Computational study on interaction energy changes during double proton transfer process

The behavior of double proton transfer occurring in a representative glycinamide-formic acid complex has been investigated at the B3LYP/6-311 + + G( * *) level of theory. Thermodynamic and, especially, kinetic parameters, such as tautomeric energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the double proton transfer process, such as geometrical changes, interaction energies, and intrinsic reaction coordinate calculations have also been studied. Computational results show that the participation of a formic acid molecule favors the proceeding of the proton transfer for glycinamide compared with that without mediate-assisted case. The double proton transfer process proceeds with a concerted mechanism rather than a stepwise one since no ion-pair complexes have been located during the proton transfer process. The calculated barrier heights are 11.48 and 0.85 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 2.95 and 2.61 kcal/mol to 8.53 and -1.76 kcal/mol if further inclusion of zero-point vibrational energy corrections, where the negative barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to that occurring between glycinamide and formamide. Furthermore, solvent effects on the thermodynamic and kinetic processes have also been predicted qualitatively employing the isodensity surface polarized continuum model within the framework of the self-consistent reaction field theory. Additionally, the oxidation process for the double H-bonded glycinamide-formic acid complex has also been investigated. Contrary to that neutral form possessing a pair of two parallel intermolecular H bonds, only a single H bond with a comparable strength has been found in its ionized form. The vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 9.40 and 8.69 eV, respectively, where ionization is mainly localized on the glycinamide fragment. Like that ionized glycinamide-formamide complex, the proton transfer in the ionized complex is characterized by a single-well potential, implying that the proton initially attached to amide N4 in the glycinamide fragment cannot be transferred to carbonyl O13 in the formic acid fragment at the geometry of the optimized complex.

In this paper a variation in density of states (DOS) of the substrate due to chemisorption of hydrogen on transition metals using composite Anderson-Newns model has been investigated for different coverages in quasi-chemical approximation of Fowler and Guggenhiem, which in the limitz→∞ gives the Bragg-Williams approximation as a special case. Variation in density of states has been studied for one-dimensional periodic substrate with change in adatom interaction energy and coverage. With increase in coverage, the bonding and antibonding (B-AB) peaks are found to shift towards higher energies and at the same time relative height of the peaks also increases. The interesting feature to observe is that both approximations for a particular coverage, give split-off states with different height for both (B-AB) peaks. It particularly indicates change in B-AB states, representing amount of chemisorption, with the change in interaction energy between adatoms. At the same time bond strength is also found to decrease with interaction between adatoms.

使用高精度从头算方法（含基组重叠误差校正）计算了水团簇（H2O）n（n=8,10,16,20,22,24）中的所有二体、三体和四体作用能,分析了水团簇中的多体效应.研究表明,二体作用对体系总作用能的贡献高达70%以上,三体作用对总作用能的贡献可高达25%,四体作用在总作用能中所占比例不超过3%,五体及以上多体作用能在总作用能中所占比例更小,不超过0.5%.本文研究还表明,两个水分子间距小于0.68 nm的二体作用、三个和四个水分子中最近的两个水分子间距小于0.31 nm的三体和四体作用对体系总作用能的贡献高达99.4%.因此,以生物体系为对象的分子模拟方法应该具备准确地模拟两个水分子间距小于0.68 nm的二体作用、三个和四个水分子中最近的两个分子间距小于0.31 nm的三体和四体作用的能力。

Ionic liquids (ILs) hold great promise in many fields including energy storage and generation, mechanical, pharmaceutical, synthetic and separation applications to name just a few. For any given application, the desired physical properties of the ideal IL may differ substantially from others and no widely applicable patterns or trends to facilitate intuitive design. The origins of physical properties lie in the characteristics of the intermolecular energetics, which consist of a complex interplay between electrostatic and dispersion forces. This thesis investigates and develops computational methodologies for calculating a reliable description of the intermolecular interactions for this challenging class of solvents and electrolytes of the future. The electrostatic approximation used in classical molecular dynamics (MD) where atomic partial charges are assigned was investigated in terms of methods based on density matrix partitioning, and the restrained electrostatic potentials (RESP) approaches. It was found that the “geodesic” atomic partial charge scheme, part of the RESP family, produced the most accurate charges. This was measured in terms of (a) charge convergence with increasing basis set size; (b) charge invariance with changes to the coordinate system; (c) insensitivity to minor structural changes on the resulting charges; (d) adequate capture of charge transfer effects; and (e) the preservation of symmetric of charges in symmetric molecules. Although charges can vary dramatically depending on the scheme used, the careful use of atomic partial charge schemes may still produce reliable forcefields, or at least serve as a rapid diagnostic tool to quantify electrostatic interactions and charge transfer. In moving towards unbiased a priori descriptions of IL intermolecular interactions, second-order Moller-Plesset perturbation theory (MP2) was used with the linear-scaling fragment molecular orbital (FMO) framework to assess the extent to which dispersion forces play a role in the intermolecular energetics. ILs of increasing size were examined such that the many-body effects may be captured. The dispersion energy contribution formed up to 20% of the total interaction energy. Furthermore, the interaction energy as produced by FMO was within 1 kJ mol−1 of the full-wavefunction MP2 interaction energy when three-body effects were included. As the dispersion interaction is purely a quantum mechanical phenomenon, correlated quantum mechanical methods, such as MP2 or coupled-cluster approaches, are required to provide an unbiased account of these effects. Ab initio methods such as MP2 and CCSD(T) scale formally as N⁵ an N⁷, respectively, with chemical system size. While the FMO approach provides a marked improvement in efficiency, the counterpoise (CP) approach to correcting the basis set superposition error (BSSE) is not amenable to fragmented approaches and requires each ion in the cluster to be calculated in the basis set of the entire system. In order to remove this bottleneck, the spin-component scaled second-order Moller Plesset perturbation theory (SCS-MP2) methodology was refined by fitting 174 non-CP corrected interaction energies at the MP2/cc-pVTZ level of theory to CP corrected CCSD(T)/CBS benchmark energies. This has resulted in an implicit BSSE correction that may be used within the highly efficient FMO framework, and is shown to yield results on par with or exceeding the accuracy of MP2/cc-pVQZ for clusters of two and four ion pairs (IPs). This new approach as been termed SCS-IL-MP2. An alternative dispersion corrected density functional theory (DFT) approach, DFT- D3, was assessed and refined in view of producing accurate interaction energies at the same CCSD(T)/CBS quality. The same test set of 174 ILs was used to fit the SCS-IL-MP2 approach was used to refit the DFT-D3 approach for both the Hartree-Fock (HF) wavefunction and the PBE and BLYP density functionals (DFs). In most cases, the selection of the DF and associated DFT-D version 3 (DFT-D3) parameters differed negligibly with all reaching within 1 to 2 kJ mol−1 per IP. HF-D3 parameters, on the other hand, showed a substantial improvement, particularly when used with the Becke-Johnson (BJ) damping function. Refitted HF-D3 and the BJ damping function was able to consistently provide interaction energy errors below 5 kJ mol−1 per IP. It would be worthwhile further investigating the application of the refined HF-D3 in its ability to produce reliable energies and geometries over a more diverse set of ILs. Both the SCS-IL-MP2 and new DFT-D3 approaches may be applied to the highly scal- able FMO framework. These form the core elements of the quantum chemistry toolbox for the study and understanding of the physicochemical properties of ILs that have so far been only superficially characterised by electronic structure theory. From this starting point, a rigorous and unbiased a priori understanding of the intermolecular interactions and resulting physicochemical properties may be predicted by means of efficient ab initio molecular dynamics (AIMD) techniques.

The equilibrium structure and binding energy of the water dimer have been determined in ab initio quantum-mechanical calculations at the correlated level using second-order Mo/ller Plesset theory (MP2) and coupled-electron pair theory (CEPA-1). Basis set superposition error was avoided by applying the counterpoise procedure throughout. Basis set convergence was monitored by studying not only the total interaction energy, but also the first and higher-order Hartree–Fock interaction energies, the partitioned intra and intermolecular components of the MP2 interaction energy, and the monomer dipole moments. This was done at a near equilibrium geometry for more than 20 progressively improved basis sets. The largest set was used in MP2 and CEPA-1 geometry optimizations in Cs symmetry, keeping all intramolecular coordinates fixed, except for the donor OH length. The equilibrium geometry is found to be ROO=2.949 (6) Å, θa=55.2 (2.0)°, θd=57.6 (2.0)°. The donor OH bond is lengthened by 0.0060 (6) Å, but this has virtually no effect upon the final ROO. The equilibrium binding energy is determined as ΔE=−4.73 (10) kcal/mol. The CEPA dipole moment is 2.60 (10) D. The error bars on these results reflect the uncertainty due to the remaining incompleteness in the one-electron basis as well as in the treatment of electron correlation. Taking into account the vibrational effects present in experimental data, the calculated results lie within the error bars of the experimental data available to date. However, the present error bars are two to seven times tighter and so some of the experimental values lie outside the present ranges. The largest discrepancy is for ΔE, which is difficult to determine experimentally. This finding is of importance for the modeling of water properties where empirical potentials with ΔE ranging from −5.0 to −5.5 kcal/mol are customarily employed.

The purpose of the present study was to determine the lead structure in cardiac glycosides at the receptor level, i.e. the minimal structural requirement for specific and powerful receptor recognition. Accordingly 73 digitalis-like acting steroids were characterized as to the concentration effecting half-maximum inhibition of Na,K-ATPase from human cardiac muscle under standardized turnover conditions. Since the Ki value equaled the apparent KD value, K'D was expressed in terms of the apparent standard Gibbs energy change delta G degrees' of steroid interaction with Na,K-ATPase. This allowed the use of the extrathermodynamic approach as a rational way of correlating in a quantitative manner, the potency and structure of the various steroidal compounds. The results of the present analysis taken in conjunction with relevant findings reported in the literature, favour the following conclusions. Cassaine, canrenone, prednisolone- and progesterone-3,20-bisguanylhydrazone, and chlormadinol acetate are compounds that are not congeneric with digitalis. The butenolide ring of cardenolides or the analogous side-chains at C17 beta of 5 beta, 14 beta-androstane-3 beta, 14-diol are not pharmacophoric substructures, but merely amplifiers of the interaction energy of the steroid lead. All modifications of the structure, geometry and spatial relationship between the steroid nucleus and butenolide side chain of digitoxigenin all at once weaken the close fit interaction with the steroid and butenolide binding subsites of the enzyme in such way that the cardenolide derivatives interact with the receptor binding site area in whatever orientation that will minimize the Gibbs energy of the steroid-receptor-solvent system. The "butenolide carbonyl oxygen distance model" (Ahmed et al. 1983) for the interpretation of the differences in potency of the cardenolide derivatives describes the change in interaction energy through structural modification as a function of the entire molecule. 5 beta, 14 beta-androstane-3 beta, 14-diol, the steroid nucleus of cardiac glycosides of the digitalis type, is the minimum structure for specific receptor recognition and the key structure for inducing protein conformational change and thus Na,K-ATPase inhibition. It is also the structural requirement for maximum contributions of the butenolide substituent at C17 beta and the sugar substituent at C3 beta-OH to the overall interaction energy, i.e. this steroid nucleus is the lead structure.(ABSTRACT TRUNCATED AT 400 WORDS)

Molecular models of the M-H(2) binding sites of experimentally characterised amorphous vanadium hydrazide gels are studied computationally using gradient corrected density functional theory, to probe the coordination number of the vanadium in the material and the nature of the interaction between the metal and the H(2) molecules. The H(2) is found to bind to the vanadium through the Kubas interaction, and the first quantum theory of atoms-in-molecules analysis of this type of interaction is reported. Strong correlation is observed between the electron density at the H-H bond critical point and the M-H(2) interaction energy. Four coordinate models give the best reproduction of the experimental data, suggesting that the experimental sites are four coordinate. The V-H(2) interaction is shown to be greater when the non-hydrazine based ligand, THF, of the experimental system is altered to a poorer π-acceptor ligand. Upon altering the metal to Ti or Cr the M-H(2) interaction energy changes little but the number of H(2) which may be bound decreases from four (Ti) to two (Cr). It is proposed that changing the metal from V to Ti may increase the hydrogen storage capacity of the experimental system. A 9.9 wt% maximum storage capacity at the ideal binding enthalpy for room temperature performance is predicted when the Ti metal is combined with a coordination sphere containing 2 hydride ligands.

Photoinduced proton-coupled electron transfer and long-range two-proton transport via a Grotthuss-type mechanism are investigated in a biomimetic construct. The ultrafast, nonequilibrium dynamics are assessed via two-dimensional electronic vibrational spectroscopy, in concert with electrochemical and computational techniques. A low-frequency mode is identified experimentally and found to promote double proton and electron transfer, supported by recent theoretical simulations of a similar but abbreviated (non-photoactive) system. Excitation frequency peak evolution and center line slope dynamics show direct evidence of strongly coupled nuclear and electronic degrees of freedom, from which we can conclude that the double proton and electron transfer processes are concerted (up to an uncertainty of 24 fs). The nonequilibrium pathway from the photoexcited Franck–Condon region to the E2PT state is characterized by an ∼110 fs time scale. This study and the tools presented herein constitute a new window into hot charge transfer processes involving an electron and multiple protons.

Molecular dynamics simulations of polyvinyl acetate-perfluorooctane based anti-stain coatings

Dynamical computer simulations have been performed on a single nitrogen particle in helium at room temperature and pressures ranging from 0.6 up to 8.7 GPa. Both the frequency and the linewidth have been determined. The ‘‘repulsive’’ contribution to the frequency is comparable to that in pure nitrogen. In contrast with the pure component case, the experimental values for the shift in the mixture are higher than those obtained from the simulations. From the difference between the experimentally determined shift and the simulation results, an estimate has been made of the change in interaction energy with the surrounding particles on excitation of a nitrogen molecule. A good fit is obtained by the addition of a weak Lennard-Jones potential. The results for the linewidth reveal a marked difference to those for a system of pure N2, which has been confirmed by experimental evidence. This behavior, is for the greater part, due to a significant difference in the time correlation of the vibration frequency and the resulting correlation time.

Tight oil reservoirs are currently a hot topic in petroleum exploration and development. However, due to the low porosity and low permeability of reservoirs and the lack of external energy supplementation, there is a significant mismatch between resources and production in tight oil. Mining and experimental studies have shown that CO2 and gaseous hydrocarbons have a high injectivity and effective oil displacement effect in tight oil reservoirs. Currently, research is mostly focused on a single energy supplement medium, and whether CO2 hydrocarbon mixtures can more effectively improve oil recovery needs to be further studied. The features of crude oil expansion capacity and interaction energy changes following various fluid interactions were investigated via molecular dynamics simulation techniques in response to the ambitious comprehension of the mechanistic changes underlying the CO2–CH4 synergistic effect during the development of tight oil reservoirs. The research results indicate that the expansion and diffusion abilities of crude oil are improved after being treated with pure CO2, CO2-CH4 (9:1), CO2-CH4 (7:3), and CO2-CH4 (1:1), and enhanced with increasing CO2 content in the injected fluid.

Insights into Saquinavir Resistance in the G48V HIV-1 Protease: Quantum Calculations and Molecular Dynamic Simulations

In the past 2 years,since the emergence of severe acute respiratorysyndrome coronavirus 2 (SARS-CoV-2), multiple SARS-CoV-2 variantshave emerged. Whenever a new variant emerges, considerable time isrequired to analyze the binding affinity of the viral surface proteinsto human angiotensin-converting enzyme 2 (hACE2) and monoclonal antibodies.To efficiently predict the binding affinities associated with hACE2and monoclonal antibodies in a short time, herein, we propose a methodapplying statistical analysis to simulations performed using molecularand quantum mechanics. This method efficiently predicted the trendof binding affinity for the binding of the spike protein of each variantof SARS-CoV-2 to hACE2 and individually to eight commercial monoclonalantibodies. Additionally, this method accurately predicted interactionenergy changes in the crystal structure for 10 of 13 mutated residuesin the Omicron variant, showing a significant change in the interactionenergy of hACE2. S375F was found to be a mutation that majorly changedthe binding affinity of the spike protein to hACE2 and the eight monoclonalantibodies. Our proposed analysis method enables the prediction ofthe binding affinity of new variants to hACE2 or to monoclonal antibodiesin a shorter time compared to that utilized by the experimental method.

Protein tyrosine phosphatase 1B (PTP1B) is one of the important regulators of signal transduction pathways. The present study aims to investigate the effect of Arg 221 on the active site of PTP1B. Six mutants were carried out using Schrödinger Suite 2007 and molecular dynamics simulation was performed by using the Tinker package. Results show that point mutations at position 221 have great influence on shape of active site, backbone movement of active site, and interaction between substrate and PTP1B. R221H and R221K lead to increased total interaction energies. R221G, R221F and R221T cause increase in total interaction energies, but decrease in interaction energies between pTyr 4 and P loop (catalytic residues). R221E results in both decreased total interaction energies and interaction energies between pTyr 4 and P loop. This indicates that Arg 221 mutated to basic residues can lead to enhanced binding affinity between substrate and protein; when mutated to acidic residues it will decrease binding affinity and catalytic activity; other kinds of mutations result in increased binding affinity but decreased catalytic activity.

Effect of the Weber number on the coalescence of relatively moving droplets in an electric field: A molecular dynamics study