bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of Kekulé valence structures and the corresponding valence bond wave function
Authors: Rashid Zahid , van Lenthe Joop H. 
Published: October 2010

AbstractA new scheme, called “list of nonredundant bonds”, is presented to record the number of bonds and their positions for the atoms involved in Kekulé valence structures of (poly)cyclic conjugated systems. Based on this scheme, a recursive algorithm for generating Kekulé valence structures has been developed and implemented. The method is general and applicable for all kinds of (poly)cyclic conjugated systems including fullerenes. The application of the algorithm in generating Valence Bond (VB) wave functions, in terms of Kekulé valence structures, is discussed and illustrated in actual VB calculations. Two types of VBSCF calculations, one involving Kekulé valence structures only and the second one involving all covalent VB structures, were performed for benzene, pentalene, benzocyclobutadiene, and naphthalene. Both strictly local and delocalised p‐orbitals were used in these calculations. Our results show that, when the orbitals are restricted to their own atoms, other VB structures (Dewar structures) also have a significant contribution in the VB wave function. When removing this restriction, the other VB structures (Dewar and also the ionic structures) are accommodated in the Kekulé valence structures, automatically. Therefore, at VBSCF delocal level, the ground states of these systems can be described almost quantitatively by considering Kekulé valence structures only at a considerable saving of time. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.
Using correlated parameters for improved ranking of protein–protein docking decoys
Authors: Mitra Pralay , Pal Debnath 
Published: October 2010

AbstractA successful protein–protein docking study culminates in identification of decoys at top ranks with near‐native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near‐native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein–protein interface. In this work, we describe a novel method combining an interface‐size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein–protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having ≤10 Å backbone root mean square deviation from true binding geometry. Comparisons with other state‐of‐art methods confirm the improved ranking power of our method without the use of any experiment‐guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less‐difficult bound binary protein–protein complexes with ≤35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with ≤5Å backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Intermolecular potential energy surface for CS2 dimer
Authors: Farrokhpour Hossein , Mombeini Zainab , Namazian Mansoor , Coote Michelle L. 
Published: October 2010

AbstractA new four‐dimensional intermolecular potential energy surface for CS2 dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center‐of‐mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller–Plesset second‐order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug‐cc‐pVxZ, x = D, T) and corrected for the basis‐set superposition error using the full counterpoise correction method. A two‐point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole–dipole dispersion coefficient (C6) of CS2 fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well‐known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol−1 at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water
Authors: Lin Bin , Pettitt B. Montgomery 
Published: October 2010

AbstractElectrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson‐Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLS‐AA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirms that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Looking for high energy density compounds applicable for propellant among the derivatives of dpo with n3, ono2, and nno2 groups
Authors: Wang Gui‐Xiang , Gong Xue‐Dong , Liu Yan , Du Hong‐Chen , Xu Xiao‐Juan , Xiao He‐Ming 
Published: October 2010

AbstractThe derivatives of DPO (2,5‐dipicryl‐1,3,4‐oxadiazole) are optimized to obtain their molecular geometries and electronic structures at the DFT‐B3LYP/6‐31G* level. The bond length is focused to primarily predict thermal stability and the pyrolysis mechanism of the title compounds. Detonation properties are evaluated using the modified Kamlet‐Jacobs equations based on the calculated densities and heats of formation. It is found that there are good linear relationships between density, detonation velocity, detonation pressure, and the number of azido, nitrate, and nitramine groups. According to the largest exothermic principle, the relative specific impulse is investigated by calculating the enthalpy of combustion (ΔHcomb) and the total heat capacity (Cp,gases). It is found that the introduction of N3, ONO2, and NNO2 groups could increase the specific impulses and II‐4, II‐5, and III‐5 are potential candidates for High Energy Density Materials (HEDMs). The effect of the azido, nitrate, and nitramine groups on the structure and the properties is discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Numerical modelling of bit–rock fracture mechanisms in percussive drilling with a continuum approach
Authors: Saksala Timo 
Published: October 2010

SUMMARYThis paper presents a numerical method for continuum modelling of the dynamic bit–rock interaction process in percussive drilling. The method includes a constitutive model based on a combination of the recent viscoplastic consistency model, the isotropic damage concept and a parabolic compression cap. The interaction between the drill bit and rock is modelled using contact mechanics by treating the bit as a rigid body. As the bit–rock interaction in percussive drilling is a transient event, the method is implemented in explicit dynamics FEM. The rock strength heterogeneity is characterized at the mesoscopic level statistically using the Weibull distribution. The bit–rock interaction is simulated under axisymmetric conditions using cylindrical and hemispherical buttons. The choice of the quite complex constitutive model accounting, e.g. for plastic compaction, viscoplastic shear and tensile failure along with induced damage and rate dependency is justified by numerical simulations. Moreover, the quasi‐static and dynamic cases are compared in plane strain simulations. Finally, some results clarifying the discrepancy of opinions found in the literature concerning the side (lateral) crack formation are obtained. Copyright © 2010 John Wiley & Sons, Ltd.
Diffuse failure in geomaterials: Experiments, theory and modelling
Authors: Daouadji A. , Darve F. , Al Gali H. , Hicher P. Y. , Laouafa F. , Lignon S. , Nicot F. , Nova R. , Pinheiro M. , Prunier F. , Sibille L. , Wan R. 
Published: October 2010

AbstractThis paper presents a synthesis of the works performed by various teams from France, Italy and Canada around the question of second‐order work criterion. Because of the non‐associative character of geomaterials plastic strains, it is now recognized that a whole bifurcation domain exists in the stress space with various possible modes of failure. In a first part these failure modes are observed in lab experimental tests and in discrete element modelling. Then a theoretical study of second‐order work allows to establish a link with the kinetic energy, giving a basis to explain the transition from a prefailure (quasi)static regime to a postfailure dynamic regime. Eventually the main features of geomaterials failure are obtained by applying second‐order work criterion to five different constitutive rate‐independent models—three being phenomenological and two micromechanical. As a whole this paper tries to gather together all the elements for a proper understanding and use of second‐order work criterion in geomechanics. Copyright © 2010 John Wiley & Sons, Ltd.
Warpage and countermeasure for injection‐molded in‐mold labeling parts
Authors: Larpsuriyakul Patcharee , Fritz Hans‐Gerhard 
Published: October 2010

AbstractDecades ago, the production of packaging with the injection in‐mold labeling (IML) has been established. With this manufacturing technique, label and packaging, both are of the same polymeric material, become inseparably connected during the injection molding process. Because thermal conductivity of the polymeric label material is clearly smaller than that of the metal mold wall, thermal‐induced warpage of injected IML parts or part surface deformation could occur. In this study, structure and warpage behavior of IML parts, which are different from those of conventional molded parts without labels were intensively investigated. It was found that it is the volume contraction difference between label and substrate that forces IML parts to warp to the opposite side of the label. In addition, IML part warpage problem can be coped by varying the mold temperature on the stationary and moving mold platen. By increasing the mold temperature on the label side, the degree of IML part warpage can be reduced with acceptable reduction in mechanical properties. The optimum mold temperature range for particular substrate material, however, was found to be more decisive in maintaining the modulus of elasticity of IML parts than the magnitude of mold temperature difference. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
Telechelic polynorbornenes with hydrogen bonding moieties by direct end capping of living chains
Authors: Kurzhals Steffen , Binder Wolfgang H. 
Published: October 2010

AbstractWe present two novel symmetric olefins bearing hydrogen bonding moieties for the direct capping of living ring opening metathesis polymerization‐chains using Grubbs catalyst 1st‐ and 3rd‐generation. The symmetric olefins are generated via homo metathesis of the corresponding α‐olefins under aid of microwave irradiation and are used to prepare polynorbornene‐chains (Mn = 4,000–10,000 g/mol, Mw/Mn = 1.1–1.4) bearing barbiturate and thymine‐moieties. A qualitative and quantitative analysis of the generated polymers is done via MALDI‐TOF MS proving the introduction of hydrogen‐bonding moieties into the polymer chain and revealing the strong dependence of the desorption on the chemical structure of the different polymer species and high efficiencies for the end group introduction (90–99%). The efficiency of this process depends strongly on the reaction time and the equivalents of terminating agent with respect to the living end. The best results for the end group introduction are achieved by reacting the living chains with an excess of the terminating agent (5–20 equiv) for 100 h. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI‐CPTC initiative perspective
Authors: Rodriguez Henry , Rivers Robert , Kinsinger Christopher , Mesri Mehdi , Hiltke Tara , Rahbar Amir , Boja Emily 
Published: October 2010

AbstractProteomics holds great promise in personalized medicine for cancer in the post‐genomic era. In the past decade, clinical proteomics has significantly evolved in terms of technology development, optimization and standardization, as well as in advanced bioinformatics data integration and analysis. Great strides have been made for characterizing a large number of proteins qualitatively and quantitatively in a proteome, including the use of sample fractionation, protein microarrays and MS. It is believed that differential proteomic analysis of high‐quality clinical biospecimen (tissue and biofluids) can potentially reveal protein/peptide biomarkers responsible for cancer by means of their altered levels of expression and/or PTMs. Multiple reaction monitoring, a multiplexed platform using stable isotope dilution‐MS with sensitivity and reproducibility approaching that of traditional ELISAs commonly used in the clinical setting, has emerged as a potentially promising technique for next‐generation high‐throughput protein biomarker measurements for diagnostics and therapeutics.
Methionyl‐tRNA synthetase from Caenorhabditis elegans: A specific multidomain organization for convergent functional evolution
Authors: Havrylenko Svitlana , Legouis Renaud , Negrutskii Boris , Mirande Marc 
Published: October 2010

AbstractMethionyl‐tRNA synthetase (MetRS) is a multidomain protein that specifically binds tRNAMet and catalyzes the synthesis of methionyl‐tRNAMet. The minimal, core enzyme found in Aquifex aeolicus is made of a catalytic domain, which catalyzes the aminoacylation reaction, and an anticodon‐binding domain, which promotes tRNA–protein association. In eukaryotes, additional domains are appended in cis or in trans to the core enzyme and increase the stability of the tRNA–protein complexes. Eventually, as observed for MetRS from Homo sapiens, the C‐terminal appended domain causes a slow release of aminoacyl‐tRNA and establishes a limiting step in the global aminoacylation reaction. Here, we report that MetRS from the nematode Caenorhabditis elegans displays a new type of structural organization. Its very C‐terminal appended domain is related to the oligonucleotide binding‐fold‐based tRNA‐binding domain (tRBD) recovered at the C‐terminus of MetRS from plant, but, in the nematode enzyme, this domain is separated from the core enzyme by an insertion domain. Gel retardation and tRNA aminoacylation experiments show that MetRS from nematode is functionally related to human MetRS despite the fact that their appended tRBDs have distinct structural folds, and are not orthologs. Thus, functional convergence of human and nematode MetRS is the result of parallel and convergent evolution that might have been triggered by the selective pressure to invent processivity of tRNA handling in translation in higher eukaryotes.
Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein
Authors: Sippel Katherine H. , Venkatakrishnan Balasubramanian , Boehlein Susan K. , Sankaran Banumathi , Quirit Jeanne G. , Govindasamy Lakshamanan , Agbandje‐McKenna Mavis , Goodison Steve , Rosser Charles J. , McKenna Robert 
Published: October 2010

AbstractMycoplasma genitalium is one of the smallest organisms capable of self‐replication and its sequence is considered a starting point for understanding the minimal genome required for life. MG289, a putative phosphonate substrate binding protein, is considered to be one of these essential genes. The crystal structure of MG289 has been solved at 1.95 Å resolution. The structurally identified thiamine binding region reveals possible mechanisms for ligand promiscuity. MG289 was determined to be an extracytoplasmic thiamine binding lipoprotein. Computational analysis, size exclusion chromatography, and small angle X‐ray scattering indicates that MG289 homodimerizes in a concentration‐dependant manner. Comparisons to the thiamine pyrophosphate binding homolog Cypl reveal insights into the metabolic differences between mycoplasmal species including identifying possible kinases for cofactor phosphorylation and describing the mechanism of thiamine transport into the cell. These results provide a baseline to build our understanding of the minimal metabolic requirements of a living organism. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Distinct second extracellular loop structures of the brain cannabinoid CB1 receptor: Implication in ligand binding and receptor function
Authors: Shim Joong‐Youn , Rudd James , Ding Tomas T. 
Published: October 2010

AbstractThe G‐protein‐coupled receptor (GPCR) second extracellular loop (E2) is known to play an important role in receptor structure and function. The brain cannabinoid (CB1) receptor is unique in that it lacks the interloop E2 disulfide linkage to the transmembrane (TM) helical bundle, a characteristic of many GPCRs. Recent mutation studies of the CB1 receptor, however, suggest the presence of an alternative intraloop disulfide bond between two E2 Cys residues. Considering the oxidation state of these Cys residues, we determine the molecular structures of the 17‐residue E2 in the dithiol form (E2dithiol) and in the disulfide form (E2disulfide) of the CB1 receptor in a fully hydrated 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine bilayer, using a combination of simulated annealing and molecular dynamics simulation approaches. We characterize the CB1 receptor models with these two E2 forms, CB1(E2dithiol) and CB1(E2disulfide), by analyzing interaction energy, contact number, core crevice, and cross correlation. The results show that the distinct E2 structures interact differently with the TM helical bundle and uniquely modify the TM helical topology, suggesting that E2 of the CB1 receptor plays a critical role in stabilizing receptor structure, regulating ligand binding, and ultimately modulating receptor activation. Further studies on the role of E2 of the CB1 receptor are warranted, particularly comparisons of the ligand‐bound form with the present ligand‐free form. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Structural and functional analysis of substrate recognition by the 250s loop in amylomaltase from Thermus brockianus
Authors: Jung Jong‐Hyun , Jung Tae‐Yang , Seo Dong‐Ho , Yoon Sei‐Mee , Choi Hyun‐Chang , Park Byoung Chul , Park Cheon‐Seok , Woo Eui‐Jeon 
Published: October 2010

AbstractAmylomaltase, or 4‐α‐glucanotransferase (EC 2.4.1.25), is involved in glycogen and maltooligosaccharide metabolism in microorganisms, catalyzing both the hydrolysis and transfer of an α‐1,4‐oligosacchraride to other sugar molecules. In this study, we determined the crystal structure of amylomaltase from Thermus brockianus at a resolution of 2.3 Å and conducted a biochemical study to understand the detailed mechanism for its activity. Careful comparison with previous amylomaltase structures showed a pattern of conformational flexibility in the 250s loop with higher B‐factor. Amylomaltase from T. brockianus exhibited a high transglycosylation factor for glucose and a lower value for maltose. Mutation of Gln256 resulted in increased Km for maltotriose and a sharp decrease of the transglycosylation factor for maltose, suggesting the involvement of Gln 256 in substrate binding between subsites +1 and +2. Mutation of Phe251 resulted in significantly lower glucose production but increased maltose production from maltopentose substrates, showing an altered substrate‐binding affinity. The mutational data suggest the conformational flexibility of the loop may be involved in substrate binding in the GH77 family. Here, we present an action model of the 250s loop providing the molecular basis for the involvement of residues Phe251, Gln256, and Trp258 in the hydrolysis and transglycosylation activities in amylomaltase. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall
Authors: Yang Yinshan , Auguin Daniel , Delbecq Stéphane , Dumas Emilie , Molle Gérard , Molle Virginie , Roumestand Christian , Saint Nathalie 
Published: October 2010

AbstractThe pore‐forming outer membrane protein OmpATb from Mycobacterium tuberculosis is a virulence factor required for acid resistance in host phagosomes. In this study, we determined the 3D structure of OmpATb by NMR in solution. We found that OmpATb is composed of two independent domains separated by a proline‐rich hinge region. As expected, the high‐resolution structure of the C‐terminal domain (OmpATb198–326) revealed a module structurally related to other OmpA‐like proteins from Gram‐negative bacteria. The N‐terminal domain of OmpATb (73–204), which is sufficient to form channels in planar lipid bilayers, exhibits a fold, which belongs to the α+β sandwich class fold. Its peculiarity is to be composed of two overlapping subdomains linked via a BON (Bacterial OsmY and Nodulation) domain initially identified in bacterial proteins predicted to interact with phospholipids. Although OmpATb73–204 is highly water soluble, current–voltage measurements demonstrate that it is able to form conducting pores in model membranes. A HADDOCK modeling of the NMR data gathered on the major monomeric form and on the minor oligomeric populations of OmpATb73–204 suggest that OmpATb73–204 can form oligomeric rings able to insert into phospholipid membrane, similar to related proteins from the Type III secretion systems, which form multisubunits membrane‐associated rings at the basal body of the secretion machinery. Proteins 2011. © 2010 Wiley‐Liss, Inc.