Molecular Modeling of Geochemical Reactions - An Introduction

Informationen zum Autor Professor James David Kubicki, Department of Geosciences, The Pennsylvania State University, USA Dr Kubicki has 25 years of experience in computational geochemistry across a variety of sub-disciplines. He has published on melts and glasses, high-pressure mineral physics, aqueous geochemistry, organic geochemistry, environmental geochemistry, biogeochemistry and isotopic geochemistry. He has been an editor of three books, two on computational geochemistry and one on geochemical kinetics. Dr Kubicki has been a professor at The Pennsylvania State University for 15 years and has taught about computational geochemistry in all of his graduate courses. In addition, he has participated in numerous multi-disciplinary research projects and mentored graduate and undergraduate students on computational geochemistry research methods. He has organized two workshops on methods and applications in computational geochemistry. Klappentext Molecular processes in nature affect human health, the availability of resources and the Earth's climate. Molecular modelling is a powerful and versatile toolbox that complements experimental data and provides insights where direct observation is not currently possible.Molecular Modeling of Geochemical Reactions: An Introduction applies computational chemistry to geochemical problems. Chapters focus on geochemical applications in aqueous, petroleum, organic, environmental, bio- and isotope geochemistry, covering the fundamental theory, practical guidance on applying techniques, and extensive literature reviews in numerous geochemical sub-disciplines.Topics covered include:* Theory and Methods of Computational Chemistry* Force Field Application and Development* Computational Spectroscopy* Thermodynamics* Structure Determination* Geochemical KineticsThis book will be of interest to graduate students and researchers looking to understand geochemical processes on a molecular level. Novice practitioners of molecular modelling, experienced computational chemists, and experimentalists seeking to understand this field will all find information and knowledge of use in their research. Zusammenfassung Molecular processes in nature affect human health, the availability of resources and the Earth s climate. Molecular modelling is a powerful and versatile toolbox that complements experimental data and provides insights where direct observation is not currently possible. Inhaltsverzeichnis List of Contributors xi Preface xiii 1 Introduction to the Theory and Methods of Computational Chemistry 1 David M. Sherman 1.1 Introduction 1 1.2 Essentials of Quantum Mechanics 2 1.2.1 The Schrödinger Equation 4 1.2.2 Fundamental Examples 4 1.3 Multielectronic Atoms 7 1.3.1 The Hartree and Hartree-Fock Approximations 7 1.3.2 Density Functional Theory 13 1.4 Bonding in Molecules and Solids 17 1.4.1 The Born-Oppenheimer Approximation 17 1.4.2 Basis Sets and the Linear Combination of Atomic Orbital Approximation 18 1.4.3 Periodic Boundary Conditions 20 1.4.4 Nuclear Motions and Vibrational Modes 21 1.5 From Quantum Chemistry to Thermodynamics 22 1.5.1 Molecular Dynamics 24 1.6 Available Quantum Chemistry Codes and Their Applications 27 References 28 2 Force Field Application and Development 33 Marco Molinari, Andrey V. Brukhno, Stephen C. Parker, and Dino Spagnoli 2.1 Introduction 33 2.2 Potential Forms 35 2.2.1 The Non-bonded Interactions 35 2.2.2 The Bonded Interactions 37 2.2.3 Polarisation Effects 37 2.2.4 Reactivity 39 2.2.5 Fundamentals of Coarse Graining 40 2.3 Fitting Procedure 42 2.3.1 Combining Rules Between Unlike Species 42 2.3.2 Optimisation Procedures for All-Atom Force Fields 43 2.3.3 Deriving CG Fo...

List of contents

List of Contributors xi
 
Preface xiii
 
1 Introduction to the Theory and Methods of Computational Chemistry 1
David M. Sherman
 
1.1 Introduction 1
 
1.2 Essentials of Quantum Mechanics 2
 
1.2.1 The Schrödinger Equation 4
 
1.2.2 Fundamental Examples 4
 
1.3 Multielectronic Atoms 7
 
1.3.1 The Hartree and Hartree-Fock Approximations 7
 
1.3.2 Density Functional Theory 13
 
1.4 Bonding in Molecules and Solids 17
 
1.4.1 The Born-Oppenheimer Approximation 17
 
1.4.2 Basis Sets and the Linear Combination of Atomic Orbital Approximation 18
 
1.4.3 Periodic Boundary Conditions 20
 
1.4.4 Nuclear Motions and Vibrational Modes 21
 
1.5 From Quantum Chemistry to Thermodynamics 22
 
1.5.1 Molecular Dynamics 24
 
1.6 Available Quantum Chemistry Codes and Their Applications 27
 
References 28
 
2 Force Field Application and Development 33
Marco Molinari, Andrey V. Brukhno, Stephen C. Parker, and Dino Spagnoli
 
2.1 Introduction 33
 
2.2 Potential Forms 35
 
2.2.1 The Non-bonded Interactions 35
 
2.2.2 The Bonded Interactions 37
 
2.2.3 Polarisation Effects 37
 
2.2.4 Reactivity 39
 
2.2.5 Fundamentals of Coarse Graining 40
 
2.3 Fitting Procedure 42
 
2.3.1 Combining Rules Between Unlike Species 42
 
2.3.2 Optimisation Procedures for All-Atom Force Fields 43
 
2.3.3 Deriving CG Force Fields 45
 
2.3.4 Accuracy and Limitations of the Fitting 47
 
2.3.5 Transferability 48
 
2.4 Force Field Libraries 48
 
2.4.1 General Force Fields 48
 
2.4.2 Force Field Libraries for Organics: Biomolecules with Minerals 49
 
2.4.3 Potentials for the Aqueous Environment 50
 
2.4.4 Current CGFF Potentials 51
 
2.4.5 Multi-scale Methodologies 53
 
2.5 Evolution of Force Fields for Selected Classes of Minerals 54
 
2.5.1 Calcium Carbonate 54
 
2.5.2 Clay Minerals 56
 
2.5.3 Hydroxides and Hydrates 60
 
2.5.4 Silica and Silicates 60
 
2.5.5 Iron-Based Minerals 61
 
2.6 Concluding Remarks 63
 
References 64
 
3 Quantum-Mechanical Modeling of Minerals 77
Alessandro Erba and Roberto Dovesi
 
3.1 Introduction 77
 
3.2 Theoretical Framework 79
 
3.2.1 Translation Invariance and Periodic Boundary Conditions 79
 
3.2.2 HF and KS Methods 80
 
3.2.3 Bloch Functions and Local BS 81
 
3.3 Structural Properties 82
 
3.3.1 P-V Relation Through Analytical Stress Tensor 83
 
3.3.2 P-V Relation Through Equation of State 85
 
3.4 Elastic Properties 86
 
3.4.1 Evaluation of the Elastic Tensor 86
 
3.4.2 Elastic Tensor-Related Properties 89
 
3.4.3 Directional Seismic Wave Velocities and Elastic Anisotropy 89
 
3.5 Vibrational and Thermodynamic Properties 91
 
3.5.1 Solid-State Thermodynamics 93
 
3.6 Modeling Solid Solutions 95
 
3.7 Future Challenges 98
 
References 99
 
4 First Principles Estimation of Geochemically Important Transition Metal Oxide Properties: Structure and Dynamics of the Bulk, Surface, and Mineral/Aqueous Fluid Interface 107
Ying Chen, Eric Bylaska, and John Weare
 
4.1 Introduction 107
 
4.2 Overview of the Theoretical Methods and Approximations Needed to Perform AIMD Calculations 109
 
4.3 Accuracy of Calculations for Observable Bulk Properties 113
 
4.3.1 Bulk Structural Properties 113
 
4.3.2 Bulk Electronic Structure Properties 118
 
4.4 Calculation of Surface Properties 12

Product details

• Authors: James D Kubicki, James D. Kubicki
• Assisted by: Jame D Kubicki (Editor), James D Kubicki (Editor), James D. Kubicki (Editor), Kubicki James D. (Editor)
• Publisher: Wiley, John and Sons Ltd
• Languages: English
• Product format: Hardback
• Released: 08.07.2016
• EAN: 9781118845080
• ISBN: 978-1-118-84508-0
• No. of pages: 440
• Subjects: Natural sciences, medicine, IT, technology > Chemistry > Organic chemistry; Chemie, Geochemie, Geowissenschaften, chemistry, Earth Sciences, Computational Chemistry u. Molecular Modeling, Computational Chemistry & Molecular Modeling, Boden- u. Geochemie, Soil & Geochemistry, Geochemie, Mineralogie, Geochemistry & Minerology, Molekulare Modellierung