bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ab initio molecular orbital study of the structures and energies of neutral and charged bimolecular complexes of NH3 with the hydrides AHn (A = N, O, F, P, S, and Cl)
Authors: Del Bene Janet E. 
Published: January 2005

AbstractHartree‐Fock 6‐31G(d) structures for the neutral, positive ion, and negative ion bimolecular complexes of NH3 with the first‐ and second‐row hydrides AHn (AHn = NH3, OH2, FH, PH3, SH2, and ClH) have been determined. All of the stable neutral complexes except (NH3)2, the positive ion complexes with NH3 as the proton acceptor, and the negative ion complexes containing first‐row anions exhibit conventional hydrogen bonded structures with essentially linear hydrogen bonds and directed lone pairs of electrons. The positive ion complex NH4+ …︁ OH2 has the dipole moment vector of H2O instead of a lone pair directed along the intermolecular line, while the complexes of NH4+ with SH2, FH, and ClH have structures intermediate between the lone‐pair directed and dipole directed forms. The negative ion complexes containing second‐row anions have nonlinear hydrogen bonds. The addition of diffuse functions on nonhydrogen atoms to the valence double‐split plus polarization 6‐31G(d,p) basis set usually decreases the computed stabilization energies of these complexes. Splitting d polarization functions usually destabilizes these complexes, whereas splitting p polarization functions either has no effect or leads to stabilization. The overall effect of augmenting the 6‐31G(d,p) basis set with diffuse functions on nonhydrogen atoms and two sets of polarization functions is to lower computed stabilization energies. Electron correlation stabilizes all of these complexes. The second‐order Møller–Plesset correlation term is the largest term and always has a stabilizing effect, whereas the third and fourth‐order terms are smaller and often of opposite sign. The recommended level of theory for computing the stabilization energies of these complexes is MP2/6‐31+G(2d,2p), although MP2/6‐31+G(d,p) is appropriate for the negative ion complexes.
Locally dense basis sets for chemical shift calculations
Authors: Chesnut D. B. , Moore K. D. 
Published: January 2005

AbstractCalculations of chemical shifts have been carried out using “locally dense” basis sets for the resonant atom of interest, and smaller, attenuated sets on other atoms in the molecule. For carbon, calculations involving a 6‐311G(d) triply split valence set with polarization on the resonant atom and 3‐21G atomic bases on other heavy atoms result in good agreement with experiment, and are virtually identical to those found employing the larger basis on all atoms. For species such as nitrogen, oxygen, and fluorine where standard balanced basis sets do not agree well with experiment, use of attenuated sets fail as well. The use of locally dense basis sets permits calculations previously impractical, and the successful application to carbon suggests that the chemical shift is most dependent on the local basis set, and less so on whether or not a balanced or unbalanced calculation is being carried out.
3S‐ Versus 1s‐type Gaussian primitives: Modifications of the 3‐21G(*) basis set for the sulfur atom
Authors: Sabio Michael , Topiol Sid 
Published: January 2005

AbstractThe complete set of second‐order Gaussian functions (6D) includes a totally symmetric second‐order Gaussian function (3s‐type) in addition to the five d‐type functions. This 3s‐type function in the 3–21G(*) basis set for the sulfur atom is described (1) in terms of its geometric and electronic effects observed in the sulfur atom and in four sulfur‐containing molecules and (2) by the ability of a single zero‐order 1s‐type Gaussian function (with various exponents) to replace it in ab initio Hartree–Fock calculations. The geometry of the molecules (dihydrogen sulfide, dihydrogen thioketone, dihydrogen disulfide, and methanesulfonamide) were obtained using various semiempirical and ab initio methods. It is found that the 3s‐type function lowers the energy relative to that calculated with the 3–21G(*) basis set with only five second‐order Gaussian functions by ca. 46–48 kcal/mol per sulfur atom. Only small changes in geometry are observed when the latter basis set is augmented with a 3s or 1s function. When the exponent of the 1s replacement function is chosen so that the resulting function has a location similar to that of the 3s function as measured by the degree of overlap or the coincidence of radial distribution maxima, the corresponding drop in energy is less than 8 kcal/mol per sulfur atom. However, when the shape of the radial distribution of the 1s function is similar to that of the 3s, i.e., when the value of the 1s exponent is ca. equal to that of the 3s function (a local maximum in the 1s energy profile), the energy lowering is similar to that produced with the 3s function. The electronic effects observed in the molecules differ from those in the atom, the largest deviations being found in the methanesulfonamide calculations.
Force field parameterization for the 4‐fluorophenyl group
Authors: Gregory D. H. , Gerig J. T. 
Published: January 2005

AbstractEmpirical intermolecular force field parameters for the fluorine atom of the 4‐fluorophenyl group have been generated for use in molecular mechanics programs. Partial charges on the ring system were obtained by Mulliken population analysis of wave functions generated by molecular orbital calculations in the STO‐3G approximation. Fluorine van der Waals parameters were obtained by non‐linear least‐squares fitting of crystallographic data following the procedure of Hagler and Lifson. The parameters developed are compared to fluorine parameters reported previously.
A simplified representation of the potential produced by Gaussian charge distributions
Authors: Fortunelli Alessandro , Salvetti Oriano 
Published: January 2005

AbstractA procedure is presented which allows a more economical representation of the potential produced by orbital charge distributions in which the orbitals are expanded in terms of a finite set of polynomial Gaussian functions. The basic idea is that the products of pairs of Gaussian basis functions, on which the charge distributions are expanded, are expressed in terms of a new basis set of optimally chosen single Gaussian functions. Such a procedure has been tested in a particular case and a few possible applications have been suggested.
Free energy calculations involving NH4+ in water
Authors: Boudon Stéphane , Wipff Georges 
Published: January 2005

AbstractThe analysis of the hydration of NH4+ and the estimation of relative or absolute free energies of hydration by means of Monte Carlo computer simulations using different 1‐6‐12 potential functions is reported. Two electrostatic representations of NH4+ (used respectively by W.L. Jorgensen and P.A. Kollman) in conjunction with two common water models (TIP3P and TIP4P) are considered. A change in relative hydration free energies of 1.7 kcal/mol is found when the NH4+ models are mutated into each other in either TIP3P or TIP4P. The NH4+ → Na+ mutation in both solvent models leads to similar but overestimated relative hydration energies of about −28.7 kcal/mol. Similarly, the NH4+ annihilation significantly overestimates the absolute free energy of hydration.
A general Brownian dynamics simulation program for biopolymer dynamics and its implementation on a vector computer
Authors: Elvingson Christer 
Published: January 2005

AbstractA Brownian dynamics simulation program for the computation of transport properties of charged polarizable macromolecules is presented. The program contains routines for simulating polymer dynamics in a gel network as well as in a quiescent fluid or in a shear field. An electric field can also be included to simulate e.g., gel electrophoresis or electric dichroism. Vector algorithms have been used where possible to obtain maximum efficiency on a vector processor. The length of the vector registers and the effect of computer memory organization have also been considered. On an IBM 3090‐150S VF, more than 1.5 · 106 steps are executed in one cpu hour for a chain with 128 subunits diffusing in a rigid gel consisting of 8828 beads.
Molecular mechanics (MM2) and conformational analysis of compounds with NCO units. Parametrization of the force field and anomeric effect
Authors: Fernández Berta , Ríos Miguel A. , Carballeira Luís 
Published: January 2005

AbstractA molecular mechanics force field was developed for systems bearing the NCO unit on the basis of 6‐31G* and 4‐21G “ab initio” calculations with full optimization of the geometry and experimental heats of formation. The parameters used, which implicitly included the anomeric effect, provided good geometric and energetic results, both for the compounds on which the parametrization was based and for others on which the validity of the predictions was checked.
Computer enumeration of walks on directed graphs
Authors: Balasubramanian K. 
Published: January 2005

AbstractA vectorized computer code is developed for the enumeration of walks through the matrix power method for directed graphs. Application of this code to several graphs is considered. It is shown that the coefficients in the generating functions for signed graphs are much smaller in magnitude. It is shown that self‐avoiding walks on some graphs can be enumerated as a linear combination of walk GFs of directed paths and rooted‐directed paths.
Ab initio study of ascorbic acid conformations
Authors: Al‐Laham Mohammad A. , Petersson G. A. , Haake Paul 
Published: January 2005

AbstractThe STO‐3G optimized structures of nine different staggered conformers of ascorbic acid are presented. The largest energy difference between the nine local minima is 5.1 kcal/mol. Comparison of the relative energies of the fully optimized structures of ascorbic acid conformers with those of nonoptimized conformers shows that full optimization is essential to obtain meaningful results. However, optimization of the ring structure is almost independent of optimization of the side‐chain structure. One of the STO‐3G optimized gas phase conformers is very close to the X‐ray structure of the crystal.
Ab initio characterization of several states of nitroxylium (NO). Comparison of fragmentation energies of nitroxylium, nitroxyl (NO3), and nitrate
Authors: Boehm Randall C. , Lohr Lawrence L. 
Published: January 2005

AbstractAb initio calculations have been performed at the self‐consistent field (HF) level, and its perturbative extensions up to fourth‐order (MPn), for several electronic states of nitroxylium (NO) as well as for a large number of reference species. Geometries are optimized at the HF/DZ and HF/DZP levels (double zeta and double zeta plus polarization bases). The ground state is found to be the D3h 1A1′ state, with the C2v 1A1 (closed Y) state higher by 0.94 eV. The relationship between adding electrons or oxygen atoms to NO+ and NO is explored, especially in relation to fragmentation energies of NO (q = 0 or 1). A comparison is drawn between NO and two isoelectronic species, CO3 and C(CH2)3, where no surprises are found.
Dependence of axon initial segment formation on Na+ channel expression
Authors: Xu Xiaorong , Shrager Peter 
Published: January 2005

AbstractSpinal motor neurons were isolated from embryonic rats, and grown in culture. By 2 days in vitro, the axon initial segment was characterized by colocalization and clustering of Na+ channels and ankyrinG. By 5 days, NrCAM, and neurofascin could also be detected at most initial segments. We sought to determine, as one important aim, whether Na+ channels themselves played an essential role in establishing this specialized axonal region. Small hairpin RNAs (shRNAs) were used to target multiple subtypes of Na+ channels for reduced expression by RNA interference. Transfection resulted in substantial knockdown of these channels within the cell body and also as clusters at initial segments. Furthermore, Na+ currents originating at the initial segment, and recorded under patch clamp, were strongly reduced by shRNA. Control shRNA against a nonmammalian protein was without effect. Most interestingly, targeting Na+ channels also blocked clustering of ankyrinG, NrCAM, and neurofascin at the initial segment, although these proteins were seen in the soma. Thus, both Na+ channels and ankyrinG are required for formation of this essential axonal domain. Knockdown of Na+ channels was somewhat less effective when introduced after the initial segments had formed. Disruption of actin polymerization by cytochalasin D resulted in multiple initial segments, each with clusters of both Na+ channels and ankyrinG. The results indicate that initial segment formation occurs as Na+ channels are transported into the nascent axon membrane, diffuse distally, and link to the cytoskeleton by ankyrinG. Subsequently, other components are added, and stability is increased. A computational model closely reproduced the experimental results. © 2005 Wiley‐Liss, Inc.
Shoreline tufa and tufaglomerate from Pleistocene Lake Bonneville, Utah, USA: stable isotopic and mineralogical records of lake conditions, processes, and climate
Authors: Nelson Stephen T. , Wood M. Jay , Mayo Alan L. , Tingey David G. , Eggett Dennis 
Published: January 2005

AbstractShoreline carbonate deposits of Pleistocene Lake Bonneville record the conditions and processes within the lake, including the evaporative balance as well as vertical and lateral chemical and isotopic gradients. Tufas (swash‐zone) and tufaglomerates (cemented, subaqueous colluvium or beachrock) on multiple, well‐developed shorelines near the Silver Island Range, Utah, also present an opportunity to examine physicochemical lake processes through time. Three shorelines are represented by carbonate deposits, including the 23–20 ka Stansbury stage, 15–14.5 ka Bonneville stage, and 14.5–14 ka Provo stage.Mean δ18OVSMOWvalues of all three shorelines are statistically indistinguishable ( ∼ 27 ± 1‰), when a few Bonneville samples of unusual composition are neglected. However, differences in primary carbonate mineralogy indicate that the correspondence is an artefact of the different fractionation factors between calcite or aragonite and water. Second, in order to sustain a much smaller, shallower lake during the colder Stansbury stage, the climate must have also been relatively dry. Third, δ18O values in tufa are higher than tufaglomerate by  ∼ 0.5‰, consistent with greater evaporative enrichment of lake water in the swash zone. Fourth, mean δ13C values for the Provo, Stansbury and Bonneville shorelines (4.4, 5.0 and 5.2‰, respectively) show that carbon species were dominated by atmospheric exchange, with the variations produced by differences in the oxidation of organic matter.Comparisons of shoreline carbonates with deep‐lake marls of the same approximate age indicate that shoreline carbonate was much higher in δ13C and δ18O values (both ∼ 2.5‰) during Bonneville time, whereas isotopic differences were minor (both ∼ 1‰) in Stansbury time. In particular, the Bonneville stage may have sustained large vertical or lateral isotopic gradients due to evaporative enrichment effects on δ18O values. In contrast, the lake during the much shallower Stansbury stage may have been well mixed.Differences in the primary mineralogy (Stansbury and Bonneville, aragonite > calcite; Provo, calcite > aragonite) reflect profound differences in lake chemistry in terms of open versus closed‐basin lakes. The establishment of a continuous outlet during Provo time probably reduced the Mg2+/Ca2+ratio of lake water. Curiously, regardless of primary mineralogy, tufaglomerate cements are enriched in Na+and Cl−and depleted in Mg2+relative to capping tufa of the same age. This probably reflects vital or kinetic effects in the swash zone (tufa). We suspect that ‘abiotic’ effects may have been important in the dark pore space of developing tufaglomerate, where the absence of light suppressed photosynthesis. Copyright © 2005 John Wiley & Sons, Ltd.
Palaeomagnetic correlation and dating of Plio/Pleistocene sediments at the southern margins of the North Sea Basin
Authors: Maher B. A. , Hallam D. F. 
Published: January 2005

AbstractA series of discontinuous sediment sequences, of Plio/Pleistocene age, occur onshore around the southern North Sea margins, notably in the East Anglian region of Britain. Intensive lithological and palaeontological analyses of these sediments have shown that they record both major and minor oscillations in climate, sea level and environmental conditions. However, significant uncertainties exist regarding the absolute and relative chronostratigraphies of many of these sequences, hindering understanding of the relative impacts of climatic, eustatic and tectonic changes on the palaeogeographic development of the southern North Sea basin. Here, a number of key East Anglian Plio/Pleistocene sites are subjected to robust palaeomagnetic and mineralogical examination, in order to determine those sediments which display reliable, syn‐depositional magnetic polarities, which are thus of use in ascribing a palaeomagnetically determined age from comparison with the Geomagnetic Polarity Timescale (GPTS). Based on a range of palaeomagnetic and complementary mineralogical methods, reliable palaeomagnetic directions were obtained from eight sites, with reversed polarities displayed by sediments from three sites. These polarity determinations can be used to infer absolute ages and test published, between‐site correlations. Copyright © 2005 John Wiley & Sons, Ltd.
Holocene sedimentation in the Skagerrak interpreted from chirp sonar and core data
Authors: Gyllencreutz Richard , Jakobsson Martin , Backman Jan 
Published: January 2005

AbstractHigh‐resolution chirp sonar profiling in the northeastern Skagerrak shows acoustically stratified sediments draping a rough‐surfaced substratum. A 32 metre long sediment core retrieved from the survey area encompasses the entire Holocene and latest Pleistocene. The uppermost seismo‐acoustic units in the chirp profiles represent Holocene marine sediments. The lowermost unit is interpreted as ice‐proximal glacial‐marine sediments rapidly deposited during the last deglaciation. The end of ice‐proximal sedimentation is marked by a strong reflector, interpreted to have been formed during latest Pleistocene time as a consequence of rapid ice retreat and drastically lowered sedimentation rate. The subsequent distal glacial‐marine sediments were deposited with initially high sedimentation rates caused by an isostatic rebound‐associated sea‐level fall. Based on correlation between the core and the chirp sonar profiles using measured sediment physical properties and AMS 14C dating, we propose a revised position for the Pleistocene/Holocene boundary in the seismo‐acoustic stratigraphy of the investigated area. Copyright © 2005 John Wiley & Sons, Ltd.
Magnetic carriers and remanence mechanisms in magnetite‐poor sediments of Pleistocene age, southern North Sea margin
Authors: Maher B. A. , Hallam D. F. 
Published: January 2005

AbstractPleistocene sedimentary sequences in the East Anglian region of Britain record both major and minor climatic oscillations, and the impact of isostatic and eustatic variations. Intensively studied in terms of their lithology and biostratigraphy, the sequences have been difficult to place in an absolute timeframe. Dating and correlation by magnetostratigraphy has been attempted over a number of years. However, these sediments are difficult to date by palaeomagnetic means because they are poor in detrital magnetite, are subject to post‐depositional deformation and diagenesis, and have unknown rates of sedimentation. Determining whether their natural remanence magnetisation (NRM) directions are reliable thus requires information on the mode and timing of remanence acquisition. Here, we apply palaeomagnetic, rock magnetic and mineralogical analyses to identify the NRM carriers in these sediments and hence their palaeomagnetic reliability. Within oxidised fluvial sediments (the Kesgrave Formation), the magnetic carriers appear to be relict magnetic minerals (ferrian ilmenites, chromites, haematite and goethite), which sometimes carry a reliable primary depositional remanence (DRM) but often an overprinting viscous (time‐varying) remanence (VRM). Within some reduced marine and intertidal sediments (within the Crag basin), the iron sulphide, greigite, has been found to carry a reliable, ‘syn’‐depositional chemical remanence (CRM). In all the sediments, magnetic inclusions within silicates are abundant, are significant for the mineral magnetic signal but contribute little to any recoverable palaeomagnetic information. Copyright © 2005 John Wiley & Sons, Ltd.
Reconstruction of Late Glacial summer temperatures from chironomid assemblages in Lac Lautrey (Jura, France)
Authors: Heiri Oliver , Millet Laurent 
Published: January 2005

AbstractA chironomid–July air temperature inference model based on chironomid assemblages in the surface sediments of 81 Swiss lakes was used to reconstruct Late Glacial July air temperatures at Lac Lautrey (Jura, Eastern France). The transfer‐function was based on weighted averaging–partial least squares (WA‐PLS) regression and featured a leave‐one‐out cross‐validated coefficient of determination (r2) of 0.80, a root mean square error of prediction (RMSEP) of 1.53 ° C, and was applied to a chironomid record consisting of 154 samples covering the Late Glacial period back to the Oldest Dryas. The model reconstructed July air temperatures of 11–12 ° C during the Oldest Dryas, increasing temperatures between 14 and 16.5 ° C during the Bølling, temperatures around 16.5–17.0 ° C for most of the Allerød, temperatures of 14–15 ° C during the Younger Dryas and temperatures of ca. 16.5 ° C during the Preboreal. The Lac Lautrey record features a two‐step July air temperature increase after the Oldest Dryas, with an abrupt temperature increase of ca. 3–3.5 ° C at the Oldest Dryas/Bølling transition followed by a more gradual warming between ca. 14 200 and 13 700 BP. The transfer‐function reconstructs a less rapid cooling at the Allerød/Younger Dryas transition than other published records, possibly an artefact caused by the poor analogue situation during the earliest Younger Dryas, and an abrupt warming at the Younger Dryas/Holocene transition. During the Allerød, two centennial‐scale 1.5–2.0 ° C coolings are apparent in the record. Although chronologically not well constrained, the first of these cold events may be synchronous with the beginning of the Gerzensee Oscillation. The second is inferred just before deposition of the Laachersee tephra at Lac Lautrey and is therefore coeval with the end of the Gerzensee Oscillation. In contrast to the Greenland oxygen isotope records, the Lac Lautrey palaeotemperature reconstruction lacks a clearly defined Greenland Interstadial (GI) event 1d and the decreasing temperature trend during the Bølling/Allerød Interstadial. Copyright © 2005 John Wiley & Sons, Ltd.