Advances in Chemical Physics, Volume 149 E-Book

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

Seitenzahl: 477

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 field 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 serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics.

This volume explores:

• Quantum Dynamical Resonances in Chemical Reactions: From A + BC to Polyatomic Systems (Kopin Liu)

• The Multiscale Coarse-Graining Method (Lanyuan Lu and Gregory A. Voth)

• Molecular Solvation Dynamics from Inelastic X-ray Scattering Measurements (R.H. Coridan and G.C.L. Wong)

• Polymers Under Confinement (M. Muthukumar)

• Computational Studies of the Properties of DNA-linked Nanomaterials (One-Sun Lee and George C. Schatz)

• Nanopores: Single-Molecule Sensors of Nucleic Acid Based Complexes (Amit Meller)

Leseprobe

Contents

Cover

Editorial Board

Title Page

Copyright

Preface to the Series

Contributors to Volume 149

Chapter 1: Quantum Dynamical Resonances in Chemical Reactions: From A + BC to Polyatomic Systems

I. Introduction

II. A Few Basic Concepts

III. Experimental Approaches

IV. The Benchmark F + HD Reaction

V. An Obvious Extension: F + Methane

VI. A Less-Obvious Reaction: Cl + Methane

VII. Summary and Outlook

Acknowledgments

Chapter 2: The Multiscale Coarse-Graining Method

I. Introduction

II. Methodology

III. Results

IV. Conclusion

Acknowledgments

Chapter 3: Molecular Solvation Dynamics from Inelastic X-Ray Scattering Measurements

I. Introduction

II. Review of High-Resolution Inelastic X-Ray Scattering on Liquid Water: Theory and Experiment

III. Green's Function Imaging of Dynamics with Femtosecond Temporal and Angstrom Spatial Resolution

IV. An excluded volume implementation for Green's Function Imaging of Dynamics

V. Conclusions and Outlook

Chapter 4: Polymers Under Confinement

I. Introduction

II. Models of a Polymer Chain

III. Anisotropic Confinement

IV. Confinement in Spherical Cavities

V. Confinement in Cylindrical Cavities

VI. Confinement in Slab-Like Geometries

VII. Conclusions

Acknowledgments

Chapter 5: Computational Studies Of The Properties Of Dna-Linked Nanomaterials

1. Introduction

II. Optical Properties of DNA-Au NPs

III. Melting Properties of DNA-Au NPs

IV. Structural Properties of the Self-Assembled Materials

V. Conformation of DNA

VI. Conclusion

Chapter 6: Nanopores: Single-Molecule Sensors of Nucleic Acid-Based Complexes

I. Introduction

II. DNA Capture and Translocation Processes

III. Probing DNA/Small Molecule Interactions

IV. Nanopore-Based Genomic Profiling Using Sequence-Specific Probes

V. Summary

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: 978-1-118-16793-9

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

Contributors to Volume 149

R. H. Coridan, Department of Bioengineering and California NanoSystems Institute, University of California, Los Angeles, CA 90024, USA

One-Sun Lee, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA

Kopin Liu, Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan; Department of Physics, National Taiwan University, Taipei 10617, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan

Lanyuan Lu, Computation Institute, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA

Amit Meller, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA

M. Muthukumar, Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA

George C. Schatz,} {Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA

Gregory A. Voth, Department of Chemistry, James Franck and Computation Institutes, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA

G. C. L. Wong, Department of Bioengineering and California NanoSystems Institute, University of California, Los Angeles, CA 90024, USA

Chapter 1

Quantum Dynamical Resonances in Chemical Reactions: From A + BC to Polyatomic Systems

Kopin Liu

Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan; Department of Physics, National Taiwan University, Taipei 10617, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan

I. Introduction

Resonance phenomenon is ubiquitous in chemistry and physics. Atomic and molecular spectroscopy is perhaps one of the most familiar examples that manifest the resonance behavior. When the photon energy is tuned to match the energy difference of two levels of a species, a sharp peak (resonance) appears provided that the optical selection rules permit the transition. The resulting spectrum, the intensity versus the photon energy, then gives the fingerprint of the species, and the energy width of the spectral peak provides the information of the lifetime of the excited states. Similar behaviors have also been observed in many particle scattering processes, notably in nuclear physics [1–3] and electron scatterings [4]. In these processes, resonances are often associated with transiently formed compound states or quasi-bound states. A quasi-bound state is a bound species that can spontaneously dissociate by converting part of its internal energy into the translational energy of unbound relative motion of dissociation fragments. Again, the energy peak position and the peak width are the two most fundamental quantities to characterize the observed resonance. Then, what is special about the reactive resonance, that is, the quantum dynamical resonance phenomenon in a bimolecular reactive event? Why has the “sighting” of reactive resonance been so elusive over the past decades? Is our current conceptual understanding about reactive resonance phenomena deep enough to have some sort of predicting power in a previously unexplored or more complex reaction system?

These are the questions we try to address in this review. Recent advances in our understanding of reactive resonances in a few A + BC benchmarks have been amply discussed in several comprehensive reviews [5–8]. Our aim is not to summarize them again, rather than to look ahead for the unexplored possibilities by distilling and conveying the essential concepts that we learned from the benchmark studies. To this end, our discussion is necessarily 3 pedagogical and intuitive; the qualitative description in some cases may not be rigorously accurate from a theoretical point of view. Nevertheless, we will leave the readers these thoughts, and hope that there will be unexpected insights from viewing these works together and new ways of thinking can be developed to make reactive resonances more readily predictable.

The paper is organized as follows: in Section I a few basic concepts are introduced and further elucidated in Section II. Section III outlines the current experimental methods in searching for the signatures of reactive resonances. Section IV summarizes the joint theory-experiment efforts on the benchmark F + HD reaction. The emphasis is placed on what we have learned and on the basic concepts that may be generalized to other more complex reaction systems. Sections V and VI exemplify two polyatomic reactions, in which the experimental sightings of reactive resonances were reported, and how these resonance conjectures or “conclusions” were reached on the basis of the general concepts drawn from Section IV. Section VII gives the summary and future perspective.

II. A Few Basic Concepts

A. What is the Quantum Dynamical or Reactive Resonance?

A chemical reaction describes an old-bond breaking and new-bond forming process. Since the motion of the electron is typically thousand times faster than that of nuclei, the Born–Oppenheimer approximation is conveniently invoked in our conceptual understanding of how a chemical bond is ruptured and another bond is formed. Within this theoretical framework, a chemical reaction is then envisioned as nuclear dynamics evolving from reactants to product on a Born–Oppenheimer potential energy surface (PES). Broadly speaking, the term “reactive resonance” refers to a transiently formed short-lived species, or a quasi-bound state, produced as the reaction occurs. However, the central questions concerning any resonance phenomenon have to do with the formation and decay of the quasi-bound state. It is this concern prompting us in a 2001 review [5] to use a loose term of “transition-state resonance” and to classify transition-state resonances into different types according to their nature. Here, we will use the term “reactive or quantum dynamical resonance” in a more restricted sense as defined in Section II.B.

B. Classification of Transition-State Resonances

To set the stage and to make the concept more concrete, illustrates the three types of transition-state resonances in chemical reactions. Case (a) is usually associated with a complex-forming reaction, for which numerous bound and quasi-bound (predissociative) states are built upon the deep intermediate potential well. It is natural to view resonances or quasi-bound states in this case as the continuation of the bound-state spectrum into the continuum. Because, in a typical complex-forming reaction, many quasi-bound state of this sort are involved, the contributions of those heavily overlapped resonances can interfere with one another (). The well-known forward–backward symmetric product angular distribution in a long-lived complex reaction can be regarded as the result of the interferences of overlapping resonances of this type. In many other cases, this type of resonance is more amenable to spectroscopic investigations; a number of beautiful examples have been documented by Reid and Reisler [9] and Bowman [10].