Showing papers on "Implicit solvation published in 2011"

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations.

Abstract: The Molecular Mechanics/Poisson−Boltzmann Surface Area (MM/PBSA) and the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free energies for macromolecules by combining molecular mechanics calculations and continuum solvation models. To systematically evaluate the performance of these methods, we report here an extensive study of 59 ligands interacting with six different proteins. First, we explored the effects of the length of the molecular dynamics (MD) simulation, ranging from 400 to 4800 ps, and the solute dielectric constant (1, 2, or 4) on the binding free energies predicted by MM/PBSA. The following three important conclusions could be observed: (1) MD simulation length has an obvious impact on the predictions, and longer MD simulation is not always necessary to achieve better predictions. (2) The predictions are quite sensitive to the solute dielectric constant, and this parameter should be carefully determined according to the characteristics of the protein/lig...

Use of Solution-Phase Vibrational Frequencies in Continuum Models for the Free Energy of Solvation

Abstract: We find that vibrational contributions to a solute’s free energy are in general insensitive to whether the solute vibrational frequencies are computed in the gas phase or in solution. In most cases, the difference is smaller than the intrinsic error in solvation free energies associated with the continuum approximation to solvation modeling, although care must be taken to avoid spurious results associated with limitations in the quantum-mechanical harmonic-oscillator approximation for very low-frequency molecular vibrations. We compute solute vibrational partition functions in aqueous and carbon tetrachloride solution and compare them to gas-phase molecular partition functions computed with the same level of theory and the same quasiharmonic approximation for the diverse and extensive set of molecules and ions included in the training set of the SMD continuum solvation model, and we find mean unsigned differences in vibrational contributions to the solute free energy of only about 0.2 kcal/mol. On the bas...

The COSMO and COSMO-RS solvation models

Abstract: The conductor-like screening model COSMO, a variant of the dielectric continuum solvation models, has become very popular due to its algorithmic simplicity, numerical stability, and its great insensitivity with respect to outlying charge errors. The advanced model COSMO-RS, i.e., COSMO for realistic solvation, is a statistical thermodynamics theory based on COSMO polarization charge densities, which overcomes many of the limitations and theoretical shortcomings of dielectric continuum models. Due to its ability to treat mixtures at variable temperatures, it has become very popular in chemical engineering and in wide areas of physical and medicinal chemistry. COSMO-RS may currently be considered the most accurate model for the prediction of solvation energies. This article provides a short description of the basic concepts of both models, of the differences with other solvation models, and of their application areas. Finally, Direct-COSMO-RS, a recent direct integration of the COSMO-RS concept into quantum chemical calculations, is briefly described. For further resources related to this article, please visit the WIREs website.

Revised self-consistent continuum solvation in electronic-structure calculations

Abstract: The solvation model proposed by Fattebert and Gygi [Journal of Computational Chemistry 23, 662 (2002)] and Scherlis et al [Journal of Chemical Physics 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability We first recast the problem in terms of induced polarization charges that act as a direct mapping of the self-consistent continuum dielectric; this allows to define a functional form for the dielectric that is well behaved both in the high-density region of the nuclear charges and in the low-density region where the electronic wavefunctions decay into the solvent Second, we outline an iterative procedure to solve the Poisson equation for the quantum fragment embedded in the solvent that does not require multi-grid algorithms, is trivially parallel, and can be applied to any Bravais crystallographic system Last, we capture some of the non-electrostatic or cavitation terms via a combined use of the quantum volume and quantum surface [Physical Review Letters 94, 145501 (2005)] of the solute The resulting self-consistent continuum solvation (SCCS) model provides a very effective and compact fit of computational and experimental data, whereby the static dielectric constant of the solvent and one parameter allow to fit the electrostatic energy provided by the PCM model with a mean absolute error of 03 kcal/mol on a set of 240 neutral solutes Two parameters allow to fit experimental solvation energies on the same set with a mean absolute error of 13 kcal/mol A detailed analysis of these results, broken down along different classes of chemical compounds, shows that several classes of organic compounds display very high accuracy, with solvation energies in error of 03-04 kcal/mol, whereby larger discrepancies are mostly limited to self-dissociating species and strong hydrogen-bond forming compounds

Practical computation of electronic excitation in solution: vertical excitation model

Abstract: We present a unified treatment of solvatochromic shifts in liquid-phase absorption spectra, and we develop a self-consistent state-specific vertical excitation model (called VEM) for electronic excitation in solution. We discuss several other approaches to calculate vertical excitations in solution as an approximation to VEM. We illustrate these methods by presenting calculations of the solvatochromic shifts of the lowest excited states of several solutes (acetone, acrolein, coumarin 153, indolinedimethine-malononitrile, julolidine-malononitrile, methanal, methylenecyclopropene, and pyridine) in polar and nonpolar solvents (acetonitrile, cyclohexane, dimethyl sulfoxide, methanol, n-hexane, n-pentane, and water) using implicit solvation models combined with configuration interaction based on single excitations and with time-dependent density functional theory.

Molecular density functional theory of solvation: from polar solvents to water.

Abstract: A classical density functional theory approach to solvation in molecular solvent is presented. The solvation properties of an arbitrary solute in a given solvent, both described by a molecular force field, can be obtained by minimization of a position and orientation-dependent free-energy density functional. In the homogeneous reference fluid approximation, limited to two-body correlations, the unknown excess term of the functional approximated by the angular-dependent direct correlation function of the pure solvent. We show that this function can be extracted from a preliminary MD simulation of the pure solvent by computing the angular-dependent pair distribution function and solving subsequently the molecular Ornstein-Zernike equation using a discrete angular representation. The corresponding functional can then be minimized in the presence of an arbitrary solute on a three-dimensional cubic grid for positions and Gauss-Legendre angular grid for orientations to provide the solvation structure and free-energy. This two-step procedure is proved to be much more efficient than direct molecular dynamics simulations combined to thermodynamic integration schemes. The approach is shown to be relevant and accurate for prototype polar solvents such as the Stockmayer solvent or acetonitrile. For water, although correct for neutral or moderately charged solute, it tends to underestimate the tetrahedral solvation structure around H-bonded solutes, such as spherical ions. This can be corrected by introducing suitable three-body correlation terms that restore both an accurate hydration structure and a satisfactory energetics.

How does halogen bonding behave in solution? A theoretical study using implicit solvation model.

Abstract: A systematic study of halogen bonding interactions in gas phase and in solution was carried out by means of quantum chemical DFT/B3LYP method Three solvents with different polarities (chloroform, acetone, and water) were selected, and solvation effects were considered using the polarized continuum model (PCM) For charged halogen-bonded complexes, the strength of the interactions tends to significantly weaken in solution, with a concomitant elongation of intermolecular distances For neutral systems, halogen bond distances are shown to shorten and the interaction energies change slightly Computations also reveal that in the gas phase the binding affinities decrease in the order Cl(-) > Br(-) > I(-), while in solution the energy gaps of binding appear limited for the three halide anions According to free energy results, many systems under investigation are stable in solution Particularly, calculated free energies of formation of the complexes correlate well with halogen-bonding association constants determined experimentally The differences of the effects of solvent upon halogen and hydrogen bonding were also elucidated This study can establish fundamental characteristics of halogen bonding in media, which would be very helpful for applying this noncovalent interaction in medicinal chemistry and material design

A coarse-grained model of DNA with explicit solvation by water and ions.

Abstract: Solvation by water and ions has been shown to be vitally important for biological molecules, yet fully atomistic simulations of large biomolecules remain a challenge due to their high computational cost. The effect of solvation is the most pronounced in polyelectrolytes, of which DNA is a paradigmatic example. Coarse-grained (CG) representations have been developed to model the essential physics of the DNA molecule, yet almost without exception, these models replace the water and ions by implicit solvation in order to significantly reduce the computational expense. This work introduces the first coarse-grained model of DNA solvated explicitly with water and ions. To this end, we combined two established CG models; the recently developed mW-ion model [DeMille, R. C.; Molinero, V. J. Chem. Phys. 2009, 131, 034107], which reproduces the structure of aqueous ionic solutions without electrostatic interactions, was coupled to the three-sites-per-nucleotide (3SPN) CG model of DNA [Knotts, T. A., IV; et al. J. Ch...

Polar solvation dynamics in water and methanol: search for molecularity

Abstract: Time-dependent Stokes shifts (TDSS) were measured for diverse polarity probes in water, heavy water, methanol, and benzonitrile, by broadband fluorescence up-conversion with 85 fs time resolution. In water the spectral dynamics is solute-independent and quantitatively described by simple dielectric continuum theory of solvation. In methanol the slower part of the TDSS is solute-dependent. A correlation with anisotropy decay suggests that methanol solvation dynamics is modulated by orientational solute diffusion. An empirical power law which links the solvation relaxation function of a mobile solute to that of an immobile solute is experimentally verified. Activation energies for the average relaxation rate are also given. Solvation dynamics in H2O and D2O are identical at and above 20 °C but diverge below.

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects

Abstract: A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σi) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules, or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σi and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for non-polar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

Modeling aqueous solvation with semi-explicit assembly

Abstract: We describe a computational solvation model called semi-explicit assembly (SEA). SEA water captures much of the physics of explicit-solvent models but with computational speeds approaching those of implicit-solvent models. We use an explicit-water model to precompute properties of water solvation shells around simple spheres, then assemble a solute’s solvation shell by combining the shells of these spheres. SEA improves upon implicit-solvent models of solvation free energies by accounting for local solute curvature, accounting for near-neighbor nonadditivities, and treating water’s dipole as being asymmetrical with respect to positive or negative solute charges. SEA does not involve parameter fitting, because parameters come from the given underlying explicit-solvation model. SEA is about as accurate as explicit simulations as shown by comparisons against four different homologous alkyl series, a set of 504 varied solutes, solutes taken retrospectively from two solvation-prediction events, and a hypothetical polar-solute series, and SEA is about 100-fold faster than Poisson–Boltzmann calculations.

Solvent effects and dynamic averaging of 195Pt NMR shielding in cisplatin derivatives.

Abstract: The influences of solvent effects and dynamic averaging on the 195Pt NMR shielding and chemical shifts of cisplatin and three cisplatin derivatives in aqueous solution were computed using explicit and implicit solvation models. Within the density functional theory framework, these simulations were carried out by combining ab initio molecular dynamics (aiMD) simulations for the phase space sampling with all-electron relativistic NMR shielding tensor calculations using the zeroth-order regular approximation. Structural analyses support the presence of a solvent-assisted “inverse” or “anionic” hydration previously observed in similar square-planar transition-metal complexes. Comparisons with computationally less demanding implicit solvent models show that error cancellation is ubiquitous when dealing with liquid-state NMR simulations. After aiMD averaging, the calculated chemical shifts for the four complexes are in good agreement with experiment, with relative deviations between theory and experiment of abo...

Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

Abstract: Continuum solvation methods are frequently used to increase the efficiency of computational methods to estimate free energies. In this paper, we have evaluated how well such methods estimate the nonpolar solvation free-energy change when a ligand binds to a protein. Three different continuum methods at various levels of approximation were considered, viz., the polarized continuum model (PCM), a method based on cavity and dispersion terms (CD), and a method based on a linear relation to the solvent-accessible surface area (SASA). Formally rigorous double-decoupling thermodynamic integration was used as a benchmark for the continuum methods. We have studied four protein-ligand complexes with binding sites of varying solvent exposure, namely the binding of phenol to ferritin, a biotin analogue to avidin, 2-aminobenzimidazole to trypsin, and a substituted galactoside to galectin-3. For ferritin and avidin, which have relatively hidden binding sites, rather accurate nonpolar solvation free energies could be obtained with the continuum methods if the binding site is prohibited to be filled by continuum water in the unbound state, even though the simulations and experiments show that the ligand replaces several water molecules upon binding. For the more solvent exposed binding sites of trypsin and galectin-3, no accurate continuum estimates could be obtained, even if the binding site was allowed or prohibited to be filled by continuum water. This shows that continuum methods fail to give accurate free energies on a wide range of systems with varying solvent exposure because they lack a microscopic picture of binding-site hydration as well as information about the entropy of water molecules that are in the binding site before the ligand binds. Consequently, binding affinity estimates based upon continuum solvation methods will give absolute binding energies that may differ by up to 200 kJ/mol depending on the method used. Moreover, even relative energies between ligands with the same scaffold may differ by up to 75 kJ/mol. We have tried to improve the continuum solvation methods by adding information about the solvent exposure of the binding site or the hydration of the binding site, and the results are promising at least for this small set of complexes.

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

Abstract: To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

DNA Molecular Solvation in Neat Ionic Liquids

Abstract: The structural and molecular mechanism of double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) solvation in ten room-temperature ionic liquids (RTILs) is disclosed herein. We show that the Drew Dickerson B DNA structure solvated in neat RTILs based on imidazolium, oxazolium, pyrrolidinium, pyrimidinium and quaternary ammonium cations, combined with hexafluorophosphate and tetrafluorobromide anions (Figure 1), is able to maintain the native dsDNA B form confor-

Anchor points for the unified Brønsted acidity scale: the rCCC model for the calculation of standard Gibbs energies of proton solvation in eleven representative liquid media

Abstract: The COSMO cluster-continuum (CCC) solvation model is introduced for the calculation of standard Gibbs solvation energies of protons. The solvation sphere of the proton is divided into an inner proton-solvent cluster with covalent interactions and an outer solvation sphere that interacts electrostatically with the cluster. Thus, the solvation of the proton is divided into two steps that are calculated separately: 1) The interaction of the proton with one or more solvent molecules is calculated in the gas phase with high-level quantum-chemical methods (modified G3 method). 2) The Gibbs solvation energy of the proton-solvent cluster is calculated by using the conductor-like screening model (COSMO). For every solvent, the solvation of the proton in at least two (and up to 11) proton-solvent clusters was calculated. The resulting Gibbs solvation energies of the proton were weighted by using Boltzmann statistics. The model was evaluated for the calculation of Gibbs solvation energies by using experimental data of water, MeCN, and DMSO as a reference. Allowing structural relaxation of the proton-solvent clusters and the use of structurally relaxed Gibbs solvation energies improved the accordance with experimental data especially for larger clusters. This variation is denoted as the relaxed COSMO cluster-continuum (rCCC) model, for which we estimate a 1σ error bar of 10 kJ mol(-1) . Gibbs solvation energies of protons in the following representative solvents were calculated: Water, acetonitrile, sulfur dioxide, dimethyl sulfoxide, benzene, diethyl ether, methylene chloride, 1,2-dichloroethane, sulfuric acid, fluorosulfonic acid, and hydrogen fluoride. The obtained values are absolute chemical standard potentials of the proton (pH=0 in this solvent). They are used to anchor the individual solvent specific acidity (pH) scales to our recently introduced absolute acidity scale.

Solvation studies of a zinc finger protein in hydrated ionic liquids.

Abstract: The solvation of the zinc finger protein with the PDB-ID “5ZNF” in hydrated ionic liquids was studied at varying water content 1-Ethyl-3-methylimidazolium and trifluoromethanesulfonate were the cation and anion, respectively The protein stability as well as the solvation structure, the shell dynamics and the shell resolved dielectric properties were investigated by means of molecular dynamics simulations The lengths of the respective trajectories extended up to 200 nanoseconds in order to cover the complete solvent dynamics Considering the above mentioned properties as a function of the water content they all exhibit a maximum or minimum at the very same mole fraction While the exact value xH2O = 0927 depends on the underlying force field, its origin may be traced back to the competition between the van der Waals and the electrostatic energy of the protein as well as to the transition from aqueous dielectric screening to ionic charge screening with decreasing water content The parameter-free Voronoi decomposition of space served as a basis for the analysis of most results In particular, solvation shells were naturally inferred from this concept In addition to the molecular analysis a mesoscopic view is given in terms of dielectric properties Thereby, the net dielectric constant is decomposed into contributions from the protein, the first and second solvation shells as well as the bulk Cross-terms between these components are given, too

Postprocessing of docked protein-ligand complexes using implicit solvation models.

Abstract: 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 ...

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: equilibrium fluctuation of cytochrome c.

Abstract: The relationship between the protein conformation and the hydration effect is investigated for the equilibrium fluctuation of cytochrome c. To elucidate the hydration effect with explicit solvent, the solvation free energy of the protein immersed in water was calculated using the molecular dynamics simulation coupled with the method of energy representation. The variations of the protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation. The roles of the attractive and repulsive components in the protein–water interaction are further examined for the solvation free energy. The attractive component represented as the average sum of protein–water interaction energy is dominated by the electrostatic effect and is correlated to the solvation free energy through the linear-response-type relationship. No correlation with the (total) solvation free energy is seen, on the other hand, for the repulsive component expressed as t...

Physical Modeling of Aqueous Solvation

Abstract: We consider the free energies of solvating molecules in water. Computational modeling usually involves either detailed explicit-solvent simulations, or faster computations, which are based on implicit continuum approximations or additivity assumptions. These simpler approaches often miss microscopic physical details and non-additivities present in experimental data. We review explicit-solvent modeling that identifies the physical bases for the errors in the simpler approaches. One problem is that water molecules that are shared between two substituent groups often behave differently than waters around each substituent individually. One manifestation of non-additivities is that solvation free energies in water can depend not only on surface area or volume, but on other properties, such as the surface curvature. We also describe a new computational approach, called Semi-Explicit Assembly, that aims to repair these flaws and capture more of the physics of explicit water models, but with computational efficiencies approaching those of implicit-solvent models.

Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free‐Energy Methods

Abstract: We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.

On the solvation of the Zn2+ ion in methanol: a combined quantum mechanics, molecular dynamics, and EXAFS approach.

Abstract: The solvation properties of the Zn(2+) ion in methanol solution have been investigated using a combined approach based on molecular dynamics (MD) simulations and extended X-ray absorption fine structure (EXAFS) experimental results. The quantum mechanical potential energy surface for the interaction of the Zn(2+) ion with a methanol molecule has been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective Zn-methanol interactions have been fitted by suitable analytical potentials, and have been utilized in the MD simulation to obtain the structural properties of the solution. The reliability of the whole procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to the EXAFS experiments.

Solvent effect on keto–enol tautomerism in a new β-diketone: a comparison between experimental data and different theoretical approaches

Abstract: The novel β-diketo compound (3-acetyl-4-oxopentanoic acid) OPAA is here synthesized and completely characterized in the solid state by means of X-ray crystallography and in solution by potentiometry and 1H and 13C NMR spectroscopy. In the solid state, OPAA exhibits the di-keto (DK) structure, however, in solution, we can observe a strong solvent dependent tautomeric equilibrium. Theoretical ab initio calculations employing DFT at the B3LYP/6-311G** level, and different methods of theoretical model chemistry (CBS-4M, G3MP2, CBS-QB3) are used to extensively investigate the tautomeric equilibrium and compare it with experimental data. Solvent effects are evaluated using a CPCM continuum solvation method; among all applied methods, CBS-4M is the one that better predicts experimental data and is able to qualitatively describe tautomeric equilibrium in solution, allowing thermodynamic calculations of pKa. Furthermore a supermolecular solvent approach is used to better analyze solvent–solute interactions in order to predict chemical properties.

Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH.

Abstract: Modern implicit solvent models for macromolecular simulations in water-proton bath are considered. The fundamental quantity that implicit models approximate is the solute potential of mean force, which is obtained by averaging over solvent degrees of freedom. The implicit solvent models suggest practical ways to calculate free energies of macromolecular conformations taking into account equilibrium interactions with water solvent and proton bath, while the explicit solvent approach is unable to do that due to the need to account for a large number of solvent degrees of freedom. The most advanced realizations of the implicit continuum models by different research groups are discussed, their accuracy are examined, and some applications of the implicit solvent models to macromolecular modeling, such as free energy calculations, protein folding, and constant pH molecular dynamics are highlighted.

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water.

Abstract: We report the development of an atomic decomposition method of the protein solvation free energy in water, which ascribes global change in the solvation free energy to local changes in protein conformation as well as in hydration structure. So far, empirical decomposition analyses based on simple continuum solvation models have prevailed in the study of protein-protein interactions, protein-ligand interactions, as well as in developing scoring functions for computer-aided drug design. However, the use of continuum solvation model suffers serious drawbacks since it yields the protein free energy landscape which is quite different from that of the explicit solvent model and since it does not properly account for the non-polar hydrophobic effects which play a crucial role in biological processes in water. Herein, we develop an exact and general decomposition method of the solvation free energy that overcomes these hindrances. We then apply this method to elucidate the molecular origin for the solvation free energy change upon the conformational transitions of 42-residue amyloid-beta protein (Aβ42) in water, whose aggregation has been implicated as a primary cause of Alzheimer's disease. We address why Aβ42 protein exhibits a great propensity to aggregate when transferred from organic phase to aqueous phase.

Evaluation of DNA Force Fields in Implicit Solvation.

Abstract: DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models.

A QM/MM study of the binding of RAPTA ligands to cathepsin B

Abstract: We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson–Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r 2) of 0.35–0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r 2 = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r 2 = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r 2 = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.

Efficient Solvation Free Energy Calculations of Amino Acid Analogs by Expanded Ensemble Molecular Simulation.

Abstract: We present an efficient, automated expanded ensemble method to calculate the residual chemical potential or solvation free energy by molecular dynamics simulation. The methodology is validated by computing the residual chemical potential of 13 amino acid analogs in water at 300 K and 1 bar and comparing to reference simulation data. Overall agreement is good, with the methodology of the present study reaching limiting precisions of less than 0.1 kBT in half of the total simulation time of the reference simulation study which utilized Bennett's acceptance ratio method. The apparent difference in the efficiencies is a result of the inherent advantages of the expanded ensemble method, which creates an improved decorrelation of simulation data and improves the sampling of the important regions of the configurational phase space of each subensemble. The present adaptation utilizes histograms of proposed transition energies collected throughout the entire simulation, to make extremely precise calculations of the relative free energy between neighboring subensembles.

Water-exclusion and liquid-structure forces in implicit solvation.

Abstract: A continuum model of solvation is proposed to describe (i) long-range electrostatic effects of water exclusion resulting from incomplete and anisotropic hydration in crowded environments and (ii) short-range effects of liquid-structure forces on the hydrogen-bond interactions at solute/water interfaces. The model is an extension of the phenomenological screened coulomb potential-based implicit model of solvation. The developments reported here allow a more realistic representation of highly crowded and spatially heterogeneous environments, such as those in the interior of a living cell. Only the solvent is treated as a continuum medium. It is shown that the electrostatic effects of long-range water-exclusion can strongly affect protein–protein binding energies and are then related to the thermodynamics of complex formation. Hydrogen-bond interactions modulated by the liquid structure at interfaces are calibrated based on systematic calculations of potentials of mean force in explicit water. The electrosta...