CE 530 Molecular Simulation

Size: px
Start display at page:

Download "CE 530 Molecular Simulation"

Transcription

1 1 CE 530 Molecular Simulation Lecture 14 Molecular Models David A. Kofke Department of Chemical Engineering SUNY Buffalo

2 2 Review Monte Carlo ensemble averaging, no dynamics easy to select independent variables lots of flexibility to improve performance Molecular dynamics time averaging, yields dynamical properties extended Lagrangians permit extension to other ensembles Models atomic systems only hard sphere, square well Lennard-Jones

3 3 Modeling Molecules Quantitative calculations require more realistic treatment of molecular interactions Quantum mechanical origins Intermolecular forces Intramolecular forces Effects of long-range interactions on properties Multibody interactions

4 4 Quantum Mechanical Origins Fundamental to everything is the Schrödinger equation Ψ HΨ= ih Nuclear coordinates t wave function Ψ( Rrt,, ) H = Hamiltonian operator time independent form HΨ= EΨ h 2 2m i H = K + U = + U Electronic coordinates Born-Oppenheimer approximation electrons relax very quickly compared to nuclear motions nuclei move in presence of potential energy obtained by solving electron distribution for fixed nuclear configuration it is still very difficult to solve for this energy routinely usually nuclei are heavy enough to treat classically

5 5 Force Field Methods Too expensive to solve QM electronic energy for every nuclear configuration Instead define energy using simple empirical formulas force fields or molecular mechanics Decomposition of the total energy N (1) (2) (3) i i i j< i i j i j< i k< j i j k U( r ) = u ( r) + u ( r, r ) + u ( r, r, r ) + K Single-atom energy (external field) Atom-pair contribution 3-atom contribution Neglect 3- and higher-order terms Force fields usually written in terms of pairwise additive interatomic potentials with some exceptions

6 6 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization U cross cross

7 7 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization U cross cross

8 8 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization U cross cross

9 9 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization U cross cross

10 10 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization U cross cross

11 11 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization U cross cross

12 12 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization Repulsion U cross cross Mixed terms

13 13 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization Repulsion U cross cross Mixed terms

14 14 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only U str stretch U bend bend U tors torsion U vdw van der Waals U el electrostatic U pol polarization Repulsion Attraction U cross cross Mixed terms

15 15 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only Repulsion U str stretch U vdw van der Waals Attraction U bend bend U el electrostatic U tors torsion U pol polarization U cross cross Mixed terms

16 16 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only Repulsion U str stretch U vdw van der Waals Attraction U bend bend U tors torsion U el electrostatic U pol polarization - + U cross cross Mixed terms

17 17 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only Repulsion U str stretch U vdw van der Waals u (2) Attraction U bend bend U el electrostatic u (2) U tors torsion U pol polarization u (N) U cross cross Mixed terms

18 18 Contributions to Potential Energy Total pair energy breaks into a sum of terms N U( r ) = U + U + U + U + U + U + U str bend tors cross vdw el pol Intramolecular only Repulsion U str stretch U vdw van der Waals u (2) Attraction U bend bend U el electrostatic u (2) U tors torsion U pol polarization u (N) + - U cross cross Mixed terms

19 19 Stretch Energy Expand energy about equilibrium position 2 o du o d U o dr o r= r dr o r= r Ur ( ) = Ur ( ) + ( r r ) + ( r r ) +K define minimum 2 (neglect) o 12 = Ur ( ) kr ( r ) Model fails in strained geometries 2 harmonic better model is the Morse potential 12 ( ) Ur ( ) = D1 e αr 12 2 Energy (kcal/mole) Morse dissociation energy force constant Stretch (Angstroms)

20 20 Bending Energy Expand energy about equilibrium position 2 o du o d U o dθ o 2 θ= θ dθ o θ= θ U( θ) = U( θ ) + ( θ θ ) + ( θ θ ) +K define minimum 2 θ (neglect) U( θ) = k( θ θ ) improvements based on including higher-order terms Out-of-plane bending o 2 harmonic u (4) o U( χ) = k( χ χ ) 2 χ

21 21 Two new features periodic Torsional Energy weak (Taylor expansion in f not appropriate) Fourier series U ( φ ) = U n 1 n cos( nφ ) = terms are included to capture appropriate minima/maxima depends on substituent atoms e.g., ethane has three mimum-energy conformations n = 3, 6, 9, etc. depends on type of bond e.g. ethane vs. ethylene usually at most n = 1, 2, and/or 3 terms are included φ

22 22 Van der Waals Attraction Correlation of electron fluctuations Stronger for larger, more polarizable molecules CCl 4 > CH 4 ; Kr > Ar > He Theoretical formula for long-range behavior U att vdw : C r O( r ) Only attraction present between nonpolar molecules reason that Ar, He, CH 4, etc. form liquid phases a.k.a. London or dispersion forces

23 Van der Waals Repulsion Overlap of electron clouds Theory provides little guidance on form of model Two popular treatments inverse power rep A exponential typically n ~ 9-12 Combine with attraction term Lennard-Jones model U vdw : r n Exp-6 two parameters A C 10 Br C LJ U = U = Ae r 12 r 6 Exp-6 6 r 8 U rep vdw : Ae Br a.k.a. Buckingham or Hill x Beware of anomalous Exp-6 short-range attraction Exp-6 repulsion is slightly softer

24 Electrostatics Interaction between charge inhomogeneities Modeling approaches point charges point multipoles Point charges assign Coulombic charges to several points in the molecule total charge sums to charge on molecule (usually zero) Coulomb potential qq i j Ur () = 4πε r 0 very long ranged Lennard-Jones Coulomb 4

25 Electrostatics 2. At larger separations, details of charge distribution are less important Multipole statistics capture basic features! Vector Dipole Quadrupole Octopole, etc. Point multipole models based on long-range behavior dipole-dipole u dd i i µ = q i r i Q = dipole-quadrupole µ 1Q2 ˆ µ 2 ˆ µ ˆ µ quadrupole-quadrupole q i r i r i Tensor µµ = 3 r 1 2 [ 3( ˆ µ rˆ)( ˆ µ rˆ) ( ˆ µ ˆ µ )] ( ) µ 0, Q = 0 µ = 0, Q 0 µ µ Q u 3 dq = ( 4 1 rˆ) 5( Q ˆ 2 rˆ) 1 2( 1 2)( Q ˆ 2 rˆ) 2 r 3 QQ u 1 2 QQ = 1 5c 5c + 2c + 35c c 20cc c 4 5 r Axially symmetric quadrupole Q 25

26 Electrostatics 3. Some Experimental/Theoretical Values Molecule µ, Debye Q, B α, A 3 He Ar O N Cl HF CO H 2 O (xx) (yy) (zz) 1.5 (xx) 1.43 (yy) 1.45 (zz) CH CCl C 6 H NH C 2 H

27 27 Polarization Charge redistribution due to influence of surrounding molecules dipole moment in bulk different from that in vacuum Modeled with polarizable charges or multipoles Involves an iterative calculation evaluate electric field acting on each charge due to other charges adjust charges according to polarizability and electric field re-compute electric field and repeat to convergence Re-iteration over all molecules required if even one is moved

28 28 Explicit Multibody Interactions Axilrod-Teller u (3) consider response of atoms 2 and 3 to fluctuation in dipole moment of atom 1 average over all fluctuations in 1 3 Eαα α u( r, r, r ) = 3cos cos cos + 1 ( θ θ θ ) r12r23r13 1 θ 1 2 3

29 29 Unlike-Atom Interactions Mixing rules give the potential parameters for interactions of atoms that are not the same type Ur () = no ambiguity for Coulomb interaction 4πε0r for effective potentials (e.g., LJ) it is not clear what to do Lorentz-Berthelot is a widely used choice 1 12 = σ ( σ σ ) ε = ε ε qq i j Treatment is a very weak link in quantitative applications of molecular simulation

30 Common Approximations in Molecular Models 30 Rigid intramolecular degrees of freedom fast intramolecular motions slow down MD calculations Ignore hydrogen atoms united atom representation Ignore polarization expensive n-body effect Ignore electrostatics Treat whole molecule as one big atom maybe anisotropic Model vdw forces via discontinuous potentials Ignore all attraction Model space as a lattice especially useful for polymer molecules Qualitative models

31 31 Summary Intermolecular forces arise from quantum mechanics too complex to include in lengthy simulations of bulk phases Empirical forms give simple formulas to approximate behavior intramolecular forms: bend, stretch, torsion intermolecular: van der Waals, electrostatics, polarization Unlike-atom interactions weak link in quantitative work

Introduction to molecular dynamics

Introduction to molecular dynamics 1 Introduction to molecular dynamics Yves Lansac Université François Rabelais, Tours, France Visiting MSE, GIST for the summer Molecular Simulation 2 Molecular simulation is a computational experiment.

More information

Structural Bioinformatics (C3210) Molecular Mechanics

Structural Bioinformatics (C3210) Molecular Mechanics Structural Bioinformatics (C3210) Molecular Mechanics How to Calculate Energies Calculation of molecular energies is of key importance in protein folding, molecular modelling etc. There are two main computational

More information

510 Subject Index. Hamiltonian 33, 86, 88, 89 Hamilton operator 34, 164, 166

510 Subject Index. Hamiltonian 33, 86, 88, 89 Hamilton operator 34, 164, 166 Subject Index Ab-initio calculation 24, 122, 161. 165 Acentric factor 279, 338 Activity absolute 258, 295 coefficient 7 definition 7 Atom 23 Atomic units 93 Avogadro number 5, 92 Axilrod-Teller-forces

More information

Lecture 11: Potential Energy Functions

Lecture 11: Potential Energy Functions Lecture 11: Potential Energy Functions Dr. Ronald M. Levy ronlevy@temple.edu Originally contributed by Lauren Wickstrom (2011) Microscopic/Macroscopic Connection The connection between microscopic interactions

More information

CE 530 Molecular Simulation

CE 530 Molecular Simulation 1 CE 530 Molecular Simulation Lecture 1 David A. Kofke Department of Chemical Engineering SUNY Buffalo kofke@eng.buffalo.edu 2 Time/s Multi-Scale Modeling Based on SDSC Blue Horizon (SP3) 1.728 Tflops

More information

Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland

Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland 1) Question. Two methods which are widely used for the optimization of molecular geometies are the Steepest descents and Newton-Raphson

More information

General Physical Chemistry II

General Physical Chemistry II General Physical Chemistry II Lecture 13 Aleksey Kocherzhenko October 16, 2014" Last time " The Hückel method" Ø Used to study π systems of conjugated molecules" Ø π orbitals are treated separately from

More information

The Potential Energy Surface (PES) And the Basic Force Field Chem 4021/8021 Video II.iii

The Potential Energy Surface (PES) And the Basic Force Field Chem 4021/8021 Video II.iii The Potential Energy Surface (PES) And the Basic Force Field Chem 4021/8021 Video II.iii Fundamental Points About Which to Be Thinking It s clear the PES is useful, so how can I construct it for an arbitrary

More information

Force fields in computer simulation of soft nanomaterials

Force fields in computer simulation of soft nanomaterials Lecture 2 Part B Force fields in computer simulation of soft nanomaterials Recommended reading: Leach Chapter 4 1 Force Field Methods Force field methods are simulation methods that use classical force

More information

Atomic and molecular interaction forces in biology

Atomic and molecular interaction forces in biology Atomic and molecular interaction forces in biology 1 Outline Types of interactions relevant to biology Van der Waals interactions H-bond interactions Some properties of water Hydrophobic effect 2 Types

More information

Molecular Mechanics. Yohann Moreau. November 26, 2015

Molecular Mechanics. Yohann Moreau. November 26, 2015 Molecular Mechanics Yohann Moreau yohann.moreau@ujf-grenoble.fr November 26, 2015 Yohann Moreau (UJF) Molecular Mechanics, Label RFCT 2015 November 26, 2015 1 / 29 Introduction A so-called Force-Field

More information

Subject of the Lecture:

Subject of the Lecture: Subject of the Lecture: Conceptual basis for the development of force fields. Implementation/validation Water - a worked example Extensions - combining molecular mechanics and quantum mechanics (QM/MM)

More information

Molecular Mechanics. C. David Sherrill School of Chemistry and Biochemistry Georgia Institute of Technology. January 2001

Molecular Mechanics. C. David Sherrill School of Chemistry and Biochemistry Georgia Institute of Technology. January 2001 Molecular Mechanics C. David Sherrill School of Chemistry and Biochemistry Georgia Institute of Technology January 2001 Introduction Molecular Mechanics uses classical type models to predict the energy

More information

Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,

Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Course,Informa5on, BIOC%530% GraduateAlevel,discussion,of,the,structure,,func5on,,and,chemistry,of,proteins,and, nucleic,acids,,control,of,enzyma5c,reac5ons.,please,see,the,course,syllabus,and,

More information

Chapter 3. Crystal Binding

Chapter 3. Crystal Binding Chapter 3. Crystal Binding Energy of a crystal and crystal binding Cohesive energy of Molecular crystals Ionic crystals Metallic crystals Elasticity What causes matter to exist in three different forms?

More information

Molecular mechanics. classical description of molecules. Marcus Elstner and Tomáš Kubař. April 29, 2016

Molecular mechanics. classical description of molecules. Marcus Elstner and Tomáš Kubař. April 29, 2016 classical description of molecules April 29, 2016 Chemical bond Conceptual and chemical basis quantum effect solution of the SR numerically expensive (only small molecules can be treated) approximations

More information

All-atom Molecular Mechanics. Trent E. Balius AMS 535 / CHE /27/2010

All-atom Molecular Mechanics. Trent E. Balius AMS 535 / CHE /27/2010 All-atom Molecular Mechanics Trent E. Balius AMS 535 / CHE 535 09/27/2010 Outline Molecular models Molecular mechanics Force Fields Potential energy function functional form parameters and parameterization

More information

T6.2 Molecular Mechanics

T6.2 Molecular Mechanics T6.2 Molecular Mechanics We have seen that Benson group additivities are capable of giving heats of formation of molecules with accuracies comparable to those of the best ab initio procedures. However,

More information

An Introduction to Quantum Chemistry and Potential Energy Surfaces. Benjamin G. Levine

An Introduction to Quantum Chemistry and Potential Energy Surfaces. Benjamin G. Levine An Introduction to Quantum Chemistry and Potential Energy Surfaces Benjamin G. Levine This Week s Lecture Potential energy surfaces What are they? What are they good for? How do we use them to solve chemical

More information

CE 530 Molecular Simulation

CE 530 Molecular Simulation 1 CE 530 Molecular Simulation Lecture 16 Dielectrics and Reaction Field Method David A. Kofke Department of Chemical Engineering SUNY Buffalo kofke@eng.buffalo.edu 2 Review Molecular models intramolecular

More information

Computational Methods. Chem 561

Computational Methods. Chem 561 Computational Methods Chem 561 Lecture Outline 1. Ab initio methods a) HF SCF b) Post-HF methods 2. Density Functional Theory 3. Semiempirical methods 4. Molecular Mechanics Computational Chemistry " Computational

More information

Intermolecular Forces I

Intermolecular Forces I I How does the arrangement of atoms differ in the 3 phases of matter (solid, liquid, gas)? Why doesn t ice just evaporate into a gas? Why does liquid water exist at all? There must be some force between

More information

Bioengineering 215. An Introduction to Molecular Dynamics for Biomolecules

Bioengineering 215. An Introduction to Molecular Dynamics for Biomolecules Bioengineering 215 An Introduction to Molecular Dynamics for Biomolecules David Parker May 18, 2007 ntroduction A principal tool to study biological molecules is molecular dynamics simulations (MD). MD

More information

The broad topic of physical metallurgy provides a basis that links the structure of materials with their properties, focusing primarily on metals.

The broad topic of physical metallurgy provides a basis that links the structure of materials with their properties, focusing primarily on metals. Physical Metallurgy The broad topic of physical metallurgy provides a basis that links the structure of materials with their properties, focusing primarily on metals. Crystal Binding In our discussions

More information

Scientific Computing II

Scientific Computing II Scientific Computing II Molecular Dynamics Simulation Michael Bader SCCS Summer Term 2015 Molecular Dynamics Simulation, Summer Term 2015 1 Continuum Mechanics for Fluid Mechanics? Molecular Dynamics the

More information

The liquid-vapour interface of QDO water. Flaviu Cipcigan Andrew Jones Jason Crain Vlad Sokhan Glenn Martyna

The liquid-vapour interface of QDO water. Flaviu Cipcigan Andrew Jones Jason Crain Vlad Sokhan Glenn Martyna The liquid-vapour interface of QDO water Flaviu Cipcigan Andrew Jones Jason Crain Vlad Sokhan Glenn Martyna The liquid-vapour interface of QDO water 1. Molecular models 2. The Quantum Drude Oscillator

More information

Introduction to Computational Chemistry

Introduction to Computational Chemistry Introduction to Computational Chemistry Vesa Hänninen Laboratory of Physical Chemistry room B430, Chemicum 4th floor vesa.hanninen@helsinki.fi September 3, 2013 Introduction and theoretical backround September

More information

Atomic Structure and Bonding. Chapter 1 Organic Chemistry, 8 th Edition John McMurry

Atomic Structure and Bonding. Chapter 1 Organic Chemistry, 8 th Edition John McMurry Atomic Structure and Bonding Chapter 1 Organic Chemistry, 8 th Edition John McMurry 1 Common Elements Groups First row Second row In most organic molecules carbon is combined with relatively few elements

More information

Why study protein dynamics?

Why study protein dynamics? Why study protein dynamics? Protein flexibility is crucial for function. One average structure is not enough. Proteins constantly sample configurational space. Transport - binding and moving molecules

More information

Session 1. Introduction to Computational Chemistry. Computational (chemistry education) and/or (Computational chemistry) education

Session 1. Introduction to Computational Chemistry. Computational (chemistry education) and/or (Computational chemistry) education Session 1 Introduction to Computational Chemistry 1 Introduction to Computational Chemistry Computational (chemistry education) and/or (Computational chemistry) education First one: Use computational tools

More information

k θ (θ θ 0 ) 2 angles r i j r i j

k θ (θ θ 0 ) 2 angles r i j r i j 1 Force fields 1.1 Introduction The term force field is slightly misleading, since it refers to the parameters of the potential used to calculate the forces (via gradient) in molecular dynamics simulations.

More information

Reactive potentials and applications

Reactive potentials and applications 1.021, 3.021, 10.333, 22.00 Introduction to Modeling and Simulation Spring 2011 Part I Continuum and particle methods Reactive potentials and applications Lecture 8 Markus J. Buehler Laboratory for Atomistic

More information

Lecture C2 Microscopic to Macroscopic, Part 2: Intermolecular Interactions. Let's get together.

Lecture C2 Microscopic to Macroscopic, Part 2: Intermolecular Interactions. Let's get together. Lecture C2 Microscopic to Macroscopic, Part 2: Intermolecular Interactions Let's get together. Most gases are NOT ideal except at very low pressures: Z=1 for ideal gases Intermolecular interactions come

More information

Imperfect Gases. NC State University

Imperfect Gases. NC State University Chemistry 431 Lecture 3 Imperfect Gases NC State University The Compression Factor One way to represent the relationship between ideal and real gases is to plot the deviation from ideality as the gas is

More information

Hyeyoung Shin a, Tod A. Pascal ab, William A. Goddard III abc*, and Hyungjun Kim a* Korea

Hyeyoung Shin a, Tod A. Pascal ab, William A. Goddard III abc*, and Hyungjun Kim a* Korea The Scaled Effective Solvent Method for Predicting the Equilibrium Ensemble of Structures with Analysis of Thermodynamic Properties of Amorphous Polyethylene Glycol-Water Mixtures Hyeyoung Shin a, Tod

More information

Polar molecules vs. Nonpolar molecules A molecule with separate centers of positive and negative charge is a polar molecule.

Polar molecules vs. Nonpolar molecules A molecule with separate centers of positive and negative charge is a polar molecule. CHM 123 Chapter 8 8.5 8.6 Polar covalent Bonds and Dipole moments Depending on the relative electronegativities of the two atoms sharing electrons, there may be partial transfer of electron density from

More information

Intermolecular Forces and Monte-Carlo Integration 열역학특수연구

Intermolecular Forces and Monte-Carlo Integration 열역학특수연구 Intermolecular Forces and Monte-Carlo Integration 열역학특수연구 2003.3.28 Source of the lecture note. J.M.Prausnitz and others, Molecular Thermodynamics of Fluid Phase Equiliria Atkins, Physical Chemistry Lecture

More information

3rd Advanced in silico Drug Design KFC/ADD Molecular mechanics intro Karel Berka, Ph.D. Martin Lepšík, Ph.D. Pavel Polishchuk, Ph.D.

3rd Advanced in silico Drug Design KFC/ADD Molecular mechanics intro Karel Berka, Ph.D. Martin Lepšík, Ph.D. Pavel Polishchuk, Ph.D. 3rd Advanced in silico Drug Design KFC/ADD Molecular mechanics intro Karel Berka, Ph.D. Martin Lepšík, Ph.D. Pavel Polishchuk, Ph.D. Thierry Langer, Ph.D. Jana Vrbková, Ph.D. UP Olomouc, 23.1.-26.1. 2018

More information

PH 548 Atomistic Simulation Techniques

PH 548 Atomistic Simulation Techniques PH 548 Atomistic Simulation Techniques Lectures: Lab: 2-0-2-6 Tuesday 12-1 PM Thursday 12-1 PM Monday 2-5 PM P. K. Padmanabhan PH548: Two Excellent Books How to do it? 1 2 F 12 F 23 3 F i = F ij j i F

More information

Lecture Presentation. Chapter 11. Liquids and Intermolecular Forces. John D. Bookstaver St. Charles Community College Cottleville, MO

Lecture Presentation. Chapter 11. Liquids and Intermolecular Forces. John D. Bookstaver St. Charles Community College Cottleville, MO Lecture Presentation Chapter 11 Liquids and Intermolecular Forces John D. Bookstaver St. Charles Community College Cottleville, MO Properties of Gases, Liquids, and Solids State Volume Shape of State Density

More information

Potentials, periodicity

Potentials, periodicity Potentials, periodicity Lecture 2 1/23/18 1 Survey responses 2 Topic requests DFT (10), Molecular dynamics (7), Monte Carlo (5) Machine Learning (4), High-throughput, Databases (4) NEB, phonons, Non-equilibrium

More information

Interatomic Potentials. The electronic-structure problem

Interatomic Potentials. The electronic-structure problem Interatomic Potentials Before we can start a simulation, we need the model! Interaction between atoms and molecules is determined by quantum mechanics: Schrödinger Equation + Born-Oppenheimer approximation

More information

An introduction to Molecular Dynamics. EMBO, June 2016

An introduction to Molecular Dynamics. EMBO, June 2016 An introduction to Molecular Dynamics EMBO, June 2016 What is MD? everything that living things do can be understood in terms of the jiggling and wiggling of atoms. The Feynman Lectures in Physics vol.

More information

Week 8 Intermolecular Forces

Week 8 Intermolecular Forces NO CALCULATORS MAY BE USED FOR THESE QUESTIONS Questions 1-3 refer to the following list. (A) Cu (B) PH 3 (C) C (D) SO 2 (E) O 2 1. Contains instantaneous dipole moments. 2. Forms covalent network solids.

More information

Molecular Geometry and intermolecular forces. Unit 4 Chapter 9 and 11.2

Molecular Geometry and intermolecular forces. Unit 4 Chapter 9 and 11.2 1 Molecular Geometry and intermolecular forces Unit 4 Chapter 9 and 11.2 2 Unit 4.1 Chapter 9.1-9.3 3 Review of bonding Ionic compound (metal/nonmetal) creates a lattice Formula doesn t tell the exact

More information

CE 530 Molecular Simulation

CE 530 Molecular Simulation CE 530 Molecular Simulation Lecture Molecular Dynamics Simulation David A. Kofke Department of Chemical Engineering SUNY Buffalo kofke@eng.buffalo.edu MD of hard disks intuitive Review and Preview collision

More information

Molecular Mechanics. I. Quantum mechanical treatment of molecular systems

Molecular Mechanics. I. Quantum mechanical treatment of molecular systems Molecular Mechanics I. Quantum mechanical treatment of molecular systems The first principle approach for describing the properties of molecules, including proteins, involves quantum mechanics. For example,

More information

Solids, Liquids and Gases

Solids, Liquids and Gases WHY? Why is water usually a liquid and not a gas? Why does liquid water boil at such a high temperature for such a small molecule? Why does ice float on water? Why do snowflakes have 6 sides? Why is I

More information

Molecular Mechanics, Dynamics & Docking

Molecular Mechanics, Dynamics & Docking Molecular Mechanics, Dynamics & Docking Lawrence Hunter, Ph.D. Director, Computational Bioscience Program University of Colorado School of Medicine Larry.Hunter@uchsc.edu http://compbio.uchsc.edu/hunter

More information

Molecular interactions. Levente Novák István Bányai Zoltán Nagy Department of Physical Chemistry

Molecular interactions. Levente Novák István Bányai Zoltán Nagy Department of Physical Chemistry Molecular interactions Levente Novák István Bányai Zoltán Nagy Department of Physical Chemistry Characterization of colloidal systems Degree of dispersion (=size) Morphology (shape and internal structure)

More information

Name: Date: Period: #: BONDING & INTERMOLECULAR FORCES

Name: Date: Period: #: BONDING & INTERMOLECULAR FORCES BONDING & INTERMOLECULAR FORCES Page 1 INTERMOLECULAR FORCES Intermolecular forces (van der Waals forces) relative weak interactions that occur between molecules. Most of the physical properties of gases,

More information

Chapter 10. Dipole Moments. Intermolecular Forces (IMF) Polar Bonds and Polar Molecules. Polar or Nonpolar Molecules?

Chapter 10. Dipole Moments. Intermolecular Forces (IMF) Polar Bonds and Polar Molecules. Polar or Nonpolar Molecules? Polar Bonds and Polar Molecules Chapter 10 Liquids, Solids, and Phase Changes Draw Lewis Structures for CCl 4 and CH 3 Cl. What s the same? What s different? 1 Polar Covalent Bonds and Dipole Moments Bonds

More information

For the following intermolecular forces:

For the following intermolecular forces: Lecturenotes 1 unit6_review_exercise_2017.odt Lecturenotes 2 unit6_review_exercise_2017.odt Lecturenotes 3 unit6_review_exercise_2017.odt Lecturenotes 4 unit6_review_exercise_2017.odt Answers: 1. Ionic

More information

6 Shapes of molecules and intermolecular forces Answers to practice questions. OCR Chemistry A. Question Answer Marks Guidance

6 Shapes of molecules and intermolecular forces Answers to practice questions. OCR Chemistry A. Question Answer Marks Guidance 1 (a) (i) HI, HBr, HCl, HF 1 (a) (ii) CF 4, CH 3 I, CH 2 Br 2, CHCl 2 F 1 (b) (i) CO 2 and HCN: linear H 2 O and SCl 2 : non-linear BF 3 and SO 3 : trigonal planar NH 3 and H 3 O + : pyramidal AlCl 4 and

More information

The change in free energy on transferring an ion from a medium of low dielectric constantε1 to one of high dielectric constant ε2:

The change in free energy on transferring an ion from a medium of low dielectric constantε1 to one of high dielectric constant ε2: The Born Energy of an Ion The free energy density of an electric field E arising from a charge is ½(ε 0 ε E 2 ) per unit volume Integrating the energy density of an ion over all of space = Born energy:

More information

Colloid Chemistry. La chimica moderna e la sua comunicazione Silvia Gross.

Colloid Chemistry. La chimica moderna e la sua comunicazione Silvia Gross. Colloid Chemistry La chimica moderna e la sua comunicazione Silvia Gross Istituto Dipartimento di Scienze di e Scienze Tecnologie Chimiche Molecolari ISTM-CNR, Università Università degli Studi degli Studi

More information

This semester. Books

This semester. Books Models mostly proteins from detailed to more abstract models Some simulation methods This semester Books None necessary for my group and Prof Rarey Molecular Modelling: Principles and Applications Leach,

More information

INTERMOLECULAR INTERACTIONS

INTERMOLECULAR INTERACTIONS 5.61 Physical Chemistry Lecture #3 1 INTERMOLECULAR INTERACTIONS Consider the interaction between two stable molecules (e.g. water and ethanol) or equivalently between two noble atoms (e.g. helium and

More information

Electric properties of molecules

Electric properties of molecules Electric properties of molecules For a molecule in a uniform electric fielde the Hamiltonian has the form: Ĥ(E) = Ĥ + E ˆµ x where we assume that the field is directed along the x axis and ˆµ x is the

More information

ICCP Project 2 - Advanced Monte Carlo Methods Choose one of the three options below

ICCP Project 2 - Advanced Monte Carlo Methods Choose one of the three options below ICCP Project 2 - Advanced Monte Carlo Methods Choose one of the three options below Introduction In statistical physics Monte Carlo methods are considered to have started in the Manhattan project (1940

More information

Molecular Dynamics Simulations. Dr. Noelia Faginas Lago Dipartimento di Chimica,Biologia e Biotecnologie Università di Perugia

Molecular Dynamics Simulations. Dr. Noelia Faginas Lago Dipartimento di Chimica,Biologia e Biotecnologie Università di Perugia Molecular Dynamics Simulations Dr. Noelia Faginas Lago Dipartimento di Chimica,Biologia e Biotecnologie Università di Perugia 1 An Introduction to Molecular Dynamics Simulations Macroscopic properties

More information

RW Session ID = MSTCHEM1 Intermolecular Forces

RW Session ID = MSTCHEM1 Intermolecular Forces RW Session ID = MSTCHEM1 Intermolecular Forces Sections 9.4, 11.3-11.4 Intermolecular Forces Attractive forces between molecules due to charges, partial charges, and temporary charges Higher charge, stronger

More information

Chap 10 Part 4Ta.notebook December 08, 2017

Chap 10 Part 4Ta.notebook December 08, 2017 Chapter 10 Section 1 Intermolecular Forces the forces between molecules or between ions and molecules in the liquid or solid state Stronger Intermolecular forces cause higher melting points and boiling

More information

Ionic Compounds and Ionic Bonding

Ionic Compounds and Ionic Bonding Ionic Compounds and Ionic Bonding Definitions Review: Crystal Lattice - 3D continuous repeating pattern of positive and negative ions in an ionic solid Formula Unit- smallest possible neutral unit of an

More information

Chem 442 Review for Exam 2. Exact separation of the Hamiltonian of a hydrogenic atom into center-of-mass (3D) and relative (3D) components.

Chem 442 Review for Exam 2. Exact separation of the Hamiltonian of a hydrogenic atom into center-of-mass (3D) and relative (3D) components. Chem 44 Review for Exam Hydrogenic atoms: The Coulomb energy between two point charges Ze and e: V r Ze r Exact separation of the Hamiltonian of a hydrogenic atom into center-of-mass (3D) and relative

More information

Intermolecular Forces

Intermolecular Forces Intermolecular Forces H covalent bond (stronger) Cl H Cl intermolecular attraction (weaker) The attractions between molecules are not nearly as strong as the covalent bonds that hold atoms together. They

More information

Kinetic Molecular Theory of Gases used to account for Ideal Gas Behavior when gases approach high temperatures and low pressures

Kinetic Molecular Theory of Gases used to account for Ideal Gas Behavior when gases approach high temperatures and low pressures LIQUIDS AND SOLIDS Kinetic Molecular Theory of Gases used to account for Ideal Gas Behavior when gases approach high temperatures and low pressures GASES are very different from solids and liquids. We

More information

Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia

Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia University of Groningen Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia IMPORTANT NOTE: You are advised to consult the publisher's version

More information

liquids_solids_15dec2017_1st.notebook Liquids and solids Chapters 11 and 12

liquids_solids_15dec2017_1st.notebook Liquids and solids Chapters 11 and 12 liquids_solids_15dec2017_1st.notebook December 15, 2017 Liquids and solids Chapters 11 and 12 Intermolecular forces Intermolecular: forces between molecules Intramolecular: within molecules (i.e. covalent)

More information

Sparks CH301. WHY IS EVERYTHING SO DIFFERENT? Gas, Liquid or Solid? UNIT 3 Day 7

Sparks CH301. WHY IS EVERYTHING SO DIFFERENT? Gas, Liquid or Solid? UNIT 3 Day 7 Sparks CH301 WHY IS EVERYTHING SO DIFFERENT? Gas, Liquid or Solid? UNIT 3 Day 7 What are we going to do today? Discuss types of intermolecular forces. Compare intermolecular forces for different molecules.

More information

PY5020 Nanoscience Scanning probe microscopy

PY5020 Nanoscience Scanning probe microscopy PY500 Nanoscience Scanning probe microscopy Outline Scanning tunnelling microscopy (STM) - Quantum tunnelling - STM tool - Main modes of STM Contact probes V bias Use the point probes to measure the local

More information

Chemistry 20 Lesson 13 Intermolecular Forces

Chemistry 20 Lesson 13 Intermolecular Forces Chemistry 20 Lesson 13 Intermolecular Forces I. Intermolecular Vs Intramolecular Forces The Kinetic Molecular Theory of gases, which we will study in a later unit, describes the behaviour of gases in terms

More information

Atoms can form stable units called molecules by sharing electrons.

Atoms can form stable units called molecules by sharing electrons. Atoms can form stable units called molecules by sharing electrons. The formation of molecules is the result of intramolecular bonding (within the molecule) e.g. ionic, covalent. Forces that cause the aggregation

More information

Intermolecular and Intramolecular Forces. Introduction

Intermolecular and Intramolecular Forces. Introduction Intermolecular and Intramolecular Forces Introduction Atoms can form stable units called molecules by sharing electrons. The formation of molecules is the result of intramolecular bonding (within the molecule)

More information

Downloaded from

Downloaded from I.I.T.Foundation - XI Chemistry MCQ #4 Time: 45 min Student's Name: Roll No.: Full Marks: 90 Chemical Bonding I. MCQ - Choose Appropriate Alternative 1. The energy required to break a chemical bond to

More information

CE 530 Molecular Simulation

CE 530 Molecular Simulation CE 530 Molecular Simulation Lecture 20 Phase Equilibria David A. Kofke Department of Chemical Engineering SUNY Buffalo kofke@eng.buffalo.edu 2 Thermodynamic Phase Equilibria Certain thermodynamic states

More information

Equations of State. Equations of State (EoS)

Equations of State. Equations of State (EoS) Equations of State (EoS) Equations of State From molecular considerations, identify which intermolecular interactions are significant (including estimating relative strengths of dipole moments, polarizability,

More information

Module17: Intermolecular Force between Surfaces and Particles. Lecture 23: Intermolecular Force between Surfaces and Particles

Module17: Intermolecular Force between Surfaces and Particles. Lecture 23: Intermolecular Force between Surfaces and Particles Module17: Intermolecular Force between Surfaces and Particles Lecture 23: Intermolecular Force between Surfaces and Particles 1 We now try to understand the nature of spontaneous instability in a confined

More information

When intermolecular forces are strong, the atoms, molecules, or ions are strongly attracted to each other, and draw closer together.

When intermolecular forces are strong, the atoms, molecules, or ions are strongly attracted to each other, and draw closer together. INTERMOLECULAR FORCES: THE FORCE BEHIND VARIOUS PROPERTIES WHY? Intermolecular forces are largely responsible for the properties of affinity, solubility, volatility, melting/ boiling point, and viscosity.

More information

Computational Modeling of Protein-Ligand Interactions

Computational Modeling of Protein-Ligand Interactions Computational Modeling of Protein-Ligand Interactions Steven R. Gwaltney Department of Chemistry Mississippi State University Mississippi State, MS 39762 Auguste Comte, 1830 Every attempt to refer chemical

More information

Water models in classical simulations

Water models in classical simulations Water models in classical simulations Maria Fyta Institut für Computerphysik, Universität Stuttgart Stuttgart, Germany Water transparent, odorless, tasteless and ubiquitous really simple: two H atoms attached

More information

Sodium, Na. Gallium, Ga CHEMISTRY Topic #2: The Chemical Alphabet Fall 2017 Dr. Susan Findlay See Exercises 9.2 to 9.7.

Sodium, Na. Gallium, Ga CHEMISTRY Topic #2: The Chemical Alphabet Fall 2017 Dr. Susan Findlay See Exercises 9.2 to 9.7. Sodium, Na Gallium, Ga CHEMISTRY 1000 Topic #2: The Chemical Alphabet Fall 2017 Dr. Susan Findlay See Exercises 9.2 to 9.7 Forms of Carbon Kinetic Molecular Theory of Matter The kinetic-molecular theory

More information

REVIEW : INTRODUCTION TO THE MOLECULAR ORIGINS OF MECHANICAL PROPERTIES QUANTITATIVE TREATMENT OF INTERATOMIC BONDING : THE LENNARD-JONES POTENTIAL

REVIEW : INTRODUCTION TO THE MOLECULAR ORIGINS OF MECHANICAL PROPERTIES QUANTITATIVE TREATMENT OF INTERATOMIC BONDING : THE LENNARD-JONES POTENTIAL LECTURE #19 : 3.11 MECANICS OF MATERIALS F3 INSTRUCTOR : Professor Christine Ortiz OFFICE : 13-422 PONE : 452-384 WWW : http://web.mit.edu/cortiz/www REVIEW : INTRODUCTION TO TE MOLECULAR ORIGINS OF MECANICAL

More information

Quantum Chemical Simulations and Descriptors. Dr. Antonio Chana, Dr. Mosè Casalegno

Quantum Chemical Simulations and Descriptors. Dr. Antonio Chana, Dr. Mosè Casalegno Quantum Chemical Simulations and Descriptors Dr. Antonio Chana, Dr. Mosè Casalegno Classical Mechanics: basics It models real-world objects as point particles, objects with negligible size. The motion

More information

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations Alexandre V. Morozov, Tanja Kortemme, Kiril Tsemekhman, David Baker

More information

Physical Chemistry - Problem Drill 01: Chemistry and Physics Review

Physical Chemistry - Problem Drill 01: Chemistry and Physics Review Physical Chemistry - Problem Drill 01: Chemistry and Physics Review No. 1 of 10 1. Chemical bonds are considered to be the interaction of their electronic structures of bonding atoms involved, with the

More information

Pair Potentials and Force Calculations

Pair Potentials and Force Calculations Molecular Dynamics simulations Lecture 04: Pair Potentials and Force Calculations Dr. Olli Pakarinen University of Helsinki Fall 01 Lecture notes based on notes by Dr. Jani Kotakoski, 010 CONSTRUCTING

More information

Computer simulation methods (2) Dr. Vania Calandrini

Computer simulation methods (2) Dr. Vania Calandrini Computer simulation methods (2) Dr. Vania Calandrini in the previous lecture: time average versus ensemble average MC versus MD simulations equipartition theorem (=> computing T) virial theorem (=> computing

More information

Surface interactions part 1: Van der Waals Forces

Surface interactions part 1: Van der Waals Forces CHEM-E150 Interfacial Phenomena in Biobased Systems Surface interactions part 1: Van der Waals Forces Monika Österberg Spring 018 Content Colloidal stability van der Waals Forces Surface Forces and their

More information

Scuola di Chimica Computazionale

Scuola di Chimica Computazionale Societa Chimica Italiana Gruppo Interdivisionale di Chimica Computazionale Scuola di Chimica Computazionale Introduzione, per Esercizi, all Uso del Calcolatore in Chimica Organica e Biologica Modellistica

More information

Intermolecular Forces & Condensed Phases

Intermolecular Forces & Condensed Phases Intermolecular Forces & Condensed Phases CHEM 107 T. Hughbanks READING We will discuss some of Chapter 5 that we skipped earlier (Van der Waals equation, pp. 145-8), but this is just a segue into intermolecular

More information

Introduction to Vibrational Spectroscopy

Introduction to Vibrational Spectroscopy Introduction to Vibrational Spectroscopy Harmonic oscillators The classical harmonic oscillator The uantum mechanical harmonic oscillator Harmonic approximations in molecular vibrations Vibrational spectroscopy

More information

Complete and precise descriptions based on quantum mechanics exist for the Coulombic/Electrostatic force. These are used to describe materials.

Complete and precise descriptions based on quantum mechanics exist for the Coulombic/Electrostatic force. These are used to describe materials. The forces of nature: 1. Strong forces hold protons and neutrons together (exchange of mesons) 2. Weak interactions are involved in some kinds of radioactive decay (β-decay) 3. Coulombic or electrostatic

More information

Material Properties & Characterization - Surfaces

Material Properties & Characterization - Surfaces 1) XPS Spectrum analysis: The figure below shows an XPS spectrum measured on the surface of a clean insoluble homo-polyether. Using the formulas and tables in this document, answer the following questions:

More information

Lecture 6 - Bonding in Crystals

Lecture 6 - Bonding in Crystals Lecture 6 onding in Crystals inding in Crystals (Kittel Ch. 3) inding of atoms to form crystals A crystal is a repeated array of atoms Why do they form? What are characteristic bonding mechanisms? How

More information

Chapter 11. Intermolecular forces. Chapter 11 1

Chapter 11. Intermolecular forces. Chapter 11 1 Chapter 11 Intermolecular Attractions and the Properties of Liquids and Solids 1 2 Intermolecular forces Forces of attraction between molecules Directly dependent on the distance between the molecules

More information

Chapter Intermolecular attractions

Chapter Intermolecular attractions Chapter 11 11.2 Intermolecular attractions Intermolecular Attractions and the Properties of Liquids and Solids Intermolecular forces control the physical properties of the substance. Intramolecular forces

More information

DIFFERENT TYPES OF INTEMOLECULAR FORCES INTERMOLECULAR FORCES

DIFFERENT TYPES OF INTEMOLECULAR FORCES INTERMOLECULAR FORCES DIFFERENT TYPES OF INTEMOLECULAR FORCES Do all the exercises in your studyguide COMPARISON OF THE THREE PHASES OF MATTER. Matter is anything that occupy space and has mass. There are three states of matter:

More information

Lecture: P1_Wk1_L1 IntraMolecular Interactions. Ron Reifenberger Birck Nanotechnology Center Purdue University 2012

Lecture: P1_Wk1_L1 IntraMolecular Interactions. Ron Reifenberger Birck Nanotechnology Center Purdue University 2012 Lecture: IntraMolecular Interactions Distinguish between IntraMolecular (within a molecule) and InterMolecular (between molecules) Ron Reifenberger Birck Nanotechnology Center Purdue University 2012 1

More information

3. An Introduction to Molecular Mechanics

3. An Introduction to Molecular Mechanics 3. An Introduction to Molecular Mechanics Introduction When you use Chem3D to draw molecules, the program assigns bond lengths and bond angles based on experimental data. The program does not contain real

More information