bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Holocene Paleoindian deposits at Nall Playa, Oklahoma Panhandle, U.S.A.
Authors: LaBelle Jason M. , Holliday Vance T. , Meltzer David J. 
Published: December 2002

AbstractFieldwork conducted at the Nall North locale and the adjacent playa documents buried Paleoindian deposits and a stratigraphic sequence dating back to the late Pleistocene. Cultural debris recovered from the surface of Nall North includes bone, tools, and lithic flake debris. Two buried paleosols at the locale date to the early Holocene and hold high potential for Paleoindian materials. The Baker paleosol, a stabilized surface above the shoreline of the adjacent playa lake, dated between ca. 6870 and 7740 yr B.P., contains a rich cultural component of tools, flakes, and bone, and represents a potential surface for Angostura and Allen/Frederick artifacts. Located below the Baker soil is the Nall soil (dated to ca. 9650 yr B.P.) that probably represents a marsh facies of the playa fill. The Nall soil represents a potential surface for Plainview/Goshen‐age artifacts, although excavations thus far have recovered no cultural debris. In the playa adjacent to the Nall North locality, a sequence dating between ca. 12,960 and 5310 yr B.P. documents localized spring flow into the playa during the late Pleistocene, followed by several thousand years of playa muds during the early Holocene, and the eventual drying of the playa in the middle Holocene. © 2003 Wiley Periodicals, Inc.
Digging for the color of life: Paleoindian red ochre mining at the Powars II site, Platte County, Wyoming, U.S.A.
Authors: Stafford Michael D. , Frison George C. , Stanford Dennis , Zeimans George 
Published: December 2002

AbstractThe Powars II site, 48PL330, located near Sunrise, Wyoming, is a significant Paleoindian site in the Hartville Uplift area of eastern Wyoming. Intensive red ochre mining took place at Powars II, as indicated by Paleoindian materials in direct association with a natural hematite deposit. Projectile points ranging in age from Clovis to Late Paleoindian have been recovered, as well as stone and bone tools, shell and bone beads, and several pieces of incised bone. It is argued that the Powars II assemblage reflects a two‐part cultural manifestation: a technological component resulting from the process of mining and processing ochre, and an ideological component derived from emic beliefs about the ochre source itself. © 2003 Wiley Periodicals, Inc.
Eolian and soil stratigraphy at a Paleoindian site along the South Platte River valley, Nebraska, U.S.A.
Authors: May David W. , Holen Steven R. 
Published: December 2002

AbstractEolian and soil stratigraphy and radiocarbon ages of soil humates were used to reconstruct landscape evolution at a site (25KH67) in western Nebraska along the South Platte River. The site is on the bluff of a short, deeply incised, dune‐blocked tributary to the South Platte. The Paleoindian component is in the lower part of the Brady Soil. The age of the lower Brady Soil where cultural material was recovered is 10,360 yr B.P., and the age of the upper Brady Soil is 6090 yr B.P. The Brady Soil formed over a longer interval at site 25KH67 than at other upland localities in southern Nebraska and Kansas. Three episodes of eolian deposition occurred after 6090 yr B.P. Discovery of additional Paleoindian sites along the South Platte River valley and across the central Great Plains will be hampered by Holocene eolian deposits that blanket the Brady Soil. © 2003 Wiley Periodicals, Inc.
Geoarchaeological investigations at the Winger site: A Late Paleoindian bison bonebed in southwestern Kansas, U.S.A.
Authors: Mandel Rolfe D. , Hofman Jack L. 
Published: December 2002

AbstractThe Winger site is a deeply buried Late Paleoindian bison bonebed in a playa basin on the High Plains of midcontinental North America. The site is one of few stratified, Late Paleoindian bison kills recorded in the region. The bonebed is exposed in the bank of an intermittent stream that cut into the edge of the playa basin. Avocational archaeologists excavated a small portion of the exposed bonebed in the early 1970s and reported flakes in association with the skeletal remains. Limited reinvestigations of the site were undertaken in 2001, and a month‐long excavation was conducted in 2002 to assess the stratigraphy, geochronology, and archaeology. The bonebed is 35 m long in a buried soil developed in fine‐grained basin fill overlain by early Holocene alluvium (arroyo fill). Recent alluvium overlies a soil developed in the early Holocene alluvium, and modern deposits of eolian sand 2 m to < 35 cm thick mantle the site area. Artifacts found at the site include two Allen points and a flake tool discovered in the bone bed, and a biface and Allen point fragment in disturbed bonebed deposits. Excavation of 9 m2 of the bone bed revealed some fully articulated skeletons, and taphonomic observations suggest some of the bison collapsed while standing in a playa or pond margin setting. The remains of at least six bison are represented in the excavated sample from 2002, but many more animals are represented in the bonebed. A 14C age of ca. 9000 yr B.P. was determined on collagen from bison rib fragments. This age is consistent with the diagnostic artifacts found at Winger. © 2003 Wiley Periodicals, Inc.
Structural and dynamical analysis of the hydration of the Alzheimer's β‐amyloid peptide
Authors: Massi Francesca , Straub John E. 
Published: December 2002

AbstractAn analysis of the water molecules in the first solvation shell obtained from the molecular dynamics simulation of the amyloid β(10‐35)NH2 peptide and the amyloid β(10‐35)NH2E22Q “Dutch” mutant peptide is presented. The structure, energetics, and dynamics of water in the hydration shell have been investigated using a variety of measures, including the hydrogen bond network, the water residence times for all the peptide residues, the diffusion constant, experimentally determined HN amide proton exchange, and the transition probabilities for water to move from one residue to another or into the bulk. The results of the study indicate that: (1) the water molecules at the peptide‐solvent interface are organized in an ordered structure similar for the two peptide systems but different from that of the bulk, (2) the peptide structure inhibits diffusion perpendicular to the peptide surface by a factor of 3 to 5 relative to diffusion parallel to the peptide surface, which is comparable to diffusion of bulk water, (3) water in the first solvation shell shows dynamical relaxation on fast (1–2 ps) and slow (10–40 ps) time scales, (4) a novel solvent relaxation master equation is shown to capture the details of the fast relaxation of water in the peptide's first solvation shell, (5) the interaction between the peptide and the solvent is stronger in the wild type than in the E22Q mutant peptide, in agreement with earlier results obtained from computer simulations [Massi, F.; Straub, J. E. Biophys J 2001, 81, 697] correlated with the observed enhanced activity of the E22Q mutant peptide. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 143–153, 2003
Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation
Authors: Jakalian Araz , Jack David B. , Bayly Christopher I. 
Published: December 2002

AbstractWe present the first global parameterization and validation of a novel charge model, called AM1‐BCC, which quickly and efficiently generates high‐quality atomic charges for computer simulations of organic molecules in polar media. The goal of the charge model is to produce atomic charges that emulate the HF/6‐31G* electrostatic potential (ESP) of a molecule. Underlying electronic structure features, including formal charge and electron delocalization, are first captured by AM1 population charges; simple additive bond charge corrections (BCCs) are then applied to these AM1 atomic charges to produce the AM1‐BCC charges. The parameterization of BCCs was carried out by fitting to the HF/6‐31G* ESP of a training set of >2700 molecules. Most organic functional groups and their combinations were sampled, as well as an extensive variety of cyclic and fused bicyclic heteroaryl systems. The resulting BCC parameters allow the AM1‐BCC charging scheme to handle virtually all types of organic compounds listed in The Merck Index and the NCI Database. Validation of the model was done through comparisons of hydrogen‐bonded dimer energies and relative free energies of solvation using AM1‐BCC charges in conjunction with the 1994 Cornell et al. forcefield for AMBER.13 Homo‐ and hetero‐dimer hydrogen‐bond energies of a diverse set of organic molecules were reproduced to within 0.95 kcal/mol RMS deviation from the ab initio values, and for DNA dimers the energies were within 0.9 kcal/mol RMS deviation from ab initio values. The calculated relative free energies of solvation for a diverse set of monofunctional isosteres were reproduced to within 0.69 kcal/mol of experiment. In all these validation tests, AMBER with the AM1‐BCC charge model maintained a correlation coefficient above 0.96. Thus, the parameters presented here for use with the AM1‐BCC method present a fast, accurate, and robust alternative to HF/6‐31G* ESP‐fit charges for general use with the AMBER force field in computer simulations involving organic small molecules. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1623–1641, 2002
Theoretical study of sheets formed by β‐peptides
Authors: Lin Jin‐Qiu , Luo Shi‐Wei , Wu Yun‐Dong 
Published: December 2002

AbstractStructural and thermodynamic features of the sheets formed by β‐peptides have been studied by quantum mechanics calculations using peptide models. Calculations using dipeptide models indicate that the intrinsic hydrogen bond strength is great for both parallel and antiparallel sheets and that it is little affected by proper substituents. Heterochiral‐β2,3‐peptides have much stronger sheet‐forming propensity than other types of peptides because their favored backbone conformation is ideal for sheet formation. A planar or ideally pleated strand has a curved geometry, which is unfavorable for the formation of sheets. Thus, sheets have to adopt twisted geometries. There is a large cooperativity in the formation of the hydrogen bond network in the sheets of β‐peptides in the perpendicular direction due to long‐range electrostatic attractions because all carbonyl groups are roughly in the same direction, in contrast to the situation in β‐sheets of α‐peptides. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1551–1558, 2002
Computational study of epoxy‐amine reactions
Authors: Okumoto Satoshi , Yamabe Shinichi 
Published: December 2002

AbstractDensity functional theory calculations were carried out for the title reactions. Ethylene oxide and methylamine were adopted as reactants. Amine clusters (dimer, trimer, tetramer, and pentamer) were considered, because the combination of one oxide and one amine molecule gave a large activation energy. An amine tetramer was found to react favorably with the oxide via various zwitterionic intermediates. A back‐side SN2 nucleophilic attack of one amine and the subsequent proton relay up to the front side provide a stabilized reaction field. The amine‐alcohol mixed reactant may react readily with the oxide, because the alcoholic OH group is in contact with the oxide oxygen with the strong hydrogen‐bond stabilization. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 244–253, 2003
Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects
Authors: Garcia‐Viloca Mireia , Alhambra Cristóbal , Truhlar Donald G. , Gao Jiali 
Published: December 2002

AbstractWe have applied molecular dynamics umbrella‐sampling simulation and ensemble‐averaged variational transition state theory with multidimensional tunneling (EA‐VTST/MT) to calculate the reaction rate of xylose‐to‐ xylulose isomerization catalyzed by xylose isomerase in the presence of two Mg2+ ions. The calculations include determination of the free energy of activation profile and ensemble averaging in the transmission coefficient. The potential energy function is approximated by a combined QM/MM/SVB method involving PM3 for the quantum mechanical (QM) subsystem, CHARMM22 and TIP3P for the molecular mechanical (MM) environment, and a simple valence bond (SVB) local function of two bond distances for the hydride transfer reaction. The simulation confirms the essential features of a mechanism postulated on the basis of kinetics and X‐ray data by Whitlow et al. (Whitlow, M.; Howard, A. J.; Finzel, B. C.; Poulos, T. L.; Winborne, E.; Gilliland, G. L. Proteins 1991, 9, 153) and Ringe, Petsko, and coworkers (Labie, A.; Allen, K.‐N.; Petsko, G. A.; Ringe, D. Biochemistry 1994, 33, 5469). This mechanism involves a rate‐determining 1,2‐hydride shift with prior and post proton transfers. Inclusion of quantum mechanical vibrational energy is important for computing the free energy of activation, and quantum mechanical tunneling effects are essential for computing kinetic isotope effects (KIEs). It is found that 85% of the reaction proceeds by tunneling and 15% by overbarrier events. The computed KIE for the ratio of hydride to deuteride transfer is in good agreement with the experimental results. The molecular dynamics simulations reveal that proton and hydride transfer reactions are assisted by breathing motions of the mobile Mg2+ ion in the active site, providing evidence for concerted motion of Mg2+ during the hydride transfer step. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 177–190, 2003
PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods
Authors: Repasky Matthew P. , Chandrasekhar Jayaraman , Jorgensen William L. 
Published: December 2002

AbstractTwo new semiempirical methods employing a Pairwise Distance Directed Gaussian modification have been developed: PDDG/PM3 and PDDG/MNDO; they are easily implemented in existing software, and yield heats of formation for compounds containing C, H, N, and O atoms with significantly improved accuracy over the standard NDDO schemes, PM5, PM3, AM1, and MNDO. The PDDG/PM3 results for heats of formation also show substantial improvement over density functional theory with large basis sets. The PDDG modifications consist of a single function, which is added to the existing pairwise core repulsion functions within PM3 and MNDO, a reparameterized semiempirical parameter set, and modified computation of the energy of formation of a gaseous atom. The PDDG addition introduces functional group information via pairwise atomic interactions using only atom‐based parameters. For 622 diverse molecules containing C, H, N, and O atoms, mean absolute errors in calculated heats of formation are reduced from 4.4 to 3.2 kcal/mol and from 8.4 to 5.2 kcal/mol using the PDDG modified versions of PM3 and MNDO over the standard versions, respectively. Several specific problems are overcome, including the relative stability of hydrocarbon isomers, and energetics of small rings and molecules containing multiple heteroatoms. The internal consistency of PDDG energies is also significantly improved, enabling more reliable analysis of isomerization energies and trends across series of molecules; PDDG isomerization energies show significant improvement over B3LYP/6‐31G* results. Comparison of heats of formation, ionization potentials, dipole moments, isomer, and conformer energetics, intermolecular interaction energies, activation energies, and molecular geometries from the PDDG techniques is made to experimental data and values from other semiempirical and ab initio methods. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1601–1622, 2002
Prediction of β‐sheet topology and disulfide bridges in polypeptides
Authors: Klepeis J. L. , Floudas C. A. 
Published: December 2002

AbstractAn ab initio method has been developed to predict β architectures in polypeptides. The approach predicts the topology of β‐sheets and disulfide bridges through a novel superstructure‐based mathematical framework originally established for chemical process synthesis problems. Two types of superstructure are introduced, both of which emanate from the principle that hydrophobic interactions drive the formation of a β‐structure. The mathematical formulation of the problem results in a set of integer linear programming (ILP) problems that can be solved to global optimality to identify the optimal β‐configuration. These (ILP) models can also predict a ranked ordered list of the best, second‐best, third‐best, etc., topologies of β‐sheets and disulfide bridges. The approach is shown to perform very well for several benchmark polypeptide systems, as well as polypeptides exhibiting challenging nonsequential β‐sheet topologies folds (56 to 187 amino acids). © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 191–208, 2003
Molecules for materials: Germanium hydride neutrals and anions. Molecular structures, electron affinities, and thermochemistry of GeHn/GeH (n = 0–4) and Ge2Hn/Ge2H (n = 0–6)
Authors: Li Qian‐Shu , Lü Rui‐Hua , Xie Yaoming , Schaefer Henry F. 
Published: December 2002

AbstractThe GeHn (n = 0–4) and Ge2Hn (n = 0–6) systems have been studied systematically by five different density functional methods. The basis sets employed are of double‐ζ plus polarization quality with additional s‐ and p‐type diffuse functions, labeled DZP++. For each compound plausible energetically low‐lying structures were optimized. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews 102, 231, 2002). The geometries predicted in this work include yet unknown anionic species, such as Ge2H−, Ge2H, Ge2H, Ge2H, and Ge2H. In general, the BHLYP method predicts the geometries closest to the few available experimental structures. A number of structures rather different from the analogous well‐characterized hydrocarbon radicals and anions are predicted. For example, a vinylidene‐like GeGeH structure is the global minimum of Ge2H. For neutral Ge2H4, a methylcarbene‐like HGë‐GeH3 is neally degenerate with the trans‐bent H2GeGeH2 structure. For the Ge2H anion, the methylcarbene‐like system is the global minimum. The three different neutral‐anion energy differences reported in this research are: the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). For this family of molecules the B3LYP method appears to predict the most reliable electron affinities. The adiabatic electron affinities after the ZPVE correction are predicted to be 2.02 (Ge2), 2.05 (Ge2H), 1.25 (Ge2H2), 2.09 (Ge2H3), 1.71 (Ge2H4), 2.17 (Ge2H5), and −0.02 (Ge2H6) eV. We also reported the dissociation energies for the GeHn (n = 1–4) and Ge2Hn (n = 1–6) systems, as well as those for their anionic counterparts. Our theoretical predictions provide strong motivation for the further experimental study of these important germanium hydrides. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1642–1655, 2002
Placenta: Regularization of neovascularization. Microvascularization pattern of the rabbit term placenta
Authors: Del Mar Yllera Maria , Alexandre‐Pires Graça Maria , Cifuentes Jose Manuel 
Published: December 2002

AbstractMammalian blastocyst produces membranes that gradually attach in the endometrial epithelium and establish a close relationship between fetal and maternal circulatory systems for physiologic exchange. This fact results in the formation of a combined organ, the placenta. Placentation includes extensive neovascularization in maternal and embryonic placental tissues. Recent studies, particularly of genetically altered mice, have greatly improved our understanding of the molecular basis of the development of the vascular system. Numerous factors have been implicated in the regulation of the neovascularization process of the placenta. The aim of this article is to highlight briefly the pattern circulation of the rabbit term placenta as an example of the microvascularization of hemochorial placenta typical of humans and to summarize the main factors responsible for modulating the growth of decidual placental vessels and the vasculogenesis of the basal plate. Microsc. Res. Tech. 60:38–45, 2003. © 2002 Wiley‐Liss, Inc.
The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology
Authors: Fogolari F. , Brigo A. , Molinari H. 
Published: December 2002

AbstractElectrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. The Poisson–Boltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution. The theoretical basis of the Poisson–Boltzmann equation is reviewed and a wide range of applications is presented, including the computation of the electrostatic potential at the solvent‐accessible molecular surface, the computation of encounter rates between molecules in solution, the computation of the free energy of association and its salt dependence, the study of pKa shifts and the combination with classical molecular mechanics and dynamics. Theoretical results may be used for rationalizing or predicting experimental results, or for suggesting working hypotheses. An ever‐increasing body of successful applications proves that the Poisson–Boltzmann equation is a useful tool for structural biology and complementary to other established experimental and theoretical methodologies. Copyright © 2002 John Wiley & Sons, Ltd.
Essential motions in a fungal lipase with bound substrate, covalently attached inhibitor and product
Authors: Peters Günther H. , Bywater Robert P. 
Published: December 2002

AbstractAs an aid to understanding the influence of dynamic fluctuations during esterolytic catalysis, we follow protein flexibility at three different steps along the catalytic pathway from substrate binding to product clearance via a covalently attached inhibitor, which represents a transition‐state mimic. We have applied a classical approach, using molecular dynamics simulations to monitor protein dynamics in the nanosecond regime. We filter out small amplitude fluctuations and focus on the anharmonic contributions to the overall dynamics. This ‘essential dynamics’ analysis reveals different modes of response along the pathway suggesting that binding, catalysis and product clearance occur along different energy surfaces. Motions in the enzyme with a covalently attached ligand are more complex and occur along several eigenvectors. The magnitudes of the fluctuations in these individual subspaces are significantly smaller than those observed for the substrate and product molecules, indicating that the energy surface is shallow and that a relatively large number of conformational substates are accessible. On the other hand, substrate binding and product release occur at distinct modes of the protein flexibility suggesting that these processes occur along rough energy surfaces with only a few minima. Detailed energetic analyses along the trajectories indicated that in all cases binding is dominated by van der Waals interactions. The carboxylate form of the product is stabilized by a tight hydrogen bond network involving in particular Ser82, which may be a potential cause of product inhibition. Considerations such as these should aid the understanding of mechanisms of substrate, inhibitor or product recognition and could become of importance in the design of new substrates or inhibitors for enzymes. Copyright © 2002 John Wiley & Sons, Ltd.