Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

Total Page:16

File Type:pdf, Size:1020Kb

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics Chem. Rev. 1999, 99, 2161−2200 2161 Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics Christopher J. Cramer* and Donald G. Truhlar* Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431 Received January 4, 1999 (Revised Manuscript Received June 4, 1999) Contents 1. Introduction 2161 2. Previous Reviews 2162 3. Elements of Continuum Solvation Theory 2163 4. Models for Equilibrium Solvation 2165 4.1. Widely Used Models 2165 4.2. Recent Methodological Extensions 2168 4.3. Electron Correlation 2169 4.4. Direct Reaction Field 2169 4.5. Individual First-Solvation-Shell Effects 2170 4.6. Universal Solvation Models 2171 4.7. Explicit Solvent in the First Solvation Shell 2172 4.8. Effect of Solute Volume 2174 5. Dipole Moments and Charge and Spin 2174 Chris Cramer received his A.B. degree summa cum laude in Chemistry Distributions and Mathematics from Washington University (St. Louis) in 1983 and his 6. Solvent Effects on Equilibria 2176 Ph.D. degree in Chemistry from the University of Illinois in 1988. Following four years of national service, he joined the faculty of the University of 7. Solvent Effects on Spectra 2177 Minnesota, where he is now an Associate Professor of Chemistry, 7.1. Electronic Spectra 2177 Chemical Physics, and Scientific Computation. His research interests 7.2. Solvent Effects on Vibrational Spectra 2183 revolve around the development and application of methods for modeling 8. Dynamics 2184 the structure and reactivity of, well, everything. 8.1. Equilibrium Solvation 2184 8.1.1. Theory 2184 8.1.2. SES and ESP Applications 2187 8.2. Nonequilibrium Solvation 2188 8.3. Nonhomogeneous Media 2190 9. Conclusion 2190 10. Acknowledgments 2191 11. References 2191 1. Introduction The present review is concerned with continuum and other implicit models of solvation effects. We will concentrate on the elements required to make such Don Truhlar received his B.A. degree in Chemistry summa cum laude models successful and on the factors that limit their from St. Mary’s College of Minnesota in 1965 and his Ph.D. degree in accuracy. We will discuss explicit solvent models only Chemistry from Caltech in 1970. In 1969, he joined the faculty of the to the extent that they provide a complementary University of Minnesota, where he is now Institute of Technology picture or a context, since physical models of solva- Distinguished Professor of Chemistry, Chemical Physics, and Scientific tion, e.g., nonequilibrium solvent coordinates, can Computation and Director of the University of Minnesota Supercomputing often be achieved using either a continuum treatment Institute for Digital Technology and Advanced Computations. His research fields are theoretical chemical dynamics, molecular structure, modeling, of solvent or one that recognizes individual solvent and scientific computation. molecules. There are two principal advantages of continuum 1-octanol. Observable structural and dynamical prop- models. The first is a reduction in the system’s erties of a solute must be averaged over these degrees number of degrees of freedom. If we treat 200 of freedom, typically by Monte Carlo or molecular molecules of a solvent explicitly, this adds 1800 dynamics techniques. If, however, we can treat the degrees of freedom for water, 9000 degrees of freedom solvent as a continuous medium bathing the solute, for ethyl ether, and 16 200 degrees of freedom for the averaging becomes implicit in the properties 10.1021/cr960149m CCC: $35.00 © 1999 American Chemical Society Published on Web 07/30/1999 2162 Chemical Reviews, 1999, Vol. 99, No. 8 Cramer and Truhlar attributed to the bath. Although approximate models continuum solvation models, a comparison of alter- are seldom perfect, we may be able to make the errors native methods, and a summary of selected applica- small enough that our attention can be focused tions. elsewhere, e.g., on a better quantitative treatment Rivail and Rinaldi5 reviewed this field in a book of the solute or the dynamics, rather than on further chapter entitled “Liquid State Quantum Chemistry: improving the description of solvent effects. Computational Applications of the Polarizable Con- The second advantage is appreciated when one tinuum Models”. This review pays particular atten- realizes that complementary methods based on ex- tion not only to the nature of the solute-solvent plicit solvent are also imperfect. Only when such interface (e.g., ideal vs nonideal cavities, size of the models are considerably refined do they model the cavities, etc.), but also to the means by which the solvent electric polarization as well as a continuum solute charge distribution is represented. The Nancy model based on the experimental dielectric constant. group has carefully examined the degree to which the Thus, the second advantage of continuum solvent continuous solute charge distribution can be realisti- models is that they provide a very accurate way to cally represented as a truncated multipolar expan- treat the strong, long-range electrostatic forces that sion at one or more positions within the solute cavity. dominate many solvation phenomena. There is a This is an alternative approach to the solution of third advantage in practice. Most explicit-solvent Poisson’s equation in terms of apparent surface simulations still neglect solute electronic polarization charges. They also review the use of analytic gradi- due to cost (a notable exception being an extensive ents for geometry optimization to study solvent body of work of Gao and co-workers1,2), whereas there influences on molecular geometries and reaction is over 20 years worth of experience with polarizable dynamics. solutes using continuum theory. At about the same time, the present authors reviewed the field in two book chapters,6,7 both 2. Previous Reviews entitled “Continuum Solvation Models”. The former review was particularly complete on the generalized- Before proceeding to discuss implicit models of Born-plus-atomic-surface-tensions approach and con- solvation, we note that the present review is but one tained extensive comparisons of the results of differ- in a steady stream of reviews of this subject in recent ent approaches applied to the same systems. The years. This high review activity stems, of course, from latter review provided a fairly complete recapitula- a large number of original papers on the subject and tion of SCRF theory and the derivation of the a concomitant steep rate of research progress. For appropriate one-electron operator for inclusion of example, the 1994 review of continuum solvation solvent effects in molecular orbital theory within the theories and calculations by Tomasi and Persico3 has context of linear response theory. A systematic clas- 838 references, with over 300 of them from 1988 or sification scheme for different continuum models was later. Furthermore, the subject continues to be in an proposed, and a complete enumeration of extant exponential growth stage with no end in sight. Thus, models to that point was attempted. In addition, the not only will our review of the literature be selective, subject of dynamical processes within the context of even our review of reviews (i.e., the following para- continuum solvation was discussed. Finally, a thor- graphs) will be selective. We note the following ough review of continuum calculations of solvent reviews that particularly complement the one pre- effects on tautomeric equilibria, particularly those of sented here (with a brief description of each). heterocycles, was presented. The 1994 review of Tomasi and Persico,3 entitled Richards8 has provided the most recent review of “Molecular Interactions in Solution: An Overview of continuum solvation models as part of a larger work Methods Based on Continuous Distributions of the focusing on the application of semiempirical quantum Solvent”, provides a particularly complete discussion mechanical methods to biological systems. Detailed of the historical development of various continuum derivations and descriptions of popular models are approximations for computing the electrostatic com- provided. We also mention the 1994 review of Rashin ponent of the solvation free energy. It describes how and Bukatin9 which discussed additional thermody- early research on idealized systems having analytic namic quantities beyond the free energy of solvation solutions to Poisson’s equation led to more general where continuum models of hydration can be com- approaches for realistic cavities and, moreover, pro- pared to experiment. vides a thorough analysis of the relative utility of Five other reviews are mentioned because of their different numerical recipes for solving Poisson’s discussion of solvation modeling in general, including equation recast as a surface integral over apparent both continuum and discrete methods. In particular, surface charges. Finally, this review provides com- the reviews of Tapia10 in 1992, Warshel11 and Smith parisons of different approaches for including the and Pettitt12 in 1994, Orozco et al.13 in 1996, and solvation free energy in the one-electron Fock or Hummer et al.14 in 1998 provide useful comparisons Kohn-Sham operator needed for various quantum of the underlying assumptions of continuum vs chemical calculations, i.e., so-called self-consistent- discrete models (including lattice dipole models) and reaction-field (SCRF) computations. A less detailed of their relative performance for different classes of but still edifying summary of accounting for nonelec- problems. The Warshel and Orozco-Luque groups trostatic components of the solvation free energy is have been particularly active in comparing different also provided. A 1997 review by Tomasi et al.4 theoretical models against one another in a variety presents an updated analysis of quantum mechanical of systems; for the general practitioner, such com- Implicit Solvation Models Chemical Reviews, 1999, Vol. 99, No. 8 2163 parisons can be very helpful in analyzing how first radii, is probably the single most important contribu- to attack a specific problem. tor to the negative impression some researchers Finally the reader is referred to two recent mono- formed of continuum models.
Recommended publications
  • Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
    processes Review Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development Outi M. H. Salo-Ahen 1,2,* , Ida Alanko 1,2, Rajendra Bhadane 1,2 , Alexandre M. J. J. Bonvin 3,* , Rodrigo Vargas Honorato 3, Shakhawath Hossain 4 , André H. Juffer 5 , Aleksei Kabedev 4, Maija Lahtela-Kakkonen 6, Anders Støttrup Larsen 7, Eveline Lescrinier 8 , Parthiban Marimuthu 1,2 , Muhammad Usman Mirza 8 , Ghulam Mustafa 9, Ariane Nunes-Alves 10,11,* , Tatu Pantsar 6,12, Atefeh Saadabadi 1,2 , Kalaimathy Singaravelu 13 and Michiel Vanmeert 8 1 Pharmaceutical Sciences Laboratory (Pharmacy), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland; ida.alanko@abo.fi (I.A.); rajendra.bhadane@abo.fi (R.B.); parthiban.marimuthu@abo.fi (P.M.); atefeh.saadabadi@abo.fi (A.S.) 2 Structural Bioinformatics Laboratory (Biochemistry), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland 3 Faculty of Science-Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; [email protected] 4 Swedish Drug Delivery Forum (SDDF), Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; [email protected] (S.H.); [email protected] (A.K.) 5 Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7 A, FI-90014 Oulu, Finland; andre.juffer@oulu.fi 6 School of Pharmacy, University of Eastern Finland, FI-70210 Kuopio, Finland; maija.lahtela-kakkonen@uef.fi (M.L.-K.); tatu.pantsar@uef.fi
    [Show full text]
  • Microscopic Dynamics of Charge Separation at the Aqueous Electrochemical Interface
    Microscopic dynamics of charge separation at the aqueous electrochemical interface John A. Kattirtzia,b, David T. Limmerc,d,e,1, and Adam P. Willarda,1 aDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02138; bCollege of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China; cDepartment of Chemistry, University of California, Berkeley, CA 94609; dKavili Energy NanoScience Institute, University of California, Berkeley, CA 94609; and eMaterial Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94609 Edited by Michael L. Klein, Temple University, Philadelphia, PA, and approved June 6, 2017 (received for review March 7, 2017) We have used molecular simulation and methods of importance the process of aqueous ion association (forward reaction above) sampling to study the thermodynamics and kinetics of ionic or dissociation (reverse reaction above) is deceptively simple. charge separation at a liquid water–metal interface. We have con- The expression omits the cooperative role of solvent, which sidered this process using canonical examples of two different must restructure to accommodate transitions between the asso- classes of ions: a simple alkali–halide pair, Na+I−, or classical ions, ciated and dissociated states (2, 11). This restructuring, which + − and the products of water autoionization, H3O OH , or water is driven by thermal fluctuations, is both collective (extending ions. We find that for both ion classes, the microscopic mecha- beyond the first solvation shell) and fleeting (12–14). These nism of charge separation, including water’s collective role in the microscopic processes are difficult to probe experimentally (15), process, is conserved between the bulk liquid and the electrode so atomistic simulation has played an important role in reveal- interface.
    [Show full text]
  • Improved Prediction of Solvation Free Energies by Machine-Learning Polarizable Continuum Solvation Model
    Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model Amin Alibakhshi1,*, Bernd Hartke1 Theoretical Chemistry, Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24118 Kiel, Germany Corresponding Author’s email: [email protected] Abstract Theoretical estimation of solvation free energy by continuum solvation models, as a standard approach in computational chemistry, is extensively applied by a broad range of scientific disciplines. Nevertheless, the current widely accepted solvation models are either inaccurate in reproducing experimentally determined solvation free energies or require a number of macroscopic observables which are not always readily available. In the present study, we develop and introduce the Machine- Learning Polarizable Continuum solvation Model (ML-PCM) for a substantial improvement of the predictability of solvation free energy. The performance and reliability of the developed models are validated through a rigorous and demanding validation procedure. The ML-PCM models developed in the present study improve the accuracy of widely accepted continuum solvation models by almost one order of magnitude with almost no additional computational costs. A freely available software is developed and provided for a straightforward implementation of the new approach. Introduction Free energy of solvation is one of the key thermophysical properties in studying thermochemistry in solution, where the majority of real-life chemistry happens.
    [Show full text]
  • FORCE FIELDS for PROTEIN SIMULATIONS by JAY W. PONDER
    FORCE FIELDS FOR PROTEIN SIMULATIONS By JAY W. PONDER* AND DAVIDA. CASEt *Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 51. Louis, Missouri 63110, and tDepartment of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 I. Introduction. ...... .... ... .. ... .... .. .. ........ .. .... .... ........ ........ ..... .... 27 II. Protein Force Fields, 1980 to the Present.............................................. 30 A. The Am.ber Force Fields.............................................................. 30 B. The CHARMM Force Fields ..., ......... 35 C. The OPLS Force Fields............................................................... 38 D. Other Protein Force Fields ....... 39 E. Comparisons Am.ong Protein Force Fields ,... 41 III. Beyond Fixed Atomic Point-Charge Electrostatics.................................... 45 A. Limitations of Fixed Atomic Point-Charges ........ 46 B. Flexible Models for Static Charge Distributions.................................. 48 C. Including Environmental Effects via Polarization................................ 50 D. Consistent Treatment of Electrostatics............................................. 52 E. Current Status of Polarizable Force Fields........................................ 57 IV. Modeling the Solvent Environment .... 62 A. Explicit Water Models ....... 62 B. Continuum Solvent Models.......................................................... 64 C. Molecular Dynamics Simulations with the Generalized Born Model........
    [Show full text]
  • Density Functional Theory for Protein Transfer Free Energy
    Density Functional Theory for Protein Transfer Free Energy Eric A Mills, and Steven S Plotkin∗ Department of Physics & Astronomy, University of British Columbia, Vancouver, British Columbia V6T1Z4 Canada E-mail: [email protected] Phone: 1 604-822-8813. Fax: 1 604-822-5324 arXiv:1310.1126v1 [q-bio.BM] 3 Oct 2013 ∗To whom correspondence should be addressed 1 Abstract We cast the problem of protein transfer free energy within the formalism of density func- tional theory (DFT), treating the protein as a source of external potential that acts upon the sol- vent. Solvent excluded volume, solvent-accessible surface area, and temperature-dependence of the transfer free energy all emerge naturally within this formalism, and may be compared with simplified “back of the envelope” models, which are also developed here. Depletion contributions to osmolyte induced stability range from 5-10kBT for typical protein lengths. The general DFT transfer theory developed here may be simplified to reproduce a Langmuir isotherm condensation mechanism on the protein surface in the limits of short-ranged inter- actions, and dilute solute. Extending the equation of state to higher solute densities results in non-monotonic behavior of the free energy driving protein or polymer collapse. Effective inter- action potentials between protein backbone or sidechains and TMAO are obtained, assuming a simple backbone/sidechain 2-bead model for the protein with an effective 6-12 potential with the osmolyte. The transfer free energy dg shows significant entropy: d(dg)=dT ≈ 20kB for a 100 residue protein. The application of DFT to effective solvent forces for use in implicit- solvent molecular dynamics is also developed.
    [Show full text]
  • Solvent Effects on the Thermodynamic Functions of Dissociation of Anilines and Phenols
    University of Wollongong Research Online University of Wollongong Thesis Collection 1954-2016 University of Wollongong Thesis Collections 1982 Solvent effects on the thermodynamic functions of dissociation of anilines and phenols Barkat A. Khawaja University of Wollongong Follow this and additional works at: https://ro.uow.edu.au/theses University of Wollongong Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorise you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: This work is copyright. Apart from any use permitted under the Copyright Act 1968, no part of this work may be reproduced by any process, nor may any other exclusive right be exercised, without the permission of the author. Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. A court may impose penalties and award damages in relation to offences and infringements relating to copyright material. Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form. Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong. Recommended Citation Khawaja, Barkat A., Solvent effects on the thermodynamic functions of dissociation of anilines and phenols, Master of Science thesis, Department of Chemistry, University of Wollongong, 1982.
    [Show full text]
  • Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces
    Minerals 2014, 4, 345-387; doi:10.3390/min4020345 OPEN ACCESS minerals ISSN 2075-163X www.mdpi.com/journal/minerals Review Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces Krishnamoorthy Arumugam and Udo Becker * Department of Earth and Environmental Sciences, University of Michigan, 1100 North University Avenue, 2534 C.C. Little, Ann Arbor, MI 48109-1005, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-734-615-6894; Fax: +1-734-763-4690. Received: 11 February 2014; in revised form: 3 April 2014 / Accepted: 13 April 2014 / Published: 24 April 2014 Abstract: Applications of redox processes range over a number of scientific fields. This review article summarizes the theory behind the calculation of redox potentials in solution for species such as organic compounds, inorganic complexes, actinides, battery materials, and mineral surface-bound-species. Different computational approaches to predict and determine redox potentials of electron transitions are discussed along with their respective pros and cons for the prediction of redox potentials. Subsequently, recommendations are made for certain necessary computational settings required for accurate calculation of redox potentials. This article reviews the importance of computational parameters, such as basis sets, density functional theory (DFT) functionals, and relativistic approaches and the role that physicochemical processes play on the shift of redox potentials, such as hydration or spin orbit coupling, and will aid in finding suitable combinations of approaches for different chemical and geochemical applications. Identifying cost-effective and credible computational approaches is essential to benchmark redox potential calculations against experiments.
    [Show full text]
  • Hydrated Sulfate Clusters SO4^2
    Article Cite This: J. Phys. Chem. B 2019, 123, 4065−4069 pubs.acs.org/JPCB 2− n − Hydrated Sulfate Clusters SO4 (H2O)n ( =1 40): Charge Distribution Through Solvation Shells and Stabilization Maksim Kulichenko,† Nikita Fedik,† Konstantin V. Bozhenko,‡,§ and Alexander I. Boldyrev*,† † Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, United States ‡ Department of Physical and Colloid Chemistry, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow 117198, Russian Federation § Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Moscow Region, Russian Federation *S Supporting Information 2− ABSTRACT: Investigations of inorganic anion SO4 interactions with water are crucial 2− for understanding the chemistry of its aqueous solutions. It is known that the isolated SO4 dianion is unstable, and three H2O molecules are required for its stabilization. In the 2− current work, we report our computational study of hydrated sulfate clusters SO4 (H2O)n (n =1−40) in order to understand the nature of stabilization of this important anion by fi 2− water molecules. We showed that the most signi cant charge transfer from dianion SO4 ≤ 2− to H2O takes place at a number of H2O molecules n 7. The SO4 directly donates its charge only to the first solvation shell and surprisingly, a small amount of electron density of 0.15|e| is enough to be transferred in order to stabilize the dianion. Upon further addition of ff ≤ H2O molecules, we found that the cage e ect played an essential role at n 12, where the fi 2− | | rst solvation shell closes.
    [Show full text]
  • Solvation Structure of Ions in Water
    International Journal of Thermophysics, Vol. 28, No. 2, April 2007 (© 2007) DOI: 10.1007/s10765-007-0154-6 Solvation Structure of Ions in Water Raymond D. Mountain1 Molecular dynamics simulations of ions in water are reported for solutions of varying solute concentration at ambient conditions for six cations and four anions in 10 solutes. The solutes were selected to show trends in properties as the size and charge density of the ions change. The emphasis is on how the structure of water is modified by the presence of the ions and how many water molecules are present in the first solvation shell of the ions. KEY WORDS: anion; cation; molecular dynamics; potential functions; solva- tion; water. 1. INTRODUCTION The behavior of aqueous solutions of salts is a topic of continuing interest [1–3]. In this note we examine how the structure of water,as reflected in the oxy- gen–oxygen pair function, is modified as the concentration of ions increases. The method of generating the pair functions is molecular dynamics using the SPC/E model for water [4] and various models for ion–water interactions taken from the literature. The solutes are LiCl, NaCl, KCl, RbCl, NaF, CaCl2, CaSO4,Na2SO4, NaNO3, and guanidinium chloride (GdmCl) [C(NH2)3Cl]. This work is an extension of earlier work [5] to a larger set of ions. The water molecules and ions interact through site–site pair interac- tions consisting of Lennard–Jones potentials and Coulomb interactions so that the interaction between a pair of sites labeled i, j and separated by an interatomic distance r is 12 6 φij (r) = 4ij (σij /r) − (σij /r) + qiqj /r (1) where qi is the charge on site i.
    [Show full text]
  • Comparative Study of Implicit and Explicit Solvation Models for Probing Tryptophan Side Chain Packing in Proteins†
    828 Bull. Korean Chem. Soc. 2012, Vol. 33, No. 3 Changwon Yang and Youngshang Pak http://dx.doi.org/10.5012/bkcs.2012.33.3.828 Comparative Study of Implicit and Explicit Solvation Models for Probing Tryptophan Side Chain Packing in Proteins† Changwon Yang and Youngshang Pak* Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 609-735, Korea *E-mail: [email protected] Received November 10, 2011, Accepted December 29, 2011 We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (beta- hairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins. Key Words : Replica exchange molecular dynamics simulation, Implicit solvation model, Tryptophan side chain packing, Protein folding Introduction develop a transferable all-atom protein force field with the GBSA model, so that free energy based native structure Developments of efficient simulation strategies in con- predictions of diverse structural motifs become feasible at junction with all-atom force fields have provided an the all-atom resolution.
    [Show full text]
  • Correlation Between Solubility and the Number of Water Molecules in the First Solvation Shell
    Pure &App/. Chem., Vol. 70, No. 10, pp. 1895-1904, 1998. Printed in Great Britain. 0 1998 IUPAC Solubility of gases in water: Correlation between solubility and the number of water molecules in the first solvation shell Pirketta Scharlin,a Rubin Battino,b Estanislao Silla,c Iiiaki Tuii6nc and Juan Luis Pascual-Ahuirc a Department of Chemistry, University of Turku, FIN-20014 Turku, Finland Department of Chemistry, Wright State University, Dayton, Ohio 45435, USA Departamento de Quimica Fisica, Universidad de Valbncia, 46100 Burjassot, Valbncia, Spain Abstract: Using a new version of a program called GEPOL, a consistent set of values for areas of three different kinds of surfaces for 53 gaseous solutes was computed by Silla et al. These surface areas, together with the volumes of space enclosed by the surfaces, are reported in the present paper. The three surfaces are the van der Waals Surface (WS), the Solvent Accessible Surface (SAS) and the Solvent-Excluding Surface (SES). Values for the number of water molecules (N) in the first solvation shell are estimated by a simple surface area approach from the SAS data. Values of N, as well as literature data on solubilities of gases in water, are used to study various semi-empirical correlations between thermodynamic changes on solution and the number of water molecules in the first solvation shell. Dilute aqueous solutions of gases have been of continuous experimental and theoretical interest. Reliable solubility data exist for a large variety of gases in water. '-18 Experimental data have been important for validating the results of theoretical calculations, computer simulations, and various practical applications.
    [Show full text]
  • Biomolecularelectrostaticsandsol
    Quarterly Reviews of Biophysics 45, 4 (2012), pp. 427–491. f Cambridge University Press 2012 427 doi:10.1017/S003358351200011X Printed in the United States of America Biomolecular electrostatics and solvation: a computational perspective Pengyu Ren1, Jaehun Chun2, Dennis G. Thomas2, Michael J. Schnieders1, Marcelo Marucho3, Jiajing Zhang1 and Nathan A. Baker2* 1 Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA 2 Pacific Northwest National Laboratory, Richland, WA 99352, USA 3 Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249, USA Abstract. An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models. 1.
    [Show full text]