Enzyme design is a steadily growing field of computational chemistry, but its successes are limited by the current available knowledge and application of enzyme conformational dynamics. In this work a series of FTIR and 2D IR spectroscopic methods, for observing the conformational dynamics of an enzymatic active site and its surrounding residues, are characterized. The enzyme model system for these studies is the promiscuous ene-reductase from Pyrococcus horikoshii (PhENR) which is capable of binding substrates in multiple orientations. In one method, the spectral lineshape of an aryl-nitrile substrate-analog vibrational label is analyzed using a frequency fluctuation correlation function (FFCF) and compared to the lineshape of a corresponding aryl-azide label. This analysis revealed dynamic and electrostatic active site anisotropy which may influence substrate catalysis. The second method utilizes the intramolecular vibrations of the enzymatic cofactor, flavin mononucleotide (FMN), which is shown to be sensitive to electric field changes associated with substrate binding. The final method places a site-specific nonnatural amino acid containing an azide probe within the enzyme’s hydrophobic core. Additionally, a double-mutant cycle was identified via a common design program, the Rosetta Modeling Suite, and used to analyze the effects of mutation on enzyme dynamics. Altogether, these methods demonstrate the ability of 2D IR spectroscopy to observe enzyme conformational dynamics. Application of these methods to various other enzyme model systems should provide valuable insight for the improvement of future dynamic enzyme design protocols.

Two-dimensional infrared spectroscopy (2D IR) is a powerful tool to investigate molecular structures and dynamics on femtosecond to picosecond time scales and is applied to diverse systems. Current technologies allow for the acquisition of a single 2D IR spectrum in a few hundreds of milliseconds using a pulse shaper and an array detector, but demanding applications require spectra for many waiting times and involve considerable signal averaging, resulting in data acquisition times that can be many days of laboratory measurement time. Compressive sampling is an emerging signal processing technique to reduce data acquisition time in diverse fields by requiring only a fraction of the traditional number of measurements while yielding much of the same information as the fully-sampled data. Here we combine cutting-edge 2D IR methodology with a novel compressive sampling reconstruction algorithm to reduce the data acquisition time of 2D IR spectroscopy without distorting lineshapes. We introduce the Generic Iteratively Reweighted Annihilating Filter (GIRAF) algorithm re-engineered to the specific problem of 2D IR reconstruction and show its effectiveness applied to various systems, including those with low signal, with multiple peaks, and with differing amounts of frequency shifting. Additionally, we lay the groundwork for 2D IR microscopic imaging using compressive sampling in the spatial image domain. The first instance of a single-pixel camera in the infrared is introduced.

The functional and pathogenic roles of biomolecules are often coupled to the self-association of their basic units into oligomers and aggregates whose structural details are difficult to distinguish because of their insoluble and heterogenous nature. This work focuses on DNA G-quadruplex motifs and amyloid peptides whose oligomers and aggregates are associated with numerous biological roles and human diseases. Infrared (IR) spectroscopy is a powerful tool which probes vibrational transitions whose signatures report on their arrangement within molecules. Advances in two-dimensional infrared (2D IR) spectroscopy have allowed structural characterization in increasingly complex biomolecules that are not amenable to traditional high-resolution techniques. However, careful consideration of the physical phenomena that lead to IR spectra are necessary to make accurate assignments. In the first portion of this work, using FTIR and 2D IR, we determine spectral markers that can differentiate size, metal ion coordination, and topology in DNA G-quadruplex motifs. IR studies aided by isotope labeling define the physical origin of these markers and allow for the construction of a structural landscape in parallel DNA G-quadruplex motifs. It is also shown that 2D IR and isotope editing probes site-specific structural changes in G-quadruplex motifs that can differentiate ion identity and location based on spectral shifts. In the latter portion of this work, we use a combination of spectroscopy and imaging techniques to show that a peptide derived from the human pro-apoptotic protein BAX forms amyloid aggregates whose structure is dependent on the presence of model membranes. Combined, the work in this thesis allows for the formulation of multiple hypotheses based on IR structural assignments regarding disease states and functional mechanisms of these systems.

Biochemische Prozesse treten in wässriger Umgebung auf und Wechselwirkungen der Wasserhülle mit Biomolekülen spielt eine Schlüsselrolle für deren Struktur und Funktion. In dieser Arbeit wird die Strukturdynamik der Wassermoleküle und Gegenionen in der umgebenden Wasserhülle der DNA mit der Methode der zweidimensionalen Infrarotspektroskopie (2D IR) sowie Anrege-Abfrage-Spektroskopie untersucht. Die Ergebnisse der vorliegenden Arbeit zeigt das starke Potenzial von Schwingungsmoden an Grenzflächen für die Abbildung und das Verständnis von Wechselwirkungen zwischen Biomolekülen und ihrer Wasserhülle. In Zukunft soll dieses Konzept auch auf andere Biomoleküle angewendet werden. / Biochemical processes occur in an aqueous environment and interactions of the water shell with biomolecules play a key role for their structure and function. In this thesis, the structural dynamics of water molecules and counterions in the hydration shell of DNA is investigated by two-dimensional infrared (2D IR) spectroscopy and pump-probe transient spectroscopy. 2D IR spectroscopy is a powerful technique that can track molecular couplings between different vibrational modes and structural fluctuations of the chemical environment on a femto- to picosecond time scale. In the present study, vibrational modes of the DNA backbone serve as probes located at the DNA-water interface. The results of this thesis demonstrate the strong potential of interfacial vibrational modes for mapping and understanding interactions between biomolecules and their water shell. In future, this concept will be applied to other biomolecular systems.

Mit Hilfe von linearer und nichtlinearer Infrarotspektroskopie im Femtosekundenbereich wurden Schwingungsdynamiken von H2PO4- und BH4- Ionen untersucht sowie ein Volumenplasmon in einem Schichtsystem aus Ga-dotiertem ZnO. Phosphatgruppen stellen Hydratisierungsstellen in Biomolekülen wie DNS oder Phospholipiden dar und wechselwirken intensiv mit wässrigen Solvatationsschalen. Die Untersuchung einer isolierten Phosphatgruppe in Wasser, dem Phosphation H2PO4-, hat ergeben, dass Phosphatschwingungen sehr sensitive Sonden für die ausgeprägte Fluktuationsdynamik von Volumenwasser darstellen, was experimentell mit homogen verbreiterten Linienformen nachgewiesen werden konnte. Komplexe Hydride wie NaBH4 werden wegen ihres großen Wasserstoffgehalts als potenzielle Wasserstoff- bzw. Energieträger für mobile Anwendungen diskutiert. Jedoch ist die Wasserstoffabsorption- bzw. emission energieaufwendig. Für ein detailliertes Verständnis der Wasserstoffdynamiken im BH4- Tetraeder wurden die Energieverlustkanäle nach optischer Anregung von B-H Schwingungen untersucht. Es konnte experimentell gezeigt werden, dass eine Energieumverteilung von hoch- zu niederfrequenten B-H Schwingungen stattfindet mit abschließender Dissipation in das umgebende Medium, z.B. ein Lösungsmittel oder ein NaBH4 Festkörper. Volumenplasmonen repräsentieren kollektive, longitudinale Anregungen eines freien Elektronengases in ionischen oder polaren Kristallstrukturen. In einer hoch Ga-dotierten ZnO-Schicht eines speziellen Schichtsystems konnte eine Volumenplasmon in Reflektionsgeometrie optisch angeregt werden. Dabei führte Intrabandanregung von Leitungsbandelektronen zur Erhitzung des Elektronengases und, durch das nichtparabolische ZnO-Leitungsband, zu einer Erhöhung der effektiven Elektronenmasse und damit zu einer Rotverschiebung der Plasmafrequenz auf einer sub-ps Zeitskala. Damit konnte ein Mechanismus aufgezeigt werden, um Plasmafrequenzen von Volumenplasmonen gezielt transient zu kontrollieren. / The vibrational dynamics of H2PO4- and BH4- ions and a bulk plasmon in Ga-doped ZnO were studied with methods of linear and nonlinear infrared spectroscopy in the femtosecond range. Phosphates constitute the major hydration sites of biomolecules such as DNA or phospholipds and, thus, strongly interact with aqueous hydrations shells. The investigation of isolated phosphate ions (H2PO4-) revealed a distinct sensitivity of phosphate vibrations on the fluctuation dynamics of bulk water that could be experimentally shown by homogeneously broadened line shapes of phosphate vibrations. Complex hydrides such as NaBH4 constitute a large hydrogen content and, accordingly, are discussed as energy- and hydrogen carriers for mobile applications. However, hydrogen uptake and release are energetically unfavourable. In order to gain detailed insights into hydrogen dynamics within the BH4- tetrahedrons energy relaxation mechanisms were studied after optical excitation of B-H vibrations. It could be experimentally shown that energy dissipation proceeds from high-frequency to low-frequency B-H vibrations into the heat bath of the environment, such as e.g. a liquid solvent or the solid state NaBH4. Bulk plasmons represent collective, longitudinal excitations of a free electron gas in an ionic or polar crystal. Within a specifically designed system of Ga-doped ZnO layers, a bulk plasmon could be optically excited in a reflection geometry. Intraband excitation of conduction band electrons resulted in a heating of the electron gas. Due to a non-parabolic ZnO conduction band hot electrons exhibit an increased effective electron mass and, thereby, reduce the plasma frequency. A redshift of the bulk plasma frequency that possesses sub-ps dynamics could be experimentally shown which represents a mechanism for the time-dependent control of plasma frequencies.

The overarching objective of the investigations discussed herein is the development of a model experimental system for surface-enhanced infrared absorption (SEIRA) spectroscopy, with potential applicability in higher order infrared spectroscopic techniques, specifically, surface-enhanced two-dimensional infrared (SE-2D IR) spectroscopy. Theoretical predictions that accurately predict the stability of functionalized nanoparticles enable guided design of their properties but are often limited by the accuracy of the parameters used as model inputs. Hence, first, such parameterization limitations for the extended DLVO (xDLVO) theory are overcome using a size-dependent Hamaker constant for gold, interfacial surface potentials, and tilt angles of self-assembled monolayers (SAMs), which collectively improves the predictive power of xDLVO theory for modeling nanoparticle stability. Measurements of electrical properties of functionalized gold nanoparticles validate the predictions of xDLVO theory using these new parameterizations illustrating the potential for this approach to improve the design and control of the properties of functionalized gold nanoparticles in various applications. Next, a series of experiments were conducted to elucidate the behavior of various infrared active molecules in the presence of spherical gold nanoparticles of average diameter ∼20 nm. Here, the spectroscopic anomalies, specifically the shifted vibrational frequency and the dispersive lineshape observed in the infrared spectra for SCN- in the presence of gold nanoparticles provide direct evidence of SIERA. Nevertheless, it was evidenced that nanomaterial with plasmonic properties that extends into the infrared wavelengths are imperative in observing efficient infrared enhancements. Hence, nanomaterial indicating plasmonic properties extending into the infrared wavelengths were synthesized via a straightforward, seedless, one-pot synthesis. The gold nanostars prepared here indicated plasmonic behavior clearly extending into the near infrared, with simple plasmonic tunability via changing the buffer concentration used during synthesis. The systematic understanding achieved here in terms of theoretical prediction of nanoparticle stability, origin of infrared spectral anomalies in the presence of nanomaterials, and the preparation of infrared plasmonic material, collectively provides a resilient framework for the further investigation of surface-enhanced infrared spectroscopic techniques including SEIRA and SE-2D IR spectroscopies.

Successful enzyme catalysis depends on many noncovalent interactions between the enzyme, cofactors, and substrate that poise the system to access a productive transition state. Motions on a variety of timescales contribute to this, but some controversy exists surrounding the role of ultrafast dynamics on catalysis. Site-specific 2D IR spectroscopy using probes of vibrational dynamics provides the opportunity to explore ultrafast motions in an enzyme active site owing to the technique’s spatial and temporal resolution. In this work, a series of aryl-azide vibrational labels were assessed using a variety of 2D IR techniques for their sensitivity to solvent and energy transfer processes, and their ability to be adapted to experiments in biomacromolecules. One of these labels, 4-azido-N-phenylmaleimide, is a substrate analog for the promiscuous ene-reductase from Pyrococcus horikoshii (PhENR). The label was covalently attached in two orientations in the enzyme active site, occupying the same position as native substrates based on X-ray crystallography and molecular dynamics simulations. FTIR and 2D IR spectroscopy were used to identify close-lying conformational states based on the strong anharmonic coupling of the label, revealing that the active site itself modulates the probe’s internal vibrational coupling. More commonly used analogous aryl-nitrile labels, however, were not sensitive to such small structural and lineshape changes. This demonstrates the importance of thoughtful label design to maximize the amount of information that can be gleaned from 2D IR studies. Using the methods herein—both spectroscopic and biochemical—provides a strategy for probing ultrafast motions that could possibly be catalytically relevant.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Die Struktur von DNS Molekülen und ihre Wechselwirkung mit Wasser werden seit langer Zeit heiß diskutiert. In der vorliegenden Arbeit wird nichtlineare Spektroskopie zur Untersuchung dieser Systeme angewendet. Oligomere, die aus 23 alternierenden Adenin-Thymin-Basenpaaren bestehen und eine Doppelhelix bilden, wurden mit Hilfe von 2D IR Spektroskopie für verschiedene Hydratisierungsgrade untersucht. Für DNS-Filme bei 0% relativer Feuchte (r.F.) erlauben die transienten Spektren eine Unterscheidung der NH Streckschwingung von Thymin ((NH)), der symmetrischen und asymmetrischen NH2 Streckschwingung von Adenin (s(NH2) and a(NH2)) sowie die Bestimmung der jeweiligen Linienprofile. Die Spektren zeigen eine homogene Verbreiterung für die (NHT) wohingegen die s(NH2) and a(NH2) eine ausgeprägte und zeitunabhängige inhomogene Verbreiterung zeigen, welche auf Unordnungen in der DNS-Struktur hinweisen. Außerdem kann Energietransfer von der a(NH2) zur (NH) beobachtet werden. Bei Erhöhung der r.F. hat die erhöhte Anzahl von Wassermolekülen nur einen geringen Einfluss auf die Positionen und Linienprofile der NH Streckschwingungen. Dadurch wird nahegelegt, dass die spektrale Dynamik vom DNS Molekül selbst und nicht vom umgebenen Wasser bestimmt ist. Im Gegensatz dazu zeigt die OH Streckmode der Wasserhülle um die DNS spektrale Diffusion auf einer 500 fs Zeitskala. Guanosin-Cytidin(GC)-Basenpaare wurden in Chloroformlösung untersucht, um die Wechselwirkung zwischen Basenpaaren zu verstehen. Dabei wurden die NH Schwingungen in einer local mode Darstellung betrachtet, die zwei freie NH Gruppen von G und C und drei wasserstoffverbrückte NH Gruppen beeinhaltet. Die Kopplungen und Relaxationsdynamik der NH Streckanregungen wurden mit Femtosekunden-Pump-Probe und 2D IR Experimenten studiert. Die Ergebnisse zeigen eine Verringerung der Lebensdauer mit der Bildung von Wasserstoffbrücken sowie Energietransfer zwischen zwei wasserstoffverbrückten NH Streckschwingungen. / The structure of DNA molecule and the interactions with its surrounding water is a hot topic for long time. In this thesis, we employ the nonlinear spectroscopy, including femtosecond pump-probe and two-dimensional infrared (2D IR) experiment, to study the vibrational dynamics of the systems. Double-stranded DNA short oligomers containing 23 alternating adenine-thymine base pairs were studied at different hydration levels by femtosecond 2D IR spectroscopy. For a DNA film at 0% relative humidity, the transient spectra enable a separation of the NH stretching mode of thymine from the symmetric and asymmetric NH2 stretching modes of adenine and determine the individual line shapes. For the NH stretch of thymine, the spectra demonstrate an essential homogeneous broadening, whereas for the symmetric and asymmetric NH2 stretches a pronounced and time-independent inhomogeneous broadening suggests a disorder in DNA structure. An energy transfer from the asymmetric NH2 stretch of adenine to the NH stretch of thymine is also observed. When the relative humidity increases, the increased water molecules have limited influence on the positions and line shapes of NH stretching frequencies, suggesting the spectral dynamics governed by DNA rather than water fluctuations. In contrast, the OH stretching mode of water shell around hydrated DNA undergoes a spectral diffusion on a 500 fs time scale, which is slower than the neat water. The guanosine-cytidine (GC) base pairs in chloroform solution were investigated to understand the interactions within base pairs. A local mode representationof NH stretching mode is adopted, consisting two free NH groups of G and C and three hydrogen bonded NH groups. The coupling and relaxation dynamics of the NH stretching excitations are studied by femtosecond pump-probe and 2D IR experiments. The results demonstrate a lifetime shortening upon the formation of hydrogen bonds, and an energy transfer between two hydrogen-bonded NH stretches.

Die Energierelaxationsdynamik und strukturelle Dynamik der DNA spielen eine entscheidende Rolle für das Verständnis der photochemischen Eigenschaften und biologischen Funktion von DNA. Die schnellsten Prozesse geschehen dabei auf Zeitskalen im Femto- bis Pikosekundenbereich und können durch zeitaufgelöste (ultraschnelle) Messungen an molekularen Schwingungsanregungen in Echtzeit beobachtet werden. In dieser Arbeit werden NH-Streck Schwingungsmoden der Nukleobasen sowie OH-Streckmoden der Hydrathülle mittels linearer infrarot (IR) Spektroskopie sowie ultraschneller Pump-Probe und zweidimensionaler IR Spektroskopie untersucht. Messungen an monomerartigen Nukleobasen, wasserstoffverbrückten Nukleobasenpaaren und kurzen DNA Fragmenten in Doppelhelixstruktur ermöglichen es, die Effekte der verschiedenen Wasserstoffbrücken und Schwingungskopplungen separat voneinander zu untersuchen. Im Zusammenspiel mit exzitonischen und quantenchemischen Rechnungen werden so weitreichende Einsichten in die spektroskopischen Eigenschaften und die Relaxationsdynamik von Schwingungsanregungen in DNA gewonnen. Es wird u.a. gezeigt, dass Wasserstoffbrücken zwischen Nukleobasen eine Lebensdauer größer 1 ps besitzen und eine beschleunigte Energierelaxation durch Fermiresonanzen mit niederfrequenten Schwingungsmoden des Fingerprintbereichs bewirken. Die DNA-Hydrathülle zeigt eine ultraschnelle strukturelle Dynamik unabhängig von der Basenpaarzusammensetzung und fungiert als effiziente Wärmesenke für hochfrequente Schwingungsanregungen. / Energy relaxation and structural dynamics in DNA play a crucial role for the understanding of the photochemical properties and biological function of DNA. The fastest of such processes occur on the femto- to picosecond time scale and can be followed in real time through time-resolved (ultrafast) measurements on molecular vibrations. In this work, NH stretching excitations of nucleobases and OH stretching modes of the hydration shell are analyzed through linear infrared (IR) spectroscopy as well as ultrafast pump-probe and two-dimensional IR spectroscopy. Measurements on monomeric nucleobases, hydrogen-bonded nucleobase pairs, and short DNA fragments in double helix structure allow one to examine the effects of the different hydrogen bonds and vibrational couplings separately from each other. The combination with excitonic and quantum chemical calculations provides profound new insights into the spectroscopic properties and relaxation dynamics of vibrational excitations in DNA. This work shows that hydrogen bonds between nucleobases have a lifetime greater than 1 ps and lead to an accelerated dissipation of energy due to Fermi resonances with vibrational modes in the fingerprint range. The hydration shell of DNA exhibits ultrafast structural dynamics independent of the base pair composition and serves as an efficient heat sink for high-energy vibrational excitations.