Abstract: Silicon–lithium clusters are promising candidates for hydrogen storage due to their lightweight composition, high gravimetric capacities, and favorable non-covalent binding characteristics. In this study, we employ density functional theory (DFT), global optimization (AUTOMATON and Kick-MEP), and Born–Oppenheimer molecular dynamics (BOMD) simulations to evaluate the structural stability and hydrogen storage performance of key Li–Si systems. Potential energy surface (PES) exploration reveals that the true global minima of Li6Si6 and Li10Si10 differ markedly from previously proposed aromatic analogs based on benzene and naphthalene motifs. Instead, these clusters adopt compact geometries composed of one or two Si4 (Td) units and a Si2 dimer, all stabilized by surrounding Li atoms. Motivated by the recurrence of the Si4–Td motif—previously shown to exhibit three-dimensional σ-aromaticity—we explore oligomers of Li4Si4, confirming additive H2 uptake across dimer, trimer, and tetramer assemblies. Within the series of Si–Li clusters evaluated the Li12Si5 sandwich complex, featuring a σ-aromatic Si5 ring encapsulated by two Li6 units, achieves the highest hydrogen capacity, adsorbing 34 H2 molecules with a gravimetric density of 23.45 wt%. Its enhanced performance arises from the high density of accessible Li⁺ adsorption sites and the electronic stabilization afforded by delocalized σ-bonding. BOMD simulations at 300 and 400 K confirm dynamic stability and reversible storage behavior, while analysis of the interaction regions confirms that hydrogen adsorption proceeds via weak, dispersion-driven physisorption. These findings clarify structure-property relationships in Si–Li clusters and provide a basis for designing modular, lightweight, and thermally stable hydrogen storage materials.

Abstract: A reduced-order model (ROM) procedure for a one-dimensional steady plug-flow reactor (PFR) is developed and used to investigate the performance of a membrane reactor (MR), or membrane module (MM), for hydrogen separation from syngas that may be produced in an integrated gasification combined cycle (IGCC). A feed syngas enters from one side into a retentate zone, while a sweep gas of nitrogen enters from the opposite side into a neighbor permeate zone. The two zones are separated by permeable palladium membrane surfaces that are selectively permeable to hydrogen. After analyzing the hydrogen permeation profile in a base case (300 °C uniform temperature, 40 atm absolute retentate pressure, and 20 atm absolute permeate pressure), the temperature of the module, the retentate-side pressure, and the permeate-side pressure were varied individually and their influence on the permeation performance is investigated. In all the simulation cases, fixed targets of 95% hydrogen recovery and 40% mole-fraction of hydrogen at the permeate exit are demanded. The module length is allowed to change in order to satisfy these targets. Other dependent permeation-performance variables that are investigated include the logarithmic mean pressure-square-root difference, the hydrogen apparent permeance, and the efficiency factor of the hydrogen permeation. Various linear and nonlinear regression models are proposed based on the obtained results. This work gives general insights into hydrogen permeation via palladium membranes in a hydrogen membrane reactor (HMR). For example, the temperature is the most effective factor to improve the permeation performance. Increasing the absolute retentate pressure from the base value of 40 atm to 120 atm results in a proportional gain in the permeated hydrogen mass flux, with about 0.05 kg/m².hr gained per 1 atm increase in the retentate pressure; while decreasing the absolute permeate pressure from the base value of 20 bar to 0.2 bar causes the hydrogen mass flux to increase exponentially from 1.15 kg/m².hr. to 5.11 kg/m².hr.

Abstract: A combined crystallographic/computational analysis focused on the supramolecular features of the crystal structure of N,N'-diethyloxamide (NNDO) is discussed in this work. The studied compound was obtained unexpectedly during the synthesis of a series of salts of cyclic oximes derivatives. In the solid state NNDO is stabilized essentially through a strong N–H···O hydrogen bond but Hirshfeld surface analysis and Density Functional Theory (DFT) calculations were carried out to evaluate the strength of the predominant hydrogen bonds observed in the X-ray structure, as well as the secondary CH···O and CH···N contacts established between the ethyl groups and the perpendicular dioxamide group. These interactions were further investigated using a combination of Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interaction Plot (NCIplot) computational tools, and were rationalized using Molecular Electrostatic Potential (MEP) surface calculations.

Abstract:

Currently in order to calculate the number of covalent bonds for cyclic unsaturated organic molecules there are equations that include the index of hydrogen deficiency (IHD), a σ-bonds derivation from the Euler characteristic for planar graphs and other empirical formulations. However the IHD which is also known as the degree of unsaturation (DOU) requires to assign a numerical value for the pi(π) bonds and rings without knowing their precise number in a molecule, and all the other equations that are used to determine the numerical value of sigma(σ) and single bonds are made up of variables such as the number of rings, double and triple bonds. In this manuscript we present a novel type of mathematical model that was deduced by using chemical graph theory and can be applied to calculate the value of covalent bonds and rings for cyclic organic molecules with double or triple bonds only knowing the number of atoms, their corresponding valences and a new chemical concept which we called total unsaturation (TU) that represents the degree of unsaturation expressed as a percentage. The objective of this study is to highlight a deeper mathematical relationship formed by multiple structural elements of a molecule in order to enhance the correlations between graph theory and organic chemistry from a different perspective that is primarly focused on the number of bonds.

Abstract: With the advancement of new synthetic techniques, 5-Methyl-2-ethylfuran (5-MEF) has emerged as a promising renewable biofuel. In this study, the potential energy surfaces for the unimolecular dissociation reaction, H-addition reaction, and H-abstraction reaction of 5-MEF were mapped at the CBS-QB3 level. The temperature- and pressure-dependent rate constants for these reactions on the potential energy surfaces were determined by solving the master equation, using both transition state theory and Rice-Ramsperger-Kassel-Marcus theory. The results showed that the dissociation reaction of the C(6) site on the branched chain of 5-MEF has the largest rate constant and is the main decomposition pathway, while the dissociation reaction of the H atom on the furan ring has a lower rate constant and is not the main reaction pathway. In addition, the dissociation of H atoms on the branched chain and intramolecular H-transfer reactions also have high-rate constants and play an important role in the decomposition of 5-MEF. H-addition reactions mainly occur at the C(2) and C(5) sites, and the generation of the corresponding products through β-breakage becomes the main reaction pathway. With the increase of temperature, the H-addition reaction at the C(2) site gradually changes to a substitution reaction, dominating the formation of C₂H₅ and 2-methylfuran.

Abstract: Oxovanadium and zinc complexes are reported as insulin-mimetics. They inhibit several proteins including enzymes which belong to the same class of membrane sensitive phosphatases, similar in terms of general architecture and biochemistry of the active site. Borrowing from this summary, we explore the structural and electronic properties of representative oxovanadium and zinc complexes as computed in isolation and upon binding to PTEN and PTP1B phosphatases. Using crystallographic data and quantum chemistry calculations, we investigate how bonding nature and structural flexibility of the studied inhibitors affects efficiency of their binding to the active sites of the enzymes: albeit different, the two active sites represent evolutionary variant choices of the same type of biochemistry of phosphatases. As a result of our studies, we address optical responses which can be suitable for diagnostics and discuss engineering of AI assisted protein embedding to alter electronic states of metal centres which may be beneficial for biomedical and quantum information applications within the bio-spintronics of tomorrow.

Abstract: For the first time, the adsorption of hydrogen on the (110) surface of the A15 Ti3Sb compound with a cubic structure (Cr3Si type; space group Pm3 ̅n) for the accumulation of hydrogen H was calculated using the density functional theory methods (DFT SGGA-PBE). Taking into account the relaxation of the Ti3Sb–H system, the equilibrium positions of hydrogen on the Ti3Sb (110) surface were determined depending on the supercell size. Hydrogen adsorption on the Ti3Sb (110) surface of supercells is preferable in pit sites. The effects of relaxation and an increase in the supercell size (3 × 3 × 3 and 5 × 5 × 5) reduce the adsorption energy compared to the unrelaxed 2 × 1 × 1 supercell. The calculated band structure, curves of local and partial densities of states of Ti3Sb–H are used to explain the interaction of hydrogen with the Ti3Sb (110) surface. The activation energy of H diffusion along the coordinates tetrahedral interstitial site → tetrahedral interstitial site (TIS–TIS) and tetrahedral interstitial site → octahedral interstitial site (TIS–OIS), as well as the diffusion coefficient of H in the cubic lattice of Ti3Sb, were calculated.

Abstract: This study introduces a fragmentation-based linear-scaling method for strongly correlated systems, specifically the divide-and-conquer Hartree-–Fock-–Bogoliubov (DC-HFB) approach. Two energy gradient formulations of the DC-HFB method are derived and implemented, enabling efficient optimization of molecular geometries in large systems. This method is applied to graphene nanoribbons (GNRs) to explore their geometries and polyradical characters. Numerical results demonstrate that the present DC-HFB method has a potential to treat the static electron correlation and predict diradical character in GNRs, offering new avenues for studying large-scale strongly correlated systems.

Abstract: This study employs DFT at the APFD/def2-TZVP level, with SMD solvation in THF, to investigate the catalytic activation of methane by [(κ3-CNC)Fe(N₂O)]2+ cation complexes. The catalytic mechanism encompasses three key steps: oxygen atom transfer (OAT), hydrogen atom abstraction (HAA), and oxygen radical rebound (ORR). Computational results identify OAT as the rate-determining step, with activation barriers of −10.2 kcal/mol and 5.0 kcal/mol for κ1-O- and κ1-N-bound intermediates in the gas and solvent phases, respectively. Methane activation proceeds via HAA, with energy barriers of 16.0–25.2 kcal/mol depending on the spin state and solvation, followed by ORR, which occurs efficiently with barriers as low as 6.4 kcal/mol. The triplet (S = 1) and quintet (S = 2) spin states exhibit critical roles in the catalytic pathway, with intersystem crossing facilitating optimal reactivity. Spin density analysis highlights the oxyl radical character of the FeIV=O intermediate as essential for activating methane’s strong C–H bond. These findings underscore the catalytic potential of CNC-ligated iron complexes for methane functionalization and demonstrate their dual environmental benefits by utilizing methane and reducing nitrous oxide, a potent greenhouse gas.

Abstract: The current paradigm of low-T combustion and autoignition of hydrocarbons is based on the sequential two-step oxygenation of fuel radicals. The addition of the first oxygen molecule forms a peroxy radical RO2, which isomerizes to a hydroperoxyalkyl radical (QOOH). The key chain-branching occurs when the second oxygenation adduct (OOQOOH) is isomerized releasing an OH radical and forming a key ketohydroperoxide (KHP) intermediate, O=POOH. Subsequent homolytic dissociation of relatively weak O-O bond in KHP generates two more radicals in the oxidation chain leading to ignition/explosion. Thus, the formation and consumption of KHPs is a key controlling process.We recently introduced a new type of intramolecular isomerization mechanism involving self-catalyzed migration of H-atoms relevant to keto-enol and other isomerization processes designated as “catalytic hydrogen atom transfer - CHAT” (J. Phys. Chem. 2024, 128, 2169), more adequately abbreviated here as SCI-HAT. On this basis, we have identified a new general unimolecular decomposition channel for the formation of enol hydroperoxides (EHP) - the classical isomers of KHPs using first-principles modeling and potential energy surface analysis. Even though the enols are currently involved in various combustion/flame chemistry models, their actual contribution in combustion processes mostly remains neglected, due to the high computed barriers for classical (“direct”) keto-enol tautomerization. Remarkably, the novel SCI-HAT mechanism dramatically reduces activation barriers for such a conversion in the case of EHPs. Here, we present detailed mechanistic and kinetic analysis of the SCI-HAT-facilitated pathways involving some models of n-hexane, n-heptane, and specifically n-pentane as a prototype molecule for gasoline, diesel and hybrid rocket fuels (HRF). We particularly examined the formation and subsequent dissociation kinetics of γ-enol-hydroperoxide (γ-EHP) isomer of the γ-KHP (γ-C5-KHP), the most abundant isomer of the pentane-derived ketohydroperoxides observed experimentally. The novel self-catalyzed bond-exchange mechanism can be regarded as an intramolecular version of the intermolecular relay transfer of H-atoms mediated by an external molecule (molecular catalyst), such as dihydrogen, water, acids, and even radicals. Earlier, we proposed a general systematization of such intermolecular processes illustrated in the simplest case of the H2-mediated reactions termed “dihydrogen catalysis” (Catal. Rev. - Sci. Eng. 2014, 56, 403). Following this systematization, the SCI-HAT catalysis can be assigned to the category of relay-transfer of H-atoms. To gain molecular level insight into the SCI-HAT catalysis, we have additionally explored the role of the catalytic moiety on SCI-HAT reactivity using selected small models. All applied models demonstrated significant reduction of the H-transfer barriers, primarily due to the decreased ring strain in transition states. The electronic and steric factors affecting reactivity and allowing this path to circumvent the geometric disadvantages of the uncatalyzed (direct) H-transfer processes, are also discussed. Depending on the dimensions and specific molecular parameters of the SCI-HAT catalytic moieties, the longer-range and sequential H-migration processes are also identified to extend the role of the new mechanism in combustion of large alkanes and paraffin-wax hybrid rocket fuels. Such processes are particularly illustrated by a combined double keto-enol conversion of heptane-2,6-diketo-4-hydroperoxide introducing a long-range H-migration as a potential chain-branching model.To assess the possible impact of the SCI-HAT channels on global fuel combustion characteristics, we present a detailed kinetic analysis of isomerization and decomposition of pentane 2,4-ketohydroperoxide comparing SCI-HAT with key alternative reactions, including direct dissociation and Korcek channels. Calculated rate parameters were implemented into a modified version of the n-pentane kinetic model developed earlier using RMG automated model generation software (ACS Omega, 2023, 8, 4908). Simulation of ignition delay times using such models revealed significant effects of the new pathways suggesting an important role of the SCI-HAT pathway in low-temperature combustion of large alkanes.

Abstract: Understanding of binding between antiretroviral agents and biomacromolecules is important for investigation of processes that proceed during therapy. The conformational stability, binding affinity and energies of interactions in the crystal, ligand-nucleobase pairs and ligand–receptor complexes were studied for 1-[2-(2-benzoylphenoxy)ethyl]-6-methyluracil (VMU-2012-05), a potential anti-HIV drug. The x-ray structure of the crystalline VMU-2012-05 was solved experimentally, and the analysis of intermolecular interactions has been performed by means of Quantum Theory “Atoms in Molecules” (QTAIM). Quantum chemical study of the isolated molecule revealed five stable conformations, their energies differ up to 14.3 kJ/mol, four of them can be described as folded and one as extended or linear. In the crystal, a folded conformation of VMU-2012-05 significantly differs from stable ones for an isolated molecule. Intermolecular interactions in the model complexes of VMU-2012-05 with nucleobases and the HIV-1 reverse transcriptase caused stabilization of the least favorable folded conformation for the molecule. QTAIM and NCI study revealed that the dimers between VMU-2012-05 and the nucleobases are assembled mainly via C-H...π and staking interactions, while in the crystal and the complex with the HIV-1 reverse transcriptase VMU-2012-05 readily forms strong hydrogen bonds. The number of potential acceptors of H-bonding in VMU-2012-05 molecule exceeds the number of donors (1 and 5) that limits the number of hydrogen bonds experimentally observed in the crystal. The number of H-bonds in the model binding pocket with extra donors and acceptors is higher, nevertheless, the energy which goes to N-H…O bonds in the crystal is nearly the same as in the binding pocket (-58.9 and -63.6 kJ/mol, respectively). However, value of the lattice energy is by 37.9 kJ/mol larger than the total energy of the intermolecular interactions with the HIV-1 receptor (-214.6 and -245.2 kJ/mol) due to additional hydrophobic interactions. These results indicate the role of weak van der Waals interactions in stabilization of VMU-2012-05 associates with nucleobases and HIV-1 reverse transcriptase.

Abstract:

Density functional theory (DFT) calculation and molecular dynamics (MD) simulation were performed to do an in-depth study on the inhibition mechanism of quaternary ammonium surfactant CI molecules with a different chain length in the presence of 1.0 M HCl and 500 ppm acetic acid on the Fe (110) metal surface. Results from DFT calculation showed that all surfactant CI molecules have good inhibition properties where the cationic quaternary ammonium groups (N⁺) and the alpha carbon act as a reactive centre to donate electrons to the metal surface with low band-gap energy of 1.26 eV. In the MD simulation, C12 with a 12-alkyl chain length showed the most promising CI molecules with high adsorption energy and binding energy values, low diffusion coefficient towards the corrosion particles and randomly scattered at low concentration that give better adsorption towards the Fe (110) metal surface. The finding on the effect of the alkyl chain length on the inhibition efficiency of all quaternary ammonium CI molecules based on computer modelling data and the success of an in-depth study on the theoretical understanding of quaternary ammonium surfactant CI molecules in the acidic medium corrosion system towards metal surface could be used as the future development of new surfactant CI molecules with ammonium-based functional groups.

Abstract: This manuscript introduces the concept of scaling factors for rotational constants. These factors are designed to bring computed equilibrium rotational constants closer to experimentally-fitted ground-state-averaged rotational constants. The parameterization of the scaling factors was performed for several levels of theory, namely DF-Dn/def2-mVP (DF=B3LYP,PBE0, n=3(BJ),4, m=S,TZ), PBEh-3c, and r2SCAN-3c. The obtained scaling factors systematically improve the consistency between theoretical and experimental rotational constants.

Abstract: Teucrium polium L. is a plant with various claims of ethnobotanical use, primarily for in-flammatory diseases. Chemical studies have already isolated different types of terpenes from the species, and studies have established the pharmacological potential. The present study evaluated the components of T. polium essential oil cultivated in Algerian Saharan Atlas. GC-MS identified the major components as Fenchone (31.25%), 3-Carene (15.77%), cis-Limonene oxide (9.77%), and Myrcene (9.15%). In the in silico prediction, molecules with more than 1% abundance were selected. Regarding Lipinski’s rule, all molecules fol-lowed the rule. All molecules were found to be toxic in at least one model, with some mol-ecules being non-genotoxic (6, 8, 10, 11, 12, 13), others being non-mutagenic (5, 7, 9, 14). Three molecules were selected that showed the best results in pharmacokinetic and toxici-ty studies: the molecules that did not present carcinogenic potential (7 - Myrtenal; 9 - Myr-tenol; 14 – Verbenol). The molecular target was established and it seems that all three bind to the Nuclear Factor NF-kappa-B. Based on the docking and molecular dynamics results. These molecules have potential as anti-inflammatory agents, with further in vitro and in vivo studies needed to evaluate their activities and toxicity.

Abstract: In this study, molecular dynamics simulations were employed to analyze interactions between phospholipid membranes and human serum albumin (HSA) in the presence of mono- and divalent cations. Two types of membranes, composed of dipalmitoyl phosphatidylcholine (DPPC) and dipalmitoyl phosphatidylethanolamine (DPPE), were utilized. The results revealed that both systems exhibited high stability, with the DPPE complexes displaying greater stability compared to those formed with DPPC. This increased stability was attributed to a higher number of ionic contacts and hydrogen bonds. The presence of mono- and divalent metal cations significantly influenced the membrane’s capacity to bind proteins. However, these effects varied depending on the phospholipid composition of the bilayer. The studies confirmed the relatively low ability of DPPC to bind potassium ions, as previously observed by others. Consequently, the DPPC/HSA/K+ complex was found to be the least stable among the systems studied. While DPPC interactions were limited to HSA domains I and II, DPPE was able to interact with all domains of the protein. Both lipid bilayers exhibited substantial structural changes and characteristic curvature induced by interactions with HSA, which confirms the formation of relatively strong interactions capable of influencing the arrangement of the phospholipids.

Abstract: Endohedral metallo-borospherenes M@B40 have received considerable attention since the discovery of B40 in 2014. However, the coordination bonding nature of most of the actinide-doped endohedral An@B40 still remains in disputes or unexplored. Extensive first-principles theory calculations performed herein unveil the ground states of triplet U@B40 (1, C2v, 3A2), quartet U@B40- (2, C2v, 4B1), quintet Np@B40+ (3, C2v, 5A1), sextet Np@B40 (4, C2, 6A), septet Pu@B40 (5, C2v, 7A2), octet Am@B40 (6, C2v, 8A2), and octet Cm@B40+ (7, C2v, 8A2) at the coupled-cluster with triple excitations CCSD(T) level. Detailed principal interacting spin orbital (PISO) and adaptive natural density partitioning (AdNDP) analyses reveal their coordination bonding patterns and show that, with the numbers of unpaired α-electrons in parallel spins varying from nα = 2, 3, 4, 5, 6, 7, to 7 in these complexes, the percentage contribution of the An 5f-involved PISO pairs to overall coordination bonding interactions decreases monotonously from 41% to 1%, the contribution of An 6d-involved PISO pairs increases monotonously from 47% to 72%, while the marginal contribution of An 7s-involved PISO pairs remains basically unchanged (4~7%). The IR, Raman, and photoelectron spectra of the most concerned species are computationally simulated to facilitate their characterizations in future experiments.

Abstract: The distortions and instability of high-symmetry configurations of polyatomic systems in nondegenerate states are usually ascribed to the pseudo-Jahn-Teller effect (PJTE). The geometries of hypericin, isohypericin, and fringelite D were optimized within various symmetry groups. Group-theoretical treatment and (TD-)DFT calculations were used to identify the corresponding electronic states during the symmetry descent. The symmetry descent paths (up to the stable structures without any imaginary vibrations) were determined using the corresponding imaginary vibrations as their kernel subgroups starting from the highest possible symmetry group. The vibronic interaction between the ground and excited electronic states relates to an increasing energy difference of both states during the symmetry decrease. This criterion was used to identify possible PJTE. We have shown that the PJTE in these naturally occurring compounds explains only the symmetry descent paths C2v → C2 and C2v → Cs in hypericin, and the D2h → C2v, D2h → C2v → Cs, and D2h → C2h ones in fringelite D. The electric dipole moments of hypericin and its analogs are determined prevailingly by the mutual orientations of the hydroxyl groups. The same holds for the energies of frontier orbitals in these systems, but their changes during the symmetry descent are less significant.

Abstract: The alkoxycarbonylation of styrene by palladium chloride is studied employing the density functional theory (DFT). Initially, [PdCl3]– reacts with methanol to form the methoxy-bound intermediate, which undergoes β-hydride elimination to form the key intermediate [PdCl2H]–. Then, a 1,2-insertion reaction to styrene takes place to form linear and branched alkyl coordinated with the PdII. Then CO coordination followed by a 1,1-insertion reaction leads to the formation of acyl intermediate. Next, the methanolysis leads to the formation of esters. Previous reports with other catalysts suggested the intermolecular/intramolecular transition state (TS) formation with a high activation barrier, and this step was the bottleneck. To the best of our knowledge, it is the first time we have considered a two-step mechanism for the alcoholysis of the ester formation mechanism. After coordination with the metal, the methanol undergoes oxidative addition to form the PdIV square pyramidal intermediate, followed by reductive elimination to form the ester with regeneration of the metal hydride active intermediate. Deeper insight into the nature of bonding at the TSs are obtained through energy decomposition with natural orbital for chemical valence (EDA-NOCV) and quantum theory of atoms in molecules (QTAIM).

Abstract: 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.

Abstract: 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.