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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]

Machine learning (ML) methods are being used in almost every conceivable area of electronic structure theory and molecular simulation. In particular, ML has become firmly established in the construction of high-dimensional interatomic potentials. Not a day goes by without another proof of principle being published on how ML methods can represent and predict quantum mechanical properties—be they observable, such as molecular polarizabilities, or not, such as atomic charges. As ML is becoming pervasive in electronic structure theory and molecular simulation, we provide an overview of how atomistic computational modeling is being transformed by the incorporation of ML approaches. From the perspective of the practitioner in the field, we assess how common workflows to predict structure, dynamics, and spectroscopy are affected by ML. Finally, we discuss how a tighter and lasting integration of ML methods with computational chemistry and materials science can be achieved and what it will mean for research practice, software development, and postgraduate training. [ABSTRACT FROM AUTHOR]

The intriguing properties of polycyclic structure known as benzenoid hydrocarbons, which are unsaturated and totally conjugated molecules with hexagonal rings, continue to entice researchers to investigate their chemical and physical molecular structure with reference to aromaticity. To correlate important molecular structural attributes such as enthalpy, melting, boiling point, and cyclicity, numerical descriptors or topological indices which have been used for decades, for variety of two and three dimensional chemical structures networks or graphs with vital physicochemical properties. To determine the degree‐based topological indices, in this study, the degrees of the chemical structure or graph of the molecule under examination are utilized. In molecular graph theory, M‐polynomial is a relatively recent approach for investigating chemical networks and structures. It shows numerical descriptors in algebraic form and highlights molecular properties as a polynomial function. In this study, we propose a polynomials presentation of two‐dimensional coronene fractal structures and compute numerous M‐polynomials, including the M‐polynomials of the first and second Zagreb indexes, as well as the Randic index. [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]

Nanoscience has progressed exponentially during the previous few decades, moving from bench science to complex applied technologies. Nanomaterials found their application in large number of industrial products which includes filters, paints, insulation, electronic components, lubricant additives, biomedical applications, etc. One such important nanomaterial is lead sulphide, an inorganic compound with the chemical formula PbS, and is one of the most common ore of Galena. The graphical depiction of the molecular structure determines how the atoms are organised in real three-dimensional space. Graphical representation encloses a detailed study of the physical and chemical properties of molecules for the calculation of degree and distance-based graph parameters. Such parameters are termed as topological indices of graph and are usually numerical parameters. The resolvability parameters of a graph are a highly innovative topic in which the entire structure is molded to obtain each atom's unique position. In this work, we consider some degree and distance-based graph parameters of an inorganic compound, namely, lead sulphide. In particular, we study its metric dimension and fault-tolerant metric dimension. We also obtain first, second, and third Zagreb index for PbS. [ABSTRACT FROM AUTHOR]

We propose a molecular theory for fluids of structured molecules based on the Born-Bogoliubov-Green-Kirkwood-Yvon (BBGKY) hierarchy for classical fluids. We treat the polyatomic molecules as an N-body mixture of its constituent moieties. The reassembly of these chemical units into the original molecules is achieved via the site-site interaction potentials. To find the usual total correlations and direct correlations, we incorporate the Lebowitz-Percus functional derivatives, i.e. the 'fluctuation-compressibility' derivatives into the first member of the BBGKY. This enables us to construct a generalised Ornstein-Zernike equation for the system of dimeric molecules. We are able to separate out from the resulting equation a part that is identified as the direct correlation functions. This equation involves higher order correlations, namely the triplet correlation functions. We contrast this direct correlation with those from the earlier reference interaction site model (RISM) and exhibit the differences between the two approaches. A new theoretical framework is established, as an alternative to other current theories for polyatomic molecular fluids. [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]

Although nanostructures self-assembled by short peptides are very promising in developing novel biomaterials and nanomaterials, it is still a great challenge to design the peptide molecular structure which will self-assemble into designated nanostructures. By combining elastic theory with molecular dynamics simulations, we introduce a multiscale computational approach to predict the β-sheet morphology self-assembled by short peptides in aqueous solution only based on the molecular structure of the peptide. In our approach, the gap between the elastic model and atomistic model is bridged by the simplified model, whose parameters are determined by enhanced sampling and extensive all-atom molecular dynamics simulation results at different levels. This multiscale approach is applied to two model peptides KIIIIK (KI4K) and IIIIKK (I4K2) to test its validity. The computational results, consistent with the previous experimental observations, show that KI4K with a higher ratio of inter-sheet interaction to intra-sheet interaction tends to form tube-like morphology with a larger width, while I4K2 with a lower ratio tends to form fibril with a smaller width. This methodology is anticipated to be helpful for computer-aided design of nanostructures self-assembled by short peptides. [ABSTRACT FROM AUTHOR]

We perceive smells as perduring complex entities within a distal array. However, odor theories have been recently criticized for their conception of the spatiotemporal nature of olfactory perception and the individuation of distal odors. The paper does not aim to dispute these criticisms. Rather, what will be shown is that molecular structure theory, a refinement of odor theory, can be further developed to handle these challenges. The theory is further refined by focusing on distal perception that requires considering the perceptual object as mereologically complex persisting odor against a background scene conceived of as a smellscape. [ABSTRACT FROM AUTHOR]

Nevadensin 2-(4-methoxyphenyl)-5,7-dihydroxy-6,8-dimethoxy-4H-1-benzo-pyran-4-one] is a natural bioactive flavonoid compound that has the potential to become a novel "natural lead" in the field of drug discovery program. The molecular structure, vibrational frequencies, and corresponding vibrational assignment of nevadensin have been investigated experimentally and theoretically by employing the B3PW91/6–311++G(d,p) method. The fundamental vibrational wave numbers as well as their intensities were calculated, and a good correlation between experimental and scaled calculated wave numbers had been accomplished. The ultraviolet spectrum of the studied molecule was recorded in the region 200–500 nm, and the electronic properties were predicted by the time-dependent density functional theory approach. 1H and 13C NMR spectra have been calculated by employing the gauge-independent atomic orbital method. Nevadensin has been reported to exhibit antimicrobial activities against both Gram-positive and Gram-negative bacteria and also against the fungal pathogens, highlighting the pharmacological importance of the molecule. [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]

New liquid crystals categorised as cholesteryl dimers have been successfully synthesised through the reaction between cholesteryl 4-(prop-2-ynyloxy)benzoate moieties with n-azido(cholesteryloxy-carbonyl)alkane. All the dimers display enantiotropic mesophases. Whilst the odd-numbered dimers exhibit chiral nematic (N*), twisted grain boundary (TGB) and chiral smectic C (SmC*) phases, the even-numbered members from the same series show chiral smectic A and C. A detailed inspection on mesophase reveals that the chiral centres and the bent conformation of the odd-numbered members are essential for the induction of TGB phase. However, upon decreasing the temperature, the ratio of the transition temperatures (TSmC*-SmA*/TSmA*-I) is found to be 0.95, which indicate the second order transition according to the McMillan's molecular theory. In addition, the X-ray diffraction study supports the presence of the smectic A phase on the even members rather than the N* by the appearance of the Bragg diffraction peaks at 190°C. A comparison study with the other analogues in which the cholesterol entity is substituted by azobenzene or biphenyl tails has been carried out to assess the relationship between the molecular structure and mesomorphic behaviour. [ABSTRACT FROM AUTHOR]

In the analysis of molecular structure and local order in heterogeneous samples, multiphoton excitation of fluorescence affords chemically specific information and high-resolution imaging. This report presents the results of an investigation that secures a detailed theoretical representation of the fluorescence polarization produced by one-, two-, and three-photon excitations, with orientational averaging procedures being deployed to deliver the fully disordered limits. The equations determining multiphoton fluorescence response prove to be expressible in a relatively simple, generic form, and graphs exhibit the functional form of the multiphoton fluorescence polarization. Amongst other features, the results lead to the identification of a condition under which the fluorescence produced through the concerted absorption of any number of photons becomes completely unpolarized. It is also shown that the angular variation of fluorescence intensities is reliable indicator of orientational disorder. [ABSTRACT FROM AUTHOR]

Recently [Y. S. Djikaev and E. Ruckenstein, J. Phys. Chem. B 111, 886 (2007)], the authors proposed a kinetic model for the nucleation mechanism of protein folding where a protein was modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads and the composition of the growing cluster of protein residues was assumed to be constant and equal to the overall protein composition. Here, they further develop the model by considering a protein as a three-component heteropolymer and by allowing the composition of the growing cluster of protein residues to vary independently of the overall one. All the bonds in the heteropolymer (now consisting of hydrophobic, hydrophilic, and neutral beads) have the same constant length, and all the bond angles are equal and fixed. As a crucial idea of the model, an overall potential around the cluster wherein a residue performs a chaotic motion is considered to be a combination of the average dihedral and average pairwise potentials assigned to the bead. The overall potential as a function of the distance from the cluster center has a double well shape which allows one to determine its emission and absorption rates by using a first passage time analysis. Knowing these rates as functions of three independent variables of a ternary cluster, one can develop a self-consistent kinetic theory for the nucleation mechanism of folding of a protein using a ternary nucleation formalism and evaluate the size and composition of the nucleus and the protein folding time. As an illustration, the model is applied to the folding of bovine pancreatic ribonuclease consisting of 124 amino acids whereof 40 are hydrophobic, 81 hydrophilic, and 3 neutral. With a reasonable choice of diffusion coefficients of the residues in the native state and potential parameters, the model predicts folding times in the range of 1–100 s. [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]

Systematic efforts to synthesize fullerene-containing liquid crystals have produced a variety of successful model compounds. We present a simple molecular theory, based on the interconverting shape approach [Vanakaras and Photinos, J. Mater. Chem. 15, 2002 (2005)], that relates the self-organization observed in these systems to their molecular structure. The interactions are modeled by dividing each molecule into a number of submolecular blocks to which specific interactions are assigned. Three types of blocks are introduced, corresponding to fullerene units, mesogenic units, and nonmesogenic linkage units. The blocks are constrained to move on a cubic three-dimensional lattice and molecular flexibility is allowed by retaining a number of representative conformations within the block representation of the molecule. Calculations are presented for a variety of molecular architectures including twin mesogenic branch monoadducts of C60, twin dendromesogenic branch monoadducts, and conical (badminton shuttlecock) multiadducts of C60. The dependence of the phase diagrams on the interaction parameters is explored. In spite of its many simplifications and the minimal molecular modeling used (three types of chemically distinct submolecular blocks with only repulsive interactions), the theory accounts remarkably well for the phase behavior of these systems. [ABSTRACT FROM AUTHOR]

Abstract We report here the synthesis and a combined experimental and theoretical study on molecular structure of 2-thioxo- 3N-(2-methoxyphenyl) −5 [4′-methyl -3′N -(2′-methoxyphenyl) thiazol-2′(3′H)-ylidene] thiazolidin-4-one. The crystal structure has been determined by X-ray diffraction. Crystallographic data revealed that the compound crystallizes in a monoclinic system with a space group of P 2 1 / c , with crystal cell parameters: a = 10.618 (3), b = 13.180 (5), c = 15.101 (3) Å, β = 97.766 (16), V = 2093.9(11) A3 and Z = 4. The final R-value was 0.0405 based on 4801 observed reflections. From the dihedral angle values, the structure was found to be significantly non planar. Density functional theory (DFT) calculation were carried out to obtain the ground state optimized geometry of the molecule using B3LYP and HSEH1PBE methods with 6-311G(d,p) basis set. The optimized geometry of the title compound was found to be consistent with the structure determined by X-ray diffraction. The stability of the title compound is due to the presence of a good number of potential donor and acceptor groups establishing intermolecular interactions like C H⋅⋅⋅O, C H⋅⋅⋅S and π-π stacking linking the molecules into dimers with C(6), R 2 2 (18) and R 2 2 (24) graph sets. In addition, the solid state behaviors of molecules in the crystal were studied using 3D Hirshfeld surface analysis and associated 2D fingerprint plots. Calculated frontier molecular orbitals (FMOs) energies and chemical reactivity parameters indicated that the molecule under investigation exhibits high first hyperpolarizability, typical of a NLO material. Graphical abstract Image 1 Highlights • Synthesis and characterization of the title compound have been reported. • X-ray single crystal and molecular structures were determined. • Hydrogen bonds were examined using Hirshfeld surface analysis. • HOMO, LUMO and MEP were investigated. • Molecular NLO properties were calculated. [ABSTRACT FROM AUTHOR]

We present a theoretical analysis of the effects that lead to distortion or symmetry restoration of the nuclear configuration in ions of weakly bound molecular systems and clusters. The vibronic coupling mechanisms involved are reviewed and discussed in terms of simple and general models. Guided by a qualitative characterization of the wave function of a loosely bound system, we study the symmetry determining effects for such ions in terms of first order (Koopmans’), relaxation and correlation distortion energies associated with electron removal from the parent system. Our discussion suggests that the Koopmans’ approximation can reasonably be expected to provide a qualitatively correct dependence of the ion energy on nuclear motion. Exceeding these expectations, it is found in numerical applications to the He+3 and He+4 ions that the relaxation and correlation energy changes accompanying symmetry breaking tend to cancel exactly. This implies, and we show in practice, that while insufficiently accurate correlation energy estimates may easily lead to incorrect geometries, the inexpensive Koopmans’ approximation can often suffice to obtain the correct energy curvature along symmetry breaking coordinates. Further preliminary results for N3 and CO+2 suggest that these findings have a much wider applicability than anticipated. [ABSTRACT FROM AUTHOR]

The development of switchable mechanically interlocked molecular architectures (MIMAs) is an active area of experimental and theoretical research because the environmental-responsiveness of these systems makes them desirable candidates for incorporation into molecular machines. Presented here is a review of the recent literature that reports theoretical and computational studies of these topologically complex systems. Modelling strategies that have been applied to switchable MIMAs are analysed and outstanding challenges to theory and computation are highlighted. [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]

Magnetic nanomaterial-based electrochemical cytosensor holds great promise to tackle the challenges in isolation and detection of circulating tumor cells (CTCs) by the combination of the selectivity of magnetic cell separation with high sensitivity of electrochemical sensing platforms. Herein, by leveraging nanomaterials with L -cysteine and folic acid, we design innovative biomaterials for electrochemical cell detection, with minimal materials and materials manufacturing steps. Folic acid- L -cysteine-capped CoFe 2 O 4 nanoparticles (CCF) are developed to magnetically capture folate-overexpressed tumor cells. Hybrids of L -cysteine-folic acid and silver nanowires (FAgNWs) are synthesized using a green, convenient and template-free approach without any surfactant. Direct immobilization of L -cysteine and folic into silver nanowires hybrids facilitates the electrode preparation and cell detection. The density functional theory and molecular dynamics simulations were also used to provide deep insight into the interaction of silver nanowires with L -cysteine coupled with folic acid (LCFA). An affordable nanocytosensor is proposed for the detection of CTCs by sandwiching the MCF-7 cells captured between CCF and FAgNWs. This nanocytosensor has the low detection limit of 5 MCF-7 cells/mL with the wide dynamic range of 50–106 cells/mL. The presented nanomaterial-based sensing platform is promising for convenient cell isolation and detection. [Display omitted] • Magnetic isolation of circulating tumor cells were carried out using functional CoFe 2 O 4 magnetic nanoparticles. • Hybrids of L -cysteine-folic acid and silver-nanowires (FAgNWs) were deveoped for cell sensing. • The presented sandwich-like electrochemical platform successfully detected MCF-7 cells with the low detection limit of 5 cells/mL. • The deep insight into the FAGNWs molecular structures provided by the density functional theory and molecular dynamic simulations. [ABSTRACT FROM AUTHOR]

Liquid-crystalline D-A dyads and A-D-A triads, based on the chemical association of electron-donor (D) triphenylene discogens and electron-acceptor (A) perylene/benzoperylene diimides, have been synthesized by the Pd-catalyzed Sonogashira coupling/DBU-promoted cyclization reactions tandem. These molecular heterojunctions spontaneously self-organize into columnar hexagonal (Col hex) or/and rectangular (Col rec) mesophases, over broad temperature ranges including room temperature, with the antagonist moieties segregated into alternated homo-molecular (homolithic) stacks within mixed columns. Their intramolecular electron and energy transfers have been studied by UV/Vis absorption and fluorescence emission spectroscopies. Due to photo-induced electron transfer between donor and acceptor units, fluorescence quenching is systematically observed for all the dyads and triads. This study further reveals that perylenediimide is a stronger electron acceptor than the larger benzoperylenediimide building block. Density function theory calculations of their molecular structures and HOMO-LUMO energy levels and gaps support the experimental results and demonstrate that these donor-acceptor systems have potential applications in various optoelectronic devices. • Dyad and triad discotic mesogens were synthesized by Sonogashira coupling/DBU-promoted cyclization reactions tandem. • Fluorescence quenching is observed for all compounds due to photo-induced electron transfer between donors and acceptors. • The compounds exhibit hexagonal and rectangular columnar mesophases over broad temperature ranges. [ABSTRACT FROM AUTHOR]

The synthesis and X-ray molecular structure of the first metal-stabilized o-dithiobenzoquinone [Cp*Ir-o-(η4-C6H4S2)] (2) are described. The presence of the metal stabilizes this elusive intermediate by p coordination and increases the nucleophilic character of the sulfur atoms. Indeed, the p-bonded dithiolene complex 2 was found to react with the organometallic solvated species [Cp*M(acetone)3][OTf]2 (M = Rh, Ir) to give a unique class of binuclear dithiolene compounds [Cp*Ir(C6H4S2)MCp*][OTf]2 [M = Rh (3), Ir (4)] in which the elusive dithiolene η-C6H4S2 acts as a bridging ligand toward the two Cp*M moieties. The electrochemical behavior of all complexes was investigated and provided us with valuable information about their redox properties. Density functional theory (DFT) calculations on the π-bonded dithiobenzoquinone ligand and related bimetallic systems show that the presence of Cp*M at the arene system of the dithiolene ligand increases the stability compared to the known monomeric species [Cp*Ir-o-(C6H4S2-κ2-S,S)] and enables these complexes Cp*Ir(C6H4S2)MCp*][OTf]2 (3 and 4) to act as electron reservoirs. Time-dependent DFT calculations also predict the qualitative trends in the experimental UV–vis spectra and indicate that the strongest transitions arise from ligand–metal charge transfer involving primarily the HOMO–1 and LUMO. All of these compounds were fully characterized and identified by single-crystal X-ray crystallography. These results illustrate the first examples describing the coordination chemistry of the elusive o-dithiobenzoquinone to yield bimetallic complexes with an o-benzodithiolene ligand. These compounds might have important applications in the area of molecular materials. [ABSTRACT FROM AUTHOR]

Latent molecular properties are not exhibited by the given molecular structure but are reproducibly exhibited by the same molecule in a different electronic state or if some molecular interactions have taken place. A consequence of the Holographic Electron Density Theorem, as applied to latent properties, provides a framework that allows an extension of the expectation value formalism, leading to 'unexpected' expectation value expressions for latent properties. Connections of special cases of this approach to earlier density matrix extrapolation methods are pointed out. [ABSTRACT FROM AUTHOR]

A molecular statistical theory of the smectic A phase is developed taking into account specific interactions between different molecular fragments which enables one to describe different microscopic scenario of the transition into the smectic phase. The effects of nanoscale segregation are described using molecular models with different combinations of attractive and repulsive sites. These models have been used to calculate numerically coefficients in the mean filed potential as functions of molecular model parameters and the period of the smectic structure. The same coefficients are calculated also for a conventional smectic with standard Gay-Berne interaction potential which does not promote the segregation. The free energy is minimized numerically to calculate the order parameters of the smectic A phases and to study the nature of the smectic transition in both systems. It has been found that in conventional materials the smectic order can be stabilized only when the orientational order is sufficiently high, In contrast, in materials with nanosegregation the smectic order develops mainly in the form of the orientational-translational wave while the nematic order parameter remains relatively small. Microscopic mechanisms of smectic ordering in both systems are discussed in detail, and the results for smectic order parameters are compared with experimental data for materials of various molecular structure. [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]

Previously (Hähnke et al., J Comput Chem 2010, 31, 2810) we introduced the concept of nonlinear dimensionality reduction for canonization of two-dimensional layouts of molecular graphs as foundation for text-based similarity searching using our Pharmacophore Alignment Search Tool (PhAST), a ligand-based virtual screening method. Here we apply these methods to three-dimensional molecular conformations and investigate the impact of these additional degrees of freedom on virtual screening performance and assess differences in ranking behavior. Best-performing variants of PhAST are compared with 16 state-of-the-art screening methods with respect to significance estimates for differences in screening performance. We show that PhAST sorts new chemotypes on early ranks without sacrificing overall screening performance. We succeeded in combining PhAST with other virtual screening techniques by rank-based data fusion, significantly improving screening capabilities. We also present a parameterization of double dynamic programming for the problem of small molecule comparison, which allows for the calculation of structural similarity between compounds based on one-dimensional representations, opening the door to a holistic approach to molecule comparison based on textual representations. © 2011 Wiley Periodicals, Inc. J Comput Chem , 2011. [ABSTRACT FROM AUTHOR]

Abstract: A new approach to describe blast loading is suggested, herein referred to as the corpuscular approach. The detonation products are modeled as a set of discrete particles following Maxwell''s original kinetic molecular theory. For numerical purposes, the number of molecules has to be greatly reduced compared to what one has in real gases. However, the total molecular mass and temperature dependent velocity distribution are the same as in an ideal gas. Pressure loading on structures is then numerically represented by the momentum transfer as particles impact and rebound from the surface of the structure. The suggested approach has significant advantages compared to today''s state-of-the-art continuum-based approaches to fully coupled blast-loading computations. The computational time can be significantly reduced, the method is numerically robust and the approach will easily cope with complex geometries in the fluid–structure interface. [Copyright &y& Elsevier]

Analytical energy gradients have been implemented in the DALTON program at the level of explicitly correlated second-order Møller-Plesset perturbation theory (MP2-R12). The implementation has been accomplished for standard approximation A using an auxiliary basis which is the same as the orbital basis for the resolution-of-the-identity, with and without frozen core. As a test calculation, the geometries of nine stationary points on the potential energy surface of the water dimer have been optimized and the results are compared with earlier studies. [ABSTRACT FROM AUTHOR]

A mathematical analysis of several algorithms, for the integration of the differential equation associated to the Intrinsic Reaction Coordinate path, is performed. This analysis first shows that the Intrinsic Reaction Coordinate path can be derived from a variational problem, so that it has the properties of an extremal curve. Then, one may borrow the mathematical methods for the integration of extremal curves, to formulate new algorithms for the integration of the Intrinsic Reaction Coordinate path. One may use also this theoretical framework, to recast recently formulated algorithms based on direct minimization of an arbitrary curve, such as the Nudged Elastic Band Method or String Method. In this view a new algorithm is proposed. Finally, the theory of broken extremals is used to analyse an Intrinsic Reaction Coordinate path possessing a valley ridge inflection point. [ABSTRACT FROM AUTHOR]

Scaling factors have been derived to obtain fundamental vibrational frequencies with the recently introduced semiempirical molecular orbital methods RM1 and PM6, implemented in MOPAC2007. A least-squares approach is used with a training set comprised of 90 singlet-state molecules and 922 distinct vibrations, extracted from the NIST Computational Chemistry Comparison and Benchmark Database (CCCBDB). Results are presented both for the conventional Scott-Radom type single-factor fitting, and for a multi-factor linear model: Semiempirical Semiglobal Self-consistently Scaled Quantum Mechanical (S4QM). The new NDDO methods in conjunction with the multi-linear fitting are shown to yield improved prediction of vibrational frequencies. To demonstrate the performance of S4QM//PM6 for calculating vibrational spectra, the examples of indene, indazole and four tetrachlorinated p-dibenzodioxins are presented. [ABSTRACT FROM AUTHOR]

The ground electronic state potential energy surfaces of the title reactions have been studied at the CCSD(T)/6-311 + G(3df, 2p) level of theory with the geometric parameters optimized at the CCSD/6-311 + G(3df, 2p) level of theory. The direct hydrogen abstraction channels and the indirect association/decomposition channels from the chemically activated methanol molecule have been considered. The barriers for the direct hydrogen abstraction processes in CH3O + H and CH2OH + H are predicted to be 0.11 and 2.2 kcal mol-1, respectively. The rate constants for decomposition of the internally excited CH3OH following the barrierless association reactions have been calculated by micro-canonical VTST/RRKM theory for all accessible product channels. The individual rate constants for the formation of CH2O + H2, predicted to occur primarily by the direct abstraction processes, are in good agreement with the available experimental data in the literature; however, the predicted total rate constants for both title reactions are much greater than those from the literature and CH3 + OH, instead of CH2O + H2, are concluded to be the major products of both processes, contrary to the assumption commonly made in the literature. The branching rate constants for all accessible product channels have been predicted for combustion modeling applications. Additionally, the rate constants for the two related reaction systems, CH3 + OH and CH2 + H2O, have been calculated and compared with the available experimental data; in both cases, agreement between theory and experiment is excellent. [ABSTRACT FROM AUTHOR]

The high-accuracy W4 computational thermochemistry protocol, and several post-W4 methods, have been applied to the P2 and P4 molecules. Contrary to previous studies, we find the experimental thermochemistry to be fundamentally sound. The reaction enthalpy for P4→2P2 has a very significant contribution from post-CCSD(T) correlation effects. We derive a gas-phase heat of formation for the phosphorus atom of [image omitted] kcal mol-1 and [image omitted] kcal mol-1, in the upper half of the CODATA uncertainty interval. [ABSTRACT FROM AUTHOR]

We calculated the variational and diffusion quantum Monte Carlo forces using the Hellmann-Feynman theorem and Pulay's correction for the first-row diatomic and triatomic molecules (CO, NO, CO2 and NO2). It is demonstrated that Pulay's correction is important for accurate calculation of forces on non-hydrogen atoms. [ABSTRACT FROM AUTHOR]

A computer program has been written to perform analytic derivative calculations of magnetic response properties based on uncontracted multireference configuration interaction (MRCI) wavefunctions. At this point, orbital relaxation is neglected in this treatment and the basis functions are assumed to be independent of the perturbation. It is therefore equivalent to an untruncated sum-over-states (SOS) approach to the g-tensor. Hence, the treatment is more rigorous than all previous MRCI g-tensor calculations that have used truncated SOS formulations. In the present calculations, MRCI calculations were performed on top of full valence complete-active space self-consistent field (CASSCF) reference wavefunctions without truncation of the reference or correlation spaces. Results are reported for two types of spin-orbit coupling operators, a simple effective nuclear charge approximation and the spin-orbit mean field (SOMF) approximation. The effects of orbital relaxation are discussed. The values obtained can be used in future calibration studies. [ABSTRACT FROM AUTHOR]

An implementation of the projected gradient method for locating the minimum energy crossing point between electronic states of different symmetry/multiplicity within the equation-of-motion coupled-cluster family of methods is reported. The method is applied to characterize the intersections between electronic states in [image omitted], NO2, and para-benzyne using the excitation energies, ionization potential, and spin-flip variants of the equation-of-motion coupled-cluster methods. The performance of the algorithm is discussed and recommendations for improving the convergence in problematic situations are given. [ABSTRACT FROM AUTHOR]

An IC-MRCI ansatz has been used in conjunction with augmented quadruple-ζ basis sets to construct an 89-point potential energy surface of the ground electronic state of [image omitted]. The equilibrium structure was predicted to be of C2v symmetry, possessing Be-H bond lengths of 1.609 Å and a H-Be-H bond angle of 29.4°. A rational Padé analytical function was fitted to the discrete IC-MRCI grid yielding a [image omitted] value of 5.20 cm-1. It was embedded in the t-coordinate Eckart-Watson Hamiltonian to calculate vibrational and rovibrational wave functions. For the vibrational ground state, the vibration-averaged bond lengths and angle were 1.647 Å and 29.2°, respectively. An embedded analytical IC-MRCI dipole moment function fitted to 73 discrete points was transformed to the space-fixed frame. Rovibrational radiative properties were calculated using this surface in conjunction with a novel integration scheme. [ABSTRACT FROM AUTHOR]

Conformational studies were carried out on acetylcholine and two nerve agents (NAs), soman and sarin, to determine the influence of the low-energy conformers of NAs in inhibiting the hydrolysis of acetylcholine using state-of-the-art quantum chemical techniques. Different enantiomers of sarin and soman were taken into account during the conformational analyses. The aqueous solvation of these molecules was studied at the density functional level using the polarized continuum model with the conductor-like reaction field approach. The results show that, compared with acetylcholine, the NAs have less conformational flexibility in the gas phase. The conformational flexibility of these molecules increases during aqueous solvation, and the transition barrier to different low-energy conformations also decreases. This property, together with the molecular electrostatic potential surfaces of the NAs, was compared with those of acetylcholine to obtain an insight into the cholinesterase inhibition properties of these molecules. [ABSTRACT FROM AUTHOR]

The reaction pathways to [image omitted] (tolyl, benzyl, and tropylium) from o-, m-, and p-chlorotoluene radical cations have been studied at the SCF level of theory using the DZ and DZP basis sets. The equilibrium structures and relative energies for the local minima and transition states have been fully optimized and the harmonic vibrational frequencies have been evaluated to differentiate the local minimum and the transition state. The lowest barrier rearrangement pathway is the formation of the benzyl cation for all three isomers, corroborating the recent experimental findings of Kim and Shin. This benzyl channel involves [1,3] α-hydrogen migration at the entrance and the activation energy is calculated to be 40.3, 39.7, and 42.2 kcal mol-1 for the o-, m-, and p-isomer, respectively. The other competing rearrangement pathway involves [1,2] α-hydrogen migration at the entrance, which leads to the tropylium ion, and the activation barrier is predicted to be 55.5, 54.2, and 56.62 kcal mol-1 for the o-, m-, and p-isomer, respectively. The highest barrier process involves direct C-Cl bond cleavage that yields the tolyl cation with a 0 K dissociation energy of 61.6, 64.6, and 68.92 kcal mol-1 for the o-, m-, and p-isomer, respectively. [ABSTRACT FROM AUTHOR]

A hydroiodic acid molecule is dissociated by more than four water molecules. Here, the effect of an excess electron on the hexahydated hydroiodic acid where the dissociated structure [H3O+(H2O)5I-] is much more stable than the undissociated one [(H2O)6HI], is investigated. Upon binding an excess electron (e-), the cluster releases a hydrogen radical and forms the stable hexahydrated iodide [(H2O)6I-] when the initial kinetic energy is above ∼200 K, due to the small transition barrier (∼0.5 eV). The system with the hydrogen radical released, [(H2O)6I- + H·], is much more stable than the systems with an excess electron, [(H3O)+{e-(H2O)5}I-] or [e-(H2O)2(H3O)+(H2O)3I-]. [ABSTRACT FROM AUTHOR]

Coupled cluster and density-functional theory calculations of the electronic circular dichroism (ECD) spectra and optical rotatory dispersion (ORD) of (S)-methyloxirane and (S)-methylthiirane have been carried out for comparison to gas-phase experimental data. Coupled cluster simulations of the ECD spectra of both molecules are in excellent agreement with experiment, both for the positions of the transitions and for the signs and magnitudes of the rotational strengths. Density-functional theory yields the correct structure of the ECD spectra, but the transition energies are shifted to lower energies by up to 0.3 eV. Density-functional ORD curves of (S)-methylthiirane exhibit incorrect dispersion due to an early onset of the Cotton pole. The coupled cluster ORD curves of (S)-methylthiirane give the correct sign of the rotations, but overestimate their magnitude by up to 50% at shorter wavelengths. Although temperature-dependent harmonic vibrational corrections improve the comparison between coupled-cluster theory and experiment at 633 nm, such corrections produce an incorrect sign of the rotation at 355 nm. [ABSTRACT FROM AUTHOR]

We investigate isotope effects in dihydrogen systems using the nuclear orbital plus molecular orbital (NOMO) theory, which simultaneously determines nuclear and electronic wave functions without the Born-Oppenheimer approximation. In order to estimate the vibrational averaging bond distances, the analytical energy gradients are used for the NOMO theory. The bond distances of three dihydrogen-bonded systems, namely H3NX+ ··· XBeH, LiX ··· XC2H and H2BX ··· XF for X = H, D and T, are obtained. The X ··· X bond distances decrease with respect to the substitution T → D → H, which is contrary to the behaviour of typical hydrogen bonds. This indicates that isotope effects strengthen the X ··· X bond. This behaviour is analogous to the Ubbelohde effect observed in the solid phase. [ABSTRACT FROM AUTHOR]

Analytic energy gradients with respect to atomic coordinates for systems with translational invariance are formulated within the framework of Kohn-Sham Density Functional Theory. The energy gradients are implemented in the BAND program for periodic DFT calculations which directly employs a Bloch basis set made up of Slater-type (STOs) and numeric atomic orbitals (NAOs). The details of our implementation are described including the use of symmetry in the reciprocal and direct spaces, as well as the application of the frozen core approximation. [ABSTRACT FROM AUTHOR]

Over twenty ways to solve the DIIS equation are introduced and discussed. Some of these solution methods are inherently inaccurate and are never recommended, others have some efficiency or accuracy advantages that may be exploited in different situations. Two of these ways, linear least squares with substitution and elimination, and linear least squares with equality constraint, have the potential to produce solutions that are significantly more accurate than the traditional normal equation solutions. The choice of the most accurate solution approach for a given problem depends on various vector and matrix norm relations which are discussed. The advantage of one of these methods is demonstrated on a model problem, which has a closed-form solution. A simple geometrical interpretation is given for the DIIS method that involves minimization of a function value within a particular multidimensional plane. [ABSTRACT FROM AUTHOR]