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Tyrosyl radicals can facilitate proton-coupled electron transfer (PCET) reactions that are linked to catalysis in many biological systems. One such protein system is ribonucleotide reductase (RNR). This enzyme is responsible for the conversion of ribonucleotides to deoxyribonucleotides. The beta2 subunit of class Ia RNRs contains a diiron cluster and a stable tyrosyl radical (Y122*). Reduction of ribonucleotides is dependent on reversible, long-distance PCET reactions involving Y122* located 35 Å from the active site. Protein conformational dynamics are postulated to precede diiron cluster assembly and PCET reactions in RNR. Using UV resonance Raman spectroscopy, we identified structural changes to histidine, tyrosine, and tryptophan residues with metal cluster assembly in beta2. With a reaction-induced infrared spectroscopic technique, local amide bond structural changes, which are associated with the reduction of Y122*, were observed. Moreover, infrared spectroscopy of tyrosine-containing pentapeptide model compounds supported the hypothesis that local amide bonds are perturbed with tyrosyl radical formation. These findings demonstrate the importance of the amino acid primary sequence and amide bonds on tyrosyl radical redox changes. We also investigated the function of a unique tyrosine-histidine cross-link, which is found in the active site of cytochrome c oxidase (CcO). Spectrophotometric titrations of model compounds that mimic the cross-link were consistent with a proton transfer role in CcO. Infrared spectroscopic data support the formation of tyrosyl radicals in these model compounds. Collectively, the effect of the local structure and the corresponding protein dynamics involved in tyrosyl radical-mediated PCET reactions are illustrated in this work.

Contemporary laser research involves the development of spectroscopic techniques to understand the microscopic structural aspects of a simple molecular system in chemical and materials to more complex biological systems such as cells. In particular, Raman spectroscopy, which provides bond specific information, has attracted considerable attention. Further with the advent of femtosecond (fs) laser, the recent trend in the field of fs chemistry is to develop nonlinear Raman techniques that allow one to acquire vibrational structural information with both fs temporal resolution as well as good spectral resolution. Among many advanced nonlinear Raman techniques, the development of fs Stimulated Raman scattering (SRS) has gathered momentum in the recent decade due to its ability to (1) provide vibrational structural information of various system including fluorescent molecules with good signal to noise ratio and (2) circumvent the limitation imposed on the spectral resolution by the necessary pulse durations according to the energy-time uncertainty principle where ‘K’ is a constant that depends on the pulse shape) unlike in the case of fs normal resonance Raman spectroscopy. We have developed a technique named “Ultrafast Raman loss spectroscopy (URLS)” that is analogues to SRS, but is more advantageous as compared to SRS and has the potential to be an alternative if not competitive tool as a vibrational structure elucidating technique. The concept and the design of this novel technique, URLS, form the core of the thesis entitled “Ultrafast Raman Loss Spectroscopy (URLS)”. Chapter 1 lays the theoretical groundwork for ultra-short pulses and nonlinear spectroscopy which forms the heart of URLS. It presents a detailed discussion on the basis behind the elementary experimental problems associated with the ultra-short laser pulses when they travel through a medium, the characterization of these ultrashort pulses as well as various non-linear phenomena induced within a medium due to the propagation of these pulses. Chapter 2 focuses on the concept of SRS which resulted into the foundation of URLS. It illustrates the theoretical as well as the experimental aspects of SRS and demonstrates the sensitivity of SRS over normal Raman spectroscopy. Chapter 3 introduces the conceptual and the technical basis which ensued into the development of URLS while Chapter 4 demonstrates its application and efficiency over its analogue SRS. URLS involves the interaction of two laser sources, viz. a picosecond (ps) pulse and a fs white light (WL), with a sample leading to the generation of loss signal on the higher energy (blue) side with respect to the wavelength of the ps pulse unlike the gain signal observed on the lower energy (red) side in SRS. These loss signals are at least 1.5 times more intense than SRS signals. Also, the very prerequisite of the experimental protocol for signal detection to be on the higher energy side by design eliminates the interference from fluorescence, which appears on the red side. Thus, the rapid data acquisition, 100% natural fluorescence rejection and experimental ease ascertain “Ultrafast Raman Loss Spectroscopy (URLS)” as a unique valuable structure determining technique. Further, the effect of resonance on the line shape of the URLS signal has been studied which forms the subject of discussion in Chapter 5. The objective of the study is to verify whether the variation of resonance Raman line shapes in URLS could provide an understanding of the mode specific response on ultrafast excitation. It is found that the URLS signal’s line shape is mode dependent and can provide information similar to Raman excitation profile (REP) in the normal Raman studies. This information can have impact on the study of various dynamical process involving vibrational modes like structural dynamics and coherent control. Chapter 6 demonstrates the application of URLS as a structure elucidating technique for monitoring ultrafast structural and reaction dynamics in both chemical and biological systems using α-terthiophene (3T) as the model system. The objective is to understand the mechanism of the molecular structure dependent electronic relaxation of the first singlet excited state, S1, of α-terthiophene using fs URLS. The URLS data along with the ab-initio calculations indicate that the electronic transition is associated with a structural rearrangement from a non-planar to a planar configuration in the singlet manifold along the ring deformation co-ordinate. The experimental findings suggest that the singlet state decays exponentially with a decay time constant ( 1/e) of about 145 ps and this decay could be assigned to the intersystem crossing (ISC) pathway from the relaxed S1 state to the vibrationally hot triplet state, T1*. Lastly, Chapter 7 summarizes the entire thesis and presents some possible future prospects for URLS. Considering the advantages of URLS, it is proposed that URLS can be exploited [1] to determine the structure of any fluorescent/non-florescent condensed materials and biological systems with a very good spectral resolution (10- 40 cm-1); [2] to obtain the vibrational signature of weak Raman scattering molecules and vibrational modes with relatively small Raman cross-section owing to its high detection sensitivity with good signal to noise ratio; [3] for performing fs time-resolved study by introducing an additional fs pulse for photo-excitation of the molecule and using URLS to probe the excited state dynamics with good temporal (fs) and spectral (10-40 cm-1) resolution; and lastly, [4] the high chemical selectivity of URLS and the fact that the signal is generated only within the focal volume of the lasers where all the beams overlap can be utilized for developing this method into a microscopy for labeled-free effective vibrational study of biological samples. Consequently, it is hoped that this technique, “Ultrafast Raman Loss Spectroscopy (URLS)”, would be a suitable alternative to other nonlinear Raman methods like coherent anti-Stokes Raman spectroscopy (CARS) that has made major inroads into biology, medicine and materials.

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It has long been recognized that course and efficiency of a chemical reaction is largely mediated by the short-lived transient species (excited state or radicals) which are formed as reactive intermediates during a chemical reaction. Subtle changes not only in the bonding and electronic distributions but also in the conformations and geometries of these intermediates have a dramatic influence on the reactivity. A detailed understanding of the structural and dynamical aspects of electronic excited states is therefore essential towards unraveling photoinduced natural processes and for designing novel photonic materials. Time-resolved techniques have been widely used to study the transient species (or intermediates) formed during photochemical and photophysical reactions for better understanding of the reaction mechanism and dynamics. Time-resolved absorption spectroscopy is a promising tool to study the temporal dynamics and the kinetics of photophysical processes. But the absorption spectra of species in solution usually consist of broad spectral band revealing little or no information about the structure of the transient species under investigation. Time-resolved resonance Raman (TR3) spectroscopy, on the other hand, is a potential sensitive modality, which not only allows one to study the dynamics but also provides the vibrational structure of the transient species of interest in microsecond to picosecond time scale. Moreover, by choosing the wavelength of excitation one can selectively probe the particular transient species from a complex molecular system especially a biological molecule. Thioxanthone (TX) is well known for its dramatic solvatochromic behavior and has drawn enormous attention in the recent years. The objective of present thesis has been to understand the solvent-induced structural changes on the lowest excited triplet state of TX and its derivatives. We have primarily employed nanosecond TR3 spectroscopy, a pump-probe technique, to investigate structure of the lowest excited triplet state. Transient absorption experiments have also been carried out to study the excited electronic states. In order to substantiate our experimental findings and also to get more insight into the triplet-state structure, we have performed density functional theory (DFT) calculations. The polarizable continuum solvation model has been employed to account for the solvent effect into the computation. Time dependent (TD) -DFT calculations have also been performed to get the energy and the structure of the excited states. The present thesis has been divided into eight chapters. Chapter 1 gives brief literature review on photochemistry and photophysics of TX and the introduction to the TR3 technique. In this chapter we have briefly introduced key concepts which form the basis of the thesis. Chapter 2 covers the experimental and theoretical methodologies used in the present thesis work. The major components of the TR3 spectrometer as well as the important technical aspect of the TR3 technique have been discussed in detail. In the section of the theoretical method, basic concepts of the computational method, density functional theory and key concepts related to the solvation are briefly discussed. Chapter 3 focuses on a systematic vibrational study of the ground and lowest triplet states of TX. TR3 experiments have been carried out and the observed vibrational frequencies have been assigned. It has been observed that electronic excitation distorts the molecule, enabling the increased electron delocalization in the central ring keeping the ground state symmetry intact. The largest structural reorganization is observed in the central ring of TX, consisting of an oxygen atom. Normal mode analyses show that the normal mode composition is significantly influenced by the electronic excitation. The C=C stretching and C=O stretching modes are coupled to a greater extent in the triplet state as compared to the ground state. In the ground state, the two high-frequency modes can be assigned almost exclusively to the C=O stretching and C=C stretching, whereas in the triplet state, both of these coordinates have comparable contributions to the two totally symmetric modes. Chapter 4 deals with a very unique observation of simultaneous detection of two triplets. This is the first time when two triplet states have been simultaneously deleted using TR3 experiments. We have performed TR3 experiments in wide variety of solvents differing in their polarities and hydrogen atom donor abilities. The transient Raman signal has been observed from both n - π∗ and π - π∗ triplet states simultaneously. The population ratio of the two triplet states has been found to be dependent on the solvent polarity. Additionally, the excitation wavelength study has revealed that the relative ratios of the transient Raman peaks (assigned to two different triplet states) change with the excitation wavelength. Our claim of simultaneous detection of two triplets has been reconfirmed by triplet quenching experiments carried out at different temperature. It has also been observed that the CO bond length is very sensitive to the solvent polarity and specific interactions play an important role in determining the structure of lowest triplet-state. In Chapter 5, we focus on the understanding of the effect of chlorine substitution on the lowest excited triplet state of TX. TR3 spectroscopy has been used as an experimental tool to study the vibrational structure of 2-chlorothioxanthone (CTX). TR3 results indicate the coexistence of two lowest triplet states in the thermal equilibrium akin to the parent compound. The above observation has been further substantiated by probe wavelength dependent study. The configuration of the T1 state has been assigned to π – π∗, whereas the T2 state has been ascribed as n - π∗. The population ratio of 3n - π∗ to 3 π - π ∗ triplet states has been found to be more for CTX as compared to TX which has been substantiated by the flash photolysis experiments. Chapter 6 highlights the influence of solvent effect on lowest triplet state structure of CTX. Transient absorption spectroscopy has been employed to understand the triplet state electronic structure; whereas solvent induced changes in the structure of the lowest triplet state have been studied using TR3 spectroscopy. Time-resolved absorption measurements show that solvent polarity has dramatic dependence on the wavelength of T1 - Tn absorption maximum. A good correlation between the wavelength of T1 - Tn absorption maximum and ET(30) value of the solvent is observed. TR3 experiments carried out in solvents of varying polarities indicate that the contribution of n - π∗ character to the lowest excited triplet state increases with the increase in the solvent polarity. Both transient absorption and TR3 studies reveal that specific solvent effect is more pronounced in comparison to the nonspecific solvent effect. Chapter 7 of the thesis deals with the study on the triplet state structure and solvent effect on 2-trifluoromethyl Thioxanthone. Flash photolysis in tandem with TR3 spectroscopy has been employed to understand both the electronic and the vibrational structures of this pharmaceutically important thioxanthone derivative. Experiments have also been carried out in solvents of varying polarities to study solvent-induced changes in the triplet-state electronic spectra. We have observed the coexistence of two lowest triplet states alike the parent compound. The T1 state has been assigned to π - π∗ state, whereas n - π∗ configuration has been attributed to the T2 state. The wavelength of triplet-triplet absorption maximum of the lowest triplet state has been found to be sensitive to the solvent polarity and good correlation has been observed with the ET(30) value. The transient Raman results indicate that the CF3 substitution leads to increase in the population ratio of n - π∗ and π - π ∗ triplet states. Finally, Chapter 8 contains overall summary of the thesis and future directions of the present investigation.

Histidinkinase-Rhodopsine (HKRs) können als besondere Gruppe der Hybrid-Histidinkinasen beschrieben werden, deren N-terminale sensorische Domäne ein mikrobielles Rhodopsin ist. HKR-codierende Sequenzen konnten in den Genomen verschiedener Algen, Pilze und Amoeben gefunden werden doch ihre Aufgaben und Wirkungsweisen sind bisher ungeklärt. Im Rahmen dieser Arbeit wurden die rekombinanten Rhodopsin-Domänen von zwei HKRs mit verschiedenen spektroskopischen Techniken charakterisiert. Sie zeigten mehrere Besonderheiten. Das Rhodopsin-Fragment von Cr-HKR1 aus Chlamydomonas reinhardtii kann durch alternierende kurzwellige und langwellige Belichtung zwischen zwei stabilen Absorptionsformen konvertiert werden: einer Blaulicht-absorbierenden (Rh-Bl) und einer UVA-Licht-absorbierenden Form (Rh-UV). Dies resultiert aus der ungewöhnlichen thermischen Stabilität des Zustandes mit deprotonierter Schiff’scher Base. Das zweite charakterisierte HKR, die Os-HKR-Rhodopsin-Domäne aus der marinen Picoalge Ostreococcus tauri, zeigt eine Dunkelabsorption von 505 nm. Auch Os-HKR ist photochrom und die deprotonierte Spezies kann effizient akkumuliert werden. Diese P400-Absorptionsform ist jedoch nicht völlig stabil sondern es kommt nach Belichtungsende zur langsamen Dunkelzustands-Regeneration. Überraschenderweise konnte die Bindung sowie die transiente Abgabe eines Anions während des Os-HKR-Photozyklus festgestellt werden. Somit beeinflusst nicht nur das Licht, sondern auch das Salz in der Umgebung die Os-HKR-Reaktionen. Aufgrund ihrer photochromen Eigenschaften werden die HKRs als wirksame lichtinduzierte Schalter für die C-terminalen Signaltransduktionsdomänen postuliert. Schwingungsspektroskopische Analysen deckten eine Heterogenität hinsichtlich der im Protein gebundenen Retinal‐Konfiguration sowie die Existenz von zwei parallelen Photozyklen auf. Jeder dieser Photozyklen geht aus einer der beiden Retinal-Isomere hervor. / Histidine kinase rhodopsins (HKRs) can be described as hybrid histidine kinases with a microbial rhodopsin as N-terminal sensory domain. HKR-encoding sequences were found in the genomes of various unicellular organisms such as algae, fungi and amoeba but their mechanistic and physiologic function is unknown. During this work the absorptive properties of the recombinant rhodopsin domains of two HKRs were studied by the usage of different spectroscopic techniques. Both HKRs showed unusual characteristics. The rhodopsin fragment of Cr‐HKR1 from Chlamydomonas reinhardtii can be interconverted between two stable absorbance forms by the alternate application of short‐ and long‐wavelength light: a blue light-absorbing dark form (Rh-Bl) and a UVA light-absorbing form (Rh-UV). This unusual photocycle results from the uncommon thermal stability of the absorbance state with a deprotonated retinal Schiff base. The second studied HKR, the Os‐HKR rhodopsin domain from the marine picoalga Ostreococcus tauri, shows an absorbance maximum at 505 nm in darkness. Likewise Cr‐HKR1 the Os‐HKR is photochromic and the deprotonated form P400 can be efficiently accumulated. But the Os-HKR P400-form is not completely stable. A slow dark state recovery occurs. Surprisingly the dark state absorbance of Os‐HKR was found to be dependent on anion binding in the protein. Furthermore during the photocycle the transient anion release occurs and therefore not only light but also salt impacts the Os-HKR-reactions. Due to their pronounced photochromic properties, the HKRs are postulated to act as effective molecular switches for the C-terminal signal transduction domains in response to the light conditions. Vibrational spectroscopy revealed the heterogeneity with regard to the retinal configuration bound in the HKRs suggesting the existence of two parallel photocycles. Either of these photocycles originates from one of the two retinal isoforms.

All life on earth depends mainly on the presence of oxygen. Largest producers of oxygen are green plants, cyanobacteria and algae. Oxygen is released from the oxygenevolving complex of photosystem II during photosynthesis and it is used in cellular respiration of all life complexes. The oxygen-evolving complex of photosystem II has the same function in each photosynthetic organism, but it has a different composition and organization of extrinsic proteins; only PsbO protein is ubiquitous in all known oxyphototrophs. Until now only low resolution electron microscopy structural models of plant PSII and crystal structures of cyanobacterial PSII are available. Higher plant extrinsic proteins (PsbP, PsbQ and PsbR) are structurally unrelated, non-homologues to the cyanobacterial extrinsic proteins (PsbO, PsbU and PsbV) and this is the reason why it is not possible to predict arrangement of these proteins on the lumenal site of higher plant PSII. Recently, models differ mainly in the structure of the oxygen-evolving complex, which could be resolved by determination of the exact binding sites for extrinsic proteins. An other question evolves: if the difference in the oxygen-evolving complex composition is the result of evolution or adaptation of photosynthetic organisms to their environment. Structural knowledge of extrinsic proteins that could help to resolve the location and subsequently the function of extrinsic proteins is still incomplete. From this case,structural analysis, interactions and probably arrangement of proteins PsbP and PsbQ was studied and is described in detail in this thesis.

Raman spectroscopy involves change in the polarizability of the molecular system on excitation and is based on scattering process. Spontaneous Raman scattering is a two photon process, in which the input light initiates the excitation, which then leads to an emission of another photon due to scattering. It is extensively used to understand molecular properties. As spontaneous Raman scattering is a weak process, the detection of these weak Raman photons are rather difficult. Alternatively, resonance Raman (RR) scattering is another technique where the excitation wavelength is chosen according to the material under study. The excitation wavelength is chosen to be within the absorption spectrum of the material under study. RR spectroscopy not only provides considerable improvement in the intensity of the Raman signal, but also provides mode specific information i.e. the modes which are Franck-Condon active in that transition can be observed. There are reports on RR studies of many systems using pulsed light as an excitation source. It is necessary to use at least two pulsed laser sources for carrying out the time resolved RR spectroscopy. A single pulse source for excitation would lead to compromise either with temporal or spectral resolution which is due to the uncertainty principle. If an excitation pulse has pulse width of ~100 femtoseconds then the spectral resolution will be ~ 150 cm-1. It is clear now that for improving the temporal and spectral resolution simultaneously, usage of single pulse for Raman experiments (spontaneous scattering) is not adequate. The usage of multiple laser pulses may provide the way out to improve the resolutions. Nonlinear spectroscopy in a broad view helps in understanding the structural and dynamical properties of the molecular systems in a deeper manner. There are a number of techniques as a part of nonlinear spectroscopy that have emerged in due course to meet different requirements and to overcome some difficulties while understanding the molecular properties. Stimulated Raman (SRS) gain, coherent anti-Stokes Raman scattering (CARS) and the inverse Raman spectroscopy are a few to mention as third order nonlinear spectroscopic techniques which give the similar kind of information about the molecular systems. Stimulated Raman scattering is a more general process involved in nonlinear Raman processes. SRS involves at least two laser pulses and the difference in their frequencies should match with the vibrational frequency of the molecule. The polarization has to be matched between the Raman pump and the Raman probe pulses. We have developed a new nonlinear Raman technique in our laboratory named as ultrafast Raman loss spectroscopy (URLS) using the principles of nonlinear Raman scattering. It involves the Raman pump (~ 1 picosecond (ps) or ~ 15 cm-1spectral resolution) and Raman probe as a white light continuum (100 fs) whose frequency components ranges from 400-900 nm. The laser system consists of Tsunami which is pumped by a Millennia laser and Spitfire-Pro, a regenerative amplifier which is pumped by an Empower laser. Tsunami provides a 100 fs, 780 nm centered, 80 MHz and ~6 nJ energy laser pulses. The Tsunami output is fed into Spitfire to amplify its energy and change the repetition rate to 1 KHz. The pulse length of the input pulse is preserved in amplification. The output of amplifier is split into two equal parts; one part is used to pump the Optical Parametric Amplifier (OPA) in order to generate wavelengths in the range 480-800 nm. The output of the OPA is utilized to generate Raman pump which has to be in ps in order to get the best spectral resolution. A small portion of the other part of amplifier output is utilized to generate white light source for the Raman probe. The remaining part of the amplifier output is used to pump TOPAS to generate wavelengths in the ultraviolet region. URLS has been applied to many molecular systems which range from non-fluorescent to highly fluorescent. URLS has been demonstrated to be very sensitive and useful while dealing with highly fluorescent systems. URLS is a unique technique due to its high sensitivity and the Raman loss signal intensity is at least 1.5-2 times higher as compared to the Raman gain signal intensities. Cresyl violet perchlorate (CVP) is a highly fluorescent system. URLS has been applied to study CVP even at resonance excitation. Rhodamine B has also been studied using URLS. Spontaneous Raman scattering is very difficult to observe experimentally in such high quantum yield fluorescent systems. The variation in the lineshapes of the Raman bands for different RP excitation wavelengths in URLS spectra shows the mode dependent behavior of the absorption spectrum. The experimental observation of variation in the lineshape has been accounted using theoretical formalism. The thesis is focused on discussing the development of the new nonlinear Raman spectroscopic technique URLS in detail and its applicability to molecular systems for better understanding. A theoretical formalism for accounting the uniqueness of URLS among the other nonlinear Raman techniques is developed and discussed in various pictorial representations i.e. ladder, Feynman and closed loop diagrams. A brief overview of nonlinear spectroscopy and nonlinear Raman spectroscopy is presented for demonstrating the difference between the URLS and the other nonlinear Raman techniques.