Semi Empirical Force Fields and Their Limitations. Potential Energy Surface (PES)
|
|
|
- Toby Blankenship
- 6 years ago
- Views:
Transcription
1 Semi Empirical Force Fields and Their Limitations Ioan Kosztin Beckman Institute University of Illinois at Urbana-Champaign Potential Energy Surface (PES) Schrödinger equation: H T Ψ( r, = E Ψ( r, H = K + K T n e + T V ( r, Born-Oppenheimer approx. Ψ( r, = ψ( r Θ( Equation of motion for electrons: ( Ke + V ) ψ( r, = Ee( ψ( r, PES quantum Equation of motion for nuclei: (motion on the PES) classical (MD) [ K E ( ] Θ( = E Θ( n + e T m d 2 R / dt 2 = E ( e 1
2 Classical Force Fields Consist of: 1. Analytical form of the interatomic potential energy U=E e ( as a function of the atomic coordinates of the molecule 2. Parameters which enter U The force field is fit to experimental data from a small set of molecules The molecule is considered to be a collection of atoms held together by simple elastic (harmonic) forces. The forces are given by the gradients of the potential energy with respect to the internal coordinates of the molecule. Components of a Force Field Any force field contains the necessary building blocks for the calculation of energy and force: - a list of atom types - a list of atomic charges - rules for atom-types - functional forms of the components of the energy expression - parameters for the function terms - rules for generating parameters that have not been explicitly defined (for some force fields) - a defined way of assigning functional forms and parameters (for some force fields) 2
3 Force Field Energy Expression General form: E = E bond + E angle + E torsion + E nonbond + E other Force fields differ: - in parameters and cross terms - methods of parameterization Types of Force Fields Classical (first-generation) force fields CHARMm AMBER CVFF (consistent valence force field) Second-generation force fields Rule-based force fields Special-purpose force fields 3
4 Force Field Variety MMFF MM2 MSI Charmm Small Molecules CFF CVFF CFF91 Proteins Nucleic acids Charmm27 Amber Langley The CHARMm Force Field 4
5 The CHARMm Energy Function: Bonded Terms E bond bond-stretching potential energy E 2 = k ( r r ) 0 bond b E θ angle-bending potential energy E θ = θ k ( θ θ ) 2 0 E UB Urey-Bradley term E UB = K ( S S ) 0 UB 2 The CHARMm Energy Function: Bonded Terms E dih dihedral angle potential energy E φ K = φ [1 + cos( nφ δ)] E impr improper dihedral angle potential energy E ω k = ω ( ω ω 2 0 ) 5
6 The CHARMm Energy Function: Nonbonded Terms E elec - electrostatic energy E elec = i j i> j ε rij E vdw - Van der Waals energy q q E vdw = R ε r min ij ij 12 R r min ij ij 6 External Files RTF Residue Topology Files Store information about atom mass, atom type, partial charges, connectivity, internal coordinates, residue definitions PRM parameter files Contain parameters for force constants, equilibrium geometries, van der Waals radii, other data PSF Protein Structure Files Files actually used by CHARMm, force field dependent, contain information from the RTF files, have a hierarchical organization of atoms, residues, segments 6
7 External Files Atoms have different environments N (N peptide N) C (CB aliphatic sp3 C) C (CA aliphatic sp3 C) C (C polar C) NH1 CT1 CT3 O (O carbonyl O) C MASS 10 HS H! thiol hydrogen MASS 11 HE H! for alkene; RHC=CR MASS 20 C C! carbonyl C, peptide backbone MASS 21 CA C! aromatic C MASS 22 CT C! aliphatic sp3 C for CH (missing data here) RESI ALA 0.00 ATOM N NH1-0.47! ATOM HN H 0.31! HN-N ATOM CA CT1 0.07! HB1 ATOM HA HB 0.09! /! HA-CA--CB-HB2 ATOM CB CT3-0.27! \ ATOM HB1 HA 0.09! HB3 ATOM HB2 HA 0.09! O=C ATOM HB3 HA 0.09!! ATOM C C 0.51 ATOM O O BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN IC -C N CA C IC N CA C +N IC +N CA *C O IC CA C +N +CA IC N C *CA CB IC N C *CA HA IC C CA CB HB IC HB1 CA *CB HB IC HB1 CA *CB HB RTF Files Alanine 7
8 RTF Files: H 2 O & Shake RESI TIP ! tip3p water model! generate using noangle nodihedral ATOM OH2 OT ATOM H1 HT ATOM H2 HT BOND OH2 H1 OH2 H2 H1 H2! the last bond is needed for shake ANGLE H1 OH2 H2! required ACCEPTOR OH2 RESI GUA -1.00! O6 ATOM P P 1.50! ATOM O1P ON3-0.78! C6 ATOM O2P ON3-0.78! / \ ATOM O5' ON2-0.57! H1-N1 C5--N7\\ ATOM C5' CN8B -0.08! C8-H8 ATOM H5' HN8 0.09! C2 C4--N9/ ATOM H5'' HN8 0.09! / \\ / \! H21-N2 N3 \ ATOM C4' CN7 0.16! \ ATOM H4' HN7 0.09! H22 \ ATOM O4' ON6B -0.50! \ ATOM C1' CN7B 0.16! O1P H5' H4' O4' \ ATOM H1' HN7 0.09! \ / \ \! -P-O5'-C5'---C4' C1' ATOM N9 NN2B -0.02! \ / \ ATOM C4 CN5 0.26! O2P H5'' C3'--C2' H1' ATOM N2 NN1-0.68! / \ / \ ATOM H21 HN1 0.32! O3' H3'O2' H2'' ATOM H22 HN1 0.35! ATOM N3 NN3G -0.74! H2' ATOM C2 CN ATOM N1 NN2G ATOM H1 HN ATOM C6 CN ATOM O6 ON ATOM C5 CN5G 0.00 ATOM N7 NN ATOM C8 CN ATOM H8 HN ATOM C2' CN7B 0.14 ATOM H2'' HN ATOM O2' ON ATOM H2' HN ATOM C3' CN ATOM H3' HN ATOM O3' ON RTF Files 8
9 RESI GNA -1.00! O6 ATOM P P 1.50! ATOM O1P ON3-0.78! C6 ATOM O2P ON3-0.78! / \ ATOM O5' ON2-0.57! H1-N1 C5--N7\\ ATOM C5' CN8B -0.08! C8-H8 ATOM H5' HN8 0.09! C2 C4--N9/ ATOM H5'' HN8 0.09! / \\ / \! H21-N2 N3 \ ATOM C4' CN7 0.16! \ ATOM H4' HN7 0.09! H22 \ ATOM O4' ON6B -0.50! \ ATOM C1' CN7B 0.16! O1P H5' H4' O4' \ ATOM H1' HN7 0.09! \ / \ \! -P-O5'-C5'---C4' C1' ATOM N9 NN2B -0.02! \ / \ ATOM C4 CN5 0.26! O2P H5'' C3'--C2' H1' ATOM N2 NN1-0.68! / \ / \ ATOM H21 HN1 0.32! O3' H3'N2' H2'' ATOM H22 HN1 0.35! / \ ATOM N3 NN3G -0.74! HN2' HN2'' ATOM C2 CN ATOM N1 NN2G ATOM H1 HN ATOM C6 CN ATOM O6 ON ATOM C5 CN5G 0.00 ATOM N7 NN ATOM C8 CN ATOM H8 HN ATOM C2' CN7B 0.14 ATOM H2'' HN ATOM N2' NN ATOM HN2' HN ATOM HN2''HN ATOM C3' CN ATOM H3' HN ATOM O3' ON Modified RTF File RTF Files Differences between RTF s for single molecules and residues First residue converted to N-terminus NH 3 + Last residue converted to C-terminus CO O Special atoms -C, -O, +N, +H, +CA Refers to atoms in residues preceding (-) or following (+) 9
10 BONDS!V(bond) = Kb(b - b0)**2!kb: kcal/mole/a**2!b0: A!atom type Kb b0! C C ! ALLOW ARO HEM! Heme vinyl substituent (KK, from propene (JCS)) CA CA ! ALLOW ARO! benzene, JES 8/25/ (missing data here) ANGLES!V(angle) = Ktheta(Theta - Theta0)**2!V(Urey-Bradley) = Kub(S - S0)**2!Ktheta: kcal/mole/rad**2!theta0: degrees!kub: kcal/mole/a**2 (Urey-Bradley)!S0: A!!atom types Ktheta Theta0 Kub S0! CA CA CA ! ALLOW ARO! JES 8/25/89 CE1 CE1 CT Parameter Files AMBER Force Field 10
11 Consistent Valence Force Field The Power of the Force Field Approach 1) Force field-based simulations can handle large systems, are several orders of magnitude faster (and cheaper) than quantum-based calculations. 2) The analysis of the energy contributions can be done at the level of individual or classes of interactions. 3) Modification of the energy expression to bias the calculation. 11
12 Limitations of the Force Field Approach Applications beyond the capability of classical force field methods include: Electronic transitions (photon absorption). Electron transport phenomena. Proton transfer (acid/base reactions). 12
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
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,
Force Fields for Classical Molecular Dynamics simulations of Biomolecules. Emad Tajkhorshid
Force Fields for Classical Molecular Dynamics simulations of Biomolecules Emad Tajkhorshid Theoretical and Computational Biophysics Group, Beckman Institute Departments of Biochemistry and Pharmacology,
TOPOLOGIES AND FORCE FIELD PARAMETERS FOR NITROXIDE SPIN LABELS
TOPOLOGIES AND FORCE FIELD PARAMETERS FOR NITROXIDE SPIN LABELS 1. Introduction The force field used in these studies is the CHARMM19 (Chemistry at HARvard Molecular Mechanics) extended atom force field
Dihedral Angles. Homayoun Valafar. Department of Computer Science and Engineering, USC 02/03/10 CSCE 769
Dihedral Angles Homayoun Valafar Department of Computer Science and Engineering, USC The precise definition of a dihedral or torsion angle can be found in spatial geometry Angle between to planes Dihedral
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
MD EXPERIMENT. Initialization : Relaxation : Equilibration : Productive run: Analysis : building molecular system; initial coordinates
MD EXPERIMENT Initialization : Relaxation : building molecular system; initial coordinates the system is brought to a state where actual Equilibration : Productive run: Analysis : dynamics can be performed
Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450
Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450 Julianna Oláh, 1 Adrian J. Mulholland* and Jeremy N. Harvey* School of
Why Proteins Fold? (Parts of this presentation are based on work of Ashok Kolaskar) CS490B: Introduction to Bioinformatics Mar.
Why Proteins Fold? (Parts of this presentation are based on work of Ashok Kolaskar) CS490B: Introduction to Bioinformatics Mar. 25, 2002 Molecular Dynamics: Introduction At physiological conditions, the
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
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
Force Fields for Classical Molecular Dynamics simulations of Biomolecules. Emad Tajkhorshid
Force Fields for Classical Molecular Dynamics simulations of Biomolecules Emad Tajkhorshid Beckman Institute Departments of Biochemistry Center for Biophysics and Computational Biology University of Illinois
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
Figure 1. Molecules geometries of 5021 and Each neutral group in CHARMM topology was grouped in dash circle.
Project I Chemistry 8021, Spring 2005/2/23 This document was turned in by a student as a homework paper. 1. Methods First, the cartesian coordinates of 5021 and 8021 molecules (Fig. 1) are generated, in
Electronic Supplementary Information for A molecular dynamics investigation on the cross-linking and physical properties of epoxy-based materials
Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2014 Electronic Supplementary Information for A molecular dynamics investigation on the cross-linking
Computational Biology & Computational Medicine
Computational Biology & Computational Medicine Homayoun Valafar Outline Why proteins? What are proteins? How do we compute them? How do we use computational approaches? Why Proteins? Molecular basis of
The Molecular Dynamics Method
H-bond energy (kcal/mol) - 4.0 The Molecular Dynamics Method Fibronectin III_1, a mechanical protein that glues cells together in wound healing and in preventing tumor metastasis 0 ATPase, a molecular
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
Force Fields for MD simulations
Force Fields for MD simulations Topology/parameter files Where do the numbers an MD code uses come from? ow to make topology files for ligands, cofactors, special amino acids, ow to obtain/develop missing
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
CHEM 498Q / CHEM 630Q: Molecular Modeling of Proteins TUTORIAL #3a: Empirical force fields
Department of Chemistry and Biochemistry, Concordia University! page 1 of 6 CHEM 498Q / CHEM 630Q: Molecular Modeling of Proteins TUTORIAL #3a: Empirical force fields INTRODUCTION The goal of this tutorial
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
CHEM 498Q / CHEM 630Q: Molecular Modeling of Proteins TUTORIAL #3a: Empirical force fields
Department of Chemistry and Biochemistry, Concordia University page 1 of 6 CHEM 498Q / CHEM 630Q: Molecular Modeling of Proteins TUTORIAL #3a: Empirical force fields INTRODUCTION The goal of this tutorial
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,
Parameterizing a Novel Residue
University of Illinois at Urbana-Champaign Luthey-Schulten Group, Department of Chemistry Theoretical and Computational Biophysics Group Computational Biophysics Workshop Parameterizing a Novel Residue
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
Molecular Simulation II. Classical Mechanical Treatment
Molecular Simulation II Quantum Chemistry Classical Mechanics E = Ψ H Ψ ΨΨ U = E bond +E angle +E torsion +E non-bond Jeffry D. Madura Department of Chemistry & Biochemistry Center for Computational Sciences
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)
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
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
The Force Field Toolkit (fftk)
Parameterizing Small Molecules Using: The Force Field Toolkit (fftk) Christopher G. Mayne, Emad Tajkhorshid Beckman Institute for Advanced Science and Technology University of Illinois, Urbana-Champaign
read rtf card append * Initial topology guesses generated by * CHARMM General Force Field (CGenFF) program version 0.9.
Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2014 * Stream file for dehydro-amino residues * If using these parameters please cite: * Turpin,
6.#Molecular#Mechanics#and# Molecular#Dynamics#Simula5on# MOLECULAR)MECHANICS) Determinant#of#Structure#(or#Lack#of#It)# Water#
BIOCH 755: Biochemistry I Fall 2015 6.#Molecular#Mechanics#and# Molecular#Dynamics#Simula5on# Jianhan#Chen# Office#Hour:#M#1:30?2:30PM,#Chalmers#034# Email:#jianhanc@ksu.edu# Office:#785?2518# Determinant#of#Structure#(or#Lack#of#It)#
Determining Force Fields
University of Illinois at Urbana-Champaign Department of Chemistry - Luthey-Schulten Group Beckman Institute for Advanced Science and Technology Theoretical and Computational Biophysics Group Summer School
Applications of Molecular Dynamics
June 4, 0 Molecular Modeling and Simulation Applications of Molecular Dynamics Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tohru
Molecular Dynamics, Monte Carlo and Docking. Lecture 21. Introduction to Bioinformatics MNW2
Molecular Dynamics, Monte Carlo and Docking Lecture 21 Introduction to Bioinformatics MNW2 Allowed phi-psi angles Red areas are preferred, yellow areas are allowed, and white is avoided 2.3a Hamiltonian
Molecular Simulation II
Molecular Simulation II Quantum Chemistry Classical Mechanics E = Ψ H Ψ ΨΨ U = E bond +E angle +E torsion +E non-bond Jeffry D. Madura Department of Chemistry & Biochemistry Center for Computational Sciences
Determining Force Fields
University of Illinois at Urbana-Champaign Theoretical and Computational Biophysics Group Summer School 2004 - University of Western Australia, Perth Determining Force Fields Rommie Amaro Brijeet Dhaliwal
Solutions to Assignment #4 Getting Started with HyperChem
Solutions to Assignment #4 Getting Started with HyperChem 1. This first exercise is meant to familiarize you with the different methods for visualizing molecules available in HyperChem. (a) Create a molecule
1 Contents. 1. Contents i. 1. Introduction Forcefields 9
1 Contents 1. Contents i 1. Introduction 1 Who should use this documentation.................. 2 What can simulation engines do?.................... 2 Energy minimization........................... 2 Molecular
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
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
Molecular Simulation III
Molecular Simulation III Jeffry D. Madura Department of Chemistry & Biochemistry Center for Computational Sciences Duquesne University Time and Length Scales Tamar Schlick s Biomolecular Structure and
Multiscale Materials Modeling
Multiscale Materials Modeling Lecture 09 Quantum Mechanics/Molecular Mechanics (QM/MM) Techniques Fundamentals of Sustainable Technology These notes created by David Keffer, University of Tennessee, Knoxville,
Energy functions and their relationship to molecular conformation. CS/CME/BioE/Biophys/BMI 279 Oct. 3 and 5, 2017 Ron Dror
Energy functions and their relationship to molecular conformation CS/CME/BioE/Biophys/BMI 279 Oct. 3 and 5, 2017 Ron Dror Outline Energy functions for proteins (or biomolecular systems more generally)
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
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
Chapter 11 Molecular Mechanics
Chapter 11 Molecular Mechanics Molecular Mechanics uses an analytical, differentiable, and relatively simple potential energy function, (R), for describing the interactions between a set of atoms specified
The Molecular Dynamics Method
H-bond energy (kcal/mol) - 4.0 The Molecular Dynamics Method Fibronectin III_1, a mechanical protein that glues cells together in wound healing and in preventing tumor metastasis 0 ATPase, a molecular
Molecular Modelling. part of Bioinformatik von RNA- und Proteinstrukturen. Sonja Prohaska. Leipzig, SS Computational EvoDevo University Leipzig
part of Bioinformatik von RNA- und Proteinstrukturen Computational EvoDevo University Leipzig Leipzig, SS 2011 Protein Structure levels or organization Primary structure: sequence of amino acids (from
Molecular Dynamics, Monte Carlo and Docking. Lecture 21. Introduction to Bioinformatics MNW2
Molecular Dynamics, Monte Carlo and Docking Lecture 21 Introduction to Bioinformatics MNW2 If you throw up a stone, it is Physics. If you throw up a stone, it is Physics. If it lands on your head, it is
HOMOLOGY MODELING. The sequence alignment and template structure are then used to produce a structural model of the target.
HOMOLOGY MODELING Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental
Nanotube AFM Probe Resolution
Influence of Elastic Deformation on Single-Wall Carbon Nanotube AFM Probe Resolution Ian R. Shapiro, Santiago D. Solares, Maria J. Esplandiu, Lawrence A. Wade, William A. Goddard,* and C. Patrick Collier*
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
DISCRETE TUTORIAL. Agustí Emperador. Institute for Research in Biomedicine, Barcelona APPLICATION OF DISCRETE TO FLEXIBLE PROTEIN-PROTEIN DOCKING:
DISCRETE TUTORIAL Agustí Emperador Institute for Research in Biomedicine, Barcelona APPLICATION OF DISCRETE TO FLEXIBLE PROTEIN-PROTEIN DOCKING: STRUCTURAL REFINEMENT OF DOCKING CONFORMATIONS Emperador
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
Revised CHARMM Force Field Parameters for Iron- Containing Cofactors of Photosystem II
WWW.C-CHEM.ORG FULL PAPER Revised CHARMM Force Field Parameters for Iron- Containing Cofactors of Photosystem II Suliman Adam, [a] Michaela Knapp-Mohammady, [b] Jun Yi, [c] and Ana-Nicoleta Bondar [a]
COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationssOverview with Details on Alkane and Benzene Compounds
7338 J. Phys. Chem. B 1998, 102, 7338-7364 COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationssOverview with Details on Alkane and Benzene Compounds H. Sun Molecular Simulations
Molecular Mechanics / ReaxFF
Molecular Dynamics simulations Lecture 09: Molecular Mechanics / ReaxFF Dr. Olli Pakarinen University of Helsinki Fall 2012 Lecture notes based on notes by Dr. Jani Kotakoski, 2010 CONTENTS Molecular mechanics
Free Radical-Initiated Unfolding of Peptide Secondary Structure Elements
Free Radical-Initiated Unfolding of Peptide Secondary Structure Elements Thesis of the Ph.D. Dissertation by Michael C. Owen, M.Sc. Department of Chemical Informatics Faculty of Education University of
Biomolecular modeling I
2016, December 6 Biomolecular structure Structural elements of life Biomolecules proteins, nucleic acids, lipids, carbohydrates... Biomolecular structure Biomolecules biomolecular complexes aggregates...
TOPOLOGY FILE TUTORIAL
University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Theoretical and Computational Biophysics Group TOPOLOGY FILE TUTORIAL Aaron Oakley Timothy Isgro Yi Wang
3. Solutions W = N!/(N A!N B!) (3.1) Using Stirling s approximation ln(n!) = NlnN N: ΔS mix = k (N A lnn + N B lnn N A lnn A N B lnn B ) (3.
3. Solutions Many biological processes occur between molecules in aqueous solution. In addition, many protein and nucleic acid molecules adopt three-dimensional structure ( fold ) in aqueous solution.
A Molecular Dynamics Simulation of a Homogeneous Organic-Inorganic Hybrid Silica Membrane
A Molecular Dynamics Simulation of a Homogeneous Organic-Inorganic Hybrid Silica Membrane Supplementary Information: Simulation Procedure and Physical Property Analysis Simulation Procedure The molecular
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
Born-Oppenheimer Approximation
Born-Oppenheimer Approximation Adiabatic Assumption: Nuclei move so much more slowly than electron that the electrons that the electrons are assumed to be obtained if the nuclear kinetic energy is ignored,
Computer simulation of Biological Systems
UNIVERSITY OF TRENTO Faculty of Mathematical, Physical and Natural Sciences Physics Department Ph.D. Thesis in Physics Computer simulation of Biological Systems Supervisors: Dr. Maurizio Dapor Dr. Giovanni
Biomolecular modeling I
2015, December 15 Biomolecular simulation Elementary body atom Each atom x, y, z coordinates A protein is a set of coordinates. (Gromacs, A. P. Heiner) Usually one molecule/complex of interest (e.g. protein,
Supporting information of Self-Assembly, Structure and Pi- Conjugation at the Interface of Poly-3-Hexylthiophene and Carbon Nanotubes
Supporting information of Self-Assembly, Structure and Pi- Conjugation at the Interface of Poly-3-Hexylthiophene and Carbon Nanotubes Details of the molecular dynamics simulations and computational procedures
Atomistic Modeling of DNA and Protein Structures
Atomistic Modeling of DNA and Protein Structures George C. Schatz Introduction In this lecture we introduce one of the most commonly used computational tools for studying protein and DNA structure, the
Dominant Paths in Protein Folding
Dominant Paths in Protein Folding Henri Orland SPhT, CEA-Saclay France work in collaboration with P. Faccioli, F. Pederiva, M. Sega University of Trento Henri Orland Annecy meeting 2006 Outline Basic notions
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
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
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
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,
Conformational Geometry of Peptides and Proteins:
Conformational Geometry of Peptides and Proteins: Before discussing secondary structure, it is important to appreciate the conformational plasticity of proteins. Each residue in a polypeptide has three
An Informal AMBER Small Molecule Force Field :
An Informal AMBER Small Molecule Force Field : parm@frosst Credit Christopher Bayly (1992-2010) initiated, contributed and lead the efforts Daniel McKay (1997-2010) and Jean-François Truchon (2002-2010)
Patrick: An Introduction to Medicinal Chemistry 5e Chapter 01
Questions Patrick: An Introduction to Medicinal Chemistry 5e 01) Which of the following molecules is a phospholipid? a. i b. ii c. iii d. iv 02) Which of the following statements is false regarding the
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
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.
Prediction of Young s Modulus of Graphene Sheets by the Finite Element Method
American Journal of Mechanical Engineering, 15, Vol. 3, No. 6, 5-9 Available online at http://pubs.sciepub.com/ajme/3/6/14 Science and Education Publishing DOI:1.1691/ajme-3-6-14 Prediction of Young s
Lecture 12: Solvation Models: Molecular Mechanics Modeling of Hydration Effects
Statistical Thermodynamics Lecture 12: Solvation Models: Molecular Mechanics Modeling of Hydration Effects Dr. Ronald M. Levy ronlevy@temple.edu Bare Molecular Mechanics Atomistic Force Fields: torsion
Dynamics. capacities of. (A.I.1) (E b ), bond. E total stretching (A.I.2) (A.I.3) A.I.1. Ebond force (A.I.4) (A.I.5)
Thermodynamics of liquids: Standard d molar entropies and heat capacities of common solvents from 2PT Molecular Dynamics Tod A Pascal, Shiang-Tai Lin and William A Goddard III Supplementary Materials Appendix
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
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
Rotamers in the CHARMM19 Force Field
Appendix A Rotamers in the CHARMM19 Force Field The people may be made to follow a path of action, but they may not be made to understand it. Confucius (551 BC - 479 BC) ( ) V r 1 (j),r 2 (j),r 3 (j),...,r
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
Advanced Quantum Chemistry III: Part 6
Advanced Quantum Chemistry III: Part 6 Norio Yoshida Kyushu University Last updated 16-1-6 2015 Winter Term 1 Quantum Chemistry for Condensed Phase Liquid phase Solid phase Biological systems 2 Divide
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
The chemical bond The topological approach
The chemical bond The topological approach Julia Contreras-García 1. Why and how studying chemical bonds? 2. Topology a) critical points b) topological partitions 3. Chemical functions a) electron density
/2Mα 2 α + V n (R)] χ (R) = E υ χ υ (R)
![/2Mα 2 α + V n (R)] χ (R) = E υ χ υ (R)](/thumbs/75/72875547.jpg "/2Mα 2 α + V n (R)] χ (R) = E υ χ υ (R)")
Spectroscopy: Engel Chapter 18 XIV 67 Vibrational Spectroscopy (Typically IR and Raman) Born-Oppenheimer approx. separate electron-nuclear Assume elect-nuclear motion separate, full wave fct. ψ (r,r) =
Organic Chemistry 112 A B C - Syllabus Addendum for Prospective Teachers
Chapter Organic Chemistry 112 A B C - Syllabus Addendum for Prospective Teachers Ch 1-Structure and bonding Ch 2-Polar covalent bonds: Acids and bases McMurry, J. (2004) Organic Chemistry 6 th Edition
Carbon Compounds. Chemical Bonding Part 2
Carbon Compounds Chemical Bonding Part 2 Introduction to Functional Groups: Alkanes! Alkanes Compounds that contain only carbons and hydrogens, with no double or triple bonds.! Alkyl Groups A part of a
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
Atomic and Molecular Dimensions
1 Atomic and Molecular Dimensions Equilibrium Interatomic Distances When two atoms approach each other, their positively charged nuclei and negatively charged electronic clouds interact. The total interaction
Journal Name ARTICLE. ESI for: CHARMM force field parameterization protocol for selfassembling peptide amphiphiles: The Fmoc moiety
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2016Please do not adjust margins ESI for: Received 00th January 20xx, Accepted 00th
COSMO-RS Theory. The Basics
Theory The Basics From µ to properties Property µ 1 µ 2 activity coefficient vapor pressure Infinite dilution Gas phase Pure compound Pure bulk compound Partition coefficient Phase 1 Phase 2 Liquid-liquid
Density Functional Theory
Density Functional Theory March 26, 2009 ? DENSITY FUNCTIONAL THEORY is a method to successfully describe the behavior of atomic and molecular systems and is used for instance for: structural prediction
Structure Determination by NMR Spectroscopy #3-1
Structure Determination by NMR Spectroscopy #3-1 3. Computational methods in NMR-spectroscopy 3.1 Nomenclature of proteins and nucleic acids 3.1.1. Classification of structural relationships between molecules
Supplementary Material for A Hybrid Potential Simulation of the Acylation of Enterococcus faecium L,D-transpeptidase by Carbapenems
Supplementary Material for A Hybrid Potential Simulation of the Acylation of Enterococcus faecium L,D-transpeptidase by Carbapenems Nicholus Bhattacharjee 1, Martin J. Field 1 Jean-Pierre Simorre 2, Michel