Revealing The Structure And Dynamics Of Small Molecule Solutions And Proteins Using Theoretical Vibrational Spectroscopy

Due to the sensitivity of vibrational chromophores to their local environments, linear and ultrafast vibrational spectroscopy have proven to be very useful techniques for studying the structure and dynamics of condensed phases. Because spectroscopic techniques encode information related to the time-dependent configuration of an entire system into spectra resolved over at most a few dimensions, however, it is very difficult to interpret vibrational line shapes in a detailed and unambiguous manner. One approach to surmounting this difficulty is to calculate vibrational line shapes from molecular dynamics (MD) simulations by employing vibrational response theory and spectroscopic maps. (The maps relate observables in classical MD simulations to quantum spectroscopic quantities.) Once validated by comparison of experimental and theoretical line shapes, MD simulations can be used as an unequivocal basis for the interpretation of vibrational spectra. Here, we employ this approach in order to gain insight into small-molecule solutions and proteins. After sketching the theoretical formalism underlying the calculations of vibrational spectra (Chapter 2), vibrational spectroscopic analysis of the urea/water (Chapter 3) and cyanide/water (Chapter 4) solutions is presented. Analysis of linear infrared (IR) line shapes provides information concerning the local solvation structure of these molecules, while analysis of two-dimensional IR and anisotropy decay yields insight into frequency and rotational dynamics. The remainder of this work concerns the vibrational spectroscopy of the amide I (mostly CO-stretch) band of proteins. After presenting additional theoretical formalism and maps for protein spectroscopy (Chapter 5), the maps are evaluated by examining IR spectra for a single conformation of an alpha-helical model peptide in the gas phase (Chapter 6). These methods are then applied to evaluate the 2D IR spectra of two important biological systems: polyglutamine (Chapter 7) and the potassium ion channel KcsA (Chapter 8). Notably, these studies employ isotope-labeling techniques to isolate the vibrational response of a subset of amide I modes in a non-perturbative fashion. Finally, extensions to the theory are presented to enable the computation of amide I vibrational sum-frequency generation spectra (Chapter 9), which are expected to be sensitive to the structures of interfacial proteins.

Theoretical Vibrational Spectroscopy of Proteins Lu Wang Under the supervision of Professor James L. Skinner At the University of Wisconsin-Madison Vibrational spectroscopy, such as linear and two-dimensional infrared (IR) spectroscopy, is widely utilized to study the structure and dynamics of peptides and proteins. Interpretation of the experiment, or a direct assignment of the complex experimental spectra to the underlying protein structure, can be difficult. Molecular dynamics (MD) simulations offer a complementary approach to provide high-resolution structural and temporal information of proteins, although they are limited by factors such as force field accuracy and are not directly comparable to spectroscopic experiments. We have developed vibrational frequency maps for proteins that generate instantaneous site frequencies directly from MD simulations. We combine the frequency maps with established nearest-neighbor frequency shift and coupling schemes and a mixed quantum/classical framework to form a theoretical strategy for calculating protein linear and 2D IR spectra in the amide I region. This theoretical method provides a means to bridge spectroscopic experiments and molecular simulations, which allows a critical assessment of MD simulations by comparison to experiment, and enables the interpretation of experimental spectra at the molecular level. In this dissertation, we present the development of the vibrational frequency maps and provide the theoretical protocol that allows the calculation of protein vibrational spectra directly from MD simulations. We validate the theoretical method by applying it to peptides with various secondary structures in aqueous solution, and apply it to a few biologically relevant problems. For instance, we have studied the thermal unfolding transition of the villin headpiece subdomain (HP36) using IR spectra calculations. We follow the unfolding process of HP36 by monitoring its spectral changes as a function of temperature. With the help of isotope labeling, we are able to capture the feature that helix 2 of HP36 loses its secondary structure before global unfolding occurs, in agreement with experiment. In collaboration with the Zanni group and the de Pablo group at University of Wisconsin, we have also carried out studies on IAPP, a peptide closely related to type 2 diabetes. By combining theoretical modeling with extensive computer simulations and spectroscopic experiments, we have investigated the structure and dynamics of IAPP in aqueous solution, in the fibril form and in the vicinity of lipid membranes.

Vibrational Dynamics of Molecules represents the definitive concise text on the cutting-edge field of vibrational molecular chemistry. The chapter contributors are a Who's Who of world leaders in the field. The editor, Joel Bowman, is widely considered as one of the founding fathers of theoretical reaction dynamics. The included topics span the field, from fundamental theory such as collocation methods and vibrational CI methods, to interesting applications such as astrochemistry, supramolecular systems and virtual computational spectroscopy. This is a useful reference for theoretical chemists, spectroscopists, physicists, undergraduate and graduate students, lecturers and software developers.

Recent advances in the study of structural and dynamic properties of solutions have provided a molecular picture of solute-solvent interactions. Although the study of thermodynamic as well as electronic properties of solutions have played a role in the development of research on the rate and mechanism of chemical reactions, such macroscopic and microscopic properties are insufficient for a deeper understanding of fast chemical and biological reactions. In order to fill the gap between the two extremes, it is necessary to know how molecules are arranged in solution and how they change their positions in both the short and long range. This book has been designed to meet these criteria. It is possible to develop a sound microscopic picture for reaction dynamics in solution without molecular-level knowledge of how reacting ionic or neutral species are solvated and how rapidly the molecular environment is changing with time. A variety of actual examples is given as to how and when modern molecular approaches can be used to solve specific solution problems. The following tools are discussed: x-ray and neutron diffraction, EXAFS, and XANES, molecular dynamics and Monte Carlo computer simulations, Raman, infrared, NMR, fluorescence, and photoelectron emission spectroscopic methods, conductance and viscosity measurements, high pressure techniques, and statistical mechanics methods. Static and dynamic properties of ionic solvation, molecular solvation, ion-pair formation, ligand exchange reactions, and typical organic solvents are useful for bridging the gap between classical thermodynamic studies and modern single-molecule studies in the gas phase. The book will be of interest to solution, physical, inorganic, analytical and structural chemists as well as to chemical kineticists.

This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics. The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, reflecting the ubiquity and importance of hydrogen-bonded networks. The final chapter provides the microscopic theory of the dynamics and spectroscopy of doped helium cluster, highly quantum systems whose unusual properties have been studied extensively in the past couple of years.

The book reviews the results of vibration-rotational spectroscopy of molecules obtained recently by combining modern computational methods of quantum chemistry with the new techniques of high-resolution rotational and vibration-rotational spectroscopy. It shows for example that the tunneling vibration-rotational spectroscopy of the van der Waals complexes provides a new look at intermolecular forces while the high precision and sensitivity of the submillimeter-wave and Fourier transform microwave spectroscopy make it possible to study complex rotational spectra of molecules in excited vibrational states. New results of high level ab initio quantum chemical computations of vibrational and rotational energy levels and dipole moment functions of unusual molecules will be discussed together with the recent discovery of clustering of energy levels in asymmetric tops. Group theoretical analysis of floppy molecules, especially the tunneling effects in nonrigid molecules, will also be discussed.

This book brings together many different relaxation phenomena in liquids under a common umbrella and provides a unified view of apparently diverse phenomena. It aligns recent experimental results obtained with modern techniques with recent theoretical developments. Such close interaction between experiment and theory in this area goes back to the works of Einstein, Smoluchowski, Kramers' and de Gennes. Development of ultrafast laser spectroscopy recently allowed study of various relaxation processes directly in the time domain, with time scales going down to picosecond (ps) and femtosecond (fs) time scales. This was a remarkable advance because many of the fundamental chemical processes occur precisely in this range and was inaccessible before the 1980s. Since then, an enormous wealth of information has been generated by many groups around the world, who have discovered many interesting phenomena that has fueled further growth in this field. As emphasized throughout the book, the seemingly different phenomena studied in this area are often closely related at a fundamental level. Biman Bagchi explains why relatively small although fairly sophisticated theoretical tools have been successful in explaining a wealth of experimental data at a semi-phenomenological level.

The workshop on "The structure of small molecules and ions" was held at the Neve-Han guest house, near Jerusalem, Israel on December 13 to 18 in mem ory of the late Professor Itzhak Plesser. Professor Plesser played a central role in the research done both at the Weizmann Institute and at Argonne National Laboratories on the "Coulomb explosion" method. His friends honored his memory by organizing a meeting in which subjects related to Plesser's interests would be discussed. Just a week be fore the conference started we were struck by another tragedy -the death of our graduate student Ms. Hana Kovner, who participated in many of the Coulomb explosion experiments at the Weizmann Institute. We would like to dedicate these proceedings to her memory as well. The goal of the workshop was to bring together chemists and physicists working on different aspects of the structural problems of small molecular en tities. The time seemed appropriate for discussing experimental and theoretical concepts, since in recent years new methods have been introduced, and a large amount of information has been accumulated on systems not studied before, like unstable molecules, ions, van der Waals molecules and clusters. The program of the workshop reflects, we believe, these new developments. The meeting was characterized by intensive discussions in which the weak nesses and strengths of new and of well established concepts were revealed. We hope that it measured up to the high standards Itzhak Plesser maintained all through his scientific life.

This book reviews various aspects of molecular spectroscopy and its application in materials science, chemistry, physics, medicine, the arts and the earth sciences. Written by an international group of recognized experts, it examines how complementary applications of diverse spectroscopic methods can be used to study the structure and properties of different materials. The chapters cover the whole spectrum of topics related to theoretical and computational methods, as well as the practical application of spectroscopic techniques to study the structure and dynamics of molecular systems, solid-state crystalline and amorphous materials, surfaces and interfaces, and biological systems. As such, the book offers an invaluable resource for all researchers and postgraduate students interested in the latest developments in the theory, experimentation, measurement and application of various advanced spectroscopic methods for the study of materials.

This book will fulfill the needs of time-domain spectroscopists who wish to deepen their understanding of both the theoretical and experimental features of this cutting-edge spectroscopy technique. Coherent Multidimensional Spectroscopy (CMDS) is a state-of-the-art technique with applications in a variety of subjects like chemistry, molecular physics, biochemistry, biophysics, and material science. Due to dramatic advancements of ultrafast laser technologies, diverse multidimensional spectroscopic methods utilizing combinations of THz, IR, visible, UV, and X-ray radiation sources have been developed and used to study real time dynamics of small molecules in solutions, proteins and nucleic acids in condensed phases and membranes, single and multiple excitons in functional materials like semiconductors, quantum dots, and solar cells, photo-excited states in light-harvesting complexes, ions in battery electrolytes, electronic and conformational changes in charge or proton transfer systems, and excess electrons and protons in water and biological systems.