The development of biomolecular Raman optical activity spectroscopy

Following its first observation over 40 years ago, Raman optical activity (ROA), which may be measured as a small difference in the intensity of vibrational Raman scattering from chiral molecules in right- and left-circularly polarized incident light or, equivalently, the intensity of a small circularly polarized component in the scattered light using incident light of fixed polarization, has evolved into a powerful chiroptical spectroscopy for studying a large range of biomolecules in aqueous solution. The long and tortuous path leading to the first observations of ROA in biomolecules in 1989, in which the author was closely involved from the very beginning, is documented, followed by a survey of subsequent developments and applications up to the present day. Among other things, ROA provides information about motif and fold, as well as secondary structure, of proteins; solution structure of carbohydrates; polypeptide and carbohydrate structure of intact glycoproteins; new insight into structural elements present in unfolded protein sequences; and protein and nucleic acid structure of intact viruses. Quantum chemical simulations of observed Raman optical activity spectra provide the complete three-dimensional structure, together with information about conformational dynamics, of smaller biomolecules. Biomolecular ROA measurements are now routine thanks to a commercial instrument based on a novel design becoming available in 2004

Raman scattering in C_{60} and C_{48}N_{12} aza-fullerene: First-principles study

We carry out large scale {\sl ab initio} calculations of Raman scattering activities and Raman-active frequencies (RAFs) in ${\rm C}_{48}{\rm N}_{12}$ aza-fullerene. The results are compared with those of ${\rm C}_{60}$. Twenty-nine non-degenerate polarized and 29 doubly-degenerate unpolarized RAFs are predicted for ${\rm C}_{48}{\rm N}_{12}$. The RAF of the strongest Raman signal in the low- and high-frequency regions and the lowest and highest RAFs for ${\rm C}_{48}{\rm N}_{12}$ are almost the same as those of ${\rm C}_{60}$. The study of ${\rm C}_{60}$ reveals the importance of electron correlations and the choice of basis sets in the {\sl ab initio} calculations. Our best calculated results for ${\rm C}_{60}$ with the B3LYP hybrid density functional theory are in excellent agreement with experiment and demonstrate the desirable efficiency and accuracy of this theory for obtaining quantitative information on the vibrational properties of these molecules.Comment: submitted to Phys.Rev.

A computational study of cyclic peptides with vibrational circular dichroism

Cyclic peptides are a class of molecules that has shown antimicrobial potential. These are complex compounds to investigate with their large conformational space and multiple chiral centers. A technique that can be used to investigate both conformational preferences and absolute configuration (AC) is vibrational circular dichroism (VCD). To extract information from the experimental VCD spectra a comparison with calculated spectra is often needed and this is the focus of this thesis: the calculation of VCD spectra. The VCD spectra are very sensitive to small structural changes, and to accurately calculate the spectra, all important conformers need to be identified. The first part of this thesis has been to establish a reliable computational protocol using meta-dynamics to sample the conformational space and ab initio methods to calculate the spectra for cyclic peptides. Using our protocol, we have investigated if VCD alone can determine the AC of cyclic tetra- and hexapeptides. We show that it is possible to determine the AC of the cyclic peptides with two chiral centers while for the peptides with three and four chiral centers, VCD is at best able to reduce the number of possible ACs and further investigation with other techniques is needed. Further, we investigated four cyclic hexapeptides with antimicrobial potential. These peptides, in contrast to the ones used for validating the protocol, consist of several amino acids with long and positively charged side chains. For these peptides, a molecular dynamics based approach provided VCD spectra in better agreement with experiment than our protocol. Reasons for this may be the lack of atomistic detail in the solvent model used during the conformational search and insufficient description of dispersion interactions during the meta-dynamics simulation

Anharmonic Effects on Vibrational Spectra Intensities: Infrared, Raman, Vibrational Circular Dichroism, and Raman Optical Activity

The aim of this paper is 2-fold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman optical activity (ROA) with the full inclusion of first- and second-order resonances for both frequencies and intensities in the framework of the generalized second-order vibrational perturbation theory (GVPT2) for all kinds of vibrational spectroscopies. Then, from a more general point of view, we want to present and validate the performance of VMS for the parallel analysis of different vibrational spectra for medium-sized molecules (IR, Raman, VCD, ROA) including both mechanical and electric/magnetic anharmonicity. For the well-known methyloxirane benchmark, careful selection of density functional, basis set, and resonance thresholds permitted us to reach qualitative and quantitative agreement between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, showing that it is now possible to interpret different spectra in terms of mass, electronegativity, polarizability, and hindrance variation between closely related substituents, chiral spectroscopies being particular effective in this connection

Coupled cluster simulation of impulsive stimulated X-ray Raman scattering

Time-dependent equation-of-motion coupled cluster (TD-EOM-CC) is used to simulate impulsive stimulated x-ray Raman scattering (ISXRS) of ultrashort laser pulses by neon, carbon monoxide, pyrrole, and p-aminophenol. The TD-EOM-CC equations are expressed in the basis of field-free EOM-CC states, where the calculation of the core-excited states is simplified through the use of the core-valence separation (CVS) approximation. The transfer of electronic population from the ground state to the core- and valence-excited states is calculated for different numbers of included core- and valence-excited states, as well as for electric field pulses with different polarizations and carrier frequencies. The results indicate that Gaussian pulses can transfer significant electronic populations to the valence states through the Raman process. The sensitivity of this population transfer to the model parameters is analyzed. The time-dependent electronic density for p-aminophenol is also showcased, supporting the interpretation that ISXRS involves localized core excitations and can be used to rapidly generate valence wavepackets.Comment: 10 pages, 5 figure

Time-dependent coupled-cluster for ultrafast spectroscopy

The ultimate reason for chemical reactivity is the electronic motion, occurring at an attosecond timescale. Until the last century, it was impossible to observe it directly, as the shortest available laser pulses had duration in the order of femtoseconds. Recent technological advances lead to sub-femtosecond laser pulses, making possible real-time observation and control of electron dynamics.My Ph.D. thesis aims to develop and implement a model for the interaction between ultrashort laser pulses and molecules. This is interesting as an extension of the theory and the computational tools available, to design experiments at laser facilities, and to predict and interpret their outcomes.The theoretical framework that we have chosen is the time-dependent coupled-cluster (TDCC) theory. We have implemented our code in the eT program, which represents the first released implementation of a TDCC method.After validating our procedures by comparison with the literature, we used our code to calculate the electronic response to a pump-probe sequence of laser pulses. We performed convergence tests of parameters on the LiH. Then, we observed and interpreted the effect of the delay between pump and probe pulses on the LiF transient absorption spectrum.We extended this implementation to a time-dependent equation-of-motion coupled-cluster (TD-EOM-CC) approach with the use of a reduced basis calculated with an asymmetric band Lanczos algorithm, and within the core-valence separation (CVS) approximation. This converged to the same spectral features as the TDCC but with much lower computational times, as we showed for LiF. We observed the limits of CVS approximation: for the LiH molecule, several peaks were not correctly retrieved. Finally, we modeled the transient absorption for the glycine molecule, which is a good candidate for experimental investigations.We also modeled the electronic impulsive stimulated Raman scattering (ISXRS) population transfer induced by an ultrashort laser pulse through the TD-EOM-CC model for Ne, CO, pyrrole, and p-aminophenol and visualized through a movie the real-time evolution of the electronic density of p-aminophenol.The significance of this work lies in the development of theoretical and computational tools to be used in attochemistry: one groundbreaking application can be the direct control of electrons, which would have a big impact on many research fields, like medicine, biology, and material science

Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.Comment: 23 pages, 17 figure

Systematic Investigation of Intermolecular Interactions in NEXAFS Spectroscopy

Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy can be used to study molecular packing and order in organic materials, but only if the spectroscopic effects of intermolecular interactions are well understood. This work aims to contribute to an improved general understanding of the roles of intermolecular interactions on NEXAFS spectroscopy by studying the effects of Rydberg quenching on the degree of Rydberg-valence mixing in saturated molecules and π-π interactions of unsaturated molecules. The effects of π-π interactions were systematically studied by using paracyclophane (PCP) molecules, in which the benzene/benzene separation distance can be systematically varied through the length of the spacer between benzene rings. The effects of Rydberg quenching on the degree of Rydberg-valence mixing in saturated molecules were systematically studied as a function of different crystalline polymorphs (orthorhombic and monoclinic) and chain lengths of n-alkane single crystals. The effects of π-π interactions with varied spacing between co-facial benzene rings in PCPs are observed and these intermolecular effects can be used to study molecular packing and order in unsaturated materials. This work explores the strengths and significance of the effects of π-π interactions on NEXAFS spectroscopy as a function of benzene-benzene separation distances. The effects of Rydberg quenching on the degree of Rydberg-valence mixing to the NEXAFS spectra are not significant between different n-alkanes crystalline polymorphs. However, linear dichroism effects were observed for these different n-alkane crystalline polymorphs. For a given a crystal structure (orthorhombic or monoclinic), the relative intensities of the two C-H peaks (287-288 eV) and the energy of the C-H band (287-288 eV) changed when X-ray linear horizontal polarization was aligned along the principal axes (X,Y) of individual crystals. In addition to the observed linear dichroism, the room temperature NEXAFS spectra of orthorhombic alkanes becomes broader as the alkane chain length decreased. This broadening of NEXAFS spectra is believed to be the result of increased molecular disorder and nuclear motion at room temperature. Nuclear motion effects refers to the energetically accessible molecular conformations present at the experimental temperature. In summary, this work is a significant contribution to the development a more comprehensive understanding of the influences of intermolecular interactions on NEXAFS spectroscopy

Inorganic Chiral Nanomaterials: Design Strategies and Their Properties

Interest in the synthesis of chiral nanostructures has been fueled by their prime fundamental and potential application of chiral nanostructures in biosensing, telecommunication, display technologies, diffraction-free patterning, and chiral catalysis. Although chirality is often associated with biochemistry due to numerous chiral biomolecules, today chiral inorganic nanostructures have attracted much attention, but their optical properties remain largely unexplored. Nanoscale inorganic chiral materials strongly rotate linear and circularly polarized light passing through them. Such optical effects are relatively easy to observe and are being actively investigated as a part of the study of chiral photonics and plasmonics. However, the opposite effects, the transfer of spin angular momenta of circularly polarized photons to materials and their subsequent nanoscale restructuring, are much less understood. In chapters II and III of this dissertation, I describe an experiment that demonstrates how circularly polarized light (CPL) affects dispersions of racemic nanoparticles (NPs). The intrinsic, non-covalent electrostatic, dipole-dipole, and van der Walls interactions, as well as hydrogen bonds between NPs combined to produce different types of NP superstructures. The transition from individual NPs to their superstructure assemblies can be easily controlled, visualized, and studied by different means. This strategy was applicable to various materials such as gold. By illuminating a seed-free gold ion dispersion with CPL, I could obtain optically active gold nanostructures. In chapter IV, I describe how I synthesized chiral cobalt oxide NPs using chiral molecules, namely, L- and D-cysteine as surface ligands. The chiral paramagnetic NPs showed ~ 10 times greater optical activity than other metal or semiconducting NPs of similar size. Moreover, the optical activities of the latter were mainly in the UV region while our NPs show practical activity in both the UV and visible ranges. The results of this study provide new opportunities for the design and synthesis of novel materials and contribute to a better understanding of materials at the nexus of magnetism and chirality.PHDMacromolecular Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/140792/1/jyeom_1.pd