Open Access. Powered by Scholars. Published by Universities.®

Physical Sciences and Mathematics Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 30 of 34

Full-Text Articles in Physical Sciences and Mathematics

Mono-N-Acyl-2,6-Diaminopimelic Acid Derivatives: Analysis By Electromigration And Spectroscopic Methods And Examination Of Enzyme Inhibitory Activity, Jan Hlaváček, Miloslava Vítovcová, Petra Sázelová, Jan Pícha, Václav Vaněk, Miloš Buděšínský, Jiří Jiráček, Danuta M. Gillner, Richard C. Holz, Ivan Mikšík, Václav Kašička Dec 2014

Mono-N-Acyl-2,6-Diaminopimelic Acid Derivatives: Analysis By Electromigration And Spectroscopic Methods And Examination Of Enzyme Inhibitory Activity, Jan Hlaváček, Miloslava Vítovcová, Petra Sázelová, Jan Pícha, Václav Vaněk, Miloš Buděšínský, Jiří Jiráček, Danuta M. Gillner, Richard C. Holz, Ivan Mikšík, Václav Kašička

Chemistry Faculty Research and Publications

Thirteen mono-N-acyl derivatives of 2,6-diaminopimelic acid (DAP)—new potential inhibitors of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18)—were analyzed and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopies and two capillary electromigration methods: capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC). Structural features of DAP derivatives were characterized by IR and NMR spectroscopies, whereas CZE and MEKC were applied to evaluate their purity and to investigate their electromigration properties. Effective electrophoretic mobilities of these compounds were determined by CZE in acidic and alkaline background electrolytes (BGEs) and by MEKC in acidic and alkaline BGEs …


Protein Expression, Characterization And Activity Comparisons Of Wild Type And Mutant Dusp5 Proteins, Jaladhi Nayak, Adam J. Gastonguay, Marat R. Talipov, Padmanabhan Vakeel, Elise A. Span, Kelsey S. Kalous, Raman G. Kutty, David R. Jensen, Phani Raj Pokkuluri, Daniel S. Sem, Rajendra Rathore, Ramani Ramchandran Dec 2014

Protein Expression, Characterization And Activity Comparisons Of Wild Type And Mutant Dusp5 Proteins, Jaladhi Nayak, Adam J. Gastonguay, Marat R. Talipov, Padmanabhan Vakeel, Elise A. Span, Kelsey S. Kalous, Raman G. Kutty, David R. Jensen, Phani Raj Pokkuluri, Daniel S. Sem, Rajendra Rathore, Ramani Ramchandran

Chemistry Faculty Research and Publications

Background

The mitogen-activated protein kinases (MAPKs) pathway is critical for cellular signaling, and proteins such as phosphatases that regulate this pathway are important for normal tissue development. Based on our previous work on dual specificity phosphatase-5 (DUSP5), and its role in embryonic vascular development and disease, we hypothesized that mutations in DUSP5 will affect its function.

Results

In this study, we tested this hypothesis by generating full-length glutathione-S-transferase-tagged DUSP5 and serine 147 proline mutant (S147P) proteins from bacteria. Light scattering analysis, circular dichroism, enzymatic assays and molecular modeling approaches have been performed to extensively characterize the protein form and function. …


Structure, Stability, And Substituent Effects In Aromatic S-Nitrosothiols: The Crucial Effect Of A Cascading Negative Hyperconjugation/Conjugation Interaction, Matthew Flister, Qadir K. Timerghazin Oct 2014

Structure, Stability, And Substituent Effects In Aromatic S-Nitrosothiols: The Crucial Effect Of A Cascading Negative Hyperconjugation/Conjugation Interaction, Matthew Flister, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Aromatic S-nitrosothiols (RSNOs) are of significant interest as potential donors of nitric oxide and related biologically active molecules. Here, we address a number of poorly understood properties of these species via a detailed density functional theory and the natural bond orbital (NBO) investigation of the parent PhSNO molecule. We find that the characteristic perpendicular orientation of the −SNO group relative to the phenyl ring is determined by a combination of the steric factors and the donor–acceptor interactions including, in particular, a cascading orbital interaction involving electron delocalization from the oxygen lone pair to the σ-antibonding S–N orbital and then …


Interactive Tool For Visualization Of Adiabatic Adjustment In Aph Coordinates For Computational Studies Of Vibrational Motion And Chemical Reactions, Alexander Teplukhin, Dmitri Babikov Oct 2014

Interactive Tool For Visualization Of Adiabatic Adjustment In Aph Coordinates For Computational Studies Of Vibrational Motion And Chemical Reactions, Alexander Teplukhin, Dmitri Babikov

Chemistry Faculty Research and Publications

The adiabatically-adjusting principal-axes hyperspherical (APH) coordinates reviewed in this letter are one of the best coordinate sets developed for computational treatment of spectroscopy and dynamics of triatomic molecules. Unfortunately, it is not so easy to understand and interpret them, compared to other simpler coordinates, like valence coordinates or Jacobi coordinates. To address this issue, we developed a desktop application called APHDemo. This tool visualizes the process of adjustment of the APH coordinates to the shape of a triatomic molecule during molecular vibrations or chemical reaction, and helps to understand their physical meaning without going into complicated math.


Supramolecular Biopolymeric Composite Materials: Green Synthesis, Characterization And Applications, Tamutsiwa Moven Mututuvari Oct 2014

Supramolecular Biopolymeric Composite Materials: Green Synthesis, Characterization And Applications, Tamutsiwa Moven Mututuvari

Dissertations (1934 -)

Macrocycles, such as crown ethers (CRs) and resorcinarenes (RESs), exhibit selective complexation of heavy metal ions and organic pollutants respectively. Consequently, they have been investigated for their suitability in adsorbing these aqueous pollutants. However, they are difficult to handle and recycle for reuse because, by themselves, they can only be fabricated in powder form. To alleviate this challenge, we developed a method to encapsulate these macrocycles into film-forming polysaccharides--cellulose (CEL) and chitosan (CS). This was achieved by using a green and recyclable solvent, an ionic liquid, to dissolve both macrocycles and polysaccharides and regenerate corresponding composites in water. Resultant composites …


Resonant Two-Photon Ionization Studies Of Non Covalent Interactions In Halo Aromatic Clusters And Spin-Orbit Coupling Modeling In Mono-Halocarbenes, Silver Nyambo Oct 2014

Resonant Two-Photon Ionization Studies Of Non Covalent Interactions In Halo Aromatic Clusters And Spin-Orbit Coupling Modeling In Mono-Halocarbenes, Silver Nyambo

Dissertations (1934 -)

Non-covalent interactions in halobenzenes (PhX) (X=F, Cl, Br) and phenylamine (C6 H5 NH2 ) have been studied here using resonance two-photon ionization (R2PI) spectroscopy combined with a linear TOF-mass spectrometer. Their interaction with polar molecules in form of ammonia (NH 3 ) and trifluorohalomethanes (CF3 X) has also been studied. DFT and TD-DFT calculations using M06-2X functionals were carried out on different cluster conformations to compliment experimental results. A general trend of broadness in homogenous dimers (PhX)2 , has been attributed to mainly the presence of multiple cluster isomers and Frank-Condon activity in the low …


Preparation Of Cyclohexenones From Acyclic (Pentadienyl)Iron(1+) Cations: Synthetic Studies Directed Toward The A-Ring Of Dihydrotachysterols, Charles Felix Manful, William A. Donaldson Oct 2014

Preparation Of Cyclohexenones From Acyclic (Pentadienyl)Iron(1+) Cations: Synthetic Studies Directed Toward The A-Ring Of Dihydrotachysterols, Charles Felix Manful, William A. Donaldson

Chemistry Faculty Research and Publications

The reaction of tricarbonyl(3-methylpentadienyl)iron(1+) cation (7) with stabilized carbon nucleophiles affords 4-methyl-5-substituted cyclohexenones. Reaction of 7 with sodium bis[(+)-2-phenylcyclohexyl]malonate afforded a mixture of diastereomers (de = 60 %); the diastereomeric allylic alcohols resulting from Luche reduction of this mixture were separable by column chromatography. Issues in diastereoselectivity in approaches to synthons for the A-ring of the tachysterols from these cyclohexenones are reported.


Synthesis Of Homo- And Heterobimetallic NiIi–MIi (M = Fe, Co, Ni, Zn) Complexes Based On An Unsymmetric Ligand Framework: Structures, Spectroscopic Features, And Redox Properties, Denan Wang, Sergey V. Lindeman, Adam T. Fiedler Sep 2014

Synthesis Of Homo- And Heterobimetallic NiIi–MIi (M = Fe, Co, Ni, Zn) Complexes Based On An Unsymmetric Ligand Framework: Structures, Spectroscopic Features, And Redox Properties, Denan Wang, Sergey V. Lindeman, Adam T. Fiedler

Chemistry Faculty Research and Publications

Several homo- and heterobimetallic NiII–MII complexes (MII = Fe, Co, Ni, Zn) supported by an unsymmetric polydentate ligand (L13−) are reported (L13− is the trianion of 2-[bis(2-hydroxy-3,5-tert-butylphenyl)aminomethyl]-4-methyl-6-[(2-pyridylmethyl)iminomethyl]phenol). The L13− chelate provides two distinct coordination environments: a planar tridentate {N2O} site (A) and a tetradentate {NO3} site (B). Reaction of L13− with equimolar amounts of NiII and MII salts provides bimetallic complexes in which the NiII ion exclusively occupies the tetragonal A-site and the MII ion is found …


Chitosan-Cellulose Composite For Wound Dressing Material. Part 2. Antimicrobial Activity, Blood Absorption Ability, And Biocompatibility, April Harkins, Simon Duri, Luther C. Kloth, Chieu D. Tran Aug 2014

Chitosan-Cellulose Composite For Wound Dressing Material. Part 2. Antimicrobial Activity, Blood Absorption Ability, And Biocompatibility, April Harkins, Simon Duri, Luther C. Kloth, Chieu D. Tran

Clinical Lab Sciences Faculty Research and Publications

Chitosan (CS), a polysaccharide derived from chitin, the second most abundant polysaccharide, is widely used in the medical world because of its natural and nontoxic properties and its innate ability for antibacterial and hemostasis effects. In this study, the novel composites containing CS and cellulose (CEL) (i.e., [CEL + CS]), which we have previously synthesized using a green and totally recyclable method, were investigated for their antimicrobial activity, absorption of anticoagulated whole blood, anti-inflammatory activity through the reduction of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6), and the biocompatibility with human fibroblasts. The [CEL + CS] composites were found to …


Synthesis, Characterization And Reactivity Studies Of Fe(Ii) Complexes With Relevance To The Radical Sam Enzymes, Xixi Hong Jul 2014

Synthesis, Characterization And Reactivity Studies Of Fe(Ii) Complexes With Relevance To The Radical Sam Enzymes, Xixi Hong

Master's Theses (2009 -)

It is well-established that S-adenosylmethionine (SAM) serves as the methyl group donor in methylations of DNA, hormones, neurotransmitters and signal transduction systems. However, a new class of enzymatic reactions involving SAM has recently attracted considerable attention. In these systems, SAM initiates radical-based reactions at the active sites of enzymes via formation of an adenosyl radical, which further abstracts a H-atom from the substrate to initiate a radical-based mechanism. However, modeling studies of radical SAM enzymes have been hindered, by difficulties in preparing adequate synthetic [Fe4S4] clusters. We prepared a novel series of Fe(II) complexes with tripodal tris(2-hydroxybenzyl)amine ligands, which replicate …


Investigations Of Synthetic Models Of Mononuclear Nonheme Iron Dioxygenases, Michael Bittner Jul 2014

Investigations Of Synthetic Models Of Mononuclear Nonheme Iron Dioxygenases, Michael Bittner

Dissertations (1934 -)

Ring cleaving dioxygenases, such as o-aminophenol dioxygenase (APDO) and extradiol catechol dioxygenases (CatD), play an important role in human metabolism and the degradation of aromatic pollutants, yet questions still remain concerning the enzymatic mechanisms. One area of the catalytic cycle that remains controversial is the geometric and electronic structure of the intermediate formed after O2 binding to the Fe(II) centers. Synthetic model systems can be useful for studying enzyme active sites, as they are easier to modify and characterize than the enzymes themselves. However, synthetic models of APDOs have been relatively rare thus far. We prepared several monoiron(II) complexes …


Fluorescence2d: Software For Accelerated Acquisition And Analysis Of Two-Dimensional Fluorescence Spectra, Evgeni L. Kovrigin Jul 2014

Fluorescence2d: Software For Accelerated Acquisition And Analysis Of Two-Dimensional Fluorescence Spectra, Evgeni L. Kovrigin

Chemistry Faculty Research and Publications

The Fluorescence2D is free software that allows analysis of two-dimensional fluorescence spectra obtained using the accelerated “triangular” acquisition schemes. The software is a combination of Python and MATLAB-based programs that perform conversion of the triangular data, display of the two-dimensional spectra, extraction of 1D slices at different wavelengths, and output in various graphic formats.


Electrochemistry And Spectroelectrochemistry Of 1,4-Dinitrobenzene In Acetonitrile And Room-Temperature Ionic Liquids: Ion-Pairing Effects In Mixed Solvents, Abderrahman Atifi, Michael D. Ryan Jul 2014

Electrochemistry And Spectroelectrochemistry Of 1,4-Dinitrobenzene In Acetonitrile And Room-Temperature Ionic Liquids: Ion-Pairing Effects In Mixed Solvents, Abderrahman Atifi, Michael D. Ryan

Chemistry Faculty Research and Publications

Room-temperature ionic liquids (RTILs) have been shown to have a significant effect on the redox potentials of compounds such as 1,4-dinitrobenzene (DNB), which can be reduced in two one-electron steps. The most noticeable effect is that the two one-electron waves in acetonitrile collapsed to a single two-electron wave in a RTIL such as butylmethyl imidazolium-BF4 (BMImBF4). In order to probe this effect over a wider range of mixed-molecular-solvent/RTIL solutions, the reduction process was studied using UV–vis spectroelectrochemistry. With the use of spectroelectrochemistry, it was possible to calculate readily the difference in E°’s between the first and …


In Vitro Biosynthesis And Chemical Identification Of Udp-N-Acetyl-D-Quinovosamine (Udp-D-Quinac), Tiezheng Li, Laurie Simonds, Evgeni L. Kovrigin, K. Dale Noel Jun 2014

In Vitro Biosynthesis And Chemical Identification Of Udp-N-Acetyl-D-Quinovosamine (Udp-D-Quinac), Tiezheng Li, Laurie Simonds, Evgeni L. Kovrigin, K. Dale Noel

Chemistry Faculty Research and Publications

N-acetyl-d-quinovosamine (2-acetamido-2,6-dideoxy-d-glucose, QuiNAc) occurs in the polysaccharide structures of many Gram-negative bacteria. In the biosynthesis of QuiNAc-containing polysaccharides, UDP-QuiNAc is the hypothetical donor of the QuiNAc residue. Biosynthesis of UDP-QuiNAc has been proposed to occur by 4,6-dehydration of UDP-N-acetyl-d-glucosamine (UDP-GlcNAc) to UDP-2-acetamido-2,6-dideoxy-d-xylo-4-hexulose followed by reduction of this 4-keto intermediate to UDP-QuiNAc. Several specific dehydratases are known to catalyze the first proposed step. A specific reductase for the last step has not been demonstrated in vitro, but previous mutant analysis suggested that Rhizobium etli gene wreQ might encode this reductase. Therefore, this gene was cloned and expressed …


The Dimerization Domain In Dape Enzymes Is Required For Catalysis, Boguslaw Nocek, Anna Starus, Magdalena Makowska-Grzyska, Blanca Gutierrez, Stephen Sanchez, Robert Jedrzejczak, Jamey C. Mack, Kenneth W. Olsen, Andzrej Joachimiak, Richard C. Holz May 2014

The Dimerization Domain In Dape Enzymes Is Required For Catalysis, Boguslaw Nocek, Anna Starus, Magdalena Makowska-Grzyska, Blanca Gutierrez, Stephen Sanchez, Robert Jedrzejczak, Jamey C. Mack, Kenneth W. Olsen, Andzrej Joachimiak, Richard C. Holz

Chemistry Faculty Research and Publications

The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) converts N-succinyl-L,L-diaminopimelic acid to L,Ldiaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role …


Dioxygen Reactivity Of Biomimetic Fe(Ii) Complexes With Noninnocent Catecholate, O-Aminophenolate, And O-Phenylenediamine Ligands, Michael M. Bittner, Sergey Lindeman, Cordina V. Popescu, Adam T. Fiedler Apr 2014

Dioxygen Reactivity Of Biomimetic Fe(Ii) Complexes With Noninnocent Catecholate, O-Aminophenolate, And O-Phenylenediamine Ligands, Michael M. Bittner, Sergey Lindeman, Cordina V. Popescu, Adam T. Fiedler

Chemistry Faculty Research and Publications

This study describes the O2 reactivity of a series of high-spin mononuclear Fe(II) complexes each containing the facially coordinating tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (Ph2TIP) ligand and one of the following bidentate, redox-active ligands: 4-tert-butylcatecholate (tBuCatH), 4,6-di-tert-butyl-2-aminophenolate (tBu2APH), or 4-tert-butyl-1,2-phenylenediamine (tBuPDA). The preparation and X-ray structural characterization of [Fe2+(Ph2TIP)(tBuCatH)]OTf, [3]OTf and [Fe2+(Ph2TIP)(tBuPDA)](OTf)2, [4](OTf)2 are described here, whereas [Fe2+(Ph2 …


Photochemical Elimination Reactions That Proceed Via Triplet Excited State Electrocyclic Ring Closures, Himali Devika Jayasekara Apr 2014

Photochemical Elimination Reactions That Proceed Via Triplet Excited State Electrocyclic Ring Closures, Himali Devika Jayasekara

Master's Theses (2009 -)

Cage compounds have become an important tool for the study of biological processes. The research focuses on new cage compounds that can unmask functional groups present in biologically important molecules such as proteins, peptides, and oligonucleosides. The project focuses on certain functional groups that are often difficult to release photochemically. These are the thiolate groups present in cysteine residues of proteins and peptides. Thiolate groups are fairly basic leaving groups, unlike the more labile groups such as the carboxylates that are present in proteins and peptides, or the phosphate groups present in nucleosides. The research takes advantage of the ability …


Acrylamide Production Using Encapsulated Nitrile Hydratase From Pseudonocardia Thermophila In A Sol–Gel Matrix, Salette Martinez, Misty L. Kuhn, James T. Russell, Richard C. Holz, Timothy E. Elgren Feb 2014

Acrylamide Production Using Encapsulated Nitrile Hydratase From Pseudonocardia Thermophila In A Sol–Gel Matrix, Salette Martinez, Misty L. Kuhn, James T. Russell, Richard C. Holz, Timothy E. Elgren

Chemistry Faculty Research and Publications

The cobalt-type nitrile hydratase from Pseudonocardia thermophila JCM 3095 (PtNHase) was successfully encapsulated in tetramethyl orthosilicate sol–gel matrices to produce a PtNHase:sol–gel biomaterial. The PtNHase:sol–gel biomaterial catalyzed the conversion of 600 mM acrylonitrile to acrylamide in 60 min at 35 °C with a yields of >90%. Treatment of the biomaterial with proteases confirmed that the catalytic activity is due to the encapsulated enzyme and not surface bound NHase. The biomaterial retained 50% of its activity after being used for a total of 13 consecutive reactions for the conversion of acrylonitrile to acrylamide. The thermostability and long-term …


Synergistic Adsorption Of Heavy Metal Ions And Organic Pollutants By Supramolecular Polysaccharide Composite Materials From Cellulose, Chitosan And Crown Ether, Tamutsiwa M. Mututuvari, Chieu D. Tran Jan 2014

Synergistic Adsorption Of Heavy Metal Ions And Organic Pollutants By Supramolecular Polysaccharide Composite Materials From Cellulose, Chitosan And Crown Ether, Tamutsiwa M. Mututuvari, Chieu D. Tran

Chemistry Faculty Research and Publications

We have developed a simple one-step method to synthesize novel supramolecular polysaccharide composites from cellulose (CEL), chitosan (CS) and benzo-15-crown 5 (B15C5). Butylmethylimidazolium chloride [BMIm+Cl], an ionic liquid (IL), was used as a sole solvent for dissolution and preparation of the composites. Since majority of [BMIm+Cl] used was recovered for reuse, the method is recyclable. The [CEL/CS + B15C5] composites obtained retain properties of their components, namely superior mechanical strength (from CEL), excellent adsorption capability for heavy metal ions and organic pollutants (from B15C5 and CS). More importantly, the [CEL/CS + B15C5] …


Resonance Raman Spectroscopy Reveals That Substrate Structure Selectively Impacts The Heme-Bound Diatomic Ligands Of Cyp17, Piotr J. Mak, Michael C. Gregory, Stephen G. Sligar, James R. Kincaid Jan 2014

Resonance Raman Spectroscopy Reveals That Substrate Structure Selectively Impacts The Heme-Bound Diatomic Ligands Of Cyp17, Piotr J. Mak, Michael C. Gregory, Stephen G. Sligar, James R. Kincaid

Chemistry Faculty Research and Publications

An important function of steroidogenic cytochromes P450 is the transformation of cholesterol to produce androgens, estrogens, and the corticosteroids. The activities of cytochrome P450c17 (CYP17) are essential in sex hormone biosynthesis, with severe developmental defects being a consequence of deficiency or mutations. The first reaction catalyzed by this multifunctional P450 is the 17α-hydroxylation of pregnenolone (PREG) to 17α-hydroxypregnenolone (17-OH PREG) and progesterone (PROG) to 17α-hydroxyprogesterone (17-OH PROG). The hydroxylated products then either are used for production of corticoids or undergo a second CYP17 catalyzed transformation, representing the first committed step of androgen formation. While the hydroxylation reactions are catalyzed by …


Spectral Data For "Probing The Human Estrogen Receptor-Alpha Binding Requirements For Phenolic Mono- And Do-Hydroxyl Compounds: A Combined Synthesis, Binding And Docking Study", Christopher Mccullough, Terrence S. Neumann, Jayapal Reddy Gone, Zhengjie He, Julie Lukesh, Rajesh K. Pandey, William A. Donaldson, Daniel S. Sem Jan 2014

Spectral Data For "Probing The Human Estrogen Receptor-Alpha Binding Requirements For Phenolic Mono- And Do-Hydroxyl Compounds: A Combined Synthesis, Binding And Docking Study", Christopher Mccullough, Terrence S. Neumann, Jayapal Reddy Gone, Zhengjie He, Julie Lukesh, Rajesh K. Pandey, William A. Donaldson, Daniel S. Sem

Natural Products Synthesis via Organoiron Methodology

Spectral data used in the course of researching "Probing the human estrogen receptor-alpha binding requirements for phenolic mono- and do-hydroxyl compounds: A combined synthesis, binding and docking study".

Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. …


Accurate Calculations Of Rotationally Inelastic Scattering Cross Sections Using Mixed Quantum/Classical Theory, Alexander Semenov, Dmitri Babikov Jan 2014

Accurate Calculations Of Rotationally Inelastic Scattering Cross Sections Using Mixed Quantum/Classical Theory, Alexander Semenov, Dmitri Babikov

Chemistry Faculty Research and Publications

For computational treatment of rotationally inelastic scattering of molecules, we propose to use the mixed quantum/classical theory, MQCT. The old idea of treating translational motion classically, while quantum mechanics is used for rotational degrees of freedom, is developed to the new level and is applied to Na + N2 collisions in a broad range of energies. Comparison with full-quantum calculations shows that MQCT accurately reproduces all, even minor, features of energy dependence of cross sections, except scattering resonances at very low energies. The remarkable success of MQCT opens up wide opportunities for computational predictions of inelastic scattering cross sections …


Rotational Quenching Of H2O By He: Mixed Quantum/Classical Theory And Comparison With Quantum Results, Mikhail V. Ivanov, Marie-Lise Dubernet, Dmitri Babikov Jan 2014

Rotational Quenching Of H2O By He: Mixed Quantum/Classical Theory And Comparison With Quantum Results, Mikhail V. Ivanov, Marie-Lise Dubernet, Dmitri Babikov

Chemistry Faculty Research and Publications

The mixed quantum/classical theory (MQCT) formulated in the space-fixed reference frame is used to compute quenching cross sections of several rotationally excited states of water molecule by impact of He atom in a broad range of collision energies, and is tested against the full-quantum calculations on the same potential energy surface. In current implementation of MQCT method, there are two major sources of errors: one affects results at energies below 10 cm−1, while the other shows up at energies above 500 cm−1. Namely, when the collision energy E is below the state-to-state transition energy ΔE the …


Isomer Dependence In The Assembly And Lability Of Silver(I) Trifluoromethanesulfonate Complexes Of The Heteroditopic Ligands, 2-, 3-, And 4-[Di(1H-Pyrazolyl)Methyl]Phenyl(Di-P-Tolyl)Phosphine, James R. Gardinier, Jeewantha S. Hewage, Sergey V. Lindeman Jan 2014

Isomer Dependence In The Assembly And Lability Of Silver(I) Trifluoromethanesulfonate Complexes Of The Heteroditopic Ligands, 2-, 3-, And 4-[Di(1H-Pyrazolyl)Methyl]Phenyl(Di-P-Tolyl)Phosphine, James R. Gardinier, Jeewantha S. Hewage, Sergey V. Lindeman

Chemistry Faculty Research and Publications

Three isomers of a new heteroditopic ligand that contains a di(1H-pyrazolyl)methyl (−CHpz2) moiety connected to a di(p-tolyl)phosphine group via a para-, meta-, or ortho-phenylene spacer (pL, mL, and oL, respectively) have been synthesized by using a palladium(0)-catalyzed coupling reaction between HP(p-tolyl)2 and the appropriate isomer of (IC6H4)CHpz2. The 1:1 complexes of silver(I) trifluoromethanesulfonate, Ag(OTf), were prepared to examine the nature of ligand coordination and the type of supramolecular isomer (monomeric, cyclic oligomeric, or polymeric) that would be obtained. …


Assembly, Structure, And Reactivity Of Cu4S And Cu3S Models For The Nitrous Oxide Reductase Active Site, CuZ*, Brittany J. Johnson, Sergey V. Lindeman, Neal P. Mankad Jan 2014

Assembly, Structure, And Reactivity Of Cu4S And Cu3S Models For The Nitrous Oxide Reductase Active Site, CuZ*, Brittany J. Johnson, Sergey V. Lindeman, Neal P. Mankad

Chemistry Faculty Research and Publications

Bridging diphosphine ligands were used to facilitate the assembly of copper clusters with single sulfur atom bridges that model the structure of the CuZ* active site of nitrous oxide reductase. Using bis(diphenylphosphino)amine (dppa), a [CuI44-S)] cluster with N–H hydrogen bond donors in the secondary coordination sphere was assembled. Solvent and anion guests were found docking to the N–H sites in the solid state and in the solution phase, highlighting a kinetically viable pathway for substrate introduction to the inorganic core. Using bis(dicyclohexylphosphino)methane (dcpm), a [CuI33-S)] cluster was assembled …


Probing The Human Estrogen Receptor-Α Binding Requirements For Phenolic Mono- And Di-Hydroxyl Compounds: A Combined Synthesis, Binding And Docking Study, Christopher Mccullough, Terrence S. Neumann, Jayapal Reddy Gone, Zhengjie He, Christian Herrild, Julie Lukesh, Rajesh K. Pandey, William A. Donaldson, Daniel S. Sem Jan 2014

Probing The Human Estrogen Receptor-Α Binding Requirements For Phenolic Mono- And Di-Hydroxyl Compounds: A Combined Synthesis, Binding And Docking Study, Christopher Mccullough, Terrence S. Neumann, Jayapal Reddy Gone, Zhengjie He, Christian Herrild, Julie Lukesh, Rajesh K. Pandey, William A. Donaldson, Daniel S. Sem

Chemistry Faculty Research and Publications

Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. Di-hydroxyl compounds were predicted to bind with their aliphatic hydroxyl group interacting with His524 in ERα. One nonsteroid-based dihdroxyl compound was 1000-fold specific for ERβ over ERα, and …


On Readout Of Vibrational Qubits Using Quantum Beats, Dmytro Shyshlov, Eduardo Berrios, Martin Gruebele, Dmitri Babikov Jan 2014

On Readout Of Vibrational Qubits Using Quantum Beats, Dmytro Shyshlov, Eduardo Berrios, Martin Gruebele, Dmitri Babikov

Chemistry Faculty Research and Publications

Readout of the final states of qubits is a crucial step towards implementing quantum computation in experiment. Although not scalable to large numbers of qubits per molecule, computational studies show that molecular vibrations could provide a significant (factor 2–5 in the literature) increase in the number of qubits compared to two-level systems. In this theoretical work, we explore the process of readout from vibrational qubits in thiophosgene molecule, SCCl2, using quantum beat oscillations. The quantum beats are measured by first exciting the superposition of the qubit-encoding vibrational states to the electronically excited readout state with variable time-delay pulses. …


Mixed Quantum/Classical Theory For Inelastic Scattering Of Asymmetric-Top-Rotor + Atom In The Body-Fixed Reference Frame And Application To The H2O + He System, Alexander Semenov, Marie-Lise Dubernet, Dmitri Babikov Jan 2014

Mixed Quantum/Classical Theory For Inelastic Scattering Of Asymmetric-Top-Rotor + Atom In The Body-Fixed Reference Frame And Application To The H2O + He System, Alexander Semenov, Marie-Lise Dubernet, Dmitri Babikov

Chemistry Faculty Research and Publications

The mixed quantum/classical theory (MQCT) for inelastic molecule-atom scattering developed recently [A. Semenov and D. Babikov, J. Chem. Phys.139, 174108 (2013)] is extended to treat a general case of an asymmetric-top-rotor molecule in the body-fixed reference frame. This complements a similar theory formulated in the space-fixed reference-frame [M. Ivanov, M.-L. Dubernet, and D. Babikov, J. Chem. Phys.140, 134301 (2014)]. Here, the goal was to develop an approximate computationally affordable treatment of the rotationally inelastic scattering and apply it to H2O + He. We found that MQCT is somewhat less accurate at lower scattering energies. For example, below E …


Cellulose-Chitosan-Keratin Composite Materials: Synthesis, Immunological And Antibacterial Properties, Meghann Rosewald, Fang Yao Stephen Hou, Tamutsiwa Moven Mututuvari, April L. Harkins, Chieu D. Tran Jan 2014

Cellulose-Chitosan-Keratin Composite Materials: Synthesis, Immunological And Antibacterial Properties, Meghann Rosewald, Fang Yao Stephen Hou, Tamutsiwa Moven Mututuvari, April L. Harkins, Chieu D. Tran

Chemistry Faculty Research and Publications

Novel composites were synthesized from keratin (KER), cellulose (CEL) and chitosan (CS). The method is recyclable because majority (>88%) of [BMIm+Cl-], an ionic liquid (IL), used as the sole solvent, was recovered for reuse. Experimentally, it was confirmed that unique properties of each component remain intact in the composites, namely bactericide (from KER and CS) and anti-inflammatory property (from KER). Specifically, the composites were examined for their anti-inflammatory influence on macrophages. The cells were imaged and immunophenotyped to determine the quantity using the macrophage marker CD11b. The 75:25 [KER+CS] composite was found to have the …


Mixed Quantum/Classical Calculations Of Total And Differential Elastic And Rotationally Inelastic Scattering Cross Sections For Light And Heavy Reduced Masses In A Broad Range Of Collision Energies, Alexander Semenov, Dmitri Babikov Jan 2014

Mixed Quantum/Classical Calculations Of Total And Differential Elastic And Rotationally Inelastic Scattering Cross Sections For Light And Heavy Reduced Masses In A Broad Range Of Collision Energies, Alexander Semenov, Dmitri Babikov

Chemistry Faculty Research and Publications

The mixed quantum/classical theory (MQCT) for rotationally inelastic scattering developed recently [A. Semenov and D. Babikov, J. Chem. Phys.139, 174108 (2013)] is benchmarked against the full quantum calculations for two molecular systems: He + H2 and Na + N2. This allows testing new method in the cases of light and reasonably heavy reduced masses, for small and large rotational quanta, in a broad range of collision energies and rotational excitations. The resultant collision cross sections vary through ten-orders of magnitude range of values. Both inelastic and elastic channels are considered, as well as differential (over scattering angle) cross sections. In …