For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
87
views
36
references
 Top references
cited by
34
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      128
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: not found

      A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys. 1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design.

          Related collections

          Most cited references36

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Why do ultrasoft repulsive particles cluster and crystallize? Analytical results from density functional theory

          Bianca M Mladek, Dieter Gottwald, Gerhard Kahl … (2007)
          We demonstrate the accuracy of the hypernetted chain closure and of the mean-field approximation for the calculation of the fluid-state properties of systems interacting by means of bounded and positive-definite pair potentials with oscillating Fourier transforms. Subsequently, we prove the validity of a bilinear, random-phase density functional for arbitrary inhomogeneous phases of the same systems. On the basis of this functional, we calculate analytically the freezing parameters of the latter. We demonstrate explicitly that the stable crystals feature a lattice constant that is independent of density and whose value is dictated by the position of the negative minimum of the Fourier transform of the pair potential. This property is equivalent with the existence of clusters, whose population scales proportionally to the density. We establish that regardless of the form of the interaction potential and of the location on the freezing line, all cluster crystals have a universal Lindemann ratio L = 0.189 at freezing. We further make an explicit link between the aforementioned density functional and the harmonic theory of crystals. This allows us to establish an equivalence between the emergence of clusters and the existence of negative Fourier components of the interaction potential. Finally, we make a connection between the class of models at hand and the system of infinite-dimensional hard spheres, when the limits of interaction steepness and space dimension are both taken to infinity in a particularly described fashion.
          Article 0 comments Cited 430 times – based on 0 reviews
          Preprint
               Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            Lattice simulation method to model diffusion and NMR spectra in porous materials

            Clare Grey, Céline Merlet, John M. Griffin … (2014)
            A coarse-grained simulation method to predict NMR spectra of ions diffusing in porous carbons is proposed. The coarse-grained model uses input from molecular dynamics simulations such as the free-energy profile for ionic adsorption, and density-functional theory calculations are used to predict the NMR chemical shift of the diffusing ions. The approach is used to compute NMR spectra of ions in slit pores with pore widths ranging from 2 to 10 nm. As diffusion inside pores is fast, the NMR spectrum of an ion trapped in a single mesopore will be a sharp peak with a pore size dependent chemical shift. To account for the experimentally observed NMR line shapes, our simulations must model the relatively slow exchange between different pores. We show that the computed NMR line shapes depend on both the pore size distribution and the spatial arrangement of the pores. The technique presented in this work provides a tool to extract information about the spatial distribution of pore sizes from NMR spectra. Such information is diffcult to obtain from other characterisation techniques.
            Article 0 comments Cited 326 times – based on 0 reviews
            Preprint
                 Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Correlated geminal wave function for molecules: an efficient resonating valence bond approach

              S. Sorella, M Casula, C Attaccalite (2004)
              We show that a simple correlated wave function, obtained by applying a Jastrow correlation term to an Antisymmetrized Geminal Power (AGP), based upon singlet pairs between electrons, is particularly suited for describing the electronic structure of molecules, yielding a large amount of the correlation energy. The remarkable feature of this approach is that, in principle, several Resonating Valence Bonds (RVB) can be dealt simultaneously with a single determinant, at a computational cost growing with the number of electrons similarly to more conventional methods, such as Hartree-Fock (HF) or Density Functional Theory (DFT). Moreover we describe an extension of the Stochastic Reconfiguration (SR) method, that was recently introduced for the energy minimization of simple atomic wave functions. Within this extension the atomic positions can be considered as further variational parameters, that can be optimized together with the remaining ones. The method is applied to several molecules from Li_2 to benzene by obtaining total energies, bond lengths and binding energies comparable with much more demanding multi configuration schemes.
              Article 0 comments Cited 303 times – based on 0 reviews
              Preprint
                   Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-ta): J Chem Theory Comput
                Journal ID (iso-abbrev): J Chem Theory Comput
                Journal ID (publisher-id): ct
                Journal ID (coden): jctcce
                Title: Journal of Chemical Theory and Computation
                Publisher: American Chemical Society
                ISSN (Print): 1549-9618
                ISSN (Electronic): 1549-9626
                Publication date (Electronic): 14 January 2014
                Publication date (Print): 11 March 2014
                Volume: 10
                Issue: 3
                Pages: 934-941
                Affiliations
                [† ]Chemical Computing Group Inc. , 1010 Sherbrooke Street West, Suite 910, Montréal, Québec, Canada, H3A 2R7
                [‡ ]Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas 77555, United States of America
                Author notes
                [* ]Current address: Vertex Pharmaceuticals, 275 boul. Armand-Frappier, Laval, Québec, H7V 4A7, Canada. Phone: +1 (450) 978-7915. E-mail: jean-francois_truchon@ 123456vrtx.com .
                Article
                DOI: 10.1021/ct4009359
                PMC ID: 3953892
                PubMed ID: 24634616
                SO-VID: 9ae194fc-cadd-42d8-94cd-416e952a63cf
                Copyright statement: Copyright © 2014 American Chemical Society
                History
                Date received : 25 October 2013
                Funding
                National Institutes of Health, United States
                Categories
                Subject: Article
                Custom metadata
                document-id-old-9 ct4009359
                document-id-new-14 ct-2013-009359
                ccc-price

                ScienceOpen disciplines: Computational chemistry & Modeling
                Data availability:
                ScienceOpen disciplines: Computational chemistry & Modeling

                Comments

                Comment on this article

                scite_

                Similar content128

                See all similar

                Cited by33

                See all cited by

                Most referenced authors2,779

                See all reference authors