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University of Nebraska - Lincoln

2006

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Articles 1 - 30 of 51

Full-Text Articles in Chemistry

Multiwalled Ice Helixes And Ice Nanotubes, Jaeil Bai, Jun Wang, Xiao Cheng Zeng Nov 2006

Multiwalled Ice Helixes And Ice Nanotubes, Jaeil Bai, Jun Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We report six phases of high-density nano-ice predicted to form within carbon nanotubes (CNTs) at high pressure. High-density nano-ice self-assembled within smaller-diameter CNT (17,0) exhibits a double-walled helical structure where the outer wall consists of four double- stranded helixes, which resemble a DNA double helix, and the inner wall is a quadruple-stranded helix. Four other double-walled nano-ices, self-assembled respectively in two larger-diameter CNTs (20,0 and 22,0), display tubular structure. Within CNT (24,0), the confined water can freeze spontaneously into a triple-walled helical nanoice where the outer wall is an 18-stranded helix and the middle and inner walls are hextuple-stranded helixes.

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Α,Ω-Dithiol Oligo(Phenylene Vinylene)S For The Preparation Of High-Quality Π-Conjugated Self-Assembled Monolayers And Nanoparticle-Functionalized Electrodes, Dwight S. Seferos, Rebecca Lai, Kevin W. Plaxco, Guillermo C. Bazan Nov 2006

Α,Ω-Dithiol Oligo(Phenylene Vinylene)S For The Preparation Of High-Quality Π-Conjugated Self-Assembled Monolayers And Nanoparticle-Functionalized Electrodes, Dwight S. Seferos, Rebecca Lai, Kevin W. Plaxco, Guillermo C. Bazan

Rebecca Lai Publications

While thioacetate-terminated oligo(phenylene vinylene)s (OPVs) have been synthesized and employed in applications involving the formation of metal–molecule–metal junctions, the synthesis and application of potentially more versatile α,ω-dithiol OPVs have not previously been described. Here, a thiomethyl-precursor route to the synthesis of α,ω-dithiol OPVs is reported and their ability to form well-ordered self-assembled monolayers (SAMs) without the addition of exogenous deprotection reagents is described. α,ω-Dithiol OPV monolayers exhibit thicknesses consistent with molecular length and are nearly defect-free, as assayed by electrochemical measurements. To demonstrate the ease with which SAMs containing these bifunctional OPVs can, in contrast to thioacetate functionalized OPVs, be …

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Acrosome Reaction Is Subfamily Specific In Sea Star Fertilization, Mia Nakachi, Hideaki Moriyama, Motonori Hoshi, Midori Matsumoto Oct 2006

Acrosome Reaction Is Subfamily Specific In Sea Star Fertilization, Mia Nakachi, Hideaki Moriyama, Motonori Hoshi, Midori Matsumoto

Hideaki Moriyama Publications

In the fertilization process of sea stars, sperm is activated to go through the acrosome reaction before cell fusion. We focused on induction of the acrosome reaction as a key process in fertilization. Six species of sea stars were used in this study: Asterias amurensis, Asterias rubens, Asterias forbesi, Aphelasterias japonica, Distolasterias nipon, and Asterina pectinifera. Acrosome reaction assays indicate that the acrosome reaction can be induced across species within Asteriinae subfamily. However, cross-fertilization assays indicate that sea stars have species specificity in fertilization. Therefore, steps after the acrosome reaction are responsible for the …

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Homogeneous Nucleation At High Supersaturation And Heterogeneous Nucleation On Microscopic Wettable Particles: A Hybrid Thermodynamic/Density-Functional Theory, T. V. Bykov, Xiao Cheng Zeng Oct 2006

Homogeneous Nucleation At High Supersaturation And Heterogeneous Nucleation On Microscopic Wettable Particles: A Hybrid Thermodynamic/Density-Functional Theory, T. V. Bykov, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Homogeneous nucleation at high supersaturation of vapor and heterogeneous nucleation on microscopic wettable particles are studied on the basis of Lennard-Jones model system. A hybrid classical thermodynamics and density-functional theory (DFT) approach is undertaken to treat the nucleation problems. Local-density approximation and weighted-density approximation are employed within the framework of DFT. Special attention is given to the disjoining pressure of small liquid droplets, which is dependent on the thickness of wetting film and radius of the wettable particle. Different contributions to the disjoining pressure are examined using both analytical estimations and numerical DFT calculation. It is shown that van der …

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Structures And Relative Stability Of Neutral Gold Clusters: AuN (N=15–19), Satya S. Bulusu, Xiao Cheng Zeng Oct 2006

Structures And Relative Stability Of Neutral Gold Clusters: AuN (N=15–19), Satya S. Bulusu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We performed a global-minimum search for low-lying neutral clusters (Aun) in the size range of n=15–19 by means of basin-hopping method coupled with density functional theory calculation. Leading candidates for the lowest-energy clusters are identified, including four for Au15, two for Au16, three for Au17, five for Au18, and one for Au19. For Au15 and Au16 we find that the shell-like flat-cage structures dominate the population of low-lying clusters, while for Au17 and Au18 spherical-like hollow-cage structures dominate the low-lying population. The transition …

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Novel Mesoscale Defect Structure On Nio(1 0 0) Surfaces By Atomic Force Microscopy, S. C. Petitto, Cindy L. Berrie, Marjorie Langell Sep 2006

Novel Mesoscale Defect Structure On Nio(1 0 0) Surfaces By Atomic Force Microscopy, S. C. Petitto, Cindy L. Berrie, Marjorie Langell

Marjorie A. Langell Publications

Cleaved NiO(1 0 0) surfaces were imaged with atomic force microscopy (AFM) to determine defect concentrations and morphology. Random (0 1 0) and (0 0 1) oriented steps, which have been previously characterized, were the most common defect observed on the cleaved surface and formed with step heights in multiples of 2.1 Å, the Ni–O nearest-neighbor distance, and terrace widths in the range of 25–100 nm. In addition, the surface showed novel mesoscale (~0.5–2 μm) square pyramidal defects with the pyramid base oriented along (1 0 0) symmetry related directions. Upon etching, the pyramidal defects converted to more stable cubic …

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Tau-Tubulin Kinase 1 (Ttbk1), A Neuron-Specific Tau Kinase Candidate, Is Involved In Tau Phosphorylation And Aggregation, Shinji Sato, Ronald Cerny, James L. Buescher, Tsuneya Ikezu Sep 2006

Tau-Tubulin Kinase 1 (Ttbk1), A Neuron-Specific Tau Kinase Candidate, Is Involved In Tau Phosphorylation And Aggregation, Shinji Sato, Ronald Cerny, James L. Buescher, Tsuneya Ikezu

Ronald Cerny Publications

Neurofibrillary tangles, which are major pathological hallmarks of Alzheimer’s disease (AD), are composed of paired helical filaments (PHFs) containing hyperphosphorylated tau. Specific kinases regulate tau phosphorylation and are closely linked to the pathogenesis of AD. We have characterized a human tau-tubulin kinase 1 (TTBK1) gene located on chromosome 6p21.1. TTBK1 is a serine/threonine/tyrosine kinase that is conserved among species and belongs to the casein kinase 1 superfamily. It is specifically expressed in the brain, especially in the cytoplasm of cortical and hippocampal neurons. TTBK1 phosphorylates tau proteins in both a Mg2+- and a Mn2+-dependent manner. Phosphopeptide …

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Single-Crystal, Polarized, Raman Scattering Study Of The Molecular And Lattice Vibrations For The Energetic Material Cyclotrimethylene Trinitramine, James C. Haycraft, Lewis L. Stevens, Craig J. Eckhardt Sep 2006

Single-Crystal, Polarized, Raman Scattering Study Of The Molecular And Lattice Vibrations For The Energetic Material Cyclotrimethylene Trinitramine, James C. Haycraft, Lewis L. Stevens, Craig J. Eckhardt

Craig J. Eckhardt Publications

The single-crystal, polarized, Raman spectra for cyclotrimethylene trinitramine (RDX) have been studied at room temperature and pressure over the region of 5–3400 cm-1. While the observed Raman bands agree well with a previous Raman study, this work provides a consistent interpretation of the Raman spectra by assignment of fundamental modes, overtones, and combination bands. A total of 56 internal vibrations were observed, 36 of which were labeled as fundamental molecular vibrations. In addition, all 24 lattice optical phonons are identified. All six possible polarizations were probed to obtain the Ag, B1g, B2 …

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“Reductive Ozonolysis” Via A New Fragmentation Of Carbonyl Oxides, Chris Schwartz, Joseph Raible, Kyle Mott, Patrick Dussault Sep 2006

“Reductive Ozonolysis” Via A New Fragmentation Of Carbonyl Oxides, Chris Schwartz, Joseph Raible, Kyle Mott, Patrick Dussault

Patrick Dussault Publications

This account describes the development of methodologies for ‘reductive’ ozonolysis, the direct ozonolytic conversion of alkenes into carbonyl groups without the intermediacy of 1,2,4-trioxolanes (ozonides). Ozonolysis of alkenes in the presence of DMSO produces a mixture of aldehyde and ozonide. The combination of DMSO and Et3N results in improved yields of carbonyls but still leaves unacceptable levels of residual ozonides; similar results are obtained using secondary or tertiary amines in the absence of DMSO. The influence of amines is believed to result from conversion to the corresponding N-oxides; ozonolysis in the presence of amine N-oxides efficiently …

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List Of Publications: Robert Powers Aug 2006

List Of Publications: Robert Powers

Robert Powers Publications

Chronological list of 57 published articles and chapters in chemistry. Current through August 2006.

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Hybrid Atomistic-Coarse-Grained Treatment Of Multiscale Processes In Heterogeneous Materials: A Self-Consistent-Field Approach, Dennis J. Diestler, H. Zhou, Ruqiang Feng, Xiao Cheng Zeng Aug 2006

Hybrid Atomistic-Coarse-Grained Treatment Of Multiscale Processes In Heterogeneous Materials: A Self-Consistent-Field Approach, Dennis J. Diestler, H. Zhou, Ruqiang Feng, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

A treatment of multiscale quasistatic processes that combines an atomistic description of microscopic heterogeneous (“near”) regions of a material with a coarse-grained (quasicontinuum) description of macroscopic homogeneous (“far”) regions is presented. The hybrid description yields a reduced system consisting of the original atoms of the near regions plus pseudoatoms (nodes of the coarse-graining mesh) of the far regions, which interact through an effective many-body potential energy Veff that depends on the thermodynamic state. The approximate nature of Veff gives rise to “ghost forces,” which are reflected in spurious heterogeneities close to interfaces between near and far regions. The …

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Comparison Of Protein Active Site Structures For Functional Annotation Of Proteins And Drug Design, Robert Powers, Jennifer C. Copeland, Katherine Germer, Kelly A. Mercier, Viswanathan Ramanathan, Peter Revesz Jul 2006

Comparison Of Protein Active Site Structures For Functional Annotation Of Proteins And Drug Design, Robert Powers, Jennifer C. Copeland, Katherine Germer, Kelly A. Mercier, Viswanathan Ramanathan, Peter Revesz

Robert Powers Publications

Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein’s activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The …

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Shape-Persistent Macrocyclic Aromatic Tetrasulfonamides: Molecules With Nanosized Cavities And Their Nanotubular Assemblies In Solid State, Lan He, Yu An, Lihua Yuan, Wen Feng, Minfeng Li, Dechun Zhang, Kazuhiro Yamato, Chong Zheng, Xiao Cheng Zeng, Bing Gong Jul 2006

Shape-Persistent Macrocyclic Aromatic Tetrasulfonamides: Molecules With Nanosized Cavities And Their Nanotubular Assemblies In Solid State, Lan He, Yu An, Lihua Yuan, Wen Feng, Minfeng Li, Dechun Zhang, Kazuhiro Yamato, Chong Zheng, Xiao Cheng Zeng, Bing Gong

Xiao Cheng Zeng Publications

Alkoxy side-chain-flanked diarylsulfonamide serves as a reliable structural motif for constructing macrocyclic aromatic tetrasulfonamides. This 90° structural motif is persistent both in solution and in the solid state, which allows the one-step formation of tetrasulfonamide macrocycles. These macrocycles adopt a cone-shaped conformation in solution and in the solid state. For each molecule, an interior cavity surrounded by the aromatic residues is formed. The cavity sizes of the macrocycles can be tuned by incorporating aromatic residues of proper sizes. Guest (solvent) molecules are found in the cavities and bound by side chains. In solution, 1H NMR shows that the cone …

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Structural And Electronic Properties Of Gd@C60: All-Electron Relativistic Total-Energy Study, Jing Lu, Wai-Ning Mei, Yi Gao, Xiao Cheng Zeng, Mingwei Jing, Guangping Li, Renat F. Sabirianov, Zhengxiang Gao, Liping You, Jun Xu, Dapeng Yu, Hengqiang Ye Jul 2006

Structural And Electronic Properties Of Gd@C60: All-Electron Relativistic Total-Energy Study, Jing Lu, Wai-Ning Mei, Yi Gao, Xiao Cheng Zeng, Mingwei Jing, Guangping Li, Renat F. Sabirianov, Zhengxiang Gao, Liping You, Jun Xu, Dapeng Yu, Hengqiang Ye

Xiao Cheng Zeng Publications

Water soluble Gd-based metallofullerenes have potential application as magnetic resonance imaging contrast agent due to its higher proton relaxivities and lower toxicity. In this letter, we have investigated the structural and electronic properties of Gd@ C60, which is the most abundantly produced Gd-based metallofullerene in carbon arc process, by using all-electron relativistic density functional theory. It is found that the Gd3+ ion is bonded to a hexagonal ring of C60 by electrostatic interaction. The total spin multiplicity of Gd@C60 is S = 7. The Gd atomic orbitals are hybridized with the C60 molecular orbitals.

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Adsorption Of Transition-Metal Atoms On Boron Nitride Nanotube: A Density-Functional Study, Xiaojun Wu, Xiao Cheng Zeng Jul 2006

Adsorption Of Transition-Metal Atoms On Boron Nitride Nanotube: A Density-Functional Study, Xiaojun Wu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Adsorption of transition atoms on a (8,0) zigzag single-walled boron nitride (BN) nanotube has been investigated using density-functional theory methods. Main focuses have been placed on configurations corresponding to the located minima of the adsorbates, the corresponding binding energies, and the modified electronic properties of the BN nanotubes due to the adsorbates.We have systemically studied a series of metal adsorbates including all 3d transition-metal elements (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn) and two group-VIIIA transition-metal elements (Pd and Pt). We found that many transition-metal atoms can be chemically adsorbed on the outer surface of the …

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Staphylococcus Aureus Helicase But Not Escherichia Coli Helicase Stimulates S. Aureus Primase Activity And Maintains Initiation Specificity, Scott A. Koepsell, Marilynn A. Larson, Mark A. Griep, Steven H. Hinrichs Jul 2006

Staphylococcus Aureus Helicase But Not Escherichia Coli Helicase Stimulates S. Aureus Primase Activity And Maintains Initiation Specificity, Scott A. Koepsell, Marilynn A. Larson, Mark A. Griep, Steven H. Hinrichs

Mark Griep Publications

Bacterial primases are essential for DNA replication due to their role in polymerizing the formation of short RNA primers repeatedly on the lagging-strand template and at least once on the leading-strand template. The ability of recombinant Staphylococcus aureus DnaG primase to utilize different single-stranded DNA templates was tested using oligonucleotides of the sequence 5’-CAGA (CA) 5 XYZ (CA) 3-3’, where XYZ represented the variable trinucleotide. These experiments demonstrated that S. aureus primase synthesized RNA primers predominately on templates containing 5’-d(CTA)-3’ or TTA and to a much lesser degree on GTA-containing templates, in contrast to results seen with the Escherichia …

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Adsorption Of Hydrogen Molecules On The Platinum-Doped Boron Nitride Nanotubes, Xiaojun Wu, J.L. Yang, Xiao Cheng Zeng Jul 2006

Adsorption Of Hydrogen Molecules On The Platinum-Doped Boron Nitride Nanotubes, Xiaojun Wu, J.L. Yang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Adsorption of hydrogen molecules on platinum-doped single-walled zigzag (8,0) boron nitride (BN) nanotube is investigated using the density-functional theory. The Pt atom tends to occupy the axial bridge site of the BN tube with the highest binding energy of −0.91 eV. Upon Pt doping, several occupied and unoccupied impurity states are induced, which reduces the band gap of the pristine BN nanotube. Upon hydrogen adsorption on Pt-doped BN nanotube, the first hydrogen molecule can be chemically adsorbed on the Pt-doped BN nanotube without crossing any energy barrier, whereas the second hydrogen molecule has to overcome a small energy barrier of …

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The Importance Of The Strictly Conserved, C-Terminal Glycine Residue In Phosphoenolpyruvate Carboxylase For Overall Catalysis: Mutagenesis And Truncation Of Gly-961 In The Sorghum C4 Leaf Isoform, Wenxin Xu, Shaheen Ahmed, Hideaki Moriyama, Raymond Chollet Jun 2006

The Importance Of The Strictly Conserved, C-Terminal Glycine Residue In Phosphoenolpyruvate Carboxylase For Overall Catalysis: Mutagenesis And Truncation Of Gly-961 In The Sorghum C4 Leaf Isoform, Wenxin Xu, Shaheen Ahmed, Hideaki Moriyama, Raymond Chollet

Hideaki Moriyama Publications

Phosphoenolpyruvate carboxylase (PEPC) is a “multifaceted,” allosteric enzyme involved in C4 acid metabolism in green plants/microalgae and prokaryotes. Before the elucidation of the three-dimensional structures of maize C4 leaf and Escherichia coli PEPC, our truncation analysis of the sorghum C4 homologue revealed important roles for the enzyme’s C-terminal α-helix and its appended QNTG961 tetrapeptide in polypeptide stability and overall catalysis, respectively. Collectively, these functional and structural observations implicate the importance of the PEPC C-terminal tetrapeptide for both catalysis and negative allosteric regulation. We have now more finely dissected this element of PEPC structure-function by modification of the absolutely conserved …

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Chromatographic Analysis Of Carbamazepine Binding To Human Serum Albumin: Ii. Comparison Of The Schiff Base And N-Hydroxysuccinimide Immobilization Methods, Hee Seung Kim, Rangan Mallik, David S. Hage Jun 2006

Chromatographic Analysis Of Carbamazepine Binding To Human Serum Albumin: Ii. Comparison Of The Schiff Base And N-Hydroxysuccinimide Immobilization Methods, Hee Seung Kim, Rangan Mallik, David S. Hage

David Hage Publications

Recent studies with carbamazepine on human serum albumin (HSA) columns have noted an appreciable degree of non-specific binding on supports prepared by the Schiff base immobilization method. This work examines an alternative immobilization method for HSA based on N-hydroxysuccinimide (NHS)-activated silica. This support was prepared by reacting HPLC-grade silica directly with disuccinimidyl carbonate. The resulting material was compared to an HSA support prepared by the Schiff base method in terms of its activity for carbamazepine and non-specific interactions with this drug. When examined by frontal analysis, both supports gave comparable association equilibrium constants for carbamazepine interactions with HSA ((0.53–0.55) …

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Kinetics Of The Dna Polymerase Pyrococcus Kodakaraensis, Mark A. Griep, Casey A. Kotera, R.M. Nelson, Hendrik J. Viljoen Jun 2006

Kinetics Of The Dna Polymerase Pyrococcus Kodakaraensis, Mark A. Griep, Casey A. Kotera, R.M. Nelson, Hendrik J. Viljoen

Mark Griep Publications

The polymerase chain reaction is one of the most important reactions in molecular biology. Single stranded DNA is copied in a complex series of steps, at the core of which lies the action of the DNA polymerase. At each nucleotide along the template, the polymerase screens the dNTP pool until it finds the complementary dNTP. The insertion of each dNMP is a balance between high fidelity and rapid elongation. In this study the kinetics of the β type polymerase pyrococcus kodakaraensis (KOD) is analyzed. The kinetics is influenced by reaction conditions such as the dNTP pool composition and temperature. In …

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Molecular Simulations Of Solid-Liquid Interfacial Tension Of Silicon, Yuk Wai Tang, Jun Wang, Xiao Cheng Zeng Jun 2006

Molecular Simulations Of Solid-Liquid Interfacial Tension Of Silicon, Yuk Wai Tang, Jun Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Silicon is an important semiconductor for manufacturing of microelectronic chips used in computers and other electronic devices. During the manufacturing process, liquid silicon is being solidified to make high-grade solid semiconductors. Thus, improved data of the solid-liquid interfacial properties of silicon will be useful towards optimizing the experiment condition for making better quality electronics. Yet it is difficult to perform experiments of liquid silicon due to its high melting point. Thus far, most experimental measurements of the solid-liquid interfacial tension are based on the measurement of rate of homogeneous crystal nucleation at a given undercooling. The first measurement of solidliquid …

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Evidence Of Hollow Golden Cages, Satya S. Bulusu, Xi Li, Lai-Sheng Wang, Xiao Cheng Zeng May 2006

Evidence Of Hollow Golden Cages, Satya S. Bulusu, Xi Li, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

The fullerenes are the first “free-standing” elemental hollow cages identified by spectroscopy experiments and synthesized in the bulk. Here, we report experimental and theoretical evidence of hollow cages consisting of pure metal atoms, Au–n (n = 16–18); to our knowledge, free-standing metal hollow cages have not been previously detected in the laboratory. These hollow golden cages (“bucky gold”) have an average diameter >5.5 Å, which can easily accommodate one guest atom inside.

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Evidence Of Hollow Golden Cages: Supplementary Materials And Supporting Information, Satya S. Bulusu, Xi Li, Lai-Sheng Wang, Xiao Cheng Zeng May 2006

Evidence Of Hollow Golden Cages: Supplementary Materials And Supporting Information, Satya S. Bulusu, Xi Li, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Figures 3A-3D: Simulated anion photoelectron spectra [based on the density-functional theory (DFT) calculation with the PBEPBE/LANL2DZ functional and basis set] for all of the candidate lowest-energy isomers of
Au¯15 (A),
Au¯16 (B),
Au¯17 (C), and
Au¯18 (D) identified in Fig. 3 A–D, respectively.

Figures 4A-4E: Top-10 lowest-energy isomers of Au¯15, Au¯16, Au¯17, Au¯18, and Au¯19 obtained from a basin-hopping global search combined with DFT optimization and total-energy calculation.

Table 2: The experimental adiabatic detachment energies (ADEs) for Au¯n (n = 15–19) measured from the threshold …

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Studies By Biointeraction Chromatography Of Binding By Phenytoin Metabolites To Human Serum Albumin, Corey M. Ohnmacht, Shirley Chen, Zenghan Tong, David S. Hage May 2006

Studies By Biointeraction Chromatography Of Binding By Phenytoin Metabolites To Human Serum Albumin, Corey M. Ohnmacht, Shirley Chen, Zenghan Tong, David S. Hage

David Hage Publications

Biointeraction studies based on high performance affinity chromatography were used to investigate the binding of human serum albumin (HSA) to two major phenytoin metabolites: 5-(3-hydroxyphenyl)-5-phenylhydantoin (m-HPPH) and 5-(4-hydroxyphenyl)-5-phenylhydantoin (p-HPPH). This was initially examined by conducting self-competition zonal elution experiments in which m-HPPH or p-HPPH were placed in both the mobile phase and injected sample. It was found that each metabolite had a single major binding site on HSA. Competitive zonal elution experiments using l-tryptophan, warfarin, digitoxin, and cis-clomiphene as site-selective probes indicated that m-HPPH and p-HPPH were interacting with the indolebenzodiazepine …

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Functional Replacement Of The Ketosynthase Domain Of Fum1 For The Biosynthesis Of Fumonisins, A Group Of Fungal Reduced Polyketides, Xiangcheng Zhu, Fengan Yu, R. S. Bojja, K. Zaleta-Rivera, Liangcheng Du May 2006

Functional Replacement Of The Ketosynthase Domain Of Fum1 For The Biosynthesis Of Fumonisins, A Group Of Fungal Reduced Polyketides, Xiangcheng Zhu, Fengan Yu, R. S. Bojja, K. Zaleta-Rivera, Liangcheng Du

Liangcheng Du Publications

The genetic manipulation of the biosynthesis of fungal reduced polyketides has been challenging due to the lack of knowledge on the biosynthetic mechanism, the difficulties in the detection of the acyclic, non-aromatic metabolites, and the complexity in genetically manipulating filamentous fungi. Fumonisins are a group of economically important mycotoxins that contaminate maize-based food and feed products worldwide. Fumonisins contain a linear dimethylated C18 chain that is synthesized by Fum1p, which is a single module polyketide synthase (PKS). Using a genetic system that allows the specific manipulation of PKS domains in filamentous fungus Fusarium verticillioides, we replaced the KS domain …

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Search For Global-Minimum Geometries Of Medium-Sized Germanium Clusters. Ii. Motif-Based Low-Lying Clusters Ge21–Ge29, S. Yoo, Xiao Cheng Zeng May 2006

Search For Global-Minimum Geometries Of Medium-Sized Germanium Clusters. Ii. Motif-Based Low-Lying Clusters Ge21–Ge29, S. Yoo, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We performed a constrained search for the geometries of low-lying neutral germanium clusters GeN in the size range of 21≤N≤29. The basin-hopping global optimization method is employed for the search. The potential-energy surface is computed based on the plane-wave pseudopotential density functional theory. A new series of low-lying clusters is found on the basis of several generic structural motifs identified previously for silicon clusters [S. Yoo and X. C. Zeng, J. Chem. Phys. 124, 054304 (2006)] as well as for smaller-sized germanium clusters [S. Bulusu et al., J. Chem. Phys. 122, 164305 (2005)]. Among the generic motifs examined, …

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Protein Structure Similarity Clustering: Dynamic Treatment Of Pdb Structures Facilitates Clustering, Bradley D. Charette, Richard G. Macdonald, Stefan Wetzel, David B. Berkowitz, Herbert Waldmann Apr 2006

Protein Structure Similarity Clustering: Dynamic Treatment Of Pdb Structures Facilitates Clustering, Bradley D. Charette, Richard G. Macdonald, Stefan Wetzel, David B. Berkowitz, Herbert Waldmann

David Berkowitz Publications

Protein structure similarity clustering (PSSC) [1]– [3] is one of a number of potential guiding principles [4], [5] that have been introduced to focus combinatorial-library design/ protein targeting. PSSC clusters protein targets with similar ligand-binding cores in which little sequence or functional similarity is evident. Lead compounds for one member of the cluster then provide novel starting points in chemical space for ligand development for other members of the PSSC.

We describe herein a new clustering procedure that lends itself to ligand docking, molecular dynamics (MD), and the vector-alignment-search-tool (VAST) [6] algorithm. This MD-assisted approach offers an alternative to the …

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Α-Vinylic Amino Acids: Occurrence, Asymmetric Synthesis, And Biochemical Mechanisms, David B. Berkowitz, Bradley D. Charette, Kannan Karukurichi, Jill M. Mcfadden Apr 2006

Α-Vinylic Amino Acids: Occurrence, Asymmetric Synthesis, And Biochemical Mechanisms, David B. Berkowitz, Bradley D. Charette, Kannan Karukurichi, Jill M. Mcfadden

David Berkowitz Publications

This report presents an overview of the family of naturally occurring “vinylic” amino acids, namely those that feature a C–C double bond directly attached to the α-carbon, along the side chain. Strategies that have been brought to bear on the stereo-controlled synthesis of these olefinic amino acids are surveyed. The mechanistic diversity by which such “vinylic triggers” can be actuated in a PLP (pyridoxal phosphate) enzyme active site is then highlighted by discussion of vinylglycine (VG), its substituted congeners, particularly AVG [4E-(2′-aminoethoxy)vinylglycine], and a naturally occurring VG-progenitor, SMM [(S)-methylmethionine].

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Structures And Relative Stability Of Medium-Sized Silicon Clusters. V. Low-Lying Endohedral Fullerenelike Clusters Si31–Si40 And Si45, Soohaeng Yoo, N. Shao, C. Koehler, T. Fraunhaum, Xiao Cheng Zeng Apr 2006

Structures And Relative Stability Of Medium-Sized Silicon Clusters. V. Low-Lying Endohedral Fullerenelike Clusters Si31–Si40 And Si45, Soohaeng Yoo, N. Shao, C. Koehler, T. Fraunhaum, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We have performed unconstrained search for low-lying structures of medium-sized silicon clusters Si31–Si40 and Si45, by means of the minimum-hopping global optimization method coupled with a density-functional based tight-binding model of silicon. Subsequent geometric optimization by using density-functional theory with the PBE, BLYP, and B3LYP functionals was carried out to determine the relative stability of various candidate low-lying silicon clusters obtained from the unconstrained search. The low-lying characteristics of these clusters can be affirmed by comparing the binding energies per atom of these clusters with previously determined lowest-energy clusters (Sin) in the size …

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Relative Stability Of Planar Versus Double-Ring Tubular Isomers Of Neutral And Anionic Boron Cluster B20 And B20-, Wei An, Satya S. Bulusu, Yi Gao, Xiao Cheng Zeng Apr 2006

Relative Stability Of Planar Versus Double-Ring Tubular Isomers Of Neutral And Anionic Boron Cluster B20 And B20-, Wei An, Satya S. Bulusu, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

High-level ab initio molecular-orbital methods have been employed to determine the relative stability among four neutral and anionic B20 isomers, particularly the double-ring tubular isomer versus three low-lying planar isomers. Calculations with the fourth-order Møller-Plessset perturbation theory [MP4(SDQ)] and Dunning’s correlation consistent polarized valence triple zeta basis set as well as with the coupled-cluster method including single, double, and noniteratively perturbative triple excitations and the 6-311G(d) basis set show that the double-ring tubular isomer is appreciably lower in energy than the three planar isomers and is thus likely the global minimum of neutral B20 cluster. In contrast, calculations …

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