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In the present study, we have employed a high-level density functional theory (DFT) model to investigate both implicit and explicit effects of solvation (i.e., the bulk solvation effect as well as microhydration) in addition to the effect of distal Histidine on the binding of CO to Ferrous and Ferric-Heme. It has been predicted that the distal N-methylimidazole (MI) in addition to microsolvation, as a simple mode of environment, leads to a significant stabilization on the binding of CO to Heme-FeII (by ∼ 4 kcal mol−1). This is while no clear alteration has been predicted for the implicit solvation model. For the Ferric heme, and in contrast to the Ferrous system, strong destabilization from the environment has been predicted for binding CO to the Ferric heme analog.

Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the nonlinear and linearized versions of the Poisson-Boltzmann equation (PBE), the domain-decomposition conductor-like screening model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatics models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least-squares style target function based on a library of 103 small-molecule solvation free energy differences. Mean signed errors for the adaptive Poisson-Boltzmann solver (APBS), ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.58 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields opens the door to their use for folding and design applications.

Time-dependent density functional theory (TD-DFT) and spectrophotometric methods were used for speciation analysis in systems disulfides (cystine, cystamine, homocystine, 3,3-dithiodipropionic acid) — [PdCl4]2− or [PtCl4]2−. We use the M06-2X and CAM-B3LYP density functionals with Def2-SVP basis set to reproduce the experimental UV-vis spectra; the polarized continuum solvation model (PCM) was fitted to take into account solvation effects of the medium (water). Used methods have shown the good agrees with the experiment — theoretical values of transition energies differ from real parameters within ±0.15 eV for functional CAM-B3LYP. Binuclear disulfide complexes of Pd(II) with cystine and cystamine have form S,N-coordination sites, instead of S,S-conformation. It was shown that Pd(II) thiolate complexes formed by cleavage of the disulfide bond exist as [PdCl3L] and [Pd2S2L2]. Pt(II)-disulfide systems have confirmed the presence of [Pt2Cl6(R-SS-R)] and [PtCl4(S-R)] complex species. The DFT/CAM-B3LYP/Def2-SVP/SMD level can be recommended for theoretical estimations of absorption spectra of complexes of palladium or platinum and sulfur-containing ligands.

International audience; The insertion reactions of the bispentamethylcyclopentadienyl bisthiolate uranium(IV) complexes [U(Cp*)(2)(SR)(2)] (Cp* = eta-C5Me5; R = Me (1), Bu-t (2), Pr-i (3), Ph (4)) with CO2 or CS2 were investigated using Density Functional Theory (DFT), solvent effects being taken into account using the SMD continuum solvation model. The optimized geometries of the bisthiolate compounds computed at the DFT/B3PW91 level are in good agreement with available X-ray experimental data. The energy profiles of their reactions with CO2 and CS2 were determined. The formation of the products can be explained by a unique reaction mechanism involving an uranium(IV)-bridged heteroallene transition state. The CO2 insertion reactions exhibit lower activation barriers than those of CS2 insertion in accordance with the experiments showing that the CO2 insertion reactions are faster. As expected, compound 2 (R = Bu-t) was found to be the most difficult to undergo the insertion reaction because of steric hindrance. The geometrical parameters of the CS2 insertion derivative [U(Cp*)(2)(StBu)((S2CSBu)-Bu-t)] (5) and the mixed insertion complex [U(Cp*)(2)((O2CSBu)-Bu-t)((S2CSBu)-Bu-t)] (6) obtained after treatment of 5 with CO2 are consistent with those determined by X-ray diffraction. The performed orbital analysis reveal the respective role of the actinide 7s, 6d and 5f orbitals, whereas the Wiberg Bond Indices (WBI) afford a good explanation of the structural variations during the insertion reactions. Finally, the Natural Population Analyses account for the different charge transfers occurring during the insertion processes. (C) 2019 Elsevier B.V. All rights reserved.

Ligand affinity prediction from docking simulations is usually performed by means of highly empirical and diverse protocols. These protocols often involve the re-scoring of poses generated by a force field (FF) based Hamiltonian to provide either estimated binding affinities—or alternatively, some empirical goodness score. Re-scoring is performed by so-called scoring functions—typically, a reweighted sum of FF terms augmented by additional terms (e.g., desolvation/entropic penalty, hydrophobicity, aromatic interactions etc.). Sometimes, the scoring function actually drives ligand positioning, but often it only operates on the best scoring poses ranked top by the initial ligand positioning tool. In either of these rather intricate scenarios, scoring functions are docking-specific models, and most require machine-learning-based calibration. Therefore, docking simulations are less straightforward when compared to “standard” molecular simulations in which the FF Hamiltonian defines the energy, and affinity emerges as an ensemble average property over pools of representative conformers (i.e., the trajectory). Paraphrasing on Occam’s Razor principle, additional model complexity is only acceptable if demonstrated to bring a significant improvement of prediction quality. In this work we therefore examined whether the complexity inherent to scoring functions is indeed justified. For this purpose we compared sampler for multiple protein–ligand entities, a general purpose conformation sampler based on the AMBER/GAFF FF, complemented with continuum solvation terms, with several state of the art docking tools that rely on calibrated scoring functions (Glide, Gold, Autodock-Vina) in terms of its ability to top-rank the actives from large and diverse ligand series associated with various proteins. There is no clear winner of this study, where each program performed well on most of the targets, but also failed with respect to at least one of them. Therefore, a well-parameterized force field with a simple, energy-based ligand ranking protocol appears to be an as effective docking protocol as intricate rescoring strategies based on scoring functions. A tool that can sample the conformational space of the free ligand, the bound ligand and the protein binding site using the same force field may avoid many of the approximations common to contemporary docking protocols and allow e.g., for docking into highly flexible active sites, when current scoring functions are not well suited to estimate receptor strain energies.

In this work, we have combined the polarizable force field based on the classical Drude oscillator with a continuum Poisson-Boltzmann/solvent-accessible surface area (PB/SASA) model. In practice, the positions of the Drude particles experiencing the solvent reaction field arising from the fixed charges and induced polarization of the solute must be optimized in a self-consistent manner. Here, we parameterized the model to reproduce experimental solvation free energies of a set of small molecules. The model reproduces well-experimental solvation free energies of 70 molecules, yielding a root mean square difference of 0.8 kcal/mol versus 2.5 kcal/mol for the CHARMM36 additive force field. The polarization work associated with the solute transfer from the gas-phase to the polar solvent, a term neglected in the framework of additive force fields, was found to make a large contribution to the total solvation free energy, comparable to the polar solute-solvent solvation contribution. The Drude PB/SASA also reproduces well the electronic polarization from the explicit solvent simulations of a small protein, BPTI. Model validation was based on comparisons with the experimental relative binding free energies of 371 single alanine mutations. With the Drude PB/SASA model the root mean square deviation between the predicted and experimental relative binding free energies is 3.35 kcal/mol, lower than 5.11 kcal/mol computed with the CHARMM36 additive force field. Overall, the results indicate that the main limitation of the Drude PB/SASA model is the inability of the SASA term to accurately capture non-polar solvation effects. © 2018 Wiley Periodicals, Inc.

International audience; The Gibbs energy of solvation measures the affinity of a solute for its solvent and is thus a key property for the selection of an appropriate solvent for a chemical synthesis or a separation process. More fundamentally, Gibbs energies of solvation are choice data for developing and benchmarking molecular models predicting solvation effects. The Comprehensive Solvation-CompSol-database was developed with the ambition to propose very large sets of new experimental solvation chemical-potential, solvation entropy, and solvation enthalpy data of pure and mixed components, covering extended temperature ranges. For mixed compounds, the solvation quantities were generated in infinite-dilution conditions by combining experimental values of pure-component and binary-mixture thermodynamic properties. Three types of binary-mixture properties were considered: partition coefficients, activity coefficients at infinite dilution, and Henry's-law constants. A rigorous methodology was implemented with the aim to select data at appropriate conditions of temperature, pressure, and concentration for the estimation of solvation data. Finally, our comprehensive CompSol database contains 21 671 data associated with 1969 pure species and 70 062 data associated with 14 102 binary mixtures (including 760 solvation data related to the ionic-liquid class of solvents). On the basis of the very large amount of experimental data contained in the CompSol database , it is finally discussed how solvation energies are influenced by hydrogen-bonding association effects.

Sugar-based surfactants are amphiphilic compounds bearing a head group derived from sugar. Such surfactants represent a good alternative to petroleum-based surfactants, because they can be prepared from bioproducts and generally have a low toxicity. The conformational flexibility of sugars is well known and since they can form competitive intramolecular hydrogen bonding-like interactions, the most stable conformations are often non-trivial. Calculating molecular descriptors in the context of Quantitative Structure-Property Relationship (QSPR) studies require relevant conformations. To find such conformations and then develop QSPR models, in this study, we carried out a conformational analysis of two anomers, octyl α- d -glucopyranoside and octyl β- d -glucopyranoside, to exhibit the main conformational parameters of glucopyranosides and their influence on some quantum chemical molecular descriptors that could be used in QSPR models of surfactants. From a starting set of 26 conformations for each anomer, optimized at B3LYP/6-31+G(d, p) level of Density Functional Theory, three most significant conformations, common for both glucopyranosides, generated by changing a single dihedral angle, were highlighted as the most significant conformations. The influence of solvent modeled by an implicit solvation model on conformations was discussed. Moreover, the influence of conformations on calculated molecular properties (partial charges, polarisability, and dipole moment) was discussed, for n-alkyl α/β- d -glucopyranosides. It was shown that for the studied alkyl glucosides, the dipole moment is influenced by the choice of conformations, but that the polarisability and the partial charges are less so.

The evaluation of solvation energies is a great challenge. We focus here on an organic molecule chemisorbed at a metal-liquid interface, as a prototypical system, essential in tribology, electrochemistry and heterogeneous catalysis. We compare an established implicit solvation scheme with a strategy based on molecular mechanics (MM) free energy perturbation (FEP) seeded by QM computations. First, we benchmark the approaches against experimental hydration energies of standard (organic) molecules and find acceptable errors in the order of 0.06 eV (1.3 kcal mol-1). Then, the impact of various parameters on the solvation energy of an adsorbate have been assessed on a typical system of interest, levulinic acid adsorbed at a Ru(0001)/water interface. We identify the need for dipole corrections or symmetric slabs when including solvation effects on metallic surfaces. The MM-FEP scheme is revealed to be as reliable as the implicit solvent for water. In the case of levulinic acid, both PCM and MM-FEP agree that the bulk solvation effect is not sufficient to change the adsorption mode from bidentate to mono-dentate, despite the fact that the COOH group is desolvated in the bidentate case. MM-FEP has the great advantage of being more easily generalized to other solvents and to be further improved which will be particularly useful to study solvent and (counter-)ion effects on interfacial reactions.

In situ FT-IR measurements and electronic structure calculations are reported for the reduction of CO2 catalyzed by the macrocyclic complex [CoIIN4H]2+ (N4H = 2,12-dimethyl-3,7,11,17-tetraazabicyclo-[11.3.1]-heptadeca-1(17),2,11,13,15-pentaene). Beginning from the [CoIIN4H]2+ resting state of the complex in wet acetonitrile solution, two different visible light sensitizers with substantially different reducing power are employed to access reduced states. Accessing reduced states of the complex with a [Ru(bpy)3]2+ sensitizer yields an infrared band at 1670 cm–1 attributed to carboxylate, which is also observed for an authentic sample of the one-electron reduced complex [CoN4H(MeCN)]+ in CO2 saturated acetonitrile solution. The results are interpreted based on calculations using the pure BP86 functional that correctly reproduces experimental geometries. Continuum solvation effects are also included. The calculations show that Co is reduced to CoI in the first reduction, which is consistent with experimental...

International audience; A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr-2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

International audience; The present contribution constitutes an extensive density functional theory (DFT) investigation of the nonlinear optical (NLO) properties of a large number of molecules belonging to the azobenzene and azothiophene families of photochromic compounds which can act as NLO switches. Toward the design of systems simultaneously presenting both large total nonlinear response values, beta(tot), and large contrast, beta(ratio), between the cis and trans isomers, we have focused not only on the monomers but also on azobenzene dimers, the latter containing two N=N bonds along the molecular backbone. After it was established that the inclusion of implicit solvation is not important in drawing qualitative conclusions on the NLO switching ability for the investigated systems, gas-phase calculations have shown that for the asymmetric pushpull azobenzene and azothiophene candidates, the combination of strong donating groups such as NPh2, N(Ph-OMe)(2), and N(Ph-NMe2)(2) with the dicyanoethene group CH=C(C=N)(2) as an acceptor delivers large ?trans (150-217 x 10(-30) esu) and non-negligible beta(cis) (18-55 x 10(-30) esu) values as well as substantial contrast, beta(ratio) (3.9-8.7). For the investigated double azobenzenes, it is found that, with a careful choice of donor and acceptor groups, the contrast, beta(ratio), can be significantly increased compared to that of the monomers while maintaining large beta values that facilitate their detection with standard experimental techniques (e.g., electric-field-induced second-harmonic generation). Our results set the stage on which further theoretical and experimental studies can be based in the search for efficient and versatile NLO switches.

International audience; In this contribution, we have combined Time-Dependent Density Functional Theory with both implicit solvation using variations of the well-known Polarisable Continuum Model (Linear-Response, corrected Linear-Response and State-Specific schemes) and explicit solvation approaches, to investigate the solva-tochromic shifts undergone by three recently synthesised dyes. These dyes, an aza-BODIPY, a BODIPY and a so-called NBO fluorophore all present excited-states developing a significant cyanine-like character, that is known to be challenging for density-based theories. Our investigation reveals dramatic influence of the selected environmental model on both the predicted sign and amplitude of the solvent shifts. The impact of solvation on the 0-0 energies and vibronic band shapes is also discussed and comparisons with experimental data are performed. (C) 2014 Elsevier B.V. All rights reserved.

International audience; In this contribution, an efficient, parallel, linear scaling implementation of the conductor-like screening model (COSMO) is presented, following the domain decomposition (dd) algorithm recently proposed by three of us. The implementation is detailed and its linear scaling properties, both in computational cost and memory requirements, are demonstrated. Such behavior is also confirmed by several numerical examples on linear and globular large-sized systems, for which the calculation of the energy and of the forces is achieved with timings compatible with the use of polarizable continuum solvation for molecular dynamics simulations.

The AtO(+) molecular ion, a potential precursor for the synthesis of radiotherapeutic agents in nuclear medicine, readily reacts in aqueous solution with organic and inorganic compounds, but at first glance, these reactions must be hindered by spin restriction quantum rules. Using relativistic quantum calculations, coupled to implicit solvation models, on the most stable AtO(+)(H2O)6 clusters, we demonstrate that specific interactions with water molecules of the first solvation shell induce a spin change for the AtO(+) ground state, from a spin state of triplet character in the gas phase to a Kramers-restricted closed-shell configuration in solution. This peculiarity allows rationalization of the AtO(+) reactivity with closed-shell species in aqueous solution and may explain the differences in astatine reactivity observed in (211)At production protocols based on "wet" and "dry" processes.

International audience; Liquid-phase pKa values play a key role in food science. Chemical properties of molecules depend largely on whether they are ionized or not. Most organic molecules are capable of gaining and/or losing a proton in aqueous solutions. Proton transfer most. frequently occurs between water and any ionizable atom of the organic molecule. The molecule’s response to profanation or deprotonation depends significantly on the site that was disturbed by proton transfer. Partial charge distribution in the molecule also varies with protonation of the acidlbase active sites. Then it can he used to determine the pKa of a molecule.First, we use the COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a statistical thermodynamics treatment fin- more Realistic Solvation (RS) simulations, for the direct prediction of pKa constants of about 50 molecules (amino-acids, dipeptides and tripeptides). Then, we compare our results with experimental data and the pKa values predicted using two other methods. We used respectively the ChemAxon method using a program based on the calculation of partial charge of atoms in the molecule and the ACD/Labs method that enables to calculate single pKa values. for all possible dissociation centers when the rest of the molecule is considered neutral, using an internal database containing chemical structures and their experimental pKa values.The averaged Root Mean Square Error (RMSE) of the predicted pKa values for each method compared to experimental results were respectively 0.596 for COSMO-RS, 0.445 for ChemAxon and 0.490 for ACD/Labs. While ACDILabs and ChemAxon are parameterized using a large set ofexperimental data (including several of the studied molecules), the COSMO- RS method was used in a fully predictive way. Regarding these results, COSMO-RS appears as a promising method to predict the pKa values of molecules of interest in food science with scarce available pKa values such as peptides. The final goal of this study is to use the pKa values in a predictive thermodynamics model for products of interest in food industry. For this purpose, the effects of several factors (like conformations set treatment in COSMO-RS calculations, ionic strength effect) that can affect the comparison between observed and predicted pKa data are discussed.; Les valeurs de constantes d’acidité (pKa) jouent un rôle très important, en particulier dans l’industrie alimentaire. Les propriétés chimiques des molécules dépendent significativement de leurs états d’ionisation. La plupart des molécules sont capables de gagner et/ou perdre un proton dans les solutions aqueuses. Ce transfert de proton apparaît la plupart du temps entre l’eau et un atome ionisable de la molécule organique. La réponse de la molécule à la protonation ou à la déprotonation dépend significativement du site concerné par le transfert de proton. La distribution partielle des charges dans la molécule varie également en fonction des sites actifs pour la protonation du couple acide; base. Par conséquent on peut l’utiliser pour déterminer le pKa d’une molécule.Dans un premier temps, nous avons utilisé la méthode COSMO-RS, une combinaison du modèle de solvatation diélectrique (COSMO) et d’un traitement de thermodynamique statistique pour des solvants plus réels (RS), pour prédire les constantes de dissociation de 50 molécules environ (des acides aminés, des dipeptides et des tripeptides). Les résultats de pKa obtenus ont été comparés aux valeurs expérimentales, ainsi qu’aux valeurs de pKa prédites par deux autres méthodes. Nous avons utilisé respectivement la méthode ChemAxon, utilisant un programme basé sur le calcul des charges partielles des atomes d’une molécule, et la méthode ACD/Labs qui permet de déterminer des valeurs de pKa pour chaque centre de dissociation en considérant que le reste de la molécule est neutre, en utilisant une base de données internes contenant des structures chimiques ainsi que leurs valeurs expérimentales de pKa.L’écart-type moyen des valeurs prédites vaut respectivement 0,596 pour la méthode COSMO-RS, 0,445 pour la méthode ChemAxon et 0,490 pour la méthode ACD/Labs. Au vu de ces résultats, la méthode COSMO-RS apparaît comme une méthode prometteuse pour prédire les valeurs de pKa de molécules d’intérêt dans l’industrie alimentaire pour lesquelles peu de données de pKa sont disponibles comme les peptides, d’autant plus que les méthodes ACD/Labs et ChemAxon ont été paramétrées en utilisant un grand nombre de données expérimentales (incluant certaines des molécules étudiées dans cet article) alors que la méthode COSMO-RS a été utilisée d’un point de vue purement prédictif.L’objectif final de cette étude est d’utiliser ces valeurs de pKa dans un modèle thermodynamique prédictif pour des produits d’intérêt dans l’industrie alimentaire. Pour ce faire, les effets de certains facteurs (comme le traitement des conformations dans les calculs COSMO-RS,l’infuence de la force ionique) pouvant influencer la comparaison entre les données expérimentales et les données prédites, seront discutés.

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 0.3 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 1.3 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 0.3-0.4 kcal/mol, whereby larger discrepancies are mostly limited to self-dissociating species and strong hydrogen-bond forming compounds., The following article has been accepted by The Journal of Chemical Physics. After it is published, it will be found at http://link.aip.org/link/?jcp/

International audience; 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.

Conformational free-energy differences are key quantities for understanding important phenomena in molecular biology that involve large structural changes of macromolecules. In this paper, an improved version of the confinement approach, which is based on earlier developments, is used to determine the free energy of individual molecular states by progressively restraining the corresponding molecular structures to pure harmonic basins, whose absolute free energy can be computed by normal-mode analysis. The method is used to calculate the free-energy difference between two conformational states of the alanine dipeptide in vacuo, and of the beta-hairpin from protein G with an implicit solvation model. In all cases, the confinement results are in excellent agreement with the ones obtained from converged equilibrium molecular dynamics simulations, which have a much larger computational cost. The systematic and statistical errors of the results are evaluated and the origin of the errors is identified. The sensitivity of the calculated free-energy differences to structure-based definitions of the molecular states is discussed. A variant of the method, which closes the thermodynamic cycle by a quasi-harmonic rather than harmonic analysis, is introduced. The latter is proposed for possible use with explicit solvent simulations.

We describe a new way to calculate the electrostatic properties of macromolecules that goes beyond the classical Poisson-Boltzmann treatment with only a small extra CPU cost. The solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. The method effectively unifies both the Poisson-centric view and the Langevin Dipole model. The model results in a variable dielectric constant \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{pmc} \usepackage[Euler]{upgreek} \pagestyle{empty} \oddsidemargin -1.0in \begin{document} \begin{equation*}{\epsilon}({\vec{r}})\end{equation*}\end{document} in the solvent region and also in a variable solvent density \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{pmc} \usepackage[Euler]{upgreek} \pagestyle{empty} \oddsidemargin -1.0in \begin{document} \begin{equation*}{\rho}({\vec{r}})\end{equation*}\end{document} that depends on the nature of the closest exposed solute atoms. The model was calibrated using small molecules and ions solvation data with only two adjustable parameters, namely the size and dipolar moment of the solvent. Hydrophobicity scales derived from the solvent density profiles agree very well with independently derived hydrophobicity scales, both at the atomic or residue level. Dimerization interfaces in homodimeric proteins or lipid-binding regions in membrane proteins clearly appear as poorly solvated patches on the solute accessible surface. Comparison of the thermally averaged solvent density of this model with the one derived from molecular dynamics simulations shows qualitative agreement on a coarse-grained level. Because this calculation is much more rapid than that from molecular dynamics, applications of a density-profile-based solvation energy to the identification of the true structure among a set of decoys become computationally feasible. Various possible improvements of the model are discussed, as well as extensions of the formalism to treat mixtures of dipolar solvents of different sizes.

Recently, the synthesis of a molecule has been reported that belongs to a Lysine based, branched cyclic peptide class. This work explores the ability of such molecules to preserve the 3D geometry of the Trypsin's Active Site (TAS) by applying an integrated framework of automated computer procedures. The following four factors a) D/L chirality, b) different amino acids at different positions of the molecular scaffold's cyclic part, c) the application of AMBER and CHARMM force fields and d) different implicit solvation models were evaluated against TAS similarity. It was found that a number of molecules exhibit satisfactory geometric affinity to the TAS during extended Molecular Dynamics runs. We estimated that more than 2000 molecules (belonging to this class) could retain good similarity to the TAS arrangement.

International audience; We have studied the microscopic solvation structure of Co2+ in liquid water by means of density functional theory (DFT)-based Car−Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co2+−water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car−Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co2+ in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car−Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co2+ solvation properties obtained using first-principle simulations.

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The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li+ and Na+ ions, and for liquid argon. First, two methods are proposed which allow, by means of simulation;to extract the quantitative speed-up in diffusion induced by the exchange events. Second,. it is shown by simple kinematic considerations that the instantaneous velocity of the solute conditions to a considerable extent the character of the exchanges. Analytic formulas are derived which quantitatively estimate this effect, and which are of general applicability to molecular diffusion in any thermal fluid. Despite the simplicity of the kinematic considerations, they are shown to well describe many aspects of solvent exchange/diffusion coupling features for nontrivial systems. (c) 2005 American Institute of Physics.

International audience; Increasingly complex schemes for representing solvent effects in an implicit fashion are being used in computational analyses of biological macromolecules. These schemes speed up the calculations by orders of magnitude and are assumed to compromise little on essential features of the solvation phenomenon. In this work we examine this assumption. Five implicit solvation models, a surface area-based empirical model, two models that approximate the generalized Born treatment and a finite difference Poisson-Boltzmann method are challenged in situations differing from those where these models were calibrated. These situations are encountered in automatic protein design procedures, whose job is to select sequences, which stabilize a given protein 3D structure, from a large number of alternatives. To this end we evaluate the energetic cost of burying amino acids in thousands of environments with different solvent exposures belonging, respectively, to decoys built with random sequences and to native protein crystal structures. In addition we perform actual sequence design calculations. Except for the crudest surface area-based procedure, all the tested models tend to favor the burial of polar amino acids in the protein interior over nonpolar ones, a behavior that leads to poor performance in protein design calculations. We show, on the other hand, that three of the examined models are nonetheless capable of discriminating between the native fold and many nonnative alternatives, a test commonly used to validate force fields. It is concluded that protein design is a particularly challenging test for implicit solvation models because it requires accurate estimates of the solvation contribution of individual residues. This contrasts with native recognition, which depends less on solvation and more on other nonbonded contributions.

In this paper we present coupled quantum mechanical/molecular dynamics simulations on the solvation of naphthalene in acetonitrile. A semiempirical treatment is introduced into classical molecular dynamics simulations to deal with the electronic polarizability of the solute. We study the structure of the solvation shell, the features of the electrostatic intermolecular interactions, the dynamics of solute and solvent molecules and the spectral shifts of the solute. For this particular system it is found that the influence of induced electrostatic interaction on the structure of the solvation shell is negligible. On the other hand, net induced dipolar contributions arise in the electrostatic interactions, in spite of the fact that the electric field is found to be inhomogeneous at the scale of the solute molecule. These induced dipolar interactions enhance the calculated absorption and emission shifts and contribute up to 40% to the electrostatic spectral shifts. They also modify or even dominate the fluct...

With the availability of accurate methods to treat the electrostatic long-range interactions, molecular dynamics simulations have resulted in refined dynamical models of the structure of the hydration shell around RNA motifs. The models reviewed here range from basic Watson-Crick to more specific noncanonical base pairs, from "simple" double helices to RNA molecules displaying more complex tertiary folds, and from DNA/RNA hybrid double helices to RNA hybrids formed with a chemically modified strand.