bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extensive theoretical studies of the hydrogen-bonded complexes (H2O)2, (H2O)2H+, (HF)2, (HF)2H+, F2H−, and (NH3)2
Authors: Frisch Michael J. , Del Bene Janet E. , Binkley J. Stephen , Schaefer Henry F. 
Published: July 2002

The structures and binding energies of the complexes (H2O)2, (H2O)2H+, (HF)2, (HF)2H+, F2H−, and (NH3)2 have been examined using much higher levels of theory than has been previously applied to these systems. These methods including large basis sets and full optimization of structures with the effects of electron correlation included, are known to give single bond energies to an accuracy of about 2 kcal mol−1 and are found in this study to give excellent agreement with the extensive experimental data available for the hydrogen fluoride and water dimers. The Cs open
form of ammonia dimer remains a very shallow minimum energy structure at these levels, in agreement with previous theoretical results but seemingly in disagreement with experiment. The theoretical enthalpy of association of H5O+2 is found to be −35.0 kcal mol−1, in slight disagreement with the most recent experimental results, but in accord with earlier ones, which suggests that these experiments should be reexamined. The enthalpy of association of H2F+ is predicted to be −33.5 kcal mol−1, and that of F− with HF to be −46.4 kcal mol−1. A study of the effects of basis set expansion on the structure of the water dimer shows that the structure is much more sensitive to basis set at the Hartree–Fock level than when correlation is included. A valence triple-zeta basis plus two sets of first polarization functions and one set of diffuse functions appears to be necessary to approach the Hartree–Fock limiting structure. Counterpoise estimates of the effects of basis set deficiencies on the structure and binding energy of this complex are shown to be misleading. Examination of the complexes (HF)2, (H2O)2, (NH3)2, (H2O)2H+, (HF)2H+, and F2H− at the MP4/6-311++G(3df ,3pd)//MP2/6-311++G(2d,2p) level of theory indicates that previous studies using fourth order perturbation theory with some smaller basis sets and Hartree–Fock optimized structures are likely to be reliable, although part of the agreement reflects a cancellation of error. HF/6-31+G(d) estimates of zero-point vibrational energy contributions to association energies are found to be satisfactory for asymmetric complexes, but can both over and underestimate the contribution of this term for symmetrically bound complexes.
Gerade Rydberg states and n
s 3Σ+u(1u,0−u) photoionization spectra of the rare gas dimers (n=2–6)
Authors: Killeen K. P. , Eden J. G. 
Published: July 2002

Transient absorption spectra of rare gas dimer Rydberg transitions in the ultraviolet, visible, and near infrared (220≤λ≤900 nm) spectral regions have been observed in electron beam excited rare gases. The most prominent molecular bands for He2, Ne2, Ar2, Kr2, and Xe2 are assigned to the mp 3Πg←ns 3Σ+u (He:n=2, 3≤m≤10; Ne:n=3, 4≤m≤10; Ar:n=4, 5≤m≤15; Kr:n=5, 6≤m≤16; Xe:n=6, 8≤m≤11) Rydberg series of the dimer. Adiabatic ionization potentials, relative to the ns 3Σ+u state, are determined by extrapolation of the series to their limits (m→∞) to be 34 361.4±30 cm−1 (4.260±0.004 eV) for He2, 34 396.3±25 cm−1 (4.265±0.003 eV) for Ne2, 29 351.9±15 cm−1 (3.639±0.002 eV) for Ar2, 28 428.5±10 cm−1 (3.525±0.001 eV) for Kr2, and 26 664.5±250 cm−1 (3.306±0.031 eV) for Xe2. Absorption bands which are ascribed to m′p 3Σ+g←ns 3Σ+u Rydberg series of Ne2(m′=4,6,8), Ar2(5≤m′≤10), Kr2(6≤m′≤10), and Xe2(m′=8,9) are also reported, and the ns 3Σ+u ionization potentials found to be identical to the respective values quoted above. All of the observed molecular Rydberg states have an A 2Σ+1/2u ion core. The lowest vibrational quanta (ΔG1/2) for the ns 3Σ+u states are determined from vibronic structure in the Rydberg transitions to be 1723 cm−1 for He2, 539 cm−1 for Ne2, 302 cm−1 for Ar2, 172 cm−1 for Kr2, and 135 cm−1 for Xe2, and are consistent with previously reported values. The instability of the ns 3Σ+u metastable state with respect to the dimer ion core potential [D0(A 2Σ+1/2u)−D0(ns
3Σ+u)] is calculated to be 0.508±0.004 eV for He2, 0.681±0.003 eV for Ne2, 0.572±0.002 eV for Ar2, 0.560±0.001 eV for Kr2, and 0.52±0.03 eV for Xe2. Using these values and those reported in the literature for the dissociation energy of the dimer ion A 2Σ+1/2u state, D0(ns 3Σ+u) is estimated (Ne2: 0.67±0.07 eV; Ar2: 0.76±0.02 eV; Kr2: 0.62±0.02 eV; Xe2: 0.52±0.03 eV). By comparing energy level spacings, quantum defects, and absorption oscillator strengths for transitions between molecular or atomic states, the mp 3Πg Rydberg levels appear to correlate with the mp[3/2]2+1S0 atomic asymptotes. An important aspect of the experimental approach is that the diatomic excited states are studied in the vicinity of Re rather than at the van der Waals (ground state) minimum. Chemical forces (as opposed to ion-induced dipole interactions) dominate at small R and the resulting spectra are largely free of congestion arising from the perturbations and avoided curve crossings that are prevalent at large R. Therefore, insight can be obtained into the structure and behavior of molecular Rydberg states in the region near the first ionization limit A 2Σ+1/2u[1(1/2)u].
Radiative lifetimes of van der Waals heteroclusters
Authors: Shalev Eli , Ben-Horin Narda , Jortner Joshua 
Published: July 2002

In this paper we advance and apply a molecular theory of pure radiative lifetimes τr of (aromatic molecule)⋅(rare gas)n heteroclusters. The modification of τr in the heterocluster, relative to the bare molecule value, originates from intermolecular interactions between molecular multicenter transition monopoles, which are described by π electron approximation, and the rare-gas atom transition dipoles, which are specified in terms of the static atomic polarizability α. The calculated changes of τr of 9,10 dichloroanthracene⋅A1 (A=Ar, Kr, Xe) heterodimers are in good agreement with experiment; the theory accounting for the nearly linear dependence of the change of τr on α.
Calculations of the radiative lifetimes of 9,10 dichloroanthracene⋅Arn (n=1–34) heteroclusters were performed using structural information from potential optimization for small (n=1–3) heteroclusters, static structural data for small and medium-sized (n=1–8) heteroclusters, and (constant energy) finite-temperature molecular dynamics simulations for medium-sized and large (n=5–34) heteroclusters. The structural sensitivity of τr is manifested by different values of τr for distinct structural isomers, by the nonmonotonous size effects on τr with increasing n, and by pronounced decrease of τr with increasing temperature. For medium-sized clusters (n=5–18), the temperature dependence of τr originates from the enhancement of atomic motion on both sides of the aromatic microsurface and the occupation of the peripheral region, while for large clusters (n≂34) two layer–one layer isomerization processes with increasing temperature result in dramatic changes of τr. Satisfactory overall agreement between theory and experiment for 9,10 dichloroanthracene⋅Arn n=1–34 heteroclusters was accomplished.
The dominating 9,10 dichloroanthracene⋅Arn structures for n=1–18, which yield agreement between theory and experimental for τr, correspond to nearly equal distribution of the rare gases on both sides of the aromatic microsurfaces at T≤20 K, while large n=34 two-layered structures in the temperature domain 22 K≤T≤40 K account for the experimental τr result. τr serves as a useful spectroscopic probe for the interrogation of the structure and isomerization dynamics in heteroclusters.
Electronic energy transfer in anisotropic systems. III. Monte Carlo simulations of energy migration in membranes
Authors: Johansson Lennart B.-Å. , Engström Sven , Lindberg Maria 
Published: July 2002

Electronic energy migration in membrane systems has been studied by means of Monte Carlo (MC) simulations according to an algorithm described previously [S. Engström, M. Lindberg, and L. B.-Å. Johansson, Chem. Phys. 89, 204 (1988)]. In the systems investigated, the interacting donor molecules are randomly localized in mono-, bi-, and multilayers and are either oriented with their transition dipoles isotropically or parallel to the layers. The mean-square displacement [〈R(t)2〉] of the excitation and experimental observables in terms of different fluorescence depolarizations were determined. All results are relevant for the ‘‘slow case,’’ which means that translational and rotational motions of the donors are much slower as compared to the rate of fluorescence. A two-particle approximation for calculating the excitation probability of the initially excited molecule [denoted by Gs(t) ] and the fluorescence depolarizations in two-dimensional systems has been published previously [J. Baumann and M. D. Fayer, J. Chem. Phys. 85, 4087 (1986)]. By using the MC algorithm, we have in this work tested this model extensively.
The excitation probability Gs(t) is found to be in excellent agreement with the MC simulations for all of the systems studied. For isotropically oriented donor molecules in multilamellar systems, the simulations show that Gs(t) is very well approximated by that of a monolayer at distances of d≥3 R0 between the layers. At distances of d≤0.5 R0, the function Gs(t) is equal to that of a three-dimensional solution. For the in-plane oriented dipoles in a multilayer system, Gs(t) is very well approximated by that for a single bilayer at d&gt;2 R0. In general, the depolarizations obtained by the two-particle model and MC simulations differ depending on the particular orientational distribution and the experimental geometry. To obtain a physically correct behavior of the fluorescence anisotropy at long times (i.e., the limiting anisotropy) is not possible within a two-particle approach. We instead propose a phenomenological model for calculating the fluorescence anisotropy which is a function of Gs(t) obtained within the two-particle approximation. This model gives a remarkably good agreement with the MC simulations and has the correct limiting anisotropy. The MC simulations of energy migration show that 〈R(t)2〉 is about twice as large for in-plane oriented donors in mono- and bilayers, as compared to the case of isotropically oriented transition dipoles. For multilayer systems consisting of layers separated by d=R0, we find that 〈R(t)2〉 is only slightly larger for the in-plane oriented transition dipoles as compared to the isotropic orientational distribution.
Quantitative determination of molecular structure in multilayered thin films of biaxial and lower symmetry from photon spectroscopies. I. Reflection infrared vibrational spectroscopy
Authors: Parikh Atul N. , Allara David L. 
Published: July 2002

A semitheoretical formalism based on classical electromagnetic wave theory has been developed for application to the quantitative treatment of reflection spectra from multilayered anisotropic films on both metallic and nonmetallic substrates. Both internal and external reflection experiments as well as transmission can be handled. The theory is valid for all wavelengths and is appropriate, therefore, for such experiments as x-ray reflectivity, uv–visible spectroscopic ellipsometry, and infrared reflection spectroscopy. Further, the theory is applicable to multilayered film structures of variable number of layers, each with any degree of anisotropy up to and including full biaxial symmetry. The reflectivities (and transmissivities) are obtained at each frequency by solving the wave propagation equations using a rigorous 4×4 transfer matrix method developed by Yeh in which the optical functions of each medium are described in the form of second rank (3×3) tensors. In order to obtain optical tensors for materials not readily available in single crystal form, a method has been developed to evaluate tensor elements from the complex scalar optical functions (n̂) obtained from the isotropic material with the limitations that the molecular excitations are well characterized and obey photon–dipole selection rules.
This method is intended primarily for infrared vibrational spectroscopy and involves quantitative decomposition of the isotropic imaginary optical function (k) spectrum into a sum of contributions from fundamental modes, the assignment of a direction in molecular coordinates to the transition dipole matrix elements for each mode, the appropriate scaling of each k vector component in surface coordinates according to a selected surface orientation of the molecule to give a diagonal im(n̂) tensor, and the calculation of the real(n̂) spectrum tensor elements by the Kramers–Kronig transformation. Tensors for other surface orientations are generated by an appropriate rotation matrix operation. To test the viability of this approach, three sets of experimentally derived infrared spectra of oriented monolayer assemblies on quite distinctively different substrates were chosen for simulation: (1) n-alkanethiols self- assembled onto gold, (2) n-alkanoic acid salt Langmuir–Blodgett (LB) monolayers on carbon, and (3) n-alkanoic acid salt LB monolayers on silica glass. The formalism developed was used to simulate the spectral response and to derive structural features of the monolayers. Good agreement was found where comparisons with independent studies could be made and, in general, the method appears quite useful for structural studies of highly organized thin films.
Shear viscosity for fluids of hard ellipsoids: A kinetic theory and molecular dynamics study
Authors: Tang Shuang , Evans Glenn T. , Mason Carl P. , Allen Michael P. 
Published: July 2002

The frequency-dependent shear viscosity η(ω) and the shear-orientation coupling parameter R are calculated for fluids of hard prolate ellipsoids of revolution, using kinetic theory and molecular dynamics. Two effects which contribute to the shear viscosity are considered. First, the D∞h particle symmetry influences both the spectrum of the collision operator and the multi-Lorentzian decay of η(ω). These multiple decays are most important at low densities for elongated particles. Second, coupling between the stress tensor and the collective molecular orientation leads to a minimum in η(ω) between its zero-frequency limit η and its infinite-frequency plateau value η∞. At densities approaching the transition to a nematic phase, the zero-frequency shear viscosity is predicted to be dominated by its infinite-frequency plateau value, i.e., η/η∞∼1. Molecular dynamics simulations, extended to longer times than those previously reported, confirm the existence of the dip in η(ω) and the importance of stress-orientation coupling in determining the value of η. Discrepancies previously thought to exist between simulation and theory are attributed to this coupling between the stress and slow collective reorientation; we now obtain good agreement between simulation and theory at low and moderate densities. The kinetic theory predicts the position of the dip quite well, but underestimates its magnitude for elongated particles at medium and high densities.
The theory also predicts a weak density dependence of the shear-orientation coupling parameter R, and a decrease in this parameter with increasing elongation, whereas the simulations show a steady increase in R with both density and elongation. Moreover, the ratio η/η∞ falls below unity, rather than approaching unity, as the density increases, in several of the cases studied. The Stokes–Einstein relation and the Stokes–Einstein–Debye relation are investigated, and a consistent picture emerges of a crossover between a regime in which kinetic theory is accurate (at low density and elongation) to one in which a hydrodynamic description with slip boundary conditions applies (at high density and elongation). The change to hydrodynamic behavior is more apparent for the rotational motion than for the translational motion.
A classification of tasks in bioinformatics
Authors: Stevens Robert , Goble Carole , Baker Patricia , Brass Andy 
Published: July 2002

Abstract
Motivation: This paper reports on a survey of bioinformatics tasks currently undertaken by working biologists. The aim was to find the range of tasks that need to be supported and the components needed to do this in a general query system. This enabled a set of evaluation criteria to be used to assess both the biology and mechanical nature of general query systems.
Results: A classification of the biological content of the tasks gathered offers a checklist for those tasks (and their specialisations) that should be offered in a general bioinformatics query system. This semantic analysis was contrasted with a syntactic analysis that revealed the small number of components required to describe all bioinformatics questions. Both the range of biological tasks and syntactic task components can be seen to provide a set of bioinformatics requirements for general query systems. These requirements were used to evaluate two bioinformatics query systems.
Contact: robert.stevens@cs.man.ac.uk
Supplementary information: The questionnaire, responses and their summaries may be found at http://img.cs.man.ac.uk/tambis/questionnaire/bio-queries.html
* To whom correspondence should be addressed.
Analysis of mRNA expression and protein abundance data: an
approach for the comparison of the enrichment of features in the
cellular population of proteins and transcripts
Authors: Greenbaum Dov , Jansen Ronald , Gerstein Mark 
Published: July 2002

Abstract
Motivation: Protein abundance is related to mRNA expression through many different cellular processes. Up to now, there have been conflicting results on how correlated the levels of these two quantities are. Given that expression and abundance data are significantly more complex and noisy than the underlying genomic sequence information, it is reasonable to simplify and average them in terms of broad proteomic categories and features (e.g. functions or secondary structures), for understanding their relationship. Furthermore, it will be essential to integrate, within a common framework, the results of many varied experiments by different investigators. This will allow one to survey the characteristics of highly expressed genes and proteins.
Results: To this end, we outline a formalism for merging and scaling many different gene expression and protein abundance data sets into a comprehensive reference set, and we develop an approach for analyzing this in terms of broad categories, such as composition, function, structure and localization. As the various experiments are not always done using the same set of genes, sampling bias becomes a central issue, and our formalism is designed to explicitly show this and correct for it. We apply our formalism to the currently available gene expression and protein abundance data for yeast. Overall, we found substantial agreement between gene expression and protein abundance, in terms of the enrichment of structural and functional categories. This agreement, which was considerably greater than the simple correlation between these quantities for individual genes, reflects the way broad categories collect many individual measurements into simple, robust averages. In particular, we found that in comparison to the population of genes in the yeast genome, the cellular populations of transcripts and proteins (weighted by their respective abundances, the transcriptome and what we dub the translatome) were both enriched in: (i) the small amino acids Val, Gly, and Ala; (ii) low molecular weight proteins; (iii) helices and sheets relative to coils; (iv) cytoplasmic proteins relative to nuclear ones; and (v) proteins involved in ‘protein synthesis,’ ‘cell structure,’ and ‘energy production.’
Supplementary information: http://genecensus.org/expression/translatome
Contact: mark.gerstein@yale.edu
* To whom correspondence should be addressed.
† These authors contributed equally to this work.
An NMR and Mutational Study of the Pseudoknot Within the Gene 32 mRNA of Bacteriophage T2: Insights into a Family of Structurally Related RNA Pseudoknots
Authors: Du Zhihua , Hoffman David W. 
Published: July 2002

Abstract
NMR methods were used to investigate a series of mutants of the pseudoknot within the gene 32messenger RNA of bacteriophage T2, for the purpose of investigating the range of sequences, stem and loop lengths that can form a similar pseudoknot structure. This information is of particular relevance since the T2 pseudoknot has been considered a representative of a large family of RNA pseudoknots related by a common structural motif, previously referred to as ‘common pseudoknot motif 1’ or CPK1. In the work presented here, a mutated sequence with the potential to form a pseudoknot with a 6 bp stem2 was shown to adopt a pseudoknot structure similar to that of the wild-type sequence. This result is significant in that it demonstrates that pseudoknots with 6 bp in stem2 and a single nucleotide in loopl are indeed feasible. Mutated sequences with the potential to form pseudoknots with either 5 or 8 bp in stem2 yielded NMR spectra that could not confirm the formation of a pseudoknot structure. Replacing the adenosine nucleotide in loopl of the wild-type pseudoknot with any one of G, C or U did not significantly alter the pseudoknot structure. Taken together, the results of this study provide support for the existence of a family of similarly structured pseudoknots with two coaxially stacked stems, either 6 or 7 bp in stem2, and a single nucleotide in loop1. This family includes many of the pseudo-knots predicted to occur downstream of the frameshift or readthrough sites in a significant number of viral RNAs.
Human Paralogs of KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms
Authors: Crosier Moira , Viggiano Luigi , Guy Jane , Misceo Doriana , Stones Robert , Wei Wenbin , Hearn Tom , Ventura Mario , Archidiacono Nicoletta , Rocchi Mariano , Jackson Michael S. 
Published: July 2002

KIAA0187 is a gene of unknown function that maps to 10q11 and has been subject to recent duplication events. Here we analyze 18 human paralogs of this gene and show that paralogs of exons 14–23 were formed through satellite-associated pericentromeric-directed duplication, whereas paralogs of exons 1–9 were created via chromosome-specific satellite-independent duplications. In silico, Northern, and RT-PCR analyses indicate that nine paralogs are transcribed, including four in which KIAA0187 exons are spliced onto novel sequences. Despite this, no new genes appear to have been created by these events. The chromosome 10 paralogs map to 10q11, 10q22, 10q23.1, and 10q23.3, forming part of a complex family of chromosome-specific repeats that includes GLUD1,Cathepsin L, and KIAA1099 pseudogenes. Phylogenetic analyses and comparative FISH indicates that the 10q23.1 and 10q23.3 repeats were created in 10q11 and relocated by a paracentric inversion 13 to 27 Myr ago. Furthermore, the most recent duplications, involving the KIAA1099 pseudogenes, have largely been confined to 10q11. These results indicate a simple model for the evolution of this repeat family, involving multiple rounds of centromere-proximal duplication and dispersal through intrachromosomal rearrangement. However, more complex events must be invoked to account for high sequence identity between some paralogs.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AJ298152 through AJ298168.]