Valence bond theory for chemical dynamics

Exploring the impact of novel thiazole-pyrazole fused benzo-coumarin derivatives on human serum albumin: Synthesis, photophysical properties, anti-cholinergic activity, and interaction studies

Derivatives of thiazole-pyrazole fused benzo-coumarin compounds were successfully synthesized and characterized, followed by a comprehensive spectroscopic investigation on various photophysical properties in different media. The multipronged approach using steady state and time resolved fluorescence spectroscopy pointed out the impact of substitution in the estimated spectroscopic and other physicochemical properties of the systems. Further, the evaluation of anti-acetylcholinesterase (anti-AChE) activity yielded significant insight into the therapeutic potential of the synthesized coumarinyl compounds for the treatment of Alzheimer's disease (AD). The findings revealed a non-competitive mode of inhibition mechanism, with an estimated IC50 value of 67.72 ± 2.00 nM observed for one of the investigated systems as AChE inhibitor. Notably, this value is even lower than that of an FDA-approved AD drug Donepezil (DON), indicating the enhanced potency of the coumarin derivatives in inhibiting AChE. Interestingly, significant diminution in inhibition was observed in presence of human serum albumin (HSA) as evidenced by the relative increase in IC50 value by 8 ∼ 39 % in different cases, which emphasized the role of albumin proteins to control therapeutic efficacies of potential medications. In-depth spectroscopic and in-silico analysis quantified the nature of interactions of the investigated systems with HSA and AChE. Overall, the outcomes of this study provide significant understanding into the biophysical characteristics of novel thiazole-pyrazole fused benzo-coumarin systems, which could aid in the development of new cholinergic agents for the treatment of AD and materials based on coumarin motifs.

Resonating holes vs molecular spin-orbit coupled states in group-5 lacunar spinels

The valence electronic structure of magnetic centers is one of the factors that determines the characteristics of a magnet. This may refer to orbital degeneracy, as for jeff = 1/2 Kitaev magnets, or near-degeneracy, e.g., involving the third and fourth shells in cuprate superconductors. Here we explore the inner structure of magnetic moments in group-5 lacunar spinels, fascinating materials featuring multisite magnetic units in the form of tetrahedral tetramers. Our quantum chemical analysis reveals a very colorful landscape, much richer than the single-electron, single-configuration description applied so far to all group-5 GaM4X8 chalcogenides, and clarifies the basic multiorbital correlations on M4 tetrahedral clusters: while for V strong correlations yield a wave-function that can be well described in terms of four V4+V3+V3+V3+ resonant valence structures, for Nb and Ta a picture of dressed molecular-orbital jeff = 3/2 entities is more appropriate. These internal degrees of freedom likely shape vibronic couplings, phase transitions, and the magneto-electric properties in each of these systems.

Zeno and Anti-Zeno Effects in Nonadiabatic Molecular Dynamics

Decoherence plays an important role in nonadiabatic (NA) molecular dynamics (MD) simulations because it provides a physical mechanism for trajectory hopping and can alter transition rates by orders of magnitude. Generally, decoherence effects slow quantum transitions, as exemplified by the quantum Zeno effect: in the limit of infinitely fast decoherence, the transitions stop. If the measurements are not sufficiently frequent, an opposite quantum anti-Zeno effect occurs, in which the transitions are accelerated with faster decoherence. Using two common NA-MD approaches, fewest switches surface hopping and decoherence-induced surface hopping, combined with analytic examination, we demonstrate that including decoherence into NA-MD slows down NA transitions; however, many realistic systems operate in the anti-Zeno regime. Therefore, it is important that NA-MD methods describe both Zeno and anti-Zeno effects. Numerical simulations of charge trapping and relaxation in graphitic carbon nitride suggest that time-dependent NA Hamiltonians encountered in realistic systems produce robust results with respect to errors in the decoherence time, a favorable feature for NA-MD simulations.

Establishment and Molecular Modeling Study of Cyclodextrin-Based Synergistic Enantioseparation Systems with Three New Amino Acid Chiral Ionic Liquids as Additives in Capillary Electrophoresis

Chiral ionic liquids (CILs) have attracted more and more attention due to their superior performance as chiral additives in capillary electrophoresis. In this work, based on the cyclodextrin (CD) derivatives and three new amino acid CILs (trifluoroacetate-L-Hydroxyproline, nitric acid-L-Hydroxyproline and trifluoroacetate-L-threonine), the new synergistic systems were established for chiral drug separation. In contrast to the traditional single glucosyl-β-CD (Glu-β-CD) separation system, the CIL/Glu-β-CD synergistic systems achieved improved resolution of three model drug racemates. Some experimental variables, such as CIL concentration, Glu-β-CD concentration, buffer pH, applied voltage, and the type and proportion of organic modifier, were optimized in the trifluoroacetate-L-Hydroxyproline/Glu-β-CD synergistic system. In addition, the recognition process in the synergistic system was studied through the molecular modeling method.

Diabatic States of Molecules

Quantitative simulations of electronically nonadiabatic molecular processes require both accurate dynamics algorithms and accurate electronic structure information. Direct semiclassical nonadiabatic dynamics is expensive due to the high cost of electronic structure calculations, and hence it is limited to small systems, limited ensemble averaging, ultrafast processes, and/or electronic structure methods that are only semiquantitatively accurate. The cost of dynamics calculations can be made manageable if analytic fits are made to the electronic structure data, and such fits are most conveniently carried out in a diabatic representation because the surfaces are smooth and the couplings between states are smooth scalar functions. Diabatic representations, unlike the adiabatic ones produced by most electronic structure methods, are not unique, and finding suitable diabatic representations often involves time-consuming nonsystematic diabatization steps. The biggest drawback of using diabatic bases is that it can require large amounts of effort to perform a globally consistent diabatization, and one of our goals has been to develop methods to do this efficiently and automatically. In this Feature Article, we introduce the mathematical framework of diabatic representations, and we discuss diabatization methods, including adiabatic-to-diabatic transformations and recent progress toward the goal of automatization.

A Critical Look at Linus Pauling's Influence on the Understanding of Chemical Bonding

The influence of Linus Pauling on the understanding of chemical bonding is critically examined. Pauling deserves credit for presenting a connection between the quantum theoretical description of chemical bonding and Gilbert Lewis's classical bonding model of localized electron pair bonds for a wide range of chemistry. Using the concept of resonance that he introduced, he was able to present a consistent description of chemical bonding for molecules, metals, and ionic crystals which was used by many chemists and subsequently found its way into chemistry textbooks. However, his one-sided restriction to the valence bond method and his rejection of the molecular orbital approach hindered further development of chemical bonding theory for a while and his close association of the heuristic Lewis binding model with the quantum chemical VB approach led to misleading ideas until today.

L-Histidinium Chiral Ionic Liquid Functionalized β-Cyclodextrin as Chiral Selector in Capillary Electrophoresis

Nowadays, ionic liquids (ILs) functionalized cyclodextrins (CDs) have drawn increasing attention in chiral separation. Herein, a novel β-CD derivative functionalized by L-histidinium IL, mono-6-deoxy-6-L-histidinium-β-cyclodextrin chloride (L-HMCDCl), was synthesized for the first time and utilized for enantioseparation of nefopam and chlorphenamine in capillary electrophoresis. The L-HMCDCl exhibited superior enantioselectivity compared with native β-CD. The effect of some key parameters such as chiral selector concentration, buffer pH and applied voltage on the enantioseparation was investigated in detail. In the interest of the chiral discrimination mechanism and the enhanced enantioselectivity of L-HMCDCl, molecular modeling with AutoDock was employed to study the interaction, which was in good agreement with experimental results.

Ab initio valence bond theory: A brief history, recent developments, and near future

This Perspective presents a survey of several issues in ab initio valence bond (VB) theory with a primary focus on recent advances made by the Xiamen VB group, including a brief review of the earlier history of the ab initio VB methods, in-depth discussion of algorithms for nonorthogonal orbital optimization in the VB self-consistent field method and VB methods incorporating dynamic electron correlation, along with a concise overview of VB methods for complex systems and VB models for chemical bonding and reactivity, and an outlook of opportunities and challenges for the near future of the VB theory.

Structural insight of two 4-Coumarate CoA ligase (4CL) isoforms in Leucaena suggests targeted genetic manipulations could lead to better lignin extractability from the pulp

4-Coumarate: coenzyme A ligase (4CL) is a key enzyme involved in the early steps of the monolignol biosynthetic pathway. It is hypothesized to modulate S and G monolignol content in the plant. Lignin removal is imperative to the paper industry and higher S/G ratio governs better extractability of lignin and economics of the pulping process. This background prompted us to predict 3D structure of two isoforms of 4CL in Leucaena leucocephala and evaluate their substrate preferences. The 3D structure of Ll4CL1 and Ll4CL2 protein were created by homology modeling and further refined by loop refinement. Molecular docking studies suggested differential substrate preferences of both the isoforms. Ll4CL1 preferred sinapic acid (- 4.91 kcal/mole), ferulic acid (- 4.84 kcal/mole), hydroxyferulic acid (- 4.72 kcal/mole), and caffeic acid (- 4.71 kcal/mole), in their decreasing order. Similarly, Ll4CL2 preferred caffeic acid (- 6.56 kcal/mole, 4 H bonds), hydroxyferulic acid (- 6.56 kcal/mole, 3 H bonds), and ferulic acid (- 6.32 kcal/mole) and sinapic acid (- 5.00 kcal/mole) in their decreasing order. Further, active site residues were identified in both the isoforms and in silico mutation and docking analysis was performed. Our analysis suggested that ASP228, TYR262, and PRO326 for Ll4CL1 and SER165, LYS247 and PRO315 for Ll4CL2 were important for their functional activity. Based on differential substrate preferences of the two isoforms, as a first step towards genetically modified Leuaena having the desired phenotype, it can be proposed that over-expression of Ll4CL1 gene and/or down-regulation of Ll4CL2 gene could yield higher S/G ratio leading to better extractability of lignin.

Wood–Moisture Relationships Studied with Molecular Simulations: Methodological Guidelines

This paper aims at providing a methodological framework for investigating wood polymers using atomistic modeling, namely, molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. Atomistic simulations are used to mimic water adsorption and desorption in amorphous polymers, make observations on swelling, mechanical softening, and on hysteresis. This hygromechanical behavior, as observed in particular from the breaking and reforming of hydrogen bonds, is related to the behavior of more complex polymeric composites. Wood is a hierarchical material, where the origin of wood-moisture relationships lies at the nanoporous material scale. As water molecules are adsorbed into the hydrophilic matrix in the cell walls, the induced fluid–solid interaction forces result in swelling of these cell walls. The interaction of the composite polymeric material, that is the layer S2 of the wood cell wall, with water is known to rearrange its internal material structure, which makes it moisture sensitive, influencing its physical properties. In-depth studies of the coupled effects of water sorption on hygric and mechanical properties of different polymeric components can be performed with atomistic modeling. The paper covers the main components of knowledge and good practice for such simulations.

Oxidation of organic diselenides and ditellurides by H2O2 for bioinspired catalyst design

The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity.

Potential Energy Surface for Large Barrierless Reaction Systems: Application to the Kinetic Calculations of the Dissociation of Alkanes and the Reverse Recombination Reactions

The isodesmic reaction method is applied to calculate the potential energy surface (PES) along the reaction coordinates and the rate constants of the barrierless reactions for unimolecular dissociation reactions of alkanes to form two alkyl radicals and their reverse recombination reactions. The reaction class is divided into 10 subclasses depending upon the type of carbon atoms in the reaction centers. A correction scheme based on isodesmic reaction theory is proposed to correct the PESs at UB3LYP/6-31+G(d,p) level. To validate the accuracy of this scheme, a comparison of the PESs at B3LYP level and the corrected PESs with the PESs at CASPT2/aug-cc-pVTZ level is performed for 13 representative reactions, and it is found that the deviations of the PESs at B3LYP level are up to 35.18 kcal/mol and are reduced to within 2 kcal/mol after correction, indicating that the PESs for barrierless reactions in a subclass can be calculated meaningfully accurately at a low level of ab initio method using our correction scheme. High-pressure limit rate constants and pressure dependent rate constants of these reactions are calculated based on their corrected PESs and the results show the pressure dependence of the rate constants cannot be ignored, especially at high temperatures. Furthermore, the impact of molecular size on the pressure-dependent rate constants of decomposition reactions of alkanes and their reverse reactions has been studied. The present work provides an effective method to generate meaningfully accurate PESs for large molecular system.

Realization of a half-metallic state on bilayer WSe2 using doping transition metals (Cr, Mn, Fe, Co, Ni) in its interlayer

The structural, electronic and magnetic properties of Cr, Mn, Fe, Co and Ni-doped bilayer WSe₂ are predicted by using first principles calculations. The doped transition-metal (TM) atoms show a covalent-binding with the nearest Se atoms. The calculated electronic structures reveal that the TM Cr, Mn, Fe and Co-doped bilayer WSe₂ exhibits a half-metallic character with a 100% spin polarization at the Fermi level, and the reason is ascribed to the strong hybridization peak between the transition metals and the parent W and Se atoms. The Ni-doped bilayer WSe₂ is still a semiconductor with nonmagnetism. The Fe-doped system has a robust stability of half-metallicity because there are three connected states peak spanning the Fermi level. The doping of Cr, Mn, Fe and Co atoms leads to a prominent total magnetism (0.93-3.65 [Formula: see text] moment per unit cell), and an induced ∼0.3 [Formula: see text] moment in parent W atoms is found in addition to the main contribution of TM atomic magnetism (0.71-3.33 [Formula: see text] moment per atom). The predicted Cr, Mn, Fe and Co-doped bilayer WSe₂ should be the candidate materials for spintronic devices due to their magnetic and half-metallic nature.

Mechanochemical syntheses and 35Cl solid-state NMR characterization of fluoxetine HCl cocrystals

Novel mechanochemical syntheses of cocrystals of fluoxetine HCl are presented, along with characterization of the molecular-level structures by ³⁵Cl solid-state NMR and DFT calculations.

Direct diabatization based on nonadiabatic couplings: the N/D method

We propose a new diabatization method that is direct, orbital-free, and adiabatic-equivalent based on directly calculated nonadiabatic couplings of states and the adiabatic energy gradients.

A novel chemosensor based on rhodamine and azobenzene moieties for selective detection of Al3+ ions

Both rhodamine and azobenzene moieties have been conjugated to prepare a novel chemosensor for the detection of Al³⁺ through CHEF-PET and the spirolactam ring opening mechanism.

Bioactive polycyclic polyprenylated acylphloroglucinols from Hypericum perforatum

Fifteen new polycyclic polyprenylated acylphloroglucinols with dual-targeted inhibitory activities for Alzheimer's disease, were isolated from Hypericum perforatum.

Stanene-hexagonal boron nitride heterobilayer: Structure and characterization of electronic property

The structural and electronic properties of stanene/hexagonal boron nitride (Sn/h-BN) heterobilayer with different stacking patterns are studied using first principle calculations within the framework of density functional theory. The electronic band structure of different stacking patterns shows a direct band gap of ~30 meV at Dirac point and at the Fermi energy level with a Fermi velocity of ~0.53 × 106 ms-1. Linear Dirac dispersion relation is nearly preserved and the calculated small effective mass in the order of 0.05mo suggests high carrier mobility. Density of states and space charge distribution of the considered heterobilayer structure near the conduction and the valence bands show unsaturated π orbitals of stanene. This indicates that electronic carriers are expected to transport only through the stanene layer, thereby leaving the h-BN layer to be a good choice as a substrate for the heterostructure. We have also explored the modulation of the obtained band gap by changing the interlayer spacing between h-BN and Sn layer and by applying tensile biaxial strain to the heterostructure. A small increase in the band gap is observed with the increasing percentage of strain. Our results suggest that, Sn/h-BN heterostructure can be a potential candidate for Sn-based nanoelectronics and spintronic applications.

Potential energy construction in the diabatic picture for quantum mechanical rate constants of intermolecular proton transfer

We propose a simple method for potential construction in the diabatic picture and the estimation of thermal rate constants for intermolecular proton transfer reactions using quantum dynamics simulations carried out on the constructed potentials.

Multireference Model Chemistries for Thermochemical Kinetics

By combining the generalized valence bond ansatz of correlated participating orbitals (CPO) with the complete-active-space prescription for selecting configurations and with the use of multireference second order perturbation theory (MRMP2) for including dynamical correlation, we define three levels of multireference (MR) theoretical model chemistries for electronic structure calculations of chemical reaction energies and barrier heights. The three levels differ in their choice of which orbitals are considered to be participating; the choices are called nominal (nom-CPO), moderate (mod-CPO), and extended (ext-CPO). Combining any of these three choices with a method for treatment of dynamical correlation energy and a one-electron basis set yields a theoretical model chemistry. Unlike the full-valence choice of active orbitals, the CPO choices lead to active spaces that contain the orbitals needed to include important static correlation effects on chemical reactions but do not increase with the size of the nonparticipating portion of the system, and hence they remain viable computational options even for many large and complex reacting systems. The accuracies of the new levels, combined with the MG3S basis set (a partially augmented, multiply polarized valence triple-ζ basis with appropriately tight d functions for 3p-block elements) and with the fully augmented correlation-consistent aug-cc-pVTZ basis set, are assessed against a previously presented database of barrier heights for diverse reaction types. We find that nom-CPO level captures the bulk of the static correlation energy, and MRMP2/nom-CPO calculations have an average error of only 1.4 kcal/mol in barrier heights, which may be compared to 5.0 kcal/mol for single-reference MP2 theory, 2.5 kcal/mol for CCSD, and 4.1 and 1.0 kcal/mol for the B3LYP and M06-2X density functionals, respectively. The accuracy of MRMP2/CPO for transition structure bond lengths and donor-acceptor distances is excellent, with a mean unsigned error of only 0.007 Å as compared to 0.018 Å for CCSD, 0.019 Å for M06-2X, and 0.039 Å for MP2 and B3LYP. We also introduce a new multireference diagnostic, called the M diagnostic, that allows one to measure the importance of static correlation in a given reagent or transition state.

Relation of molecular structure to Franck-Condon bands in the visible-light absorption spectra of symmetric cationic cyanine dyes

A Franck-Condon (FC) model is used to study the solution-phase absorbance spectra of a series of seven symmetric cyanine dyes having between 22 and 77 atoms. Electronic transition energies were obtained from routine visible-light absorbance and fluorescence emission spectra. Harmonic normal modes were computed using density functional theory (DFT) and a polarizable continuum solvent model (PCM), with frequencies corrected using measured mid-infrared spectra. The model predicts the relative energies of the two major vibronic bands to within 5% and 11%, respectively, and also reproduces structure-specific differences in vibronic band shapes. The bands themselves result from excitation of two distinct subsets of normal modes, one with frequencies between 150 and 625cm(-1), and the other between 850 and 1480cm(-1). Vibronic transitions excite symmetric in-plane bending of the polymethine chain, in-plane bends of the polymethine and aromatic C-H bonds, torsions and deformations of N-alkyl substituents, and in the case of the indocyanines, in-plane deformations of the indole rings. For two dyes, the model predicts vibronic coupling into symmetry-breaking torsions associated with trans-cis photoisomerization.

Quest for a universal density functional: the accuracy of density functionals across a broad spectrum of databases in chemistry and physics

Kohn-Sham density functional theory is in principle an exact formulation of quantum mechanical electronic structure theory, but in practice we have to rely on approximate exchange-correlation (xc) functionals. The objective of our work has been to design an xc functional with broad accuracy across as wide an expanse of chemistry and physics as possible, leading--as a long-range goal--to a functional with good accuracy for all problems, i.e. a universal functional. To guide our path towards that goal and to measure our progress, we have developed-building on earlier work of our group-a set of databases of reference data for a variety of energetic and structural properties in chemistry and physics. These databases include energies of molecular processes, such as atomization, complexation, proton addition and ionization; they also include molecular geometries and solid-state lattice constants, chemical reaction barrier heights, and cohesive energies and band gaps of solids. For this paper, we gather many of these databases into four comprehensive databases, two with 384 energetic data for chemistry and solid-state physics and another two with 68 structural data for chemistry and solid-state physics, and we test two wave function methods and 77 density functionals (12 Minnesota meta functionals and 65 others) in a consistent way across this same broad set of data. We especially highlight the Minnesota density functionals, but the results have broader implications in that one may see the successes and failures of many kinds of density functionals when they are all applied to the same data. Therefore, the results provide a status report on the quest for a universal functional.

Verdict: Time-Dependent Density Functional Theory "Not Guilty" of Large Errors for Cyanines

We assess the accuracy of eight Minnesota density functionals (M05 through M08-SO) and two others (PBE and PBE0) for the prediction of electronic excitation energies of a family of four cyanine dyes. We find that time-dependent density functional theory (TDDFT) with the five most recent of these functionals (from M06-HF through M08-SO) is able to predict excitation energies for cyanine dyes within 0.10-0.36 eV accuracy with respect to the most accurate available Quantum Monte Carlo calculations, providing a comparable accuracy to the latest generation of CASPT2 calculations, which have errors of 0.16-0.34 eV. Therefore previous conclusions that TDDFT cannot treat cyanine dyes reasonably accurately must be revised.

SPIN DENSITY OF SPIN-FREE VALENCE BOND WAVE FUNCTIONS AND ITS IMPLEMENTATION IN VB2000

The expressions for computing the spin density of spin-free valence bond wave functions are derived based on the bonded tableaux approach. The new expressions, although similar to the original forms given by Cooper and McWeeny in the 1960s, are simpler and thus easier for coding. The new formulation was implemented in VB2000, an ab initio valence bond program based on algebrant algorithm and group function theory. The spin density calculation for multi-group VB wave functions is also briefly discussed. As examples of applications, the spin densities of allyl radical and diazide anion [Formula: see text] were computed at different VB levels.