COMPUTATIONAL CHEMISTRY: PRACTICAL APPLICATIONS

By I. KISAM

CONTENTS 1 INTRODUCTION MODELS, APPROXIMATIONS, AND REALITY HOW COMPUTATIONAL CHEMISTRY IS USED BIBLIOGRAPHY PART I BASIC TOPICS 2 FUNDAMENTAL PRINCIPLES ENERGY ELECTROSTATICS ATOMIC UNITS THERMODYNAMICS QUANTUM MECHANICS STATISTICAL MECHANICS 3 AB INITIO METHODS HARTREE±FOCK APPROXIMATION CORRELATION MÙLLER±PLESSET PERTURBATION THEORY CON®GURATION INTERACTION MULTI-CON®GURATIONAL SELF-CONSISTENT FIELD MULTI-REFERENCE CON®GURATION INTERACTION COUPLED CLUSTER QUANTUM MONTE CARLO METHODS NATURAL ORBITALS 3 10 CONCLUSIONS 4 SEMIEMPIRICAL METHODS HUÈCKEL EXTENDED HUÈCKEL PPP CNDO MINDO MNDO INDO ZINDO 4 10 PRDDO 4 13 PM3/TM 4 14 FENSKE±HALL METHOD 4 15 TNDO 4 17 GAUSSIAN THEORY 4 18 RECOMMENDATIONS 5 DENSITY FUNCTIONAL THEORY BASIC THEORY LINEAR SCALING TECHNIQUES PRACTICAL CONSIDERATIONS RECOMMENDATIONS 6 MOLECULAR MECHANICS EXISTING FORCE FIELDS 7 MOLECULAR DYNAMICS AND MONTE CARLO SIMULATIONS MOLECULAR DYNAMICS MONTE CARLO SIMULATIONS SIMULATION OF MOLECULES SIMULATION OF LIQUIDS CONTENTS 8 PREDICTING MOLECULAR GEOMETRY SPECIFYING MOLECULAR GEOMETRY BUILDING THE GEOMETRY COORDINATE SPACE FOR OPTIMIZATION OPTIMIZATION ALGORITHM LEVEL OF THEORY 9 CONSTRUCTING A Z-MATRIX Z-MATRIX FOR A DIATOMIC MOLECULE Z-MATRIX FOR A POLYATOMIC MOLECULE LINEAR MOLECULES RING SYSTEMS 10 USING EXISTING BASIS SETS CONTRACTION SCHEMES NOTATION TREATING CORE ELECTRONS COMMON BASIS SETS STUDIES COMPARING RESULTS 11 MOLECULAR VIBRATIONS HARMONIC OSCILLATOR APPROXIMATION ANHARMONIC FREQUENCIES PEAK INTENSITIES ZERO-POINT ENERGIES AND THERMODYNAMIC CORRECTIONS 12 POPULATION ANALYSIS MULLIKEN POPULATION ANALYSIS LOÈWDIN POPULATION ANALYSIS NATURAL BOND-ORDER ANALYSIS ATOMS IN MOLECULES ELECTROSTATIC CHARGES CHARGES FROM STRUCTURE ONLY CONTENTS 13 OTHER CHEMICAL PROPERTIES METHODS FOR COMPUTING PROPERTIES MULTIPOLE MOMENTS FERMI CONTACT DENSITY ELECTRONIC SPATIAL EXTENT AND MOLECULAR VOLUME ELECTRON A½NITY AND IONIZATION POTENTIAL HYPER®NE COUPLING DIELECTRIC CONSTANT OPTICAL ACTIVITY BIOLOGICAL ACTIVITY 13 10 BOILING POINT AND MELTING POINT 13 11 SURFACE TENSION 13 12 VAPOR PRESSURE 13 13 SOLUBILITY 13 14 DI¨USIVITY 13 15 VISUALIZATION 13 16 CONCLUSIONS 14 THE IMPORTANCE OF SYMMETRY WAVE FUNCTION SYMMETRY TRANSITION STRUCTURES 15 E½CIENT USE OF COMPUTER RESOURCES TIME COMPLEXITY LABOR COST PARALLEL COMPUTERS 16 HOW TO CONDUCT A COMPUTATIONAL RESEARCH PROJECT WHAT DO YOU WANT TO KNOW? HOW ACCURATELY? WHY? HOW ACCURATE DO YOU PREDICT THE ANSWER WILL BE? HOW LONG DO YOU PREDICT THE RESEARCH WILL TAKE? WHAT APPROXIMATIONS ARE BEING MADE? WHICH ARE SIGNI®CANT? CONTENTS PART II ADVANCED TOPICS 17 FINDING TRANSITION STRUCTURES INTRODUCTION MOLECULAR MECHANICS PREDICTION USE OF SYMMETRY OPTIMIZATION ALGORITHMS FROM STARTING AND ENDING STRUCTURES REACTION COORDINATE TECHNIQUES RELAXATION METHODS POTENTIAL SURFACE SCANS 17 10 SOLVENT E¨ECTS 17 11 VERIFYING THAT THE CORRECT GEOMETRY WAS OBTAINED 17 12 CHECKLIST OF METHODS FOR FINDING TRANSITION STRUCTURES 18 REACTION COORDINATES MINIMUM ENERGY PATH LEAST MOTION PATH REACTION DYNAMICS WHICH ALGORITHM TO USE 19 REACTION RATES ARRHENIUS EQUATION RELATIVE RATES HARD-SPHERE COLLISION THEORY TRANSITION STATE THEORY VARIATIONAL TRANSITION STATE THEORY TRAJECTORY CALCULATIONS STATISTICAL CALCULATIONS ELECTRONIC-STATE CROSSINGS 20 POTENTIAL ENERGY SURFACES PROPERTIES OF POTENTIAL ENERGY SURFACES COMPUTING POTENTIAL ENERGY SURFACES FITTING PES RESULTS TO ANALYTIC EQUATIONS FITTING PES RESULTS TO SEMIEMPIRICAL MODELS 21 CONFORMATION SEARCHING GRID SEARCHES MONTE CARLO SEARCHES SIMULATED ANNEALING GENETIC ALGORITHMS DISTANCE-GEOMETRY ALGORITHMS THE FRAGMENT APPROACH CHAIN-GROWTH RULE-BASED SYSTEMS USING HOMOLOGY MODELING 21 10 HANDLING RING SYSTEMS 21 11 LEVEL OF THEORY 21 12 RECOMMENDED SEARCH ALGORITHMS 22 FIXING SELF-CONSISTENT FIELD CONVERGENCE PROBLEMS POSSIBLE RESULTS OF AN SCF PROCEDURE HOW TO SAFELY CHANGE THE SCF PROCEDURE WHAT TO TRY FIRST 23 QM/MM NONAUTOMATED PROCEDURES PARTITIONING OF ENERGY ENERGY SUBTRACTION SELF CONSISTENT METHOD TRUNCATION OF THE QM REGION REGION PARTITIONING OPTIMIZATION INCORPORATING QM TERMS IN FORCE FIELDS 24 SOLVATION PHYSICAL BASIS FOR SOLVATION E¨ECTS EXPLICIT SOLVENT SIMULATIONS ANALYTIC EQUATIONS GROUP ADDITIVITY METHODS CONTINUUM METHODS 25 ELECTRONIC EXCITED STATES SPIN STATES CIS INITIAL GUESS BLOCK DIAGONAL HAMILTONIANS HIGHER ROOTS OF A CI NEGLECTING A BASIS FUNCTION IMPOSING ORTHOGONALITY: DFT TECHNIQUES IMPOSING ORTHOGONALITY: QMC TECHNIQUES PATH INTEGRAL METHODS 25 10 TIME-DEPENDENT METHODS 25 11 SEMIEMPIRICAL METHODS 25 12 STATE AVERAGING 25 13 ELECTRONIC SPECTRAL INTENSITIES 25 14 RECOMMENDATIONS 26 SIZE CONSISTENCY CORRECTION METHODS 27 SPIN CONTAMINATION HOW DOES SPIN CONTAMINATION A¨ECT RESULTS? RESTRICTED OPEN-SHELL CALCULATIONS SPIN PROJECTION METHODS HALF-ELECTRON APPROXIMATION 28 BASIS SET CUSTOMIZATION WHAT BASIS FUNCTIONS DO CREATING BASIS SETS FROM SCRATCH COMBINING EXISTING BASIS SETS CUSTOMIZING A BASIS SET BASIS SET SUPERPOSITION ERROR CONTENTS 29 FORCE FIELD CUSTOMIZATION POTENTIAL PITFALLS ORIGINAL PARAMETERIZATION ADDING NEW PARAMETERS 30 STRUCTURE±PROPERTY RELATIONSHIPS QSPR QSAR 3D QSAR COMPARATIVE QSAR 31 COMPUTING NMR CHEMICAL SHIFTS AB INITIO METHODS SEMIEMPIRICAL METHODS EMPIRICAL METHODS 32 NONLINEAR OPTICAL PROPERTIES NONLINEAR OPTICAL PROPERTIES COMPUTATIONAL ALGORITHMS 33 RELATIVISTIC E¨ECTS RELATIVISTIC TERMS IN QUANTUM MECHANICS EXTENSION OF NONRELATIVISTIC COMPUTATIONAL TECHNIQUES CORE POTENTIALS EXPLICIT RELATIVISTIC CALCULATIONS E¨ECTS ON CHEMISTRY 34 BAND STRUCTURES MATHEMATICAL DESCRIPTION OF ENERGY BANDS COMPUTING BAND GAPS COMPUTING BAND STRUCTURES DESCRIBING THE ELECTRONIC STRUCTURE OF CRYSTALS COMPUTING CRYSTAL PROPERTIES DEFECT CALCULATIONS 35 MESOSCALE METHODS BROWNIAN DYNAMICS DISSIPATIVE PARTICLE DYNAMICS DYNAMIC MEAN-®ELD DENSITY FUNCTIONAL METHOD NONDYNAMIC METHODS VALIDATION OF RESULTS 36 SYNTHESIS ROUTE PREDICTION SYNTHESIS DESIGN SYSTEMS APPLICATIONS OF TRADITIONAL MODELING TECHNIQUES PART III APPLICATIONS 37 THE COMPUTATIONAL CHEMIST'S VIEW OF THE PERIODIC TABLE ORGANIC MOLECULES MAIN GROUP INORGANICS, NOBLE GASES, AND ALKALI METALS TRANSITION METALS LANTHANIDES AND ACTINIDES 38 BIOMOLECULES METHODS FOR MODELING BIOMOLECULES SITE-SPECI®C INTERACTIONS GENERAL INTERACTIONS 39 SIMULATING LIQUIDS PERIODIC BOUNDARY CONDITION SIMULATIONS 40 POLYMERS SIMULATION CONSTRUCTION PROPERTIES 41 SOLIDS AND SURFACES CONTINUUM MODELS CLUSTERS BAND STRUCTURES MOLECULAR DYNAMICS AND MONTE CARLO METHODS AMORPHOUS MATERIALS