Combining Quantum Mechanics and Molecular Mechanics. Some Recent Progresses in QM/MM Methods (eBook)

Sylvio Canuto (Herausgeber)

eBook Download: PDF | EPUB

2010 | 1. Auflage
432 Seiten
Elsevier Science (Verlag)
978-0-12-380899-8 (ISBN)

Infos

Advances in Quantum Chemistry presents surveys of current developments in this rapidly developing field. With invited reviews written by leading international researchers, each presenting new results, it provides a single vehicle for following progress in this interdisciplinary area.

* Publishes articles, invited reviews and proceedings of major international conferences and workshops
* Written by leading international researchers in quantum and theoretical chemistry
* Highlights important interdisciplinary developments

Inhalt

Cover 1
Editorial Board 3
Titlte page 
4 
Copyright page 5
Contents 6
Preface 10
Contributors 14
CHAPTER 1 18
Implementing Quantum Mechanics into Molecular Mechanics-Combined QM/MM Modeling Methods 18
Introduction 18
Partition of a System into QM and MM Parts 20
Treatment of the QM/MM Boundary 21
Interactions in the QM/MM Coupling 24
Computational Aspects 27
Future Prospects 29
References 30
CHAPTER 2 34
Extending the Range of Computational Spectroscopy by QM/MM Approaches: Time-Dependent and Time-Independent Routes 34
Introduction 35
The QM/MM Framework for Spectroscopic Studies 36
Applications 54
Final Remarks and Conclusions 70
Acknowledgments 71
References 71
CHAPTER 3 76
Use of the Average Solvent Potential Approach in the Study of Solvent Effects 76
Introduction 77
The Mean Field Approximation 78
The ASEP/MD Method 80
Validity of the Mean Field Approximation 88
Examples of Applications 91
Summary 111
References 112
CHAPTER 4 116
QM/MM Approaches to the Electronic Spectra of Hydrogen-Bonding Systems with Connection to Many-Body Decomposition Schemes 116
Introduction 117
Theoretical Methods 118
Applications 136
Final Remarks and Conclusions 157
References 158
CHAPTER 5 162
Molecular Dynamics of Polypeptides and Their Inclusion Compounds with rbeta-Cyclodextrin in Aqueous Solution Using DC-SCC-DFTB/UFF Approach 162
Introduction 163
Theoretical Approach 164
Polypeptides and their inclusion compounds with rbeta-cyclodextrin in aqueous solution 174
Final Remarks 194
Acknowledgments 195
References 195
CHAPTER 6 198
Computer Simulations of Photobiological Processes: The Effect of the Protein Environment 198
Introduction 199
Theory 199
Applications 220
Final Remarks and Conclusions 227
References 228
CHAPTER 7 230
Ab Initio Quantum Mechanical Charge Field Molecular Dynamics-A Nonparametrized First-Principle Approach to Liquids and Solutions 230
Introduction 231
Methodology 233
Application of the QMCF MD Methodology 244
Outlook 259
References 261
CHAPTER 8 264
Applications of Mixed-Quantum/Classical Trajectories to the Study of Nuclear Quantum Effects in Chemical Reactions and Vibrational Relaxation Processes 264
Introduction 264
Mixed-Q/C Propagations Schemes 266
Hydrogen Transfer in Gas Phase 272
Proton and Hydride Transfer in Condensed Phase 277
Vibrational Energy Relaxation 287
Concluding Remarks 295
Acknowledgments 295
References 295
CHAPTER 9 300
Development of a Quantum Chemical Method Combined with a Theory of Solutions-Free-Energy Calculation for Chemical Reactions by Condensed Phase Simulations 300
Introduction 301
Quantum Chemical Approach 306
Theory of Solutions 318
Combination of Quantum Chemical Method with Theory of Solutions 343
Conclusions and Perspectives 364
References 366
CHAPTER 10 370
A Guide to QM/MM Methodology and Applications 370
Introduction 371
Basic Concepts of QM/MM Methodology 372
QM/MM Optimization Techniques for Potential Energy Surfaces 384
QM/MM Approaches to the Simulation of Kinetics and Thermodynamics in the Condensed Phase 390
Beyond Conventional QM/MM Dynamics: Explicit Account of Nuclear Quantum Effects 402
Summary of Alternatives to QM/MM Methodology 405
Applications to Biochemical Simulation 406
Conclusions and Perspectives 409
Acknowledgments 410
References 410
Index 418

Textauszug

Chapter 1

Implementing Quantum Mechanics into Molecular Mechanics—Combined QM/MM Modeling Methods

Yaoquan [e-mail]; Aatto [e-mail]    a Biophysical and Theoretical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
b Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden

1 INTRODUCTION

Quantum chemistry is a very powerful tool to study the properties of molecules and their reactions. The recent years’ development in quantum chemistry methods, especially that of density functional theory (DFT) methods [1], has made it possible for quantum chemistry calculations to reach accuracies comparable to those obtained in experiments for molecules of moderate sizes. The rapid development of computer technologies has greatly encouraged chemists to use quantum chemistry to understand, model, and predict molecular properties and their reactions, properties of nanometer materials, and reactions and processes taking place in biological systems [2–4].

To develop quantum chemistry methods, capable of treating large or complicated systems, has been one of the important subjects in quantum chemistry. In the early days, quantum chemists developed mostly semiempirical molecular orbital methods for the study of large systems [5–7]. These methods often involve many empirical parameters that are optimized by reproducing the properties of some reference molecules. Usually, the parameters are accurate for the systems they are parameterized for. For many properties, such as the relative energies of different conformations of a large molecule, the bonding energy, and structure of a hydrogen-bonded system, the results from semiempirical calculations are not reliable. This limits their applications to large systems, especially those where hydrogen bonds are important. In recent years, many first-principles quantum chemistry methods aimed for large molecular systems have been introduced [8–11].

For large systems, pure ab initio calculations are still very expensive. In many practical applications, we are only interested in the properties of a few molecules of a system or part of a large molecule. Many calculations are therefore only limited to these molecules or part of a large molecule. These studies can provide us with very useful information, but there are often cases where the effects from the surrounding molecules or the remaining part of a large molecule cannot be neglected. Typical examples involve the properties of a solute molecule in a solvent. If we use quantum chemistry to calculate the properties of the solute molecule and neglect the effects from the solvent molecules, the properties obtained correspond only to those of the isolated solute molecule. Another example is the enzymatic reactions occurring in biological systems. Usually, the active center of an enzyme consists typically of about 100 atoms or more, which already reaches the computational limit of many high-level quantum chemistry methods. Using a smaller cluster to represent an active center and studying it carefully with high-level quantum chemistry methods is the standard way usually carried out. However, such an approach may not be adequate since the surrounding atoms could obviously affect the barriers obtained [12,13]. Usually, the surrounding atoms can often stabilize the reactants and products and lower the barrier of a reaction. Without the surrounding atoms, the barrier calculated according to a smaller cluster becomes often overestimated.

In conventional quantum chemistry calculations, the effects from the surrounding atoms of a molecule or cluster are often recovered by using the polarizable continuum model (PCM) [14] in which the surrounding atoms are represented by a dielectric continuum with dielectric constant ε. In PCM, the microscopic structure of the surrounding atoms of a molecule is not considered, thus it is not adequate in cases where the structure of the surrounding atoms is important.

Combined quantum mechanical and molecular mechanical (QM/MM) methods, pioneered by Warshel and Levitt [15], can be considered as a compromise between the full QM calculation of a system and the QM treatment of part of the system with the surroundings being modeled by the PCM. In combined QM/MM methods [15–17], the surroundings of a molecule or cluster are explicitly represented as atoms, but their effects are modeled by an MM force field. Because all the atoms are explicitly represented and the interactions between the atoms are considered, the results obtained from a combined QM/MM calculation could be more accurate than those from a QM calculation with the PCM. Compared with the full QM treatment of a system, a combined QM/MM calculation is much faster since only a small part of the system is treated quantum mechanically. Therefore, combined QM/MM methods have the potentials of studying the properties and processes happening at the electronic scale in very large systems.

In the last decade, much effort has been made in developing reliable and accurate combined QM/MM methods, especially in the treatment of the boundary and interactions between the QM and MM parts [18–33]. There are increasing publications each year in applying the QM/MM methods to larger and more complicated systems. The purpose of this chapter is to introduce the reader to the area of combined QM/MM methods. We will not, however, consider different applications, but rather consider methodological aspects in the area, with the focus on the progress made in the last decade in the treatment of the QM/MM boundary and the QM/MM coupling.

2 PARTITION OF A SYSTEM INTO QM AND MM PARTS

In a combined QM/MM method, the system to be studied is partitioned into two parts; a QM part and an MM part (see Figure 1.1) [17]. The QM part has small number of atoms. It may be a molecule (such as a solute molecule in a solution) or several molecules, a fragment (or part) of a large molecule or a molecular complex (such as the active center of an enzymatic catalyzed reaction). The QM part corresponds to what we need to study in detail. Atoms in this part are explicitly expressed as electrons and nuclei and are described quantum mechanically. When a combined QM/MM method is used to study a system involving charge transfer, electron excitations, or chemical reactions, the corresponding region is always treated quantum mechanically. That is, the region is always included in the QM part.

Figure 1.1 The combined QM/MM model.

The MM part is the “environment” to the QM part. Usually, it has much larger number of atoms than the QM part. This part is most often “nonreactive” and is treated by using a classical MM force field. “Nonreactive” also means that there is no charge transfer or other “chemical” exchange between the QM and MM parts.

For a large molecule, it becomes necessary to divide it into a QM part and an MM part. This division is often quite natural, especially for a large biomolecule where the main interest may be in the active site or a reaction center. In such a case, there are chemical bonds connecting the QM and the MM parts. Because the MM part is treated by a classical force field, the properties and electron densities of the QM atoms bonded to the MM atoms may change drastically. Therefore, the intermediate region between the two parts should be treated so that the effects from partitioning the QM and the MM parts across the bonds on the QM atoms are minimized. In practice, well-localized single bonds are terminated and the valences are satisfied on the QM atoms. The reason to choose well-localized single bonds is to make the theoretical treatment easier. Saturation of the valences on the QM atoms is done to keep the chemical properties of these atoms unchanged.

The choice of the QM/MM boundary can affect greatly the accuracy of a combined QM/MM calculation, such as the charge distribution of the QM part and the overall energy of the system, especially when the QM/MM boundary is within a molecule. It has been found that MM atoms with large magnitudes of charges close to the QM/MM boundary can lead to significant errors in energy [34]. Therefore, care must be taken when choosing a QM/MM boundary.

3 TREATMENT OF THE QM/MM BOUNDARY

There are several ways to treat the QM/MM boundary when a large molecule is divided into a QM part and an MM part [20–33]. Among the widely used ways are those using a hybrid orbital or a link atom to satisfy the valence of the QM atom on a QM/MM bond. In the early work of Warshel and Levitt [15], one single hybrid atomic orbital was placed on each MM atom, originally connected to a QM atom. These hybrid atomic orbitals are then involved in the calculation of the QM part to satisfy the valences. Rivail and coworkers [20,35–37] also used hybrid atomic orbitals in their localized self-consistent field (LSCF) method to treat the QM part. They assumed that the bond connecting a QM atom and an MM atom could be described by a “strictly localized bond orbital (SLBO),” considered to be one of the molecular orbitals of the QM part. However, the orbital is assumed to be “frozen” and therefore is not involved in the QM calculation. This is implemented by letting all the molecular orbitals (MOs), appearing in...

Produkt-Details

• Erscheint lt. Verlag: 14.6.2010
• Mitarbeit: Herausgeber (Serie): John R. Sabin
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Chemie ► Physikalische Chemie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Atom- / Kern- / Molekularphysik
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Quantenphysik
• Themenwelt: Technik
• ISBN-10: 0-12-380899-5 / 0123808995
• ISBN-13: 978-0-12-380899-8 / 9780123808998