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Articles 271 - 300 of 690
Full-Text Articles in Chemistry
On Molecular Origin Of Mass-Independent Fractionation Of Oxygen Isotopes In The Ozone Forming Recombination Reaction, Mikhail V. Ivanov, Dmitri Babikov
On Molecular Origin Of Mass-Independent Fractionation Of Oxygen Isotopes In The Ozone Forming Recombination Reaction, Mikhail V. Ivanov, Dmitri Babikov
Chemistry Faculty Research and Publications
Theoretical treatment of ozone forming reaction is developed within the framework of mixed quantum/classical dynamics. Formation and stabilization steps of the energy transfer mechanism are both studied, which allows simultaneous capture of the delta zero-point energy effect and η-effect and identification of the molecular level origin of mass-independent isotope fractionation. The central role belongs to scattering resonances; dependence of their lifetimes on rotational excitation, asymmetry; and connection of their vibrational wave functions to two different reaction channels. Calculations, performed within the dimensionally reduced model of ozone, are in semiquantitative agreement with experiment.
Reactive Pathways In The Chlorobenzene–Ammonia Dimer Cation Radical: New Insights From Experiment And Theory, Scott A. Reid
Reactive Pathways In The Chlorobenzene–Ammonia Dimer Cation Radical: New Insights From Experiment And Theory, Scott A. Reid
Chemistry Faculty Research and Publications
Building upon our recent studies of noncovalent interactions in chlorobenzene and bromobenzene clusters, in this work we focus on interactions of chlorobenzene (PhCl) with a prototypical N atom donor, ammonia (NH3). Thus, we have obtained electronic spectra of PhCl···(NH3)n (n = 1–3) complexes in the region of the PhCl monomer S0 −S1 (ππ*) transition using resonant 2-photon ionization (R2PI) methods combined with time-of-flight mass analysis. Consistent with previous studies, we find that upon ionization the PhCl···NH3 dimer cation radical reacts primarily via Cl atom loss. A second channel, HCl loss, is …
Intramolecular Hydrogen Bonding In CuIi Complexes With 2,6-Pyridinedicarboxamide Ligands: Synthesis, Structural Characterization, And Physical Properties, Denan Wang, Sergey V. Lindeman, Adam T. Fiedler
Intramolecular Hydrogen Bonding In CuIi Complexes With 2,6-Pyridinedicarboxamide Ligands: Synthesis, Structural Characterization, And Physical Properties, Denan Wang, Sergey V. Lindeman, Adam T. Fiedler
Chemistry Faculty Research and Publications
The significance of second-sphere interactions in synthetic catalysts and metalloenzyme active sites has encouraged the development of ligand frameworks capable of supporting intramolecular hydrogen-bonding networks. With this approach in mind, we prepared a series of 2,6-pyridinedicarboxamide ligands (H2LX) that feature outer-sphere heterocyclic groups (pyridine, pyrimidine, or quinoline rings). Reaction with CuCl2 yields complexes with the general formula [CuCl2(LX{H}2)] (1X), in which the pincer ligands coordinate to the CuII center in a tridentate fashion through the central pyridine and two amidato nitrogen atoms. The LX …
Π-Stacking, C–H/Π, And Halogen Bonding Interactions In Bromobenzene And Mixed Bromobenzene–Benzene Clusters, Scott A. Reid, Silver Nyambo, Lloyd Muzangwa, Brandon Uhler
Π-Stacking, C–H/Π, And Halogen Bonding Interactions In Bromobenzene And Mixed Bromobenzene–Benzene Clusters, Scott A. Reid, Silver Nyambo, Lloyd Muzangwa, Brandon Uhler
Chemistry Faculty Research and Publications
Noncovalent interactions play an important role in many chemical and biochemical processes. Building upon our recent study of the homoclusters of chlorobenzene, where π–π stacking and CH/π interactions were identified as the most important binding motifs, in this work we present a study of bromobenzene (PhBr) and mixed bromobenzene–benzene clusters. Electronic spectra in the region of the PhBr monomer S0–S1 (ππ*) transition were obtained using resonant two-photon ionization (R2PI) methods combined with time-of-flight mass analysis. As previously found for related systems, the PhBr cluster spectra show a broad feature whose center is red-shifted from the monomer absorption, …
Photoisomerization And Photoinduced Reactions In Liquid Ccl4 And Chcl3, Scott A. Reid, Fawzi Abou-Chahine, Thomas J. Preston, Greg T. Dunning, Andrew J. Orr-Ewing, Gregory M. Greetham, Ian P. Clark, Mike Towrie
Photoisomerization And Photoinduced Reactions In Liquid Ccl4 And Chcl3, Scott A. Reid, Fawzi Abou-Chahine, Thomas J. Preston, Greg T. Dunning, Andrew J. Orr-Ewing, Gregory M. Greetham, Ian P. Clark, Mike Towrie
Chemistry Faculty Research and Publications
Transient absorption spectroscopy is used to follow the reactive intermediates involved in the first steps in the photochemistry initiated by ultraviolet (266-nm wavelength) excitation of solutions of 1,5-hexadiene, isoprene, and 2,3-dimethylbut-2-ene in carbon tetrachloride or chloroform. Ultraviolet and visible bands centered close to 330 and 500 nm in both solvents are assigned respectively to a charge transfer band of Cl-solvent complexes and the strong absorption band of a higher energy isomeric form of the solvent molecules (iso-CCl3–Cl or iso-CHCl2–Cl). These assignments are supported by calculations of electronic excitation energies. The isomeric forms have …
In Situ Study Of The Photodegradation Of Carbofuran Deposited On Tio2 Film Under Uv Light, Using Atr-Ftir Coupled To Hs-Mcr-Als, Abderrahman Atifi, Kazimierz Czarnecki, Hafida Mountacer, Michael D. Ryan
In Situ Study Of The Photodegradation Of Carbofuran Deposited On Tio2 Film Under Uv Light, Using Atr-Ftir Coupled To Hs-Mcr-Als, Abderrahman Atifi, Kazimierz Czarnecki, Hafida Mountacer, Michael D. Ryan
Chemistry Faculty Research and Publications
The in situ study of the photodegradation of carbofuran deposited on a TiO2 catalyst film under UV light was carried out using the ATR-FTIR technique. The data were analyzed using a Hard–Soft Multivariate Curve Resolution-Alternating Least Squares (HS-MCR-ALS) methodology. Using S-MCR-ALS, four factors were deduced from the evolving factor analysis of the data, and their concentrations and spectra were determined. These results were used to draw qualitative and quantitative analyses of the major products of carbofuran photodegradation. The results of this analysis were in good agreement with GC-MS results and with reported mechanisms. Hard-MCR-ALS was then used to refine …
Recyclable Synthesis, Characterization, And Antimicrobial Activity Of Chitosan-Based Polysaccharide Composite Materials, Chieu D. Tran, Simon Duri, April L. Harkins
Recyclable Synthesis, Characterization, And Antimicrobial Activity Of Chitosan-Based Polysaccharide Composite Materials, Chieu D. Tran, Simon Duri, April L. Harkins
Chemistry Faculty Research and Publications
We have successfully developed a simple and totally recyclable method to synthesize novel, biocompatible, and biodegradable composite materials from cellulose (CEL) and chitosan (CS). In this method, [BMIm+Cl−], an ionic liquid (IL), was used as a green solvent to dissolve and synthesize the [CEL+CS] composites. Since, the IL can be removed from the composites by washing them with water, and recovered by distilling the washed solution, the method is totally recyclable. Spectroscopic and imaging techniques including XRD, FTIR, NIR, and SEM were used to monitor the dissolution, to characterize and to confirm that CEL and CS …
Cyclic Versus Polymeric Supramolecular Architectures In Metal Complexes Of Dinucleating Ligands: Silver(I) Trifluoromethanesulfonate Complexes Of The Isomers Of Bis(Di(1h-Pyrazolyl)Methyl)-1,1′-Biphenyl, James R. Gardinier, Heidi M. Tatlock, Jeewantha S. Hewage, Sergey V. Lindeman
Cyclic Versus Polymeric Supramolecular Architectures In Metal Complexes Of Dinucleating Ligands: Silver(I) Trifluoromethanesulfonate Complexes Of The Isomers Of Bis(Di(1h-Pyrazolyl)Methyl)-1,1′-Biphenyl, James R. Gardinier, Heidi M. Tatlock, Jeewantha S. Hewage, Sergey V. Lindeman
Chemistry Faculty Research and Publications
In the search for new examples of systems that self-assemble into cyclic metal–organic architectures, the six isomers of X,Y′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, LXY, and their silver(I) trifluoromethanesulfonate complexes were prepared. Five of the six silver complexes gave crystals suitable for single crystal X-ray diffraction, with only the microcrystalline derivative of 2,3′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, L23, proving to be unsuitable for this analysis. Of the structurally characterized silver(I) complexes, that with L22 showed an unusual trans-spanning chelating coordination mode to silver. At the same time the ligand was also bound to a second silver center …
Synthetic, Spectroscopic And Dft Studies Of Iron Complexes With Iminobenzo(Semi)Quinone Ligands: Implications For O-Aminophenol Dioxygenases, Michael M. Bittner, David S. Krause, Sergey V. Lindeman, Cordina V. Popescu, Adam T. Fiedler
Synthetic, Spectroscopic And Dft Studies Of Iron Complexes With Iminobenzo(Semi)Quinone Ligands: Implications For O-Aminophenol Dioxygenases, Michael M. Bittner, David S. Krause, Sergey V. Lindeman, Cordina V. Popescu, Adam T. Fiedler
Chemistry Faculty Research and Publications
The oxidative CC bond cleavage of o-aminophenols by nonheme Fe dioxygenases is a critical step in both human metabolism (the kynurenine pathway) and the microbial degradation of nitroaromatic pollutants. The catalytic cycle of o-aminophenol dioxygenases (APDOs) has been proposed to involve formation of an FeII/O2/iminobenzosemiquinone complex, although the presence of a substrate radical has been called into question by studies of related ring-cleaving dioxygenases. Recently, we reported the first synthesis of an iron(II) complex coordinated to an iminobenzosemiquinone (ISQ) ligand, namely, [Fe(Tp)(tBuISQ)] (2 a; where Tp=hydrotris(3,5-diphenylpyrazol-1-yl)borate and tBu …
Case Of The Missing Isomer: Pathways For Molecular Elimination In The Photo-Induced Decomposition Of 1,1-Dibromoethane, Aimable Kalume, Lisa George, Nicole Cunningham, Scott A. Reid
Case Of The Missing Isomer: Pathways For Molecular Elimination In The Photo-Induced Decomposition Of 1,1-Dibromoethane, Aimable Kalume, Lisa George, Nicole Cunningham, Scott A. Reid
Chemistry Faculty Research and Publications
We report an experimental and computational study of the photodecomposition pathways of a prototypical gem-dihalide, 1,1-dibromoethane (1,1-EDB), in the condensed phase. Following photolysis of the matrix isolated parent compound in Ar at 5 K, photoproducts are observed corresponding to Br2 elimination (+ C2H4 or C2H2) and HBr elimination (+ vinyl bromide). The elimination products are observed in the matrix as complexes. In contrast to our recent studies of the photolysis of matrix isolated polyhalomethanes, no evidence for the iso-1,1-EDB species is found, although studies of the matrix isolated 1,1-dibromo-2,2,2-trifluoroethane analogue show that …
Preparation Of A Semiquinonate-Bridged Diiron(Ii) Complex And Elucidation Of Its Geometric And Electronic Structures, Amanda E. Baum, Sergey V. Lindeman, Adam T. Fiedler
Preparation Of A Semiquinonate-Bridged Diiron(Ii) Complex And Elucidation Of Its Geometric And Electronic Structures, Amanda E. Baum, Sergey V. Lindeman, Adam T. Fiedler
Chemistry Faculty Research and Publications
The synthesis and crystal structure of a diiron(II) complex containing a bridging semiquinonate radical are presented. The unique electronic structure of this S = 7/2 complex is examined with spectroscopic (absorption, EPR, resonance Raman) and computational methods.
Identification Of An Active Site-Bound Nitrile Hydratase Intermediate Through Single Turnover Stopped-Flow Spectroscopy, Natalie Gumataotao, Misty L. Kuhn, Natalia Hajnas, Richard C. Holz
Identification Of An Active Site-Bound Nitrile Hydratase Intermediate Through Single Turnover Stopped-Flow Spectroscopy, Natalie Gumataotao, Misty L. Kuhn, Natalia Hajnas, Richard C. Holz
Chemistry Faculty Research and Publications
Stopped-flow kinetic data were obtained for the iron-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase) using methacrylonitrile as the substrate. Multiple turnover experiments suggest a three-step kinetic model that allows for the reversible binding of substrate, the presence of an intermediate, and the formation of product. Microscopic rate constants determined from these data are in good agreement with steady state data confirming that the stopped-flow method used was appropriate for the reaction. Single turnover stopped-flow experiments were used to identify catalytic intermediates. These data were globally fit confirming a three-step kinetic model. Independent absorption spectra acquired between 0.005 …
Differential Hydrogen Bonding In Human Cyp17 Dictates Hydroxylation Versus Lyase Chemistry, Michael Gregory, Piotr J. Mak, Stephen G. Sligar, James R. Kincaid
Differential Hydrogen Bonding In Human Cyp17 Dictates Hydroxylation Versus Lyase Chemistry, Michael Gregory, Piotr J. Mak, Stephen G. Sligar, James R. Kincaid
Chemistry Faculty Research and Publications
Consequences of alternative H-bonding: Raman spectra of oxygenated intermediates of Nanodisc-incorporated human CYP17 in the presence of natural substrates (pregnenolone and progesterone) directly confirm that substrate structure effectively alters hydrogen-bonding interactions with the critical Fe–O–O fragment and dictates its predisposition for one of two alternative reaction pathways. Such substrate control has profound physiological implications.
Rhodium Complexes Of A New Structurally Adaptive Pnn-Pincer Type Ligand, Sarath Wanniarachchi, Jeewantha S. Hewage, Sergey V. Lindeman, James R. Gardinier
Rhodium Complexes Of A New Structurally Adaptive Pnn-Pincer Type Ligand, Sarath Wanniarachchi, Jeewantha S. Hewage, Sergey V. Lindeman, James R. Gardinier
Chemistry Faculty Research and Publications
A new PNN-pincer type ligand with pyrazolyl and diphenylphosphine flanking donors on a diarylamido anchor has been prepared. Its bis(tert-butyl isocyanide)rhodium(I) complex exhibits hemilabile behavior in solution, and its solid-state structure verified the elusive κ2P,N coordination mode for this type of ligand. Reactions between (PNN)Rh(CNtBu)2 and iodomethane afford both fac- and cis,mer-[(PNN)Rh(CNtBu)2(Me)](I), which further showcases the structural versatility of the ligand.
Chitosan-Cellulose Composite Materials: Preparation, Characterization And Application For Removal Of Microcystin, Chieu D. Tran, Simon Duri, Ambra Delneri, Mladen Franko
Chitosan-Cellulose Composite Materials: Preparation, Characterization And Application For Removal Of Microcystin, Chieu D. Tran, Simon Duri, Ambra Delneri, Mladen Franko
Chemistry Faculty Research and Publications
We developed a simple and one-step method to prepare biocompatible composites from cellulose (CEL) and chitosan (CS). [BMIm+Cl−], an ionic liquid (IL), was used as a green solvent to dissolve and prepare the [CEL + CS] composites. Since majority (>88%) of IL used was recovered for reuse by distilling the aqueous washings of [CEL + CS], the method is recyclable. XRD, FTIR, NIR, 13C CP-MAS-NMR and SEM were used to monitor the dissolution and to characterize the composites. The composite was found to have combined advantages of their components: superior mechanical strength (from CEL) …
Supramolecular Composite Materials From Cellulose, Chitosan, And Cyclodextrin: Facile Preparation And Their Selective Inclusion Complex Formation With Endocrine Disruptors, Simon Duri, Chieu D. Tran
Supramolecular Composite Materials From Cellulose, Chitosan, And Cyclodextrin: Facile Preparation And Their Selective Inclusion Complex Formation With Endocrine Disruptors, Simon Duri, Chieu D. Tran
Chemistry Faculty Research and Publications
We have successfully developed a simple one-step method of preparing high-performance supramolecular polysaccharide composites from cellulose (CEL), chitosan (CS), and (2,3,6-tri-O-acetyl)-α-, β-, and γ-cyclodextrin (α-, β-, and γ-TCD). In this method, [BMIm+Cl–], an ionic liquid (IL), was used as a solvent to dissolve and prepare the composites. Because a majority (>88%) of the IL used was recovered for reuse, the method is recyclable. XRD, FT-IR, NIR, and SEM were used to monitor the dissolution process and to confirm that the polysaccharides were regenerated without any chemical modifications. It was found that unique properties …
Solution Structures Of Mycobacterium Tuberculosis Thioredoxin C And Models Of Intact Thioredoxin System Suggest New Approaches To Inhibitor And Drug Design, Andrew Lawrence Olson, Terrence S. Neumann, Sheng Cai, Daniel S. Sem
Solution Structures Of Mycobacterium Tuberculosis Thioredoxin C And Models Of Intact Thioredoxin System Suggest New Approaches To Inhibitor And Drug Design, Andrew Lawrence Olson, Terrence S. Neumann, Sheng Cai, Daniel S. Sem
Chemistry Faculty Research and Publications
Here, we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared with the solution structure. On the basis of these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis …
Lysine Biosynthesis In Bacteria: A Metallodesuccinylase As A Potential Antimicrobial Target, Danuta Gillner, Daniel P. Becker, Richard C. Holz
Lysine Biosynthesis In Bacteria: A Metallodesuccinylase As A Potential Antimicrobial Target, Danuta Gillner, Daniel P. Becker, Richard C. Holz
Chemistry Faculty Research and Publications
In this review, we summarize the recent literature on dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) enzymes, with an emphasis on structure–function studies that provide insight into the catalytic mechanism. Crystallographic data have also provided insight into residues that might be involved in substrate and hence inhibitor recognition and binding. These data have led to the design and synthesis of several new DapE inhibitors, which are described along with what is known about how inhibitors interact with the active site of DapE enzymes, including the efficacy of a moderately strong DapE inhibitor.
Protein Control Of S-Nitrosothiol Reactivity: Interplay Of Antagonistic Resonance Structures, Marat R. Talipov, Qadir K. Timerghazin
Protein Control Of S-Nitrosothiol Reactivity: Interplay Of Antagonistic Resonance Structures, Marat R. Talipov, Qadir K. Timerghazin
Chemistry Faculty Research and Publications
There is currently great interest in S-nitrosothiols (RSNOs) because formation of protein-based RSNOs—protein S-nitrosation—has been recently recognized as a major pathway of the biological function of nitric oxide, NO. Despite the growing number of S-nitrosated proteins identified in vivo, enzymatic processes that control reactions of biological RSNOs are still not well understood. In this article, we use a range of models to computationally demonstrate that specific interactions of RSNOs with charged and polar residues in proteins can result in dramatic modification of RSNO structure, stability, and reactivity. This unprecedented sensitivity of the −SNO group toward interactions with …
Generation Of Molecular Complexity From Cyclooctatetraene: Preparation Of Optically Active Protected Aminocycloheptitols And Bicyclo[4.4.1]Undecatriene, Mohamed F. El-Mansy, Anobick Sar, Sergey V. Lindeman, William A. Donaldson
Generation Of Molecular Complexity From Cyclooctatetraene: Preparation Of Optically Active Protected Aminocycloheptitols And Bicyclo[4.4.1]Undecatriene, Mohamed F. El-Mansy, Anobick Sar, Sergey V. Lindeman, William A. Donaldson
Chemistry Faculty Research and Publications
The racemic (6-cyclo-heptadienyl)Fe(CO)3+ cation ((±)-7), prepared from cyclooctatetraene, was treated with a variety of carbon and heteroatom nucleophiles. Attack took place at the less hindered C1 dienyl carbon and decomplexation of the (cycloheptadiene)Fe(CO)3 complexes gave products rich in functionality for further synthetic manipulation. In particular, a seven-step route was developed from racemic (6-styryl-2,4-cycloheptadien-1-yl)phthalimide ((±)-9 d) to afford the optically active aminocycloheptitols (−)-20 and (+)-20.
Concerted And Sequential Pathways Of Proton-Coupled Electron Transfer In Hydrogen Halide Elimination, Aimable Kalume, Lisa George, Nicole Cunningham, Scott A. Reid
Concerted And Sequential Pathways Of Proton-Coupled Electron Transfer In Hydrogen Halide Elimination, Aimable Kalume, Lisa George, Nicole Cunningham, Scott A. Reid
Chemistry Faculty Research and Publications
Proton-coupled electron transfer (PCET) is a key reaction in a diverse array of chemical and biochemical processes. Concerted PCET, a single step process where no intermediates are expected, is often difficult to distinguish from sequential electron transfer/proton transfer (or proton transfer/electron transfer) events that involve one or more reactive intermediates. Here we demonstrate that in an apparently simple and fundamental organic reaction, hydrogen halide elimination (dehydrohalogenation), both mechanisms occur, with concerted PCET kinetically favored over sequential ET/PT. The latter involves a well-defined reactive intermediate, the corresponding iso-halon.
No Longer A Complex, Not Yet A Molecule: A Challenging Case Of Nitrosyl O-Hydroxide, Hoon, Majher I. Sarker, Tasnuva Shahrin, Mark G. Steinmetz, Qadir K. Timerghazin
No Longer A Complex, Not Yet A Molecule: A Challenging Case Of Nitrosyl O-Hydroxide, Hoon, Majher I. Sarker, Tasnuva Shahrin, Mark G. Steinmetz, Qadir K. Timerghazin
Chemistry Faculty Research and Publications
N-(9-Oxothioxanthenyl)benzothiophene carboxamides bearing leaving groups (LG− = Cl−, PhS−, HS−, PhCH2S−) at the C-3 position of the benzothiophene ring system photochemically cyclize with nearly quantitative release of the leaving group, LG−. The LG− photoexpulsions can be conducted with 390 nm light or with a sunlamp. Solubility in 75% aqueous CH3CN is achieved by introducing a carboxylate group at the C-6 position of the benzothiophene ring. The carboxylate and methyl ester derivatives regiospecifically cyclize at the more hindered C-1 position of the thioxanthone ring. …
Photochemical Electrocyclic Ring Closure And Leaving Group Expulsion From N-(9-Oxothioxanthenyl)Benzothiophene Carboxamides, Majher I. Sarker, Tasnuva Shahrin, Mark G. Steinmetz, Qadir K. Timerghazin
Photochemical Electrocyclic Ring Closure And Leaving Group Expulsion From N-(9-Oxothioxanthenyl)Benzothiophene Carboxamides, Majher I. Sarker, Tasnuva Shahrin, Mark G. Steinmetz, Qadir K. Timerghazin
Chemistry Faculty Research and Publications
N-(9-Oxothioxanthenyl)benzothiophene carboxamides bearing leaving groups (LG− = Cl−, PhS−, HS−, PhCH2S−) at the C-3 position of the benzothiophene ring system photochemically cyclize with nearly quantitative release of the leaving group, LG−. The LG− photoexpulsions can be conducted with 390 nm light or with a sunlamp. Solubility in 75% aqueous CH3CN is achieved by introducing a carboxylate group at the C-6 position of the benzothiophene ring. The carboxylate and methyl ester derivatives regiospecifically cyclize at the more hindered C-1 position of the thioxanthone ring. …
Global Permutationally Invariant Potential Energy Surface For Ozone Forming Reaction, Mehdi Ayouz, Dmitri Babikov
Global Permutationally Invariant Potential Energy Surface For Ozone Forming Reaction, Mehdi Ayouz, Dmitri Babikov
Chemistry Faculty Research and Publications
We constructed new global potential energy surface for O + O2 → O3 reaction. It is based on high level electronic structure theory calculations and employs fitting by permutationally invariant polynomial functions. This method of surface construction takes full advantage of permutation symmetry of three O nuclei and allows reducing dramatically the number of ab initio data points needed for accurate surface representation. New potential energy surface offers dramatic improvement over older surface of ozone in terms of dissociation energy and behavior along the minimum energy path. It can be used to refine the existing theories of ozone …
Frozen Rotor Approximation In The Mixed Quantum/Classical Theory For Collisional Energy Transfer: Application To Ozone Stabilization, Alexander Teplukhin, Mikhail V. Ivanov, Dmitri Babikov
Frozen Rotor Approximation In The Mixed Quantum/Classical Theory For Collisional Energy Transfer: Application To Ozone Stabilization, Alexander Teplukhin, Mikhail V. Ivanov, Dmitri Babikov
Chemistry Faculty Research and Publications
A frozen-rotor approximation is formulated for the mixed quantum/classical theory of collisional energy transfer and ro-vibrational energy flow [M. Ivanov and D. Babikov, J. Chem. Phys.134, 144107 (Year: 2011)]. Numerical tests are conducted to assess its efficiency and accuracy, compared to the original version of the method, where rotation of the molecule in space is treated explicitly and adiabatically. New approach is considerably faster and helps blocking the artificial ro-vibrational transitions at the pre- and post-collisional stages of the process. Although molecular orientation in space is fixed, the energy exchange between rotational, vibrational, and translational digresses of freedom still occurs, …
Equivalence Of The Ehrenfest Theorem And The Fluid-Rotor Model For Mixed Quantum/Classical Theory Of Collisional Energy Transfer, Alexander Semenov, Dmitri Babikov
Equivalence Of The Ehrenfest Theorem And The Fluid-Rotor Model For Mixed Quantum/Classical Theory Of Collisional Energy Transfer, Alexander Semenov, Dmitri Babikov
Chemistry Faculty Research and Publications
The theory of two seemingly different quantum/classical approaches to collisional energy transfer and ro-vibrational energy flow is reviewed: a heuristic fluid-rotor method, introduced earlier to treat recombination reactions[M. Ivanov and D. Babikov, J. Chem. Phys.134, 144107 (Year: 2011)10.1063/1.3576103], and a more rigorous method based on the Ehrenfest theorem. It is shown analytically that for the case of a diatomic molecule + quencher these two methods are entirely equivalent. Notably, they both make use of the average moment of inertia computed as inverse of average of inverse of the distributed moment of inertia. Despite this equivalence, each of the two formulations …
Identification Of A Histidine Metal Ligand In The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Wade C. Mcgregor, Danuta Gillner, Sabina I. Swierczek, Dali Liu, Richard C. Holz
Identification Of A Histidine Metal Ligand In The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Wade C. Mcgregor, Danuta Gillner, Sabina I. Swierczek, Dali Liu, Richard C. Holz
Chemistry Faculty Research and Publications
The H355A, H355K, H80A, and H80K mutant enzymes of the argE-encoded N-acetyl-L-ornithine deacetylase (ArgE) from Escherichia coli were prepared, however, only the H355A enzyme was found to be soluble. Kinetic analysis of the Co(II)-loaded H355A exhibited activity levels that were 380-fold less than Co(II)-loaded WT ArgE. Electronic absorption spectra of Co(II)-loaded H355A-ArgE indicate that the bound Co(II) ion resides in a distorted, five-coordinate environment and Isothermal Titration Calorimetry (ITC) data for Zn(II) binding to the H355A enzyme provided a dissociation constant (Kd) of 39 μM. A three-dimensional homology model of ArgE was generated using the …
Molecular Docking And Nmr Binding Studies To Identify Novel Inhibitors Of Human Phosphomevalonate Kinase, Pornthip Boonsri, Terrence S. Neumann, Andrew Lawrence Olson, Sheng Cai, Timothy J. Herdendorf, Henry M. Miziorko, Supa Hannongbua, Daniel S. Sem
Molecular Docking And Nmr Binding Studies To Identify Novel Inhibitors Of Human Phosphomevalonate Kinase, Pornthip Boonsri, Terrence S. Neumann, Andrew Lawrence Olson, Sheng Cai, Timothy J. Herdendorf, Henry M. Miziorko, Supa Hannongbua, Daniel S. Sem
Chemistry Faculty Research and Publications
Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based 1H–15N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (Kd). Tight binding compounds with Kd’s ranging from 6–60 μM were identified. These compounds tended to have significant polarity and negative charge, similar to the natural …
Mixed Quantum/Classical Theory Of Rotationally And Vibrationally Inelastic Scattering In Space-Fixed And Body-Fixed Reference Frames, Alexander Semenov, Dmitri Babikov
Mixed Quantum/Classical Theory Of Rotationally And Vibrationally Inelastic Scattering In Space-Fixed And Body-Fixed Reference Frames, Alexander Semenov, Dmitri Babikov
Chemistry Faculty Research and Publications
We formulated the mixed quantum/classical theory for rotationally and vibrationally inelastic scattering process in the diatomic molecule + atom system. Two versions of theory are presented, first in the space-fixed and second in the body-fixed reference frame. First version is easy to derive and the resultant equations of motion are transparent, but the state-to-state transition matrix is complex-valued and dense. Such calculations may be computationally demanding for heavier molecules and/or higher temperatures, when the number of accessible channels becomes large. In contrast, the second version of theory requires some tedious derivations and the final equations of motion are rather complicated …
Ro-Vibrational Quenching Of Co (V = 1) By He Impact In A Broad Range Of Temperatures: A Benchmark Study Using Mixed Quantum/Classical Inelastic Scattering Theory, Alexander Semenov, Mikhail V. Ivanov, Dmitri Babikov
Ro-Vibrational Quenching Of Co (V = 1) By He Impact In A Broad Range Of Temperatures: A Benchmark Study Using Mixed Quantum/Classical Inelastic Scattering Theory, Alexander Semenov, Mikhail V. Ivanov, Dmitri Babikov
Chemistry Faculty Research and Publications
The mixed quantum/classical approach is applied to the problem of ro-vibrational energy transfer in the inelastic collisions of CO(v = 1) with He atom, in order to predict the quenching rate coefficient in a broad range of temperatures 5 < T < 2500 K. Scattering calculations are done in two different ways: direct calculations of quenching cross sections and, alternatively, calculations of the excitation cross sections plus microscopic reversibility. In addition, a symmetrized average-velocity method of Billing is tried. Combination of these methods allows reproducing experiment in a broad range of temperatures. Excellent agreement with experiment is obtained at 400 < T < 2500 K (within 10%), good agreement in the range 100 < T < 400 K (within 25%), and semi-quantitative agreement at 40 < T < 100 K(within a factor of 2). This study provides a stringent test of the mixed quantum/classical theory, because the vibrational quantum in CO molecule is rather large and the quencher is very light (He atom). For heavier quenchers and closer to dissociation limit of the molecule, the mixed quantum/classical theory is expected to work even better.