New Models for Aqueous Systems: Construction of Vibrational Wave Functions for use in Monte Carlo Simulations.

Size: px
Start display at page:

Download "New Models for Aqueous Systems: Construction of Vibrational Wave Functions for use in Monte Carlo Simulations."

Transcription

1 New Models for Aqueous Systems: Construction of Vibrational Wave Functions for use in Monte Carlo Simulations. Maria A. Gomez and Lawrence R. Pratt T-12 and CNLS Theoretical Division Los Alamos National Laboratory Los Alamos, NM There has been great interest recently in simulation of proton exchange events in liquid water. The obvious limitations of rigid water models have led to a long and continuing history of flexible and dissociative water models for simulation of aqueous systems. One idea for improving the fidelity of simulations of chemistry in aqueous solution is to consider the model from the perspective of the quantum mechanical distribution of internal coordinates. For example, an accurate and compact wave function might be used as a model in a simulation to sample configurations of the system. Here we investigate constructing simple intramolecular wave functions for aqueous species. In particular, we describe some new Monte Carlo techniques for construction of compact wave functions for the internal atomic motion of the D 3 O + ion. Proton Transfer Water, water everywhere, Nor any drop to drink. Samuel Coleridge, Rhyme of the Ancient Mariner. From acid/base chemistry in water to synthetic proton conductors to photosynthesis, proton transfer events play a pivotal role. Proton conduction though polymer membranes, zeolites, ceramics, aluminas, and metal oxides has many potential applications to fuel cells, catalysis, steam electrolysis, solid state gas sensors, and solid state batteries. Without doubt, proton conduction is a crucial phenomenon spanning a wide variety of areas [1]. Despite its importance, even the simplest reaction, proton transfer in water, is not completely understood. Bernal and Fowler originally proposed the existence of a connected hydrogen bond pathway such as seen in Fig. 1. An excess proton on one side of this pathway causes a sequence of proton shifts and results in an excess proton in the other side of the chain.

2 Fig. 1. A proton on one side of the chain causes a sequence of proton shifts. Today, although the general idea is accepted the details are still debated. Does the proton transfer occur via a hydronium or a Zundel or an Eigen cation? (See Fig. 2.) Just what species is involved is important because it determines energy barriers and hence pathways to reactions. Studies suggest that a definitive answer to these question needs to include quantum dynamical treatment of the proton [2, 3]. Fig. 2. Various forms of a solvated proton. Modeling of Chemistry in Water Flexible and dissociative models for simulation of liquid water have often been used in classical statistical mechanical studies of aqueous materials. They present technical advantages for carrying out simulations and are of the essence where dissociation of water molecules is necessary to the chemistry being studied. However, since studies suggest that quantum mechanics plays a non-negligible role in

3 proton transfer [2, 3], a simple way to include the effects of quantum mechanics is desired. Our idea is to attempt to produce an accurate, compact wave function that might be incorporated into simulation tools to sample configurations of the system. This idea is the basis of the present contribution. Of course, such wave functions should be of interest for their own sake. One background point of conceptual interest: the vast majority of simulation calculations assume classical statistical mechanics. Simulations may be carried out on a potential generated by electronic structure theory but atoms move as point particles classically on this surface, i.e., vibrational excitations are generally not considered. By and large, these quantum mechanical effects are incorporated only implicitly through empirical parameterizations of potential energy functions and through constraints such as rigid approximations to internal degrees of freedom. Hydrogen however has a very small mass and so this point picture is not completely appropriate. Schrödinger s equation instead suggests that we look at probability distributions of the atoms and follow these in space. These probability distributions are the square of wave functions. Methods like Diffusion Monte Carlo (DMC) [4] find wave functions, i.e., eigenfunctions of Schrödinger s equation. The ground state wave function is the appropriate probability distribution at zero temperature. (See Fig. 3.) Fig. 3. Methods used to study molecular systems and the temperatures at which they are valid. At any given temperature only some of the eigenstates of the Schrödinger equation are accessible. Path integral [5] approaches incorporate only the relevant states. In this case, each atom is replaced by a path and statistical averages are obtained from distributions of paths at some temperature. At high temperatures, the classical limit is reached and only a single point is needed for the path. At low temperatures, many points are needed and the calculation becomes computationally expensive. It would be nice to have a less expensive technique just for these types of situations. (See Fig. 3.)

4 Goal We would like to do Monte Carlo simulations that sample from a simple probability distribution. Classically, molecules move on the thermally accessible regions of a potential energy surface. Their distribution on this surface is the Boltzmann distribution,, where V(x) is the potential. Quantum mechanically, however, their distribution depends on thermally accessible quantum states. For some systems, sampling from just a few vibrational wave functions ( relevant quantum mechanics. ) is sufficient to capture the Our goal is to determine the complication and accuracy in constructing wave functions that might be transferable and useful in studies of chemistry in water. We seek high accuracy in compact wave functions for the ground state and a few excited states of solutes that raised quantum mechanical questions. Model Wave Functions for Atomic Motion Instead of using the Schrödinger equation to obtain wave functions, it is convenient to use its corresponding integral equation. In this format, a new quantity is introduced namely, the density matrix or the propagator. It is easy to see that the wave functions are eigenfunctions of the density matrix. Sethia, Sanyal, and Singh [6] developed a useful method for obtaining the natural orbitals of the density matrix in 1-D. If the density matrix were known, its natural orbitals could be obtained from the propagator equation by following Mark Kac s advice: be wise, discretize! In fact, the short time or high temperature asymptotic limit of the density matrix is known analytically. At short time or high temperature, it is a great approximation to the propagator. As a result, this asymptotic limit has been a cornerstone in methods such as DMC. Here too, using this asymptotic limit yields numerically exact orbitals except for a time step error. For higher dimensional problems, we can exploit the analytically known asymptotic density matrix to produce the necessary reasonable pair orbitals after tracing out all other degrees of freedom. Basically, we will focus on a particular bond, OD, and trace over the rest of the molecule. Tracing is essentially performing integrals via Monte Carlo. After tracing over the rest of the molecule, we end up with a reduced density matrix that can be diagonalized to obtain pair functions for the ground and a few excited

5 states of the OD vibration. Similarly, pair functions for DD vibrations can be found. Our wave functions will be comprised of a product of OD pair functions and a product of DD pair functions. It is interesting to draw analogies with electronic structure. Viewing this problem from a Hartree-Fock perspective. The oxygen and deuteriums play the roles of nucleus and electrons respectively. The single particle orbitals are the natural OD orbitals. Finally, the DD functions play the role of introducing pair correlation effects. Later, we will consider how to include 3 and 4 body correlations. Accuracy of Pair-Product Wave Functions Using the variational principle and some distribution theory, we develop a measure of how well optimized are our pair wave functions? First, we would like to find the extremum in the energy. Simple manipulations of that extremum and expressing the wave function as an exponential of pair interactions lead to this stationary requirement. Note that this stationary requirement is satisfied for the exact ground state function since the local energy is spatially constant. This stationary requirement essentially removes correlation between the local energy and the two particle joint density operator. Any deviation from this stationary requirement is defined as the error of the wave function. To get a fractional error, we divide by the pair distribution.

6 Figure 4 shows the fractional error in the OD pair distribution. Notice, that the errors are smaller than 1.5 %. Comparing the fractional error with the pair distribution, we see that the largest errors are in the tails of the orbitals. Fig. 4. The OD pair distribution and its fractional error. Correlations Beyond Pairs The pair product wave functions are suitable to use within variational Monte Carlo, including excited states, and density matrix Monte Carlo calculations [7, 8]. Together with the pair product wave functions, the traditional variational theorem permits identification of wave function features with significant potential for further optimization. Such variables are principal candidates for construction of explicitly correlated wave functions. Consideration of several natural possibilities for such structural variables identified the the vector triple product u=r OD1 * (r OD2 X r OD3 ) as more correlated with the local energy of the pair product wave function than any other combination considered for the D 3 O + ion. Fig. 5. The wave function distribution of this vector triple product (solid line) and the optimization deficit (dashed line).

7 Note that there is significant correlation at u=0. This suggests adding a product of the form to the pair product wave function. The pair product wave function with moving and scaling parameters times this new multiplicative many-body factor was optimized using Variational Monte Carlo (VMC). The energies obtained are about as good as the VMC result with mixing of 9 states. The new distribution and optimization deficit for the OSS potential are shown in Fig. 6. Fig. 6.The correlated, optimized wave function distribution of u is shown by the solid line. The new optimization deficit is the dashed line. Using pair product wave functions with this correlation piece as the basis in a McMillan VMC calculation with 9 functions reduced the ground state energy errors to 5-6%. Conclusion A pair product wave function for D 3 O + has been obtained from an approximate density matrix. This pair product wave function captures two body interactions fairly well. VMC includes correlation by mixing in excited states. However, it takes about 99 states to get to an error of 4-6%. Density Matrix Monte Carlo gets accurate energies with 9 wave functions. However, it does not provide a simple wave function. A compact ground state function is obtained by using the variational principle to identify the most significant many-body terms and including it directly into the wave function. For the D 3 O + ion the most significant such variable was the vector triple product, u=r OD1 * (r OD2 X r OD3 ). Variational Monte Carlo with 9 of these correlated functions yields a ground state wave function with an error of 5-6% in the zero point energy.

8 Future Directions Having constructed wave functions for small molecules, we can now explore how these might be transferable and useful in studies of proton transfer. Ideally, we would like to do Monte Carlo simulations that include the quantum mechanics of small molecules present in larger systems while sampling from a simple probability distribution. This Research Highlights is based on the paper: M. A. Gomez and L. R. Pratt, Construction of simulation wave functions for aqueous species: D 3 O +, J. Chem. Phys. 109, 8783 (1998). References 1. P. Colomban. Proton Conductors: Solids, Membranes and Gels: Materials and Devices (Cambridge University Press, Great Britain, 1992). 2. M. Pavese, S. Chawla, J. Lobaugh, and G. A. Voth. J. Chem. Phys. 107, 7428 (1997). 3. M. E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello. Science 275, 817 (1997). 4. B. L. Hammond, W. A. Lester, Jr., and P. J. Reynolds, Monte Carlo Methods in Ab Initio Quantum Chemistry (World Scientific, River Edge, NJ, 1994). 5. R. P. Feynman and A. R. Hibbs, Quantum Mechanics and Path Integrals (McGraw-Hill, Inc., New York, 1965). 6. A. Sethia, S. Sanyal, and Y. Singh, J. Chem. Phys. 93, 7268 (1990). 7. D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988). 8. B. Bernu, D. M. Ceperley, and W. A. Lester, Jr., J. Chem. Phys. 93, 552 (1990).

QUANTUM AND THERMAL MOTION IN MOLECULES FROM FIRST-PRINCIPLES

QUANTUM AND THERMAL MOTION IN MOLECULES FROM FIRST-PRINCIPLES QUANTUM AND THERMAL MOTION IN MOLECULES FROM FIRST-PRINCIPLES 1 Tapio T. Rantala, Department of Physics, Tampere University of Technology http://www.tut.fi/semiphys CONTENTS MOTIVATION PATH INTEGRAL APPROACH

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

GCSE CHEMISTRY REVISION LIST

GCSE CHEMISTRY REVISION LIST GCSE CHEMISTRY REVISION LIST OCR Gateway Chemistry (J248) from 2016 Topic C1: Particles C1.1 Describe the main features of the particle model in terms of states of matter and change of state Explain, in

More information

Supporting Online Materials: Nature of proton. transport in a water-filled carbon nanotube and in. liquid water

Supporting Online Materials: Nature of proton. transport in a water-filled carbon nanotube and in. liquid water Supporting Online Materials: Nature of proton transport in a water-filled carbon nanotube and in liquid water Ji Chen, Xin-Zheng Li,,, Qianfan Zhang, Angelos Michaelides, and Enge Wang, ICQM and School

More information

Electrolytes for Fuel Cells

Electrolytes for Fuel Cells Electrolytes for Fuel Cells Tom Zawodzinski Materials Science and Technology Division Los Alamos National Laboratory Air-Breather Fuel Cell Stack Systems Laptop Demo DCH/Enable Prototype Small Battery

More information

Understanding Chemical Reactions through Computer Modeling. Tyler R. Josephson University of Delaware 4/21/16

Understanding Chemical Reactions through Computer Modeling. Tyler R. Josephson University of Delaware 4/21/16 Understanding Chemical Reactions through Computer Modeling Tyler R. Josephson University of Delaware 4/21/16 A little about me B.S. in Chem E from U of M, 2011 Currently, Ph.D. student at University of

More information

Quantum Monte Carlo methods

Quantum Monte Carlo methods Quantum Monte Carlo methods Lubos Mitas North Carolina State University Urbana, August 2006 Lubos_Mitas@ncsu.edu H= 1 2 i i 2 i, I Z I r ii i j 1 r ij E ion ion H r 1, r 2,... =E r 1, r 2,... - ground

More information

Oxygen Reduction Reaction

Oxygen Reduction Reaction Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2016 Oxygen Reduction Reaction Oxygen is the most common oxidant for most fuel cell cathodes simply

More information

CHEMISTRY Topic #1: Bonding What Holds Atoms Together? Spring 2012 Dr. Susan Lait

CHEMISTRY Topic #1: Bonding What Holds Atoms Together? Spring 2012 Dr. Susan Lait CHEMISTRY 2000 Topic #1: Bonding What Holds Atoms Together? Spring 2012 Dr. Susan Lait Why Do Bonds Form? An energy diagram shows that a bond forms between two atoms if the overall energy of the system

More information

Molecular Aggregation

Molecular Aggregation Molecular Aggregation Structure Analysis and Molecular Simulation of Crystals and Liquids ANGELO GAVEZZOTTI University of Milano OXFORD UNIVERSITY PRESS Contents PART I FUNDAMENTALS 1 The molecule: structure,

More information

Molecular Dynamics Simulation Study of the Ionic Mobility of OH Using the OSS2 Model

Molecular Dynamics Simulation Study of the Ionic Mobility of OH Using the OSS2 Model 1154 Bull. Korean Chem. Soc. 2006, Vol. 27, No. 8 Song Hi Lee Molecular Dynamics Simulation Study of the Ionic Mobility of OH Using the OSS2 Model Song Hi Lee Department of Chemistry, Kyungsung University,

More information

An Overview of Quantum Monte Carlo Methods. David M. Ceperley

An Overview of Quantum Monte Carlo Methods. David M. Ceperley An Overview of Quantum Monte Carlo Methods David M. Ceperley Department of Physics and National Center for Supercomputing Applications University of Illinois Urbana-Champaign Urbana, Illinois 61801 In

More information

Computational Physics. J. M. Thijssen

Computational Physics. J. M. Thijssen Computational Physics J. M. Thijssen Delft University of Technology CAMBRIDGE UNIVERSITY PRESS Contents Preface xi 1 Introduction 1 1.1 Physics and computational physics 1 1.2 Classical mechanics and statistical

More information

Liquid Chromatography

Liquid Chromatography Liquid Chromatography 1. Introduction and Column Packing Material 2. Retention Mechanisms in Liquid Chromatography 3. Method Development 4. Column Preparation 5. General Instrumental aspects 6. Detectors

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

This is a very succinct primer intended as supplementary material for an undergraduate course in physical chemistry.

This is a very succinct primer intended as supplementary material for an undergraduate course in physical chemistry. 1 Computational Chemistry (Quantum Chemistry) Primer This is a very succinct primer intended as supplementary material for an undergraduate course in physical chemistry. TABLE OF CONTENTS Methods...1 Basis

More information

Orbital-dependent backflow transformations in quantum Monte Carlo

Orbital-dependent backflow transformations in quantum Monte Carlo transformations in quantum Monte Carlo P. Seth, P. López Ríos, and R. J. Needs TCM group, Cavendish Laboratory, University of Cambridge 5 December 2012 VMC and DMC Optimization Wave functions Variational

More information

QMC dissociation energy of the water dimer: Time step errors and backflow calculations

QMC dissociation energy of the water dimer: Time step errors and backflow calculations QMC dissociation energy of the water dimer: Time step errors and backflow calculations Idoia G. de Gurtubay and Richard J. Needs TCM group. Cavendish Laboratory University of Cambridge Idoia G. de Gurtubay.

More information

2 Electronic structure theory

2 Electronic structure theory Electronic structure theory. Generalities.. Born-Oppenheimer approximation revisited In Sec..3 (lecture 3) the Born-Oppenheimer approximation was introduced (see also, for instance, [Tannor.]). We are

More information

CE 530 Molecular Simulation

CE 530 Molecular Simulation 1 CE 530 Molecular Simulation Lecture 14 Molecular Models David A. Kofke Department of Chemical Engineering SUNY Buffalo kofke@eng.buffalo.edu 2 Review Monte Carlo ensemble averaging, no dynamics easy

More information

Sparks CH301. Quantum Mechanics. Waves? Particles? What and where are the electrons!? UNIT 2 Day 3. LM 14, 15 & 16 + HW due Friday, 8:45 am

Sparks CH301. Quantum Mechanics. Waves? Particles? What and where are the electrons!? UNIT 2 Day 3. LM 14, 15 & 16 + HW due Friday, 8:45 am Sparks CH301 Quantum Mechanics Waves? Particles? What and where are the electrons!? UNIT 2 Day 3 LM 14, 15 & 16 + HW due Friday, 8:45 am What are we going to learn today? The Simplest Atom - Hydrogen Relate

More information

Independent electrons in an effective potential

Independent electrons in an effective potential ABC of DFT Adiabatic approximation Independent electrons in an effective potential Hartree Fock Density Functional Theory MBPT - GW Density Functional Theory in a nutshell Every observable quantity of

More information

Multi-Scale Modeling from First Principles

Multi-Scale Modeling from First Principles m mm Multi-Scale Modeling from First Principles μm nm m mm μm nm space space Predictive modeling and simulations must address all time and Continuum Equations, densityfunctional space scales Rate Equations

More information

QUANTUM MECHANICAL STUDY OF THE FLEISCHMANN-PONS EFFECT

QUANTUM MECHANICAL STUDY OF THE FLEISCHMANN-PONS EFFECT Session 9 O_4 Theory (III) QUANTUM MECHANICAL STUDY OF THE FLEISCHMANN-PONS EFFECT Douglas G. Tasker 1, Jonathan L. Mace 1, Steven J. Pemberton 1 1 Los Alamos National Laboratory, Los Alamos, NM 87545,

More information

Chapter 5 Light and Matter: Reading Messages from the Cosmos. What is light? Properties of Waves. Waves. The Electromagnetic Spectrum

Chapter 5 Light and Matter: Reading Messages from the Cosmos. What is light? Properties of Waves. Waves. The Electromagnetic Spectrum Chapter 5 Light and Matter: Reading Messages from the Cosmos What is light? Light is a form of radiant energy Light can act either like a wave or like a particle (photon) Spectrum of the Sun 1 2 Waves

More information

2m dx 2. The particle in a one dimensional box (of size L) energy levels are

2m dx 2. The particle in a one dimensional box (of size L) energy levels are Name: Chem 3322 test #1 solutions, out of 40 marks I want complete, detailed answers to the questions. Show all your work to get full credit. indefinite integral : sin 2 (ax)dx = x 2 sin(2ax) 4a (1) with

More information

Chapter 1 INTRODUCTION AND BASIC CONCEPTS

Chapter 1 INTRODUCTION AND BASIC CONCEPTS Heat and Mass Transfer: Fundamentals & Applications 5th Edition in SI Units Yunus A. Çengel, Afshin J. Ghajar McGraw-Hill, 2015 Chapter 1 INTRODUCTION AND BASIC CONCEPTS Mehmet Kanoglu University of Gaziantep

More information

Exp. 4. Quantum Chemical calculation: The potential energy curves and the orbitals of H2 +

Exp. 4. Quantum Chemical calculation: The potential energy curves and the orbitals of H2 + Exp. 4. Quantum Chemical calculation: The potential energy curves and the orbitals of H2 + 1. Objectives Quantum chemical solvers are used to obtain the energy and the orbitals of the simplest molecules

More information

Density Functional Theory

Density Functional Theory Chemistry 380.37 Fall 2015 Dr. Jean M. Standard October 28, 2015 Density Functional Theory What is a Functional? A functional is a general mathematical quantity that represents a rule to convert a function

More information

Bloch Wilson Hamiltonian and a Generalization of the Gell-Mann Low Theorem 1

Bloch Wilson Hamiltonian and a Generalization of the Gell-Mann Low Theorem 1 Bloch Wilson Hamiltonian and a Generalization of the Gell-Mann Low Theorem 1 Axel Weber 2 arxiv:hep-th/9911198v1 25 Nov 1999 Instituto de Física y Matemáticas, Universidad Michoacana de San Nicolás de

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

PhET Interactive Chemistry Simulations Aligned to an Example General Chemistry Curriculum

PhET Interactive Chemistry Simulations Aligned to an Example General Chemistry Curriculum PhET Interactive Chemistry Simulations Aligned to an Example General Chemistry Curriculum Alignment is based on the topics and subtopics addressed by each sim. Sims that directly address the topic area

More information

Ab Initio Molecular Dynamics: Proton Transport In Water. Felix Groß Supervisor: Frank Uhlig Talk: April 19, 2016

Ab Initio Molecular Dynamics: Proton Transport In Water. Felix Groß Supervisor: Frank Uhlig Talk: April 19, 2016 Ab Initio Molecular Dynamics: Proton Transport In Water Felix Groß Supervisor: Frank Uhlig Talk: April 19, 2016 1 1 Introduction This handout and the corresponding talk is about ab initio molecular dynamics

More information

Quantum Monte Carlo wave functions and their optimization for quantum chemistry

Quantum Monte Carlo wave functions and their optimization for quantum chemistry Quantum Monte Carlo wave functions and their optimization for quantum chemistry Julien Toulouse Université Pierre & Marie Curie and CNRS, Paris, France CEA Saclay, SPhN Orme des Merisiers April 2015 Outline

More information

Excited States Calculations for Protonated PAHs

Excited States Calculations for Protonated PAHs 52 Chapter 3 Excited States Calculations for Protonated PAHs 3.1 Introduction Protonated PAHs are closed shell ions. Their electronic structure should therefore be similar to that of neutral PAHs, but

More information

Elements and Chemical Bonds

Elements and Chemical Bonds Name Elements and Chemical Bonds How do elements join together to form chemical compounds? Before You Read Before you read the chapter, think about what you know about elements and chemical bonds Record

More information

Sharon Hammes-Schiffer a) Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556

Sharon Hammes-Schiffer a) Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 An analytical derivation of MC-SCF vibrational wave functions for the quantum dynamical simulation of multiple proton transfer reactions: Initial application to protonated water chains Karen Drukker Laboratory

More information

Brain regions related to quantum coherence

Brain regions related to quantum coherence Brain regions related to quantum coherence Research since 2007 has shown that quantum coherence is utilised in increasing the efficiency of energy transfer in photosynthetic systems. What has not been

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

Lecture 5. Hartree-Fock Theory. WS2010/11: Introduction to Nuclear and Particle Physics

Lecture 5. Hartree-Fock Theory. WS2010/11: Introduction to Nuclear and Particle Physics Lecture 5 Hartree-Fock Theory WS2010/11: Introduction to Nuclear and Particle Physics Particle-number representation: General formalism The simplest starting point for a many-body state is a system of

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

6 Hydrophobic interactions

6 Hydrophobic interactions The Physics and Chemistry of Water 6 Hydrophobic interactions A non-polar molecule in water disrupts the H- bond structure by forcing some water molecules to give up their hydrogen bonds. As a result,

More information

Chemistry 4560/5560 Molecular Modeling Fall 2014

Chemistry 4560/5560 Molecular Modeling Fall 2014 Final Exam Name:. User s guide: 1. Read questions carefully and make sure you understand them before answering (if not, ask). 2. Answer only the question that is asked, not a different question. 3. Unless

More information

QUANTUM MONTE CARLO METHOD: PERFORMANCE ANALYSIS ON MODEL SYSTEMS

QUANTUM MONTE CARLO METHOD: PERFORMANCE ANALYSIS ON MODEL SYSTEMS Vol. 79 (1991) ACTA PHYSICA POLONICA A No 6 ΟΝ THE FIXED-NODE IMPORTANCE-SAMPLING QUANTUM MONTE CARLO METHOD: PERFORMANCE ANALYSIS ON MODEL SYSTEMS A. CHŁOBOWSKI Κ. Gumiński Department of Theoretical Chemistry,

More information

1 Rayleigh-Schrödinger Perturbation Theory

1 Rayleigh-Schrödinger Perturbation Theory 1 Rayleigh-Schrödinger Perturbation Theory All perturbative techniques depend upon a few simple assumptions. The first of these is that we have a mathematical expression for a physical quantity for which

More information

arxiv:physics/ v2 [physics.chem-ph] 9 Apr 2005

arxiv:physics/ v2 [physics.chem-ph] 9 Apr 2005 Electronic Quantum Monte Carlo Calculations of Atomic Forces, Vibrations, and Anharmonicities arxiv:physics/0411209v2 [physics.chem-ph] 9 Apr 2005 Myung Won Lee a), Massimo Mella b), and Andrew M. Rappe

More information

Batteries (Electrochemical Power Sources)

Batteries (Electrochemical Power Sources) Batteries (Electrochemical Power Sources) 1. Primary (single-discharge) batteries. => finite quantity of the reactants 2. Secondary or rechargeable batteries => regeneration of the original reactants by

More information

Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water

Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water Rajib Biswas, William Carpenter, Gregory A Voth * and Andrei Tokmakoff * Department of Chemistry,

More information

Reactive Empirical Force Fields

Reactive Empirical Force Fields Reactive Empirical Force Fields Jason Quenneville jasonq@lanl.gov X-1: Solid Mechanics, EOS and Materials Properties Applied Physics Division Los Alamos National Laboratory Timothy C. Germann, Los Alamos

More information

Ab-initio molecular dynamics for High pressure Hydrogen

Ab-initio molecular dynamics for High pressure Hydrogen Ab-initio molecular dynamics for High pressure Hydrogen Claudio Attaccalite Institut d'electronique, Microélectronique et Nanotechnologie (IEMN), Lille Outline A brief introduction to Quantum Monte Carlo

More information

International Physics Course Entrance Examination Questions

International Physics Course Entrance Examination Questions International Physics Course Entrance Examination Questions (May 2010) Please answer the four questions from Problem 1 to Problem 4. You can use as many answer sheets you need. Your name, question numbers

More information

Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory

Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory Ondrej Marsalek 1 1, a) and Thomas E. Markland Department of Chemistry,

More information

New Haven Public Schools Chemistry Curriculum Pacing. Quarter Unit Sequence of instruction Timeline 1 Matter Types of Matter

New Haven Public Schools Chemistry Curriculum Pacing. Quarter Unit Sequence of instruction Timeline 1 Matter Types of Matter CHEMISTRY Chemistry is a study of the fundamental structure of matter that serves as a basic understanding of science needed in today s world. It is a study of matter, energy, atomic and molecular structure,

More information

On the Uniqueness of Molecular Orbitals and limitations of the MO-model.

On the Uniqueness of Molecular Orbitals and limitations of the MO-model. On the Uniqueness of Molecular Orbitals and limitations of the MO-model. The purpose of these notes is to make clear that molecular orbitals are a particular way to represent many-electron wave functions.

More information

High Energy D 2 Bond from Feynman s Integral Wave Equation

High Energy D 2 Bond from Feynman s Integral Wave Equation Applying the Scientific Method to Understanding Anomalous Heat Effects: Opportunities and Challenges High Energy D Bond from Feynman s Integral Wave Equation By: Thomas Barnard Sponsored by: Coolesence

More information

5.80 Small-Molecule Spectroscopy and Dynamics

5.80 Small-Molecule Spectroscopy and Dynamics MIT OpenCourseWare http://ocw.mit.edu 5.80 Small-Molecule Spectroscopy and Dynamics Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. LECTURE

More information

Commentary on Probing the Orbital Energy of an Electron in an Atom

Commentary on Probing the Orbital Energy of an Electron in an Atom Commentary on Probing the Orbital Energy of an Electron in an Atom Roger DeKock Department of Chemistry and Biochemistry Calvin College Grand Rapids, MI 49546 dekock@calvin.edu Frank Rioux Department of

More information

Yingwei Wang Computational Quantum Chemistry 1 Hartree energy 2. 2 Many-body system 2. 3 Born-Oppenheimer approximation 2

Yingwei Wang Computational Quantum Chemistry 1 Hartree energy 2. 2 Many-body system 2. 3 Born-Oppenheimer approximation 2 Purdue University CHM 67300 Computational Quantum Chemistry REVIEW Yingwei Wang October 10, 2013 Review: Prof Slipchenko s class, Fall 2013 Contents 1 Hartree energy 2 2 Many-body system 2 3 Born-Oppenheimer

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

All-electron quantum Monte Carlo calculations for the noble gas atoms He to Xe

All-electron quantum Monte Carlo calculations for the noble gas atoms He to Xe All-electron quantum Monte Carlo calculations for the noble gas atoms He to Xe A. Ma, N. D. Drummond, M. D. Towler, and R. J. Needs Theory of Condensed Matter Group, Cavendish Laboratory, University of

More information

ARTICLES. Normal-mode analysis without the Hessian: A driven molecular-dynamics approach

ARTICLES. Normal-mode analysis without the Hessian: A driven molecular-dynamics approach JOURNAL OF CHEMICAL PHYSICS VOLUME 119, NUMBER 2 8 JULY 2003 ARTICLES Normal-mode analysis without the Hessian: A driven molecular-dynamics approach Joel M. Bowman, a) Xiubin Zhang, and Alex Brown Cherry

More information

3. DIFFERENT MODEL TYPES

3. DIFFERENT MODEL TYPES 3-1 3. DIFFERENT MODEL TYPES It is important for us to fully understand a physical problem before we can select a solution strategy for it. Models are convenient tools that enhance our understanding and

More information

Ab-initio molecular dynamics: from the basics up to quantum effects Roberto Car Princeton University

Ab-initio molecular dynamics: from the basics up to quantum effects Roberto Car Princeton University Ab-initio molecular dynamics: from the basics up to quantum effects Roberto Car Princeton University Hands-on Tutorial Workshop on Ab-Initio Molecular Simulations, Fritz- Haber-Institut, Berlin, July 12-21,

More information

Joint ICTP-IAEA Workshop on Fusion Plasma Modelling using Atomic and Molecular Data January 2012

Joint ICTP-IAEA Workshop on Fusion Plasma Modelling using Atomic and Molecular Data January 2012 2327-3 Joint ICTP-IAEA Workshop on Fusion Plasma Modelling using Atomic and Molecular Data 23-27 January 2012 Qunatum Methods for Plasma-Facing Materials Alain ALLOUCHE Univ.de Provence, Lab.de la Phys.

More information

Applications of Quantum Theory to Some Simple Systems

Applications of Quantum Theory to Some Simple Systems Applications of Quantum Theory to Some Simple Systems Arbitrariness in the value of total energy. We will use classical mechanics, and for simplicity of the discussion, consider a particle of mass m moving

More information

Rotation in liquid 4 He: Lessons from a highly simplified model

Rotation in liquid 4 He: Lessons from a highly simplified model JOURNAL OF CHEMICAL PHYSICS VOLUME 114, NUMBER 10 8 MARCH 2001 Rotation in liquid 4 He: Lessons from a highly simplified model Kevin K. Lehmann a) Department of Chemistry, Princeton University, Princeton,

More information

Electronic structure simulations of water solid interfaces

Electronic structure simulations of water solid interfaces Electronic structure simulations of water solid interfaces Angelos Michaelides London Centre for Nanotechnology & Department of Chemistry, University College London www.chem.ucl.ac.uk/ice Main co-workers:

More information

Estimation of Boron Ground State Energy by Monte Carlo Simulation

Estimation of Boron Ground State Energy by Monte Carlo Simulation American Journal of Applied Mathematics 2015; 3(3): 106-111 Published online April 30, 2015 (http://www.sciencepublishinggroup.com/j/ajam) doi: 10.11648/j.ajam.20150303.15 ISSN: 2330-0043 (Print); ISSN:

More information

International Atomic Energy Agency, Vienna, Austria. Charge Transfer in Collisions of Ions with atoms and molecules.

International Atomic Energy Agency, Vienna, Austria. Charge Transfer in Collisions of Ions with atoms and molecules. International Centre for Theoretical Physics (ICTP), Trieste, Italy International Atomic Energy Agency, Vienna, Austria Training Workshop on Atomic and Molecular Data for Fusion Energy Research Charge

More information

Structure of diatomic molecules

Structure of diatomic molecules Structure of diatomic molecules January 8, 00 1 Nature of molecules; energies of molecular motions Molecules are of course atoms that are held together by shared valence electrons. That is, most of each

More information

Chemistry 3502/4502. Final Exam Part I. May 14, 2005

Chemistry 3502/4502. Final Exam Part I. May 14, 2005 Advocacy chit Chemistry 350/450 Final Exam Part I May 4, 005. For which of the below systems is = where H is the Hamiltonian operator and T is the kinetic-energy operator? (a) The free particle

More information

Introduction to Solving the Time- Dependent Schrödinger Equation. Tom Penfold

Introduction to Solving the Time- Dependent Schrödinger Equation. Tom Penfold Introduction to Solving the Time- Dependent Schrödinger Equation Tom Penfold Outline 1 Introduction to Solving the Time-Dependent Schrödinger Equation What problems are we trying to solve? How can we use

More information

Crosswalk of Georgia Performance Standards & Georgia Standards of Excellence GSE Implementation in Chemistry

Crosswalk of Georgia Performance Standards & Georgia Standards of Excellence GSE Implementation in Chemistry Implementation in 2017-18 SC1. Students will analyze the nature of matter and its classifications. a. Relate the role of nuclear fusion in producing essentially all elements heavier than helium. b. Identify

More information

Foundations in Microbiology Seventh Edition

Foundations in Microbiology Seventh Edition Lecture PowerPoint to accompany Foundations in Microbiology Seventh Edition Talaro Chapter 2 The Chemistry of Biology Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

More information

Introduction to Path Integral Monte Carlo. Part I.

Introduction to Path Integral Monte Carlo. Part I. Introduction to Path Integral Monte Carlo. Part I. Alexey Filinov, Jens Böning, Michael Bonitz Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, D-24098 Kiel, Germany

More information

Chem 1140; Molecular Modeling

Chem 1140; Molecular Modeling P. Wipf 1 Chem 1140 $E = -! (q a + q b )" ab S ab + ab!k

More information

Exercise 1: Structure and dipole moment of a small molecule

Exercise 1: Structure and dipole moment of a small molecule Introduction to computational chemistry Exercise 1: Structure and dipole moment of a small molecule Vesa Hänninen 1 Introduction In this exercise the equilibrium structure and the dipole moment of a small

More information

Beyond the Hartree-Fock Approximation: Configuration Interaction

Beyond the Hartree-Fock Approximation: Configuration Interaction Beyond the Hartree-Fock Approximation: Configuration Interaction The Hartree-Fock (HF) method uses a single determinant (single electronic configuration) description of the electronic wavefunction. For

More information

ATOMIC STRUCTURE. Atomic Structure. Atomic orbitals and their energies (a) Hydrogenic radial wavefunctions

ATOMIC STRUCTURE. Atomic Structure. Atomic orbitals and their energies (a) Hydrogenic radial wavefunctions ATOMIC STRUCTURE Atomic orbitals and their energies (a) Hydrogenic radial wavefunctions Bundet Boekfa Chem Div, Fac Lib Arts & Sci Kasetsart University Kamphaeng Saen Campus 1 2 Atomic orbitals and their

More information

PROJECT C: ELECTRONIC BAND STRUCTURE IN A MODEL SEMICONDUCTOR

PROJECT C: ELECTRONIC BAND STRUCTURE IN A MODEL SEMICONDUCTOR PROJECT C: ELECTRONIC BAND STRUCTURE IN A MODEL SEMICONDUCTOR The aim of this project is to present the student with a perspective on the notion of electronic energy band structures and energy band gaps

More information

Performance of Palladium Diffusers for Reliable Purification of Hydrogen

Performance of Palladium Diffusers for Reliable Purification of Hydrogen Performance of Palladium Diffusers for Reliable Purification of Hydrogen By Ed Connor, GC Product Specialist, Peak Scientific Instruments Ltd Performance of Palladium Diffusers for Reliable Purification

More information

CHEM-UA 127: Advanced General Chemistry I

CHEM-UA 127: Advanced General Chemistry I 1 CHEM-UA 127: Advanced General Chemistry I Notes for Lecture 6 I MOLECULAR GEOMETRY AND COORDINATES Consider a diatomic molecule AB Imagine fixing this molecule at a very specific spatial location, as

More information

Quantum mechanics can be used to calculate any property of a molecule. The energy E of a wavefunction Ψ evaluated for the Hamiltonian H is,

Quantum mechanics can be used to calculate any property of a molecule. The energy E of a wavefunction Ψ evaluated for the Hamiltonian H is, Chapter : Molecules Quantum mechanics can be used to calculate any property of a molecule The energy E of a wavefunction Ψ evaluated for the Hamiltonian H is, E = Ψ H Ψ Ψ Ψ 1) At first this seems like

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

Lecture- 08 Emission and absorption spectra

Lecture- 08 Emission and absorption spectra Atomic and Molecular Absorption Spectrometry for Pollution Monitoring Dr. J R Mudakavi Department of Chemical Engineering Indian Institute of Science, Bangalore Lecture- 08 Emission and absorption spectra

More information

1. a Draw a labelled diagram of an atom that has 9 protons and electrons and 9 neutrons.

1. a Draw a labelled diagram of an atom that has 9 protons and electrons and 9 neutrons. Topic review Using scientific language Design and construct a crossword using the following words: atom; proton; molecule; ion; lattice; shell; element; compound; bond; conductor; insulator; electrolysis;

More information

Insights on Interfacial Structure, Dynamics and. Proton Transfer from Ultrafast Vibrational Sum. Frequency Generation Spectroscopy of the

Insights on Interfacial Structure, Dynamics and. Proton Transfer from Ultrafast Vibrational Sum. Frequency Generation Spectroscopy of the Insights on Interfacial Structure, Dynamics and Proton Transfer from Ultrafast Vibrational Sum Frequency Generation Spectroscopy of the Alumina(0001)/Water Interface Aashish Tuladhar, Stefan M. Piontek,

More information

Ab initio molecular dynamics. Simone Piccinin CNR-IOM DEMOCRITOS Trieste, Italy. Bangalore, 04 September 2014

Ab initio molecular dynamics. Simone Piccinin CNR-IOM DEMOCRITOS Trieste, Italy. Bangalore, 04 September 2014 Ab initio molecular dynamics Simone Piccinin CNR-IOM DEMOCRITOS Trieste, Italy Bangalore, 04 September 2014 What is MD? 1) Liquid 4) Dye/TiO2/electrolyte 2) Liquids 3) Solvated protein 5) Solid to liquid

More information

Introduction to materials modeling and simulation

Introduction to materials modeling and simulation 1 Introduction to materials modeling and simulation With the development of inexpensive, yet very fast, computers and the availability of software for many applications, computational modeling and simulation

More information

4.2 A Scientific View of Energy Kinetic Energy

4.2 A Scientific View of Energy Kinetic Energy 4. A Universe of Matter and Energy 4.1 Matter and Energy in Everyday Life The eternal mystery of the world is its comprehensibility. The fact that it is comprehensible is a miracle. Albert Einstein (1879

More information

Gustavus Adolphus College. Lab #5: Computational Chemistry

Gustavus Adolphus College. Lab #5: Computational Chemistry CHE 372 Gustavus Adolphus College Lab #5: Computational Chemistry Introduction In this investigation we will apply the techniques of computational chemistry to several of the molecular systems that we

More information

1 Imaginary Time Path Integral

1 Imaginary Time Path Integral 1 Imaginary Time Path Integral For the so-called imaginary time path integral, the object of interest is exp( τh h There are two reasons for using imaginary time path integrals. One is that the application

More information

Advanced Analytical Chemistry Lecture 12. Chem 4631

Advanced Analytical Chemistry Lecture 12. Chem 4631 Advanced Analytical Chemistry Lecture 12 Chem 4631 What is a fuel cell? An electro-chemical energy conversion device A factory that takes fuel as input and produces electricity as output. O 2 (g) H 2 (g)

More information

where n = (an integer) =

where n = (an integer) = 5.111 Lecture Summary #5 Readings for today: Section 1.3 (1.6 in 3 rd ed) Atomic Spectra, Section 1.7 up to equation 9b (1.5 up to eq. 8b in 3 rd ed) Wavefunctions and Energy Levels, Section 1.8 (1.7 in

More information

Chapter 2: Chemistry & Life

Chapter 2: Chemistry & Life Chapter 2: Chemistry & Life 1. Atoms 2. Molecules 3. Water 1. Atoms A Generic Atom All Matter is made of Atoms Atoms are the smallest indivisible unit of matter 92 different types of atoms: ELEMENTS Atoms

More information

Chapter 2: Chemistry & Life. 1. Atoms. 2. Molecules. 3. Water. 1. Atoms. A Generic Atom

Chapter 2: Chemistry & Life. 1. Atoms. 2. Molecules. 3. Water. 1. Atoms. A Generic Atom Chapter 2: Chemistry & Life 1. Atoms 2. Molecules 3. Water 1. Atoms A Generic Atom 1 All Matter is made of Atoms Atoms are the smallest indivisible unit of matter 92 different types of atoms: ELEMENTS

More information

Plasma Spectroscopy Inferences from Line Emission

Plasma Spectroscopy Inferences from Line Emission Plasma Spectroscopy Inferences from Line Emission Ø From line λ, can determine element, ionization state, and energy levels involved Ø From line shape, can determine bulk and thermal velocity and often

More information

Molecular Bonding. Molecular Schrödinger equation. r - nuclei s - electrons. M j = mass of j th nucleus m 0 = mass of electron

Molecular Bonding. Molecular Schrödinger equation. r - nuclei s - electrons. M j = mass of j th nucleus m 0 = mass of electron Molecular onding Molecular Schrödinger equation r - nuclei s - electrons 1 1 W V r s j i j1 M j m i1 M j = mass of j th nucleus m = mass of electron j i Laplace operator for nuclei Laplace operator for

More information

Static Fields as Mass-Currents and Mercury's Perihelion Shift

Static Fields as Mass-Currents and Mercury's Perihelion Shift Static Fields as Mass-Currents and Mercury's Perihelion Shift by Paul R. Gerber Gerber Molecular Design, Forten 649, CH-8873 Amden Email: Paul.Gerber@moloc.ch 03.65.Pm 95.30.Sf 04.60.-m 98.80.Jk Relativistic

More information

Circumventing the pathological behavior of path-integral Monte Carlo for systems with Coulomb potentials

Circumventing the pathological behavior of path-integral Monte Carlo for systems with Coulomb potentials Circumventing the pathological behavior of path-integral Monte Carlo for systems with Coulomb potentials M. H. Müser and B. J. Berne Department of Chemistry, Columbia University, New York, New York 10027

More information