Advanced in silico drug design

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

Computational Chemistry. An Introduction to Molecular Dynamic Simulations

Computational Chemistry An Introduction to Molecular Dynamic Simulations Computational chemistry simulates chemical structures and reactions numerically, based in full or in part on the fundamental laws

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

ONETEP PB/SA: Application to G-Quadruplex DNA Stability. Danny Cole

ONETEP PB/SA: Application to G-Quadruplex DNA Stability Danny Cole Introduction Historical overview of structure and free energy calculation of complex molecules using molecular mechanics and continuum

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

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

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

4 th Advanced in silico Drug Design KFC/ADD Molecular Modelling Intro. Karel Berka, Ph.D.

4 th Advanced in silico Drug Design KFC/ADD Molecular Modelling Intro Karel Berka, Ph.D. UP Olomouc, 21.1.-25.1. 2019 Motto A theory is something nobody believes, except the person who made it An experiment

Advanced in silico Drug Design KFC/ADD

Advanced in silico Drug Design S pozdravem KFC/ADD Molecular Karel Berka Docking Intro Karel Berka, Ph.D. Jindřich Fanfrlík, Ph.D. Martin Lepšík, Ph.D. Pavel Polishchuk, Ph.D. UP Olomouc, 30.1.-1.2. 2017

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

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

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.

Molecular dynamics simulation of Aquaporin-1. 4 nm

Molecular dynamics simulation of Aquaporin-1 4 nm Molecular Dynamics Simulations Schrödinger equation i~@ t (r, R) =H (r, R) Born-Oppenheimer approximation H e e(r; R) =E e (R) e(r; R) Nucleic motion described

Protein-Ligand Interactions* and Energy Evaluation Methods

Protein-Ligand Interactions* and Energy Evaluation Methods *with a revealing look at roles of water Glen E. Kellogg Department of Medicinal Chemistry Institute for Structural Biology, Drug Discovery &

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

Drug Design. Molecular docking. RNDr. Karel Berka, PhD RNDr. Jindřich Fanfrlík, PhD RNDr. Martin Lepšík, PhD

Drug Design Molecular docking RNDr. Karel Berka, PhD RNDr. Jindřich Fanfrlík, PhD RNDr. Martin Lepšík, PhD Dpt. Physical Chemistry, RCPTM, Faculty of Science, Palacky University in Olomouc Motto tj. 18

Molecular Interactions F14NMI. Lecture 4: worked answers to practice questions

Molecular Interactions F14NMI Lecture 4: worked answers to practice questions http://comp.chem.nottingham.ac.uk/teaching/f14nmi jonathan.hirst@nottingham.ac.uk (1) (a) Describe the Monte Carlo algorithm

Interaction energy of DNA base pairs and amino acid pairs: DFT, DFTB and WFT calculations

Interaction energy of DNA base pairs and amino acid pairs: DFT, DFTB and WFT calculations Tomáš Kubař, Petr Jurečka, Jirka Černý, Honza Řezáč, Michal Otyepka, Haydée Valdés and Pavel Hobza* Institute of

Docking. GBCB 5874: Problem Solving in GBCB

Docking Benzamidine Docking to Trypsin Relationship to Drug Design Ligand-based design QSAR Pharmacophore modeling Can be done without 3-D structure of protein Receptor/Structure-based design Molecular

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

The Molecular Dynamics Method

The Molecular Dynamics Method Thermal motion of a lipid bilayer Water permeation through channels Selective sugar transport Potential Energy (hyper)surface What is Force? Energy U(x) F = d dx U(x) Conformation

Ab initio calculations for potential energy surfaces. D. Talbi GRAAL- Montpellier

Ab initio calculations for potential energy surfaces D. Talbi GRAAL- Montpellier A theoretical study of a reaction is a two step process I-Electronic calculations : techniques of quantum chemistry potential

MD Simulation in Pose Refinement and Scoring Using AMBER Workflows

MD Simulation in Pose Refinement and Scoring Using AMBER Workflows Yuan Hu (On behalf of Merck D3R Team) D3R Grand Challenge 2 Webinar Department of Chemistry, Modeling & Informatics Merck Research Laboratories,

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

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

What is Classical Molecular Dynamics?

What is Classical Molecular Dynamics? Simulation of explicit particles (atoms, ions,... ) Particles interact via relatively simple analytical potential functions Newton s equations of motion are integrated

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

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

Free Energy Simulation Methods

Free Energy Simulation Methods Free energy simulation methods Many methods have been developed to compute (relative) free energies on the basis of statistical mechanics Free energy perturbation Thermodynamic

Introduction to computational chemistry Exercise I: Structure and electronic energy of a small molecule. Vesa Hänninen

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

High-level Quantum Chemistry Methods and Benchmark Datasets for Molecules

High-level Quantum Chemistry Methods and Benchmark Datasets for Molecules Markus Schneider Fritz Haber Institute of the MPS, Berlin, Germany École Polytechnique Fédérale de Lausanne, Switzerland دانشگاه

Free energy simulations

Free energy simulations Marcus Elstner and Tomáš Kubař January 14, 2013 Motivation a physical quantity that is of most interest in chemistry? free energies Helmholtz F or Gibbs G holy grail of computational

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

Softwares for Molecular Docking. Lokesh P. Tripathi NCBS 17 December 2007

Softwares for Molecular Docking Lokesh P. Tripathi NCBS 17 December 2007 Molecular Docking Attempt to predict structures of an intermolecular complex between two or more molecules Receptor-ligand (or drug)

Statistical Mechanics for Proteins

The Partition Function From Q all relevant thermodynamic properties can be obtained by differentiation of the free energy F: = kt q p E q pd d h T V Q ), ( exp 1! 1 ),, ( 3 3 3 ),, ( ln ),, ( T V Q kt

Potential Energy (hyper)surface

The Molecular Dynamics Method Thermal motion of a lipid bilayer Water permeation through channels Selective sugar transport Potential Energy (hyper)surface What is Force? Energy U(x) F = " d dx U(x) Conformation

AN INTRODUCTION TO QUANTUM CHEMISTRY. Mark S. Gordon Iowa State University

AN INTRODUCTION TO QUANTUM CHEMISTRY Mark S. Gordon Iowa State University 1 OUTLINE Theoretical Background in Quantum Chemistry Overview of GAMESS Program Applications 2 QUANTUM CHEMISTRY In principle,

Potassium(I) in water from Theoretical Calculations

Potassium(I) in water from Theoretical Calculations Maria Rudbeck U.U.D.M. Project Report 2006:9 Examensarbete i matematik, 20 poäng Handledare: Daniel Spånberg, Institutionen för materialkemi och Lars-Erik

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

Introduction to Computational Chemistry Computational (chemistry education) and/or (Computational chemistry) education First one: Use computational tools to help increase student understanding of material

GEM4 Summer School OpenCourseWare

GEM4 Summer School OpenCourseWare http://gem4.educommons.net/ http://www.gem4.org/ Lecture: Molecular Mechanics by Ju Li. Given August 9, 2006 during the GEM4 session at MIT in Cambridge, MA. Please use

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,

Alek Marenich Cramer -Truhlar Group. University of Minnesota

and Computational Electrochemistry Alek Marenich Cramer -Truhlar Group University of Minnesota Outline Solvation and charge models Energetics and dynamics in solution Computational electrochemistry Future

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

MD Thermodynamics. Lecture 12 3/26/18. Harvard SEAS AP 275 Atomistic Modeling of Materials Boris Kozinsky

MD Thermodynamics Lecture 1 3/6/18 1 Molecular dynamics The force depends on positions only (not velocities) Total energy is conserved (micro canonical evolution) Newton s equations of motion (second order

( R)Ψ el ( r;r) = E el ( R)Ψ el ( r;r)

Born Oppenheimer Approximation: Ĥ el ( R)Ψ el ( r;r) = E el ( R)Ψ el ( r;r) For a molecule with N electrons and M nuclei: Ĥ el What is E el (R)? s* potential surface Reaction Barrier Unstable intermediate

METHODS FOR TREATING SOLVENT EFFECTS AND INTERMOLECULAR FORCES. Mark S. Gordon Iowa State University Ames Laboratory

METHODS FOR TREATING SOLVENT EFFECTS AND INTERMOLECULAR FORCES Mark S. Gordon Iowa State University Ames Laboratory OUTLINE Solvation Methods Explicit vs. implicit methods Explicit Methods TIP3P, TIP4P

OVERVIEW OF QUANTUM CHEMISTRY METHODS

OVERVIEW OF QUANTUM CHEMISTRY METHODS Outline I Generalities Correlation, basis sets Spin II Wavefunction methods Hartree-Fock Configuration interaction Coupled cluster Perturbative methods III Density

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

Supporting Information: Predicting the Ionic Product of Water

Supporting Information: Predicting the Ionic Product of Water Eva Perlt 1,+, Michael von Domaros 1,+, Barbara Kirchner 1, Ralf Ludwig 2, and Frank Weinhold 3,* 1 Mulliken Center for Theoretical Chemistry,

Structure of Cement Phases from ab initio Modeling Crystalline C-S-HC

Structure of Cement Phases from ab initio Modeling Crystalline C-S-HC Sergey V. Churakov sergey.churakov@psi.ch Paul Scherrer Institute Switzerland Cement Phase Composition C-S-H H Solid Solution Model

Biomolecules are dynamic no single structure is a perfect model

Molecular Dynamics Simulations of Biomolecules References: A. R. Leach Molecular Modeling Principles and Applications Prentice Hall, 2001. M. P. Allen and D. J. Tildesley "Computer Simulation of Liquids",

CHE3935. Lecture 4 Quantum Mechanical Simulation Methods Continued

CHE3935 Lecture 4 Quantum Mechanical Simulation Methods Continued 1 OUTLINE Review Introduction to CPMD MD and ensembles The functionals of density functional theory Return to ab initio methods Binding

Electronic structure calculations: fundamentals George C. Schatz Northwestern University

Electronic structure calculations: fundamentals George C. Schatz Northwestern University Electronic Structure (often called Quantum Chemistry) calculations use quantum mechanics to determine the wavefunctions

Molecular Mechanics: The Ab Initio Foundation

Molecular Mechanics: The Ab Initio Foundation Ju Li GEM4 Summer School 2006 Cell and Molecular Mechanics in BioMedicine August 7 18, 2006, MIT, Cambridge, MA, USA 2 Outline Why are electrons quantum? Born-Oppenheimer

Fragmentation methods

Fragmentation methods Scaling of QM Methods HF, DFT scale as N 4 MP2 scales as N 5 CC methods scale as N 7 What if we could freeze the value of N regardless of the size of the system? Then each method

Level-Set Variational Solvation Coupling Solute Molecular Mechanics with Continuum Solvent

Level-Set Variational Solvation Coupling Solute Molecular Mechanics with Continuum Solvent Bo Li Department of Mathematics and Center for Theoretical Biological Physics (CTBP) University of California,

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

74 these states cannot be reliably obtained from experiments. In addition, the barriers between the local minima can also not be obtained reliably fro

73 Chapter 5 Development of Adiabatic Force Field for Polyvinyl Chloride (PVC) and Chlorinated PVC (CPVC) 5.1 Introduction Chlorinated polyvinyl chloride has become an important specialty polymer due to

The Basics of Theoretical and Computational Chemistry

Bernd M. Rode, Thomas S. Hofer, and Michael D. Kugler The Basics of Theoretical and Computational Chemistry BICENTENNIA BICENTBNN I AL. WILEY-VCH Verlag GmbH & Co. KGaA V Contents Preface IX 1 Introduction

Lecture 3: methods and terminology, part I

Eritis sicut Deus, scientes bonum et malum. Lecture 3: methods and terminology, part I Molecular dynamics, internal coordinates, Z-matrices, force fields, periodic boundary conditions, Hartree-Fock theory,

Introduction to Computational Chemistry: Theory

Introduction to Computational Chemistry: Theory Dr Andrew Gilbert Rm 118, Craig Building, RSC andrew.gilbert@anu.edu.au 3023 Course Lectures Introduction Hartree Fock Theory Basis Sets Lecture 1 1 Introduction

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.

Introduction to Computational Chemistry

Introduction to Computational Chemistry Vesa Hänninen Laboratory of Physical Chemistry Chemicum 4th floor vesa.hanninen@helsinki.fi September 10, 2013 Lecture 3. Electron correlation methods September

Quantum Chemistry for Supramolecular Complexes

Quantum Chemistry for Supramolecular Complexes Stefan Grimme Mulliken Center for Theoretical Chemistry, University of Bonn COSMO Symposium, March 2015 Supramolecular chemistry: chemistry beyond the covalent

A Nobel Prize for Molecular Dynamics and QM/MM What is Classical Molecular Dynamics? Simulation of explicit particles (atoms, ions,... ) Particles interact via relatively simple analytical potential

Introduction to Computational Quantum Chemistry: Theory

Introduction to Computational Quantum Chemistry: Theory Dr Andrew Gilbert Rm 118, Craig Building, RSC 3108 Course Lectures 2007 Introduction Hartree Fock Theory Configuration Interaction Lectures 1 Introduction

Electron Correlation

Electron Correlation Levels of QM Theory HΨ=EΨ Born-Oppenheimer approximation Nuclear equation: H n Ψ n =E n Ψ n Electronic equation: H e Ψ e =E e Ψ e Single determinant SCF Semi-empirical methods Correlation

Non-covalent force fields computed ab initio

Non-covalent force fields computed ab initio Supermolecule calculations Symmetry-adapted perturbation theory (SAPT) Supermolecule calculations Requirements: E = E AB E A E B. Include electron correlation,

Noncovalent interactions in biochemistry

Noncovalent interactions in biochemistry Kevin E. Riley 1 and Pavel Hobza 2,3 Noncovalent interactions are known to play a key role in biochemistry. The knowledge of stabilization (relative) energies and

DFT: Exchange-Correlation

DFT: Local functionals, exact exchange and other post-dft methods Stewart Clark University of Outline Introduction What is exchange and correlation? Quick tour of XC functionals (Semi-)local: LDA, PBE,

2~:J~ -ryej- r- 2 Jr. A - f3. sr(djk nv~tor rn~ +~ rvjs (::-CJ) ::;-1-.'--~ -. rhd. ('-.Ji.L.~ )- r'-d)c, -r/~ JJr - 2~d ~2-Jr fn'6.

.~, ~ I, sr(djk nv~tor rn~ +~ rvjs (::-CJ) ::;-1-.'--~ -. rhd. ('-.Ji.L.~ )- r'-d)c, -r/~ JJr - 2~d ~2-Jr fn'6.)1e'" 21t-ol Je C'...-------- lj-vi, J? Jr Jr \Ji 2~:J~ -ryej- r- 2 Jr A - f3 c _,~,= ~,.,w._..._.

Anion-π and π-π cooperative interactions

Chapter 5 Anion-π and π-π cooperative interactions 5.1 Introduction The design of selective receptors of anionic species is a very active area of research within supramolecular chemistry due to the potential

DENSITY FUNCTIONAL THEORY FOR NON-THEORISTS JOHN P. PERDEW DEPARTMENTS OF PHYSICS AND CHEMISTRY TEMPLE UNIVERSITY

DENSITY FUNCTIONAL THEORY FOR NON-THEORISTS JOHN P. PERDEW DEPARTMENTS OF PHYSICS AND CHEMISTRY TEMPLE UNIVERSITY A TUTORIAL FOR PHYSICAL SCIENTISTS WHO MAY OR MAY NOT HATE EQUATIONS AND PROOFS REFERENCES

Alanine: Then There Was Water

Chemistry Publications Chemistry 6-2009 Alanine: Then There Was Water Jonathan M. Mullin Iowa State University Mark S. Gordon Iowa State University, mgordon@iastate.edu Follow this and additional works

Modeling Chemical Reactions in Aqueous Solutions

University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 8-2013 Modeling Chemical Reactions in Aqueous Solutions Osman Uner University of Arkansas, Fayetteville Follow this and additional

Electronic structure theory: Fundamentals to frontiers. 2. Density functional theory

Electronic structure theory: Fundamentals to frontiers. 2. Density functional theory MARTIN HEAD-GORDON, Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley

Multi-scale modelling of transition metal enzymes

Degree Project C in Chemistry, 15 c Multi-scale modelling of transition metal enzymes Nathalie Proos Vedin 18th June 2015 Supervisor: Marcus Lundberg Uppsala University Department of Chemistry Ångström

Ab initio molecular dynamics and nuclear quantum effects

Ab initio molecular dynamics and nuclear quantum effects Luca M. Ghiringhelli Fritz Haber Institute Hands on workshop density functional theory and beyond: First principles simulations of molecules and

MO Calculation for a Diatomic Molecule. /4 0 ) i=1 j>i (1/r ij )

MO Calculation for a Diatomic Molecule Introduction The properties of any molecular system can in principle be found by looking at the solutions to the corresponding time independent Schrodinger equation

Same idea for polyatomics, keep track of identical atom e.g. NH 3 consider only valence electrons F(2s,2p) H(1s)

XIII 63 Polyatomic bonding -09 -mod, Notes (13) Engel 16-17 Balance: nuclear repulsion, positive e-n attraction, neg. united atom AO ε i applies to all bonding, just more nuclei repulsion biggest at low

Molecular Dynamics. Molecules in motion

Molecular Dynamics Molecules in motion 1 Molecules in mo1on Molecules are not sta1c, but move all the 1me Source: h9p://en.wikipedia.org/wiki/kine1c_theory 2 Gasses, liquids and solids Gasses, liquids

Density functional theory in solution: Implementing an implicit solvent model for CASTEP and ONETEP

Density functional theory in solution: Implementing an implicit solvent model for CASTEP and ONETEP, November 2016 James C. Womack University of Southampton, Southampton, UK Overview Background The model

Intermolecular Forces in Density Functional Theory

Intermolecular Forces in Density Functional Theory Problems of DFT Peter Pulay at WATOC2005: There are 3 problems with DFT 1. Accuracy does not converge 2. Spin states of open shell systems often incorrect

Solvatochromic shifts of a polarity probe implicit and explicit solvent modeling

Solvatochromic shifts of a polarity probe implicit and explicit solvent modeling Andrzej Eilmes Faculty of Chemistry, Jagiellonian University, Kraków solvent effects in absorption spectra Absorption spectra

Chem 1140; Molecular Modeling

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

MM-GBSA for Calculating Binding Affinity A rank-ordering study for the lead optimization of Fxa and COX-2 inhibitors

MM-GBSA for Calculating Binding Affinity A rank-ordering study for the lead optimization of Fxa and COX-2 inhibitors Thomas Steinbrecher Senior Application Scientist Typical Docking Workflow Databases

Kd = koff/kon = [R][L]/[RL]

Taller de docking y cribado virtual: Uso de herramientas computacionales en el diseño de fármacos Docking program GLIDE El programa de docking GLIDE Sonsoles Martín-Santamaría Shrödinger is a scientific

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

Accounting for Solvation in Quantum Chemistry. Comp chem spring school 2014 CSC, Finland

Accounting for Solvation in Quantum Chemistry Comp chem spring school 2014 CSC, Finland In solution or in a vacuum? Solvent description is important when: Polar solvent: electrostatic stabilization Solvent

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

1 Density functional theory (DFT)

1 Density functional theory (DFT) 1.1 Introduction Density functional theory is an alternative to ab initio methods for solving the nonrelativistic, time-independent Schrödinger equation H Φ = E Φ. The

Extrapolation of Atomic Natural Orbitals of basis set to complete basis set limit

Extrapolation of Atomic Natural Orbitals of basis set to complete basis set limit Jaroslav Granatier Institute of Physical Chemistry and Chemical Physisc, Slovak University of Technology in Bratislava,

SUPPORTING INFORMATION. Table S1: Use of different functionals and variation of HF exchange on IS/HS splitting

SUPPORTING INFORMATION List of Contents Table S1: Use of different functionals and variation of HF exchange on IS/HS splitting S2 Table S2: Structural parameters using the B3LYP** functional for the IS

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

MM-PBSA Validation Study. Trent E. Balius Department of Applied Mathematics and Statistics AMS

MM-PBSA Validation Study Trent. Balius Department of Applied Mathematics and Statistics AMS 535 11-26-2008 Overview MM-PBSA Introduction MD ensembles one snap-shots relaxed structures nrichment Computational

Design of Efficient Catalysts with Double Transition Metal. Atoms on C 2 N Layer

Supporting Information Design of Efficient Catalysts with Double Transition Metal Atoms on C 2 N Layer Xiyu Li, 1, Wenhui Zhong, 2, Peng Cui, 1 Jun Li, 1 Jun Jiang 1, * 1 Hefei National Laboratory for

Molecular Simulation III

Molecular Simulation III Quantum Chemistry Classical Mechanics E = Ψ H Ψ ΨΨ U = E bond +E angle +E torsion +E non-bond Molecular Dynamics Jeffry D. Madura Department of Chemistry & Biochemistry Center

Introduction to Electronic Structure Theory

CSC/PRACE Spring School in Computational Chemistry 2017 Introduction to Electronic Structure Theory Mikael Johansson http://www.iki.fi/~mpjohans Objective: To get familiarised with the, subjectively chosen,

Homology modeling. Dinesh Gupta ICGEB, New Delhi 1/27/2010 5:59 PM

Homology modeling Dinesh Gupta ICGEB, New Delhi Protein structure prediction Methods: Homology (comparative) modelling Threading Ab-initio Protein Homology modeling Homology modeling is an extrapolation

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.