I present in this paper Diatomic, an open-source Excel application that calculates molar ther-modynamic properties for diatomic ideal gases. This application is very easy to use and requires only a limited number of molecular constants, which are freely available online. Despite its sim-plicity, Diatomic provides methodologies and results that are usually unavailable in general quantum chemistry packages. This application uses the general formalism of statistical mechanics, enabling two models to describe the rotational structure and two models to describe the vibra-tional structure. In this work, Diatomic was used to calculate standard molar thermodynamic properties for a set of fifteen diatomic ideal gases. Special emphasis was placed on the analysis of four properties (standard molar enthalpy of formation, molar heat capacity at constant pressure, average molar thermal enthalpy and standard molar entropy), which were compared with ex-perimental values. The results obtained lead to the following main conclusions: (i) the theoretical model used to describe rotational structure has a small effect on the accuracy of the results, (ii) at moderate and high temperatures, the Morse model gives better results than the harmonic model, and (iii) at the lowest temperatures both models give similar results.

Euler's theorem about the relationship between the numbers of individual elements of planar graphs (vertices, edges, faces) is also satisfied when the graph has zero vertices. The problem of the existence or not of such graphs has so far been the subject of very few studies. Plus, research that didn't prove anything. The paper presents an interpretation of this kind of graphs as mathematical formations lying on piecewise smooth surfaces. The lines of intersection of two or more smooth surfaces (faces of a graph) form edges without a vertex of the graph. The elementary properties of such graphs are discussed, the method of counting non-isomorphic 0-vertex graphs and their importance in physics and chemistry are given.

Polarizable continuum methods (PCM) have been widely employed for simulating solvent effects, in spite of the fact that they either ignore specific interactions in solution or only partially reproduce non-specific contributions. Examples of three solvatochromic dyes with a negative, a positive and a reverse behavior illustrate the achievements and shortcomings of PCM calculations, and the causes for their variable success. As shown with a theoretical model that rationalizes and predicts the solvatochromism of phenolate merocyanines based on structural parameters, PCM shortcomings are to be held responsible for their eventual failure in reproducing experimental data.

The reaction mechanisms of C-S borylation of aryl sulfides catalyzed by the 1,4-benzoquinone (BQ), were investigated by employing M06-2X-D3/ma-def2SVP method and basis set. In this study, the SMD model was taken to simulate the solvent effect of 1,4-dioxane. Also, TD-DFT calculations of BQ and methyl(p-tolyl)sulfane were performed in SMD solvent model. The computational results indicated that BQ and methyl(p-tolyl)sulfane, serving as a photo-catalyst, would be excited under blue LED of 450 nm, aligning well with experimental observations. Additionally, the role of 3O2 was investigated, revealing that it could be activated to 1O2 from the released energy of 1[BQ+methyl(p-tolyl)sulfane]* or 3[BQ+ methyl(p-tolyl)sulfane]*→BQ+ methyl(p-tolyl)sulfane process. Then 1O2, bis(pinacolato)diboron, and methyl(p-tolyl)sulfane would through a series of reactions to yield the final product P. The Gibbs free energy surface show that path a2-2 is optimal and this path has less steps and lower energy barrier. The electron spin density isosurface graphs were employed to analyze structures and elucidate the single electron distribution. These computational results offer valuable insights into the studied interactions and related processes and shed light on the mechanisms governing C–S borylation from aryl sulfides and b2pin2 catalyzed by BQ and methyl(p-tolyl)sulfane.

The study reveals correlations between the parameters of ions and their HOMO and LUMO orbital energy level values. In particular, it demonstrates a clear correlation for the ion adsorption parameters on model electrodes: the aluminum oxide (0001) surface, graphene and Au (111) surface. Correlations are also observed for the parameters of ion binding to water and dimethyl carbonate molecules, which are often used as solvents. In addition, the dipole moment, polarizability and solvation energy of ions are well correlated with the values of the molecular orbital energies, and for anions a dependence on the oxidation potential is observed. The obtained descriptors make it possible to select ions with desired values for a specific problem. As an illustrative example, in this work we consider the problem of displacement of water molecules from the inner electric double layer by ions, which is one of the factors increasing the potential window in electrolytes of aqueous batteries. This approach can be applied in the rapidly developing field of aqueous electrolytes for battery or supercapacitor design, catalysis control through surface composition variations, as well as in studies of heavy metal ion binding to sorption materials.

In this research work, we examined the decomposition mechanisms of N-substituted diacetamides. We focused on the substituent effect on the nitrogen lone pair electron delocalization, withdrawing and electron donor groups. DFT functionals used included: B1LYP, B3PW91, CAMB3LYP, LC-BLYP, and X3LYP. Dispersion functions gd3bj were applied when necessary to improve non-covalent interactions in the transition state. Pople with higher angular moments and def2-TZVP basis sets were also applied and were crucial for obtaining consistent thermodynamic parameters. The proposed mechanism involves a six-membered transition state with the extraction of an α hydrogen. Several conformers of N-diacetamides were used to account for the decrease in entropy in the transition state in the rate-determining state. All calculations, including Natural Bond Orbital (NBO) analyses, were performed using the Gaussian16 computational package and its GaussView 6.0 visualizer, along with VMD and GNUPLOT software. The isosurfaces and IBSI indexes were calculated using MultiWFN and IGMPlot, respectively.

Here, we present a general framework for computing the infrared anharmonic vibrational spectra of polyatomic molecules using the Born-Oppenheimer molecular dynamics (BOMD) with the software PyRAMD. To account for the nuclear quantum effects, we suggest using the simplified Wigner sampling (SWS) approach [\textit{Phys. Chem. Chem. Phys.}, 2023, \textbf{25}, 18406-18423] simultaneously coupled with the Andersen and Berendsen thermostats. We propose a new criterion for selecting the parameter of the SWS based on the molecules' harmonic vibrational frequencies and usage of the large-time-step blue shift correction, allowing for a decrease in computational expenses. For the Fourier transform of the dipole moment autocorrelation function, we propose to use the regularized least-squares analysis, which allows us to obtain higher frequency resolution than the direct application of fast Fourier transform. Finally, we suggest the usage of the pre-parameterized scaling factors for the IR spectra from BOMD, also providing the scaling factors for the spectra at the BLYP-D3(BJ)/6-31G, PBE-D3(BJ)/6-31G, and PBEh-3c levels of theory.

Quantum chemical topology addresses the study of the chemical structure by applying the tools of differential topology to scalar and vector fields obtained by quantum mechanics. Here the magnetically induced isotropically averaged Lorentz force density has been computed and topologically analysed for 11 small molecules. Critical points (attractors, repellers and saddles) have been determined and trajectories connecting the attractors have been computed. It is shown that kinds and numbers of the critical points are rather transferable in similar molecules. CC bonds of different order are endowed with critical points of different kind close to their centre. The long range behaviour of the force allows understanding the value of the sum of topological indices of the isolated critical points.

In this work, we will study at a basic level, a series of possible new three-dimensional monoclinic allotropes of silicon, with sp3 hybridization, of the bct type; where hexahedrons and octahedrons are combined, with other cluster shapes, with basic silicon geometries such as: triangles ( Si3 ), squares ( Si4 ), pentagons ( Si5 ) and hexagons ( Si6 ); similar to two-dimensional, sp2 hybridized graphene allotropes. Calculating its electron density, bandgap energy and electronic mobility.

In this work, we will study metallic clusters equivalent to the organic ones intercalated with metals, of solid benzene type, Ba anthracene and K3.45picene; and we will try to calculate its superconducting Tc, for each of these compounds, from electronic correlations at room temperature. We will also study metal hydrides and clusters, totally composed of metals, which adopt forms analogous to molecular organic picene and anthracene; also calculating its TC.

Abstract: A perspective is provided which illustrates the central role of quantum mechanics in the structure and periodically varying properties of atoms and in the formation of molecules. Despite having only about one hundred basic building blocks for all substances, chemistry is a subtle discipline due to it’s fundamentally quantum mechanical origin. The atoms, and their behavior as systematized in the Periodic Table, intimately reflect mechanisms natural to quantum mechanics but foreign to classical mechanics. Given their very small mass, the electrons form atomic structures only predictable by the use of quantum mechanics. Thereby the foundation of chemistry is totally dominated by quantum effects which are generally known only empirically, e.g. as in the Periodic Table. Recently these quantum effects have increasingly become known computationally, but not necessarily understood physically and therefore still challenge students and users of chemistry. In order to provide physical insight we extract here, from known facts and relations of quantum mechanics, but without reliance on detailed mathematics or numerical analysis, a simplest, yet fully consistent, physical explanation of atomic structure and periodically variable reactivity. Atomic reactivity is found to arise due to dynamical constraints on electron motion which lead to degeneracy in the atomic energy spectrum. There is a strong correlation between energy degeneracy and reactivity with the inert gas atoms found to display no degeneracy. Chemical bonding follows as a means of atomic reactivity relaxation and reduction of energy degeneracy, achieved by permanent electron rearrangement (ionic bonding) or by oscillatory electron motion between atoms (covalent bonding). Ionic bonding is directly related to the variable stability of atomic structures which extends from neutral atoms to atomic ions. These stable ions then form molecular structures by electrostatic attraction in neutral ionic clusters. The covalent bonding mechanism is fundamentally dynamical and interatomic since it depends directly on the facility with which electrons can move between atomic centers in a molecule. Both the ionic and the covalent mechanism, interatomic displacement and oscillation of electrons, are active in any bond between atoms of different species.

Oxidation of a mixture of nonlabelled (14N2H4) and 15N labeled (15N2H4) hydrazine in aqueous solutions produces 14N15N molecules, indicating the intermediate existence of N4H6 or N4H4 dimers with subsequent transfers of H atoms and splitting of lateral N-N bonds. To explain the key part of hydrazine oxidation reaction, the structures, thermodynamics, and electron characteristics of N4H4 molecules in aqueous solution are investigated at CCSD/cc-pVTZ level of theory. We have not found any spontaneous splitting of the bond between lateral nitrogen atoms in tetrazenes N4H4 during geometry optimization. The most probable N4H4 oxidation products are H2N-NH2 and N2, which are obtained by splitting the bond between central nitrogen atoms and so only 15N2 and 14N2 molecules are formed. Additionally, the formation of H3N-NH and N2 oxidation products is also preferred to structures without any N-N fissions. The formation of H2N=N and HN=NH reaction products is energetically less advantageous. Cyclo-N4H4 structures are stable, without any N-N fissions, but their very high Gibbs energies indicate their vanishing abundance in aqueous solution, so their involvement in hydrazine oxidation is highly improbable. Hydrazine oxidation to 14N15N molecules cannot be explained by tetrazene N4H4 intermediates.

Graphene oxide (GO) is considered as one of the promising adsorbents for the removal of various heavy metal contaminants in aquatic environment, due to its beneficial structural, chemical and electronic properties. Using the density functional theory (DFT) approach, we investigate the reactivity of a model GO nanoparticule (C30H14O15) toward neutral and charged lead (Pb) and cadmium (Cd) atoms. We found the model metal-free GO to have a high chemical reactivity. To study the adsorption of the metal atoms on the GO nanoparticle, we have used a single and doubly-adsorbed neutral (Pb0 and Cd0) and charged (Pb2+, Cd2+) atoms. After identified possible adsorption sites on the GO, we found that a single charged metal ion binds more strongly than a neutral atom of the same type. To determine the possibility of multiple adsorptions of GO nanoparticle, two metal atoms of the same species are co-adsorbed on its surface. Our calculations reveals a site-dependent adsorption energy such that when two atoms of the same specie are adsorbed at sites Si and Sj , the binding energy per atom depends on the whether one of the two atoms is adsorbed firstly on the Si or Sj sites. It is also found that the binding energy per atom for two co-adsorbed atoms of the same specie is less than the binding energy of a singly-adsorbed atom which suggests that atoms may become less likely to be adsorbed on the GO nanoparticle when their concentrations increase. This applies to both neutral and charged atoms. We adduce the origin of this observation to be interplay between metal-metal interaction on the one hand and GO-metal on the other, with the former resulting in a less binding for the charged adsorbed metals in particular, due to repulsive interaction between two positively charged ions. The frontier molecular orbitals analysis and the calculated global reactivity descriptors of the respective GO- metal complexes revealed that all the GO-metal complexes have a smaller HOMO-LUMO gap (HLG) relative to that of pristine metal-free GO nanoparticle. This suggests that although the GO-metal complexes are stable, they are less stable compared to metal-free GO nanoparticles. The negative values of the chemical potentials obtained for all the GO-metal complexes further confirms their stability. Our work calculates parameters that will be crucial to rational design of GO nanoparticles for Pb abd Cd ions contaminants removal, and may find application in water purification for example.

The existences of the N→C dative bonds in the complexes between N-containing molecules and fullerenes have been verified both theoretically and experimentally. However, finding stable N→C dative bonds is still a highly challenging task. In this work, we investigated computationally the N→C dative bonds in the complexes formed by fullerene C60 with 1,2,5-chalcogenadiazoles, 2,1,3-benzochalcogenadiazoles and 1,2,4,5-chalcogenatriazoles, respectively. It was found that the N→C dative bonds are formed along with the formation of the N–Ch···C (Ch = S, Se, Te) chalcogen bonds. In the gas phase, from S-containing complexes through Se-containing complexes to Te-containing complexes, the intrinsic interaction energies become more and more negative, which indicates that the N–Ch···C chalcogen bonds can facilitate the formation of the N→C dative bonds. The intrinsic interaction energies are compensated by the large deformation energy of fullerene C60. The total interaction energies of Te-containing complexes are negative, while both of the total interaction energies of S-containing complexes and Se-containing complexes are positive. This means that the N→C dative bonds in the Te-containing complexes are more easily observed in experiments in comparison with those in the S-containing complexes and Se-containing complexes. This study provides a new theoretical perspective on the experimental observation of the N→C dative bonds in the complexes involving fullerenes. Further, the formation of stable N→C dative bonds in the complexes involving fullerenes can significantly change the properties of fullerenes, which will greatly simulate and expand the application range of fullerenes.

In this exploratory work, we have examined the impact of an external static electric field on the H2 storage capacity of clathrate hydrates. To this end, we have chosen the 512 clathrate hydrate and examined the encapsulation of 1 - 4 H2 molecules within it. Results suggest that with the help of moderate electric fields (±0.10 to ±0.31V/Å), the encapsulation of 1 H2 molecule within the 512 clathrate hydrate becomes thermodynamically more favorable. In the cases of 4H2@512 and 2H2@512, however, the concerned processes become thermodynamically more favorable only when the field is applied along a specific direction. No favorable outcome could be observed in the case of 3H2@512, irrespective of the direction of the applied field. It appears from the results obtained herein that it might be possible to design a suitable external electric field to facilitate the hydrogen storage capacity of clathrate hydrates at ambient conditions, at least in certain cases.

Auxins are chemical compounds of wide interest, mostly due to their role in plant metabolism and development. Since the latter half of the XX century, synthetic auxins have been used as herbicides, presenting notable advantages, such as low toxicity in humans. As of today, extensive descriptions of syntetic and natural auxins have been made; yet studies centered on the molecular recognition process of auxins are scarce. Herein, we present a comprehensive in silico characterization of auxin receptor TIR1, using structure based methods to aid de novo design of putative ligands. In addition, we conducted binding site characterization using cosolvent molecular dynamics and enhanced sampling simulations with reference ligands. We also present a database of putative auxins and decoy compounds which can aid further studies focusing on synthetic auxin design. To the best of our knowledge, this study is the first of its kind focusing on TIR1.

Motivated by experimental success in designing linear amphiphilic copolymers with selective demicellization capabilities through head-to-tail depolymerization triggered by specific stimuli, we advanced the design paradigm by increasing the number of triggering groups on the copolymer chain through architectural modifications. Utilizing molecular dynamics simulations, we explored the demicellization and cargo release dynamics of linear and miktoarm copolymers, featuring one, two and three hydrophobic block or branches, each capable for head-to-tail depolymerization. Our findings revealed that, under stoichiometric trigger molecule concentrations, miktoarms with three branches exhibited consistently faster depolymerization rates than those with two branches and linear copolymers. Conversely, at constant trigger molecule concentrations, the depolymerization rates of copolymers exhibited more complex behavior influenced by two opposing factors: the excess of trigger molecules, which increased with a decrease in the number of hydrophobic branches or blocks, and simultaneous head-to-tail depolymerization, which intensified with an increasing number of branches. Our study elucidates the intricate interplay between copolymer architecture, trigger molecule concentrations, and depolymerization dynamics, providing valuable insights for the rational design of amphiphilic copolymers with tunable demicellization and cargo release properties.

Recently, the composite materials consisting of ionic liquids (ILs) and metal-organic frameworks (MOFs) have attracted a great of attention due to their fantastic properties. Many theoretical studies have been performed towards its special structures and applications. Yet, the mechanism for the diffusion of ILs inside MOFs channels still remain unclear. Here, the DFT calculations together with frontier orbital analysis, natural charge analysis, and energy decomposition analysis were performed to investigate the diffusion behavior of a typical IL, [C4mim][PF6], into the ZIF-8 SOD cage. The potential energy surface (PES) profiles indicate that it is quite difficult for the cation [C4min]+ to diffuse into the cage of ZIF-8 through the pristine pores because of its large imidazole steric hindrance. Moreover, the PES reveals that a success diffusion could be obtained by the thermal contributions, by which the pore size is enlarged through the swing effects at a higher temperature. Subsequently, electronic structure analyses reveal that the main interactions between [PF6]-or [C4mim]+ and ZIF-8 is the steric repulsion interactions. Finally, the effects of amounts of [C4mim][PF6]on the ZIF-8 were investigated, and the results show that two pairs of [C4mim][PF6] per SOD cage is more reasonable in terms of interaction energies and structural changes.

The study reports the effect of some metal carbides (niobium carbide, vanadium carbide, titanium carbide, and manganese sulfide) on hydrogen embrittlement in the pipeline industry using plane wave’s density functional theory (DFT). Our results predicted that the interaction of hydrogen molecules with these metals carbide occurs in the long range with binding energy varying in the energy window [0.70eV to 0.043eV]. Also, our study shows the desorption of H2 molecules from these metal carbides in the chemisorptions. Since, hydrogen embrittlement, occurs in the atomic state of hydrogen, therefore our finding in the atomic interaction of hydrogen with NbC, VC, TiC, and MnS showed that the strength of the trapping of the hydrogen atom could be classified as: TiC+H>VC+H>NbC+H> MnS+H. In addition, our study reveals that the carbon site is the most favorable hydrogen trapping site than the metal one. Furthermore, our results demonstrate that increasing the layer can also be an efficient way to enhance the trapping capacity.

The dimethylaminophenyl-substituted silver phthalocyanine [dmaphPcAg] can be used as a UV-vis photoinitiator for in situ preparation of a silver/polymer nanocomposite. To verify early steps of the supposed mechanism of radical polymerization, we performed quantum chemical calculations of m[dmaphPcAg]q complexes with charges q = +1 to -2 in the two lowest spin states m, of a free ligand and its dehydrogenated/deprotonated products m[dmaphPcHn]q, n = 2 to 0, q= 0, -1 or -2, in the lowest spin states m. The calculated electronic structures and electron transitions of all the optimized structures in CHCl3 solutions are compared with experimental EPR and UV-vis spectra, respectively. The unstable 3[dmaphPcAg]+ species deduced only from previous EPR spin trap experiments was identified. In addition to 2[dmaphPcAg]0, our results suggest the coexistence of both reaction intermediates 1[dmaphPcAg]- and 3[dmaphPcAg]- in reaction solutions. Silver nanoparticle formation is a weak point of the supposed reaction mechanism from the energetic, stereochemistry, and electronic structure points of view.

Many industrial processes, several natural processes involving non-living matter, and all the processes occurring within living organisms take place in solution. This means that the molecules playing active roles in the processes are present within another medium, called solvent. The solute molecules are surrounded by solvent molecules and interact with them. Understanding the nature and strength of these interactions, and the way in which they modify the properties of the solute molecules, is important for a better understanding of the chemical processes occurring in solution, including possible roles of the solvent in those processes. Computational studies can provide a wealth of information on solute-solvent interactions and their effects. Two major models have been developed to this purpose: a model viewing the solvent as a polarizable continuum surrounding the solute molecule, and a model considering a certain number of explicit solvent molecules around a solute molecule. Each of them has its advantages and challenges, and one selects the model that is more suitable for the type of information desired for the specific system under consideration. These studies are important in many areas of chemistry research, from the investigation of the processes occurring within a living organism to drug design and to the design of environmentally benign solvents meant to replace less benign ones in the chemical industry, as envisaged by the green chemistry principles. The paper presents a quick overview of the modelling approaches and an overview of concrete studies, with reference to selected crucial investigation themes.

In this work, Density Functional Theory (DFT) calculations were employed to study the photocatalytic CO2 to CO reduction by a series of Pt(II) square planar complexes with general formula [Pt(5-R-dpb)Cl] (dpb = 1,3-di(2-pyridyl)benzene anion, R = H, N,N-dimethylaniline,T thiophene, diazaborinine). The CO2 to CO conversion process is thought to proceed via two main steps, namely the photocatalytic/reduction step and the main catalytic step. The simulated absorption spectra exhibit strong bands in the 200 – 400 nm UV-Vis region. The calculated excited state reduction potentials are in the range 0.32 — -0.36 V revealing that the reductive quenching of the T1 state of the complexes could be modulated with suitable changes of the N^C^N pincer ligands. The CO2 fixation and activation by the ‘real’ three coordinated Pt(II) catalyst/intermediate is predicted to be favorable with Pt-CO2 bond dissociation energies, D0 in the range -36.9—-10.3 kcal/mol. The nature of the Pt-CO2 bond is complex with covalent, hyperconjugative and H-bonding interactions prevailing the repulsive electrostatic interactions. The main catalytic cycle is estimated to be a favorable exergonic process.

Density functional theory (DFT) and coupled cluster theory (CCSD(T)) calculations are performed to investigate the geometric, electronic structures and chemical bonding of a series of Cu-doped zinc oxide clusters, CunZn3O3 (n = 1-4). The structural evolution of CunZn3O3 (n = 1-4) clusters are elaborated in our work. The planar seven-membered ring of CuZn3O3 cluster plays an important role in the structural evolution, that is, the Cu atom, Cu dimer (Cu2) and Cu trimer (Cu3) anchor on the CuZn3O3 cluster. The aggregate behavior of Cu atoms on Zn3O3 may offer insight into the study of Cu/ZnO-based catalysts. Additionally, it is found that the CunZn3O3 clusters become more stable as the Cu content (n) increases. Bader charge analysis points out that as the Cu atoms doping, the reducibility of Cu aggregation (Cun-1) on the CuZn3O3 cluster increases. Combined with the d-band centers and the surface electrostatic potential (ESP), the reactivity and the possible reaction sites of CunZn3O3 (n = 1-4) clusters are also illustrated.

The surface configurations of the low-index facets of a set of spinel oxides are investigated using DFT+U calculations to derive surface energies and predict equilibrium nanoparticle shapes via the Wulff construction. Two very different conditions are investigated, corresponding to application either in heterogeneous catalysis or in electrocatalysis. First, the bare stoichiometric surfaces of NiFe₂O₄, CoFe₂O₄, NiCo₂O₄, ZnCo₂O₄ spinels are studied to model their use as high-temperature oxidation catalysts. Second, focusing attention on the electrochemical oxygen evolution reaction (OER), and on the CoFe₂O₄ inverse spinel as the most promising OER catalyst, we generate surface configurations by adsorbing OER intermediates, and, in an innovative study, we recalculate surface energies taking into account adsorption and environmental conditions, i.e., applied electrode potential and O₂ pressure. We predict that, under OER operating conditions, (111) facets are dominant in CoFe₂O₄ nanoparticle shapes, in fair agreement with microscopy measurements. Importantly, in the OER case we predict a strong dependence of nanoparticle shape upon O₂ pressure. Increasing O₂ pressure increases the size of the higher-index (111) and (110) facets at the expense of the (001) more catalytically active facet, whereas the opposite occurs at low O₂ pressure. These predictions should be experimentally verifiable and help define the optimal OER operative conditions.

NiO-based nanomaterials have attracted a great deal of interest in view of various applications, that have stimulated the implementation of various synthetic approaches to control their chemico-physical properties as a function of the desired end-use. In this regard, their bottom-up preparation starting from suitable precursors plays an important role, but a molecular level in-sight into their reactivity remains an open challenge. In this study, we focus on the fragmentation of Ni(II) diketonate-diamine adducts, of interest as precursors for Ni(II) oxide systems, by com-bined electrospray ionization mass spectrometry (ESI-MS) with multiple collisional experiments (ESI-MSn) and theoretical calculations. The joint analyses revealed common features in the frag-mentation pattern of the target compounds: i) in the first-fragmentation, all three complexes form analogous base-peak cations by losing a negatively charged diketonate; in these cations, Ni-O and Ni-N interactions are stronger and the Ni positive charge is lower than in the neutral complexes; ii) the tendency of ligand electronic charge to migrate towards Ni further increases in the subsequent fragmentation processes, leading to the formation – in all three cases – of a tetracoordinated Ni environment involving an interesting cation-π intramolecular interaction.

Atomic force microscopes are used, beside their principal function as surface imaging tools, in surface manipulation and measurement of interfacial properties. In particular, they can be modified to measure lateral friction forces that occur during the sliding of the tip against the underlying substrate. However, the shape, size, and deformation of the tips profoundly affect the measurements in a manner that is difficult to predict. In this work, we investigate the contribution of these effect to the magnitude of the lateral forces during sliding. The surface substrate is chosen to be few-layer AB-stacked graphene surface whereas the tip is initially constructed from face-centered cubic gold. In order to separate the effect of deformation from shape, rigid tips of three different shapes were considered first, namely a cone, a pyramid and a hemisphere. The shape was seen to dictate all aspects of the interface during sliding, from temperature dependence to stick-slip behavior. Deformation was investigated next by comparing a rigid hemispherical tip to one of identical shape and size but with all but the top three layers of atoms free to move. The deformation, as also verified by an indentation analysis, occurs by means of the lower layers collapsing on the upper ones, thereby increasing the contact area. This collapse mitigates the friction force and decreases it with respect to the rigid tip for the same vertical distance. Finally, the size effect is studied by means of calculating the friction forces for a much larger hemispherical tip whose atoms are free to move. In this case, the deformation is found to be much smaller but the stick-slip behavior is much more clearly seen.

The electronic structure of 7/9-AGNR superlattices with up to eight unit cells has been studied by means of state of the art DFT and a model Hamiltonian that follows two different approaches: Hubbard type (Hu) and including long range Coulomb interaction (PPP), solved in the mean field approximation. We show that 7/9 interfaces stabilizes non polarized solutions at the mean field level. Considering non-polarized solutions, Hu and PPP Hamiltonians gives solutions with a gap that is closed as the size is increased. This is in line with DFT results. However the density of states around the Fermi level is not correctly described neither in Hu nor in the PPP model. We also interpret the DFT density of states in terms of bands of topological states: localized edge topological states and extended bulk topological states which interacts between them due to the long range Coulomb terms of Hamiltonian. In this line, we show that a screened long range interaction instead describe correctly DFT results and the interaction between topological states. Screening consists of introducing a parameter for an exponential decay in the long range potential of the model Hamiltonian, to vary its spatial range. Calculations on the superlattice just mentioned, illustrate the relevance of include appropriate long range interactions in determining the density of states around the Fermi level (Dirac point).

Support effect is an important issue in heterogeneous catalysis while the explicit role of a catalytic support is often unclear for catalytic reactions. A systematic density functional theory computational study is reported in this paper to elucidate the effect of a model boron nitride (BN) support on the first N-H bond activation step of NH3 on Run (n =1, 2, 3) metal clusters. Geometry optimizations and energy calculations were carried out using density functional theory (DFT) calculation for intermediates and transition state from the starting materials undergoing the N-H activation process. The primary findings are summarized as follows. The involvement of the model BN support does not significantly alter the equilibrium structure of intermediates and transition state in the most favorable pathway (MFP). Moreover, the involvement of BN support decreases the free energy of activation, ΔG≠, thus improving the reaction rate constant. This improvement is more obvious at high temperatures like 673 K than low temperatures like 298 K. The BN support effect leading to the ΔG≠ decrease is most significant for the single Ru atom case among all three cases studied. Finally, the involvement of model BN may change the spin transition behavior of the reaction system during the N-H bond activation process. All these findings provide a deeper insight into the support effect on the N-H bond activation of NH3 for supported Ru catalyst in particular and for supported transition metal catalysts in general.

The surprisingly high catalytic activity of gold has been known to the heterogeneous catalysis community since the mid-1980s. Significant effort has been directed towards improving the reactivity of these surfaces towards important industrial reactions. One such strategy is the introduction of small amounts of other metals to create Au-based surface alloys. In this work, we investigate the synergistic effect of Pt doping of the Au(111) surface towards decreasing the activation barrier of the methanol dehydrogenation elementary step, within first-principles density functional theory. To this aim we construct several models of \ce{Pt}-doped Au(111) surfaces, including a full \ce{Pt} overlayer and monolayer. The effect of \ce{Pt} surface doping is then investigated via the computation of adsorption energies of the various chemical species involved in the catalytic step, and the estimation of activation barriers of methanol dehydrogenation. Both electronic and strain effects induced by \ce{Pt} surface doping concur in substantially lowering the activation energy barrier of this important reaction elementary step. Morever, in the presence of preadsorbed atomic oxygen, \ce{Pt} surface doping can be used to reduce the activation energy for methanol dehydrogenation to as low as 0.1 eV.

This Article demonstrates how an eigendecomposition problem is inputted into a quantum circuit, how gates are applied in the quantum circuit, and how the output measurements are the correct eigenvalues. This process is known as quantum phase estimation (QPE). A quantum harmonic oscillator example, a foundational quantum physical chemistry problem, is demonstrated within the context of QPE. A particle in a box example, another quantum physical chemistry problem, may be solved by QPE with a caveat. These examples are of the limiting cases of diagonal matrices. Future advances in taking matrix inverses for solving linear sets of equations or finding ground state energies in the Schrödinger equation will use the principles implemented in this Article.

The redox properties of quinones underlie their unique characteristics as organic battery components that outperform the conventional inorganic ones. Furthermore, the redox properties could be precisely shaped by using different substituent groups. Machine learning and statistics, onthe other hand, have proven to be very powerful approaches for efficient in silico design of novel materials. Herein, we demonstrated the machine learning approach for the prediction of the redox activity of quinones that potentially can serve as organic battery components. For the needs of the present study, a database of small quinone-derived molecules was created. A large number of quantum chemical and chemometrics descriptors was generated for each molecule and subsequently different statistical approaches were applied to select the descriptors that most prominently characterize the relationship between structure and redox-potential. Various machine-learning methods for screening of prospective organic battery electrode materials were deployed to select the most trustworthy strategy for machine learning aided design of organic redox materials. It was found that ridge regression models perform better than regression decision tree and decision tree based ensemble algorithms.

A mixture of nonlabeled (14N2H4) and 15N labeled hydrazine (15N2H4) in an aqueous solution is oxidized to 15N2, 14N2, and 14N15N molecules, indicating the intermediate existence of the 14NH2-14NH-15NH-15NH2 with subsequent hydrogen transfers and splitting of side N-N bonds. Structures, thermodynamics, and electron characteristics of various N4H6 molecules in aqueous solutions are investigated using theoretical treatment at the CCSD/cc-pVTZ level of theory to explain the crucial part of the hydrazine oxidation reaction. Most N4H6 structures in aqueous solutions are decomposed during geometry optimization. Splitting the bond between central nitrogen atoms is the most frequent, but the breakaway of the side nitrogen is energetically the most preferred. The N-N fissions are enabled by suitable hydrogen rearrangements. Gibbs free energy data indicate the dominant abundance of NH3... N2... NH3 species. The side N atoms have very high negative charges, which should support hydrogen transfers in aqueous solutions. The only stable cyclo-(NH)4…H2 structure has a too high Gibbs energy and breaks the H2 molecule. The remaining initial cyclic structures are split into hydrazine and HN≡NH or H2N≡N species, and their relative abundance in aqueous solutions is vanishing.

DFT-D3 calculations based on structural X-ray diffraction data obtained for 3-oxo-camphorsulfonyl imine (1), camphorsulfonyl chloride (2) and seven camphor sulfonimines (O2SNC10H13NR, L1-L7) from which L2 (R=4-OHC6H4), L4 (R=4-ClC6H4) and L6 (R=3,5-(CH3)2C6H3) are new, provide information into the intra and inter molecular interactions with concomitant elucidation of the supramolecular arrangement of the compounds. The DFT D3 calculations performed in small clusters of 2 or 3 molecular units reproduce the interactions observed by X-ray analyses showing that as a general trend the structural arrangement of the molecules is driven by electronic rather than by packing parameters. In all compounds the self-assembly of 3D structures involves the sulfonyl imine group ( NSO2) either to establish hydrogen bonds, through the oxygen atoms or non-classic oxygen-aliphatic hydrogen or non-bonding interactions (NBI) which also involve the sulfonyl oxygens. Interestingly, the camphor sulfonimine compounds (L2, L3) having protic groups (R=C6H4X: X=OH, L2 or X=NH2, L3) at the aromatic imine substituents (=NR) present an extra π-π stacking which is absent in the other compounds aromatic derivatives. The X-ray analysis shows that all the reported camphor sulfonimine compounds display the E configuration with respect to the imine substituent (R). The study of the redox behavior of the compounds by cyclic voltammetry allows an insight into the solution properties of the compounds and the rationalization of the molecular interactions that stand in the solid and solution states. Camphor sulfonimine compounds (L) display appropriate binding atoms to coordinate transition metals. The herein results show that monodentate coordination through the nitrogen atom of the sulfonimine 5-membered ring to the {Ag(NO3)} metal center is favored. When this imine nitrogen atom is not itself involved in the Organic Framework DFT-D3 calculations shows that the complexation does not affect the non-covalent interactions that are reproduced in the MOF structure.

The Randić index of a graph G is the sum of (dG(u)dG(v))−1/2 over all edges uv of G, where dG(u) denotes the degree of vertex u in G. In this paper, we investigate a few graph transformations that decrease Randić index of graph. By applying those transformations, we determine the minimum Randić index on tricyclic graphs, and characterize the corresponding extremal graphs.

The structures of Ag complexes with dimethyl amino phenyl substituted phtalocyanine m[dmaphPcAg]q of various charges q and in two lowest spin states m were optimized using the B3LYP method within the D4h symmetry group and its subgroups. The most stable reaction intermediate in the supposed photoinitiation reaction is 3[dmaphPcAg]-. Group-theoretical analysis of the optimized structures and of their electron states reveals two symmetry-descent mechanisms. Stable structures of maximal symmetry of complexes 1[dmaphPcAg]+, 3[dmaphPcAg]+, 2[dmaphPcAg]0 and 4[dmaphPcAg]2- correspond to the D4 group as a consequence of the pseudo-Jahn-Teller effect within unstable D4h structure. Complexes 4[dmaphPcAg]0, 1[dmaphPcAg]-, 3[dmaphPcAg]- and 2[dmaphPcAg]2- with double degenerate electron ground states in D4h symmetry structures undergo a symmetry descent to stable structures corresponding to maximal D2 symmetry not because of a simple Jahn-Teller effect but due to hidden pseudo-Jahn-Teller effect (strong vibronic interaction between excited electron states). The reduction of the neutral photoinitiator causes symmetry descent to its anionic intermediate because of vibronic interactions that must significantly affect the polymerization reactions.

Molecules sourced from marine environments hold immense promise for the development of novel therapeutic drugs, owing to their distinctive chemical compositions and valuable medicinal attributes. Notably, Talarolide A and Talaropeptides A-D have gained recent attention as potential candidates for pharmaceutical applications. This study aims to explore the chemical reactivity of Talarolide A and Talaropeptides A-D through the application of molecular modeling and computational chemistry techniques, specifically employing Conceptual Density Functional Theory (CDFT). By investigating their chemical behaviors, the study seeks to contribute to the understanding of the potential pharmacological uses of these marine-derived compounds. The investigation involves the utilization of molecular modeling and computational chemistry tools, with a specific focus on Conceptual DFT. These techniques are applied to examine the chemical reactivity of Talarolide A and Talaropeptides A-D, shedding light on their potential for interacting with various biological targets. The research reveals insights into the chemical reactivity of Talarolide A and Talaropeptides A-D, uncovering active reaction sites and potential biological targets. Talarolide A demonstrates robust anti-inflammatory properties and antitumor activity against diverse cancer cell lines, while Talaropeptide A displays antimicrobial efficacy against both bacteria and fungi. The study underscores the significance of comprehending the chemical reactivity of natural marine products for advancing pharmaceutical development. By employing computational tools such as Conceptual DFT, this research uncovers crucial information about the active sites and potential targets of Talarolide A and Talaropeptides A-D. The findings contribute to the broader understanding of marine-derived peptides and their prospects as pharmaceutical agents, though further investigations are necessary to fully elucidate their pharmacological attributes.

Stellatolides are natural compounds that have shown promising biological activities, including antitumor, antimicrobial, and anti-inflammatory properties, making them potential candidates for drug development. Chemical Reactivity Theory (CRT) is a branch of chemistry that explains and predicts the behavior of chemical reactions based on the electronic structure of molecules. Conceptual Density Functional Theory (CDFT) and Computational Peptidology (CP) are computational approaches used to study the behavior of atoms, molecules, and peptides. In this study, we present the results of our investigation of the chemical reactivity and ADMET properties of Stellatolides A-H using a novel computational approach called Conceptual DFT-based Computational Peptidology (CDFT-CP). Our study uses CDFT and CP to predict the reactivity and stability of molecules and to understand the behavior of peptides at the molecular level. We also predict the ADMET properties of the Stellatolides A-H to provide insight into their effectiveness, potential side effects, and optimal dosage and route of administration. This study sheds light on the potential of Stellatolides A-H as promising candidates for drug development and highlights the potential of CDFT-CP for the study of other natural compounds and peptides.

Tyrosinases (TYR) play an important role in oxidizing phenols and catechols, leading to the formation of catechols and ortho-quinones, respectively. In mammals, TYR catalyzes the conversion of L-Tyrosine to quinone, a pivotal step in melanogenesis, which generates melanin pigments responsible for protecting against UV radiation and oxidative stress. Given TYR's importance in melanin-related disorders and cosmetic applications, the inhibition of TYR has garnered attention for controlling melanin production. However, current inhibitors like hydroquinone, arbutin, and kojic acid (KA) have limitations in terms of side effects and effectiveness. A novel class of TYR inhibitors featuring arylpiperidine and arylpiperazine components has demonstrated potent inhibitory activity. This study presents a computational analysis of these inhibitors using molecular docking, molecular dynamics (MD) simulations, and the Linear Interaction Energy (LIE) method was used to estimate binding free energies. The arylpiperidine and arylpiperazine inhibitors exhibit remarkable stability within the TYR active site during simulations. The van der Waals interactions are notably sustained, indicating effective inhibition mechanisms. The results from LIE calculations closely align with experimental binding affinities. In summary, these results contribute to the understanding of TYR inhibition and underscore the potential of arylpiperidine and arylpiperazine derivatives as effective agents for modulating melanin production in both cosmetic and pharmaceutical applications. Overall, this study sheds light on the intricate interactions between inhibitors and TYR, opening avenues for the development of novel therapies and interventions.

Antioxidants are molecules that neutralize free radicals. In general, the reaction mechanisms of antioxidants are well known. The main reaction mechanisms of antioxidants are electron transfer (ET), proton transfer (PT), H atom transfer (HAT) and radical adduction (RAF). The study of these mechanisms is helpful to understand how antioxidants control high free radical levels on the cell. There are many studies focused on determine the main mechanism of an antioxidant to neutralize a wide spectrum of radicals, mainly reactive oxygen species (ROS) type radicals. Most of these antioxidants are polyphenols type compounds. Some esters, amides and metal-antioxidants have shown antioxidant activity. There are few experimental and theoretical studies about the antioxidant reaction mechanism of the aforementioned compounds. In this work, we shown the reaction mechanism proposed of an amide and its metal-antioxidant counterpart. We show how the presence of the metal increase the electron transfer on polar media and the H transfer in non-polar media. Even though, esters and amides are non-polar compound, the scavenger activity is good for the metal-antioxidant compound in no-polar media

Photophysical properties of a series of bis(arylydene)cycloalkanone dyes with various donor substituentns are studied by quantum chemistry. Their capacity for luminescence and nonradiative relaxation through trans-cis isomerization is related to their structure, in particular, to the donor capacity of the substituents and the degree of conjugation due to the central cycloalkanone moiety. It is shown that cyclohexanone central moiety introduces distortions and disrupts the conjugation, thus leading to a nonmonotonic change in their properties. The increasing donor capacity of the substituents causes increase in the HOMO energy (raise of the oxidation potential) and decrease in the HOMO-LUMO gap, which results in the red shift of the absorption spectra. The ability of the excited dye to relax through fluorescence or through trans-cis isomerization is governed by the height of the barrier between the Franck–Condon and S1-S0 conical intersection regions on the potential energy surface of the lowest π-π* excited state. This barrier also correlates with the donor capacity of the substituents and the degree of conjugation between the central and donor moieties. The calculated fluorescence and trans-cis isomerization rates are in good agreement with the observed fluorescence quantum yields.

A series of derivatives, involving two dithienylethene (DTE), groups, connected by several molecular linkers (bis(ethylene-1,2-dithiolato)Ni- (NiBDT), naphthalene, quasilinear oligothiophene chains) are investigated with the aid of computational quantum chemistry methods. This involves the computation of the second- and third-order nonlinear optical properties, i.e. molecular hyperpolarizabilities of the designed/selected derivatives. These properties can be efficiently controlled by DTE switches, in connection with light of appropriate frequency. We found that NiBDT, as a linker, is associated with a greater contrast, in comparison to naphthalene, between the first and second hyperpolarizabilities of the “open-open” and the “closed-closed” isomers. This is explained by invoking the low lying excited states of NiBDT. It has been found that the second hyperpolarizability can be used as an index, which follows the structural changes induced by photochromism. The two-photon absorption, which is related to the imaginary part of second hyperpolarizability, has also been investigated for the S0S1 transition. Furthermore, the intramolecular excited-state energy transfer (EET) is studied as well as the overlap between the absorption and emission spectra of the donor and acceptor groups of the molecules. The electronic coupling, VDA, between the donor and acceptor fragments, as well as the emission spectrum of the donor and the absorption spectrum of the acceptor have been computed, assuming a Förster type transfer mechanism. EET is a critical factor governing the photochromism. Two methods were used to compute VDA, one based on linear response and one based on the distributed multipole analysis (DMA); both techniques give very similar results for the dominating Coulomb contribution. For NiBDT as the linker a low VDA value has been computed. We found that VDA is affected by the molecular geometry. Our results clearly show that the linker strongly influences the communication between the open-closed DTE groups and thus, photochromism. The present computations show that full photochromism is attained in derivatives where two DTE groups are linked by a tetrathiophene chain, in agreement with experiment. The sensitivity of molecular linear and nonlinear optical properties upon photochromism can assist with the identification of the molecular isomers.

This study aims to investigate the spectroscopic and structural properties of the compound Lumefantrine which is important in pharmacology because of its anti-malarial effect. The structural and spectroscopic properties of this molecule such as bond lengths, bond angles, FT-IR and NMR spectra were handled computationally using a computational chemistry suite: Spar-tan’14. Both HF and DFT methods were used with different basis sets for the calculations. The re-sults calculated by the software were compared to experimental results from the literature. Both Computational and experimental results were exhibited as tables. Also some calculated results such as HOMO-LUMO boundary orbitals and electrostatic potential map, were given as graphics and pictures.

With the evolution of toxic chemicals continuing to progress, developing methods for the destruction of chemical warfare agents (CWAs) has become an increasingly important research topic. Metal-organic frameworks (MOFs) are a class of porous crystalline solids that have sparked interest in this area. Due to their exceptional porosities and large surface areas, MOFs possess superior adsorption, reactivity, and catalytic abilities, making them structurally ideal candidates for the capture and decomposition of target species. Additionally, the tunable networks of MOFs allow their chemical functionalities to be customized for various applications and operating conditions, making them practicable in personal protective equipment and adjustable to dynamic environments. This paper reviews experimental and computational studies on CWA removal by MOFs, with a special emphasis on nerve agent (GB, GD, and VX) removal via hydrolysis and sulfur mustard (HD) removal via selective photooxidation. With extraordinary structural stability and reusability, zirconium-based MOFs are the most promising materials for hydrolytic and photooxidative degradation of CWAs and are thus the primary focus of this work. First-principles approximations of the intrinsic catalytic reaction mechanisms towards different agents in Zr-MOFs are summarized, and developments in the structure-property relationships governing Zr-MOF design rules for efficient degradation in the aqueous and solid phases are discussed. We also examine recent progress in tuning and functionalizing MOFs to promote practical CWA removal under realistic battlefield conditions.

The development of high-performance sensing materials for detecting or removing SF₆ decomposition gases is crucial for gas-insulated switchgear (GIS). In this work, the adsorption characteristics of the pristine porphyrin (Pr) and Fe-doped porphyrin (FePr) monolayers towards SF₆ decomposition gases were investigated using the first-principles calculations. Additionally, the electronic properties and sensing-mechanism were also examined. The findings indicate that both Pr and FePr monolayers exhibit thermodynamic stability. The intrinsic Pr monolayer only exhibits a moderate affinity towards the SO₂ molecule, however, its poor sensitivity of the Pr monolayer renders it unsuitable as the sensing-material. In contrast, the FePr monolayer exhibits favorable adsorption strength towards all five toxic gases (H₂S, SO₂, SOF₂, SO₂F₂, HF). The FePr monolayer exhibits chemisorption towards SO₂/SOF₂ gases, Furthermore, the microscopic mechanism of gases-substrate interaction is elucidated through the analysis of charge density difference, charge transfer, and density of states. Moreover, the FePr has excellent sensitivity for H₂S, SO₂, SO₂F₂, SOF₂ and HF molecules owing to the significant variations of the band gap, electrical conductivity and work function. In addition, the τ of H₂S, SO₂, and SOF₂ is 12.6 μs, 18.5 s and 15.4 s at 298 K, respectively. Our calculated results can offer theoretical guidance for the practical application of FePr-based sensing materials to detect SF6 decompositions gases.

Azapeptides have gained much attention due to their ability to enhance the stability and bioavailability of peptide drugs. Their structural preferences, essential to understanding their function and potential applica-tion in the peptide drug design, remain largely unknown. In this work, we systematically investigated the conformational preferences of three azaamino acid residues in tripeptide models, Ac-azaXaa-Pro-NHMe [Xaa= Asn (4), Asp (5), Ala (6)], using the popular DFT functionals, B3LYP and B3LYP-D3. A solvation model density (SMD) was used to mimic the solvation effect on the conformational behaviors of azapep-tides in water. During the calculation, we considered the impact of the amide bond in the azapeptide mod-els on the conformational preferences of models 4-6. We analyzed the effect of the hydrogen bond be-tween the side-chain main chain and main-chain main-chain on the conformational behaviors of azapep-tides 4-6. We found that the predicted lowest energy conformation for the three models differs depending on the calculation methods. In the gas phase, B3LYP functional indicates that the conformers tttANP-1 and tttADP-1 of azapeptides 4 and 5 correspond to the type I of -turn, the lowest energy conformation with all-trans amide bonds, respectively. Considering the dispersion correction, B3LYP-D3 functional predicts the conformers tctANP-2 and tctADP-3 of azapeptide 4 and 5, which contain the cis amide bond preceding the Pro residue, as the lowest energy conformation in the gas phase. The results imply that azaAsx and Pro residues may involve cis-trans isomerization in the gas phase. In water, the predict-ed lowest energy conformer of azapeptides 4 and 5 differs from the gas phase results and depends on the calculational method. For azapeptide 6, regardless of calculation methods and phases, tttAAP-1 (-I turn) is predicted as the lowest energy conformer. The results imply that the effect of the side chain that can form hydrogen bonds on the conformational preferences of azapeptides 4 and 5 may not be negligible. We compared the theoretical results of azaXaa-Pro models with those of Pro-azaXaa models, showing that in-corporating azaamino acid residue in peptides at different positions can significantly impact the folding patterns and stability of azapeptides.

This study scrutinizes the complexities of designing and exploring the potential energy surface (PES) of systems containing more than twenty atoms with planar tetracoordinate carbons (ptCs). To tackle this issue, we utilized an established design rule to design a Naphtho [1,2-b:4,3-b′:5,6-b′′:8,7-b′′′]tetrathiophene derivative computationally. This process began with substituting S atoms with CH– units, then replacing three sequential protons with two Si2+ units in the resultant polycyclic aromatic hydrocarbon polyanion. Despite not representing the global minimum, the newly designed Si8C22 system with four ptCs provided valuable insights into strategic design and PES exploration. Our results underscore the importance of employing adequate methodologies to confirm the stability of newly designed molecular structures containing planar hypercoordinate carbons.

In this article, we delve into the intricate behavior of electronic mechanisms underlying NMR magnetic shieldings, σ, in molecules containing heavy atoms such as cadmium, platinum, and mercury. Specifically, we explore PtXn^{−2} (X = F, Cl, Br, I; n = 4, 6) and XCl2 Te2 Y2 H6 (X = Cd, Hg; Y = N, P) molecular systems. It is known that the leading electronic mechanisms responsible for the relativistic effects on σ are well characterized by the linear response with elimination of small components model (LRESC). In this study, we present results obtained from the innovative LRESC-Loc model, which offers the same outcomes as the LRESC model but employs localized molecular orbitals (LMOs) instead of canonical MOs. These LMOs provide a chemist’s representation of atomic core, lone pairs, and bonds. The whole set of electronic mechanisms responsible of the relativistic effects can be expressed in terms of both non-ligand-dependent and ligand-dependent contributions. We elucidate the electronic origins of trends and behaviors exhibited by these di- verse mechanisms in the aforementioned molecular systems. In PtX4^{−2} molecules, the predominant relativistic mechanism is the well-established one-body spin-orbit (σ^SO(1) ) mechanism, while the paramagnetic mass-velocity (σ^Mv ) and Darwin (σ^Dw ) contributing mechanisms also demand con- sideration. However, in PtX6−2 molecules, the σ Mv+ Dw contribution surpasses that of the SO(1) mechanism, thus influencing the overall ligand-dependent contributions. As for complexes con- taining Cd and Hg, the ligand-dependent contributions exhibit similar magnitudes when nitrogen is substituted with phosphorus. The only discrepancy arises from the σ^SO(1) contribution, which changes sign between the two molecules due to the contribution of bond orbitals between the metal and tellurium atoms.

The design of highly efficient sensitizers is one of the most significant areas in dye-sensitized solar cell (DSSC) research. We have studied a series of benzothiadiazole-based D-π-π-A organic dyes, putting emphasis on the influence of the donor moiety on the DSSC’s efficiency. Using linear response time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional different donor groups were characterized in terms of electronic absorption spectra and key photovoltaic parameters. As a reference a dye has been considered which has a benzothiadiazole fragment linked via thiophene rings to a diphenylamine donor and a cyanoacrylic acid acceptor. The different systems are first studied in terms of individual performance parameters, which are eventually aggregated into the power conversion efficiency. Here only the amino-substituted species shows a modest increase, whereas the dimethylamino case even shows a decrease.

The ability of 2D hybrid structures formed by boron, nitrogen and carbon atoms (h-BNCs) as potential substrates for surface enhanced Raman spectroscopy (SERS) detection of dioxin-like pollutants is theoretically analyzed. The strong confinement and high tunability of the electromagnetic response of the carbon nanostructures embedded within the h-BNC sheets point out that these hybrid structures could be promising for applications in optical spectroscopies, such as SERS. In this work, two model dioxin-like pollutants, TCDD and TCDF, and a model h-BNC surface composed by a carbon nanodisk of ninety-six atoms surrounded by a string of borazine rings, BNC96, are employed for the simulation of the adsorption complexes and the static and pre-resonance Raman spectra of the adsorbed molecules. A large affinity of BNC96 by these pollutants is reflected on the large interaction energies obtained for the most stable stacking complexes, with dispersion being the most important contribution to their stability. The large vibrational coupling of some active modes of TCDF and, specially, of TCDD makes the Raman static spectra display a ‘pure’ chemical enhancement of one order of magnitude. On the other hand, due to the strong electromagnetic response of BNC96, confined within the carbon nanodisk, pre-resonance Raman spectra obtained for TCDD and TCDF display large enhancement factors of 108 and 107, respectively. Promisingly, laser excitation wavelengths frequently used in SERS experiments also provoke significant Raman enhancements, around 104, for the TCDD and TCDF signals. Both the strong confinement of the electromagnetic response within the carbon domains and the high modulation of the resonance wavelengths within the visible and/or UV ranges in h-BNCs should lead to a higher sensitivity than graphene and white graphene parent structures, solving one of the main disadvantages of using 2D substrates for SERS applications.

Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are central eukaryotic messengers. These very highly phosphorylated molecules can exist in two distinct conformations, a canonical one with five phosphoryl groups in equatorial positions, and a “flipped” axial conformation. Using 13C-labeled InsPs / PP-InsPs, the behavior of these molecules was investigated by 2D-NMR under solution conditions reminiscent of a cytosolic environment. Remarkably, the most highly phosphorylated messenger InsP8 readily adopts both conformations at physiological conditions. Environmental factors - such as pH, metal cation composition, and temperature - strongly influence the conformational equilibrium. Thermodynamic data revealed that the transition of InsP8 from the equatorial to the axial conformation is, in fact, an exothermic process. The speciation of InsPs and PP-InsPs also affects their interaction with protein binding partners; addition of Mg2+ decreased the binding constant Kd of InsP8 to an SPX protein domain. The results illustrate that PP-InsP speciation reacts very sensitively to solution conditions, suggesting it might act as an environment-dependent molecular switch.

The thermal conductivity of the products of the interaction of molten core with concrete was derived using number theory. A formula has been found that describes the thermal conductivity of ZrO₂, ZrSiO₄, (U,Zr)SiO₄ and UO₂ over a wide temperature range. Formula is expressed in terms of the atomic numbers of elements, their valencies, the crystal structure of substances, and the thermal conductivities of individual chemical elements of the corium.

Controlling the selectivity of detonation initiation reaction of explosive is a Holy Grail, and it seems to be an “idiot's daydream”, by strengthening external electric field, to reduce the explosive sensitivity. The effects of external electric fields on the initiation reactions in NH2NO2∙∙∙NH3, a model system of the nitroamine explosive with alkaline additive, were investigated at the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p) level. The concerted effect in the intermolecular hydrogen exchange is characterized by an index of the imaginary vibrations. Due to the weakened concerted effects by the electric field along the −x-direction opposite to the “reaction axis”, the dominant reaction changes from the hydrogen exchange to 1,3-intramolecular hydrogen transference with the increase of the field strengths. Furthermore, the stronger the field strengths, the higher the barrier heights become, indicating the lower sensitivities. Therefore, by strengthening the field strength and adjusting the orientation between the field and “reaction axis”, not only can the reaction selectivity be controlled, but also the sensitivity can be reduced, in particular under a super-strong field. Thus, a traditional concept, which the explosive is dangerous under the super-strong external electric field, is broken theoretically. Compared to the neutral medium, the low sensitivity of the explosive with alkaline can be achieved under the stronger field. Employing atoms in molecules, reduced density gradient and surface electrostatic potentials, the origin of the reaction selectivity and sensitivity change is revealed. This work provides a new idea to the technical improvement for adding the external electric field into the explosive system.

The electrochemical CO2 reduction reaction can lead to high value-added molecules production while helping decrease anthropogenic CO2 emissions. Copper can reduce CO2 to more than thirty different hydrocarbons and oxygenates, but it lacks the required selectivity. We present a computational investigation of the role of nano-structuring and alloying in Cu-based catalysts on the activity and selectivity of CO2 reduction to one-carbon products: carbon monoxide, formic acid, formaldehyde, methanol, and methane. The adsorption, activation, and conversion of CO2 were computed on monometallic and bimetallic (decorated and core-shell) 55-atom Cu-based clusters. The dopant metals considered were Ag, Cd, Pd, Pt, and Zn, located at different coordination sites. The relative binding strength of the intermediates at different applied potentials were used to identify the optimal catalyst for the selective CO2 conversion to one carbon products. It was discovered that single atom doping with Cd and Zn is optimal for the CO2 to carbon monoxide conversion. The core-shell models with Ag, Pd, and Pt provided higher selectivity for formic acid and formaldehyde. The Cu-Pt and Cu-Pd showed lowest overpotential for methane formation.

The permeation of dioxin-like pollutants, namely, chlorinated dibenzodioxins and dibenzofurans, through lipid membranes has been simulated using classic molecular dynamics (CMD) combined with the umbrella sampling approach. The most toxic forms of chlorinated dibenzodioxin and dibenzofuran, 2,3,7,8-tetrachloro-p-dibenzodioxin (TCDD) and 2,3,7,8-tetrachlorodibenzofuran (TCDF), and a dioleyl-phosphatidylcholine (DOPC) lipid membrane of 50 Å wide have been chosen for our study. The free energy profile shows the penetration process is largely favoured thermodynamically (DG≈-12 kcal/mol), with a progressively decrease of the free energy until reaching the energy minima at distances of 8Å and 9.5Å from the centre of the membrane for, respectively, TCDD and TCDF. At the centre of the membrane, both molecules display subtle local maxima with free energy differences of 0.5 and 1 kcal/mol with respect to the energy minima for TCDD and TCDF, respectively. Furthermore, the intermolecular interactions between the molecules and the lipid membrane have been characterized at the minima and the local maxima using hybrid quantum mechanics/molecular mechanics energy decomposition analysis (QM/MM-EDA). Total interaction energies of -17.5 and -16.5 kcal/mol have been found at the energy minima for TCDD and TCDF, respectively. In both cases, the dispersion forces govern the molecule-membrane interactions, no significant changes have been found at the local maxima, in agreement with the classical free energy profile. The small differences found in the results obtained for TCDD and TCDF point out the adsorption and diffusion processes through the cell membrane are not related to the different toxicity shown by these pollutants.

Controlling and understanding Cu-catalyzed homocoupling reaction is crucial to prompt the development of efficient Cu-catalyzed cross-coupling reactions. The presence of a coordinating base (hydroxide, methoxide) enables the B-to-Cu(II) transmetalation from aryl boronic acid to CuIICl2 in methanol, through formation of a mixed Cu-(μ-OH)-B intermediates. A second B-to-Cu transmetalation to form bis-aryl Cu(II) complexes is disfavored. Instead, organocopper(II) dimers undergo a coupled transmetalation-electron-transfer (TET) allowing the formation of a bis-organocopper(III) complexes readily promoting reductive elimination. Based on this mechanism some guidelines are suggested to control the undesired formation of homocoupling product in Cu-catalyzed cross-coupling reactions.

Epidermal Growth Factor Receptor (EGFR) tyrosine kinase is a cell surface receptor whose overexpression has been associated with different types of cancers including brain cancer (glioblastoma multiforme). The ability of the extract of Scutellaria baicalensis to inhibit the proliferation of malignant glioma cells have been reported. Thus, in this study we report the identification of 307 bioactive constituents responsible for the anti-glioblastoma multiforme effect from S. baicalensis using in silico studies such as molecular docking, binding free energy calculations, pharmacophore modelling, induced-fit docking, gene enrichment analysis, molecular dynamic simulations and ADMET predictions. A total of 307 chemical constituents of S. baicalensis were screened and the top 10 scoring compounds indicated different binding affinities ranging from -9.010 to -6.427 kcal/mol towards the EGFR tyrosine kinase; Ganhuangenin, 5,7,2',5'-tetrahydroxyflavone, (2R)-2-(2,6-dihydroxyphenyl)-3,4-dihydro-2H-chromene-5,7-diol, and tenaxin I possess higher binding affinities (-9.010 to -8.649 kcal/mol) compared to the standard ligand, erlotinib having -8.539 kcal/mol. The compounds interacted with amino acids of clinical importance such as MET 769, GLU 738, THR 766 via H-bond. The structural features involved in the interaction with the target were mostly two aromatic rings, H-bond donors and acceptors and some hydrophobic interactions which varies between the ligands. Better docking scores in the induced-fit docking further validates the inhibitory potential of the compounds against the flexible protein. All the top-scoring ligands from S. baicalensis had zero Lipinski violation and also obeyed other drug-likeness rules by Ghose, Veber, Egan, and Muegge with the exception of breviscapine. Interestingly, all the compounds are not likely to be hepatotoxic, mutagenic, or cytogenic, making them potentially safe as anti-cancer agents.

Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug design (CADD) has contributed to drug discovery research, mitigating costs and time. In this sense, compound databases represent a fundamental element for the CADD. This work reviews the progress toward developing compound databases of natural origin, particularly databases developed in Latin America, and their practical applications in the drug discovery area. We also survey the computational methods, emphasizing chemoinformatic approaches to profile natural product databases.

Using density functional theory (DFT) and the information-theoretic approach (ITA) quantities to appreciate the energetics and properties of biopolymers is still an unaccomplished and ongoing task. To this end, we studied the building blocks of nucleic acid base pairs and small peptides. For base pairs, we have dissected the relative importance of energetic components by using two energy partition schemes in DFT. Our results convincingly show that the exchange-correlation effect predominantly governs the molecular stability of base pairs while the electrostatic potential plays a minor but indispensable role, and the steric effect is trivial. Furthermore, we have revealed that simple density-based ITA functions are in good relationships with molecular polarizabilities for a series of 30 hydrogen-bonded base pairs and all 20 natural α-amino acids, 400 dipeptides, and 8000 tripeptides. Based on these lines, one can easily predict the molecular polarizabilities of larger peptides, even proteins as long as the total molecular wavefunction is available, rather than solving the computationally demanding coupled-perturbed Hartree-Fock (CPHF) equation or its DFT counterpart coupled-perturbed Kohn-Sham (CPKS) equation.

The paper presents a new procedure for assessing the polarity and hydrophobicity of deep eutectic solvents (DESs) based on the measurement of the DES contact angle on glass. DESs consisting of benzoic acid derivatives and quaternary ammonium chlorides – tetrabutylammonium chloride (TBAC) and benzyldimethylhexadecylammonium chloride (16-BAC) in selected mole ratios were chosen for the study. To investigate the DESs polarity, an optical goniometer and an ET(30) solvatochromic scale based on the Reichardt’s dye were used. The research demonstrated the high accuracy and precision of the developed procedure. The simplicity of the examination and the availability of basic equipment allow the implementation of the developed procedure in routine investigations of DESs.

The molecular clusters ((HO)3Si-O-Si(OH)3, and (HO)3Al-O-Si(OH)3 ) representative of aluminosilicate mineral surface were employed to study the dissolution of aluminosilicate in acidic condition via density functional theory with the M06-2X+G(d,p) methodology. The surface termination sites (Si and Al) were both tetra-coordinated and the terminal oxygen was protonated in acidic condition. In the dissolution reaction, the calculated barrier height of the six-membered ring transition state complex containing two water molecules was predicted to be lower than that of four-membered ring transition state complex containing one water molecule. In addition, the calculated barrier heights for Al-terminated sites were predicted to be lower than those for the Si-terminated sites, suggesting that breaking the Al-O bond is easier than Si-O bond in the aluminosilicate mineral surface; the barrier heights of the surface termination sites with protonated terminal oxygen were lower than those without protonated terminal oxygen. With the fracture of Si-O and Al-O bonds, the Si and Al release from the aluminosilicate. These results confirm the experimental conclusions that the acidic condition facilitates the release of Si and Al from the aluminosilicate, and the concentration of Al leaching from aluminosilicate is higher than Si.

The one-to-one structural correspondence between any conjugated hydrocarbon CnHm and the borane BnHm+n is extended here, with the B3LYP/cc-pVDZ model, to pure conjugated carbon systems with the example of buckminsterfullerene C60 with the corresponding icosahedral isoelectronic system closo-borane B60H60, and the fluorine substituted systems B60F30H30 and B60F60 , all with icosahedral Ih symmetry. All systems correspond to energy minima in the potential energy hypersurface, except for B60(F30)in(H30)out . Selected electronic structure methods are used to characterize all systems: molecular electrostatic potentials (MEP), atomic charges, bond orders, and topological properties of the electron density within quantum theory of atoms-in-molecules (QTAIM) and electron-localization function (ELF) theory. In the particular case of B60H60 we use the recently developed Hückeloid model to characterize this system. The stability of the energy minimum icosahedral structure B60F60 could have an origin in F···F attractive interactions of the inner fluorine atoms of the cage.

The rational fabrication of low-dimensional materials with a well-defined topology and functions is an incredibly important aspect of nanotechnology. In particular, the on-surface synthesis (OSS) methods based on the bottom-up approach enable facile construction of sophisticated molecular architectures unattainable by traditional methods of wet chemistry. Among such supramolecular constructs especially interesting are surface-supported metal-organic networks (SMONs), composed of low-coordinated metal atoms and π-aromatic bridging linkers differing in size, shape and functionalization scheme. In this work, the lattice Monte Carlo (MC) simulation technique was used to extract the chemical information encoded in a family of Y-shaped positional isomers coadsorbed with trivalent metal atoms on a flat metallic surface with (111) geometry. For this purpose the investigated tritopic molecules/metal atoms were carefully mapped on a triangular lattice as interconnected/isolated segments with appropriatelly embedded anisotropic interactions. Depending on the intramolecular distribution of active centers (functional groups) within the simulated molecular bricks, we observed the metal-directed self-assembly of two-dimensional (2D) openwork patterns, aperiodic mosaics and metal-organic ladders. The obtained theoretical findings could be especially relevant for the scanning tunneling microscopy (STM) experimentalists interested in a surface-assisted construction of complex nanomaterials stabilized by directional coordination bonds.

The past two decades have witnessed the introduction of and then a steady increase in the use of computational techniques in the study and development of molecularly imprinted polymers (MIPs). Molecular dynamics (MD) based studies have had a significant role in this development as they can provide insights concerning the mechanisms governing the molecular level events underlying MIP synthesis and MIP-ligand interactions and can be used for the identification of preferred monomer compositions and for the prediction of MIP properties. We here review the role that MD has played in the development of molecular imprinting and examine the different types of MD strategies that have been used, including their advantages and challenges. Recent trends in the application of MD to the study of MIPs are presented, along with a perspective on the future importance of MD-based studies for the development of molecular imprinting science and technology.

This study reports a computational investigation on the antioxidant activity of five plant food benzoic acid derivatives, namely gallic acid (GA), para-hydroxybenzoic acid (PHBA), protocatechuic acid (PCA), syringic acid (SA), and vanillic acid (VA). Based on computed thermodynamics parameters, a detailed comparative debate is developed concerning their free radical scavenging activity in the gas phase and polar solutions (in water and methanol solvents). This discussion goes on to elucidate both the most preferred mechanism and the order of antioxidant activity for these molecules in each environment. Paradoxically, calculations using the harmonic oscillator model of aromaticity (HOMA) suggest that H abstraction radicals gain in stability as the central benzene ring loses in structural aromaticity. Finally, spin densities and fukui function f⁰ seem to be good indicators of the local reactivity of these compounds towards free radicals.

An overview of the chemical compounds forming the rare smectic T phases is cited with references to the historical context. Thermodynamics (transition temperatures, enthalpies) along with the factors (stereochemical constraints, electrostatic interactions, aliphatic chain stacking, intermolecular forces) contributing to the adoption of tetragonal scaffolds are also discussed. Characteristic optical microscopy textures and x-rays diffraction patterns are presented. In parallel, a comparison of the geometrical parameters such as distances between atoms, molecular areas, volumes, and lattice parameters with the closest two-dimensional and three-dimensional organizations, is performed.

In the present manuscript, we report new insights into the concept of (a)synchronicity in Diels-Alder (DA) reactions in the framework of the reaction force analysis, in conjunction with natural population calculations and atomic resolution of energy derivatives along the intrinsic reaction coordinate (IRC) path. Our findings suggest that the DA reaction transitions between a preferentially concerted mechanism to a stepwise one in a 0.10 Å window of synchronicity indices, ranging from 0.90 to 1.00 Å. We have also shown that the relative position of the global minimum of the reaction force constant with respect to the TS is an alternative and quantifiable indicator of the (a)synchronicity in DA reactions. Moreover, the atomic resolution of energy derivatives reveals that the mechanism of the DA reaction involves two inner elementary processes associated with the formation of each of the two C-C bonds. This resolution goes on to indicate that, in asynchronous reactions, the driving and retarding components of the reaction force are mostly due the fast and slow-forming C-C bonds (elementary process) respectively, while in synchronous ones both elementary processes retard and drive the process concomitantly and equivalently.

There is experimental evidence of high vibronic activity that accompanies the strongly allowed transition between the ground state and the lowest electronic singlet excited state of oligofurans that contain 2,3, and 4 furan rings. The absorption and emission spectra of the three lowest oligofurans measured in liquid nitrogen temperature show distinct fine structures that are reproduced using the projection-based model of vibronic coupling (with Dushinsky rotation included) parameterized utilizing either DFT (with several different exchange-correlation functionals) or ab initio (CC2) quantum chemistry calculations. Using as reference the experimental data concerning the electronic absorption and fluorescence for the 8 lowest oligofurans we first analyze the performance of the exchange-correlation functionals for the electronic transition energies and the reorganization energies. Subsequently, we use the best functionals alongside the CC2 method to explore how the reorganization energies are distributed among the totally symmetric vibrations, identify the normal modes that dominate in the fine structures present in the absorption and emission bands, and trace their evolution with the increasing number of rings in the oligofuran series. Confrontation of the simulated spectra with the experiment allows for verification of the performance of the selected DFT functionals and the CC2 method.

In this theoretical study we report on molecular electrostatic potential (MEP) of titled molecules confined by repulsive potentials of cylindrical symmetry mimicking a topology. Our calculations show that the spatial restriction significantly changes the picture of MEP of molecules in quantitative and qualitative sense. In particular, the drastic changes of MEP as a function of the strength of spatial confinement are observed for the BrCN molecule. This preliminary study is the first step in the investigations of the behavior of MEP of molecular systems under the orbital compression.

The minimum energy structures of the Si3C5 and Si4C8 clusters are planar and contain planar tetracoordinate carbons (ptCs). These species have been classified, qualitatively, as global () and local () aromatics according to the adaptive natural density partitioning (AdNDP) method, which is an orbital localization method. This work evaluates these species' aromaticity, focusing on confirming and quantifying their global and local aromatic character. For this purpose, we use an orbital localization method based on the partitioning of the molecular space according to the topology of the electronic localization function (LOC-ELF). In addition, the magnetically induced current density is analyzed. The LOC-ELF-based analysis coincides with the AdNDP study (double aromaticity, global and local). Besides, the current density analysis detects global and local ring currents. The strength of the global and local current circuit is significant, involving 4n+2 - and -electrons, respectively. The latter implicates the Si-ptC-Si fragment, which would be related to the 3c-2e -bond detected by the orbital localization methods in this fragment.

Azobenzene-containing molecules may associate with each other in systems such as self-assembled monolayers or micelles. The interaction between azobenzene units leads to a formation of exciton states in these molecular assemblies. Apart from local excitations of monomers, the electronic transitions to the exciton states may involve charge transfer excitations. Here, we perform quantum chemical calculations and apply transition density matrix analysis to quantify local and charge transfer contributions to the lowest electronic transitions in azobenzene dimers of various arrangements. We find that the transitions to the lowest exciton states of the considered dimers are dominated by local excitations, but charge transfer contributions become sizable for some of the lowest ππ* electronic transitions in stacked and slip-stacked dimers at short intermolecular distances. In addition, we assess different ways to partition the transition density matrix between fragments. In particular, we find that the inclusion of the atomic orbital overlap has a pronounced effect on quantifying charge transfer contributions if a large basis set is used.

Knowledge of the interaction between inorganic and organic phosphates with soil minerals is vital for improving the soil P fertility. To achieve an in-depth understanding we combined adsorption experiments and hybrid ab initio molecular dynamics simulations to analyze the adsorption of common phosphates, i.e. orthophosphate (OP), glycerolphosphate (GP) and inositolhexaphosphate (IHP), onto the 100 surface plane of goethite. Experimental adsorption data per mol P-molecule basis fitted to the Freundlich model show the adsorption strength increases in the order GP < OP < IHP, and IHP adsorption being saturated faster followed by GP and OP. Modeling results show that OP and GP form stable monodentate (M) and binuclear bidentate (B) motifs with B being more stable than M, whereas IHP forms stable M and 3M motifs. Interfacial water plays an important role through hydrogen bonds and proton transfers with OP/GP/IHP and goethite. It also controls the binding motifs of phosphates with goethite. Combining both experimental and modeling results, we propose that the B motif dominates for OP, whereas GP forms M and IHP forms a combination of M and 3M motifs. The joint approach plausibly explains why IHP is the predominant organically bound P form in soil. This study could be considered as a preliminary step for further studies for understanding the mechanisms of how microbes and plants overcome the strong IHP–mineral binding to implement the phosphate groups into their metabolism.

The calculation of the vapour pressure of organic molecules at 298.15K is presented using a commonly applicable computer algorithm based on the group-additivity method. The basic principle of this method rests on the complete breakdown of the molecules into their constituting atoms, further characterized by their immediate neighbour atoms. The group contributions are calculated by means of a fast Gauss-Seidel fitting algorithm using the experimental data of 2036 molecules from literature. A ten-fold cross-validation procedure has been carried out to test the applicability of this method, which confirmed excellent quality for the prediction of the vapour pressure, expressed in log(pa), with a cross-validated correlation coefficient Q2 of 0.9938 and a standard deviation  of 0.26. Based on these data, the molecules' standard Gibbs free energy G°vap has been calculated. Furthermore, using their enthalpies of vaporization, predicted by an analogous group-additivity approach published earlier, the standard entropy of vaporization S°vap has been determined and compared with experimental data of 1129 molecules, exhibiting excellent conformance with a correlation coefficient R2 of 0.9598, a standard error  of 8.14 J/mol/K and a medium absolute deviation of 4.68%.

This work presents the results of a computational study of the chemical reactivity and bioactivity properties of the members of the Theopapuamides A-D family of marine peptides by making use of our own proposed methodology named Computational Peptidology (CP) that has been successfully considered in previous studies of this kind of molecular systems. CP allowed for the determination of the global and local descriptors that come from Conceptual Density Functional Theory (CDFT) that can give an idea of the chemical reactivity properties of the marine natural products under study which are already known to be related to their bioactivity. At the same time, the validity of the procedure based on the adoption of the KID (Koopmans in DFT) technique as well as the MN12SX/Def2TZVP/H2O model chemistry has been successfully verified. Together with several Chemoinformatic tools that can be used for the improvement of process of Virtual Screening, some additional properties of these marine peptides were identified related to their ability to behave as useful drugs. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) parameters related to the Theopapuamides A-D pharmacokinetics are also reported.

This review summarizes experimental and theoretical studies of transition metal complexes with two types of novel metal-carbon bonds. One type features complexes with carbones CL2 as ligands, where the carbon(0) atom has two electron lone pairs which engage in double (σ and π) donation to the metal atom [M] CL2. The second part of this review reports complexes which have a neutral carbon atom C as ligand. Carbido complexes with naked carbon atoms may be considered as endpoint of the series [M]-CR3 → [M]-CR2 → [M]-CR → [M]-C.

A methodology based on the concepts that arise from Density Functional Theory named Conceptual Density Functional Theory (CDFT) was chosen for the calculation of some global and local reactivity descriptors of the Discodermins A-H family of marine peptides through the consideration of the KID (Koopmans in DFT) technique that was successfully used in previous studies of this kind of molecular systems. The determination of active sites of the studied molecules for different kind of reactivities was achieved by resorting to some CDFT-based descriptors like the Fukui functions as well as the Parr functions derived from Molecular Electron Density Theory (MEDT). A few properties identified with their ability to behave as a drug and the bioactivity of the peptides considered in this examination were acquired by depending on a homology model by studying the correlation with the known bioactivity of related molecules in their interaction with various biological receptors. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADME (Absorption, Distribution, Metabolism, and Excretion) parameters related to the Discodermins A-H pharmacokinetics are also reported.

The KID (Koopmans in DFT) procedure usually applies in organic molecules of the closed–shell type. We used the KID procedure in an open–shell system for the first time to choose the most suitable density functional to compute global and local reactivity descriptors coming from the Conceptual Density–Functional Theory. From a set of 18 density functionals spread from the second until the fourth rung of the Jacob’s ladder: BP86, B97-D, BLYP, CAM-B3LYP, M06-L, M11-L, MN12-L, B3LYP, PBE0, N12-SX, M06-2X, M11, MN12-SX, CAM-B3LYP, LC-ωHPBE, ωB97X-D, APFD, MN15 and MN15-L, we concluded that CAM-B3LYP provides the best outcome.

In the present work, we provide an electronic structure based method for the “on-the-fly” deter- mination of vibrational sum frequency generation (v-SFG) spectra. The predictive power of this scheme is demonstrated at the air-water interface. While the instantaneous fluctuations in dipole moment are obtained using the maximally localized Wannier functions, the fluctuations in polar- izability are approximated to be proportional to the second moment of Wannier functions. The spectrum henceforth obtained captures the signatures of hydrogen bond stretching, bending, as well as low-frequency librational modes.

Italian, Spanish, French vs German, Austrian or Norwegian COVID-19 tracks? Antibiotics might have a partial impact on COVID-19 death rates in various countries. Our working hypotheses based on recent publications is that that antibiotics may be a major factor that negatively affects patients’ immune system during viral infections. We are all aware that there is no specific and effective medical treatment for COVID-19 so far. However, we know that our immune system is the only efficient weapon that fights against this syndrome right now. In fact, antibiotics are very often prescribed to prevent secondary infections following an antiviral immune response. Various antibiotic therapies have also been commonly applied to support COVID-19 treatments in China and Italy. Unfortunately, the frequent antibiotic off-site targets include mitochondria that are genetically and evolutionary closely linked to bacteria. Mitochondria are multifunctional organelles responsible for bioenergetics in nearly all our cells, acting as signaling hubs in antiviral and antibacterial immune responses. Several studies have demonstrated that mitochondria are vulnerable to antibacterial treatments, interrupting their physiology. Inhibition of these processes by antibiotics might render the immune system less capable of fighting acute COVID-19 viral infections. Some antibiotics, including those prescribed for COVID-19 in Wuhan, have been shown to inhibit the synthesis of mitochondrial DNA. The question is whether antibiotics support such a treatment or weaken patient immune responses in this case. This hypothesis should be evaluated based on comparative clinical data that seem to be unavailable at the moment. Possibly the COVID-19 risk group should be extended to all patients being treated with antibiotics, including those who finished antibiotic therapies days up to several months before SARS-CoV-2 infection. We therefore urge health service response groups to evaluate the impact of antibiotics on COVID-19 recovery vs death retrospective data. We would like to motivate international, national and local health authorities to share available clinical treatment data, discuss and optimize treatment strategies.

Around the World, the number of compound databases of natural products in the public domain is rising. This is in line with the increasing synergistic combination of natural product research and chemoinformatics. Towards this global endeavor, countries in Latin America are assembling, curating, and analyzing the contents and diversity of natural products available in their geographical regions. In this manuscript we collect and analyze the efforts that countries in Latin America have made so far to build natural product databases. We further encourage the scientific community in particular in Latin America, to continue their efforts to building quality natural product databases and, whenever possible, to make them publicly accessible. It is proposed that all compound collections could be assembled into a unified resource called LANaPD: Latin America Natural Products Database. Opportunities and challenges to build, distribute, and maintain LANaPD are also discussed

History is often thought to be dull and boring – where large numbers of facts are memorized for passing exams. But the past informs the present and future, especially in delineating the context surrounding specific events that, in turn, help provide a deeper understanding of their causes and implications. Scientific progress (whether incremental or breakthroughs) is built upon prior work. Chronological examination of computational chemistry’s evolution reveals the existence of major “epochs” (e.g., transition from semi-empirical methods to first principles calculations), and the centrality of key ideas (e.g., Schrodinger equation and Born Oppenheimer approximation) in potentiating progress in the field. The longstanding question of whether computing power (both capacity and speed) or theoretical insights play a more important role in advancing computational chemistry was examined by taking into account the field’s development holistically. Specifically, availability of large amount of computing power at declining cost, and advent of graphics processing unit (GPU) powered parallel computing are enabling tools for solving hitherto intractable problems. On the other hand, this essay argues (using Born Oppenheimer approximation as an example) that theoretical insights’ role in unlocking problems through simple (but insightful) assumptions is often overlooked. Collectively, the essay should be useful as a primer for appreciating major development periods in computational chemistry, from which counterfactual questions illuminate the relative importance of theoretical insights and advances in computer science in moving the field forward.

Conjugated singlet ground state diradicals have received remarkable attention owing to their potential applications in optoelectronic devices. A distinctive character of these systems is the location of the double exciton state, a low lying excited state dominated by the doubly excited H,H→L,L configuration, which may influence optical and other photophysical properties. In this contribution we investigate this specific excited state, for a series of recently synthesized conjugated diradicals, employing time dependent density functional theory based on the unrestricted parallel spin reference configuration in the spin-flip formulation (SF-TDDFT) and standard TD calculations based on the unrestricted antiparallel spin reference configuration (TDUDFT). The quality of the computed results is assessed considering diradical and multiradical descriptors and the excited state wavefunction composition.

The Rosetta software suite for macromolecular modeling, docking, and design is widely used in pharmaceutical, industrial, academic, non-profit, and government laboratories. Considering its broad modeling capabilities, Rosetta consistently ranks highly when compared to other leading methods created for highly specialized protein modeling and design tasks. Developed for over two decades by a global community of scientists at more than 60 institutions, Rosetta has undergone multiple refactorings, and now comprises over three million lines of code. Here we discuss the methods developed in the last five years, involving the latest protocols for structure prediction, protein–protein and protein–small molecule docking, protein structure and interface design, loop modeling, the incorporation of various types of experimental data, and modeling of peptides, antibodies and other proteins in the immune system, nucleic acids, non-standard amino acids, carbohydrates, and membrane proteins. We briefly discuss improvements to the energy function, user interfaces, and usability of the ­­software. Rosetta is available at www.rosettacommons.org.

Clean production of renewable fuels is a great challenge of our scientific community. Iridium complexes have demonstrated a superior catalytic activity in the water oxidation (WO) reaction, which is a crucial step in water splitting process. Herein we have used a defective zirconium MOF with UiO-66 structure as support of a highly active Ir complex based on EDTA with formula [Ir(HEDTA)Cl]Na. The defects are induced by the partial substitution of tereftalic acid with smaller formiate groups. Anchoring of the complex occurs through a post-synthetic exchange of formiate anions, coordinated at the zirconium clusters of the MOF, with the free carboxylate group of the [Ir(HEDTA)Cl]-complex. The modified material was tested as heterogenous catalyst for the WO reaction by using Cerium Ammonium Nitrate as sacrificial agent. Although TOF and TON values are comparable to those of other iridium heterogenized catalysts, the MOF exhibits iridium leaching not limited at the first catalytic run, as usually observed, suggesting a lack of stability of the hybrid system under strong oxidative conditions.

This study deals with computational analysis of dominant fatty acid ethyl esters characterized from the biodiesel produced from waste beef tallow by means of KOH catalyzed ethanol based transesterification. Ethyl palmitate, Ethyl Oleate, Ethyl Stearate and Ethyl Myristate were identified as dominant fatty acid esters and were computed for molecular analysis in Gaussian 09 software using Density Functional Theory (B3LYP method) with 6-31G* as basis set. Geometric parameters were in accordance with existing experimental values and population analysis exhibited negative charge for oxygen atoms, both positive & negative charge for carbon atoms in all ester molecules. The molecular dipole moment was higher for unsaturated ester molecule and quadruple moment proposed electronic dislocation in X+Y direction. Also, energy gap decreased slightly with increasing carbon chain but reduced drastically with increase in unsaturation. Electrostatic potential mapping displayed negative electrostatic potential for oxygen atoms in ester linkage of all ester molecules.

Systems Chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the Graded Autocatalysis Replication Domain (GARD) formalism embodied in a Lipid World scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in Molecular Dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions and micellar formation, growth and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with Molecular Dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various Molecular Dynamics methodologies. We review different approaches for testing the validity of the GARD model, by following micellar accretion and fission events and examining compositional changes over time. Near future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.

The consideration toward Waste Cooking Oils (WCOs) is changing from hazardous waste to valuable raw material for industrial application. During the last five years some innovative processes based on the employment of recycled WCO have appeared in the literature. In the present review article, the most recent applications of recycled Waste Cooking Oil are reported and discussed. These include the production of bio-plasticizers, the application of chemicals derived from WCOs as energy vectors, and the use of WCOs as solvent for pollutant agents.

Polychlorinated phenoxathiins (PCPTs), polychlorinated dibenzothiophenes (PCDTs), and polychlorinated thianthrenes (PCTAs) are sulfur analogues of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/DFs). Chlorothiophenols(CTPs) and chlorophenols (CPs) are key precursors to form PCTA/PT/DTs, which can form chloro(thio)phenoxy radical, sulfydryl/hydryl-substituted phenyl radical and (thio)phenoxyl diradicals. The available radical/radical PCTA/DT formation mechanism failed to explain the higher concentration of PCDTs than that of PCTAs under the pyrolysis or combustion conditions. Thus in this work, a detailed thermodynamics and kinetic calculations were carried out to investigate the pre-intermediates formation for PCTA/PT/DTs from radial/molecule coupling of 2-C(T)P with their key radical species. Our study found that the radial/molecule mechanism can thermodynamically and kinetically contribute to the gas-phase formation of PCTA/PT/DT/s. The S/C coupling modes to form thioether-(thio)enol intermediats are preferable over the O/C coupling modes to form ether-(thio)enol intermediats. Thus, although the radial/molecule coupling of chlorophenoxy radical with 2-C(T)P have no effect on the PCDD/PTs formation, the radial/molecule coupling of chlorothiophenoxy radical with 2-C(T)P play an important role in the PCDT/PT formation. Most importantly, the pre-PCDT intermediates formation pathways from the coupling of sulfydryl/hydryl-substituted phenyl radical with 2-C(T)P and the coupling of (thio)phenoxyl diradicals with 2-C(T)P are more favorable to pre-PCTA/PT intermediates formation pathways from the coupling of chlorothiophenoxy radical with 2-C(T)P, which can give reasonable explanation for the high PCDT-to-PCTA ratio in the environment.

The beginning of industrialization human being has observed a variety of environmental troubles in the world. This industrialization has not only brought growth and affluence but ultimately troubled the ecosystem. One of the crashes is visible, in form of water contamination. Here the current study heavy metal contamination of water body has been discussed. Effluents from a great number of industries viz., tannery, textile, pigment & dyes, paint, wood processing, petroleum refining, electroplating, leather etc., have a major amount of heavy metals in their wastewater. The conventional technique of handling heavy metal pollution includes chemical oxidation, chemical precipitation, ion exchange, reverse osmosis, membrane separation, electrodialysis etc. These processes are expensive, energy intensive and frequently related with generation of poisonous by-product. Therefore, the adsorption has been examined as a cost-efficient technique of elimination of heavy metals from wastewater. In the current study different low-cost adsorbent has been a review as an abatement of heavy metal contamination from wastewater. These adsorbent comprise materials of natural origin like peat moss, zeolites, clay, and chitin are found to be an effective agent for removal of deadly heavy metals like Pb, Cd, Zn, Cu, Ni, Hg, Cr etc. Separately from these, a variety of agricultural wastes like rice husk, waste tea, neem bark, black gram; Turkish coffee, walnut shell etc. were also known as a powerful adsorbent for heavy metal removal. at the side of that low-cost industrial byproduct like fly ash, lignin, iron (III) hydroxide and red mud, coffee husks, Areca waste, tea factory waste, sugar beet pulp, battery industry waste, blast furnace sludge, waste slurry, sea nodule remains and grape stalk wastes have been discovered for their technical possibility to eliminate toxic heavy metals from impure water.

Fostering fruitful collaboration between chemistry and physics scholars, the analysis of the differences in the practical approach to single atoms in chemistry and in physics affords a number of conceptual outcomes pointing to a more balanced relationship between chemistry and physics.

2-Hydroxypropyl-β-cyclodextrin (HPβCD) has unique properties to enhance the stability and the solubility of low water-soluble compounds by inclusion complexation. Understanding of the structural properties of HPβCD and its derivatives based on the number of 2-hydroxypropyl (HP) substituents at the a-D-glucopyranose subunits is rather important. In this work, replica exchange molecular dynamics simulations were performed to investigate the conformational changes of single- and double-sided HP-substitution called as 6-HPβCDs and 2,6-HPβCDs, respectively. The results show that glucose subunits in both 6-HPβCDs and 2,6-HPβCDs have lower chance to flip than in βCD. Also, HP groups are occasionally blocking the hydrophobic cavity of HPβCDs, thus hindering the drug inclusion. We found that HPβCDs with high number of HP-substitutions are more likely to be blocked, while HPβCDs with double-sided HP-substitution are even more probable to be blocked. Overall, 6-HPβCDs with three and four HP-substitutions are highlighted as the most suitable structures for guest encapsulation based on our conformational analyses such as structural distortion, radius of gyration, circularity and cavity self-closure of the HPβCDs.

We have performed first-principles calculations to study the interfacial exchange coupling and magnetocrystalline anisotropy (MCA) energy in a SmCo₅/Sm₂Co₁₇ multilayer model systems. The phase of SmCo₅ and Sm₂Co₁₇ stacking along (0001) direction are structurally well matched. The atomic structure, including the alignment and the separation between layers, were firstly optimized. Then the non-collinear magnetic structures were calculated to explore the exchange coupling across the interface and the variation of MCA energy. We found that the inter-phase exchange coupling strength, rotating behavior and MCA energy are strongly dependent on the atomic thickness of the SmCo₅ and Sm₂Co₁₇ phase.

We show that combining vibrational spectroscopy with signal processing can result in a scheme for ultrasensitive detection of molecules. We consider the vibrational spectrum as a signal on the energy axis and apply a matched filter on that axis. On the example of a nerve agent molecule, we show that this allows detecting a molecule by its vibrational spectrum even when the recorded spectrum is completely buried in noise, when conventional spectroscopic detection is impossible. Detection is predicted to be possible with signal-to-noise ratios in recorded spectra as low as 0.1. We study the importance of spectral range used for detection as well as of the quality of the computed spectrum used to program the filter, specifically, the role of anharmonicity, of the exchange correlation functional, and of the basis set. The use of the full spectral range rather than of a narrow spectral window with key vibrations is shown to be advantageous, as well as accounting for anharmonicity.

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds from natural origin is increasing. Several countries have initiatives in place to construct and maintain compound databases that are representative of their diversity. Examples are Brazil, France, Panama and recently Vietnam. Herein, we discuss the first version of BIOFACQUIM, a novel compound database with natural products isolated and characterized in Mexico. We discuss its construction, curation, and a complete chemoinformatic characterization of the content and coverage in chemical space. It is reported the profile of physicochemical properties, scaffold content, and diversity, as well as structural diversity based on molecular fingerprints. BIOFACQUIM is freely available.

The multidrug resistance transporter NorM is an important drug resistance pump and plays a critical role in multidrug resistance in bacteria and mammals. In this study we carried out molecular dynamics simulation to study the mechanism of Na+ binding and dynamical structures of two long loops in the substrate-releasing process in substrate binding NorM. Our simulation study identified several key residues (D41, E261 D377) along the Na+ binding pathway and a multi-state ion-binding mechanism is proposed based on the simulation study. In this proposed model, the transport of Na+ is a multi-stage process with D41 being the first station for binding to Na+, followed by Na+ binding to the second station E262 and finally to the cation-binding site of E262 and D377. During the transport of Na+, the transmembrane components TM1, TM7 and TM2 are rearranged to facilitate the ion transport as well conformational changes of NorM to a closed state. Further, substrate-bound simulation revealed that Loop3-4 and Loop9-10 control the substrate-releasing process.

Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years, only recently microscopic aspects of these processes became more clear. In this work, we present a review on current theoretical understanding of the molecular mechanisms of the protein target search. A comprehensive discrete-state stochastic method to explain the dynamics of the protein search phenomena is introduced and explained. Our theoretical approach utilizes a first-passage analysis and it takes into account the most relevant physical-chemical processes. It is able to describe many fascinating features of the protein search, including unusually high effective association rates, high selectivity and specificity, and the robustness in the presence of crowders and sequence heterogeneity.

For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM, and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound, and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.

Amorphous solid dispersions are considered a promising formulation strategy for the oral delivery of poorly soluble drugs. The limiting factor for the applicability of this approach is the physical (in)stability of the amorphous phase in solid samples. Minimizing the risk of reduced shelf life for a new drug by establishing a suitable excipient/polymer-type from first principles would be desirable to accelerate formulation development. Here we perform Molecular Dynamics simulations to determine properties of blends of eight different polymer-small molecule drug combinations for which stability data is available from a consistent set of literature data. We calculate thermodynamic factors (mixing energies) as well as mobilities (diffusion rates and roto-vibrational fluctuations). We find that either of the two factors, mobility and energetics, can determine the relative stability of the amorphous form for a given drug. Which factor is rate limiting depends on physico-chemical properties of the drug and the excipients/polymers. The methods outlined here can be readily employed for an in-silico pre-screening of different excipients for a given drug to establish a qualitative ranking of the expected relative stabilities, thereby accelerating and streamlining formulation development.

One of the principal hallmarks of Alzheimer’s disease (AD) is related to the aggregation of amyloid-β fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists either in blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-Epigallocatechin-3-gallate, Quercetin, and Rosmarinic acid) with the amyloid-β(1-40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulate the double-layered structure stability.

X-ray crystallographic and theoretical charge density data for a series of compounds [(Co(Ts3tren))M(Co(Ts3tren))] (M = Mg, Ca, Sr and Ba) is examined. The crystal structures are isostructural and the alkaline earth metal ions have the same arrangement of donor oxygen atoms despite the large variation in ionic radii. The isomorphism of these molecules is surprising and a theoretical examination of the electronic structures, with the different metal ions along the series, provides detailed insight into their stabilities. The theoretical and experimental data are consistent and agree well. The local properties of the Co(II) ion and its donor atoms are relatively independent of the alkali earth metal.