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Articles 61 - 82 of 82
Full-Text Articles in Life Sciences
Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner
Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C···O bonds in the most stable heterodimer, bound by some 2 kcal mol(-1), NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O···O chalcogen bond. The NBO picture is that of two transfers in opposite …
Effects Of Charge And Substituent On The S∙∙∙N Chalcogen Bond, U. Adhikari, Steve Scheiner
Effects Of Charge And Substituent On The S∙∙∙N Chalcogen Bond, U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of …
An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner
An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal …
Strongly Bound Noncovalent (So3)N:H2co Complexes (N = 1, 2), L. M. Azofra, I. Alkorta, Steve Scheiner
Strongly Bound Noncovalent (So3)N:H2co Complexes (N = 1, 2), L. M. Azofra, I. Alkorta, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by SO chalcogen bonds, supplemented by weaker CHO and/or OC bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol(-1). Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original …
Membrane Lipid-Modulated Mechanism Of Action And Non-Cytotoxicity Of Novel Fungicide Aminoglycoside Fg08, Sanjib Shrestha, Michelle Grilley, Marina Y. Fosso, Cheng-Wei Tom Chang, Jon Y. Takemoto
Membrane Lipid-Modulated Mechanism Of Action And Non-Cytotoxicity Of Novel Fungicide Aminoglycoside Fg08, Sanjib Shrestha, Michelle Grilley, Marina Y. Fosso, Cheng-Wei Tom Chang, Jon Y. Takemoto
Chemistry and Biochemistry Faculty Publications
A novel aminoglycoside, FG08, that differs from kanamycin B only by a C8 alkyl chain at the 4″-O position, was previously reported. Unlike kanamycin B, FG08 shows broad-spectrum fungicidal but not anti-bacterial activities. To understand its specificity for fungi, the mechanism of action of FG08 was studied using intact cells of the yeast Saccharomyces cerevisiae and small unilamellar membrane vesicles. With exposure to FG08 (30 µg mL−1), 8-fold more cells were stained with fluorescein isothiocyanate, cells had 4 to 6-fold higher K+ efflux rates, and 18-fold more cells were stained with SYTOX Green in comparison to exposure to kanamycin B …
Mesobiliverdin Ixα Enhances Rat Pancreatic Islet Yield And Function, Taihei Ito, Dong Chen, Cheng-Wei Tom Chang, Takashi Kenmochi, Tomonori Saito, Satoshi Suzuki, Jon Y. Takemoto
Mesobiliverdin Ixα Enhances Rat Pancreatic Islet Yield And Function, Taihei Ito, Dong Chen, Cheng-Wei Tom Chang, Takashi Kenmochi, Tomonori Saito, Satoshi Suzuki, Jon Y. Takemoto
Chemistry and Biochemistry Faculty Publications
The aims of this study were to produce mesobiliverdin IXα, an analog of anti-inflammatory biliverdin IXα, and to test its ability to enhance rat pancreatic islet yield for allograft transplantation into diabetic recipients. Mesobiliverdin IXα was synthesized from phycocyanobilin derived from cyanobacteria, and its identity and purity were analyzed by chromatographic and spectroscopic methods. Mesobiliverdin IXα was a substrate for human NADPH biliverdin reductase. Excised Lewis rat pancreata infused with mesobiliverdin IXα and biliverdin IXα-HCl (1–100 μM) yielded islet equivalents as high as 86.7 and 36.5%, respectively, above those from non-treated controls, and the islets showed a high degree of …
The Role Of The Global Cryosphere On The Fate Of Organic Contaminants., Amanda M. Grannas, Christian Bogdal, Kimberly J. Hageman, Frank Wania
The Role Of The Global Cryosphere On The Fate Of Organic Contaminants., Amanda M. Grannas, Christian Bogdal, Kimberly J. Hageman, Frank Wania
Chemistry and Biochemistry Faculty Publications
The cryosphere is an important component of global organic contaminant cycles. Snow is an efficient scavenger of atmospheric organic pollutants while a seasonal snowpack, sea ice, glaciers and ice caps are contaminant reservoirs on time scales ranging from days to millennia. Important physical and chemical processes occurring in the various cryospheric compartments impact contaminant cycling and fate. A variety of interactions and feedbacks also occur within the cryospheric system, most of which are susceptible to perturbations due to climate change. In this article, we review the current state of knowledge regarding the transport and processing of organic contaminants in the …
Characterization Of A Novel Fusion Protein Of Ipab And Ipad Of Shigella And Its Potential As A Pan-Shigella Vaccine, F. J. Martinez-Becerra, X. Chen, Nicholas E. Dickenson, S. P. Choudhari, K. Harrison, J. D. Clements, W. D. Picking, L. L. Van De Verg, R. I. Walker, W. L. Picking
Characterization Of A Novel Fusion Protein Of Ipab And Ipad Of Shigella And Its Potential As A Pan-Shigella Vaccine, F. J. Martinez-Becerra, X. Chen, Nicholas E. Dickenson, S. P. Choudhari, K. Harrison, J. D. Clements, W. D. Picking, L. L. Van De Verg, R. I. Walker, W. L. Picking
Chemistry and Biochemistry Faculty Publications
Shigellosis is an important disease in the developing world, where about 90 million people become infected with Shigella spp. each year. We previously demonstrated that the type three secretion apparatus (T3SA) proteins IpaB and IpaD are protective antigens in the mouse lethal pulmonary model. In order to simplify vaccine formulation and process development, we have evaluated a vaccine design that incorporates both of these previously tested Shigella antigens into a single polypeptide chain. To determine if this fusion protein (DB fusion) retains the antigenic and protective capacities of IpaB and IpaD, we immunized mice with the DB fusion and compared …
The Magnitude And Mechanism Of Charge Enhancement Of Ch∙∙O H-Bonds, U. Adhikari, Steve Scheiner
The Magnitude And Mechanism Of Charge Enhancement Of Ch∙∙O H-Bonds, U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Quantum calculations find that neutral methylamines and thioethers form complexes, with N-methylacetamide (NMA) as proton acceptor, with binding energies of 2–5 kcal/mol. This interaction is magnified by a factor of 4–9, bringing the binding energy up to as much as 20 kcal/mol, when a CH3+ group is added to the proton donor. Complexes prefer trifurcated arrangements, wherein three separate methyl groups donate a proton to the O acceptor. Binding energies lessen when the systems are immersed in solvents of increasing polarity, but the ionic complexes retain their favored status even in water. The binding energy is reduced when the methyl …
Effects Of Carbon Chain Substituent On The P∙∙∙N Noncovalent Bond, U. Adhikari, Steve Scheiner
Effects Of Carbon Chain Substituent On The P∙∙∙N Noncovalent Bond, U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The effects of carbon chains placed on the electron-accepting P atom of a P⋯N bond are examined via ab initio calculations. Saturated alkyl groups have a mild weakening effect, regardless of chain length. In contrast, incorporation of double bonds into the chain strengthens the interaction, Ctriple bond; length of mdashC triple bonds even more so. These effects are only slightly enhanced by additional conjugated double bonds or an aromatic ring. Placing F atoms onto the carbon chains strengthens the P⋯N bond, but only by a small amount, which wanes as the F atom is displaced further from the P along …
Contributions Of Various Noncovalent Bonds To The Interaction Between An Amide And S-Containing Molecules, U. Adhikari, Steve Scheiner
Contributions Of Various Noncovalent Bonds To The Interaction Between An Amide And S-Containing Molecules, U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
N-Methylacetamide, a model of the peptide unit in proteins, is allowed to interact with CH3SH, CH3SCH3, and CH3SSCH3 as models of S-containing amino acid residues. All of the minima are located on the ab initio potential energy surface of each heterodimer. Analysis of the forces holding each complex together identifies a variety of different attractive forces, including SH⋅⋅⋅O, NH⋅⋅⋅S, CH⋅⋅⋅O, CH⋅⋅⋅S, SH⋅⋅⋅π, and CH⋅⋅⋅π H-bonds. Other contributing noncovalent bonds involve charge transfer into σ* and π* antibonds. Whereas some of the H-bonds are strong enough that they represent the sole attractive force in several dimers, albeit not usually in the …
Sensitivity Of Noncovalent Bonds To Intermolecular Separation: Hydrogen, Halogen, Chalcogen, And Pnicogen Bonds, Steve Scheiner
Sensitivity Of Noncovalent Bonds To Intermolecular Separation: Hydrogen, Halogen, Chalcogen, And Pnicogen Bonds, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
It is well known that noncovalent bonds are weakened when stretched from their equilibrium intermolecular separation. Quantum chemical calculations are used to examine and compare the sensitivity to stretches of hydrogen, halogen, chalcogen, and pnicogen bonds. NH3 was taken as the universal electron donor, paired with HOH and FH in H-bonds, as well as with FPH2, FSH, and FCl. Even though the binding energies span a wide range, stretching the intermolecular separation by 1 Å cuts this quantity by the same proportion, roughly in half, for each system. Taking the sum of van der Waals radii as an arbitrary cutoff, …
Preferred Configurations Of Peptide-Peptide Interactions, U. Adhikari, Steve Scheiner
Preferred Configurations Of Peptide-Peptide Interactions, U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The natural and fundamental proclivities of interaction between a pair of peptide units are examined using high-level ab initio calculations. The NH···O H-bonded structure is found to be the most stable configuration of the N-methylacetamide (NMA) model dimer, but only slightly more so than a stacked arrangement. The H-bonded geometry is destabilized by only a small amount if the NH group is lifted out of the plane of the proton-accepting amide. This out-of-plane motion is facilitated by a stabilizing charge transfer from the CO π bond to the NH σ* antibonding orbital. The parallel and antiparallel stacked dimers are nearly …
Evaluation Of Dft Methods To Study Reactions Of Benzene With Oh Radical, Steve Scheiner
Evaluation Of Dft Methods To Study Reactions Of Benzene With Oh Radical, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Several density functional theory” (DFT) methods are applied to two different reaction channels involving OH• + C6H6, and the results compared with high-level ab initio calculations. The OH• adds directly to one C atom in the first channel, first forming an encounter complex with the OH• poised above the aromatic plane. B3LYP, BH&HLYP, and MPW1K compute an accurate estimate of the overall exothermicity, whereas M05-2X, PBE0, and PBEPBE overestimate this quantity to some degree. With the exceptions of PBEPBE and PBE0, the other methods produce an acceptable barrier to addition. All approaches except BH&HLYP correctly predict an exothermic H• abstraction, …
First Steps In Growth Of A Polypeptide Toward Β-Sheet Structure, U. Adhikari, Steve Scheiner
First Steps In Growth Of A Polypeptide Toward Β-Sheet Structure, U. Adhikari, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. …
Extrapolation To The Complete Basis Set Limit For Binding Energies Of Noncovalent Interactions, Steve Scheiner
Extrapolation To The Complete Basis Set Limit For Binding Energies Of Noncovalent Interactions, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
A means of extrapolating from double and triple-valence basis sets to a complete basis set is examined in the context of the pnicogen bonds in the BH2P⋯NH3 complexes, with B = CH3, H, NH2, CF3, OH, Cl, F, and NO2. Binding energies converge smoothly, and the trends for the various substituents B are unaffected by the basis set size, extrapolation, or level of inclusion of electron correlation, including MP2 and CCSD(T). The approach appears to be successful also for H-bonded systems, in particular the water dimer. In the event that full extrapolation within the context of CCSD(T) is not feasible, …
Interfamily Variation In Amphibian Early Life-History Traits: Raw Material For Natural Selection?, Gareth R. Hopkins, Brian G. Gall, Susannah S. French, Edmund D. Brodie Jr.
Interfamily Variation In Amphibian Early Life-History Traits: Raw Material For Natural Selection?, Gareth R. Hopkins, Brian G. Gall, Susannah S. French, Edmund D. Brodie Jr.
Biology Faculty Publications
The embryonic development and time to hatching of eggs can be highly adaptive in some species, and thus under selective pressure. In this study, we examined the underlying interfamily variation in hatching timing and embryonic development in a population of an oviparous amphibian, the rough-skinned newt (Taricha granulosa). We found significant, high variability in degree of embryonic development and hatching timing among eggs from different females. Patterns of variation were present regardless of temperature.We also could not explain the differences among families by morphological traits of the females or their eggs. This study suggests that the variation necessary for natural …
Detailed Comparison Of The Pnicogen Bond With Chalcogen, Halogen And Hydrogen Bonds, Steve Scheiner
Detailed Comparison Of The Pnicogen Bond With Chalcogen, Halogen And Hydrogen Bonds, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The characteristics of the pnicogen bond are explored using a variety of quantum chemical techniques. In particular, this interaction is compared with its halogen and chalcogen bond cousins, as well as with the more common H-bond. In general, these bonds are all of comparable strength. More specifically, they are strengthened by the presence of an electronegative substituent on the electron-acceptor atom, and each gains strength as one moves down the appropriate column of the periodic table, for example, from N to P to As. These noncovalent bonds owe their stability to a mixture in nearly equal parts of electrostatic attraction …
A New Noncovalent Force: Comparison Of P∙∙∙N Interaction With Hydrogen And Halogen Bonds, Steve Scheiner
A New Noncovalent Force: Comparison Of P∙∙∙N Interaction With Hydrogen And Halogen Bonds, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
When PH(3) is paired with NH(3), the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom. Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ(∗) antibond of a P-H covalent bond. Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P-H σ(∗) orbital that is closest to the P. In …
Subcutaneous Administration Of Tc007 Reduces Disease Severity In An Animal Model Of Sma, Virginia B. Mattis, Marina Y. Fosso, Cheng-Wei Tom Chang, Christian L. Lorson
Subcutaneous Administration Of Tc007 Reduces Disease Severity In An Animal Model Of Sma, Virginia B. Mattis, Marina Y. Fosso, Cheng-Wei Tom Chang, Christian L. Lorson
Chemistry and Biochemistry Faculty Publications
Background Spinal Muscular Atrophy (SMA) is the leading genetic cause of infantile death. It is caused by the loss of functional Survival Motor Neuron 1 (SMN1). There is a nearly identical copy gene, SMN2, but it is unable to rescue from disease due to an alternative splicing event that excises a necessary exon (exon 7) from the majority of SMN2-derived transcripts. While SMNΔ7 protein has severely reduced functionality, the exon 7 sequences may not be specifically required for all activities. Therefore, aminoglycoside antibiotics previously shown to suppress stop codon recognition and promote translation read-through have been examined to increase the …
Liposomes Recruit Ipac To The Shigella Flexneri Type Iii Secretion Apparatus Needle As A Final Step In Secretion Induction, C. R. Epler, Nicholas E. Dickenson, A. J. Olive, W. L. Picking, W. D. Picking
Liposomes Recruit Ipac To The Shigella Flexneri Type Iii Secretion Apparatus Needle As A Final Step In Secretion Induction, C. R. Epler, Nicholas E. Dickenson, A. J. Olive, W. L. Picking, W. D. Picking
Chemistry and Biochemistry Faculty Publications
Shigella flexneri contact with enterocytes induces a burst of protein secretion via its type III secretion apparatus (TTSA) as an initial step in cellular invasion. We have previously reported that IpaD is positioned at the TTSA needle tip (M. Espina et al., Infect. Immuno. 74:4391-4400, 2006). From this position, IpaD senses small molecules in the environment to control the presentation of IpaB to the needle tip. This step occurs without type III secretion induction or IpaC recruitment to the S. flexneri surface. IpaC is then transported to the S. flexneri surface when target cell lipids are added, and this event …
Characterization Of Power Induced Heating And Damage In Fiber Optic Probes For Near-Field Scanning Optical Microscopy, Nicholas E. Dickenson, E. S. Erickson, O. L. Mooren, R. C. Dunn
Characterization Of Power Induced Heating And Damage In Fiber Optic Probes For Near-Field Scanning Optical Microscopy, Nicholas E. Dickenson, E. S. Erickson, O. L. Mooren, R. C. Dunn
Chemistry and Biochemistry Faculty Publications
Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to ~55–60°C as output powers reach ~50 nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of ~450 nW. The sample heating profiles measured for etched NSOM probes are consistent with …