Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

Origin of Local Structures of U-Co Melts: A First-Principles Study

The local structures of U-Co melts have been studied by first-principle calculations. Two sub-peaks are observed in the first peaks of U-U pair distribution functions. The Voronoi polyhedral analyses also show two separate core-shell U-U distances. Therefore, the calculated results propose that U atoms will play dual roles, “chemical” and “topological”, in the local structures of U-Co melts. In addition, the chemical effect of U atoms will be strengthened when containing more U atoms. The interaction of Co and U atoms is slightly affected by the compositions. The Co-centered clusters are mostly prism-like or antiprism-like polyhedral, which can be predicted by the solute-solvent model. The distribution of the coordinated numbers of Co atoms is much narrower than that of U atoms, showing relatively stable Co-centered clusters. The chemical and topological roles of U atoms are intuitively observed in the electron density of U-Co melts, which presents both metallic and covalent bonding characteristics for U-U bonds. In the end, we conclude that the partial localization of U 5f-electron is responsible for the dual roles of U atoms. The present results provide a theoretical understanding of the origin of the local structures of U-Co melts.

Ritonavir and xk263 Binding-Unbinding with HIV-1 Protease: Pathways, Energy and Comparison

Understanding non-covalent biomolecular recognition, which includes drug–protein bound states and their binding/unbinding processes, is of fundamental importance in chemistry, biology, and medicine. Fully revealing the factors that govern the binding/unbinding processes can further assist in designing drugs with desired binding kinetics. HIV protease (HIVp) plays an integral role in the HIV life cycle, so it is a prime target for drug therapy. HIVp has flexible flaps, and the binding pocket can be accessible by a ligand via various pathways. Comparing ligand association and dissociation pathways can help elucidate the ligand–protein interactions such as key residues directly involved in the interaction or specific protein conformations that determine the binding of a ligand under certain pathway(s). Here, we investigated the ligand unbinding process for a slow binder, ritonavir, and a fast binder, xk263, by using unbiased all-atom accelerated molecular dynamics (aMD) simulation with a re-seeding approach and an explicit solvent model. Using ritonavir-HIVp and xk263-HIVp ligand–protein systems as cases, we sampled multiple unbinding pathways for each ligand and observed that the two ligands preferred the same unbinding route. However, ritonavir required a greater HIVp motion to dissociate as compared with xk263, which can leave the binding pocket with little conformational change of HIVp. We also observed that ritonavir unbinding pathways involved residues which are associated with drug resistance and are distal from catalytic site. Analyzing HIVp conformations sampled during both ligand–protein binding and unbinding processes revealed significantly more overlapping HIVp conformations for ritonavir-HIVp rather than xk263-HIVp. However, many HIVp conformations are unique in xk263-HIVp unbinding processes. The findings are consistent with previous findings that xk263 prefers an induced-fit model for binding and unbinding, whereas ritonavir favors a conformation selection model. This study deepens our understanding of the dynamic process of ligand unbinding and provides insights into ligand–protein recognition mechanisms and drug discovery.

GENERIC-compliant simulations of Brownian multi-particle systems: modeling stochastic lubrication

A stochastic Lagrangian model for simulating the dynamics and rheology of a Brownian multi-particle system interacting with a simple liquid medium is presented. The discrete particle model is formulated within the GENERIC framework for Non-Equilibrium Thermodynamics and therefore it satisfies discretely the First/Second Laws of Thermodynamics and the Fluctuation Dissipation Theorem (FDT). Long-range fluctuating hydrodynamics interactions between suspended particles are described by an explicit solvent model. To this purpose, the Smoothed Dissipative Particle Dynamics method is adopted, which is a GENERIC-compliant Lagrangian meshless discretization of the fluctuating Navier–Stokes equations. In dense multi-particle systems, the average inter-particle distance is typically small compared to the particle size and short-range hydrodynamics interactions play a major role. In order to bypass an explicit—computationally costly—solution for these forces, a lubrication correction is introduced based on semi-analytical expressions for spheres under Stokes flow conditions. We generalize here the lubrication formalism to Brownian conditions, where an additional thermal-lubrication contribution needs to be taken into account in a way that discretely satisfies FDT. The coupled lubrication dynamics is integrated in time using a generalized semi-implicit splitting scheme for stochastic differential equations. The model is finally validated for a single particle diffusion as well as for a Brownian multi-particle system under homogeneous shear flow. Results for the diffusional properties as well as the rheological behavior of the whole suspension are presented and discussed.

Computational Estimation of the Acidities of Pyrimidines and Related Compounds

Pyrimidines are key components in the genetic code of living organisms and the pyrimidine scaffold is also found in many bioactive and medicinal compounds. The acidities of these compounds, as represented by their pKas, are of special interest since they determine the species that will prevail under different pH conditions. Here, a quantum chemical quantitative structure–activity relationship (QSAR) approach was employed to estimate these acidities. Density-functional theory calculations at the B3LYP/6-31+G(d,p) level and the SM8 aqueous solvent model were employed, and the energy difference ∆EH2O between the parent compound and its dissociation product was used as a variation parameter. Excellent estimates for both the cation → neutral (pKa1, R2 = 0.965) and neutral → anion (pKa2, R2 = 0.962) dissociations were obtained. A commercial package from Advanced Chemical Design also yielded excellent results for these acidities.

Influence of Solvents on the Oxidation Kinetics of Aldehydic Group Compounds by Diethylammonium Chloro-chromate

The redox studies of some compounds containing aldehydic functional groups by diethyl ammonium chloro-chromate (DEACC) in dimethyl sulfoxide leading a product forming to acid of correspondimg order. Reactions are found to be in unit order with oxidant while a fractional order (less than unity) was found w.r.t. reductants. The redox reactions are influenced with acid, the acid dependence is governed by this equation: kobs = a + b[H+].. When isomeric form of aldehyde, that is Me-CDO is oxidised with the same oxidant it was observed a considerable K.I.E. (Deuterium effect; kH/kD = 05.69 at 298 K). The reaction of Acetaldehyde was done in various non aqueous medium, soluble or miscible in DMSO. The effect of solvent is studied fitting our data in the solvent model of Taft's and Swain's applied for this purpose.. Rate constants are correlating very well with already reported Taft’s values of *; further the reaction constants are negative in nature. Suitable mechanism involving are proposed with transfer of hydride ion..

OS100: A Benchmark Set of 100 Digitized UV-Visible Spectra and Derived Experimental Oscillator Strengths

Excited-state quantum chemical calculations typically report excitation energies and oscillator strengths, ƒ, for each electronic transition. On the other hand, UV-visible spectrophotometric experiments report energy-dependent molar extinction/attenuation coefficients, ε(v), that determine the absorption band line shapes. ε(v) and ƒ are related, but this relation is complicated by various broadening and solvation effects. We fit and integrated experimental UV-visible spectra to obtain ƒexp values for absorption bands and estimated the uncertainty in the fitting. We derived 164 ƒexp values from 100 organic molecules ranging in size from 6-34 atoms. The corresponding computed oscillator strengths (ƒcomp) were obtained with time-dependent density functional theory and a polarizable continuum solvent model. By expressing experimental and computed absorption strengths using a common quantity, we directly compared ƒcomp and ƒexp. While ƒcomp and ƒexp are well correlated (linear regression R2=0. 921), ƒcomp in most cases significantly overestimates ƒexp (regression slope=1.34). The agreement between absolute ƒcomp and ƒexp values was substantially improved by accounting for a solvent refractive index factor, as suggested in some derivations in the literature. The 100 digitized UV-visible spectra are included as plain text files in the supporting information to aid in benchmarking computational or machine-learning approaches that aim to simulate realistic UV-visible absorption spectra.

Computational Study of Catalytic Urethane Formation

Polyurethanes (PUs) are widely used in different applications, and thus various synthetic procedures including one or more catalysts are applied to prepare them. For PU foams, the most important catalysts are nitrogen-containing compounds. Therefore, in this work, the catalytic effect of eight different nitrogen-containing catalysts on urethane formation will be examined. The reactions of phenyl isocyanate (PhNCO) and methanol without and in the presence of catalysts have been studied and discussed using the G3MP2BHandHLYP composite method. The solvent effects have also been considered by applying the SMD implicit solvent model. A general urethane formation mechanism has been proposed without and in the presence of the studied catalysts. The proton affinities (PA) were also examined. The barrier height of the reaction significantly decreased (∆E0 > 100 kJ/mol) in the presence of the studied catalysts, which proves the important effect they have on urethane formation. The achieved results can be applied in catalyst design and development in the near future.

Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides

Many renewable energy technologies, such as hydrogen gas synthesis and carbon dioxide reduction, rely on chemical reactions involving hydride anions. When selecting molecules to be used in such applications, an important quantity to consider is the thermodynamic hydricity, which is the free energy required for a species to donate a hydride anion. Theoretical calculations of thermodynamic hydricity depend on several parameters, mainly the density functional, basis set, and solvent model. In order to assess the effects of the above three parameters, we carry out hydricity calculations for a set of molecules with known experimental hydricity values, generate linear �fits, and compare the R-squared, root-mean-squared error, and Akaike Information Criterion across different combinations of density functionals, basis sets, and solvent models. Based on these results we are able to quantify the accuracy of theoretical predictions of hydricity and recommend the parameters with the best compromise between accuracy and computational cost.

A mosaic bulk-solvent model improves density maps and the fit between model and data

Bulk solvent is a major component of bio-macromolecular crystals and therefore contributes significantly to diffraction intensities. Accurate modeling of the bulk-solvent region has been recognized as important for many crystallographic calculations, from computing of R-factors and density maps to model building and refinement. Owing to its simplicity and computational and modeling power, the flat (mask-based) bulk-solvent model introduced by Jiang & Brunger (1994) is used by most modern crystallographic software packages to account for disordered solvent. In this manuscript we describe further developments of the mask-based model that improves the fit between the model and the data and aids in map interpretation. The new algorithm, here referred to as mosaic bulk-solvent model, considers solvent variation across the unit cell. The mosaic model is implemented in the computational crystallography toolbox and can be used in Phenix in most contexts where accounting for bulk-solvent is required. It has been optimized and validated using a sufficiently large subset of the Protein Data Bank entries that have crystallographic data available.