bluuebunny/crossref_metadata_2025 huggingface dataset:
Arsenobetaine and arsenocholine: Two marine arsenic compounds without embryotoxity
Authors: Irvin T Rick , Irgolic Kurt J
Published: January 2005

The embryotoxicity of carboxymethyl(trimethyl)arsonium bromide [arsenobetaine,(CH3)3As+CH2COO−] and of 2‐hydroxyethyl(trimethyl)arsonium bromide [arsenobetaine, (CH3)3As+CH2CH2OHBr] was explored. Sprague‐Dawley rat embryos with intact yolk sacs were removed on day 11 of gestation and grown in a culture medium for 24 h in the presence and absence of rat liver (S‐9) homogenate. Solutions of arsenobetaine or arsenocholine in dimethyl sulfoxide [DMSO, (CH3)2SO] (0.03 cm3) were added to the media to achieve concentrations of 20 m̈g arsenic compound per cm3 of medium. After 24 h the circulation and heart beat were monitored (indicator of embryolethality); in addition the crown‐to‐rump lengths were measured and the neural structures (somites) and limb buds observed (indicator of embryotoxicity). No evidence for embryotoxicity or embryolethality was found in the absence or the presence of S‐9. These results indicate that arsenobetaine, the most common arsenic compound found in seafood at concentrations from several micrograms to several hundred micrograms arsenic per gram, lacks subacute and acute prenatal toxicity.
119Sn Mössbauer studies of bis[cysteinato(1−)‐S]‐ and bis[penicillaminato(1−)‐S]‐diorganotin(IV) species in the crystalline state and in frozen aqueous solution
Authors: Barbieri Renato , Silvestri Arturo , Huber Friedo
Published: January 2005

The bonding and the configuration of the tin environment in the title compounds {R2Sn[SCH2CH(NH3+)COO−]2 and R2Sn[SC(CH3)2CH(NH3+)COO−]2, indicated in the following as R2Sn(cysH)2 and R2Sn(penH)2 respectively} has been investigated through the determination of the Mössbauer‐Zeeman spectra of Ph2Sn(cysH)2 and Ph2Sn(penH)2 in the solid state, and through conventional Mössbauer spectroscopy of Me2Sn(penH)2 in the solid state as well as of Me2Sn(cysH)2 and Me2Sn(penH)2 in aqueous solution (frozen). The treatment of the data by the pointcharge model approach suggested the general occurrence of a tetrahedral C2SnS2 core. In aqueous Hepes buffer, a tertiary amino nitrogen atom has been observed to coordinate tin in Me2Sn(cysH)2 and Me2Sn(penH)2, with formation of trigonal bipyramidal tin environments. The latter solutions undergo slow decomposition reactions at room temperature. From (Me2SnS)3 occurs, as well as formation of soluble complex species in the presence of glycylglycine; Me2Sn(penH)2 appears to undergo a slow desulfuration reaction.
Distribution and fate of tributyltin in the united states marine environment
Authors: Seligman Peter F , Grovhoug Joseph G , Valkirs Aldis O , Stang Peter M , Fransham Roy , Stallard Martha O , Davidson Bradley , Lee Richard F
Published: January 2005

Tributyltin (TBT) has been measured in water in 12 of 15 harbors studied during US Navy baseline surveys. The highest concentrations of TBT (some exceeding laboratory toxicity limits) have been found in yacht harbors and near vessel repair facilities. Many sites (75%) in harbors and estuaries had no detectable (<5 ng dm−3) TBT. TBT monitoring studies with increased detection limits (<1 ng dm−3) have documented a high degree of TBT variability associated with tide, season and intermittent point source discharges. Although yacht harbors were shown to be the principal TBT source in most regions, dry‐docks can be significant sources. Tributyltin degradation studies were conducted using unfiltered seawater from four geographic regions and incubated under natural conditions. Degradation half‐lives were always in the range of 4–19 days, providing evidence that TBT is not highly persistent in the water column at environmental concentrations. Preliminary degradation experiments suggest that TBT has a longer residence time in sediment with a half‐life of several months. Tributyltin is primarily in the dissolved form in unfiltered seawater, although the association with particulate fractions may increase in samples collected near yacht repair facilities, Partition coefficients for particulate TBT versus bulk water are frequently near 3000 and vary with the particulate concentration, salinity and presence of natural organics.
Environmental sources and sinks of alkyllead compounds
Authors: Harrison Roy M , Allen A G
Published: January 2005

Evidence is presented in favour of a natural environmental alkylation process as a source of atmospheric vapour‐phase alkyllead. Several species of marine flora have been cultured under laboratory conditions with added doses of inorganic lead, and production of alkyllead, predominantly trimethyllead (Me3Pb+), has been measured. Atmospheric concentrations and ratios of alkyl and inorganic lead at urban, rural and remote sites suggest that differential decay and deposition processes for different species, together with an environmental alkylation source, may explain enhanced ratios of total alkyllead/total lead in maritime air masses.
Arsenic speciation in clams of British Columbia
Authors: Cullen William R , Dodd Matthew
Published: January 2005

The water‐soluble arsenic compounds in five species of clams – Butter clam (Saxidomus giganteus), Horse clam (Schizothoerus nuttalli), Soft‐shelled clam (Mya arenaria), Native littleneck clam (Protothaca staminea), and Manila clam (Venerupis japonica) – are described. Varying amounts of arsenobetaine and tetramethylarsonium ion are the major arsenicals found in all species. Butter clams show the presence of a third compound which appears to be trimethylarsine oxide. Small amounts of as‐yet‐unidentified arsenicals can also be isolated.
Synthesis, storage, and transfer of [210Pb]‐(CH3)3PbCl across tomato fruit cuticle
Authors: Blais J S , Momplaisir G M , Marshall W D
Published: January 2005

An improved synthetic route to [210Pb]‐(CH3)3PbCl is described in which chelated 210Pb2+ is methylated to [210Pb]‐(CH3)4Pb with methylmagnesium bromide (CH3MgBr) in the presence of methyl iodide. Controlled oxidation of the product with anhydrous hydrochloric acid and purification of the crude product by reversed‐phase high‐pressure liquid chromotography (HPLC) resulted in [210Pb]‐(CH3)3PbCl in 71% radiochemical yield. Whereas storage of the purified product at −10 °C resulted in complete conversion to Pb2+ during one year, storage in 20% acetic acid at 4 °C resulted in less than 15% decomposition during six months. Periodic complexometric extractions to remove 210Pb radioactive daughters (210Bi, 100% β, Emax = 1.16 MeV; 210Po, 100% α, E = 5.305 MeV) from the storage solution did not alter the rate of decomposition. The rate of translocation of [210Pb]‐(CH3)3Pb+ across an isolated tomato cuticle was approximately twice the rate of transfer of inorganic lead(II) and was not influenced by the presence of increasing amounts of disodium ethylenediamine‐tetra‐acetate.
A study of methylation of inorganic tin by iodomethane in an aquatic environment with 13C carbon isotope tracer technique
Authors: Shugui Dai , Guolan Huang , Yong Cai
Published: January 2005

The methylation of tin(II) [Sn(II)] by iodomethane (CH3I) under environmental conditions has been further demonstrated by a 13C carbon isotope tracer method. Methylation products are mainly monomethyltin, and very small amounts of dimethyltin. The reaction of Sn(II) and CH3I was investigated at pH 2, 4, 6, 8, 10 and salinity (S) 8, 15, 22, 28, 35%; it has been found the reaction was affected by pH and salinity, the tin methylation activity being highest at about pH 6 and S = 28% . The methylation reaction is first‐order for both CH3I and Sn(II), and the rate equation has been obtained as follows:

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Näherungsformeln zur Bestimmung der Bodenpressungen von Turmfundamenten mit unterschiedlichen symmetrischen Querschnitten
Authors: Merz Klaus
Published: January 2005

Türme und Maste für den Antennenbau, den Energietransport oder für Windenergieanlagen werden üblicherweise auf kreisrunden, quadratischen oder achteckigen Fundamenten gegründet.

In diesem Beitrag werden aus den Gleichgewichtsbeziehungen zwischen einwirkenden Schnittgrößen und den für die jeweilige Fundamentgeometrie sich einstellenden Sohlspannungen Näherungsformeln sowohl zur Ermittlung der max. Spannung als auch zur Nullinienbestimmung hergeleitet. Weiter kann mit den vorgestellten Formeln auf einfache Weise bereits in der Entwurfsphase einer wirtschaftlichen Gestaltung Rechnung getragen bzw. eine Optimierung der Fundamentfläche erzielt werden.
Age and probabilistic reasoning: Biases in conjunctive, disjunctive and Bayesian judgements in early and late adulthood
Authors: Fisk John E.
Published: January 2005

Probabilistic reasoning plays an essential part in many aspects of our daily routine and it has been argued that as we grow older, the need to make judgements under uncertainty becomes increasingly important. Two studies were conducted to establish whether the propensity to commit probabilistic reasoning errors increased with age. Young (aged 16–24), middle aged (25–54), and older persons (55 years and above) were included. Study 1 revealed systematic biases and errors across a range of judgement tasks. However, no evidence of any age effect in Bayesian inference, the incidence of the conjunction fallacy, or in the number of disjunction errors was found. The results obtained in Study 1 were replicated in Study 2, where the potential mediating role of working memory processes and intellectual capacity were explicitly assessed. While some aspects of probabilistic reasoning performance were correlated with measures of intelligence and working memory functioning among young adults, this was much less evident in older persons. The present findings are discussed in relation to the evolution of the dualistic heuristic–analytical system over the adult lifespan. Copyright © 2005 John Wiley & Sons, Ltd.
Predicting postoperative morbidity by clinical assessment
Authors: Markus P M , Martell J , Leister I , Horstmann O , Brinker J , Becker H
Published: January 2005

Background

The aim of this study was to determine the accuracy of prediction of the surgeon's ‘gut-feeling’ in estimating postoperative outcome.

Methods

A prospective series of 1077 consecutive patients undergoing major hepatobiliary or gastrointestinal surgery were studied. Patients having elective (n = 827) and emergency (n = 250) procedures were included. The surgeon predicted the development of postoperative complications immediately after completion of surgery on a scale from 0 to 100 per cent. These predictions were compared with the actual outcome and with predictions made using the Physiological and Operative Severity Score for the enUmeration of Mortality and morbidity (POSSUM). The Portsmouth predictor equation (P-POSSUM) was applied for the estimation of mortality.

Results

The observed morbidity and mortality rates were 29·5 and 3·4 per cent respectively. POSSUM predicted a morbidity rate of 46·4 per cent and P-POSSUM a mortality rate of 6·9 per cent. The surgeon's gut-feeling was more accurate in the prediction of morbidity at 32·1 per cent. On the basis of gut-feeling, surgeons overpredicted morbidity in elective surgery, but underestimated the risk of complications in the emergency setting. The (P)-POSSUM scoring system overpredicted morbidity and mortality for elective and emergency operations.

Conclusion

The surgeon's gut-feeling is a good predictor of postoperative outcome, especially after elective surgery. (P)-POSSUM overpredicted morbidity and mortality in this series of major gastrointestinal and hepatobiliary operations.
Gastrectomy with extended lymphadenectomy for primary treatment of gastric cancer
Authors: McCulloch P , Niita M Eidi , Kazi H , Gama-Rodrigues J J
Published: January 2005

Background

The appropriate extent of lymph node clearance during gastrectomy for cancer remains controversial.

Methods

Medline, Embase, the Cochrane register and other databases were searched for studies reporting node dissection technique, 5 year survival and mortality after gastrectomy. Comparisons with systematic bias in treatment allocation and patients who received perioperative chemotherapy were excluded. Meta-analysis was performed separately for randomized and non-randomized comparisons.

Results

Two randomized and two non-randomized comparisons of limited (D1) versus extended (D2) node dissection and 11 reports of one dissection type were analysed. For D2 the randomised trials showed no overall survival benefit (Risk ratio (RR) = 0·95, 95 per cent c.i. 0·83–1·09) and an increased postoperative mortality (RR = 2·23, c.i. 1·45–3·45), apparently related to pancreatico-splenectomy and surgical inexperience. A trend towards survival benefit for D2 was observed for T3+ tumours (RR = 0·68, c.i. 0·42–1·10). Non-randomized comparisons found no survival benefit for D2 (RR = 0·92, c.i. 0·83–1·02), but decreased postoperative mortality (RR = 0·65, c.i. 0·45–0·93). Nine observational studies of D2 reported better results than two studies of D1 surgery, but in very different settings.

Conclusions

Evidence for D2 dissection is inconclusive. No overall survival advantage has emerged, but some patients with intermediate stage disease may benefit. Excess operative mortality appears to be associated with pancreatico-splenectomy, low case volume and lack of specialist training.
Neoadjuvant chemotherapy in breast cancer
Authors: Charfare H , Limongelli S , Purushotham A D
Published: January 2005

Background

Neoadjuvant chemotherapy for breast cancer was originally used in locally advanced inoperable disease in order to achieve surgical resection. It was then extended to operable breast cancer with a view to downstaging tumours to facilitate breast-conserving surgery. Increasingly, it is being considered as a treatment for earlier-stage disease.

Methods

A Medline literature search was performed to identify articles relating to neoadjuvant chemotherapy in breast cancer published in the English language between 1960 and 2004. Secondary references were obtained from key articles. Search words included ‘neoadjuvant chemotherapy’, ‘breast cancer’, ‘tumour biology’, ‘tumour markers’ and ‘sentinel lymph node biopsy’.

Results

Long-term results from randomized studies have shown no difference in disease-free or overall survival between neoadjuvant and adjuvant chemotherapy. The main benefit of neoadjuvant chemotherapy is its ability to downstage large tumours with a view to treatment by breast-conserving surgery, although there is a non-significant increase in the local recurrence rate. Initial results of neoadjuvant chemotherapy trials using newer agents such as taxanes have demonstrated a greater pathological complete response. Whether this will translate into better long-term survival remains to be seen.
BJS—in good health
Authors: Murie J
Published: January 2005

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

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

We 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

The 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

BACKGROUND

The 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.

METHODS

Available 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.

RESULTS

The 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.

CONCLUSIONS

Further 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

Fire 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

A 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

Orbital 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

The 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

Empirical 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

Ab 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

A 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

The 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

We 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

Compact, 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

The 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.
Experimental mathematics. I. Computational study on the limit cycle behavior of a two‐dimensional chemical oscillator
Authors: Szamosi Janos , Kristyan Sandor
Published: January 2005

A computational procedure, developed from the power series method, is used to investigate oscillating systems. In addition to its great accuracy and reduced computer time, the method is very easily programmable since the algorithm is provided by the reaction mechanism itself.
Group equivalents for converting ab initio energies to enthalpies of formation
Authors: Wiberg Kenneth B.
Published: January 2005

Group equivalents which are useful for converting energies derived from ab initio calculations into enthalpies of formation have been obtained. They allow ΔHf to be estimated from 6‐31G* energies with an uncertainty on the order of ±2 kcal/mol.
Conformational analysis of allylamine. An ab initio molecular orbital study
Authors: Kao James , Seeman Jeffrey I.
Published: January 2005

The 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

The 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

A 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

The 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

The 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 construction of the molecular distance matrix
Authors: Müller W. R. , Szymanski K. , Knop J. V. , Trinajstić N.
Published: January 2005

A simple computer‐oriented method is presented for constructing the (molecular) distance matrix. The distance matrix considered is the graph‐theoretical (topological) distance matrix.
An algorithm for geometry optimization without analytical gradients
Authors: Baker Jon
Published: January 2005

A 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

We 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

Stereochemistry 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.
Hamiltonian dynamics of chemical reactions. Consecutive first‐order reactions and reactions possessing one autocatalytic intermediate
Authors: Georgian T. , Halpin J. M. , Findley G. L.
Published: January 2005

A recently proposed Hamiltonian approach to phenomenological chemical kinetics [T. Georgian and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 10, 331 (1983); T. Georgian, J.M. Halpin, and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 11, 347 (1984)] is applied to all consecutive first‐order, single‐step reactions, and to all reactions possessing one autocatalytic intermediate. The reaction Hamiltonians presented are shown to be consistent with the phenomenological rate equations and the relationship between reaction form and the form of the reaction potential is discussed. In particular, we show: (1) that the interaction between consecutive reactions manifests itself as a coupling term in the reaction potential, a term which may be eliminated via transition to “normal reaction coordinates” for the chemical system; and (2) that coupled sets of autocatalytic reactions give rise to coupling terms in the reaction Hamiltonian which are characteristic of the reaction mechanism.
Charge calculations in molecular mechanics IV: A general method for conjugated systems
Authors: Abraham Raymond J. , Smith Paul E.
Published: January 2005

A general method for calculating pi charges based on the Hückel molecular orbital (HMO) approach is incorporated into an existing scheme for calculating partial atomic charges in saturated systems. The parametrization of the Hückel coulomb and resonance integrals is given based on (a) the CNDO pi densities and (b) the observed molecular dipole moments. The results for these two schemes are compared both with other theoretical methods and also with the observed dipole moments of a variety of conjugated and aromatic compounds. The dipole moment (DM) parametrization gives in general more consistent results and is to be preferred. The compounds studied include substituted olefins and aromatics (with substituents R, F, Cl, Br, I, OR), aldehydes, ketones, acids, esters, amides, and the heterocyclic ring systems of furan, pyrrole, pyridine, and indole.
Combinatorial models and algorithms in chemistry. Search for isomorphisms and automorphisms of molecular graphs
Authors: Stankevitch M. I. , Tratch S. S. , Zefirov N. S.
Published: January 2005

An algorithm for the recognition of all isomorphisms for any pair of labeled graphs as well as for generation of the graph group is described. Some results obtained with computer realization of the suggested algorithm are briefly discussed.
Conformational preferences in alkylbenzenes and aryl‐alkylamines: A comparative study using CAMSEQ, MM2 and molecular dynamics methods
Authors: Grunewald Gary L. , Creese Mary W. , Weintraub H. J. R.
Published: January 2005

Conformational preferences in a series of alkylbenzenes and protonated and neutral aryl‐alkylamines of biological interest have been examined. First, a general picture was obtained for the 25 compounds in the series by means of the CAMSEQ empirical potential software system. This provided solution as well as vacuum data. A low‐energy “folded” conformation (alkyl chain coiled toward aromatic ring) was observed in every case. The presence of an amino nitrogen atom in the alkyl chain did not significantly influence conformational preference. Secondly, a group of 14 compounds, representative of the subgroupings within the main series, was selected and the previously established (CAMSEQ) folded and extended minimum positions were further examined by means of a modified MM2 program. Energy differences between conformers were also calculated, and the presence of a stable folded form was confirmed. A feature common to many of the folded conformations is the positioning over the ring of a hydrogen atom from the terminal group of the chain. The MM2 folded/extended energy differences were in some cases smaller than those determined by CAMSEQ, with the “extended” form in many cases being about 1 or 2 kcal/mol more stable. Thirdly, three representative compounds from the series were examined by means of a molecular dynamics program which permitted the sampling of conformational space throughout the transition from extended to folded forms. This method gave energy differences between folded and extended conformations which agreed with the corresponding MM2 differences.
Calculating the electrostatic potential of molecules in solution: Method and error assessment
Authors: Gilson Michael K. , Sharp Kim A. , Honig Barry H.
Published: January 2005

We present a numerical method for calculating the electrostatic potential of molecules in solution, using the linearized Poisson‐Boltzmann equation. The emphasis in this work is on applications to biological macromolecules. The accuracy of the method is assessed by comparisons with analytic solutions for the case of a single charge in a dielectric sphere (Tanford‐Kirkwood theory), which serves as a model for a macromolecule. We find that the solutions are generally accurate to within 5%. Larger errors occur close to the charge and the dielectric boundary, but the maximum error found at ion‐bonding distance (3 Å) from a charge close to the boundary (1 Å deep) is only ∼15%. Several algorithmic improvements, described here, contribute to the accuracy of the method. The programs involved compose a coherent software package, called Del Phi, which goes from a Brookhaven Protein Data Bank format file to calculated electrostatic fields.
A method for calculating atomic charges in large molecules
Authors: Mullay John
Published: January 2005

A simple electronegativity method is used to calculate atomic charges for molecules of interest to biochemistry. These include purines, pyrimidines, and amino acids. Results are compared to those obtained from other theoretical methods (ab initio and semiempirical) as well as to nuclear magnetic resonance (NMR) data. Correlation is fair with CNDO results but very good for ab initio, DelRe, and other electronegativity methods. Good correlation was also achieved with NMR data. It is shown that a correction factor may be required in some cases and that important resonance effects need to be taken into account. Because of the small amount of calculational effort involved, these results suggest that this method could be quite useful in this field.
Ab initio vibrational analysis of three rotamers of 2‐propen‐1‐imine, H2CCHHCNH, and methanimine, H2CNH
Authors: Panchenko Yurii N. , Krasnoshchiokov Sergei V. , Bock Charles W.
Published: January 2005

The results of complete Hartree‐Fock (HF)/6–31G geometry optimization and HF/6–31G//HF/6–31G force fields evaluations of three rotamers of the H2CCH–HCNH molecule (s‐trans–d‐trans–, s‐trans–d‐cis‐ and s‐cis–d‐trans‐2‐propen‐1‐imine) and the H2C=N–H molecule are reported. All three conformers were found to be planar with the s‐trans–d‐trans conformer lowest in energy. This was corroborated by further complete optimizations of the geometries of the s‐trans–d‐trans and s‐trans–d‐cis conformers at the HF/6–31G*(5D) level as well as single‐point MP4/6–31G*//HF/6–31G*(5D) calculations. The assignment of the vibrational frequencies of the propenimine rotamers and some isotopomers of methanimine are also reported. The majority of the experimental frequencies of propenimine in the gaseous phase are found to belong to the s‐trans–d‐trans form, but a few frequencies are attributed to the high‐energy s‐trans–d‐cis conformer.
Efficient calculation of electrically based intermolecular potentials of weakly bonded clusters
Authors: Dykstra Clifford E.
Published: January 2005

Electrical interactions between molecules are important effects in weak and long‐range attractions. With quantum mechanical techniques now capable of yielding values of all multipole polarizabilities, hyperpolariabilities, and beyond, exhaustive treatment of electrical interaction is no longer out of the question. An efficient computational strategy is presented for the evaluation of electrical interaction energies to any desired level for small, medium, and large (ca. 100 molecules) clusters. With incorporation of repulsive, hard‐wall potentials, global surfaces may be examined. Example calculations are presented.