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Ultrafast Dynamics And Structures Of Biomolecules Using Multi Dimensional Infrared Spectroscopy
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Book Synopsis Ultrafast Dynamics and Structures of Biomolecules Using Multi-dimensional Infrared Spectroscopy by : Soohwan Sul
Download or read book Ultrafast Dynamics and Structures of Biomolecules Using Multi-dimensional Infrared Spectroscopy written by Soohwan Sul and published by . This book was released on 2009 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Fast Dynamics of Aqueous Biological Molecules Investigated with 2D IR Spectroscopy by : Jean K. Chung
Download or read book Fast Dynamics of Aqueous Biological Molecules Investigated with 2D IR Spectroscopy written by Jean K. Chung and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are dynamic structures that are in constant fluctuations, and their ability to undergo structural changes is critical to their function. However, their fastest dynamics in thermal equilibrium have remained largely unexplored. In this work, studies that examine the dynamics of aqueous proteins using two-dimensional infrared echo spectroscopy (2D IR) are presented. In particular, investigations of fast fluctuations in proteins and peptides within the context of structural changes upon denaturation are discussed. 2D IR is a nonlinear optical spectroscopic technique that can measure ultrafast dynamics of complex molecules in the picoseconds regime, timescales ~6-10 orders of magnitude faster than nuclear magnetic resonance. In addition, the relatively low energy mid-IR laser pulses used in this study probe the relevant nuclear degrees of freedom without significantly perturbing the protein structure or dynamics. Brief descriptions of the experimental setup and methods, as well as analysis and interpretation, are given.
Book Synopsis Ultrafast Dynamics and Interfacial Structural Orientation Investigated with Multidimensional Vibrational Spectroscopy by : Jiaxi Wang
Download or read book Ultrafast Dynamics and Interfacial Structural Orientation Investigated with Multidimensional Vibrational Spectroscopy written by Jiaxi Wang and published by . This book was released on 2019 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis, two multidimensional spectroscopic methods--two-dimensional infrared (2D IR) spectroscopy and heterodyne 2D sum frequency generation (HD 2D SFG) spectroscopy--are applied to investigate ultrafast chemical exchange of organometallics in bulk solution and structural orientation of surface catalysts at interface, respectively. 2D IR spectroscopy is used to study the ultrafast chemical exchange of two organometallics compound ( Ru(S2C2(CF3)2)(CO)(PPh3)2 and Co(CNArMes2)4 ) occurring on the picosecond time scale. Combined with DFT simulation results, 2D IR provides direct evidence of the existence of various isomers. For the five-coordinate Ru complex, one isomers that serves as the intermediate of the axial-equatorial exchange was observed for the first time. Furthermore, our 2D IR works find the kinetic barriers of dynamic exchange between multiple isomers surprisingly low, consider both of the transition metal complexes under study have relatively large ligands. The low kinetic barriers are attributed to the small core-angle movement involved in the chemical exchange. 2D IR is also applied to W(CO)6/dual cavity system to observe ultrafast intercavity nonlinear polariton interactions. Combined with a newly developed theory model, we show that the nonlinear interaction is realized by shared molecular anharmonicities among cavity modes, e.g. through mode delocalization, some molecules (with anharmonicity) are coupled by cavity modes adjacent to each other. HD 2D SFG spectroscopy is used to study a model CO2 reduction catalyst, Re(diCNbpy)(CO)3Cl, as a monolayer on a gold surface. We show that short-range interactions with the surface can cause substantial line-shape differences between vibrational bands from the same molecules. This interaction can be explained as the result of couplings between CO vibrational modes of the catalyst molecules and the image dipoles on gold surface, which are sensitive to the relative distance between the molecule and the surface. Thus, by analysis of HD 2D SFG lineshape differences and polarization dependences of IR spectra, the ensemble-averaged orientation of the molecules on the surface can be determined unambiguously. The high sensitivity of HD 2D SFG spectra to short-range interactions can be applied to many other adsorbate-substrate interactions and therefore serve as a unique tool to determine adsorbate orientations on surfaces. Meanwhile, surface molecules of the monolayers can adopt conformations with many different orientations. Thus, it is necessary to describe the orientations of surface molecular monolayers using both mean tilt angle and orientational distribution, which together we refer to as orientation heterogeneity. Orientation heterogeneity is difficult to measure. In most cases, in order to calculate the mean tilt angle, it is assumed that the orientational distribution is narrow. This assumption causes ambiguities in determining the mean tilt angle and loss of orientational distribution information, which is known as the "magic angle" challenge. Using HD 2D SFG spectroscopy, we report a novel method to solve the "magic angle" challenge, by simultaneously measuring mean tilt angle and orientational distribution of molecular monolayers. Although applied to a specific system, this method is a general way to determine the orientation heterogeneity of an ensemble-averaged molecular interface.
Book Synopsis Ultrafast Infrared Vibrational Spectroscopy by : Michael D. Fayer
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.
Book Synopsis Ultrafast Dynamics at the Nanoscale by : Stefan Haacke
Download or read book Ultrafast Dynamics at the Nanoscale written by Stefan Haacke and published by CRC Press. This book was released on 2017-01-06 with total page 550 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ultrafast Dynamics at the Nanoscale provides a combined experimental and theoretical insight into the molecular-level investigation of light-induced quantum processes in biological systems and nanostructured (bio)assemblies. Topics include DNA photostability and repair, photoactive proteins, biological and artificial light-harvesting systems, plasmonic nanostructures, and organic photovoltaic materials, whose common denominator is the key importance of ultrafast quantum effects at the border between the molecular scale and the nanoscale. The functionality and control of these systems have been under intense investigation in recent years in view of developing a detailed understanding of ultrafast nanoscale energy and charge transfer, as well as fostering novel technologies based on sustainable energy resources. Both experiment and theory have made big strides toward meeting the challenge of these truly complex systems. This book, thus, introduces the reader to cutting-edge developments in ultrafast nonlinear optical spectroscopies and the quantum dynamical simulation of the observed dynamics, including direct simulations of two-dimensional optical experiments. Taken together, these techniques attempt to elucidate whether the quantum coherent nature of ultrafast events enhances the efficiency of the relevant processes and where the quantum–classical boundary sets in, in these high-dimensional biological and material systems. The chapters contain well-illustrated accounts of the authors’ research work, including didactic introductory material, and address a multidisciplinary audience from chemistry, physics, biology, and materials sciences. The book is, therefore, a must-have for graduate- and postgraduate-level researchers who wish to learn about molecular nanoscience from a combined spectroscopic and theoretical viewpoint.
Book Synopsis Multidimensional Time-Resolved Spectroscopy by : Tiago Buckup
Download or read book Multidimensional Time-Resolved Spectroscopy written by Tiago Buckup and published by Springer. This book was released on 2018-12-07 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: The series Topics in Current Chemistry Collections presents critical reviews from the journal Topics in Current Chemistry organized in topical volumes. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field.
Book Synopsis Ultrafast Infrared Vibrational Spectroscopy by : Michael D. Fayer
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 475 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 su
Book Synopsis Coherent Multidimensional Spectroscopy by : Minhaeng Cho
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.
Book Synopsis Accessing Ultrafast Protein Dynamics Through 2DIR Spectroscopy of Intrinsic Ligand Vibrations by : Niall Simpson
Download or read book Accessing Ultrafast Protein Dynamics Through 2DIR Spectroscopy of Intrinsic Ligand Vibrations written by Niall Simpson and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are complex molecular machines that facilitate the chemical reactions fundamental to life. Their functions are encoded in a linear sequence of amino acids, of which only 20 species are found in nature. Yet the functional and structural diversity accessible through these building blocks is vast. Molecular and atomic-level protein studies have been crucial to our understanding of health and treatment of disease, with increasingly sophisticated experimental and computational methods continuing to provide new information with which to advance medicine. However, the requirement for more detailed understanding of proteins has risen through the emergence of multi-antibiotic-resistant bacteria and also through the potential to design synthetic proteins of novel function. Paradigms of protein function have evolved significantly since early studies, though few all-encompassing descriptions have been proposed, owing to the complex, dynamic structures of these large biomolecules. Presently, the relationship between protein structural motions at different timescales appears to hold vital significance to the elusive aspects of biological mechanisms. No single measurement technique is capable of accessing the multitude of timescales over which protein motions occur, and thus concerted investigation is necessary. Observation of dynamics at the femtosecond-picosecond timescale has only recently become possible through the development of new experimental techniques, allowing a new class of protein motions to be investigated. In this thesis, the advanced technique of two-dimensional infrared spectroscopy (2DIR) is employed to study three biomolecular systems with implications to ubiquitous protein interactions. The aims of these investigations are, firstly, to demonstrate the suitability of 2DIR spectroscopy in gathering novel dynamic information from biological systems that is not accessible via other methods, and secondly, to derive the potential physical significance of these dynamics as they relate to biological function. A description of the underlying theory of 2DIR is presented in this Chapter, along with the considerations that must be made in the application of such a technique to complex biological case-studies. In Chapter (2), descriptions are given for the experimental setups used to acquire infrared spectra, specifically, Fourier transform infrared (FTIR), pump-probe and 2DIR spectroscopies. In Chapter (3) the catalytic-site dynamics of two closely-related haem proteins are each studied by monitoring the vibrational evolution of a nitric oxide (NO) probe molecule bound to the haem centre. A comparison of the active site dynamics is performed in order to correlate the observed differences with discrepancies between the protein reaction mechanisms. Chapter (4) explores the potential of a coenzyme with high protein-binding promiscuity to serve as an intrinsic reporter of the dynamics that occur at substrate binding sites. Infrared analysis and categorisation of the free coenzyme molecule is performed in order to establish its effectiveness as a probe. In Chapter (5), method-development strategies are proposed for the extraction of 2DIR data from large, complex protein-protein systems, with the objective of expanding the range of interactions on which 2DIR can effectively report. Both well-established and novel strategies are employed, and the potential and limitations of the technique are discussed in the context of these demanding case-studies. Chapter (6) draws together conclusions and an overview of progress made and discusses future directions.
Book Synopsis Vibrational Dynamics in Peptides and Proteins Using Two Dimensional Infrared Spectroscopy by : Ayanjeet Ghosh
Download or read book Vibrational Dynamics in Peptides and Proteins Using Two Dimensional Infrared Spectroscopy written by Ayanjeet Ghosh and published by . This book was released on 2012 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Ultrafast Infrared And Raman Spectroscopy by : M.D. Fayer
Download or read book Ultrafast Infrared And Raman Spectroscopy written by M.D. Fayer and published by CRC Press. This book was released on 2001-03-16 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt: A description of procedures for probing bond activation, H-bonded systems, molecular dynamical mechanisms, vibrational dephasing, simple liquids, and proteins and energy flow effects using ultrafast vibrational spectroscopy experiments. It discusses experimental and theoretical methods of ultrafast infrared and Raman measurements.
Book Synopsis Protein Structure, Stability, and Folding by : Kenneth P. Murphy
Download or read book Protein Structure, Stability, and Folding written by Kenneth P. Murphy and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Protein Structure, Stability, and Folding, Kenneth P. Murphy and a panel of internationally recognized investigators describe some of the newest experimental and theoretical methods for investigating these critical events and processes. Among the techniques discussed are the many methods for calculating many of protein stability and dynamics from knowledge of the structure, and for performing molecular dynamics simulations of protein unfolding. New experimental approaches presented include the use of co-solvents, novel applications of hydrogen exchange techniques, temperature-jump methods for looking at folding events, and new strategies for mutagenesis experiments. Unique in its powerful combination of theory and practice, Protein Structure, Stability, and Folding offers protein and biophysical chemists the means to gain a more comprehensive understanding of some of this complex area by detailing many of the major techniques in use today.
Book Synopsis Watching Ultrafast Molecular Motions with 2D IR Chemical Exchange Spectroscopy by : Michael D. Fayer
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.
Book Synopsis Ultrafast Vibrational Dynamics of Hydrated DNA by : Lukasz Szyc
Download or read book Ultrafast Vibrational Dynamics of Hydrated DNA written by Lukasz Szyc and published by Sudwestdeutscher Verlag Fur Hochschulschriften AG. This book was released on 2012-03 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biochemical processes in living organisms predominantly take place in aqueous environments where the structure and function of biomolecules are greatly modulated through interactions with water. One and two-dimensional infrared spectroscopy provides rich structural information since each chemical structure exhibits a unique set of vibrational frequencies. However, following the fastest changes of the DNA hydration shell geometries, occurring in the time domain below 1ps, can only be achieved using ultrafast vibrational spectroscopy. The author first provides a short introduction to the field of nonlinear spectroscopy, in particular the formalism and methodology of the pump-probe technique is explained. In the main part of this book, ukasz Szyc discusses the experiments he performed on base-pair model systems and adenine-thymine oligomers aimed at understanding the vibrational dynamics and couplings in DNA at different levels of hydration, as well as establishing the role of water in the dissipation of excess energy originating from the decay of electronic and/or vibrational excitations in DNA molecules.
Book Synopsis Transient 2D-IR Spectroscopy by : Jens Bredenbeck
Download or read book Transient 2D-IR Spectroscopy written by Jens Bredenbeck and published by . This book was released on 2005 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Modern Techniques of Spectroscopy by : Dheeraj Kumar Singh
Download or read book Modern Techniques of Spectroscopy written by Dheeraj Kumar Singh and published by Springer Nature. This book was released on 2021-04-01 with total page 663 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book highlights recent developments in the field of spectroscopy by providing the readers with an updated and high-level of overview. The focus of this book is on the introduction to concepts of modern spectroscopic techniques, recent technological innovations in this field, and current examples of applications to molecules and materials relevant for academia and industry. The book will be beneficial to researchers from various branches of science and technology, and is intended to point them to modern techniques, which might be useful for their specific problems. Spectroscopic techniques, that are discussed include, UV-Visible absorption spectroscopy, XPS, Raman spectroscopy, SERS, TERS, CARS, IR absorption spectroscopy, SFG, LIBS, Quantum cascade laser (QCL) spectroscopy, fluorescence spectroscopy, ellipsometry, cavity-enhanced absorption spectroscopy, such as cavity ring-down spectroscopy (CRDS) and evanescent wave-CRDS both in gas and condensed phases, time-resolved spectroscopy etc. Applications introduced in the different chapters demonstrates the usefulness of the spectroscopic techniques for the characterization of fundamental properties of molecules, e.g. in connection with environmental impact, bio-activity, or usefulness for pharmaceutical drugs, and materials important e.g. for nano-science, nuclear chemistry, or bio-applications. The book presents how spectroscopic techniques can help to better understand substances, which have also great impact on questions of social and economic relevance (environment, alternative energy, etc.).
Book Synopsis Infrared Spectroscopy of Biomolecules by : Henry H. Mantsch
Download or read book Infrared Spectroscopy of Biomolecules written by Henry H. Mantsch and published by Wiley-Liss. This book was released on 1996-03 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: Infrared Spectroscopy of Biomolecules Edited by Henry H. Mantsch and Dennis Chapman Dramatic new advances in the application of infrared spectroscopy to biomolecules and instrumentation are revolutionizing this branch of molecular spectroscopy. Infrared Spectroscopy of Biomolecules provides an up-to-date, detailed look at the different spectroscopic techniques now available and offers a framework for progression in the field, including the evolution of Fourier transform methods, the development of time-resolved techniques and difference spectroscopy, as well as new modulation methods. The book begins with a fundamental introduction to the theories behind both infrared spectroscopy and the Fourier transform method, which lays the groundwork for the instrumental and mathematical chapters that follow. Once the basics of the infrared methods are established, the proceeding chapters cover the application of infrared spectroscopy to proteins, lipids, enzymes, nucleic acids, carbohydrates, and biomembranes. Other chapters in this excellent reference include: Theoretical Analyses of the Amide I Infrared Bands of Globular Proteins Slow and Fast Infrared Kinetic Studies Fourier Transform Infrared Spectroscopy of Cell Surface Polysaccharides What Can Infrared Spectroscopy Tell Us About the Structure and Composition of Intact Bacterial Cells Biomedical Infrared Spectroscopy Editors Henry Mantsch and Dennis Chapman, leading experts in the field, conclude with an exciting look at much-anticipated future developments, including the use of caged compounds and studies of oxidation reduction systems within the IR spectrometer. A solid introduction to the basics with up-to-the-minute coverage of the latest developments in the field, Infrared Spectroscopy of Biomolecules is an indispensable reference tool for biochemists, biophysicists, and structural biologists alike.
