bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solution structure and backbone dynamics of an antigen‐free heavy chain variable domain (VHH) from Llama
Authors: Renisio Jean‐Guillaume , Pérez Janice , Czisch Michael , Guenneugues Marc , Bornet Olivier , Frenken Leon , Cambillau Christian , Darbon Hervé 
Published: October 2004

AbstractCamelids, (dromedaries, camels, and llamas) produce heavy‐chains antibodies, with their antigen recognition sites composed of a single VH‐like domain, referred to as VHH. The solution structure of one of these VHHs domains (VHH‐H14), raised against the α subunit of the human chorionic gonadotropin hormone (hCG), has been determined by 15N heteronuclear three‐dimensional NMR spectroscopy. The framework is well resolved within the set of 20 best‐calculated NMR structures and is close to that of classical VH domains from vertebrate antibodies, consisting of two antiparallel β‐sheets organized in a β‐barrel. Loops display a lower precision, especially the Complementarity Determining Regions (CDRs), involved in antigen recognition. Comparison of the three‐dimensional VHH‐H14 solution structure with its previously solved crystal structure (Spinelli et al., Nature Struct. Biol. 1996;3:752–757) reveals a high similarity to the framework, whereas significant conformational differences occur on CDRs, leading to the assumption that the antigen recognition site is a more mobile part. In order to deepen our insights into the dynamics of VHH‐H14 in solution, 15N relaxation was measured with longitudinal R1 and transverse R2 self‐relaxation rates, and 15N steady‐state heteronuclear nuclear Overhauser enhancements (NOE), making it possible to probe picosecond‐to‐millisecond internal motions. Determination of dynamic parameters (S2, τe, and Rex) through the Lipari‐Szabo Model‐free approach enables the identification of several regions with enhanced dynamics. Especially, the mobility measurements from NMR confirm that the antigen recognition site is the most mobile part of the VHH‐H14 domain on picosecond‐to‐nanosecond fast time scales. Several residues belonging to the three CDRs are submitted to chemical exchange processes occurring on slow microsecond‐to‐millisecond time scales, suggesting that the formation of the VHH/antigen complex should be accompanied by structural changes. Proteins 2002;47:546–555. © 2002 Wiley‐Liss, Inc.
Principles of docking: An overview of search algorithms and a guide to scoring functions
Authors: Halperin Inbal , Ma Buyong , Wolfson Haim , Nussinov Ruth 
Published: October 2004

AbstractThe docking field has come of age. The time is ripe to present the principles of docking, reviewing the current state of the field. Two reasons are largely responsible for the maturity of the computational docking area. First, the early optimism that the very presence of the “correct” native conformation within the list of predicted docked conformations signals a near solution to the docking problem, has been replaced by the stark realization of the extreme difficulty of the next scoring/ranking step. Second, in the last couple of years more realistic approaches to handling molecular flexibility in docking schemes have emerged. As in folding, these derive from concepts abstracted from statistical mechanics, namely, populations. Docking and folding are interrelated. From the purely physical standpoint, binding and folding are analogous processes, with similar underlying principles. Computationally, the tools developed for docking will be tremendously useful for folding. For large, multidomain proteins, domain docking is probably the only rational way, mimicking the hierarchical nature of protein folding. The complexity of the problem is huge. Here we divide the computational docking problem into its two separate components. As in folding, solving the docking problem involves efficient search (and matching) algorithms, which cover the relevant conformational space, and selective scoring functions, which are both efficient and effectively discriminate between native and non‐native solutions. It is universally recognized that docking of drugs is immensely important. However, protein–protein docking is equally so, relating to recognition, cellular pathways, and macromolecular assemblies. Proteins function when they are bound to other molecules. Consequently, we present the review from both the computational and the biological points of view. Although large, it covers only partially the extensive body of literature, relating to small (drug) and to large protein–protein molecule docking, to rigid and to flexible. Unfortunately, when reviewing these, a major difficulty in assessing the results is the non‐uniformity in the formats in which they are presented in the literature. Consequently, we further propose a way to rectify it here. Proteins 2002;47:409–443. © 2002 Wiley‐Liss, Inc.
Calculated geometries of dications of bis odd‐membered π‐ring systems containing a NCN fragment and related π‐systems. An opposite out‐of‐plane rotation of the 4nπ‐ring subsystems
Authors: Buck Henk 
Published: October 2004

AbstractQuantum chemical calculations have been carried out on dications of bis odd‐membered π‐ring systems containing a NCN fragment and related π‐systems. An opposite out‐of‐plane rotation of both subsystems was found if these systems contain 4nπ‐electrons (antiaromatic). A planar situation was found for 4n+2 π‐electrons (aromatic). The geometric representations could be compared with X‐ray crystallographic three‐dimensional structures of related compounds. Calculations at different levels clearly show that separation of the σ‐ and π‐electron contribution is an effective way to elucidate the origin of the geometrical changes. We also give attention to some fundamental aspects of the subsystems related to the 1,3‐azolium cations because of their biochemical relevance such as fast C2H proton exchange. We postulate that at least two molecules of water are involved in this process. The significance of a trigonal pyramidal (TP) geometry has been emphasized. © 2001 Wiley Periodicals, Inc. Int J Quantum Chem, 2001
Computing the Kekulé structure count for alternant hydrocarbons
Authors: Torrens F. 
Published: October 2004

AbstractA fast computer algorithm brings computation of the permanents of sparse matrices, specifically, molecular adjacency matrices. Examples and results are presented, along with a discussion of the relationship of the permanent to the Kekulé structure count. A simple method is presented for determining the Kekulé structure count of alternant hydrocarbons. For these hydrocarbons, the square of the Kekulé structure count is equal to the permanent of the adjacency matrix. In addition, for alternant structures the adjacency matrix for N atoms can be written in such a way that only an N/2 × N/2 matrix need be evaluated. The Kekulé structure count correlates with topological indices. The inclusion of the number of cycles improves the fit. When comparing with previous results, the variance decreases 74%. The calculated standard heat of formation correlates with the logarithm of the Kekulé structure count. This heat increments 349 kJ/mol each time the Kekulé structure count increases by one order of magnitude. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Potential energy surfaces of fluorobenzene radical anions
Authors: Beregovaya Irina V. , Shchegoleva Lyudmila N. 
Published: October 2004

AbstractAb initio ROHF/6‐31+G* and MP2/6‐31+G*//ROHF/6‐31+G* calculations were used to consider fluorination's effect on potential energy surfaces (PESs) of benzene radical anion's (RAs). The Hartree–Fock PESs of symmetrically fluorinated radical anions were found to be pseudorotation surfaces. Unlike the benzene anion PES, pseudorotation surfaces include nonplanar structures. A Möbius band may represent the pseudorotation scheme of C6H stationary structures. Cutting the band out, we may obtain a pseudorotation scheme peculiar to C6F. This way of PES scheme building is also applicable to partially fluorinated RAs. A complicated structure of fluorinated anions' PES results from the avoided crossing of π states closed in energy together with the presence of a low‐lying vibronically active excited σ state. The number of stationary structures involved in pseudorotation varies in the series of anions, and may be changed at a higher level of calculations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
A graphical scheme for representing many‐electron spin‐free configurations
Authors: Sarma C. R. , Shankar N. Ravi , Rettrup S. 
Published: October 2004

AbstractThe present approach is a graphical technique for representing and generating primitive configurations of space orbitals for electronic systems. The graph is developed as a tree whose paths define the allowed space configurations of electrons admitting at most double occupancy for each orbital. The emphasis in the graph is on the nodes representing occupied orbitals rather than on the arcs compared with previous graphical procedures used in graphical unitary and symmetric group approaches. This leads to a compact representation of the orbital configurations and provides a computationally very efficient indexing scheme. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Ab initio through‐space/bond interaction analysis of the long C–C bonds in Bi(anthracene‐9,10‐dimethylene) photoisomers
Authors: Orimoto Yuuichi , Aoki Yuriko 
Published: October 2004

AbstractThe bi(anthracene‐9,10‐dimethylene) photoisomer has remarkably long C–C single bonds. To examine the lengthening of the C–C bond, we propose a novel procedure for quantitatively analyzing orbital interactions in a molecule at the level of the ab initio molecular orbital method. In this procedure, we can cut off the specific through‐space/bond interactions in a molecule by artificially increasing the absolute magnitude of the exponents in a Gaussian function. Then, the spatial orbital interactions were perfectly cut off, and, each term that makes up the total energy, that is, the nuclear–electron attractions, the electron–electron repulsions, and the nuclear–nuclear repulsions cancel each other. Several model molecules of the photoisomer were analyzed by this procedure. It was found that the orbital interaction between the p orbital on the benzene ring and the σ* orbital on the C–C bond in question, σ→σ* electron transfer through π orbital, weakens the C–C bond efficiently when these orbitals were located in the “periplanar” conformation. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Simultaneous determination of nuclear and electronic wave functions without Born–Oppenheimer approximation: Ab initio NO+MO/HF theory
Authors: Nakai Hiromi 
Published: October 2004

AbstractWe develop a simultaneous determination method of nuclear and electronic wave functions without the Born–Oppenheimer approximation. We examine two expanding methods, namely, molecular orbital (MO)‐type and valence bond (VB)‐type expansions for a nuclear orbital, which is a one‐particle wave function of a nucleus. The VB‐type expansion is shown to be more accurate than the MO‐type one because of the local nature of the nuclei. We also investigate the basis function expansion of the nuclear orbital and propose a scheme to determine the orbital exponent for the nuclear basis function. Numerical calculations confirm the accuracy and feasibility of the present method. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Surface segregation in bimetallic nanoclusters: Geometric and thermodynamic effects
Authors: Mainardi Daniela S. , Balbuena Perla B. 
Published: October 2004

AbstractNanocluster morphology (size, crystallographic faces, surface defects), coupled to thermodynamic driving forces, influence surface segregation phenomena. These geometric and thermodynamic effects are studied at several temperatures and overall compositions for Cu–Ni, Ag–Cu, and Ag–Rh. The bond order metal simulation model [Zhu, L.; DePristo, A. E. J Catal 1997, 167, 400] is used in Monte Carlo simulations to describe interatomic interactions. Nanoclusters from 110 to 729 atoms are arranged on stacks of layers corresponding to face‐centered cubic crystals. The exposed surfaces are (111), (110), and (331) faces, and the overall composition of the clusters defined in terms of the segregating atoms ranges from 5 to 95%. The effect of surface steps on surface segregation is also investigated. It is found that as overall concentration increases, the effect of surface defects on segregation phenomena becomes more pronounced. The increase in the number of low coordination sites due to the presence of surface steps modifies the layer‐by‐layer composition profile, causing surface and inner sites in the proximity of the step to become occupied by the segregating atoms. The population on other surfaces becomes depleted, resulting in a lowered total surface segregation. These effects are more noticeable not only at high overall composition but also at high temperatures, especially for the less segregating system, Ag–Cu. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Geometries and electronic structures of W4 and W clusters
Authors: Wang J. P. , Niu C. J. , Wu Z. J. 
Published: October 2004

AbstractGeometries and electronic structures of W4 and W clusters were studied by use of density functional methods B3LYP, B3P86, B3PW91, BHLYP, BLYP, and MPW1PW91. The calculated results indicate that the three‐dimensional structure of singlet state with either D2d symmetry (B3LYP, B3P86, B3PW91, BLYP, and MPW1PW91) or C2v symmetry (BHLYP) is the ground state for the W4 cluster. For the W cluster, the doublet state is preferred, and the most stable structure is also 3D with either D2d symmetry (B3LYP, B3PW91, BHLYP, BLYP) or C2v symmetry (B3P86 and MPW1PW91). The calculated electron affinity at B3P86 gives the best performance compared with experiment. For the dissociation channel, W + W3 is suggested to be the possible route for the W4 cluster. For the W cluster, W + W is the most likely route for dissociation, in agreement with experiment. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Van der Waals density functional theory with applications
Authors: Langreth D. C. , Dion M. , Rydberg H. , Schröder E. , Hyldgaard P. , Lundqvist B. I. 
Published: October 2004

AbstractThe details of a density functional that includes van der Waals (vdW) interactions are presented. In particular we give some key steps of the transition from a form for fully planar systems to a procedure for realistic layered compounds that have planar symmetry only on large‐distance scales, and which have strong covalent bonds within the layers. It is shown that the random‐phase approximation of that original functional can be replaced by an approximation that is exact at large separation between vdW interacting fragments and seamless as the fragments merge. An approximation to the latter which renders the functional easily applicable and which preserves useful accuracy in both limits and in between is given. We report additional data from applications to forms of graphite, boron nitride, and molybdenum sulfide not reported in our previous communication. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Systemic administration of 1R,4S‐4‐amino‐cyclopent‐2‐ene‐carboxylic acid, a reversible inhibitor of GABA transaminase, blocks expression of conditioned place preference to cocaine and nicotine in rats
Authors: Ashby Charles R. , Paul Mousumi , Gardner Eliot L. , Gerasimov Madina R. , Dewey Stephen L. , Lennon Ian C. , Taylor Stephen J.C. 
Published: October 2004

AbstractWe examined the effect of 1R,4S‐4‐amino‐cyclopent‐2‐ene‐carboxylic acid (ACC), a reversible inhibitor of GABA transaminase, on the expression of conditioned place preference response to cocaine and nicotine in rats. Cocaine (20 mg/kg i.p.) and nicotine (0.4 mg/kg s.c.), but not vehicle or 300 mg/kg i.p. of ACC, produced a significant conditioned place preference response. Pretreatment of animals with 300 and 75 mg/kg i.p. of ACC significantly attenuated the expression of the cocaine‐ and nicotine‐induced conditioned place preference responses, respectively. These results are the first to suggest that reversible inhibition of GABA transaminase may be useful in blocking cue‐induced relapse to nicotine and cocaine. Synapse 44:61–63, 2002. © 2002 Wiley‐Liss, Inc.
Geometric morphometrics of corpus callosum and subcortical structures in the fetal‐alcohol‐affected brain
Authors: Bookstein Fred L. , Sampson Paul D. , Streissguth Ann P. , Connor Paul D. 
Published: October 2004

AbstractBackgroundAlthough experienced clinicians have been diagnosing fetal alcohol syndrome (FAS) for nearly 30 years, the rest of the spectrum of fetal alcohol damage is not being classified effectively. This article describes a quantification of neuroanatomical structure that may supply a useful discriminator of prenatal brain damage from alcohol. It is demonstrated in a data set of adults of both sexes.MethodsNinety adults (45 males) were examined by magnetic resonance imaging (MRI). These subjects were group‐matched for age and ethnicity across three diagnoses: FAS, fetal alcohol effects (FAE), and normals. All FAS and FAE were heavily alcohol‐exposed in utero; normals were not. From T1‐weighted MR brain images, we extracted 3D morphometric representations of shape for 33‐landmark point configurations and 40‐point outlines of the corpus callosum along its midline (a slightly nonplanar structure).ResultsThere are striking differences between exposed and unexposed in the statistical distributions of these two shapes. The differences are better characterized by excess variance in the exposed group than by any change in average landmark or outline shape. For each sex, combining the callosal outline data with the landmark data leads to a powerful quadratic discriminator of exposed from unexposed. The discriminating features include the relationship of brain stem to diencephalon, and localized variabilities of callosal outline shape, but not diagnosis (FAS vs. FAE).ConclusionsStatistical analysis of brain shape is a powerful new source of information relevant to fetal alcohol spectrum nosology and etiology. Patients with FAS and FAE do not differ in these brain shape features, but both differ from the unexposed. The aspects of brain shape that are especially variable may be entailed in the underlying neuroteratogenetic mechanisms. Teratology 64:4–32, 2001. © 2001 Wiley‐Liss, Inc.
Effect of early fetal irradiation on the postnatal development of mouse
Authors: Uma Devi P. , Hossain M. 
Published: October 2004

AbstractBackgroundAn earlier study has shown that irradiation at the late fetal stage of Swiss albino mice disturbed postnatal growth and appearance of physiological markers. The present study was done to determine the effect of irradiation at the early fetal stage on the postnatal development of mouse.MethodsFourteen‐day pregnant Swiss albino mice were exposed to 0.1–1.5 Gy of cobalt‐60 γ‐rays. F1 pups were observed for ≤6 weeks of age. Postnatal mortality, body weight and length, head length and width, tail length, and the time of appearance of physiological markers (pinna detachment, eye opening, fur development, vaginal opening and testes descent) were noted.ResultsThere was no increase in congenital anomalies. Postnatal mortality and percentage of growth‐retarded pups increased significantly at doses of 0.5–1.5 Gy. A significant delay in the appearance of all the physiological markers was also noted at these doses. Body length, head length, and tail length remained significantly lower than in the controls throughout the observation period at doses of 0.3–1.5 Gy, whereas body weight and head width showed such a persistent change only at ≥0.5 Gy.ConclusionsThe early fetal day 14 in mouse is sensitive to radiation‐induced postnatal mortality and impairment of growth and temporal development of physiological markers, but not to induction of congenital anomalies. While mortality and physiological markers are not affected at <0.5 Gy, growth retardation appears to have a lower threshold of ∼0.3 Gy. Teratology 64:45–50, 2001. © 2001 Wiley‐Liss, Inc.
Career management issues for flexpatriate international staff
Authors: Mayerhofer Helene , Hartmann Linley C. , Herbert Anne 
Published: October 2004

AbstractThis article reports findings from an in‐depth study of a small number of European men and women that identifies organizational activities and their own initiatives to successfully manage their international careers within the context of their personal and family lives. In contrast to prior studies that have focused on issues for expatriate international work assignments, this study focused on flexpatriates—the frequent flyers of international work. The results indicated that, with minimal human resource management (HRM) assistance, flexpatriates were proactive and self‐managing in dealing with career issues and the family and personal demands linked to their flexpatriate lifestyles. Similar career issues were evident for men and women, but the impact of home life seemed more significant for women, and the implications of this for HRM are explored. © 2004 Wiley Periodicals, Inc.
Expatriate selection: An empirical study identifying significant skill profiles
Authors: Graf Andrea 
Published: October 2004

AbstractEffective selection procedures constitute an important factor in increasing expatriate success. However, research lacks findings regarding which skills to screen in international selection processes and whether to base expatriate selection on a culture‐specific or culture‐general skill profile. In an attempt to gather such evidence, an empirical study was conducted in the United States and Germany. Managers in both nations judge intercultural communication skills and intercultural sensitivity to be important intercultural competencies. Moreover, culture‐specific skills seem to be required when engaged in both a U.S. and German working context. Recommendations for complementing culture‐general and culture‐specific skill profiles are discussed. © 2004 Wiley Periodicals, Inc.
Attitudes toward foreign assignments among Danish economists
Authors: Andersen Torben , Scheuer Steen 
Published: October 2004

AbstractThis article addresses attitudinal issues toward foreign assignments and reports on data collected from a distinct sample of respondents—Danish economists. One of the much‐debated questions is whether foreign assignments are becoming less attractive, in particular among the younger employees, who tend to follow more narrow self‐interests and stay home. This is supposed to be reinforced by deteriorating corporate policies (i.e., offers being less attractive). The present study provides the basis for rather significant findings. The economists tend to look quite positively on expatriation (across age, gender, seniority, former foreign assignment, and unemployment), and this finding is supported by the fact that about 25% of the respondents already had experiences with foreign assignment. © 2004 Wiley Periodicals, Inc.
An empirical study of executive nationality staffing practices in foreign‐owned MNC subsidiaries in Ireland
Authors: Thompson Karen , Keating Mary 
Published: October 2004

AbstractThis study provides empirical evidence of executive nationality staffing practices in foreign‐owned multinational company (MNC) subsidiaries in Ireland. Aiming to both describe current practice and understand the factors that influence the choice of practice, the study involved the collection of data from 238 foreign‐owned companies in Ireland. The findings negate previous findings (Harzing, 1999a, b) that all foreign‐owned MNC subsidiaries in Ireland are managed by Irish nationals. The employment of parent country nationals was found to differ according to country‐of‐origin, industry, subsidiary, and MNC factors. The study has relevance theoretically in providing empirical evidence in an area dominated by conceptual assertions and for practice in explaining the strategic staffing decisions of MNCs. © 2004 Wiley Periodicals, Inc.