Advances in Chemical Physics, Volume 150 E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Advances in Chemical Physics
• Sprache: Englisch

Seitenzahl: 600

Veröffentlichungsjahr: 2012

Beschreibung

The Advances in Chemical Physics series--the cutting edge of research in chemical physics The Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series presents contributions from internationally renowned chemists and serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics. This volume explores: * Multidimensional Incoherent Time-Resolved Spectroscopy and Complex Kinetics (Mark A. Berg) * Complex Multiconfigurational Self-Consistent Field-Based Methods to Investigate Electron-Atom/Molecule Scattering Resonances (Kousik Samanta and Danny L. Yeager) * Determination of Molecular Orientational Correlations in Disordered Systems from Diffraction Data (Szilvia Pothoczki, László Temleitner, and László Pusztai) * Recent Advances in Studying Mechanical Properties of DNA (Reza Vafabakhsh, Kyung Suk Lee, and Taekjip Ha) * Viscoelastic Subdiffusion: Generalized Langevin Equation Approach (Igor Goychuk) * Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics (Xiongwu Wu, Ana Damjanovic, and Bernard R. Brooks)

Leseprobe

Contents

Cover

Editorial Board

Title Page

Copyright

Contributors to Volume 150

Preface to the Series

Chapter 1: Multidimensional Incoherent Time-Resolved Spectroscopy and Complex Kinetics

I. Introduction

II. Multidimensional Correlation Functions

III. Spectral Representations of Kinetic Data

IV. Theory of MUPPETS Measurements

V. Experimental Implementation of MUPPETS

VI. Experimental Examples of Analyzing MUPPETS Data

VII. Future of MUPPETS

Acknowledgments

References

Chapter 2: Complex Multiconfigurational Self-Consistent Field-Based Methods to Investigate Electron-Atom/Molecule Scattering Resonances

I. Introduction

II. Theory

III. Applications: Results and Discussions

IV. Summary and Conclusions

Acknowledgments

REFERENCES

Chapter 3: Determination of Molecular Orientational Correlations in Disordered Systems from Diffraction Data

I. Introduction

II. Preparation of Particle Configurations from Diffraction Data

III. Methods for Characterizing Orientational Correlations from Particle Configurations

IV. Summary

Acknowledgments

References

Chapter 4: Recent Advances in Studying Mechanical Properties of DNA

I. Introduction

II. The Worm-Like Chain (WLC) Model for DNA

III. Ensemble Methods for Studying DNA Mechanical Properties

IV. Single-Molecule Techniques to Study DNA Mechanical Properties

V. Different Stretching Modes of DNA

VI. ION and Temperature Effect

VII. Sequence Dependence of DNA Flexibility

VII. The Dynamical Properties of DNA

IX. Outlook

References

Chapter 5: Viscoelastic Subdiffusion: Generalized Langevin Equation Approach

I. Introduction

II. Phenomenological Description of Linear Viscoelasticity in Complex Media

III. Generalized Langevin Equation

IV. Anomalous Dielectric Response and Aging

V. Subdiffusive Escape and Bistable Dynamics

VI. Subdiffusion and Transport in Periodic Potentials

VII. Periodically Driven Subdiffusion and Anomalous Subdiffusive Ratchets

VIII. Summary

Acknowledgments

Appendix A: Standard Hamiltonian Model of Generalized Brownian Motion

Appendix B: Exact Solutions of GLE and Fokker–Planck Equations

References

Chapter 6: Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics

I. The Conformational Search Problem

II. History of the SGMD and SGLD Methods

III. Thermodynamics of SGMD and SGLD

IV. Characteristics of the Self-Guided Langevin Dynamics

V. Applications

IV. Summary

Acknowledgments

References

Author Index

Subject Index

Editorial Board

Moungi G. Bawendi, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

Kurt Binder, Condensed Matter Theory Group, Institut für Physik, Johannes Gutenberg-Universität Mainz, Mainz, Germany

William T. Coffey, Department of Electronics and Electrical Engineering, Trinity College, University of Dublin, Dublin, Ireland

Karl F. Freed, Department of Chemistry, James Franck Institute, University of Chicago, Chicago, Illinois, USA

Daan Frenkel, Department of Chemistry, Trinity College, University of Cambridge, Cambridge, United Kingdom

Pierre Gaspard, Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, Brussels, Belgium

Martin Gruebele, School of Chemical Sciences and Beckman Institute, Director of Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

Jean-Pierre Hansen, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Gerhard Hummer, Chief, Theoretical Biophysics Section, NIDDK-National Institutes of Health, Bethesda, Maryland, USA

Ronnie Kosloff, Department of Physical Chemistry, Institute of Chemistry and Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Israel

Ka Yee Lee, Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois, USA

Todd J. Martinez, Department of Chemistry, Stanford University, Stanford, California, USA

Shaul Mukamel, Department of Chemistry, University of California at Irvine, Irvine, California, USA

Jose Onuchic, Department of Physics, Co-Director Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California, USA

Steven Quake, Department of Physics, Stanford University, Stanford, California, USA

Mark Ratner, Department of Chemistry, Northwestern University, Evanston, Illinois, USA

David Reichmann, Department of Chemistry, Columbia University, New York, New York, USA

George Schatz, Department of Chemistry, Northwestern University, Evanston, Illinois, USA

Norbert Scherer, Department of Chemistry, James Franck Institute, University of Chicago, Chicago, Illinois, USA

Steven J. Sibener, Department of Chemistry, James Franck Institute, University of Chicago, Chicago, Illinois, USA

Andrei Tokmakoff, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

Donald G. Truhlar, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA

John C. Tully, Department of Chemistry, Yale University, New Haven, Connecticut, USA

Copyright © 2012 by John Wiley & Sons, Inc. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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Library of Congress Catalog Number: 58-9935

ISBN: 978-1-118-16784-7

Contributors to Volume 150

Mark A. Berg, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA

Bernard R. Brooks, Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 5635 Fishers Lane, Bethesda, MD 20892-9314, USA

Ana Damjanovic, Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 5635 Fishers Lane, Bethesda, MD 20892-9314, USA; Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA

Igor Goychuk, Institute of Physics, University of Augsburg, Universitätsstr. 1, D-86135 Augsburg, Germany

Taekjip Ha, Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, Urbana, IL 61801, USA

Kyung Suk Lee, Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Szilvia Pothoczki, Grup de Caracterització de Materials, Departament de Física i Enginyeria Nuclear, ETSEIB, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Catalonia, Spain

László Pusztai, Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences (RISSPO HAS), H-1121 Budapest, Konkoly Thege út 29-33, Hungary

Kousik Samanta, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; Department of Chemistry, Rice University, Houston, TX 77005, USA

László Temleitner, Japan Synchrotron Radiation Research Institute (SPring-8/JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan

Reza Vafabakhsh, Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Xiongwu Wu, Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 5635 Fishers Lane, Bethesda, MD 20892-9314, USA

Danny L. Yeager, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA

Preface to the Series

Advances in science often involve initial development of individual specialized fields of study within traditional disciplines, followed by broadening and overlapping, or even merging, of those specialized fields, leading to a blurring of the lines between traditional disciplines. The pace of that blurring has accelerated in the last few decades, and much of the important and exciting research carried out today seeks to synthesize elements from different fields of knowledge. Examples of such research areas include biophysics and studies of nanostructured materials. As the study of the forces that govern the structure and dynamics of molecular systems, chemical physics encompasses these and many other emerging research directions. Unfortunately, the flood of scientific literature has been accompanied by losses in the shared vocabulary and approaches of the traditional disciplines, and there is much pressure from scientific journals to be ever more concise in the descriptions of studies, to the point that much valuable experience, if recorded at all, is hidden in supplements and dissipated with time. These trends in science and publishing make this series, Advances in Chemical Physics, a much needed resource.

The Advances in Chemical Physics is devoted to helping the reader obtain general information about a wide variety of topics in chemical physics, a field that we interpret very broadly. Our intent is to have experts present comprehensive analyses of subjects of interest and to encourage the expression of individual points of view. We hope that this approach to the presentation of an overview of a subject will both stimulate new research and serve as a personalized learning text for beginners in a field.

Stuart A. Rice

Aaron R. Dinner

Chapter 1

Multidimensional Incoherent Time-Resolved Spectroscopy and Complex Kinetics

Mark A. Berg

Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA

I. Introduction

A. Multidimensional Kinetics Versus Multidimensional Coherent Spectroscopy

Chemical kinetics dates back to the start of quantitative measurement in chemistry. From our current perspective, those measurements were both incoherent and one dimensional (1D). They are one dimensional in the sense that a single perturbation is applied to the system, followed by a single period of evolution, before the final state is measured. Coherent time-resolved spectroscopy started with the discovery of the spin echo in 1950 [1]. This field has since evolved into a powerful array of techniques. They are applicable in the fields of NMR [2], electronic [3–5], Raman [6], and infrared [7–10] spectroscopies and have been used to extract many different structural and dynamic properties from many different systems. The surprising abilities of these methods are often attributed to the properties of quantum mechanical coherence. However, in addition to exploiting coherence, these techniques are also multidimensional: more than one excitation is used to prepare the system, and there are multiple periods of evolution before detection. Yet while the field of multidimensional coherent spectroscopy has expanded vigorously, interest in multidimensional measurements of incoherent states has been only sporadic.

This chapter will review a research program to define and develop the potential of multidimensional incoherent spectroscopy [11–20]. In principle, one might retrace the development of 1D kinetics by first developing multidimensional measurements of slow reactions, for example, by working on multidimensional stopped-flow methods. In fact, the theoretical and experimental methods developed for coherent spectroscopy are very powerful, and we have relied heavily on borrowing methods and ideas from that field. As a result, it has been easier to start by developing the multidimensional version of ultrafast kinetics. However, there is no fundamental barrier to extending these methods to longer timescales for slower process. Our approach to multidimensional kinetics has been named multiple population period transient spectroscopy (MUPPETS) to recognize its connections to multidimensional coherent spectroscopy.

The analogy between coherent and incoherent spectroscopies can be seen in a simple way. Coherent time evolution is described by factors of e±iωt, where ω is a transition frequency, whereas incoherent time evolution is describe by factors of e−kt, where k is a decay rate. Wherever a property of a spectral transition can be measured by coherent spectroscopy, there is an analogous property of rates that can be measured by an incoherent experiment. The first coherent spectroscopy, the spin echo [1], measured a homogeneous line shape within an inhomogeneously broadened line. In kinetics, the analogue of a broadened spectral line is a nonexponential decay.

Exponential kinetics and a single rate constant are easily justified for elementary unimolecular processes. However, nonexponential kinetics are increasingly common as the material examined becomes more complex [21–27]. Polymers, supercooled liquids and glasses [28–32], and biomolecules [33, 34] are classic examples of systems with nonexponential relaxation; nanoparticles [35, 36] and ionic liquids [37] are more recent ones. A nonexponential decay appears to have multiple rate constants and so is also called rate dispersion. One possible explanation is rate heterogeneity: each molecule in the sample has an exponential decay, but different molecules have different rate constants. Often, one can propose an alternative mechanism in which every molecule has a nonexponential decay—in other words, homogeneous rate dispersion.

One-dimensional kinetics cannot distinguish between these mechanisms, just as 1D coherent spectroscopy cannot distinguish between homogeneous and inhomogeneous line broadening mechanisms. However, a 2D kinetics experiment can measure a homogeneous decay within a system with rate heterogeneity, just as a 2D coherent experiments can measure a homogeneous line shape within an inhomogeneous band. Thus, the difference between coherent and incoherent spectroscopies is whether frequencies or rates are measured. The ability to detect heterogeneity is a property of a multidimensional experiment, whether coherent or incoherent.

The comparison to coherent spectroscopy suggests that multidimensional kinetics can be of both intellectual interest and practical utility. A further comparison indicates some of the challenges of turning these concepts into robust experiments. Two-dimensional (2D) coherent optical spectroscopy is generally a χ(3) process. Although experiments can be done with only two input beams, to reach its full potential, a four-beam experiment is needed. In comparison, a 2D kinetics experiment is a χ(5) process. It can be done with as few as three beams, but to reach its full potential, six beams are needed. Three-dimensional (3D) kinetics experiments are also attractive, and they would be χ(7) processes requiring up to eight beams. The difficulty with such high-order experiments is partly the small size of the signals, but just as important is the complexity of building and maintaining the necessary optical apparatus.

Experiments using six or more optical beams have been performed previously [38–43] but have a reputation for being heroic experiments aimed at specific, high-value questions. In contrast, kinetics with rate dispersion is a broad issue covering diverse systems, processes, and timescales. Thus, it is important to develop experimental methods that do not work on just one system but that are robust and adaptable to many problems.

Developing MUPPETS has required simultaneous progress along several fronts: the concepts of homogeneous and heterogeneous rates needed to be refined, a general theory of incoherent spectroscopy in multiple dimensions had to be devised, experimental methods that are practical on a broad array of systems had to be developed, and methods to quantitatively analyze the results had to be implemented. Much remains to be done in each of these areas. The completed studies focus on distinguishing homogeneous and heterogeneous contributions to the electronic relaxation of two-state systems—the incoherent analogue of the spin-echo experiment, the simplest multidimensional coherent experiment.