Solvatochromism and solvation of ternary iron-diimine-cyanide complexes

Summary The solvatochromic behaviour of several complexes [Fe(LL)₂(CN)₂] with LL=Schiff base diimine has been established in a series of non-aqueous solvents, as has that of two analogues containing diazabutadiene ligands. Transfer chemical potentials have been derived from appropriate solubility measurements for several iron(II)-and iron(III)-diimine-cyanide complexes into aqueous methanol, and for [Fe(bipy)₂(CN)₂] into several binary aqueous solvent series. The usefulness of solvatochromic shifts and transfer chemical potentials as indicators of selective solvation is discussed. Kinetics of oxidation of catechol and of 4-t-butyl catechol by [Fe(bipy)(CN)₄]^– in aqueous solution are described.     

Decomposition of electronic properties and calculation of solvation energies for surface-active molecules

For ions and polar molecules located near a surface, we derived and analyzed the general formulas to calculate their solvation energies. St. Petersburg State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 6, pp. 3–12, November-December, 1994. Translated by A. Arbuznikov     

Influence of solvation and adsorption on acid-base properties of o-nitrophenol

Transmission spectra were obtained of o-nitrophenol in aqueous solutions at various pH values and in the adsorbed state on the surface of monocation-substituted forms of kaolinite. An interpretation of the electronic spectra of the adsorbed indicator was carried out using quantum-chemical calculations by the CNDO/2 and PPP SCF MO LCAO methods, taking into account the disturbing effect of cations within a point charge model. It was found that the mechanism of the interaction of the dye molecules with active centers on a solid suface differs from its behavior in solution, and this results in changes in the acid-base properties of o-nitrophenol due to changes in the phase composition of the medium. It was concluded that the indicator molecules are adsorbed simultaneously on electron-acceptor and electron-donor centers of the aluminosilicate surface.Translated from Teoreticheskaya i Éksperimental'naya, Khimiya, Vol. 25, No. 2, pp. 226–230, March–April, 1989.     

Dynamics of adsorption: A model calculation for HD activated adsorption

We have recently developed a model potential for the interaction of a diatomic molecule with a rigid solid surface. In this note, we report some results of classical trajectory studies designed to simulate the adsorption of a diatomic molecule. Model potentials with different barrier heights are used and a variety of different initial conditions for the incident molecule are studied. In common with gas-phase results, we find that translational energy is most effective in surmounting early barriers and enhancing adsorption.     

Density functional calculation for ozone-ethylene complexes

The density functional method (exchange correlation functional Becke3LYP) is used to calculate the potential energy profiles for the reaction of ozone with ethylene. It is shown that “direct” epoxidation of the C = C double bond demands high activation energy and is unlikely for both themwchemical and photochemical reactions of ozonolysis. Translated fromZhumal Struktumoi Khimii, Vol. 41, No. 2, pp. 240–247,     

Efficient and accurate solvation energy calculation from polarizable continuum models

A new approach is proposed to enhance the efficiency and accuracy for calculation of the long-range electrostatic interaction from implicit solvation models, i.e., the polarizable continuum model (PCM) and its variants, conductorlike PCM/conductorlike screening model and integral equation formalism PCM. In these methods the solvent electrostatics effects are represented by a set of discrete apparent charges distributed on tesserae of the molecular cavity surface embedding the solute. In principle, the accuracy of these methods is improved if the cavity surface is tessellated to finer tesserae; however, the computational time is increased rapidly. We show that such undesired dependency between accuracy and efficiency is a result of the inaccurate treatment of the apparent charge self-contribution to the potential and/or electric field. By taking into account the full effects due to the size and curvature of the segment occupied by each apparent charge, the error in calculated electrostatic solvation free energy is essentially zero for ions (point charge at the center of a sphere) regardless of the degree of tessellation used. For molecules where gradient of apparent charge density is nonzero at the cavity surface, we propose a multiple-sampling technique which significantly lowers the calculated error compared to the original PCM methods, especially when very few numbers of tesserae are used.     

Role of solvation energy in starch adsorption on oxide surfaces

The effect of potassium and sodium cations on the adsorption of starch onto hematite and quartz was investigated. The role of these ions was analyzed in terms of their water structure-making or -breaking capabilities. In the presence of Na⁺, a structure maker, the polymer adsorption density did not change compared to the adsorption levels observed in distilled water. However, in the solutions of K⁺, a structure-breaking cation, the adsorption density of starch significantly increased. Assuming hydrogen bonding and chemical interaction to be the driving adsorption mechanism, it was proposed that the starch–oxide interactions can be envisioned as the competition between chemical interaction/hydrogen bonding and solvation energy:

K⁺ reduces solvation energy by disturbing interfacial water structure and thus increases the free energy of adsorption, allowing the polymer to more closely approach the oxide surfaces. In contrast, Na⁺ which is indifferent to solvation energy does not interfere with the free energy of adsorption.     

A desk computer program for the calculation of rate constants

A desk computer program has been written in BASIC programming language to optimize the values of rate constants determined from kinetic measurements of time and concentration data. The program is capable of the simultaneous refinement of a maximum of 5 rate constants. A FORTRAN version using the Gear method is also available.

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AcquaAlta: a directional approach to the solvation of ligand-protein complexes

Water molecules mediating polar interactions in ligand-protein complexes can substantially contribute to binding affinity and specificity. To account for such water molecules in computer-aided drug design, we performed an extensive search in the Cambridge Structural Database (CSD) to identify the geometrical criteria defining interactions of water molecules with ligand and protein. In addition, with ab initio calculations the propensity of ligand hydration was evaluated. Based on this information, we developed an algorithm (AcquaAlta) to reproduce water molecules bridging polar interactions between ligand and protein moieties. This approach was validated with 20 crystal structures and yielded a match of 76% between experimental and calculated water positions. When water molecules establishing only weak interactions with the protein were neglected, the match could be improved to 88%. Supported by a pharmacophore-based alignment tool, the solvation algorithm was then applied to the docking of oligopeptides to the periplasmic oligopeptide binding protein A (OppA). Calculated waters based on the crystal poses matched an average of 66% of the experimental waters. With water molecules calculated based on the docked ligands, the average match with the experimental waters dropped to 53%.     

Postprocessing of docked protein-ligand complexes using implicit solvation models

Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein-ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson-Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein-ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GB(HCT+SA) model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) A(q) protein. These results indicate that the protocol for the postprocessing of docked protein-ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.     

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

This study compares generalized Born (GB) and Poisson (PB) methods for calculating electrostatic solvation energies of proteins. A large set of GB and PB implementations from our own laboratories as well as others is applied to a series of protein structure test sets for evaluating the performance of these methods. The test sets cover a significant range of native protein structures of varying size, fold topology, and amino acid composition as well as nonnative extended and misfolded structures that may be found during structure prediction and folding/unfolding studies. We find that the methods tested here span a wide range from highly accurate and computationally demanding PB-based methods to somewhat less accurate but more affordable GB-based approaches and a few fast, approximate PB solvers. Compared with PB solvation energies, the latest, most accurate GB implementations were found to achieve errors of 1% for relative solvation energies between different proteins and 0.4% between different conformations of the same protein. This compares to accurate PB solvers that produce results with deviations of less than 0.25% between each other for both native and nonnative structures. The performance of the best GB methods is discussed in more detail for the application for force field-based minimizations or molecular dynamics simulations.     

Molecular complexes and solvation interactions in the reaction of quinone imines with thiols

This study aims to investigate the role of complexation between reagents and the role of solvation of reagents by solvents in the kinetics of chain reactions of quinone imines with thiols. The thermodynamic characteristics of the complexation of quinone imines with thiophenol in CCl₄, chlorobenzene, and ethanol, as well as of the complexation of quinone imines and thiophenol with these solvents were calculated by quantum chemical methods (DFT calculations at the PBE/cc-pVDZ level of theory) and in terms of the additive-multiplicative model. Both approaches give consistent results. The formation of molecular complexes in quinone imine–thiphenol systems is accompanied by a 10–30 kJ mol^–1 decrease in enthalpy and has only a slight effect on the reaction mechanism.     

Modeling the solvation shell of complexes in solution for quantum chemical calculations of electronic spectra

A procedure that allows for solvation effects is suggested; it is designed for quantum chemical calculations of the electronic spectra of complex compounds. Based on Monte Carlo (MC) simulation of the solvation shell one can calculate the electrostatic potential created by the solvation shell at the sites of all atoms of the complex; appropriate corrections are added to the diagonal elements of the Fock matrix and to the matrix elements of the Hamiltonian in the configuration interaction method. The method suggested has been implemented based on the semiempirical (CINDO) version of the CI (configuration interaction) technique and tested on the following compounds: [Ru(NH₃)₅(py)]²⁺, [Ru(NH₃)₅(pyz)]²⁺, [Ru(bpy)(CN)₄]^2?, [Ru(NO)(py)₄-NC-Ru(py)₄(CN)]³⁺.     

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the PB (Poisson-Boltzmann) model. Our calculated chemical shifts of (1)H and (13)C for these four proteins are in excellent agreement with experimentally measured values and represent clear improvement over that from the gas phase calculation. However, although the inclusion of the solvent effect also improves the computed chemical shifts of (15)N, the results do not agree with experimental values as well as (1)H and (13)C. Our study also demonstrates that AF-QM/MM calculated results accurately reproduce the separation of α-helical and β-sheet chemical shifts for (13)C(α) atoms in proteins, and using the (1)H chemical shift to discriminate the native structure of proteins from decoys is quite remarkable.     

New equation of adsorption for the calculation of parameters of microporous structure

A new equation describing the equilibrium adsorption of vapors of substances with different physicochemical properties was obtained on the basis of the lognormal distribution of pore volume within the theory of volume filling of micropores. Unlike the existing equations, this equation is more general since it is not related to a specific geometrical model of pores. Adsorption isotherms described by this equation for active carbons with wide pore-size distributions have smaller mean square deviations than those calculated using the Dubinin-Stoeckli equation.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1931–1933, October, 1995.This study was financially supported by the Russian Foundation for Basic Research (Project No. 94-03-09550).