bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution
Authors: Haberthür Urs , Majeux Nicolas , Werner Philipp , Caflisch Amedeo 
Published: January 2004

AbstractWe propose an analytical approach to calculate the effective dielectric function of proteins in aqueous solution. The screening effect if quantified by a measure of enclosure which is based on the distribution of solute atomic volumes around a pair of charges in a macromolecule. For protein conformations that vary significantly in size and shape, a comparison with finite difference Poisson calculations shows that pair interaction energies, their sums and solvation energies are well reproduced. The approach rivals the speed of simple distance dependent dielectric functions and the accuracy of the generalized Born model. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1936–1949, 2003
Chemical structures from the analysis of domain‐averaged Fermi holes: Multiple metalmetal bonding in transition metal compounds
Authors: Ponec Robert , Yuzhakov Gleb , Carbó‐Dorca Ramon 
Published: January 2004

AbstractThe recently proposed approach based on the analysis of domain‐averaged Fermi holes was applied to the study of the nature of metalmetal bonding in transition metal complexes and clusters. The main emphasis was put on the scrutiny of the systems assumed to contain direct multiple metalmetal bonds. The studied systems involve: (1) systems of the type M2X6 (M = Mo, W, X = CH3) anticipated to contain metalmetal triple bonds; (2) the molecule of W2Cl8(4−) as the representative of the systems with quadruple metalmetal bonding; (3) diatomic molecules Mo2 and V2 considered as the potential candidates for higher than quadruple metalmetal bonding. Although the resulting picture of bonding has been usually shown to agree with the original expectations based on early simple MO models, some examples were also found in which the conclusions of the reported analysis display dramatic sensitivity to the quality of the wave function used for the generation of the Fermi holes. In addition to this we also report some examples where the original theoretical predictions of multiplicity of metalmetal bonds have to be corrected. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1829–1838, 2003
Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field
Authors: MacCallum Justin L. , Tieleman D. Peter 
Published: January 2004

AbstractWe calculated the free energy of solvation of the neutral analogs of 18 amino acid side‐chains (not including glycine and proline) using the OPLS all‐atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1930–1935, 2003
Docking macromolecules with flexible segments
Authors: Bastard Karine , Thureau Aurélien , Lavery Richard , Prévost Chantal 
Published: January 2004

AbstractWe address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein‐DNA complex of known 3‐D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1910–1920, 2003
Gaussian‐type function set without prolapse for the Dirac–Fock–Roothaan equation
Authors: Tatewaki Hiroshi , Watanabe Yoshihiro 
Published: January 2004

AbstractA Gaussian‐type function (GTF) set without a prolapse (variation collapse) is generated for the Dirac–Fock–Roothaan (DFR) equation. The test atom was mercury. The number of primitive GTFs used is between 7and 62 (abbreviated as 7–62), 6–62, 6–62, 4–36, 4–36, 3–36, and 3–36 for s+, p−, p+, d−, d+, f−, and f+ symmetries. The respective exponent parameters were determined with even‐tempered manner, which requires the minimum and maximum exponents for the respective symmetries. We prepared several sets of these. The total energy (TE) given by the numerical DF (NDF) is −19648.849250 hartree; one of the present sets with largest number of expansion terms gave −19648.849251 hartree. The error (ΔTE) relative to the NDR TE is quite small. We then applied this set to the inert gas atoms Ne (10), Ar (18), Kr (36), Xe (54), Rn (86), and No (102), and also to Es (99) as the representative of the open shell atoms. The absolute values of ΔTE were at most 2.8 × 10−6 hartree, showing the potential of this set as a universal set. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1823–1828, 2003
Critical assessment of side‐chain conformational space sampling procedures designed for quantifying the effect of side‐chain environment
Authors: Gautier R. , Tufféry P. 
Published: January 2004

AbstractWe introduce a family of procedures designed to sample side‐chain conformational space at particular locations in protein structures. These procedures (CRSP) use intensive cycles of random assignment of side‐chain conformations followed by minimization to determine all the conformations that a group of side‐chains can adopt simultaneously. First, we consider a procedure evolving in the dihedral space (dCRSP). Our results suggest that it can accurately map low‐energy conformations adopted by clusters of side‐chains of a protein. dCRSP is relatively insensitive to various important parameters, and it is sufficiently accurate to capture efficiently the constraint induced by the environment on the conformations a particular side‐chain can adopt. Our results show that dCRSP, compared with molecular dynamics (MD), can overcome the problem of the limited set of conformations reached in a reasonable amount of simulations. Next, we introduce procedures (vCRSP) in which valence angles are relaxed, and we assess how efficiently they quantify the conformational entropy of side‐chains in the protein native state. For simple peptides, entropies obtained with vCRSP are fully compatible with those obtained with a Monte Carlo procedure. For side‐chains in a protein environment, however, vCRSP appears of limited use. Finally, we consider a two‐step procedure that combines dCRSP and vCRSP. Our tests suggest that it is able to overcome the limitations of vCRSP. We also note that dCRSP provides a reasonable initial approximation. This family of procedures offers promise in quantifying the contribution of conformational entropy to the energetics of protein structures. © 2003 Wiley Periodicals, Inc. J Comput Chem 15: 1950–1961, 2003
Adaptive integration of molecular dynamics
Authors: Horenko Illia , Weiser Martin 
Published: January 2004

AbstractThis article presents a particle method framework for simulating molecular dynamics. For time integration, the implicit trapezoidal rule is employed, where an explicit predictor enables large time steps. Error estimators for both the temporal and spatial discretization are advocated, and facilitate a fully adaptive propagation. The framework is developed and exemplified in the context of the classical Liouville equation, where Gaussian phase‐space packets are used as particles. Simplified variants are discussed briefly. The concept is illustrated by numerical examples for one‐dimensional dynamics in double well potential. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1921–1929, 2003
Adsorption of organic substances on broken clay surfaces: A quantum chemical study
Authors: Aquino Adélia J.A. , Tunega Daniel , Haberhauer Georg , Gerzabek Martin H. , Lischka Hans 
Published: January 2004

AbstractHydrogen‐bonded interactions between local defect structures on broken clay surfaces modeled as molecular clusters and the organic molecules acetic acid, acetate, and N‐methylacetamide (NMA) have been investigated. Density functional theory and polarized basis sets have been used for the computation of optimized interaction complexes and formation energies. The activity of the defect structures has been characterized as physical or chemical in terms of the strength of the hydrogen bonds formed. Chemical defects lead to significantly enhanced interactions with stronger hydrogen bonds and larger elongation of OH bonds in comparison to the physical defects. The type of interaction with the defect structure significantly influences the planarity of the model peptide bond in NMA. Both cases, enhancement of the planarity by increase of the CN double bond character and strong deviations from planarity, are observed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1853–1863, 2003
Molecular caps for full quantum mechanical computation of peptide–water interaction energy
Authors: Zhang D. W. , Chen X. H. , Zhang J. Z. H. 
Published: January 2004

AbstractWe present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein–molecule interaction energy. A previously studied pentapeptide (Gly‐Ser‐Ala‐Asp‐Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One‐dimensional potential energy curves are generated for a number of peptide–water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1846–1852, 2003
Theoretical studies for structures and energetics of RgnN2O (RgHe, Ne, Ar) clusters
Authors: Zhu Hua , Xie Daiqian , Yan Guosen 
Published: January 2004

AbstractMinimum‐energy structures of the Rg2N2O (RgHe, Ne, Ar) clusters have been determined with ab initio MP2 optimization, whereas the minimum‐energy structures of the RgnN2O clusters with n = 3–7 have been obtained with the pairwise additive potentials. Interaction energies and nonadditive three‐body effects of the Rg2N2O ternary complex have been calculated using supermolecule method at MP4 and CCSD(T) levels. It was found from the calculations that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The nonadditive three‐body effects were found to be small for Rg2N2O complexes. Our calculations also indicated that, for HenN2O and NenN2O clusters, the first six He and Ne atoms form the first solvation ring around the middle nitrogen of the N2O monomer, while for ArnN2O, the first five Ar atoms form the first solvation ring. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1839–1845, 2003
Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin
Authors: Díaz Natalia , Suárez Dimas , Sordo Tomás L. 
Published: January 2004

AbstractHerein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6‐31G* and B3LYP/6‐31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH · · · O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring‐puckering motions, and the correlation of side chain and ring‐puckering motions. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1864–1873, 2003
New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases
Authors: Ryjáček Filip , Kubař Tomáš , Hobza Pavel 
Published: January 2004

AbstractThe Cornell et al. empirical potential (Cornell et al., J Am Chem Soc 1995, 117, 5197) was modified by the introduction of nonplanarity of the amino group in guanine, adenine, and cytosine. Reparameterization was performed for 12 bond parameters of the amino group (three valence angles (C–N–H1, C–N–H2, and H1–N–H2) and the improper dihedral angle at nitrogen, four dihedral angles (X–C–N–H1, Y–C–N–H2, X–X–C–N, Y–Y–C–N), three valence angles (X–C–N, Y–C–N, X–C–Y), and the improper dihedral angle at the adjacent carbon), and was based on correlated ab initio potential energy surfaces. Calculations were performed using the resolution of identity MP2 (RIMP2) method with SVP (3s2p1d/2s1p), TZVP (5s3p1d/3s1p), TZVPP (5s3p2d1f/3s2p1d), and augTZVPP (6s4p3d2f/4s3p2d) basis sets. Results obtained on the latter two levels are practically identical with the literature reference data [MP2/6‐311++G(2df,p)] and the RIMP2/augTZVPP data can be considered a new reference set. The potential energy surface used for reparameterization was evaluated at the RIMP2/SVP level because respective geometry as well as energy data were close to the reference ones, and the computational time was very favorable. The modified potential was tested for 19 H‐bonded and eight stacked nucleic acid base pairs. Interaction energies as well as geometries were described by the modified potential considerably better than by the original one and significant improvement resulted in the description of the nonplanar H‐bonded and stacked complexes. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1891–1901, 2003
Determination of atomic valence indices from population analyses at correlated level
Authors: Bochicchio R. , Lain L. , Torre A. 
Published: January 2004

AbstractThis work carries out a study of atomic valences within molecular systems based on Mulliken and topological population analyses at correlated level. The use of the unpaired electron densities leads to suitable relationships between valences, free valence indices, and bond indices, which turn out to be quite useful for computational purposes. The results arising from both methods at correlated and uncorrelated levels are compared in a large series of chemical compounds. Several interesting conclusions are drawn out and analyzed in detail. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1902–1909, 2003
From sneaker to parental male: Change of reproductive traits in the black goby, Gobius niger (Teleostei, Gobiidae)
Authors: Immler Simone , Mazzoldi Carlotta , Rasotto Maria Berica 
Published: January 2004

AbstractThis study focuses on the consequences of the switch of tactic from parasitic to parental male in the black goby, Gobius niger (Teleostei: Gobiidae), a species showing two alternative male mating tactics. Older and larger males defend nests, court, and perform parental care on eggs, while younger and smaller ones behave as parasites, sneaking into nests while spawning occurs. Males adopting different tactics are known to present differences in primary and secondary sex traits. The social context of sneaker males was manipulated to induce a tactic switch. Sneakers were kept under two different experimental treatments with or without a female, and under exclusion of male‐male competition. Males changed tactics, courting females, spawning, and performing parental care. All males showed substantial changes in primary sexual traits, such as a reduction in gonadal development and an increase in the investment in accessory structures. The experimental groups differed in the functionality of gonads and accessory organs and in the development of the secondary sex traits. These results demonstrate that the moment of switching is not genetically fixed in the black goby. Sneaker males are able to quickly reallocate energy in primary and secondary sex traits, in accordance with the adopted tactic. Several aspects of this flexible reproductive pattern resemble the socially controlled sex change found in sequential hermaphrodites. J. Exp. Zool. 301A:177–185, 2004. © 2004 Wiley‐Liss, Inc.
Green fluorescent protein gene‐transfected peafowl somatic cells participate in the development of chicken embryos
Authors: Xi Yongmei , Nada Yoich , Soh Tomoki , Fujihara Noboru , Hattori Masa‐aki 
Published: January 2004

AbstractThis study was performed to investigate whether the embryonic somatic cells are capable of reconstituting and participating in the embryonic development of chickens to produce chimeras. In order to track the migration behavior of the donor cells, a cell line, originally isolated from an Indian peafowl embryo, was fluorescent‐labeled by transfection of the cells with enhanced Green Fluorescent Protein (GFP) and Neomycin resistant (Neo) genes prior to injection into the stage X blastoderm of White Leghorn chickens. The injection was performed with a medium in the presence of 1–5% polyethylene glycol. The development of putative chimeric embryos between the stages three and 24 was examined for GFP expression under fluorescent light. To trace the peafowl cells in the developing chicken embryos, both a species‐specific genetic marker originating from the mitochondrial DNA cytochrome b (cyt b) gene and a DNA fragment of GFP gene were used. Of the 185 fertile eggs manipulated, 173 developed into embryos. Fifty‐five of them showed positive GFP patches in extra‐embryonic tissues, and 15 expressed GFP in intra‐embryonic tissues such as those of the head, heart, and gonad. PCR analysis revealed that PCR fragments for the peafowl mitochondrial DNA cyt b and GFP genes were detected in the samples of the GFP positive extra‐ and intra‐embryonic tissues of the chimeras. The present results provide evidence that fluorescent‐labeled peafowl embryonic cells carrying GFP and Neo genes are able to participate in the development of chicken embryos to generate chimeras. J. Exp. Zool. 301A:139–149, 2004. © 2004 Wiley‐Liss, Inc.
Daily organization of laying in Japanese and European quail: Effect of domestication
Authors: Cécilia Houdelier , Catherine Guyomarc'h , Sophie Lumineau , Jean‐Pierre Richard 
Published: January 2004

AbstractIn the present study, we aimed to examine the possible effects of domestication on the daily organization of laying in female quail. To achieve this we compared laying patterns in a laboratory strain of Japanese quail with those in European quail originating from a wild population. Under LD 14:10, the same specific laying window was observed, with ovipositions occurring mainly between 7h and 15h after lights on. Thus, domestication did not modify the specific daily organization of laying in females laying in the afternoon. Research about the functional value of this temporal organization in the field thus seems justified. At an individual level, two distinct laying profiles were recorded, as in a previous experiment on an industrial Japanese quail strain selected for meat and egg production. However, different frequencies were noted. Whereas stable profile females (laying at the same time each day) were predominant (80.4%, N=102) in the industrial Japanese quail strain, delayed profile females (laying successively later each day) appeared dominant in the European quail (81%, N=22). The Japanese quail from the laboratory strain constituted an intermediate group with a slight dominance of the stable profile (58.8%, N=17). Thus, domestication has changed the frequencies of the laying profiles, favoring stable females, which are the most productive birds. A model involving interaction between one circadian rhythm and one ultradian rhythm can explain the observed laying profiles. J. Exp. Zool. 301A:186–194, 2004. © 2004 Wiley‐Liss, Inc.
Treatment with the neurosteroid dehydroepiandrosterone promotes recovery of motor behavior after moderate contusive spinal cord injury in the mouse
Authors: Fiore Christelle , Inman Denise M. , Hirose Shijiro , Noble Linda J. , Igarashi Takuji , Compagnone Natalie A. 
Published: January 2004

AbstractThe neurosteroid dehydroepiandrosterone (DHEA) has neuroprotective properties after ischemic and excitatory insults to the brain. In the developing embryo, it is produced in discrete regions of the central nervous system (CNS), where it specifically promotes axonal growth of differentiated neurons. To test if DHEA could be beneficial after spinal cord injury (SCI), we used a model of moderate contusive SCI developed and characterized in the mouse. Immediately after surgery, we applied treatment with DHEA or with vehicle only and compared treatment groups (n = 12 in each group) over a 42‐day period. Locomotor recovery was assessed in an open field using a standardized 21‐point scale, according to gait analysis on paw print recordings and using foot fault analyses on an inclined ladder beam. The DHEA‐treated group showed improved function compared to vehicle‐treated animals in these tests. More strikingly, DHEA enhanced recovery of left‐right coordination and fine motor control. In an attempt to correlate functional recovery with spinal cord neuropathology in the different experimental groups, we studied the area of spared white matter at the epicenter and reactive gliosis/scar formation 42 days post‐injury (DPI). DHEA significantly increased the area of white matter spared at the epicenter and reduced the area of reactive gliosis surrounding the lesion. These data demonstrate the effectiveness of DHEA in promoting functional recovery in the adult murine injured spinal cord. © 2003 Wiley‐Liss, Inc.