Resonance Raman, Time-Resolved Resonance Raman and Density Functional Theory Study of Benzoin Diethyl Phosphate, Selected P-Hydroxy and P-Methoxy Substituted Phenacyl Ester Phototrigger and Model Compounds


Book Description

This dissertation, "Resonance Raman, Time-resolved Resonance Raman and Density Functional Theory Study of Benzoin Diethyl Phosphate, Selected P-Hydroxy and P-methoxy Substituted Phenacyl Ester Phototrigger and Model Compounds" by Wing-sum, Chan, 陳穎心, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: RESONANCE RAMAN, TIME-RESOLVED RESONANCE RAMAN AND DENSITY FUNCTIONAL THEORY STUDY OF BENZOIN DIETHYL PHOSPHATE, SELECTED P-HYDROXY AND P-METHOXY SUBSTITUTED PHENACYL ESTER PHOTOTRIGGER AND MODEL COMPOUNDS Submitted by Wing Sum CHAN for the degree of Doctor of Philosophy at The University of Hong Kong in August 2005 Resonance Raman (RR) spectroscopy and density functional theory (DFT) calculations were done to characterize the structure and dynamics of selected phototrigger and model compounds. Nanosecond time-resolved resonance Raman (ns-TR ) spectra of p-hydroxyphenacyl diethyl phosphate (HPDP), 4-methxoyphenacyl diethyl phosphate (MPDP) and its model compound 4''-methoxyacetophenone (MPA) in acetonitrile and in the water/acetonitrile mixed solvents are reported. The results from the DFT calculations and the ns-TR spectra indicate hydrogen-bonding leads to substantial modification of both the electronic properties and structural conformation of the triplet state MAP molecule. The free triplet MAP molecule was found to have a slightly twisted geometry with a delocalized ππ* character whereas the H-bonded MAP complex has a planar geometry with a significant ring localized biradical ππ nature. A strong solvent effect on the triplet quenching dynamics was observed for the HPDP molecule. This in conjunction with the leaving group dependence of the triplet decay observed in HPDP and related molecules are consistent with a solvent assisted triplet heterolytic cleavage pathway for the HPDP photodeprotection reaction. Intermolecular hydrogen-bonding of the HPDP molecule with the solvent water molecules appears to be essential to drive its cleavage or deprotection reaction. A spiroketone intermediate was proposed to be an intermediate after the deprotection reaction of HPDP and before the rearrangement process that results in the formation of the p-hydroxyphenylacetic acid (HPAA) final product. The results reported here provide important kinetics and structural data for the photodeprotection reactions of p-hydroxy and p-methoxy phenacyl ester phototriggers. This new data provides an improved understanding of the reaction mechanism occurring after photolysis of HPDP and related phototrigger compounds in various solvents. The RR spectra of benzoin diethyl phosphate (BDP) were obtained in acetonitrile solvent with excitation to its nπ* and ππ* excited states. DFT calculations were done to determine the structure and vibrational frequencies for the ground state and the excitation energies and molecular orbitals for the lower excited states of the BDP molecule. The DFT results were used to assign the observed RR bands and for comparison and interpretation of the resonance enhancement of the experimental RR spectra. It was found that Raman modes exhibiting strong enhancement are mainly related to the benzoinyl moiety for both excited states. The results for BDP indicate there is only a relatively small displacement between the nπ* excited state and the ground state but a larger displacement between the ππ* state and the ground state. The absence of RR bands in the RR spectra related to the cleavage motion of the diethyl phosphate group rules out any direct photodissociation pathway for the BDP photodeprotection




Ab-initio Implementation of Ground and Excited State Resonance Raman Spectroscopy


Book Description

We discuss the development and application of multiple methodologies which will either make the traditional electronic structure methods more efficient or reveal the structural insight of condensed or gas-phase systems. The main idea revolves around the development and application of \textit{ab initio} resonance-Raman (RR) spectroscopy and how to achieve the efficiency to simulate the resonance-Raman spectra for biomolecules. To tackle this, the first step was the development of new quadrature grids for high precision integration of modern density functionals, as the choice of density functional for RR simulation stems from the former's accuracy and cost-effectiveness. Our pruned integration grids, SG-2 and SG-3 work well for modern difficult-to-integrate functionals alongside finding a balance between accuracy and computational cost. To calculate the vibrational spectra for a biomolecule, getting the optimized structure is important as normal mode analysis can be erroneous at a non-stationary point. All quantum-mechanical optimization of enzyme active sites can be tricky geometric constraints that need to be introduced to prevent the structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. To calculate the RR intensities using all-electron quantum chemistry, we used the excited state gradient method under the independent mode displaced harmonic oscillator (IMDHO) approximation. Using the RR spectroscopy we get insightful information about the structure of the hydrated electron, which caused a decade long debate. Furthermore, we have integrated the \textit{ab-initio} molecular dynamics (AIMD) simulation of excited states along with the resonance Raman calculation to substantiate the experimental femtosecond stimulated Raman spectra (FSRS) spectra. This formalism helps us to understand the time-dependent evolution of specific vibrational modes.




Biomolecular Spectroscopy: Advances from Integrating Experiments and Theory


Book Description

Published continuously since 1944, Advances in Protein Chemistry and Structural Biology has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. - Covers reviews of methodology and research in all aspects of protein chemistry - Brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics







Molecular Spectroscopy, 2 Volume Set


Book Description

Uniquely creates a strong bridge between molecular spectroscopy and quantum chemistry This two-volume book consists of many reviews reporting new applications of quantum chemistry to molecular spectroscopy (Raman, infrared, near-infrared, terahertz, far-ultraviolet, etc.). It contains brief introductions to quantum chemistry for spectroscopists, and to the recent progress on molecular spectroscopy for quantum chemists. Molecular Spectroscopy: A Quantum Chemistry Approach examines the recent progress made in the field of molecular spectroscopy; the state of the art of quantum chemistry for molecular spectroscopy; and more. It offers multiple chapters covering the application of quantum chemistry to: visible absorption and fluorescence, Raman spectroscopy, infrared spectroscopy, near-infrared spectroscopy, terahertz spectroscopy, and far-ultraviolet spectroscopy. It presents readers with hydrogen bonding studies by vibrational spectroscopy and quantum chemistry, as well as vibrational spectroscopy and quantum chemistry studies on both biological systems and nano science. The book also looks at vibrational anharmonicity and overtones, and nonlinear and time-resolved spectroscopy. -Comprehensively covers existing and recent applications of quantum chemistry to molecular spectroscopy -Introduces the quantum chemistry for the field of spectroscopy and the advancements being made on molecular spectroscopy for quantum chemistry -Edited by world leading experts who have long standing, extensive experience and international standing in the field Molecular Spectroscopy: A Quantum Chemistry Approach is an ideal book for analytical chemists, theoretical chemists, chemists, biochemists, materials scientists, biologists, and physicists interested in the subject.




Application of Quantum Force Computations for Raman Spectroscopy and Molecular Dynamics


Book Description

Electronic structure calculations have undergone incredible advancement in the past century. Using modern methods and supercomputing infrastructure we are now able to compute precise electron behavior in a variety of large and complex systems. However, these computations are only as good as their applications. To further these computations we consider two applications of efficient force calculations using first principles density functional theory. We compute the vibrational and Raman spectra for B-doped, P-doped, and B-P codoped Si nanocrystals using real-space pseudopotentials constructed within density functional theory. An experimental peak in the Raman spectra near 650 cm−1 observed in codoped nanocrystals can be best explained by the presence of B-P bonds, which are located near the surface of the nanocrystal. We propose that the spectral details of this peak are related to quantum confinement and the breaking of local symmetry associated with the phonon modes involving dopant bonds. We also illustrate an improved method for calculation of nonlocal contributions to interatomic forces is used to perform molecular dynamics simulations. This method results from the real space density functional theory Hamiltonian utilizing a high order Gaussian integration scheme in real space. The efficacy of this method is demonstrated through molecular dynamics simulations of an O2 molecule and a benzene molecule. Our method improves convergence of dynamic variables including stability and vibrational frequency




Molecular Spectroscopy


Book Description

Uniquely creates a strong bridge between molecular spectroscopy and quantum chemistry This two-volume book consists of many reviews reporting new applications of quantum chemistry to molecular spectroscopy (Raman, infrared, near-infrared, terahertz, far-ultraviolet, etc.). It contains brief introductions to quantum chemistry for spectroscopists, and to the recent progress on molecular spectroscopy for quantum chemists. Molecular Spectroscopy: A Quantum Chemistry Approach examines the recent progress made in the field of molecular spectroscopy; the state of the art of quantum chemistry for molecular spectroscopy; and more. It offers multiple chapters covering the application of quantum chemistry to: visible absorption and fluorescence, Raman spectroscopy, infrared spectroscopy, near-infrared spectroscopy, terahertz spectroscopy, and far-ultraviolet spectroscopy. It presents readers with hydrogen bonding studies by vibrational spectroscopy and quantum chemistry, as well as vibrational spectroscopy and quantum chemistry studies on both biological systems and nano science. The book also looks at vibrational anharmonicity and overtones, and nonlinear and time-resolved spectroscopy. -Comprehensively covers existing and recent applications of quantum chemistry to molecular spectroscopy -Introduces the quantum chemistry for the field of spectroscopy and the advancements being made on molecular spectroscopy for quantum chemistry -Edited by world leading experts who have long standing, extensive experience and international standing in the field Molecular Spectroscopy: A Quantum Chemistry Approach is an ideal book for analytical chemists, theoretical chemists, chemists, biochemists, materials scientists, biologists, and physicists interested in the subject.




Frontiers of Surface-Enhanced Raman Scattering


Book Description

A comprehensive presentation of Surface-Enhanced Raman Scattering (SERS) theory, substrate fabrication, applications of SERS to biosystems, chemical analysis, sensing and fundamental innovation through experimentation. Written by internationally recognized editors and contributors. Relevant to all those within the scientific community dealing with Raman Spectroscopy, i.e. physicists, chemists, biologists, material scientists, physicians and biomedical scientists. SERS applications are widely expanding and the technology is now used in the field of nanotechnologies, applications to biosystems, nonosensors, nanoimaging and nanoscience.




Time-Resolved Resonance Raman and Density Functional Theory Studies of Selected Arylnitrenium Ions and Their Reactions with Guanosine Derivatives and Aryl Azides


Book Description

This dissertation, "Time-resolved Resonance Raman and Density Functional Theory Studies of Selected Arylnitrenium Ions and Their Reactions With Guanosine Derivatives and Aryl Azides" by Jiadan, Xue, 薛佳丹, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. DOI: 10.5353/th_b4129091 Subjects: Nitrenes - Spectra Ions Nucleotides Azides - Spectra Time-resolved spectroscopy Raman spectroscopy Raman effect, Resonance Density functionals