Ultrafast Time-resolved Infrared Spectroscopy of Molecular Monolayers and Solute-solvent Complexes

Ultrafast Time-resolved Infrared Spectroscopy of Molecular Monolayers and Solute-solvent Complexes
Author: Daniel Edward Rosenfeld
Publisher:
Total Pages:
Release: 2012
Genre:
ISBN:

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Ultrafast time-resolved infrared spectroscopy has been a powerful tool in resolving and studying ultrafast motions in bulk chemical and biological systems. The utility of ultrafast time-resolved infrared spectroscopy is illustrated through two studies of solute-solvent complexes. The same experimental methods used to study bulk systems are then extended to study surface systems through the development of both surface molecular probes and new spectroscopic techniques. Ultrafast polarization and wavelength selective IR pump-probe spectroscopy is used to measure the inertial and long time orientational dynamics of pi-hydrogen bonding complexes. The complexes studied are composed of phen-d-ol (phenol-OD) and various pi-base solvents with different electron donating or withdrawing substituents. The inertial motion is found to be insensitive to the strength of the hydrogen bond, but highly sensitive to the local solvent structure as reported on by inhomogeneous line broadening. The local solvent structure therefore acts as the controlling influence in determining the extent of inertial orientational relaxation, and thus the angular potential. Variation in the pi-hydrogen bond strength is of secondary importance. Hydrogen bonded complexes between phenol and phenylacetylene are studied using ultrafast two-dimensional infrared (2D IR) chemical exchange spectroscopy. Phenylacetylene has two possible pi-hydrogen bonding acceptor sites (phenyl or acetylene) that compete for hydrogen bond donors in solution at room temperature. The chemical exchange process occurs in ~5 ps, and is assigned to direct hydrogen bond migration along the phenylacetylene molecule. The observation of direct hydrogen bond migration can have implications for macromolecular systems. 2D IR vibrational echo spectroscopy and heterodyne detected transient grating (HDTG) spectroscopy (an ultra-sensitive analog of pump-probe spectroscopy) are developed as means of study of the structural and vibrational dynamics of surfaces. The surfaces studied are silica surfaces functionalized with a transition metal carbonyl complex, tricarbonyl (1,10)-phenanthroline rhenium chloride. The functionalization process produces chromophore surface density of 1-2 × 10^14 per cm squared. The high surface density achieved indicates that energy transfer between molecules on the surface could impact the experimental observables probed in 2D IR and HDTG spectroscopy. The theory of excitation transfer induced spectral diffusion has been developed and is capable of calculating the effect of the energy transfer on any spectroscopic observable through a master equation approach. Initial estimates of surface structural dynamics, based on both experimental 2D IR data and theoretical calculations, showed sub-100ps structural dynamics in the molecular monolayers even without the presence of solvent. Furthermore, solvent is shown to accelerate the structural dynamics in a manner that is different from that of bulk solution. Additional surface density dependent experiments indicate the negligible nature of excitation transfer even in these dense systems. The functionalized molecular monolayers are found to have a ~40 ps structural dynamics relaxation time in the absence of solvent. Further investigation of the effects of solvents on the RePhen(CO)3Cl monolayers has been carried out. Immersion in solvent is found to change the infrared spectrum, structural dynamics and vibrational dynamics in ways that differ from the changes evidenced in the bulk. The monolayers were immersed in both solvents that can dissolve RePhen(CO)3Cl and those that cannot. For both hexadecane and D2O, which cannot dissolve the headgroup, the structural dynamics of the monolayer are slowed by the presence of solvent while the vibrational dynamics are not impacted. Polar organic solvents, which can dissolve the headgroup, accelerate the dynamics. Dimethylformamide (DMF) is found to have a particularly strong effect on the structural dynamics of the monolayers, accelerating the timescale from 40 ps to 15 ps, yet DMF has little impact on the vibrational dynamics. Chloroform is found to enhance the vibrational lifetime of the CO symmetric stretch of the RePhen(CO)3Cl headgroups in the monolayer by 50%. These results indicate that the properties of thin films can be modified by the presence of solvent, even in the case when the solvent is repelled by the monolayer.

Watching Ultrafast Molecular Motions with 2D IR Chemical Exchange Spectroscopy

Watching Ultrafast Molecular Motions with 2D IR Chemical Exchange Spectroscopy
Author: Michael D. Fayer
Publisher: World Scientific
Total Pages: 383
Release: 2011
Genre: Science
ISBN: 9814355623

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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.

Ultrafast Infrared Vibrational Spectroscopy

Ultrafast Infrared Vibrational Spectroscopy
Author: Michael D. Fayer
Publisher: CRC Press
Total Pages: 491
Release: 2013-03-04
Genre: Science
ISBN: 1466510137

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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.

Biological and Biomedical Infrared Spectroscopy

Biological and Biomedical Infrared Spectroscopy
Author: Andreas Barth
Publisher: IOS Press
Total Pages: 448
Release: 2009
Genre: Science
ISBN: 1607500450

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Although infrared spectroscopy has been applied with success to the study of important biological and biomedical processes for many years, key advances in this vibrant technique have led to its increasing use, ranging from characterization of individual macromolecules (DNA, RNA, lipids, proteins) to human tissues, cells and their components. Infrared spectroscopy thus has a significant role to play in the analysis of the vast number of genes and proteins being identified by the various genomic sequencing projects. Whilst this book gives an overview of the field, it highlights more recent developments, such as the use of bright synchrotron radiation for recording infrared spectra, the development of two-dimensional infrared spectroscopy and the ability to record infrared spectra at ultra fast speeds.

Biological Water

Biological Water
Author: Gertz I. Likhtenshtein
Publisher: Springer Nature
Total Pages: 523
Release: 2021-10-21
Genre: Science
ISBN: 3030825035

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This book embraces all physiochemical aspects of the structure and molecular dynamics of water, focusing on its role in biological objects, e.g. living cells and tissue, and in the formation of functionally active structures of biological molecules and their ensembles. Water is the single most abundant chemical found in all living things. It offers a detailed look into the latest modern physical methods for studying the molecular structure and dynamics of the water and provides a critical analysis of the existing literature data on the properties of water in biological objects. Water as a chemical reagent and as a medium for the formation of conditions for enzymatic catalysis is a core focus of this book. Although well suited for active researchers, the book as a whole, as well as each chapter on its own, can be used as fundamental reference material for graduate and undergraduate students throughout chemistry, physics, biophysics and biomedicine.

Concepts and Methods of 2D Infrared Spectroscopy

Concepts and Methods of 2D Infrared Spectroscopy
Author: Peter Hamm
Publisher: Cambridge University Press
Total Pages: 297
Release: 2011-02-24
Genre: Science
ISBN: 1139497073

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2D infrared (IR) spectroscopy is a cutting-edge technique, with applications in subjects as diverse as the energy sciences, biophysics and physical chemistry. This book introduces the essential concepts of 2D IR spectroscopy step-by-step to build an intuitive and in-depth understanding of the method. This unique book introduces the mathematical formalism in a simple manner, examines the design considerations for implementing the methods in the laboratory, and contains working computer code to simulate 2D IR spectra and exercises to illustrate involved concepts. Readers will learn how to accurately interpret 2D IR spectra, design their own spectrometer and invent their own pulse sequences. It is an excellent starting point for graduate students and researchers new to this exciting field. Computer codes and answers to the exercises can be downloaded from the authors' website, available at www.cambridge.org/9781107000056.

Water in Biological and Chemical Processes

Water in Biological and Chemical Processes
Author: Biman Bagchi
Publisher: Cambridge University Press
Total Pages: 383
Release: 2013-11-14
Genre: Medical
ISBN: 1107037298

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A unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.

The Weak Hydrogen Bond

The Weak Hydrogen Bond
Author: Gautam R. Desiraju
Publisher: International Union of Crystal
Total Pages: 530
Release: 2001
Genre: Hydrogen bonding
ISBN: 9780198509707

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The weak or non-conventional hydrogen bond has been subject of intense scrutiny over recent years in several fields, in particular in structural chemistry, structural biology, and also in the pharmaceutical sciences. There is today a large body of experimental and theoretical evidenceconfirming that hydrogen bonds like C-H...O, N-H...pi, C-H...pi and even bonds like O-H...metal play distinctive roles in molecular recognition, guiding molecular association, and in determining molecular and supramolecular architectures. The relevant compound classes include organometalliccomplexes, organic and bio-organic systems, and also DNA and proteins. The book provides a comprehensive assessment of this interaction type, and is of interest to all those interested in structural and supramolecular science, including fields as crystal engineering and drug design.