Showing papers on "Solvation published in 1993"

Free energy calculations : applications to chemical and biochemical phenomena

Abstract: The author will review the applications of free energy calculations employing molecular dynamics or Monte Carlo methods to a variety of chemical and biochemical phenomena. The focus is on the applications of such calculations to molecular solvation, molecular association, macromolecular stability, and enzyme catalysis. The molecules discussed range from monovalent ions and small molecules to proteins and nucleic acids.

Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation

Abstract: We apply a new restrained electrostatic potential fit charge model (two-stage RESP) to conformational analysis and the calculation of intermolecular interactions Specifically, we study conformational energies in butane, methyl ethyl thioether, three simple alcohols, three simple amines, and 1,2-ethanediol as a function of charge model (two-stage RESP us standard ESP) and 1-4 electrostatic scale factor We demonstrate that the two-stage RESP model with a 1-4 electrostatic scale factor of ∼1/12 is a very good model, as evaluated by comparison with high-level ab initio calculations For methanol and N-methylacetamide interactions with TIP3P water, the two-stage RESP model leads to hydrogen bonds only slightly weaker than found with the standard ESP changes

Frozen density functional approach for ab initio calculations of solvated molecules

Abstract: A new density functional method for treatment of chemical processes in solution is presented. The method is based on freezing the electron density of the solvent molecules, while solving the eigenvalue problem for the solute Hamiltonian, which includes the effective potential of the solvent molecules. The method is developed and examined in the simple case of one solvent and one solute molecule. The results are encouraging and the deviation between the unfrozen and frozen treatments can be attributed to the kinetic energy functional used. The method can be implemented in ab initio calculations of solvation free energies, following a recent pseudopotential approach [Vaidehi et al., 19921.

Macroscopic Models of Aqueous Solutions: Biological and Chemical Applications

Abstract: A theoretical approach to the treatment of solute-solvent interactions is described. The solute is described as a low dielectric cavity immersed in a dielectric continuum. However, the cavity is not assigned a simple geometric form but rather is determined from the van der Waals envelope of the molecule. Real and partial charges are placed on atomic nuclei as in any molecular mechanics force field. Dielectric and ionic strength effects are obtained through numerical solutions to the Poisson-Boltzmann equation, which has proved to be remarkably accurate for a wide range of applications

Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs

Abstract: Different microscopic and semimicroscopic approaches for calculations of electrostatic energies in macromolecules are examined. This includes the Protein Dipoles Langevin Dipoles (PDLD) method, the semimicroscopic PDLD (PDLD/S) method, and a free energy perturbation (FEP) method. The incorporation of these approaches in the POLARIS and ENZYMIX modules of the MOLARIS package is described in detail. The PDLD electrostatic calculations are augmented by estimates of the relevant hydrophobic and steric contributions, as well as the effects of the ionic strength and external pH. Determination of the hydrophobic energy involves an approach that considers the modification of the effective surface area of the solute by local field effects. The steric contributions are analyzed in terms of the corresponding reorganization energies. Ionic strength effects are studied by modeling the ionic environment around the given system using a grid of residual charges and evaluating the relevant interaction using Coulomb's law with the dielectric constant of water. The performance of the FEP calculations is significantly enhanced by using special boundary conditions and evaluating the long-range electrostatic contributions using the Local Reaction Field (LRF) model. A diverse set of electrostatic effects are examined, including the solvation energies of charges in proteins and solutions, energetics of ion pairs in proteins and solutions, interaction between surface charges in proteins, and effect of ionic strength on such interactions, as well as electrostatic contributions to binding and catalysis in solvated proteins. Encouraging results are obtained by the microscopic and semimicroscopic approaches and the problems associated with some macroscopic models are illustrated. The PDLD and PDLD/S methods appear to be much faster than the FEP approach and still give reasonable results. In particular, the speed and simplicity of the PDLD/S method make it an effective strategy for calculations of electrostatic free energies in interactive docking studies. Nevertheless, comparing the results of the three approaches can provide a useful estimate of the accuracy of the calculated energies. © 1993 John Wiley & Sons, Inc.

Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation

Abstract: Numerical solutions of the Poisson-Boltzmann equation (PBE) have found wide application in the computation of electrostatic energies of hydrated molecules, including biological macromolecules. However, solving the PBE for electrostatic forces has proved more difficult, largely because of the challenge of computing the pressures exerted by a high dielectric aqueous solvent on the solute surface. This paper describes an accurate method for computing these forces. We begin by presenting a novel derivation of the forces acting in a system governed by the PBE

An effective solvation term based on atomic occupancies for use in protein simulations

Abstract: Several approaches to the treatment of solvent effects based on continuum models are reviewed and a new method based on occupied atomic volumes (occupancies) is proposed and tested. The new method describes protein-water interactions in terms of atomic solvation parameters, which represent the solvation free energy per unit of volume. These parameters were determined for six different atoms types, using experimental free energies of solvation. The method was implemented in the GROMOS and PRESTO molecular simulation program suites. Simulations with the solvation term require 20-50% more CPU time than the corresponding vacuum simulations and are approximately 20 times faster than explicit water simulations. The method and parameters were tested by carrying out 200 ps simulations of BPTI in water, in vacuo, and with the solvation term. The performance of the solvation term was assessed by comparing the structures and energies from the solvation simulations with the equivalent quantities derived from...

Dynamical theory of proton tunneling transfer rates in solution: general formulation

Abstract: A general dynamical theory is presented for the rate constant of weak coupling, nonadiabatic proton-tunneling reactions in solution The theory incorporates the critical role of the solvent and the vibration of the separation of the heavy particles between which the proton transfers, including their dynamics The formulation which allows the computation of the quantum rate constant k via classical molecular dynamics simulation techniques is presented, as are a number of approximate analytic results for k in a variety of different important regimes The frequent appearance of (nearly) classical Arrhenius behavior for k — even though the intrinsic reactive event is quantum proton tunneling — is discussed, together with the solvent and vibrational contributions to the apparent activation energy In certain weak solvation limits, however, non-Arrhenius behavior for k is found and is related to vibrational Franck-Condon features in the reaction

A simple interpretation of polar solvation dynamics

Abstract: In this letter the authors describe an approximate relationship between the solvation response to changes in solute charge, C[sub v](t), and the reorientational dynamics of molecules in the pure solvent, C[sub 1](t). Computer simulations show that the function [l brace]C[sub 1](t)[r brace][sup [alpha][sub s]], where [alpha][sub s] is the solvent dipole density, provides a good approximation to C[sub v](t) in a wide variety of systems. This result leads to a simple and intuitive interpretation of the solvation response in terms of molecular motions. 17 refs., 4 figs., 1 tab.

Photoelectron spectra of the hydrated iodine anion from molecular dynamics simulations

Abstract: In this paper, we present the first calculations, based on molecular dynamics techniques, of vertical electron binding energies for the ionic clusters I−(H2O)n, (n=1–15). In these studies, we employ the polarizable water model developed recently by Dang [J. Chem. Phys. 97, 2659 (1992)]. We construct the ion–water potential so that the successive binding energies for the ionic clusters, the hydration enthalpy, and the structural properties of the aqueous ionic solution agree with the results obtained from experiments. The simulated vertical electron binding energies compare well with recent data from photoelectron spectroscopy experiments by Markovich, Giniger, Levin, and Cheshnovsky [J. Chem. Phys. 95, 9416 (1991)]. Interestingly, we obtain coordination numbers of 4 to 5 for the ionic clusters, I−(H2O)n, for n≥6. This result is smaller than the coordination number, based on the energetic properties predicted by Markovich et al. Possible reasons for this discrepancy are discussed in the paper. Furthermore,...

The role of hydrogen bonding in carbohydrates: molecular dynamics simulations of maltose in aqueous solution

Abstract: Molecular dynamics simulations of maltose in two different conformations in vacuum and aqueous (TIP3P) solution have been used to examine the types of hydrogen bonds made by this carbohydrate molecule. Maltose was found to be extensively hydrogen bonded to solvent molecules in aqueous solution, and these hydrogen bonds were found to have potential conformational consequences. The exchange of an intramolecular O2-O3' hydrogen bond found in the crystal structure for hydrogen bonds to solvent was observed to produce significant changes in the solvation of the sugar molecule

Nonequilibrium solvation: An ab initio quantum‐mechanical method in the continuum cavity model approximation

Abstract: The electrostatic relationships necessary for the quantum‐mechanical evaluation of the properties of a solute experiencing sudden changes in its internal charge distribution are here presented in a form suitable to perform accurate quantum‐mechanical calculations of the solute properties. Attention has been paid to express the boundary conditions in the most convenient form and to avoid further constraints on the elaboration of the computational procedures. The approach exploits the separation of orientational (inertial) and electronic (inertialess) components of the polarization and complements the polarizable continuum method [Chem. Phys. 65, 239 (1982)], usually employed for static descriptions. Examples of application of the method to photoionization and electronic transitions processes are shown.

Molecular dynamics simulations of aqueous ionic clusters using polarizable water

Abstract: The solvation properties of a chlorine ion in small water clusters are investigated using state‐of‐the‐art statistical mechanics. The simulations employ the polarizable water model developed recently by Dang [J. Chem. Phys. 97, 2659 (1992)]. The ion–water interaction potentials are defined such that the successive binding energies for the ionic clusters, and the solvation enthalpy, bulk vertical binding energy, and structural properties of the aqueous solution agree with the best available results obtained from experiments. Simulated vertical electron binding energies of the ionic clusters Cl−(H2O)n, (n=1–6) are found to be in modest agreement with data from recent photoelectron spectroscopy experiments. Minimum energy configurations for the clusters as a function of ion polarizability are compared with the recent quantum chemical calculations of Combariza, Kestner, and Jortner [Chem. Phys. Lett. 203, 423 (1993)]. Equilibrium cluster configurations at 200 K are described in terms of surface and interior s...

Quantum Chemical Conformational Analysis of Glucose in Aqueous Solution

Abstract: We have calculated the aqueous solvation effects on the anomeric and conformational equilibria of D-glucopyranose using a quantum chemical solvation model based on a continuum treatment of dielectric polarization and solvent accessible surface area. The solvation model puts the relative ordering of the hydroxymethyl conformers in linewith the experimentally determined ordering of populations. Our calculations indicatethat the anomeric equilibrium is controlled primarily by effects that are also present in the gas-phase potential energy function, that the gauche/trans O-C(6)-C(5)-O hydroxymethyl conformational equilibrium is dominated by favorable solute-solvent hydrogen bonding interactions, and that other rotameric equilibria are controlled mainly by dielectric polarization of the solvent

Proton transfer dynamics in substituted 3‐hydroxyflavones: Solvent polarization effects

Abstract: The spectroscopy and excited state proton transfer (ESPT) dynamics of 4’‐N,N‐dimethylamino‐3HF (I) and 4’‐N,N‐diethylamino‐3HF (II) have been studied in acetonitrile/benzene solvent mixtures. Solvent composition‐dependent spectral shifts are observed and can be understood in terms of an Onsager cavity model. Analysis of these spectral shifts accurately predicts solvent composition‐dependent excited state equilibrium constants, which are also experimentally determined. The ESPT rates are analyzed within the framework of a transition state theory treatment of solvent polarization‐mediated proton transfer. This treatment is analogous to electron transfer theory. In this treatment, the energetics of the transition state are largely determined by known solvent properties and the solvent‐dependent spectroscopy. This analysis yields solvent‐dependent ESPT activation energies. The corresponding calculated ESPT rates are in excellent agreement with the experimentally determined rates.

An infrared spectroscopic study of the preferential solvation in water-acetonitrile mixtures

Abstract: Mixtures of water and acetonitrile in the full concentration range have been studied by infrared spectroscopy. OD and CN stretching vibrations of HDO and CD 3 CN molecules have been used as probes of the structural environments. Acetonitrile molecules which are unaffected by water molecules are found for a broad concentration range (0.1≤xH 2 O≤0.8), showing that a preferential solvation occurs. The strong tendency for self-association of water molecules is evident from the occurrence of a broad OD stretching band. Chains of water molecules linked by hydrogen bonds are suggested to be formed rather than spherical clusters

Application of solvation equations to chemical and biochemical processes

Abstract: Two solvation equations that can be used either as LSERs or as QSARs have been applied to various processes that involve transfer of a series of solutes from the gas phase to a condensed phase or transfer of a series of solutes from one condensed phase to another. In the former class, the processes include gas-liquid chromatography, gas-solid chromatography, the solubility of gases and vapours in polymers and organic solvents, and upper respiratory tract imtation in mice. The latter class includes water-octanol and other partitions, the inhibition of firefly luciferase enzyme by aqueous nonelectrolytes, and general anaesthesia.

Water clusters: Contributions of binding energy and entropy to stability

Abstract: The binding energies of water cluster cations are obtained by measuring decay fractions of metastable dissociation and employing Klots’ model of evaporative dissociation Their variation with degree of solvation shows the commonly observed decrease, followed by a slow rise in magnitude, which typifies the trend found for solvated cations There is no observed abrupt change in the vicinity of the well‐known magic number (H2O)21⋅H+ corresponding to (H2O)20⋅H3O+ Other data are used to deduce free energies for water clusters up to size n=28, allowing a determination of entropy changes with size All of the thermochemical data, including prior literature values, are assessed in terms of calculations made using the liquid drop model and standard statistical mechanical equations It is concluded that entropic rather than energetic effects give rise to the referred to magic number

Vibrational and rotational relaxation times of solvated molecular ions

Abstract: Infrared pump–probe and infrared polarization spectroscopy have been used to measure the vibrational relaxation times (T1) of the antisymmetric stretching mode and the reorientation times (TR) for N3−, NCS−, and NCO− in D2O and/or methanol. For N3−, experiments were also conducted in H2O and hexamethyl–phosphamide (HPMA) solutions. The rapid vibrational relaxation and slow reorientation observed demonstrate strong coupling between the ions and the solvents. Longer vibrational relaxation and shorter reorientation times measured for NCS− reveal weaker solvent interactions that may be due to the importance of the charge distribution and the form of the normal coordinate. A comparison of the T1 and TR times in different solvents permits a determination of the relative interaction strengths for the solvents investigated. The relatively weaker coupling of N3− in the aprotic solvent HMPA demonstrates the importance of hydrogen bonding in strong solvent interactions in ionic solutions. The experimental results ar...

NH4+ in zeolites : coordination and solvation effects

Abstract: Proton transfer from a zeolitic cluster to NH3 and subsequent coordination of the ammonium cation onto the zeolitic cluster are studied by using ab initio quantum chemical cluster calculations. Proton transfer from the zeolite cluster to NH3 is favorable if, after proton transfer, the resulting NH4+ cation is coordinated to the zeolitic cluster with two or three hydrogen bonds. These structures are referred to as 2H and 3H, respectively. Their adsorption energies the energy needed for the process of proton transfer followed by the binding of the NH4+ cation, are calculated to be -1 14 and -1 13 kJ/mol, respectively. The geometries were optimized at the SCF level and the adsorption energies were calculated at the second-order Mprller-Plesset perturbation theory level (MP2), using the counterpoise correction (CPC) to avoid the basis set superposition error (BSSE). The basis set is the 6-3 1 l+G(d,p)/STO-3G one, which has previously been shown to give proper binding and proton transfer energies. The calculated heats of adsorption compare well with experimental heats of desorption. Proton transfer also occurs when another NH3 molecule is coadsorbed. However, the process of coadsorption is energetically less favorable than the 2H and 3H structures: the adsorption energy per NHs molecule is only -30 kJ/mol. For the clusters the N-H stretching frequencies have been calculated at the SCF level in the harmonic approach. They have been compared with experimental spectra of the NH4+ forms of some zeolites. The N-H stretching region of these spectra can be explained as a superposition of the spectra of the 2H and 3H structures. By comparison of the adsorption energy on a geometry optimized cluster and on a fixed geometry cluster, it was found that the choice of the geometry is important. On enlarging the fixed geometry cluster the adsorption energy remained constant.

Relative viscosities and quasi-thermodynamics of solutions of tert-butyl alcohol in the methanol–water system: a different view of the alkyl–water interaction

Abstract: Viscosity B coefficients for tert-butyl alcohol (TBA) in water, methanol and mixtures of the two have been obtained at 25 and 35 °C. Hence solute contributions to the activation parameters for viscous flow of the solutions have been calculated, as well as the Gibbs energy, enthalpy and entropy of transfer from the ground-state solvent to the hypothetical viscous ‘transition-state solvent’. The enthalpies of mixing of the two transition-state solvents and their relative partial molar enthalpies L′1 and L′2 are also given.In water, B is large and positive and dB/dT large and negative; in methanol B is small and dB/dT near zero. The classical explanation of these observations, which is solely in terms of water–water (1,1) interactions in an ‘iceberg’ around the alkyl group, is inconsistent with the Compensation Principle because B is proportional to a Gibbs energy function, and this requires that solute–solvent (3, 1) interactions must determine B.It is proposed that in water the alkyl group occupies a ‘cage’ in which the strength of the bonding with respect to the pure solvent is of minor importance. The ‘caging’ of the alkyl group enhances its van der Waals interactions with its nearest neighbours. The expected dependence of such interactions on distance leads to energy–reaction coordinate diagrams in the form required to explain the inversion in sign of the solvation energies from ground-state solvent to transition-state solvent in highly aqueous media.These results are consistent with, though independent of, recent structural studies by neutron diffraction with isotopic substitution.

Calculation of solvation free energies using a density functional/molecular dynamics coupled potential

Abstract: Recently there has been much interest in the development of methods which couple quantum mechanical and molecular mechanical computational models. Herein, we report the first coupling of a density functional Hamiltonian with a molecular mechanical method. The AMBER force field was coupled with a density functional Hamiltonian as implemented in the deMon program. Test calculations of solvation energies were carried out for a small group of ions. We find that our coupled potential method slightly underestimates the solvation energy of the chloride ion while it overestimates the solvation energy of the other ions studied. Nonetheless, this method will allow a chemist to study condensed-phase systems at a level of accuracy currently not available

Thermodynamics of solvation of ions. Part 6.—The standard partial molar volumes of aqueous ions at 298.15 K

Abstract: The standard partial molar volumes at 298.15 K of 138 aqueous ions ranging in their charges from –4 to +4 have been compiled. They are described by essentially the same model that was used previously to describe thermodynamic functions of ion hydration. This model involves a hydration shell of specified thickness, where most of the electrostriction takes place, so that the volume of the ion is the difference between that of the hydrated ion and the electrostriction caused by the charge. Hydrophobic ions have an extra structural contribution to their volume.

Hydration of uranyl (UO22+) cation and its nitrate ion and 18-crown-6 adducts studied by molecular dynamics simulations

Abstract: Molecular dynamics simulations have been performed first on the UO[sub 2][sup 2+] cation in a box of water molecules in order to investigate the sensitivity of hydration pattern to the electrostatic models used. The coordination number of water to the U and O atoms is not very sensitive to the charges on these atoms. With the different charges, UO[sub 2][sup 2+] is surrounded by five water molecules in the equatorial plane. It bends slightly and the U-O bond lengthens, due to strong coordination of water molecules in the first shell. However, free energy changes upon mutation of one electrostatic model into the other demonstrate the high dependence of hydration energies to the electrostatic distribution in the solute. A van der Waals parameter, 1.6 A, is proposed for the U atom in water. The UO[sub 2][sup 2+], 2NO[sub 3][sup [minus]] salt simulated in water remains as an intimate ion pair with bis(monodentate) coordination and three water molecules in the first shell. In contrast, an inclusion complex of UO[sub 2][sup 2+] with 18-crown-6 displays dissociative behavior to form a second sphere complex, in agreement with experimental evidence. 78 refs., 7 figs., 7 tabs.