Chemistry Commons^™

Spectroscopic And Computational Studies Of Reversible O2 Binding By A Cobalt Complex Of Relevance To Cysteine Dioxygenase, Anne A. Fischer, Sergey V. Lindeman, Adam T. Fiedler

Chemistry Faculty Research and Publications

The substitution of non-native metal ions into metalloenzyme active sites is a common strategy for gaining insights into enzymatic structure and function. For some nonheme iron dioxygenases, replacement of the Fe(II) center with a redox-active, divalent transition metal (e.g., Mn, Co, Ni, Cu) gives rise to an enzyme with equal or greater activity than the wild-type enzyme. In this manuscript, we apply this metal-substitution approach to synthetic models of the enzyme cysteine dioxygenase (CDO). CDO is a nonheme iron dioxygenase that initiates the catabolism of L-cysteine by converting this amino acid to the corresponding sulfinic acid. Two mononuclear …

Racemic And Enantiopure Forms Of 3‐Ethyl‐3‐Phenylpyrrolidin‐2‐One Adopt Very Different Crystal Structures, Arcadius V. Krivoshein, Sergey V. Lindeman, Tatiana V. Timofeeva, Victor N. Khrustalev

Chemistry Faculty Research and Publications

3‐Ethyl‐3‐phenylpyrrolidin‐2‐one (EPP) is an experimental anticonvulsant based on the newly proposed α‐substituted amide group pharmacophore. These compounds show robust activity in animal models of drug‐resistant epilepsy and are thus promising for clinical development. In order to understand pharmaceutically relevant properties of such compounds, we are conducting an extensive investigation of their structures in the solid state. In this article, we report chiral high‐performance liquid chromatography (HPLC) separation, determination of absolute configuration of enantiomers, and crystal structures of EPP. Preparative resolution of EPP enantiomers by chiral HPLC was accomplished on the Chiralcel OJ stationary phase in the polar‐organic mode. Using …

Spectral Characterization Of Cytochromes P450 Active Sites Using Nmr And Resonance Raman Spectroscopy, Remigio Usai

Dissertations (1934 -)

The Cytochrome P450 (P450s) has been the subject of intense research for over six decades. An efficient approach for isotopic labeling of the prosthetic group in heme proteins was exploited to produce an analogue of the soluble bacterial cytochrome P450cam (P450cam) that contains a 13C labeled-protoheme prosthetic group. HU227 strain of E. coli, which lacks the δ-aminolevulinic acid (δ-ALA) synthase gene, was employed in the heterologous expression of P450cam harboring a prosthetic group labeled with 13C at the Cm and Cα positions by growing cells in the presence of [5-13C] δ-ALA, which was synthesized in four steps from [2-13C] glycine. …

Nucleotide-Dependent Preferential Localization Of Ras In Model Membranes With Lipid Raft Nanodomains, Anna Shishina

Dissertations (1934 -)

Membrane proteins constitute a third of all proteins in the cell and more than 50% of drug targets. However, the analysis of membrane proteins has many challenges owing to their partially hydrophobic surfaces, flexibility and lack of stability. One example of an essential membrane protein is Ras superfamily. Ras is a small monomeric GTPase involved in regulation of cell growth, proliferation and differentiation. Therefore, Ras and its effectors are among the most important targets for cancer therapy. A detailed knowledge of the processes occurring during signal propagation via Ras might help to elucidate the mechanisms of the involved signal cascades. …

Spin Crossover Behavior Of N-Confused C-Scorpionate Complexes Of Iron(Ii) Trifluoromethanesulfonate, Kristin Joy Meise

Master's Theses (2009 -)

An understanding of the molecular properties that influence highly-cooperative SCO behavior is critical in the development of new electronic materials. The purpose of this thesis work is to more fully examine whether hydrogen bonding interactions can be used to assemble iron(II) scorpionate complexes and whether this leads to abruptness in the SCO behavior. In this contribution, new N-confused C-scorpionate ligands are prepared with two ‘normal’ pz* groups ( = 3,5-dimethylpyrazol-1yl) and a ‘confused’ pyrazolyl with either an N-H, HL*, or an N-Tosyl (Tosyl = p-toluenesulfonyl), TsL*, bound to a central methine. These bulky ligands complement those previously described, HL and …

Ruthenium Catalyzed Deaminative Coupling Reaction Of Amines Via C-N Bond Activation, Pandula T. Kirinde Arachchige

Master's Theses (2009 -)

C–N bond activation via transition-metal catalyst has attracted much attention during the past two decades. This strategy has become one of the most promising way to generate secondary amines, which are very important in a broad spectrum of applications in pharmaceutical industry, synthetic organic chemistry and material science. The secondary amines can be utilized as an important synthetic intermediate for further manipulations. The in-situ formed catalytic system generated from the tetranuclear Ru–H complex with 4-(1,1-dimethylethyl)-1,2-benzenediol ligand was found to be effective for the synthesis of secondary amines from the direct deaminative coupling of amines. The ruthenium catalyst was highly effective …

Altering The Coordination Of Iron Porphyrins By Ionic Liquid Nanodomains In Mixed Solvent Systems, Abderrahman Atifi, Michael D. Ryan

Chemistry Faculty Research and Publications

The solvent environment around iron porphyrin complexes was examined using mixed molecular/RTIL (room temperature ionic liquid) solutions. The formation of nanodomains in these solutions provides different solvation environments for substrates that could have significant impact on their chemical reactivity. Iron porphyrins (Fe(P)), whose properties are sensitive to solvent and ligation changes, were used to probe the molecular/RTIL environment. The addition of RTILs to molecular solvents shifted the redox potentials to more positive values. When there was no ligation change upon reduction, the shift in the E° values were correlated to the Gutmann acceptor number, as was observed for other …

When Substituents Do Not Matter: Frontier Orbitals Explain The Unusually High And Invariant Oxidation Potential In Alkoxy-, Alkyl-, And H-Substituted Iptycenes, Maxim V. Ivanov, Denan Wang, Shriya Wadumethrige, Rajendra Rathore

Chemistry Faculty Research and Publications

Frontier molecular orbitals (FMOs) have played a critical role in predicting reactivity/selectivity of pericyclic reactions. Here we show that the structurally similar iptycene-based hydroquinone ether (HE), that is, ^MeOIpt and ^BOHE/^BHHE, molecules have drastically different ordering of bisallylic and quinoidal FMOs. They are almost degenerate in ^BOHE/^BHHE, while in ^MeOIpt, the bisallylic orbital lies far below the quinoidal HOMO. Oxidation of ^BOHE/^BHHE induces coplanarization of the methoxy group and destabilizes the bisallylic HOMO, leading to a relatively low oxidation potential. In ^MeOIpt, considerable energy …

Bimetallic Cooperativity In Proton Reduction With An Amido‐Bridged Cobalt Catalyst, Kenneth K. Kpogo, Shivnath Mazumder, Denan Wang, H. Bernhard Schlegel, Adam T. Fiedler, Cláudio N. Verani

Chemistry Faculty Research and Publications

The bimetallic catalyst [Co^II₂(L¹)(bpy)₂]ClO₄ (1), in which L¹ is an [NN′₂O₂] fused ligand, efficiently reduced H⁺ to H₂ in CH₃CN in the presence of 100 equiv of HOAc with a turnover number of 18 and a Faradaic efficiency of 94 % after 3 h of bulk electrolysis at −1.6 V (vs. Ag/AgCl). This observation allowed the proposal that this bimetallic cooperativity is associated with distance, angle, and orbital alignment of the two Co centers, as promoted by the unique Co−N_{amido …}

Mqct. I. Inelastic Scattering Of Two Asymmetric-Top Rotors With Application To H2O + H2O, Alexander Semenov, Dmitri Babikov

Chemistry Faculty Research and Publications

A mixed quantum/classical theory (MQCT) for the inelastic collision of two asymmetric-top rotor molecules is developed. In this method, the quantum state-to-state transitions between the rotational states of molecules (internal) are treated quantum mechanically using the time-dependent Schrodinger equation, whereas their relative translational motion (responsible for scattering) is treated classically, using the average trajectory approach. Two versions of the formula for transition matrix elements are presented: a straightforward approach that uses numerical multidimensional quadrature over all the internal degrees of freedom and a more standard analytic approach that uses the expansion of the PES over the basis set of spherical …

Unraveling The Coulombic Forces In Electronically Decoupled Bichromophoric Systems During Two Successive Electron Transfers, Maxim V. Ivanov, Shriya Wadumethrige, Denan Wang, Rajendra Rathore

Chemistry Faculty Research and Publications

Coulombic forces are vital in modulating the electron transfer dynamics in both synthetic and biological polychromophoric assemblies, yet quantitative studies of the impact of such forces are rare, as it is difficult to disentangle electrostatic forces from simple electronic coupling. To address this problem, the impact of Coulombic interactions in the successive removal of two electrons from a model set of spirobifluorenes, where the interchromophoric electronic coupling is nonexistent, is quantitatively assessed. By systematically varying the separation of the bifluorene moieties using model compounds, ion pairing, and solvation, these interactions, with energies up to about 0.4 V, are absent at …

Analysis Of Ultrafast Transient Absorption Spectroscopy Data Using Integrative Data Analysis Platform: 1. Data Processing, Fitting, And Model Selection, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

This manuscript describes a workflow for analysis of transient absorption (TA) spectroscopy data using Integrative Data Analysis Platforms (IDAP) software package. Time-dependent spectral series are analyzed through evaluation of the isosbestic point and kinetics of excited state and ground-state bleach decays. Model fitting and selection based on Akaike's Information Criterion is discussed. As a practical example, we analyze excitation decays of a common protein label, Alexa Fluor 647.

Redox And Spectroscopic Properties Of Protonated Species Of Iron Porphyrin Nitroxlys And Their Analogues, Md. Hafizur Rahman

Dissertations (1934 -)

Nitrite reduction to ammonia or nitrous oxide involves a series of electron transfer and protonation steps which are carried out by assimilatory or dissimilatory nitrite reductases. In the assimilatory process, nitrite incorporated into the biomass while in the dissimilatory process, it is excreted from the cell and the reaction is a source of energy. The complexes that will be studied in this work are models for assimilatory (siroheme) and dissimilatory (heme d1 ) nitrite reductases. Iron porphyrin nitrosyls were reduced in the presence of weak acids such as phenol and substituted phenols. Voltammetric techniques such as cyclic and rotating ring …

Design And Synthesis Of Selective Estrogen Receptor Β Agonists And Their Pharmacology, K. L. Iresha Sampathi Perera

Dissertations (1934 -)

Estrogens (17β-estradiol, E2) have garnered considerable attention in influencing cognitive process in relation to phases of the menstrual cycle, aging and menopausal symptoms. However, hormone replacement therapy can have deleterious effects leading to breast and endometrial cancer, predominantly mediated by estrogen receptor-alpha (ERα) the major isoform present in the mammary gland and uterus. Further evidence supports a dominant role of estrogen receptor-beta (ERβ) for improved cognitive effects such as enhanced hippocampal signaling and memory consolidation via estrogen activated signaling cascades. Creation of the ERβ selective ligands is challenging due to high structural similarity of both receptors. Thus far, several ERβ …

Mixed Quantum/Classical Theory (Mqct) For Rotationally And Vibrationally Inelastic Scattering And Its Application To The Molecules Of Astrochemical Importance, Alexander Semenov

Dissertations (1934 -)

This thesis presents developments and applications of the mixed quantum/classical theory (MQCT) for inelastic scattering. In this approach, translational motion of collision partners is treated classically, while the internal degrees of freedom – rotational and/or vibrational motion – are treated quantum mechanically. Within this framework calculations of rotationally inelastic cross sections are carried out in a broad range of collision energies and results are compared against the exact full quantum data for several real systems. For CO +He, N2 + Na and H2 + He the agreement is excellent through six orders of magnitude range of cross sections values and …

Functional And Structural Studies Of Cytochromes P450 By Resonance Raman Spectroscopy, Yilin Liu

Dissertations (1934 -)

Cytochrome P450 is a broad class of heme monooxygenase enzymes which catalyze various oxidative transformations. There are two main kinds of mammalian P450s: steroidogenic and drug metabolizing P450s. The first project involves a steroidogenic P450, CYP17A1, occupying a central role in the biosynthesis of steroid hormones. It catalyzes hydroxylation reaction on pregnenolone and progesterone, generating 17OH-pregnenolone and 17OH-progesterone, presumably utilizing a “Compound I” species. However, these hydroxylated products can be further processed in a second oxidative cycle to cleave the C17–C20 bond to form dehydroepiandrosterone or androstenedione, respectively, a crucial step in androgen production. Interestingly, it is well known that …

Reactivity Of (1-Methoxycarbonylpentadienyl)Iron(1+) Cations With Hydride, Methyl, And Nitrogen Nucleophiles, Yuzhi Ma, Young K. Yun, Julie L. Wondergem, Anobick Sar, Jayapal Reddy Gone, Sergey V. Lindeman, William A. Donaldson

Chemistry Faculty Research and Publications

The reaction of tricarbonyl and (dicarbonyl)triphenylphosphine (1-methoxycarbonyl-pentadientyl)iron(1+) cations 7 and 8 with methyl lithium, NaBH₃CN, or potassium phthalimide affords (pentenediyl)iron complexes 9a-c and 11a-b, while reaction with dimethylcuprate, gave (E,Z-diene)iron complexes 10 and 12. Oxidatively induced-reductive elimination of 9a-c gave vinylcyclopropanecarboxylates 17a-c. The optically active vinylcyclopropane (+)-17a, prepared from (1S)-7, undergoes olefin cross-metathesis with excess (+)-18 to yield (+)-19, a C9C16 synthon for the antifungal agent ambruticin. Alternatively reaction of 7 with methanesulfonamide or …

Toward Reliable Modeling Of S-Nitrosothiol Chemistry: Structure And Properties Of Methyl Thionitrite (Ch3sno), An S-Nitrosocysteine Model, Dmitry Khomyakov, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Methyl thionitrite CH₃SNO is an important model of S-nitrosated cysteine aminoacid residue (CysNO), a ubiquitous biological S-nitrosothiol (RSNO) involved in numerous physiological processes. As such, CH₃SNO can provide insights into the intrinsic properties of the —SNO group in CysNO, in particular, its weak and labile S—N bond. Here, we report an ab initio computational investigation of the structure and properties of CH₃SNO using a composite Feller-Peterson-Dixon scheme based on the explicitly correlated coupled cluster with single, double, and perturbative triple excitations calculations extrapolated to the complete basis set limit, CCSD(T)-F12/CBS, with a number of …

Effect Of Facial Encumbrance On Excimer Formation And Charge Resonance Stabilization In Model Bichromophoric Assemblies, Brandon Uhler, Maxim V. Ivanov, Damian Kokkin, Neil Reilly, Rajendra Rathore, Scott A. Reid

Chemistry Faculty Research and Publications

Excimer formation and charge resonance stabilization in covalently linked bichromophoric systems with flexible spacers are important processes relevant to biochemistry and functional materials. Requiring a π-stacked cofacial arrangement of a pair of aromatic molecules at a van der Waals contact, the underlying geometrical reorganization that accompanies these events continues to be debated. Here we use a variety of methods including two-color resonant two-photon ionization spectroscopy (2CR2PI), ion yield measurements, hole-burning spectroscopy (HB), and laser-induced fluorescence (LIF) excitation and emission spectroscopy to compare the gas-phase spectroscopy and dynamics of the van der Waals dimers of fluorene, 9-methylfluorene (MF), and 9,9′-dimethylfluorene (F1). …

Resolving Three-State Ligand-Binding Mechanisms By Isothermal Titration Calorimetry: A Simulation Study, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

In this paper, I theoretically analyzed ITC profiles for three-state equilibria involving ligand binding coupled to isomerization or dimerization transitions. Simulations demonstrate that the mechanisms where the free or ligand-bound protein undergoes dimerization (such that the ligand cannot bind to or dissociate from the dimer) produce very distinctive titration profiles. In contrast, profiles of the pre-existing equilibrium or induced-fit models cannot be distinguished from a simple two-state process, requiring data from additional techniques to positively identify these mechanisms.

Serendipitous Discovery Of Light-Induced (In Situ) Formation Of An Azo-Bridged Dimeric Sulfonated Naphthol As A Potent Ptp1b Inhibito, Robert D. Bongard, Michael Lepley, Khushabu Thakur, Marat R. Talipov, Jaladhi Nayak, Rachel A. Jones Lipinski, Chris Bohl, Noreena Sweeney, Ramani Ramchandran, Rajendra Rathore, Daniel S. Sem

Chemistry Faculty Research and Publications

Background

Protein tyrosine phosphatases (PTPs) like dual specificity phosphatase 5 (DUSP5) and protein tyrosine phosphatase 1B (PTP1B) are drug targets for diseases that include cancer, diabetes, and vascular disorders such as hemangiomas. The PTPs are also known to be notoriously difficult targets for designing inihibitors [sic] that become viable drug leads. Therefore, the pipeline for approved drugs in this class is minimal. Furthermore, drug screening for targets like PTPs often produce false positive and false negative results.

Results

Studies presented herein provide important insights into: (a) how to detect such artifacts, (b) the importance of compound re-synthesis and verification, and …

Nmr Line Shape Analysis Of A Multi-State Ligand Binding Mechanism In Chitosanase, Shoko Shinya, Mariana G. Ghinet, Ryszard Brzezinski, Kyoko Furuita, Chojiro Kojima, Sneha Shah, Evgenii L. Kovrigin, Tamo Fukamizo

Chemistry Faculty Research and Publications

Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomerization of the bound-state into the final conformation. Mapping of the chemical shift perturbations in two sequential steps of the mechanism highlighted involvement of the substrate-binding subsites and the hinge region in the binding reaction. Equilibrium parameters of the three-state model agreed with the overall thermodynamic dissociation constant determined by ITC. This study presented the first …

Synthesis And Study Of The Electrochemical And Optoelectronic Properties Of Π-Conjugated Poly-P-Phenylene-Based Molecular Wires, Anitha Boddeda

Dissertations (1934 -)

Organic photovoltaics will play an important role in supplementing the energy needs of the twenty first century in a most cost-effective way to convert the solar energy into usable forms of energy. One of the bottlenecks in promoting widespread use of photovoltaic devices for solar energy storage is the inefficiency of the devices, which in part arises due to the inefficient charge separation and long-range charge transport. Design and synthesis of efficient charge-transfer materials would require one to first identify and establish the structural features necessary in a given molecular wire, which may promote effective charge transfer to long distances. …

Computational Modeling Of S-Thiolation Reaction: Toward Discovering The Enzymatic Mechanisms Of Endogenous Hno Formation, Elena Ivanova

Dissertations (1934 -)

S-nitrosothiols (RSNOs) have long been proposed as potential sources of the elusive endogenous nitroxyl (HNO) via S-thiolation reaction with thiols. It is however not clear how S-thiolation can compete with the trans-S-nitrosation pathway commonly observed in vitro. Based on the insights into the highly unusual, antagonistic chemical nature of RSNO molecules, we hypothesize that, while difficult in vitro, S-thiolation could easily lend itself to enzymatic catalysis. To explore this possibility, we adopted a bottom-up computational approach that aims to identify possible catalytic mechanisms able to steer the RSNO + thiol reaction toward HNO production. Inspired by recent discovery of small …

Ruthenium-Catalyzed Dehydrogenative And Dehydrative C-H Coupling Reactions Of Arenes With Alcohols And Carbonyl Compounds, Hanbin Lee

Dissertations (1934 -)

Despite their outstanding achievements, the requirement of preformed functional groups and wasteful byproduct formation are inherent disadvantages associated with the transition metal catalyzed cross-coupling methods. Inspired by the needs for green and sustainable chemistry, transition metal catalyzed dehydrogenative and dehydrative coupling methods have been recognized as environmentally sustainable and atom economical synthetic routes for the new C-C bond formation. The catalytic activation of C-H and C-O bonds allows the formation of coupling products from ubiquitous hydrocarbon substrates by releasing hydrogen or water byproduct. However, these novel protocols require relatively harsh conditions due to their low reactivity of C-H and C-O …

Theoretical Study Of Ozone Forming Recombination Reaction And Anomalous Isotope Effect Associated With It, Alexander Teplukhin

Dissertations (1934 -)

The ozone forming recombination reaction stands out among many chemical processes that take place in the atmosphere. This reaction is responsible for the reconstruction of ozone layer, which protects life on Earth from harmful ultra-violate radiation and is a source of so-called anomalous isotope effect in ozone. The reaction was intensively studied, but at a very basic level. There were only couple of papers where the recombination rate coefficient was computed and found to roughly agree with the experimental data. In this dissertation, the recombination process in ozone is approached using new and efficient method, which includes several modern techniques. …

On The Structure And Properties Of S-Nitrosated Cysteine Models: A Computational Study, Dmitry Khomyakov

Dissertations (1934 -)

S-Nitrosation of cysteine (Cys) residues, a covalent modification of its S atom by NO group, is a major post-translational modification of proteins. Despite the importance of S-nitrosoproteins in numerous physiological processes, lability of the S-nitrosothiol (-SNO) group hinders the research progress. In this work, computational chemistry methods were applied to S-nitrosated cysteine (CysNO) models to gain a deeper insight into its structure and properties. First, we obtained the most accurate at the moment computational estimation of the molecular structure and properties of CH3SNO model molecule using Feller-Peterson-Dixon (FPD) ab initio protocol. The S–N bond length in cis- CH3SNO is calculated …

Oxygen Activation By Mononuclear Mn, Co, And Ni Centers In Biology And Synthetic Complexes, Adam T. Fiedler, Anne A. Fischer

Chemistry Faculty Research and Publications

The active sites of metalloenzymes that catalyze O₂-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O₂ at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O₂ reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or …

Isolation Of A Chiral Anthracene Cation Radical: X-Ray Crystallography And Computational Interrogation Of Its Racemization, Mikhail V. Ivanov, Khushabu Thakur, Anshul Bhatnagar, Rajendra Rathore

Chemistry Faculty Research and Publications

Chiral cation-radical salts hold significant promise as charge-transfer materials, chiroptical switches, and electron-transfer catalysts for enantioselective synthesis. Herein we demonstrate that the readily-available chiral 9,10-diphenyleanthracene derivative (i.e.^SANT) forms a robust cation radical, whose structure was elucidated by X-ray crystallography and DFT calculations. While ^SANT was observed to racemize on a timescale (t_1/2) of 1.1 hours, a computational conformational search and kinetic analysis of the racemization pathway led us to identify a simple methyl substituted ^SANT derivative, which does not racemize (racemization t_1/2 10¹³–10¹⁷ years).

Modeling Of S‐Nitrosothiol–Thiol Reactions Of Biological Significance: Hno Production By S‐Thiolation Requires A Proton Shuttle And Stabilization Of Polar Intermediates, Lena V. Ivanova, Daniel Cibich, Gregory Deye, Marat R. Talipov, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S‐thiolation reaction between thiols and S‐nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S‐thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge‐separated zwitterionic intermediate structure RSS⁺(R)N(H)O⁻ (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S−S …