Download or read book Revealing the Structure and Dynamics of Small molecule Solutions and Proteins Using Theoretical Vibrational Spectroscopy written by and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Theoretical Vibrational Spectroscopy of Proteins written by and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Vibrational Dynamics Of Molecules written by Joel M Bowman and published by World Scientific. This book was released on 2022-06-14 with total page 603 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Structure and Dynamics of Solutions written by H. Ohtaki and published by Elsevier. This book was released on 2013-10-22 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Molecular Relaxation in Liquids written by Biman Bagchi and published by Oxford University Press. This book was released on 2012-01-30 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Molecular Spectroscopy Experiment and Theory written by Andrzej Koleżyński and published by Springer. This book was released on 2018-10-10 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Coherent Multidimensional Spectroscopy written by Minhaeng Cho and published by Springer. This book was released on 2019-08-06 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Theoretical Investigation of the Vibrational Spectroscopic Signatures of Ion water Clusters and Peptide water Clusters written by Xijun Wang and published by . This book was released on 2016 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this work is to develop theoretical approaches to compute vibrational spectra beyond the harmonic approximation and to investigate the performance of the self-consistent-charge density-functional tight-binding model (SCC-DFTB) in studying the vibrational spectra of large systems. For this purpose, vibrational spectra of ion-water clusters and peptide-water clusters are computed from molecular dynamics (MD) simulations using the Fourier transform of the autocorrelation function of the dipole moment (FTACF). The performance of the SCC-DFTB model is evaluated by comparing computed spectra with available experimental results and ab initio or first-principles results. There are four distinct aspects to this work: (1) To demonstrate how the FTACF approach overcomes the limitations of the harmonic approximation, vibrational spectra of the ?Zundel ion?, the protonated water dimer, are computed from ab initio MD simulations based on second-order Møller–Plesset (MP2) Perturbation Theory. The splitting of the band of the proton transfer mode is well reproduced, and its coupling with other modes is characterized by examining the correlation spectra of a combination of selected internal coordinates. Computed spectra at different temperatures further confirm the ability of the approach to unveil temperature-dependent features of vibrational modes coupling. (2) To confirm the spectral signature of ?free water? at the surface of aqueous droplets seeded by sulfate ions proposed by experimentalists, theoretical vibrational spectra of sulfate-water clusters are generated using the SCC-DFTB model. Computed spectra not only reproduce the spectral signature of free surface water molecules, hence confirming the hypothesis, but also reveal the distance within which the sulfate ion may affect the structure and dynamics of water molecules in the gas phase, within the accuracy of the approximate model employed and the possible limitations of conformational sampling. (3) To investigate the hydration effect on the CN stretch band of the guanidinium ion, vibrational spectra of guanidinium-water clusters are obtained with the SCC-DFTB model. Computed spectra reveal a redshift in the band position, in agreement with ab initio calculations of harmonic frequencies. The SCC-DFTB spectra are also in good agreement with those obtained from Car-Parrinello molecular dynamics (CPMD) simulations employing more rigorous density-functional theory (DFT). (4) To validate the suitability of the approach to describe the interactions and dynamics of peptide-water binary systems, vibrational spectra of several model clusters containing prototype peptides are generated from MD simulations at different temperatures, with the ultimate goal of gaining insight into solvation effects on the spectra of hydrated proteins. Computed spectra are in excellent agreement with available experimental results and reported theoretical results. Altogether, these findings not only shed light onto understanding the properties of ion-water and peptide-water clusters, but also validate an efficient approach to compute vibrational spectra of large systems with satisfactory performance and accuracy.

Download or read book Watching Ultrafast Molecular Motions with 2D IR Chemical Exchange Spectroscopy written by Michael D. Fayer and published by World Scientific. This book was released on 2011 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique volume presents a comprehensive but accessible introduction to the field of ultrafast two-dimension infrared (2D IR) vibrational echo spectroscopy based on the pioneering work of Professor Michael D Fayer, Department of Chemistry, Stanford University, USA. It contains in one place a qualitative introduction to the field of 2D IR spectroscopy and a comprehensive set of scientific papers that underlie the qualitative discussion. The introductory material contains several detailed illustrations, and is based on the Centenary Lecture at the Indian Institute of Science given by Professor Fayer July 16, 2008 as part of the celebration of the 100th anniversary of the founding of IIS in Bangalore, India. The second part of the volume contains reprints of Fayer's relevant papers. The compilation will be very useful because it presents the historical background, motivation, methodology, and experimental results at a level that is accessible to the non-expert. The reprints of the scientific papers, from review articles to detailed theoretical papers, provide rigorous supporting material so that the reader can delve as deeply as desired into the subject.

Download or read book Ultrafast Infrared Vibrational Spectroscopy written by Michael D. Fayer and published by CRC Press. This book was released on 2013-03-04 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advent of laser-based sources of ultrafast infrared pulses has extended the study of very fast molecular dynamics to the observation of processes manifested through their effects on the vibrations of molecules. In addition, non-linear infrared spectroscopic techniques make it possible to examine intra- and intermolecular interactions and how such interactions evolve on very fast time scales, but also in some instances on very slow time scales. Ultrafast Infrared Vibrational Spectroscopy is an advanced overview of the field of ultrafast infrared vibrational spectroscopy based on the scientific research of the leading figures in the field. The book discusses experimental and theoretical topics reflecting the latest accomplishments and understanding of ultrafast infrared vibrational spectroscopy. Each chapter provides background, details of methods, and explication of a topic of current research interest. Experimental and theoretical studies cover topics as diverse as the dynamics of water and the dynamics and structure of biological molecules. Methods covered include vibrational echo chemical exchange spectroscopy, IR-Raman spectroscopy, time resolved sum frequency generation, and 2D IR spectroscopy. Edited by a recognized leader in the field and with contributions from top researchers, including experimentalists and theoreticians, this book presents the latest research methods and results. It will serve as an excellent resource for those new to the field, experts in the field, and individuals who want to gain an understanding of particular methods and research topics.

Download or read book Biological NMR Spectroscopy written by John L. Markley and published by Oxford University Press. This book was released on 1997-01-30 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a critical assessment of progress on the use of nuclear magnetic resonance spectroscopy to determine the structure of proteins, including brief reviews of the history of the field along with coverage of current clinical and in vivo applications. The book, in honor of Oleg Jardetsky, one of the pioneers of the field, is edited by two of the most highly respected investigators using NMR, and features contributions by most of the leading workers in the field. It will be valued as a landmark publication that presents the state-of-the-art perspectives regarding one of today's most important technologies.

Download or read book Modern Methods for Theoretical Physical Chemistry of Biopolymers written by Evgeni Starikov and published by Elsevier. This book was released on 2011-08-11 with total page 605 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern Methods for Theoretical Physical Chemistry of Biopolymers provides an interesting selection of contributions from an international team of researchers in theoretical chemistry. This book is extremely useful for tackling the complicated scientific problems connected with biopolymers' physics and chemistry. The applications of both the classical molecular-mechanical and molecular-dynamical methods and the quantum chemical methods needed for bridging the gap to structural and dynamical properties dependent on electron dynamics are explained. Also included are ways to deal with complex problems when all three approaches need to be considered at the same time. The book gives a rich spectrum of applications: from theoretical considerations of how ATP is produced and used as ‘energy currency’ in the living cell, to the effects of subtle solvent influence on properties of biopolymers and how structural changes in DNA during single-molecule manipulation may be interpreted. · Presents modern successes and trends in theoretical physical chemistry/chemical physics of biopolymers · Topics covered are of relevant importance to rapidly developing areas in science such as nanotechnology and molecular medicine · Quality selection of contributions from renowned scientists in the field

Download or read book Femtochemistry and Femtobiology written by Monique M. Martin and published by Elsevier. This book was released on 2004-04-16 with total page 589 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reflects the heights of knowledge of ultrafast chemical processes attained in these early years of the 21st century : the latest research in femtosecond and picosecond molecular processes in Chemistry and Biology, carried out around the world, is described here in more than 110 articles. The results were presented and discussed at the VIth International Conference on Femtochemistry, in Paris, France, from July 6 to July 10, 2003. The articles published here were reviewed by referees selected from specialists in the Femtochemistry community, guaranteeing a collective responsability for the quality of the research reported in the next 564 pages. Femtochemistry is an ever-growing field, where new research areas are constantly opening up, and one which both stimulates and accompanies the development of ultrafast technologies. The increasing interest in femtobiology and chemistry at the frontier with biology is an obvious indicator of the present impact of life sciences in our society. New materials and reactions at surfaces are also some of the relatively new topics that promise rapid developments. New methodologies and technologies for probing and following in real time molecular dynamical phenomena have appeared within the last ten years or so. These methods, based on multidimensional IR spectroscopies, ultrafast X-ray and electron diffraction techniques, are well represented in this book. Of ever-improving performance, they are now applied to the characterization of structural dynamics of an increasing number of chemical and biological systems.This book reports the state of research in Femtochemistry and Femtobiology presented at Paris, at the Maison de la Chimie, in July 2003, representing the tenth anniversary of the conference. * Overview of the most recent research on ultrafast events* Application of new methodologies on chemical and biological systems* Contributions by key players in the field

Download or read book Structure and Dynamics of Supramolecular Systems One Molecule particle at a Time written by Pierre Karam and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past years, the possibility of visualizing single fluorescent molecules with exquisite spatial and temporal resolution has given rise to the field of Single Molecule Spectroscopy (SMS). The technique has enabled establishing new paradigms in biophysics and chemical biology by revealing unique information otherwise hidden in traditional ensemble measurements. In this work, we apply SMS methodologies to address problems in the field of chemistry and self-assembled structures, specifically to sense small molecules bound to a lipid membrane, to unravel exciton migration in conjugated polyelectrolytes, to study protein-RNA interactions and to characterize DNA nanotubes in solution. We discuss here the preparation and characterization of a liposome beacon platform for sensing small molecules. This platform relies on the interaction of conjugated polyelectrolytes with lipid membranes. The effect different lipids have on the photophysical properties of the ...

Download or read book Frontiers of Molecular Spectroscopy written by Jaan Laane and published by Elsevier. This book was released on 2011-08-11 with total page 741 pages. Available in PDF, EPUB and Kindle. Book excerpt: Much of what we know about atoms, molecules, and the nature of matter has been obtained using spectroscopy over the last one hundred years or so. In this book we have collected together twenty chapters by eminent scientists from around the world to describe their work at the cutting edge of molecular spectroscopy. These chapters describe new methodology and applications, instrumental developments, and theory which is taking spectroscopy into new frontiers. The range of topics is broad. Lasers are utilized in much of the research, but their applications range from sub-femtosecond spectroscopy to the study of viruses and also to the investigation of art and archeological artifacts. Three chapters discuss work on biological systems and three others represent laser physics. The recent advances in cavity ringdown spectroscopy (CRDS), surface enhanced Raman spectroscopy (SERS), two-dimensional correlation spectroscopy (2D-COS), and microwave techniques are all covered. Chapters on electronic excited states, molecular dynamics, symmetry applications, and neutron scattering are also included and demonstrate the wide utility of spectroscopic techniques. Provides comprehensive coverage of present spectroscopic investigations Features 20 chapters written by leading researchers in the field Covers the important role of molecular spectroscopy in research concerned with chemistry, physics, and biology

Download or read book Antifreeze Proteins Volume 2 written by Hans Ramløv and published by Springer Nature. This book was released on 2020-06-30 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second volume, written in four parts, offers the reader a thorough review on molecular, structural and applied aspects of antifreeze proteins. The first part treats the structure-function relationship and the physicochemical properties of antifreeze proteins; the second part provides insight into molecular mechanisms affected by antifreeze proteins; the third part presents some of the potential applications in various professional sectors and in the last part the book content is summarized and future research directions and ideas are discussed. Together with the first volume on the environment, systematic and evolution of antifreeze proteins, this book represents a unique, comprehensive work and a must-have for students and scientists in biochemistry, molecular biology, biotechnology and physical chemistry.

Download or read book Handbook of High resolution Spectroscopy written by Martin Quack and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 2236 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of High-Resolution Spectroscopy has been considerably extended and even redefined in some areas. Combining the knowledge of spectroscopy, laser technology, chemical computation, and experiments, Handbook of High-Resolution Spectroscopy provides a comprehensive survey of the whole field as it presents itself today, with emphasis on the recent developments. This essential handbook for advanced research students, graduate students, and researchers takes a systematic approach through the range of wavelengths and includes the latest advances in experiment and theory that will help and guide future applications. The first comprehensive survey in high-resolution molecular spectroscopy for over 15 years Brings together the knowledge of spectroscopy, laser technology, chemical computation and experiments Brings the reader up-to-date with the many advances that have been made in recent times Takes the reader through the range of wavelengths, covering all possible techniques such as Microwave Spectroscopy, Infrared Spectroscopy, Raman Spectroscopy, VIS, UV and VUV Combines theoretical, computational and experimental aspects Has numerous applications in a wide range of scientific domains Edited by two leaders in this field Provides an overview of rotational, vibration, electronic and photoelectron spectroscopy Volume 1 - Introduction: Fundamentals of Molecular Spectroscopy Volume 2 - High-Resolution Molecular Spectroscopy: Methods and Results Volume 3 - Special Methods & Applications