bluuebunny/crossref_metadata_2025_split huggingface dataset:
One gene, two diseases and three conformations: Molecular dynamics simulations of mutants of human prion protein at room temperature and elevated temperatures
Authors: Shamsir Mohd S. , Dalby Andrew R. 
Published: February 2005

AbstractFatal familial insomnia (FFI) and Creutzfeldt‐Jakob disease (CJD) are associated to the same mutation at codon 178 but differentiate into clinicopathologically distinct diseases determined by this mutation and a naturally occurring methionine–valine polymorphism at codon 129 of the prion protein gene. It has been suggested that the clinical and pathological difference between FFI and CJD is caused by different conformations of the prion protein. Using molecular dynamics (MD), we investigated the effect of the mutation at codon 178 and the polymorphism at codon 129 on prion protein dynamics and conformation at normal and elevated temperatures. Four model structures were examined with a focus on their dynamics and conformational changes. The results showed differences in stability and dynamics between polymorphic variants. Methionine variants demonstrated a higher stability than valine variants. Elongation of existing β‐sheets and formation of new β‐sheets was found to occur more readily in valine polymorphic variants. We also discovered the inhibitory effect of proline residue on existing β‐sheet elongation. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Statistical criteria for the identification of protein active sites using theoretical microscopic titration curves
Authors: Ko Jaeju , Murga Leonel F. , André Pierrette , Yang Huyuan , Ondrechen Mary Jo , Williams Ronald J. , Agunwamba Akochi , Budil David E. 
Published: February 2005

AbstractTheoretical Microscopic Titration Curves (THEMATICS) may be used to identify chemically important residues in active sites of enzymes by characteristic deviations from the normal, sigmoidal Henderson–Hasselbalch titration behavior. Clusters of such deviant residues in physical proximity constitute reliable predictors of the location of the active site. Originally the residues with deviant predicted behavior were identified by human observation of the computed titration curves. However, it is preferable to select the unusual residues by mathematically well‐defined criteria, in order to reduce the chance of error, eliminate any possible biases, and substantially speed up the selection process. Here we present some simple statistical tests that constitute such selection criteria. The first derivatives of the predicted titration curves resemble distribution functions and are normalized. The moments of these first derivative functions are computed. It is shown that the third and fourth moments, measures of asymmetry and kurtosis, respectively, are good measures of the deviations from normal behavior. Results are presented for 44 different enzymes. Detailed results are given for 4 enzymes with 4 different types of chemistry: arginine kinase from Limulus polyphemus (horseshoe crab); β‐lactamase from Escherichia coli; glutamate racemase from Aquifex pyrophilus; and 3‐isopropylmalate dehydrogenase from Thiobacillus ferrooxidans. The relationship between the statistical measures of nonsigmoidal behavior in the predicted titration curves and the catalytic activity of the residue is discussed. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Molecular characterization and biological response to respiration inhibitors of Pyricularia isolates from ctenanthe and rice plants
Authors: Paplomatas Epaminondas J , Pappas Athanasios C , Syranidou Elene 
Published: February 2005

AbstractThe molecular profile and the biological response of isolates of Pyricularia oryzae Cavara obtained from ctenanthe to two strobilurins (azoxystrobin, kresoxim‐methyl) and the phenylpyridinamine fungicide fluazinam were characterized, and compared with isolates from rice plants. Five different isozymes (α‐esterase, lactate, malate, isocitrate and sorbitol dehydrogenases) and five random decamer primers for RAPD‐PCR were used to generate molecular markers. Using unweighted pair‐group with arithmetic average analysis, ctenanthe isolates were found to form a separate group distinct from that of the rice isolates for both sets of markers. Amplified polymorphic sequences of mitochondrial cytochrome b that were digested with Fnu4HI or StyI revealed no differences among Pyricularia isolates at amino acid positions 143 or 129 which confer resistance to strobilurins in several fungi. In absence of the alternative respiration inhibitor salicylhydroxamic acid (SHAM) the three fungicides showed inferior and variable efficacy, with a trend toward the rice isolate being less sensitive. The addition of SHAM enhanced the effectiveness of all fungicides against isolates regardless of their origin. Appressorium formation was the most vulnerable target of action of the respiration inhibitors and azoxystrobin the most effective. This is the first report of a comparison between the molecular profiles and sensitivities to respiration inhibitors for Pyricularia oryzae isolates from a non‐gramineous host and from rice. Copyright © 2005 Society of Chemical Industry
Influence of vapor transport equilibration on spectroscopic parameters of Er3+ in LiNbO3 crystals
Authors: Zhang De‐Long , Wang Dun‐Chun , Pun E. Y. B. 
Published: February 2005

AbstractA number of X‐, Y‐ and Z‐cut Er(/Yb):LiNbO3 crystals with six different doping levels of rare earth ions were annealed at 1110 °C for 120 h using the vapor transport equilibration (VTE) technique. At room temperature, α‐polarized or unpolarized absorption spectra of these VTE‐treated crystals and corresponding as‐grown crystals were recorded in the wavelength range 280–1700 nm. The absorption characteristics of the VTE‐treated crystals are summarized and compared with those of the as‐grown crystals. The (Li+ + RE3+)/Nb5+(RE3+ = Er3+ or Er3+ + Yb3+) ratios in the VTE‐treated Er(/Yb):LiNbO3 crystals were evaluated using the optical absorption edge or Raman linewidth of the 153 cm–1 E(TO) phonon. Based upon the measured spectral data, spectroscopic parameters of Er3+ ions in as‐grown and VTE‐treated crystals were calculated using the Judd–Ofelt (J–O) theory. The influences of Er3+ doping level, type of crystal cut and VTE treatment on the key spectroscopic parameters, including integrated absorption coefficient, oscillator strength, J–O parameters and radiative lifetimes of three dominant emission manifolds (4I13/2 (∼1530 nm), 4F9/2 (∼660 nm) and 4S3/2 (∼560 nm)), are discussed and summarized and compared with the results for as‐grown crystals. The results for as‐grown crystals are also compared with those reported previously. The present theoretical result concerning the VTE effect on the 1530 nm lifetime is in rough agreement with the experimental result reported previously. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
White light electroluminescence in zinc sulfide: polyflourene blends
Authors: Sundar Manoharan S. , Mohammad Qureshi 
Published: February 2005

AbstractWe document white light emission from ZnS:Cu–PFO blend in the device structure involving indium tin oxide (ITO)/poly(3,4‐ethylenedioxythiophene):poly(4‐styrenesulfonate) (PEDOT:PSS)/ZnS–poly(9,9‐dioctylfluorene) (PFO)/Al layers, with varying ZnS:Cu dopant concentrations in the PFO matrix. We observe that with the increase in the ZnS:Cu dopant concentration in PFO from 1 to 10 wt%, the turn‐on‐voltage shifts from 7 V to 4 V. Initial brightness of the device with 1 wt% doping is 30 cd/m2 at 7 V and 40 cd/m2 at 9 V. For a 10‐wt% ZnS:Cu–PFO blend, luminescence up to 25 cd/m2 at 4 V is achieved. The broad spectral feature in electroluminescence is attributed to the partial energy transfer from PFO to ZnS:Cu, due to π–π*, n–π*, and CT–(π–π*) transitions arising out of polyfluorene–polyfluorenone chromophores. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Appearance of copper d9 defect centres in wide‐gap CdSe nanoparticles: A high‐frequency EPR study
Authors: Poolton N. R. J. , Smith G. M. , Riedi P. C. , Allen J. W. , Firth A. V. , Cole‐Hamilton D. J. , McInnes E. J. L. 
Published: February 2005

AbstractWhen preparing CdSe nanoparticles in polybutadiene‐based polymer matrices, quantum confinement in the smaller particles leads to the usual increase in the band‐gap energy, with associated, well defined, band‐edge luminescence emission. However, for samples whose size is smaller than 3 nm, new broad luminescence features appear, with the simultaneous appearance of a new paramagnetic defect centre that has not previously been reported in the literature. This work concentrates on analyzing the electron paramagnetic resonance of the new defect, which is found to be located at a trigonally‐distorted tetrahedral site, with a spin S = 1/2 and g‐values g|| = 2.321 ± 0.006 and g⊥ = 2.053 ± 0.006. With the attribution of very poorly resolved hyperfine interaction to a nucleus of spin I = 3/2, the identity of the defect is ascribed to copper in its d9 state, which would be expected to act as a simple acceptor centre in CdSe. Conclusions are drawn to the effect that the defect normally resides within the valence band for bulk and large particles, only becoming apparent as a defect within the band‐gap as the energy increases above 2.6 eV in the smaller particles. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Many‐body interactions of carbon monoxide cyclic oligomers: A computational study
Authors: Sahu Prabhat K. , Lee Shyi‐Long 
Published: February 2005

AbstractStructural properties and energetics for the optimized carbon monoxide cyclic oligomers are analyzed at the correlated ab initio second‐order Møller–Plesset (MP2) and density functional methods (B3LYP and mPW1PW), using Dunning's cc‐pVXZ (X = D, T, Q) basis set, augmented with diffuse functions. Many‐body interactions of the stable carbon monoxide cyclic oligomers, (CO)4 and (CO)5 are computed at the MP2/aug‐cc‐pVTZ level. Contributions of two‐ to five‐body terms to each of these oligomers for their interaction energies, including corrections for basis set superposition error (BSSE) are investigated by using function counterpoise and its generalized version. It has been found that three‐body terms are attractive in nature and essential in order to describe the cooperative effects in the stable cyclic CO oligomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Theoretical principles of single‐molecule electronics: A chemical and mesoscopic view
Authors: Xue Yongqiang , Ratner Mark A. 
Published: February 2005

AbstractExploring the use of individual molecules as active components in electronic devices has been at the forefront of nanoelectronics research in recent years. Compared to semiconductor microelectronics, modeling transport in single‐molecule devices is much more difficult due to the necessity of including the effects of the device electronic structure and the interface to the external contacts at the microscopic level. Theoretical formulation of the problem therefore requires integrating the knowledge base in surface science, electronic structure theory, quantum transport, and device modeling into a single unified framework starting from the first principles. In this article, we introduce the theoretical framework for modeling single‐molecule electronics and present a simple conceptual picture for interpreting the results of numerical computation. We model the device using a self‐consistent matrix Green's function method that combines nonequilibrium Green's function theory of quantum transport with atomic‐scale description of the device's electronic structure. We view the single‐molecule device as “heterostructures” composed of chemically well‐defined atomic groups, and analyze the device characteristics in terms of the charge and potential response of these atomic groups to perturbation induced by the metal–molecule coupling and the applied bias voltage. We demonstrate the power of this approach using as examples devices formed by attaching benzene‐based molecules of different size and internal structure to the gold electrodes through sulfur end atoms. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Full quantum mechanical study of binding of HIV‐1 protease drugs
Authors: Zhang Da W. , Zhang John Z. H. 
Published: February 2005

AbstractFully quantum mechanical studies of detailed binding interactions between HIV‐1 protease and six FDA (Food and Drug Administration)‐approved drugs (saquinavir, indinavir, ritonavir, nelfinavir, amprenavir, and lopinavir) are carried out using a recently developed MFCC (molecular fractionation with conjugate caps) method. The MFCC calculation produces a quantum mechanical interaction spectrum for any protease drug binding complex. Detailed quantitative analysis on binding of lopinavir to specific residues of the protease is given from the current study. The present calculation shows that the dominant binding of lopinavir to the protease is through the formation of a strong hydrogen bond between the central hydroxyl group of the drug to the aspartate oxygen of Asp25 in one of the two chains of the protease (A chain). This is closely followed by hydrogen binding of the drug to Asp29 in the B chain and somewhat weak hydrogen bonding to Asp30, Gly27, Gly48, and Ile50 in both chains. By partitioning all six drugs into four building blocks besides the central component containing the hydroxyl group, MFCC calculation finds that block III has essentially no binding interaction with the protease and the major binding interactions of these drugs are from blocks II and IV, in addition to the dominant central hydroxyl group. This detailed quantitative information on drug binding to the protease is very useful in rational design of new and improved inhibitors of HIV‐1 protease and its mutants. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
First‐principles investigation of structure and stability of AlnNm clusters
Authors: Guo Ling , Wu Hai‐Shun , Jin Zhi‐Hao 
Published: February 2005

AbstractVarious structural possibilities for AlnN and AlnN2 (n = 1–7) neutral and cationic isomers are investigated, using the density functional method of Becke's three‐parameter hybrid exchange functional with the Lee–Yang–Parr nonlocal correlation. Structural optimization and frequency analyses are performed with the basis of 6‐311+G(d) for both the neutrals and cations. The calculations predicted the existence of a number of previously unknown isomers (i.e., Al5N2 and Al6N2). The resulting geometries show that the nitrogen atom prefers to be trapped and not to be on the periphery. Frequency analyses indicate that the 3‐D Al5N, which was previous proposed as the ground‐state structure, is in fact a first‐order stationary point with an imaginary frequency at 45i (a2). The optimized ground‐state structure of Al5N obtained in this work is a planar configuration with the symmetry of C2v. The calculated adiabatic ionization potentials in their ground states showed that AlN, Al2N, Al3N, and Al4N2 clusters are more stable than any others in AlnN and AlnN2 (n = 1–7) species, being consistent with the observed time‐of‐flight (TOF) signal intensities. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Photodetachment dynamics from closed‐shell anions in the presence of a bichromatic field
Authors: Mondal Chandan Kumar 
Published: February 2005

AbstractI have studied the dynamics of photodetachment from closed‐shell anions in the presence of a two‐color (bichromatic) laser field. The electronic states of halide ions are modeled by a 1‐D Hamiltonian with a potential V(x) = −V0e. The two parameters V0 and σ are fixed by requiring V(x) to reproduce the experimentally observed ground‐state ionization energy of the halide ions concerned. The potentials so generated are shown to support only one bound state in each case. The time‐dependent Fourier grid Hamiltonian method is used to follow the detachment dynamics with fairly high intensities of light. The environmental effects on the dynamics are sought to be modeled by allowing the well depth (V0) to fluctuate randomly (V0(t) = V0[1 + ΔVR(t)]; R(t) randomly fluctuates between +1 and −1 with time, when ΔV is fixed). The average detachment rate constants kav are seen to increase with increase in the intensities of used bichromatic field. An alternative model potential, V(x) = −V0e−σx, is also shown to yield similar results. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Review of multistep methods for the numerical solution of the radial Schrödinger equation
Authors: Vigo‐Aguiar Jesús , Simos T. E. 
Published: February 2005

AbstractA review of multistep methods for the numerical solution of the Schrödinger equation is presented. Since the literature reports difficulties in the production of some of the Bettis–Cowell methods, we have included a simple way that permits production of these methods for any algebraic and trigonometric order. Numerical comparisons on resonance problems and bound‐states problems are also described. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
DFT investigation of sites of protonation of antitumor of 2‐(4‐aminophenyl)benzazoles in the gas phase and in solution
Authors: Hilal Rifaat , Elroby Shabaan A. K. 
Published: February 2005

AbstractThe proton affinity on each of the possible sites in the antitumor 2‐(4‐aminophenyl)benzazoles has been calculated at the B3LYP/6‐311G** level of theory in the gas phase and in solution. The N3‐site of protonation is found to be strongly favored over the NH2‐site for the studied compounds both in gas phase and in solution. The stability of N3‐protonated species is explained by the resonance interaction of the NH2‐group with the heterocyclic ring. The potential energy surface (PES) for the protonation process was studied at the density functional theory (DFT)/B3LYP/6‐311++G** level of theory. Solvent effects on the PES were also examined using two models: Onsager self‐consistent field and polarizable continuum model (PCM). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Atomic softness‐based QSAR study of testosterone
Authors: Srivastava H. K. , Pasha F. A. , Singh P. P. 
Published: February 2005

AbstractIonization potential of an atom in a molecule, electron affinity of an atom in a molecule, and quantum chemical descriptor atomic softness values En‡‐based quantitative structure–activity relationship (QSAR) study of testosterone derivatives have been done with the help of PM3 calculations on WinMOPAC 7.21 software. The 3D modeling and geometry optimization of all the compounds have been done with the help of PCMODEL software. The biological activities of testosterone derivatives have been taken from literature. The predicted values of biological activity with the help of multiple linear regression (MLR) analysis is very close to observed biological activity. The cross‐validation coefficient and correlation coefficient also indicate that the QSAR model is valuable. Regression analysis shows a very good relationship with biological activity and En‡ values. With the help of these values, prediction of the biological activity of any unknown compound is possible. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Long‐range π‐type hydrogen bond in the dimers CH2OHF, CH2OH2O, and CH2ONH3
Authors: Li Ruiyan , Li Zhiru , Wu Di , Hao Xiyun , Li Rujiao , Sun Chiachung 
Published: February 2005

AbstractUsing four basis sets, 6‐311G(d,p), 6‐31+G(d,p), 6‐311++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for dimers CH2OHF, CH2OH2O, CH2ONH3, and CH2OCH4. The structures of CH2OHF, CH2OH2O, and CH2ONH3 are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…HY (YF, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the acidic H atoms of CH2O and lone pair(s) on the F atom in HF, the O atom in H2O, or the N atom in NH3. By contrast with above the three dimers, for CH2OCH4, because there is not a π‐type hydrogen‐bond to bend its linear hydrogen bond, the structure of CH2OCH4 is a noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD(T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Accurate energy eigenvalues and eigenfunctions for the two‐dimensional confined hydrogen atom
Authors: Aquino N. , Campoy G. , Flores‐Riveros A. 
Published: February 2005

AbstractA study of the two‐dimensional hydrogen atom confined within a circle of impenetrable walls is presented. The potential inside the box is Coulomb type, whereas outside it is infinite. The energy eigenvalues and some radial wave function properties are computed with high accuracy for different box sizes. We derive the polarizability in the Kirkwood approximation, calculate the Fermi contact term as a function of the confinement radius, and investigate the filling order of the one‐electron states. When the electronic configuration of many electrons is constructed by means of the Aufbau principle, the model predicts the inversion 2s–3d levels in the N atom. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Localized hybrid exchange‐correlation potentials for Kohn–Sham DFT calculations of NMR and EPR parameters
Authors: Arbuznikov Alexei V. , Kaupp Martin 
Published: February 2005

AbstractIn contrast to the conventional, nonlocal, and nonmultiplicative implementation of hybrid exchange‐correlation functionals in self‐consistent calculations, the exact‐exchange contribution to the functional has been implemented as a proper local and multiplicative Kohn–Sham potential, using the localized Hartree–Fock approximation to the optimized effective potential. The resulting localized hybrid potentials provide improved performance over nonlocal implementations in density functional theory (DFT) calculations of nuclear shielding constants of main‐group molecules and electronic g‐tensors of 3d transition–metal complexes. Optimum performance of the localized potentials is found at very similar amounts of exact‐exchange admixture for both properties and is almost independent of the “pure‐DFT” exchange and correlation functionals combined with exact exchange. Based on local kinetic energy density, a measure of exact‐exchange admixture is constructed that helps rationalize the relatively large optimal exact‐exchange contributions found. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Valence and valence–core interactions in transition‐metal diatomic molecules
Authors: Boudreaux Edward A. , Baxter Eric 
Published: February 2005

AbstractIn this study, the correlation between open‐shell valence and closed‐shell valence‐core electrons is shown to be significant, with regard to an adequate description of the bonding in transition metal diatomic molecules. The SCMEH‐MO (self‐consistent modified extended Huckel molecular orbital) method is well suited for partitioning these two influences, in terms of their independent and collective effects on the electrons within the occupied mo‐s. Two test cases, Cr2 and Mo2 are presented to demonstrate the nature and magnitude of these valence/valence‐core interactions. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005