bluuebunny/crossref_metadata_2025_split huggingface dataset:
Letter: Evolution of surgical treatment for pharyngeal pouch (Br J Surg 2004; 91: 657–664)
Authors: Lerut T 
Published: January 2005

Abstract
The Editors welcome topical correspondence from readers relating to articles published in the Journal. Responses can be sent electronically via the BJS website (www.bjs.co.uk) or by post. All letters will be reviewed and, if approved, appear on the website. A selection of these will be edited and published in the Journal. Letters must be no more than 250 words in length. Letters submitted by post should be typed on A4-sized paper in double spacing and should be accompanied by a disk.
Structural Characterization of Artificial Self‐Assembling Porphyrins That Mimic the Natural Chlorosomal Bacteriochlorophylls c, d, and e
Authors: Balaban Teodor Silviu , Linke‐Schaetzel Myriam , Bhise Anil D. , Vanthuyne Nicolas , Roussel Christian , Anson Christopher E. , Buth Gernot , Eichhöfer Andreas , Foster Keir , Garab Gyözö , Gliemann Hartmut , Goddard Richard , Javorfi Tamas , Powell Annie K. , Rösner Harald , Schimmel Thomas 
Published: January 2005

AbstractWe report two crystal structures of a synthetic porphyrin molecule which was programmed for self‐assembly. The same groups which ensure that bacteriochlorophylls c, d, and e can self‐assemble into the chlorosomal nanorods, the photosynthetic antenna system of some green bacteria, have been engineered into desired positions of the tetrapyrrolic macrocycle. In the case of the 5,15‐meso‐substituted anchoring groups, depending upon the concentration, by using the same crystallization solvents, either a tetragonal or a layered structure of porphyrin stacks were encountered. Surprinsingly, π–π interactions combined with extensive dispersive interactions, which also encompass cyclohexane, one of the crystallization solvents, win over putative hydrogen bonding. We are aware that our compounds differ considerably from the natural bacteriochlorophylls, but based upon our findings, we now question the hydrogen‐bonding network, previously proposed to organize stacks of bacteriochlorophylls. Transmission electron microscopy (TEM), atomic force microscopy (AFM), and small‐angle X‐ray scattering (SAXS) on various isomeric compounds support our challenge of current models for the chlorosomal antenna as these show structures, astonishingly similar to those of chlorosomes.
Carbohydrate Microarrays: An Advanced Technology for Functional Studies of Glycans
Authors: Shin Injae , Park Sungjin , Lee Myung‐ryul 
Published: January 2005

AbstractThe biological significance of glycans in the post‐genomic era requires the development of new technologies to enable functional studies of carbohydrates in a high‐throughput manner. Recently, carbohydrate microarrays have been exploited as an advanced technology for this purpose. Efficient immobilization methods for carbohydrate probes on the proper surface are essential for the successful fabrication of carbohydrate microarrays. Up to date, several techniques have been developed to attach simple or complex carbohydrates to a solid surface. The developed glycan microarrays have been applied for functional glycomics, drug discovery, and diagnosis. In this concept article, we discuss the progress of immobilization methods of carbohydrates on solid surfaces, their potential uses for biological research and biomedical applications, and possible solutions for some remaining challenges to improve this new technology.
Estimating the optimal utilization rates of radiotherapy for hematologic malignancies from a review of the evidence
Authors: Featherstone Carolyn , Delaney Geoff , Jacob Susannah , Barton Michael 
Published: January 2005

AbstractBACKGROUNDThe objective of this study was to estimate the ideal proportion of new patients with leukemia and myeloma who should receive radiotherapy at some time during the course of their illness based on the best evidence.METHODSAvailable evidence of the efficacy of radiotherapy in most clinical situations for leukemia and myeloma was identified through extensive literature reviews and treatment guideline searches. Epidemiologic data concerning the distribution of types, disease stages, and other factors that influence the use of radiotherapy were identified. Decision trees were constructed to merge the evidence‐based recommendations with the epidemiological data to calculate the optimal proportion of patients who should receive radiotherapy according to the best available evidence. Actual radiotherapy utilization rates also were identified.RESULTSThe proportion of patients diagnosed with myeloma in Australia who should receive radiotherapy based on the evidence was 38%. There was wide variation in the proportion of patients who actually received radiotherapy for myeloma from 24% up to 55%. The recommended proportion of patients diagnosed with myeloma in Australia who, according to the best available evidence, should receive at least a single course of radiotherapy was 38%. The proportion of patients diagnosed in Australia with leukemia who should receive radiotherapy at some point in their management, according to the best available evidence, was calculated at 4%, which corresponded with actual practice.CONCLUSIONSFurther research will be required to determine why more patients who are diagnosed with myeloma are not treated with radiotherapy. Cancer 2005. © 2004 American Cancer Society.
Thermal properties of lightweight‐framed construction components at elevated temperatures
Authors: Bénichou Noureddine , Sultan Mohamed A. 
Published: January 2005

AbstractFire resistance behaviour of lightweight‐framed assemblies is determined by defining the thermal and structural performances of the assembly when exposed to fire. To adequately model thermal behaviour in a lightweight wood‐framed assembly, thermal properties of the components of the assembly at elevated temperatures must be well defined. This paper presents results of measurements of thermal properties at elevated temperatures of construction materials commonly used to build lightweight wood‐framed assemblies that were conducted at the National Research Council of Canada since 1990. The test results, in graphical form, are given as a function of temperature for thermal conductivity, specific heat, mass loss and thermal expansion/contraction for wood, gypsum and insulation. In addition, the effects of temperature on the thermal conductivity, specific heat, mass loss and thermal expansion/contraction of these materials are discussed. Finally, in addition to providing a resource of information, this paper also identifies the additional thermal property tests required to complete the matrix of information. Copyright © 2005 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.
Orbital topology. I. A basic topological model for chemical systems, an orbital mapping technique, and analyses of model, thermal electrocyclic reactions
Authors: Kelsey Donald R. 
Published: January 2005

AbstractA topological model which provides a unifying framework for chemical reactions and molecular structure is proposed. Such basic concepts as overlap, orthogonality, reaction continuity, reaction reversibility, and orbital correspondence are incorporated into the model in a logical fashion. A chemical reaction pathway is regarded as a function that transforms a reactant topological space into its equivalent product space. The unique character usually ascribed to reactants, products, and their wavefunctions is superfluous. The model also allows considerable approximation of the wavefunctions and the reaction pathway without affecting the overall result. A simple orbital mapping technique consistent with the model which traces the transformation of orbitals using intermolecular overlaps of the orbitals is also proposed. The suitability of a given pathway (“allowed” or “forbidden”) can be deduced explicitly without invoking symmetry (or other) rules and without resorting to detailed calculation of reaction energy surfaces. The validity of the mapping procedure has been confirmed by several thermal electrocyclic reactions: the ring‐opening isomerizations of substituted cyclopropyl cations, cyclopropyl anion, cyclopropanone, cyclobutene, benzocyclobutene, Dewar benzenes, and 1,3‐cyclohexadiene. Orbital mapping with EHT and CNDO/2 MOs correctly predicts the reaction stereochemistry (conrotatory or disrotatory) in every case.
Orbital topology. II. Orbital mapping of unsymmetrical molecules. A survey of the thermal isomerizations of dewar isomers of isoelectronically substituted benzenes, cyclopentadienes, and cyclopentadienyl ions
Authors: Kelsey Donald R. 
Published: January 2005

AbstractOrbital mapping analysis, based on EHT and CNDO/2 semiempirical molecular orbitals, has been used to survey the thermal, disrotatory, ring‐opening isomerizations of bicyclo[2.2.0]hexa‐2,5‐dienes (Dewar benzenes), bicyclo[2.1.0]pent‐2‐enes, and bicyclo[2.1.0]pent‐2‐en‐5‐yl ions to their planar isomers. Results indicate that isoelectronic substitution (CH replaced by C−, O+, N, NH+, etc.) in the molecular framework may favor allowed thermal reactions in some cases, in contrast to the disallowed reaction predicted for the parent hydrocarbons.
A simplex optimized INDO calculation of 13C chemical shifts in hydrocarbons
Authors: Chesnut D. B. , Whitehurst F. W. 
Published: January 2005

AbstractThe variable‐size simplex optimization method is used to reparametrize the I + A and β parameters of an INDO approximation to the perturbed Hartree–Fock calculation of 13C chemical shifts in hydrocarbons. The absolute shifts for 39 nuclei in a set of molecules containing up to four carbons are reproduced within a standard error of 9.9 ppm for an unconstrained optimization and to a standard error of 10.0 ppm for an optimization constrained to yield gross atomic charges in agreement with double‐zeta ab initio calculations.
On the gearing of methyl groups in hexamethylbenzene
Authors: Iroff Linda D. 
Published: January 2005

AbstractEmpirical force field calculations were performed on hexamethylbenzene to elucidate the internal motions of the methyl groups. When the benzene ring is constrained to be planar (as in solid‐phase studies), the methyl groups undergo a geared, disrotatory motion. When this constraint is relaxed, results are force field dependent. Calculated barriers are in good agreement with experimentally determined values.
Isomeric structures of protonated ozone: A theoretical study
Authors: Kausch Michael , Von Ragué Schleyer Paul 
Published: January 2005

AbstractAb initio molecular orbital calculations have been used to determine the structure of protonated ozone. Four stable minima were found on the O3H+ singlet potential energy surface. Three forms correspond to ozone protonated at the central oxygen (C2v) or at the terminal oxygen (two Cs isomers, E and Z). The fourth isomer (Cs) is a derivative of trioxirane. The most stable structure is the planar E form I. The proton affinity of ozone (to give I) is given as 123.6 kcal/mole (MP2/6‐31G*//4‐31G). The energy difference between I and protonated trioxirane VI is greater than that between ozone and trioxirane.
The application of molecular mechanics to the structures of carbohydrates
Authors: Jeffrey G. A. , Taylor R. 
Published: January 2005

AbstractA study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2‐methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI‐CARB, a version of MMI with changes in some of the equilibrium CO bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the CCOH torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for CC and CO bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.
Ab initio studies of structural features not easily amenable to experiment. 30. Conformational analysis and molecular structures of propanal and butanal
Authors: Klimkowski V. J. , Van Nuffel P. , Van Den Enden L. , Van Alsenoy C. , Geise H. J. , Scarsdale J. N. , Schäfer Lothar 
Published: January 2005

AbstractThe geometries of several conformations of propanal and butanal have been refined by geometrically unconstrained ab initio gradient relaxation on the 4‐21G level. Both compounds possess energy minima at OCCC torsional angles of 0° and in the 120° region, and energy maxima in the 70° region and at 180°. The structure of the aldehyde functional group is found to be relatively invariant both when different systems or when different conformations of the same system are compared. Conformationally dependent geometrical trends in propanal and butanal are discussed and found to be subtle yet noticeable.
An approach to computing electrostatic charges for molecules
Authors: Singh U. Chandra , Kollman Peter A. 
Published: January 2005

AbstractWe present an approach for deriving net atomic charges from ab initio quantum mechanical calculations using a least squares fit of the quantum mechanically calculated electrostatic potential to that of the partial charge model. Our computational approach is similar to those presented by Momany [J. Phys. Chem., 82, 592 (1978)], Smit, Derissen, and van Duijneveldt [Mol. Phys., 37, 521 (1979)], and Cox and Williams [J. Comput. Chem., 2, 304 (1981)], but differs in the approach to choosing the positions for evaluating the potential. In this article, we present applications to the molecules H2O, CH3OH, (CH3)2O, H2CO, NH3, (CH3O)2PO, deoxyribose, ribose, adenine, 9‐CH3 adenine, thymine, 1‐CH3 thymine, guanine, 9‐CH3 guanine, cytosine, 1‐CH3 cytosine, uracil, and 1‐CH3 uracil. We also address the question of inclusion of “lone pairs,” their location and charge.
Compact contracted Gaussian‐type basis sets for halogen atoms. Basis‐set superposition effects on molecular properties
Authors: Andzelm Jan , Kłobukowski Mariusz , Radzio‐Andzelm Elżbieta 
Published: January 2005

AbstractCompact, contracted Gaussian basis sets for halogen atoms are generated and tested in ab initio molecular calculations. These basis sets have similar structure to that of Huzinaga and co‐workers' (HTS) sets; however, they give both better atomic total energies and better properties of atomic valence orbitals. These sets, after splitting of valence orbitals and augmenting with polarization functions, provide molecular results that agree well with those given by extended calculations. Basis set superposition error (BSSE) is calculated using the counterpoise method. BSSE has only slight influence on calculated equilibrium geometry, shape of potential curve, and electric properties (dipole and quadrupole moments) of molecules. However, atomization energies may be significantly changed by the BSSE.
Ab initio studies of structural features not easily amenable to experiment. 32. Conformational analysis and molecular structures of isopropyl and ethyl formate and comparison with spectroscopic data
Authors: Klimkowski V. J. , Schäfer Lothar , Bohn Robert K. 
Published: January 2005

AbstractThe geometries of several conformations of ethyl and isopropyl formate were optimized by the ab initio gradient method on the 4‐21G level. The calculations are in agreemnt with the existence of two conformers of ethyl formate of nearly equal energy. The COCC torsional angle in one is anti (180°) and in the other is gauche (about 80°). The equilibrium configuration of the isopropyl group in the formate is found to be unsymmetrical, with a COCH torsional angle of about 40°. A second minimum of torsional energy, at COCH = 180°, is 1.2 kcal/mol less stable than the unsymmetrical form. The calculations demonstrate the tranferability of internal rotational‐potential parameters and of conformationally dependent geometrical trends between ethyl and isopropyl formate. There is good agreement between the calculated results and empirical potential‐energy functions and rotational constants determined from microwave spectroscopy.
Conformational analysis of allylamine. An ab initio molecular orbital study
Authors: Kao James , Seeman Jeffrey I. 
Published: January 2005

AbstractThe conformational characteristics of allylamine were investigated by the ab initio STO‐3G basis set. The results indicate that the molecule exists in a number of stable conformations through rotations about the CCNH and CCCN bonds. The TE (trans‐CCNLP, LP representing lone‐pair electrons, and eclipsed‐CCCH) is the most stable, while TC (trans‐CCNLP and cis‐CCCN), GE (gauche‐CCNLP and eclipsed‐CCCH), G′C(gauche′‐CCNLP and cis‐CCCN), and G′E (gauche′‐CCNLP and eclipsed‐CCCH) conformations are less stable, respectively, by 0.41, 0.67, 0.92, and 1.14 kcal mol−1. These results are in general consistent with previous experimental results. Rationale for the conformational characteristics and order of stabilities are explored.
Comparison of the RHF, NDDO, and MOM molecular one‐electron expectation values calculated using minimum basis sets with Slater, Burns, Clementi, and BLMO exponents
Authors: Zeiss G. D. , Whitehead M. A. 
Published: January 2005

AbstractThe effect of different exponents, Slater, Burns, Clementi, and Best Limited Molecular Orbital (BLMO) on the approximate one‐electron property expectation values from minimum basis‐set calculations is reported for Roothaan–Hartree–Fock (RHF), neglect of diatomic differential overlap (NDDO), and maximum overlap method (MOM) calculations on FH, CO, and LiH.
Combination of MOMM and VEH methods to calculate electronic properties of polymers
Authors: Burke L. A. , Kao J. , Lilly A. C. 
Published: January 2005

AbstractA Molecular‐Orbital‐Based Molecular Mechanics method (MOMM) has been employed to calculate the structures of cyclopentadiene, pyrrole, furan, thiophene, dibenzocyclopentadiene (fluorene), dibenzopyrrole, dibenzofuran, and dibenzothiophene. The dimer structures of the above compounds have also been calculated using the same method to derive the unit cells of polycyclopentadiene, polypyrrole, polyfuran, polythiophene, polydibenzocyclopentadiene, polydibenzopyrrole, polydibenzofuran, and polydibenzothiophene. The band structures, densities of states, ionization potentials, band gaps, reduction potentials, and oxidation potentials of these polymers then have been calculated by using the Valence Effective Hamiltonian method (VEH). The structural effects on electronic properties are discussed.
Comparison of the use of the MNDO and MINDO/3 methods with ab initio methods to study tautomerism in histamine, 2‐ and 4‐methylhistamine
Authors: Topiol Sid 
Published: January 2005

AbstractThe semiempirical MNDO and MINDO/3 methods are used to study the various tautomeric forms of histamine, 2‐methylhistamine, and 4‐methylhistamine. Comparisons of the optimized structures and tautomerization energies are made with values obtained from ab initio Hartree‐Fock calculations using the 3‐21G and STO‐3G basis sets. Based on these results and previous comparisons of STO‐3G results with x‐ray structures, the present results indicate that while there are some differences in the values of the structural parameters, the changes in structure upon tautomerization and/or protonation are very similar. Further analysis of the MNDO and MINDO/3 structures by means of their utilization in 3‐21G and STO‐3G calculations indicates that either of these semiempirical methods provides reliable values for the structural parameters. Both methods give good qualitative agreement with the ab initio calculations for the relative energies of the various tautomers in the three compounds. In these studies the MNDO method appears to give better quantitative agreement with the 3‐21G and STO‐3G results than the MINDO/3 method.
Theoretical study on the mechanism of the thermal decarboxylation of acrylic and benzoic acids. Models for aqueous solution
Authors: Ruelle P. 
Published: January 2005

AbstractThe mechanism of acrylic and benzoic acid decarboxylation in aqueous solution has been investigated by ab initio methods using the STO‐3G and 3‐21G basis sets. In those reactions, the solvent is represented successively by one and two water molecules. Their active participation as a proton relay in the chemical process is demonstrated by the large decrease in the activation energy with respect to the reaction studied in the absence of water. In the absence of any intermediate found along the reaction pathway, the proposed mechanism is the concerted process; the free acid being the species that undergoes decarboxylation via a pseudounimolecular mechanism by interaction with a chain of water molecules. At the transition state, the carboxylic hydrogen transfer to one water molecule, the reorganization of the chain of water molecules through which the proton is transferred and the cleavage of the CC bond are much more advanced than the proton transfer from the last water molecule to the α‐carbon atom of the carboxyl group.
An algorithm for geometry optimization without analytical gradients
Authors: Baker Jon 
Published: January 2005

AbstractA numerical algorithm for locating both minima and transition states designed for use in the ab initio program package GAUSSIAN 82 is presented. It is based on the RFO method of Simons and coworkers and is effectively the numerical version of an analytical algorithm (OPT = EF) previously published in this journal. The algorithm is designed to make maximum use of external second derivative information obtained from prior optimizations at lower levels of theory. It can be used with any wave function for which an energy can be calculated and is about two to three times faster than the default DFP algorithm (OPT = FP) supplied with GAUSSIAN 82.
Fast vector‐scalar‐multiply‐and‐add subroutines for VAX computers
Authors: Cisneros Gerardo , Bunge Carlos F. , Roothaan C. C. J. 
Published: January 2005

AbstractWe describe a set of simple VAX assembly language, Fortran‐callable subroutines for performing vectorscalar‐multiply‐and‐add operations which can increase processing speed by more than 10%. The routines are simple enough that they may be translated readily for use on other machines.
Molecular graphs as topological objects in space
Authors: Simon Jonathan 
Published: January 2005

AbstractStereochemistry deals primarily with distinctions based on rigid geometry, e.g., bond angles and lengths. But some chemical species have molecular graphs (such as knots, catenanes, and nonplanar graphs K5 and K3.3) that reside in space in a topologically nontrivial way. For such molecules there is hope of using topological methods to gain chemical information. Viewing a molecular graph as a topological object in space makes it unrealistically flexible; but if one proves that a certain graph is “topologically chiral” or that two graphs are “topological diastereomers,” then one has ruled out interconversion under any physical conditions for which the molecular graph still makes sense. In this paper, we consider several kinds of topological questions one might ask about graphs in space, methology and results available, and specific topological properties of various molecules.