Statistical Models of Solvation Eva Zurek Chemistry 699.08 Final Presentation.

Slides:



Advertisements
Similar presentations
Electrolyte Solutions - Debye-Huckel Theory
Advertisements

Simulazione di Biomolecole: metodi e applicazioni giorgio colombo
Review Of Statistical Mechanics
Transfer FAS UAS SAINT-PETERSBURG STATE UNIVERSITY COMPUTATIONAL PHYSICS Introduction Physical basis Molecular dynamics Temperature and thermostat Numerical.
Bare Surface Tension and Surface Fluctuations of Clusters with Long–Range Interaction D.I. Zhukhovitskii Joint Institute for High Temperatures, RAS.
Molecular Simulations of Metal-Organic Frameworks
Tine Porenta Mentor: prof. dr. Slobodan Žumer Januar 2010.
Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field Gaurav Chopra 07 February 2005 CS 379 A Alan GrossfeildPengyu Ren Jay W. Ponder.
Chem 388: Molecular Dynamics and Molecular Modeling Continuum Electrostatics And MM-PBSA.
Incorporating Solvent Effects Into Molecular Dynamics: Potentials of Mean Force (PMF) and Stochastic Dynamics Eva ZurekSection 6.8 of M.M.
The Calculation of Enthalpy and Entropy Differences??? (Housekeeping Details for the Calculation of Free Energy Differences) first edition: p
Lecture 3 The Debye theory. Gases and polar molecules in non-polar solvent. The reaction field of a non-polarizable point dipole The internal and the direction.
1 Lecture 4 1. Statistical-mechanical approach to dielectric theory. 2.Kirkwood-Fröhlich's equation. 3.The Kirkwood correlation factor. 4.Applications:
Objectives of this course
Molecular Modeling Fundamentals: Modus in Silico C372 Introduction to Cheminformatics II Kelsey Forsythe.
Ch 23 pages Lecture 15 – Molecular interactions.
Introduction to (Statistical) Thermodynamics
Monte-Carlo simulations of the structure of complex liquids with various interaction potentials Alja ž Godec Advisers: prof. dr. Janko Jamnik and doc.
1 Physical Chemistry III Molecular Simulations Piti Treesukol Chemistry Department Faculty of Liberal Arts and Science Kasetsart University :
Molecular Information Content
On independence of the solvation of interaction sites of a water molecule M. Předota 1, A. Ben-Naim 2, I. Nezbeda 1,3 1 Institute of Chemical Process Fundamentals,
Free energies and phase transitions. Condition for phase coexistence in a one-component system:
Statistical Thermodynamics CHEN 689 Fall 2015 Perla B. Balbuena 240 JEB
1 CE 530 Molecular Simulation Lecture 17 Beyond Atoms: Simulating Molecules David A. Kofke Department of Chemical Engineering SUNY Buffalo
Ch 9 pages Lecture 23 – The Hydrogen Atom.
Chicago, July 22-23, 2002DARPA Simbiosys Review 1 Monte Carlo Particle Simulation of Ionic Channels Trudy van der Straaten Umberto Ravaioli Beckman Institute.
12/01/2014PHY 711 Fall Lecture 391 PHY 711 Classical Mechanics and Mathematical Methods 10-10:50 AM MWF Olin 103 Plan for Lecture 39 1.Brief introduction.
Basic Monte Carlo (chapter 3) Algorithm Detailed Balance Other points.
Rosa Ramirez ( Université d’Evry ) Shuangliang Zhao ( ENS Paris) Classical Density Functional Theory of Solvation in Molecular Solvents Daniel Borgis Département.
1 CE 530 Molecular Simulation Lecture 6 David A. Kofke Department of Chemical Engineering SUNY Buffalo
1.Solvation Models and 2. Combined QM / MM Methods See review article on Solvation by Cramer and Truhlar: Chem. Rev. 99, (1999)
Intermolecular Forces:Electrostatics “Dielectrics Different classical electrostatic interactions.
Molecular Dynamics Simulation
The Ideal Monatomic Gas. Canonical ensemble: N, V, T 2.
8. Selected Applications. Applications of Monte Carlo Method Structural and thermodynamic properties of matter [gas, liquid, solid, polymers, (bio)-macro-
Surface and Bulk Fluctuations of the Lennard-Jones Clusrers D. I. Zhukhovitskii.
1 M.Sc. Project of Hanif Bayat Movahed The Phase Transitions of Semiflexible Hard Sphere Chain Liquids Supervisor: Prof. Don Sullivan.
Study of Pentacene clustering MAE 715 Project Report By: Krishna Iyengar.
Dissipative Particle Dynamics. Molecular Dynamics, why slow? MD solves Newton’s equations of motion for atoms/molecules: Why MD is slow?
Understanding Molecular Simulations Introduction
Molecular Mechanics Studies involving covalent interactions (enzyme reaction): quantum mechanics; extremely slow Studies involving noncovalent interactions.
Fluid-substrate interactions; structure of fluids inside pores.
Thermal Surface Fluctuations of Clusters with Long-Range Interaction D.I. Zhukhovitskii Joint Institute for High Temperatures, RAS.
Molecular Modelling - Lecture 2 Techniques for Conformational Sampling Uses CHARMM force field Written in C++
ChE 452 Lecture 25 Non-linear Collisions 1. Background: Collision Theory Key equation Method Use molecular dynamics to simulate the collisions Integrate.
Thermophysical properties of fluids: From simple models to applications Ivo NEZBEDA E. Hala Lab. of Thermodynamics, Acad. Sci., Prague, Czech Rep.
حرارة وديناميكا حرارية
Interacting Molecules in a Dense Fluid
An Introduction to Monte Carlo Methods in Statistical Physics Kristen A. Fichthorn The Pennsylvania State University University Park, PA
Monte Carlo in different ensembles Chapter 5
Chapter 16 Kinetic Theory of Gases. Ideal gas model 2 1. Large number of molecules moving in random directions with random speeds. 2. The average separation.
Lecture 9: Theory of Non-Covalent Binding Equilibria Dr. Ronald M. Levy Statistical Thermodynamics.
Generalized van der Waals Partition Function
Monatomic Crystals.
Kinetic Theory of Gases
Theory of dilute electrolyte solutions and ionized gases
1 Molecular Simulations Macroscopic EOS (vdW, PR) Little molecular detail Empirical parameters (  ) Seeking understanding of complex systems Surfactants.
--Experimental determinations of radial distribution functions --Potential of Mean Force 1.
Tao Peng and Robert J. Le Roy
Statistical Mechanics and Multi-Scale Simulation Methods ChBE
Chapter 32 – STRUCTURE FACTORS FOR PARTICULATE SYSTEMS 32:1. THE ORNSTEIN-ZERNIKE EQUATION 32:2. THE PERCUS-YEVICK APPROXIMATION 32:3. THE MEAN SPHERICAL.
1 Calculation of Radial Distribution Function (g(r)) by Molecular Dynamic.
Perturbation Theory. Perturbation theory for the square-well potential Hard spheres is one of the few cases in which we can find the radial distribution.
General Physics 1 Hongqun Zhang The Department of Physics, Beijing Normal University June 2005.
Overview of Molecular Dynamics Simulation Theory
Chapter 9: Molecular-dynamics
Modified by Jed Macosko
Lecture 7: Distribution functions in classical monatomic liquids
Volume 107, Issue 3, Pages (August 2014)
Physical Chemistry Chapter VI Interaction between Molecules 2019/5/16
Presentation transcript:

Statistical Models of Solvation Eva Zurek Chemistry Final Presentation

Methods n Continuum models: macroscopic treatment of the solvent; inability to describe local solute-solvent interaction; ambiguity in definition of the cavity n Monte Carlo (MC) or Molecular Dynamics (MD) Methods: computationally expensive n Statistical Mechanical Integral Equation Theories: give results comparable to MD or MC simulations; computational speedup on the order of 10 2

Statistical Mechanics of Fluids n A classical, isotropic, one-component, monoatomic fluid. n A closed system, for which N, V and T are constant (the Canonical Ensemble). Each particle i has a potential energy U i. n The probability of locating particle 1 at dr 1, etc. is n The probability that 1 is at dr 1 … and n is at dr n irrespective of the configuration of the other particles is n The probability that any particle is at dr 1 … and n is at dr n irrespective of the configuration of the other particles is

Radial Distribution Function n If the distances between n particles increase the correlation between the particles decreases. n In the limit of |r i -r j |  the n-particle probability density can be factorized into the product of single-particle probability densities. n If this is not the case then n In particular g (2) (r 1,r 2 ) is important since it can be measured via neutron or X-ray diffraction n g (2) (r 1,r 2 ) = g(r 12 ) = g(r)

Radial Distribution Function n g(r 12 ) = g(r) is known as the radial distribution function n it is the factor which multiplies the bulk density to give the local density around a particle If the medium is isotropic then 4  r 2  g(r)dr is the number of particles between r and r+dr around the central particle

Correlation Functions n Pair Correlation Function, h(r 12 ), is a measure of the total influence particle 1 has on particle 2 h(r 12 ) = g(r 12 ) - 1 n Direct Correlation Function, c(r 12 ), arises from the direct interactions between particle 1 and particle 2

Ornstein-Zernike (OZ) Equation n In 1914 Ornstein and Zernike proposed a division of h(r 12 ) into a direct and indirect part. n The former is c(r 12 ), direct two-body interactions. n The latter arises from interactions between particle 1 and a third particle which then interacts with particle 2 directly or indirectly via collisions with other particles. Averaged over all the positions of particle 3 and weighted by the density.

Closure Equations

Thermodynamic Functions from g(r) n If you assume that the particles are acting through central pair forces (the total potential energy of the system is pairwise additive),, then you can calculate pressure, chemical potential, energy, etc. of the system. n For an isotropic fluid

Molecular Liquids n Complications due to molecular vibrations ignored. n The position and orientation of a rigid molecule i are defined by six coordinates, the center of mass coordinate r i and the Euler angles n For a linear and non-linear molecule the OZ equation becomes the following, respectively

Integral Equation Theory for Macromolecules n If s denotes solute and w denotes water than the OZ equation can be combined with a closure to give This is divided into a  dependent and independent part

More Approximations n is obtained via using a radial distribution function obtained from MC simulation which uses a spherically- averaged potential. n is used to calculate b 0 (r sw ) for SSD water. n For BBL water b 0 (r sw ) = 0, giving the HNC-OZ. n The orientation of water around a cation or anion can be described as a dipole in a dielectric continuum with a dielectric constant close to the bulk value. Thus,

The Water Models n BBL Water: –Water is a hard sphere, with a point dipole  = 1.85 D. n SSD Water: –Water is a Lennard-Jones soft-sphere, with a point dipole  = 2.35 D. Sticky potential is modified to be compatible with soft-sphere. hard-sphere potential potential energy of two dipoles for a given orientation sticky potential used to mimic hydrogen-bond interactions. Attractive square-well potential, dependant upon orientation

Results for SSD Water n Position of the first peak, excellent agreement. n Coordination number, excellent agreement except for anions which differ ~13-16% from MC simulation. n Solute-water interaction energy for water differs between ~9-14% and for ions/ion-pairs ~1-24%. Greatest for Cl -.

Results for BBL Water Radial distribution function around five molecule cluster of water from theory (line) and MC simulation (circles) Twenty-five molecule cluster of water

Conclusions n Solvation models based upon the Ornstein-Zernike equation could be used to give results comparable to MC or MD calculations with significant computational speed-up. n Problems: –which solvent model? –which closure? –how to calculate and ? n Thanks: –Dr. Paul