DYNAMICS FOR BEGINNERS
CONTENTS CHAPTER INTRODUCTION TO GAUSSIAN AND GAUSSVIEW PACKAGE, GEOMETRY OPTIMIZATION, AND FREQUENCY ANALYSIS INTRODUCTION ELECTRONIC STRUCTURE THEORY BASIS SETS GETTING STARTED WITH GAUSSIAN AND GAUSSVIEW THEORY OF GEOMETRY OPTIMIZATION AND FREQUENCY ANALYSIS GEOMETRY OPTIMIZATION FREQUENCY ANALYSIS EXAMPLE: GEOMETRY OPTIMIZATION OF ETHANOL MOLECULE FREQUENCY ANALYSIS OF ETHANOL MOLECULE DISPLAY THE SPECTRUM POPULATION ANALYSIS EXAMPLE: POPULATION ANALYSIS ON ETHANOL MOLECULE THERMOCHEMISTRY ANALYSIS SPECTROSCOPY ANALYSIS UV?VISIBLE SPECTRA RAMAN SPECTRA IR SPECTRA NMR REFERENCES CHAPTER NATURAL BONDING ORBITAL AND FRONTIER MOLECULAR ORBITAL ANALYSIS NBO CHARGE ANALYSIS HOMO?LUMO ANALYSIS CALCULATION STEPS GLOBAL SCALAR PROPERTIES CHEMICAL POTENTIAL (?) GLOBAL HARDNESS AND SOFTNESS ELECTRONEGATIVITY ACKNOWLEDGMENT THEORY OF HYDROGEN BONDING: ATOMS?IN?MOLECULES, AND NON?COVALENT INTERACTION ANALYSIS THEORY OF HYDROGEN BONDING INTRODUCTION TO MULTIWFN PACKAGE REAL SPACE FUNCTION SUPPORTED BY MULTIWFN INPUT FILE SUPPORTED BY MULTIWFN GRAPHIC FORMATS AND IMAGE SIZE DETAILS ON INPUT FILES AND WAVEFUNCTION TYPES PREPARATION OF WFN, CHK, AND MOL FILE WFN FILE CHK FILE MOL FILE THEORY OF QUANTUM THEORY OF ATOM IN MOLECULES (QTAIM) AND ITS ANALYSIS THEORY OF QTAIM QTAIM ANALYSIS USING PHENOL DIMER AS EXAMPLE THEORY OF NON?COVALENT INTERACTION (NCI) AND ITS ANALYSIS THEORY OF NON?COVALENT INTERACTION (NCI) NCI ANALYSIS USING PHENOL DIMER AS AN EXAMPLE QM/MM METHODS FOR SOLVENT STUDIES 4 1 1 IMPLICIT MODEL OF SOLVATION EXPLICIT SOLVATION MODEL USING EXPLICIT SOLVATION FOR ETHANOL SOLVATION USING THE WATER CLUSTER ONIOM BACKGROUND ONIOM METHOD SETTING?UP ONIOM CALCULATION FOR THE TWO?LAYER PROPANAL ONIOM CALCULATION SET?UP FOR PROPANAL USING THE 3?LAYER MODEL ONIOM 3?LAYER CALCULATION FOR A COMPLEX STRUCTURE OF DEOXYADENOSINE (DAN) TRANSITION STATE ANALYSIS POTENTIAL ENERGY SURFACE INTRINSIC RATE COORDINATE TRANSITION STATE THEORY IMPLEMENTATION IN GAUSSIAN VARIABLE DEFINITIONS ANALYSIS INTRODUCTION TO MOLECULAR DYNAMICS SIMULATION MOLECULAR DYNAMICS SIMULATION GENERATING INPUT FILES IN GAUSSIAN FORCE FIELD PARAMETERS FROM AMBER (ANTECHAMBER) GENERATING SYSTEM BOX IN PACKMOL RUNNING THE LEAP ALGORITHM NAMD SIMULATION SETUP MINIMIZATION HEATING EQUILIBRATION PRODUCTION CASE STUDY OF MOLECULAR DYNAMICS SIMULATION HOMOGENEOUS SYSTEM ACETONE–METHANOL SYSTEM (BENZENE+DECANE) (BENZENE+DODECANE) HETEROGENEOUS SYSTEM (BENZENE–WATER) STRUCTURAL PROPERTIES NONBONDED INTERACTION ENERGY HYDROGEN BONDING DYNAMIC PROPERTY