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Five stable tautomer and rotamers of the 2-(2-Mercaptophenyl)-1-azaazulene (thiol, thione, R1, R2, and R3) molecules were studied using density functional theory (DFT). The geometries of the studied tautomer and rotamers were fully optimized at the B3LYP/6-31G(d,p) level. Thermodynamic calculations were performed at M06-2X/6-311G++(2d,2p) and ωB97XD/6-311G++(2d,2p) in the gas phase and ethanol solution conditions modeled by the solvation model based on density (SMD). The kinetic constant of tautomer and rotamers conversion was calculated in the temperature range 270–320 K using variational transition state theory (VTST) accompanied by one-dimensional wigner tunneling correction. Energy refinement at CCSD(T)/6–311++G(2d,2p) in the gas phase has been calculated. All the studied DFT methods qualitatively give similar tautomer stability orders in the gas phase. The ethanol solvent causes some reordering of the relative stability of 2-(2-Mercaptophenyl)-1-azaazulene conformers. The transition states for the 2-(2-Mercaptophenyl)-1-azaazulene tautomerization and rotamerization processes were also determined. The reactivity, electric dipole moment, and spectroscopic properties of the studied tautomer and rotamers were computed. The hyper-Rayleigh scattering (βHRS), and depolarization ratio (DR) exhibited promising optical properties when nonlinear optical properties were calculated. [ABSTRACT FROM AUTHOR]

Five stable tautomer and rotamers of the 2-(2-Mercaptophenyl)-1-azaazulene (thiol, thione, R1, R2, and R3) molecules were studied using density functional theory (DFT). The geometries of the studied tautomer and rotamers were fully optimized at the B3LYP/6-31G(d,p) level. Thermodynamic calculations were performed at M06-2X/6-311G++(2d,2p) and ωB97XD/6-311G++(2d,2p) in the gas phase and ethanol solution conditions modeled by the solvation model based on density (SMD). The kinetic constant of tautomer and rotamers conversion was calculated in the temperature range 270–320 K using variational transition state theory (VTST) accompanied by one-dimensional wigner tunneling correction. Energy refinement at CCSD(T)/6–311++G(2d,2p) in the gas phase has been calculated. All the studied DFT methods qualitatively give similar tautomer stability orders in the gas phase. The ethanol solvent causes some reordering of the relative stability of 2-(2-Mercaptophenyl)-1-azaazulene conformers. The transition states for the 2-(2-Mercaptophenyl)-1-azaazulene tautomerization and rotamerization processes were also determined. The reactivity, electric dipole moment, and spectroscopic properties of the studied tautomer and rotamers were computed. The hyper-Rayleigh scattering (βHRS), and depolarization ratio (DR) exhibited promising optical properties when nonlinear optical properties were calculated. [ABSTRACT FROM AUTHOR]

Recently, the upper bounds on the static time-reversal (T) and spatial parity (P)-violating electron electric dipole moment (eEDM) and dimensionless constant, characterizing the strength of the T , P -violating scalar–pseudoscalar nucleus–electron interaction, have been updated in the JILA experiment using the HfF+ cations. We considered two other sources of the T , P -violation in HfF+–axion-like-particle (ALP)-mediated scalar–pseudoscalar electron–electron and nucleus–electron interactions. To estimate the magnitude of effects, induced by such interactions in HfF+ we have developed and applied a method which implies the direct use of the ab initio relativistic coupled cluster theory to calculate molecular parameters that characterize the interactions. Using these parameters, we showed that an order of magnitude updated laboratory constraints on the ALP-mediated electron–electron and nucleus–electron interactions can be derived from the experimental data on T , P -violating effects in HfF+ for a wide range of ALP masses. [ABSTRACT FROM AUTHOR]

An Aristotelian philosophy of nature offers an alternative to reduction for the conception of the inter-theoretical relationships between molecular chemistry and quantum mechanics. A basic ingredient for such an approach is an ontology of fundamental causal powers, and this work aims to develop such an ontology by drawing on quantum-chemical entities, particularly, the electron density. This notion is central to the Quantum Theory of Atoms in Molecules, a theory of molecular structure developed by Richard F. W. Bader, which describes molecules and atoms in terms precisely of the electron density. Then, by identifying a philosophical tension in Bader's discourse about the nature of electron density, the work will analyze this central notion in terms of the categorical/dispositional distinction regarding properties. The central idea is that electron density can be conceived as categorical and dispositional at once, and this very characterization can avoid Bader's philosophical tension. [ABSTRACT FROM AUTHOR]

Theoretical frames for analyzing information in biological and molecular multicomponent structures are proposed. The mathematical foundations of the proposal are presented. Both the information encoded in structures is defined and the method of calculating the amount of this information is introduced. The proposed approach is applied to the operation of a molecular multicomponent machine. [ABSTRACT FROM AUTHOR]

[Display omitted] The previously observed effects of nonpolar additives on the scission energy and rheological properties of surfactant wormlike micelles can be explained in terms of the spatial distribution of the additive within the micelles. The dependence of the scission energy with the molecular organization of the system can be analyzed with a molecular theory capable of describing the thermodynamics and structure of the micelles. A new theoretical method to determine the scission energy of surfactant wormlike micelles is introduced. This methodology is based on a molecular theory that explicitly considers molecular details of all components of the micelles, and their inter- and intramolecular interactions without the use of fitting and/or empirical macroscopic parameters. The predicted effects of the concentration, molecular structure and hydrophobicity of the additive on the scission energy of cetyltrimethylammonium bromide (CTAB) wormlike micelles are found to be in qualitative agreement with previous experimental observations. In particular, our theory captures the decrease of micellar length with increasing content of highly hydrophobic additives and the non-monotonic dependence of the viscosity with additive hydrophobicity. The latter effect arises because highly and mildly hydrophobic additives affect the scission energy of wormlike micelles via markedly different molecular mechanisms. [ABSTRACT FROM AUTHOR]

Recently, A. Kovalenko et al. reported the computational study of molecular structure and energetics of CO2 + H2 reduction reaction on Cu-, Cu2O-, Fe-, and Fe3O4-based nanocatalysts in the J. Mol. Model., 26, 267 (2020). The authors claim that they developed and tested the multiscale modeling description of this process by combining the periodical boundary condition density functional theory (PBC DFT) and molecular theory of solvation. However, due to inappropriate selection of intermediate strictures, in particular, the unfavorite structure of CO* adsorbed on Cu-, Cu2O-, Fe-, and Fe3O4-nanoparticles, and some inconsistency in preparation of initial structures by DFT approach, there are serious concerns about the correctness and quality of the presented results. In addition, by this comment, I would like to help other researchers working on the development of new catalysts for electrochemical reduction of CO2 to avoid further misunderstandings following this study. [ABSTRACT FROM AUTHOR]

This article introduces potential wells around nuclei and their roles in chemical bonds. The approach uses one-electron Bohr atomic model concept. Multi-electron atoms are converted to one-electron atoms by grounding all inactive, non-reacting electrons using the Apparent Nuclear Charge (ANC) and Electron Shielding Effect (ESE) concepts introduced in earlier publications. Then, the resulting two one-electron atoms and their potential wells are utilized to obtain the related chemical bond length. The methodology is applicable to all elements of periodic table without a need for any additional tool. To test the concept, calculated bond lengths were compared to experimental ones for about 90 different bonds, which showed an average error of less than 5%. The article discusses some nontraditional views for chemical bonds which may contradict the traditional beliefs in chemistry. Hopefully, readers would consider the calculated results in support of the presented views. Attached to this article is a computer software program which was prepared with sample input and output files for readers. The software can be utilized to obtain any interested bond length. The software is applicable to all elements in the periodic table up to the element Hassium with the atomic number of 108. [ABSTRACT FROM AUTHOR]

The main purpose of this work is to analyze the effect of steric hindrance on the photoelectric performance of three different donor sensitizers (ZHG5, ZHG6, and ZHG7) by molecular theory simulation engineering. Photoelectric physical and photoelectric chemical parameters are investigated by means of frontier molecular orbital, global reactivity descriptors, optical absorption properties, fluorescent lifetime, charge density difference, and influence of external electric field. The results showed that the performance of the quinoxaline sensitizer was deteriorated by gradually increasing the steric hindrance to auxiliary donors. The optical properties of the hybridization of cir-coronene graphene quantum dot (GR) with the three dyes have been revealed, and the results show that graphene quantum dots can indeed improve the optical properties of solar cells. In addition, nine new molecules were designed by inserting six functional groups; it is found that inserting -CN in the acceptor part of the molecular structure is beneficial to the performance of the sensitizer. [ABSTRACT FROM AUTHOR]

[Display omitted] • Enhanced thermal conductivity by tuning the polymer intrinsic structure. • Enhancement of polymer thermal conductivity using external conditions. • Analysis of thermal conductivity contribution factors by bonding cooperation. • Modulation of polymer thermal conductivity by cross-linking degree. The inherent thermal transport properties of epoxy resin are vital factors to be studied in applications. In the present work, we constructed the amorphous crosslinking structure, the step crosslinking structure and the ordered crosslinking structure based on molecular dynamics theory, and used the reverse nonequilibrium molecular dynamics (RNEMD) method to calculate the thermal conductivity (TC) of different structures. Based on the numerical verification of the reliability of the method, the contribution of bonding to the TC was enhanced by increasing the molecular arrangement orderliness to reduce phonon scattering, taking the composition of the TC contribution as the guide. Meanwhile, the contribution of non-bonding interaction to the TC was enhanced by using compression process to achieve TC increase in the epoxy resin intrinsic structure, followed by exploring the effect of cross-linking degree on the TC of different structures. The results showed that the TC of amorphous epoxy resin decreased with the increase of crosslinking degree, and the relative high-frequency VDOS increased, but the influence of crosslinking degree on TC was minor in the range. For amorphous epoxy resin four-sided pressurization varied in the range of 0–7 Gpa, the non-bond energy percentage increased in the range of 0–60%, and the increase of non-bond energy made its contribution to TC increased significantly. The epoxy resin achieved 215% improvement in intrinsic TC by changing the molecular arrangement orderliness. The ordered structure TC varied from 0.3 to 3.5 W/(m⋅K) in the pressure variation range of 0–7 GPa. As the structure becomes more ordered, the TC increased significantly with the degree of cross-linking. The study provided the theoretical basis for the realization of resin preparation and resin thermal property evaluation with regulated intrinsic TC. [ABSTRACT FROM AUTHOR]

[Display omitted] • Benzothiazole based Schiff bases showed excellent anticorrosive property in 1 M HCl. • Electrochemical study unveiled corrosion inhibition efficiency of the studied inhibitors. • Heteroatoms and molecular structure effecting corrosion inhibition has been explained. • FESEM, AFM and contact angle confirmed inhibitors' adsorption on mild steel surface. • DFT, Fukui indices, NCI-RDG, MD simulation and RDF analysis validated experimental findings. Synthesis of challenging corrosion inhibitors is of prime importance to inhibit hydrogen-induced and localised metallic corrosion occur in the corrosive acidic solution. In this regard, the present research has been focused on the development of functionalised Schiff bases, namely, 1-(benzo[ d ]thiazol-2-yl)-2-((furan-2-yl)methylene)hydrazine (BTFMH), 1-(benzo[ d ]thiazol-2-yl)-2-((thiophen-2-yl)methylene)hydrazine (BTTMH), 1-(benzo[ d ]thiazol-2-yl)-2-((5-methylthiophen-2-yl)methylene)hydrazine (BTMMH) with an aim of effectively curtailing the issues associated to hydrogen-induced cracking and subsequent inhibition of metallic corrosion taking place in the corrosive acidic solution. The corrosion inhibiting performances of the synthesized inhibitors have been assessed for mild steel surfaces exposed in 1 M HCl medium using gravimetric measurement, potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) techniques. Potentiodynamic polarization study revealed that the synthesized inhibitor molecules retarded the cathodic hydrogen evolution reaction at cathodic site and subsequently minimized the oxidation of metals at anode; thereby, these Schiff bases acted as the mixed type inhibitors. The EIS study revealed that the corrosion inhibition phenomenon is being controlled through charge transfer processes. All of these three synthesized inhibitor molecules showed approximately 96–98 % corrosion inhibiting efficiency at exceedingly low concentration (0.5 mM). The inhibition efficacy obtained for these synthesized inhibitor molecules follows the order: BTMMH > BTTMH > BTFMH. The adsorption nature of these inhibitor molecules on mild steel surfaces have been revealed through surface morphology, topography and water contact angle studies. Thereafter, the insight of corrosion inhibition mechanism at atomic level have been explored by density functional theory (DFT). The optimized geometrical structure, electron density distribution of frontier molecular orbitals and their corresponding energy parameters obtained from DFT as well as Fukui indices analysis have been explored to unveil the plausible modes of adsorption or the reactive sites present within the inhibitor molecules which facilitate their interactions with surface atoms of metals. The non-covalent interaction based on reduced density gradient have been explored to study intrinsic feeble interaction acting with the molecules. Afterwards, molecular dynamics simulation has been employed to validate the spontaneity along with the nature of interaction at the metal inhibitor interface. Furthermore, the equilibrium adsorption configuration of the synthesized inhibitor molecules on the targeted metal surface atoms have been envisaged and the interfacial phenomenon has been explained. [ABSTRACT FROM AUTHOR]

Abstract: Statistical–mechanical, 3D-RISM-KH molecular theory of solvation is an integral equation theory of molecular liquids capable of describing, from the first principles, solvation structure and thermodynamics in complex nanoscale systems. The 3D-RISM-KH theory accurately yields the solvation structure for biomolecular systems as large as chaperonins and ion channels. It predicts 3D maps of ligand binding affinity at once without using empirical scoring functions, and has significant potential for computer-aided drug design. Recently, the 3D-RISM-KH theory was coupled with MD simulations by contracting solvent degrees of freedom to treat solvated biomolecules, and the MD/3D-RISM-KH multiscale method was implemented in the Amber molecular dynamics package [T. Luchko et al., 2010, []]. The MD/3D-RISM-KH method allows one to study biomolecular processes on extremely long timescales, as the statistics of rare solvent and ligand events is accounted for analytically. We further replaced the MM/GB(PB)SA post-processing which evaluates the free energy by empirical treatment of non-polar solvation effects with the MM/3D-RISM-KH method which employs 3D-RISM-KH to evaluate the solvation thermodynamics. In this paper, we briefly review the 3D-RISM-KH theory as well as the MD/3D-RISM-KH multiscale method implemented in the Amber package. We illustrate the MM/3D-RISM-KH method on binding of thiamine (vitamin of group B) to extracytoplasmic thiamine-binding lipoprotein MG289, and on the microscopic solvation properties of the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) homologue. [Copyright &y& Elsevier]

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule's chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule's stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol). [ABSTRACT FROM AUTHOR]

A combined theoretical and experimental study on the fragmentation of the mono-halogenated biphenyls; 2-chlorobiphenyl, 2-bromobiphenyl and 2-iodobiphenyl upon electron impact is presented. The appearance energies of the fragments observed and the energy dependence of their relative cross sections are reported. This is a follow up on our previous report (Barclay et al., 2019) [ 24 ] on the influence of the dihedral angle on the ionization energy of these compounds, but here we report the appearance energies and the energy dependence of the relative cross-section for all the major fragments. The appearance energies are compared to quantum mechanical threshold calculations at the coupled cluster level of theory and possible molecular structures and reaction pathways are discussed for the observed m / z ratios. For the loss of the halogen along with 1–2 H the agreement between the experiment and theory is good as reported earlier. However, the discrepancy is considerably larger for the ring rupture channels. Image 1 [ABSTRACT FROM AUTHOR]

The Raman spectra of all-trans- β -carotene (β -Car) liquefied in dimethyl sulfoxide (DMSO) with the decrease of temperature from 333 K to 263 K were recorded with the aim to reveal the molecular structure properties during phase transition. The CC stretching mode of β -Car shows red shift during liquid and solid phase, while blue shift during the liquid-solid phase transition. The 1425 cm−1 Raman band of DMSO shows the inverse characters for β -Car. Raman shift and intensity in coalescence caused by phase transition are studied by means of density functional theory and the molecular vibration mechanism is found out. The calculated Raman spectra of β -Car and DMSO accurately assign the vibrational modes. The potential energy was calculated to investigate the effect of β -ring rotation on Raman shift during phase transition. The latent 1452 cm−1 Raman band of β -Car crops up when temperature drops to the transformation point of 288 K and the 1425 cm−1 Raman band of DMSO split into two peaks at 1417 cm−1 and 1427 cm−1 after phase transition. Phase transition inducing individual methyl groups vibrations helps to interpret the dwindling intensity of 1425 cm−1 Raman peak of DMSO and the increase of 1452 cm−1 Raman peak of β -Car. A visualisation of nuclear motions is illustrated for better understanding the characteristics of vibronic variations of β -Car molecule in critical phenomena. The implication of these analyses is expected to be helpful for the understanding of the effect of phase transition on biomolecules in solution. Image 1 • Phase transition induced Raman shift and intensity of β -Car has been proposed. • β ring rotation plays key role for Raman shift during liquid-solid phase transition. • Individual methyl group vibrations lead to the Raman intensity variation during phase transition. [ABSTRACT FROM AUTHOR]

The Einstein-Brillouin-Keller semiclassical quantization and the topological Maslov index are used to deduce the correct quantum mechanical values for the energy of a one-electron atom (both nonrelativistically and relativistically) and a three-dimensional harmonic oscillator. The development is concise, transparent, and involves only elementary integral calculus and provides a conceptual and intuitive introduction to the quantum nature of the atomic and molecular structure of matter. [ABSTRACT FROM AUTHOR]