bluuebunny/crossref_metadata_2025 huggingface dataset:
Amino acid sequence specificities of an adhesive recognition signal
Authors: Yamada Kenneth M. , Kennedy Dorothy W.
Published: December 2004

Synthetic peptides derived from the cell‐binding domain of fibronectin have previously been found to inhibit fibronectin‐mediated adhesion in vitro competitively and reversibly, as well as inhibiting cell migratory events in vivo. The amino acid sequence specificity required for this inhibitory activity has been examined further using variations of the originally identified active peptide sequences. The most active small peptide was found to be the pentapeptide Gly‐Arg‐Gly‐Asp‐Ser. Although the tetrapeptide Arg‐Gly‐Asp‐Ser was found to retain substantial activity, it was approximately threefold less active. An “inverted” peptide sequence with these same four amino acids arranged in the mirror sym‐metrical sequence Ser‐Asp‐Gly‐Arg was found to be nearly as active as the forward sequence. However, the same inverted tetrapeptide sequence embedded in a synthetic decapeptide derived from a sequence of histocompatibility antigens has minimal activity, suggesting the importance of adjacent sequences in modifying the activity of such peptides. Neither substitution of amino acids of the same charge nor reversal of the positions of the two charged amino acids retains biological activity. Decreasing the spacing between the charged residues also causes a loss of activity. Our results suggest the hypothesis that this adhesive recognition signal consists of a specific arrangement of one acidic and one basic charged group and additional information provided by adjacent amino acids.
Site‐specific mutagenesis of dihydrofolate reductase from Escherichia coli
Authors: Chen Jin‐Tann , Mayer Ruth J. , Fierke Carol A. , Benkovic Stephen J.
Published: December 2004

Two site‐specific mutations of dihydrofolate reductase from Escherichia coli based on the x‐ray crystallographic structure were constructed. The first mutation (His‐45 → Gln) is aimed at assessing the interaction between the imidazole moiety and the pyrophosphate backbone of NADPH. The second (Thr‐113 → Val) is part of a hydrogen bonding network that contacts the dihydrofolate substrate and may be involved in proton delivery to the N5‐;C6 imine undergoing reduction. The first mutation was shown to alter both the association and dissociation rate constants for the cofactor so that the dissociation constant was increased 6–40‐fold. A corresponding but smaller (fourfold) effect was noted in V/K but not in V compared to the wild‐type enzyme. The second was demonstrated to increase the dissociation rate constant for methotrexate 20–30‐fold, and presumably dihydrofolate also, with it corresponding 20–30‐fold increase in the dissociation constant. In this case an identical effect was noted on V/K but not in V relative to the native enzyme. Thus, in both mutant enzymes the decrease in binding has not been translated into a loss of catalytic efficiency.
Increasing and decreasing protein stability: Effects of revertant substitutions on the thermal denaturation of phage λ repressor
Authors: Hecht Michael H. , Hehir Kathleen M. , Nelson Hillary C. M. , Sturtevant Julian M. , Sauer Robert T.
Published: December 2004

The thermal denaturations of five revertant λ repressors containing single amino acid substitutions in their N‐terminal domains have been studied by differential scanning calorimetry. Two substitutions slightly decrease stability, and the remaining three render the protein more stable than wild type. The Gly48 → Asn and Gly48 → Ser proteins are 4°C more stable than wild type. These two substitutions replace an α helical residue, and in each case a poor helix forming residue, glycine, is replaced by a residue with a higher helical propensity. We also present data showing that one revertant, Tyr22 → Phe, has reduced operator DNA binding affinity despite its enhanced stability.
Amplification of RNA and DNA specific for erb B in unbalanced 1;7 chromosomal translocation associated with myelodysplastic syndrome
Authors: Woloschak Gayle E. , Dewald Gordon W. , Bahn Rebecca S. , Kyle Robert A. , Greipp Philip R. , Ash Robert C.
Published: December 2004

Previous work has established the presence of an unbalanced chromosome abnormality [+der(1),t(1;7)(p11;p11)] in some therapy‐associated myelodysplastic disorders. Recently the EGF receptor has been found to reside at 7p11. Using a probe specific for erb B oncogene, which encodes a truncated form of the EGF receptor, we examined RNA and DNA derived from bone marrow and peripheral blood mononuclear cells from three patients with myelodysplastic syndromes (MDS) and one with acute lymphocytic leukemia (ALL), all bearing an abnormal clone in their bone marrow with a similar unbalanced 1;7 translocation. DNA‐excess slot blot hybridization to 5′‐32p‐labeled cellular RNA revealed from ten‐ to thirtyfold enhancement in accumulation of mRNA specific for erb B in both peripheral blood and bone marrow cells of the three MDS patients when compared to normal controls. In addition, enhancement of H‐ras mRNA accumulation was detected in some, though expression of other genes such as actin, N‐ras, myc, src, B‐lym, and 20 other genes was not found to be enhanced. Increased erb B expression was not apparent in mononuclear cells from patients with other hematologic disorders such as chronic lymphocytic leukemia, Hodgkin's disease, or lymphoma. Southern blot analysis of restriction‐enzyme‐cleaved DNA from three MDS patients with an unbalanced 1;7 translocation revealed that erb B gene was amplified at least twentyfold in peripheral blood white blood cells, while levels of actin hybridization were comparable to those of the controls. No such amplification was evident in the ALL patient. Our data suggest that +der(1),t(1;7)(p11;p11) chromosomal anomalies can be specifically associated with amplification of erb B DNA and RNA sequences.
Differential induction of transcription of c‐myc and c‐fos proto‐oncogenes by 12‐O‐tetradecanoylphorbol‐13‐acetate in mortal and immortal human‐urothelial cells
Authors: Skouv Jan , Christensen Britta , Autrup Herman
Published: December 2004

The effect of the skin tumor‐promoter TPA (12‐O‐tetradecanoylphorbol‐13‐ace‐tate) on expression of cellular proto‐oncogenes has been examined in cell lines derived from human urothelium. A single treatment with TPA (1 μg/ml) increased the transcription of c‐fos and c‐myc proto‐oncogenes at least 20‐fold in the mortal cell line HU 1752. The induction was transient and was accompanied by a rapid but transient change in cell morphology. When immortalized cell lines were treated with TPA a similar rapid and transient morphological response was observed, but the TPA treatment only increased the level of c‐fos mRNA. suggesting that the normal regulation of c‐myc transcription is altered in immortalized cells irrespective of their tumorigenic properties. The levels of c‐Ha‐ras and c‐Ki‐ras mRNAs were unaffected by TPA treatment in all cell lines.
Spontaneous fusion between metastatic mammary tumor subpopulations
Authors: Miller Fred R. , McInerney Donna , Rogers Clare , Miller Bonnie E.
Published: December 2004

This study describes a differential frequency of spontaneous fusion between metastatic and nonmetastatic subpopulations derived from a single mouse mammary tumor. Subpopulations 66, 66cl4 (a variant of 66 which is resistant to both thioguanine and ouabain), 410.4, and 44FTO (a thioguanine‐resistant, ouabain‐resistant derivative of 410.4) spontaneously metastasize from subcutaneous and mammary fatpad sites. Subpopulations 168, 168FARO (a diaminopurine‐resistant, ouabain‐resistant derivative of 168), 67, 68H, and 410 do not. The ability of these subpopulation lines to fuse spontaneously in vitro was determined after coculturing a drug‐resistant line with a wild‐type line in nonselective media. After 16–20 h of coculture, cells were plated in the appropriate media to select for fusion products—either HAT (hypoxanthine, aminopterin, thymidine) plus ouabain or AA (alanosine, adenine) plus ouabain—to determine the number of colony‐forming cells (fusion products) present per 104 cells plated. When both subpopulations of the pair in the fusion mixture were metastatic, a significantly greater number of fusion products was recovered than if one or both of the subpopulations in the fusion mixture was nonmetastatic, with one exception: line 410 readily fused with both 66cl4 and 44FTO. Subline 410 was highly metastatic when originally isolated but lost its metastatic competence after a brief time in tissue culture.
Conformational energy surfaces of triplet‐state isomeric methyloxiranes
Authors: Demaré G. R. , Peterson M. R. , Csizmadia I. G. , Strausz O. P.
Published: January 2005

A conformational study was carried out on the three ring‐opened structures of triplet methyloxirane with a minimal Gaussian basis set, within the unrestricted Hartree–Fock framework. For the two structures
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energy surfaces E(θ1, θ2) were generated, where θ1 measures the methyl rotation and θ2 is associated with the torsion about the other CC bond. For the third structure
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an energy hypersurface E(θ1, θ2, θ3) was generated, where energy was a function of methyl rotation θ1 and two nonequivalent CO rotations θ2 and θ3. Analysis of the surfaces revealed the locations and relative energies of the critical points (minima, saddle points, and maxima). The overall stereochemical finding was that these ring‐opened triplet C3H6O species possessed rather flexible structures.
A theoretical comparison of cationic and anionic homoaromaticity: Reinforcement of cationic homoaromaticity by σ‐nonclassical effects
Authors: Wirth David , Bauld Nathan L.
Published: January 2005

A MINDO/3 study of homoaromaticity in the 3‐cyclobutenyl cation and the Mobius 3‐cyclobutenyl anion has been used to evaluate cationic and anionic homoaromaticity quantitatively. π Homodelocalization energies of the two are found equal in isostructural planar comparisons. In planar optimized structures, the homodelocalization energy of the cation is slightly (about 4 kcal) greater than that of the anion, a consequence of the greater 1,3 distance in the latter. Full optimization produces a highly puckered and further stabilized cation, but engenders no change in the Mobius anion. The total stabilization of the cation relative to the anion is 13 kcal, in accord with the generalization that cationic homoaromaticity is more potent than the anionic variety. The fully optimized cation is revealed to actually have a much smaller π homodelocalization energy than the optimized anion, in contrast to the order of overall stabilities. σ‐Nonclassical effects, which are stabilizing in the cation but destabilizing in the Mobius anion, provide the rationale for the above.
Evaluation of MINDO/3 calculated structures. II. Branching errors in alkanes and cycloalkanes
Authors: McManus Samuel P. , Smith Maurice R. , Smith Margaret B. , Shafer Steven G.
Published: January 2005

MINDO/3 calculations have been carried out for a series of branched chain alkanes in order to assess effects of branching on calculated geometries and heats of formation (ΔHf). With vicinal branching, MINDO/3 calculates the central CC bond to be too long. Bond angles are also found to be distorted. Errors in calculated heats of formation are large when geminal branching is present and significant with vicinal branching. Branching error corrections for ΔHf have been derived and applied to a separate series of branched acyclic and cyclic compounds. For the test sample, application of the branching error corrections gave calculated structures of acyclic branched hydrocarbons with heats of formation having an average absolute error of 1.3 kcal/mole rather than 17.3 kcal/mole before correction. Cyclic branched hydrocarbons are shown to be less well corrected. Calculations of heats of reaction have also been carried out for some isomerization and cyclization reactions using the MINDO/3 and MNDO methods. It is clear from the comparisons that MNDO calculations give less severe errors for highly branched compounds but the errors are still substantial. For prediction of heats of reaction, the error‐corrected calculations are shown to be superior to the “raw” calculations obtained by MINDO/3 or MNDO.
Graphite: A molecular mechanics treatment
Authors: Sprague Joseph T. , Allinger Norman L.
Published: January 2005

Graphite is the limiting case of an infinite aromatic hydrocarbon, and as such is an important benchmark in force‐field calculations. Using experimentally determined physical properties for graphite, a force‐field parameter set was developed for molecular mechanics calculations with unsaturated hydrocarbons and is described and discussed.
Quantum chemical investigations of charge transfer interactions in relation to the electronic theory of cancer. II
Authors: Ball John R. , Thomson Colin
Published: January 2005

The results of ab initio “supermolecule” calculations of the charge transfer between formamide and methylglyoxal, ethylglyoxal, and dimethylglyoxal are compared for several different relative conformations of the constituent molecules. The charge transfer properties of ethylglyoxal were found to be quite different to those of the other two glyoxals.
Ab initio calculations of the rotational potential functions for propanol and ethyl methyl ether
Authors: Burkert Ulrich
Published: January 2005

Calculations at the STO‐3G and 4–31G levels have been carried out on propanol and ethyl methyl ether, with geometries obtained from molecular mechanics calcualations. Full relaxation was allowed in all degrees of freedom except for the torsion about the central bond, which was varied at 30° increments. A butane‐type potential was found, the maximum and minimum values of energy are from 0° to 180° 5.55, 0.00, 4.02, and 0.00 kcal/mole for propanol, and 8.35, 2.74, 3.31, and 0.00 kcal/mole for ethyl methyl ether (4–31G).
Electronic structure of benzaldehyde: A comparative study of the lowest excited singlet π* ← π and π* ← n states
Authors: Srivastava S. K. , Mishra P. C.
Published: January 2005

VE‐PPP, CNDO/2, and CNDO/s‐CI methods have been used to investigate the electronic spectrum and structure of benzaldehyde. Electronic charge distributions and bond orders in the ground and lowest excited singlet π* ← π and π* ← n states of the molecule have been studied. The molecule has been shown to be nonplanar in the lowest π* ← n excited singlet state, in agreement with the conclusions drawn from the study of vibrational spectra. Dipole moments in both excited states have been shown to be larger than the ground‐state value. Thus, the ambiguity in the experimental result for the π* ← π n excited singlet state dipole moment has been resolved. It has been shown that the n orbital is mainly localized on the CHO group. Furthermore, charge distributions, dipole moments, and molecular geometries are shown to be very different in the excited singlet π* ← π and π* ← n states.
A theoretical approach to substituent effects. Structural consequences of electrostatic and orbital interactions in model mono‐ and disubstituted methanes
Authors: Pross Addy , Radom Leo
Published: January 2005

Ab initio molecular orbital theory is used to examine the effect of substituents on bond lengths in mono‐ and disubstituted methanes. The relative importance of electrostatic and orbital interaction terms are assessed. The results suggest that for substituents (X) which show powerful σ effects and weak π interactions (e.g., F), the changes in bond length are due primarily to the electrostatic component except in some disubstituted methanes in which case the change in the hyperconjugative ability of the C—X bond is also important. On the other hand, substituents X which show weak σ effects but powerful π interactions (e.g., NH2) affect bond lengths primarily through hyperconjugative interaction of a filled or vacant π‐type orbital on X with the adjacent bonds.
Spectroscopic CNDO/CI study of some cyclic polyenes
Authors: Zuccarello Felice , Buemi Giuseppe , Raudino Antonio
Published: January 2005

CNDO/S calculations are carried out on 1,3,5‐cycloheptatriene (I), 1,3,5,7‐cyclooctatetraene (II), all‐cis‐1,3,5,7‐cyclononatetraene (III), and all‐cis‐1,4,7‐cyclononatriene (IV), for which π‐σ separability is a questionable matter. When disparate choices are available for the geometries, preferences are based on the agreement between calculated and experimental spectra. The microwave structure for I and an unsymmetrical conformation for III are suggested. In the electronic spectra, conjugative contributions are assigned to the lowest‐energy weak band, while an ethylenic nature is to be attributed to the intense band in the range of 6 eV. The possibility of through‐space π interactions is examined qualitatively. An appreciable degree of such interaction is shown by IV.
Molecular charge distribution and chemical binding in five‐membered heterocycles. I
Authors: Hilal Rifaat
Published: January 2005

Electron density maps for the heterocycles thiophene, furan, and pyrrole are determined from ab initio 4‐31G wavefunctions. The charge distributions in these molecules are analyzed in terms of the total molecular density and difference density maps and their profiles. The atomiclike core, especially the L core of sulfur, is found to play an important role, via its polarization and interaction, in determining the extent and direction of valence density transfer from the carbon to the heteroatom. The changes in the charge distributions that occur in the immediate vicinity of the heteroatoms and the relation of density quantities to binding and antibinding characteristics are discussed. The quantum topological features of the molecular charge distributions of the three heterocycles are analyzed and discussed and the different bonding situations, e.g., ring strain, ionic and covalent binding, etc., are compared in a model‐independent way.
Localized molecular orbitals and chemical binding in five‐membered heterocycles. II
Authors: Hilal Rifaat
Published: January 2005

The localized molecular orbitals (LMOs) of thiophene, furan, and pyrrole are derived from ab initio 4‐31G wavefunctions using Boys' criteria for localization. From the transferability point of view, these LMOs are classified as (i) completely different and nontransferable LMOs (these are the lone‐pair orbitals on O and N on one hand and those on S on the other hand), (ii) chemically similar lone pairs and inner shells on O and N (of furan and pyrrole, respectively), and (iii) chemically equivalent CC, CC, and CH LMOs in the three heterocycles. The sp3 hybridization of the L core of sulfur, its appreciable polarization, and considerable involvement in bonding in the CS bond region have been discussed. The present investigation indicates the limitation of the application of semiempirical MO methods to molecules that contain second‐row atoms due to both the appreciable core—valence and π‐σ interactions involving such atoms. Qualitative investigation of aromaticity and reactivity of the studied heterocycles agrees satisfactorily with experimental observations and shows that conclusions drawn based solely on static factor considerations (charge distribution in the noninteracting molecules) might very well be misleading and such factors determine the ease rather than the final orientation of the substituent.
Prediction of the crystal structure of a cyclic tetrapeptide
Authors: Hall David , Wood Murray K.
Published: January 2005

Prediction of the known crystal structure of cyclic‐L‐Ser(O‐t‐Bu)‐β‐Ala‐Gly‐L‐β‐Asp(OMe) has been attempted by establishing the low‐energy conformations of the isolated molecule by conformational analysis, and then regarding each of these as a rigid molecule, by establishing the favorable crystal packing arrangements by molecular packing analysis. The theoretical model closest to the observed structure was one of the lowest‐energy solutions and was recognized as essentially correct by reference to the x‐ray data. The limitations of the model follow from the fact that the side chain conformations are somewhat affected by packing interactions.
Gas‐phase nitrosation of benzene: Theoretical investigations
Authors: Raghavachari Krishnan , Reents W. D. , Haddon R. C.
Published: January 2005

The structures and energetics involved in the nitrosation of benzene are explored by means of ab initio molecular orbital computations. The effects of polarization functions and electron correlation are included in these calculations. Good agreement is obtained in cases where experimental energies are available. The nitrosation of ethylene is considered as a model system to simulate the behavior of the larger nitrosyl cation (NO)+/benzene system. Detailed comparison reveals that careful use of such model systems can yield useful information.
An unconventional scf method for calculations on large molecules
Authors: Cremer Dieter , Gauss JüRgen
Published: January 2005

An unconventional SCF method for calculations on large molecules with more than 100 basis functions is described. Storage problems which arise in conventional SCF schemes when storing more than 107 integrals are avoided by repeated calculation of integrals. The resulting increase in computational times is kept at a reasonable level by (a) improving the initial guess, (b) accelerating convergence, (c) employing a recursive construction of the Fock matrix, and (d) eliminating insignificant integrals from the calculation by a density‐weighted cutoff criterion. Sample calculations show that, compared with conventional SCF calculations, computational times increase by 25%–75% depending on the basis set and the shape of the molecule.
On the Use of Constraints in Molecular Mechanics. Rigid Group Refinement
Authors: Dillen Jan L. M.
Published: January 2005

It is shown how the refinement of groups of atoms as rigid entities can be implemented in a molecular mechanics program. The method is worked out for the Newton‐Raphson scheme and eventually combined with other constraints, including the Eckart conditions. An example is also given.
Atomic Physicochemical Parameters for Three‐Dimensional Structure‐Directed Quantitative Structure‐Activity Relationships I. Partition Coefficients as a Measure of Hydrophobicity
Authors: Ghose Arup K. , Crippen Gordon M.
Published: January 2005

Earlier we showed (A. K. Ghose and G. M. Crippen,J. Med. Chem., 28, 333, 1985) the necessity of atomic physicochemical parameters in three‐dimensional receptor mapping. Here we derive more refined and widely applicable hydrophobicity parameters. Carbon, hydrogen, oxygen, nitrogen, sulfur, and halogens are classified into 110 atom types. Among these, the hydrophobic contributions of 90 atom types have been evaluated from the logP(water‐octanol)values of 494 molecules, using the additive model and leastsquares technique. It gave a standard deviation of 0.347, a correlation coefficient of 0.962, and an explained variance of 0.908. These atomic values were used to predict the logPvalues of 69 compounds. The predicted values showed a standard deviation of 0.404 and a correlation coefficient of 0.896. This work has been compared with more conventional approaches.
Ab initio studies on van der Waals molecules. A comparative study with several basis sets of the C2v HeLi2 system
Authors: Matías Manuel , Tel Luis M. , Novoa Juan J.
Published: January 2005

The potential energy surface of the van der Waals system HeLi2 is computed for the case in which the system has C2v symmetry and at the Li‐Li distance (5.005 bohrs). A comparative study of the results for the two methods used, ab initio Hartree‐Fock and second‐order Møller‐Plesset, and several basis sets, ranging from minimal to near Hartree‐Fock quality, is also done. The results show the importance of correcting the basis set superposition error, and the need, in order to obtain a good description of the potential, of basis sets with polarization functions on all the atoms, when the Møller‐Plesset method is used. At the Hartree‐Fock level, the MINI‐1 basis gives results almost of the same quality as the near Hartree‐Fock basis.
Numerical calculation of eigenvalues for the Schrödinger equation. III
Authors: Neuberger J. W. , Noid D. W.
Published: January 2005

A recently developed method for calculation of eigenvalues is applied to a four coupled oscillator system previously used to test more approximate methods. Analysis is presented to show how the present method scales for systems of two, three, and four coupled oscillator systems.
The modeling of chemical phenomena using topological indices
Authors: Rouvray Dennis H.
Published: January 2005

A class of graph invariants known today as topological indices are being increasingly realized by chemists and others to be powerful tools in the description of chemical phenomena. Topological indices generally characterize both the size and shape of chemical species; in recent years a number of such indices have been put forward that sensitively reflect the amount of branching present in molecules. Chemists are thus able to model accurately the chemical behavior of an extensive range of chemical substances in all three thermodynamic states. In discussing the manifold applications of topological indices to the description of physicochemical properties, we present a survey of the progress to date in this area and point out some of the advantages and drawbacks of using topological indices.
Bond critical points in the electronic structures of the main group diatomic hydrides of lithium through bromine
Authors: Boyd Russell J. , Edgecombe Kenneth E.
Published: January 2005

The bond critical points and associated electronic properties of the diatomic hydrides of the twenty‐one main group elements from lithium to bromine have been calculated with large basis sets. As part of a systematic study of the polarity of chemical bonds, the position of the bond critical point, the charge density at the bond critical point, the Laplacian of the charge density at the bond critical point, and the molecular dipole moment of each molecule have been calculated. Particular attention has been paid to the effect of bond length elongation and contraction on the electronic properties. Variation of the bond length reveals that with atoms of low electronegativity, the bond critical point of AH tends to follow atom A, whereas with atoms of high electronegativity, the bond critical point tends to follow the hydrogen atom as the bond lengthens. Furthermore, it is shown that some properties of the diatomic hydrides vary monotonically within each row of the periodic table, while others effect a classification according to the character of the bond.
Some methods and applications of electron density distribution analysis
Authors: Ritchie James P. , Bachrach Steven M.
Published: January 2005

Accurate and efficient integration of the electron density function over arbitrary regions has been previously achieved by exploiting a separation of variables. Recently, a computer program has been written that calculates ρ, \documentclass{article}\pagestyle{empty}\begin{document}$ \buildrel{\rightharpoonup}\over{\nabla} $\end{document}ρ, and ∇2ρ in an expeditious fashion, taking advantage of the separation of variables in the electron density function. Accurate integrations of ∇2ρ over arbitrary regions can also be accomplished. The structure of the program is suited especially to vector processors. As a result of the efficiencies of these programs, functions of the electron density, such as the density itself, the surrounding electrostatic potential, ∇ρ, and ∇2ρ have been calculated in three dimensions. Results of calculations for nitrated cubanes are presented illustrating how the effects of the nitro groups are manifested in the electron density and associated properties.
Graph generators
Authors: Randić Milan , Woodworth Wayne L. , Kleiner Alexander F. , Hosoya Haruo
Published: January 2005

We consider the construction of highly symmetrical vertex transitive graphs. Some such graphs represent the degenerate rearrangements in which a molecule or an ion is formed by breaking and making bonds so that the final and the initial skeleton is identical. The approach is closely related to Cayley's graphs for selected groups. We restrict the choice of generators to symmetric matrices. Successive multiplications of such matrices generate other permutation matrices of the same dimension, each new matrix representing a new vertex for a transitive graph under the construction. In particular we restrict our discussion to matrices of dimension 3 and 4 and proceed to construct systematically all transitive graphs using 4 × 4 symmetric matrices as generators.
Molecular orbital theory of the properties of inorganic and organometallic compounds. 6. Extended basis sets for second‐row transition metals
Authors: Dobbs K. D. , Hehre W. J.
Published: January 2005

A series of efficient split‐valence basis sets for second‐row transitions metals, termed 3‐21G, has been constructed based on previously formulated minimal expansions of Huzinaga, and in a manner analogous to the previous development of 3‐21G basis sets for first‐row metals. The Huzinaga three Gaussian expansions for s‐ and p‐type orbitals of given n quantum number have been fit by least squares to new three Gaussian combinations in which the two sets of functions share the same Gaussian exponents. The original three Gaussian expansions for 1s, 3d, and 4d atomic orbitals have been employed as is. The valence description comprises 4d‐ 5s‐ and 5p‐type functions, each of which has been split into two and one Gaussian parts. 5p functions, while not populated in the ground state of the free atom, are believed to be important in the description of the bonding in molecules.

The performance of the 3‐21G basis sets is examined with regard to the calculation of equilibrium geometries and normal‐mode vibrational frequencies for a variety of simple inorganic and organometallic compounds incorporating second‐row transition metals.
On the out‐of‐plane deformation of aromatic rings, and its representation by molecular mechanics
Authors: Liljefors Tommy , Tai Julia C. , Li Shusen , Allinger Norman L.
Published: January 2005

It has been found that the previous MM2 (or MMP2) description of out‐of‐plane deformation of aromatic rings sometimes yields distortions which are much too large. As a result, rotational barriers involving distortions of such rings may be calculated to have values which are too low. Examples are collected and discussed. An alternative formulation, which appears to significantly reduce the calculational error, is presented.
Cooperative effects in extended hydrogen bonded systems involving OH groups. Ab initio studies of the cyclic S4 water tetramer
Authors: Koehler J. E. H. , Saenger W. , Lesyng B.
Published: January 2005

The additional energy stabilization due to cooperative effects was calculated in extended hydrogen bonded systems OH ⃛OH ⃛OH with unidirectional (homodromic) orientation of the OH groups. Ab initio restricted Hartree Fock, MP2 and MP3 calculations with geometry optimization and BSSE correction have been performed using the GAUSSIAN 83 program package for the ground states of the linear water dimer with Cs symmetry and the cyclic water tetramer with S4 symmetry. The latter represents the smallest possible, experimentally observed cooperative structure. A new definition for a cooperativity parameter is proposed. The definition is based on the two‐body, non‐neighbour interaction energy, plus three‐ and four‐body contributions, including one‐body deformation terms in relation to the total interaction energy of the water tetramer. The advantage of this definition is its independence of the reference system, which is necessary in complicated molecular systems with an undefined number of hydrogen bonds, such as disordered or flip‐flop systems. According to this definition the energy gain based on cooperativity in the S4 water tetramer is 29% with the MP3/6‐31G** approximation, (30% with HF/4‐31G* and 46% with HF/3‐21G). The largest contribution of 18% is due to the three‐body term on the MP3/6‐31G** level, followed by the two‐body, non‐neighbour term with 11%. The four‐body term and the deformation term are in the order of 1% and cancel each other because they have opposite sign.
Nonbonded interactions. 1. Anisotropic hydrogen‐hydrogen interactions
Authors: Wiberg Kenneth B. , Murcko Mark A
Published: January 2005

The hydrogen‐hydrogen nonbonded potential which may be derived from the calculated interactions between hydrogen molecules has been obtained. The best three‐parameter Buckingham function gave an RMS error of 0.18 kcal/mol in fitting Price and Stone's ab initio data for 130 pairs of hydrogen molecules, which may be compared with an RMS error of 0.74 kcal/mol using the parameters in the MM2 force field. Burton's basis set is also considered. A better fit to these data requires that the angular relationship between the bonds be included. The data for hydrogen as well as experimental data for chlorine show that these atoms appear “larger” normal to the bond axis than along the axis, and this is probably also the case for other atoms. When simple angular terms are added it is possible to fit the Price and Stone data set with an RMS error of less than 0.06 kcal/mol. The preferred function was: V = [a0 + a1(sin θ1 + sin θ2)4 + a2r]e−3r − [c0 + c1(1 + sinθ1sinθ2)]/r5. Deficiencies in the current ab initio data are discussed.
Calculation of enthalpies of hydrogenation of hydrocarbons
Authors: Ibrahim Mustafa R. , Fataftah Zacharia A. , von Ragué Schleyer Paul , Stout Peter D.
Published: January 2005

Sets of hydrogen molecule equivalents have been developed which permit the calculation of hydrogenation of different types of carbon‐carbon bonds from ab initio total energies (3‐21G and 6‐31G* basis sets, and, to a more limited extent, for MP2/6‐31G* data) of reactants and products. The calculated enthalpies of hydrogenation are in good agreement with experiment for unstrained molecules, with average errors on the order of 2 kcal/mol. The 6‐31G* equivalents allow the enthalpies for strained molecules to be calculated accurately, but the 3‐21G equivalents do not. The equivalents for both basis sets have been tested by calculating the enthalpies of hydrogenation of carbon‐carbon bonds in nitrogen‐ and oxygen‐containing organic molecules, free radicals, and classical carbocations. The results are in good agreement with experiment in most cases.
MNDO Calculations on [n]metacyclophanes
Authors: Jenneskens Leonardus W. , de Kanter Franciscus J.J. , de Wolf Willem H. , Bickelhaupt Friedrich
Published: January 2005

MNDO calculations on [n]metacyclophanes and a variety of related compounds are reported. An analysis of the strain, imposed by the oligomethylene bridge, and its distribution over the distorted benzene ring and the oligomethylene bridge is presented. The effect of strain and bending of the benzene ring on aromatic delocalization is investigated by a comparison of ΔHof of the bent benzene systems with that of a correspondingly bent, but localized 1,3,5‐cyclohexatriene. The results indicate that, even in the case of the highly bent [4]metacyclophane (1a), localization is unfavorable by about 10 kcal/mol.
Acetylcholine in water: Ab‐initio potential and Monte Carlo simulation
Authors: Margheritis C. , Corongiu G.
Published: January 2005

Ab initio SCF‐LCAO‐MO computations using a minimal basis set have been carried out on the acetylcholine ion in different conformations. The rotational barrier around the C9‐C8‐O1‐C2 dihedral angle (τ1) has been also calculated: the curve presents a broad minimum. SCF calculations have been carried out on the system Ach‐water at 468 different separations and/or orientations; the interaction energies were then fitted to a pair potential function used in Monte Carlo (MC) simulations of Ach water solution. The rdfs indicate a global first hydration shell with about 38 waters. Details about the hydration shell are presented. The overall MC results indicate that for the Ach ion in water solution at room temperature relative free rotation is possible around τ1, and that Ach is well represented as a large positively charged hydrated globe with a small mobile tail free of strong interactions with the surrounding water molecules.
The computation of floating functions and their use in force constant calculations
Authors: Hurley A. C.
Published: January 2005

It is shown how standard computer programs for calculating the equilibrium geometry of a molecule may be adapted to yield floating functions. These functions satisfy the Hellmann–Feynman theorem and so lead to simple electrostatic interpretations of intramolecular forces and vibrations. The theory is illustrated by detailed calculations for the water molecule.
A molecular mechanics study of neutral molecule complexation with crown ethers
Authors: Damewood Jr. James R. , Anderson Wayne P. , Urban Joseph J.
Published: January 2005

Molecular mechanics methods are applied to the study of neutral molecule complexation with crown ethers. Protocols for the development of parameters necessary to describe these molecule‐molecule interactions are presented. Application of these methods to the study of 1:1 and 2:1 (guest:host) complexation between acetonitrile (1), nitromethane (2), malononitrile (3) and dimethylsulfone (4) reveals positive cooperativity in formation of the 2:1 complexes in isolation.
Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability‐directed search procedure
Authors: Lambert Millard H. , Scheraga Harold A.
Published: January 2005

A procedure that finds the most probable conformational states of a protein chain is described. Single‐residue conformations are represented in terms of four conformational states, α, ϵ, α*, and ϵ*. The conformation of the entire chain is represented by a sequence of single‐residue conformational states; the distinct conformations in this representation are called “chain‐states.” The first article in this series described a procedure that computes tripeptide conformational probabilities from the amino acid sequence using pattern recognition techniques. The procedure described in this article uses the tripeptide probabilities to estimate the probabilities of the chain‐states. The chain‐state probability estimator is a product of conditional and marginal probabilities (obtained from the tripeptide probabilities), with a penalty factor to eliminate conformations containing α‐helices and ϵ‐strands of excessive length. The probability estimator considers short‐range conformational information, medium‐range sequence information and some simple long‐range information (through the restrictions on helix and strand lengths). Energy minimization calculations can be carried out in the region of conformational space corresponding to a particular chain‐state. By selecting the most probable chain‐states, the search can be focused on the most probable, or “important,” regions of the conformational space. These energy calculations are described in the third article of the series. The complete procedure described by the three articles is called PRISM, for pattern recognition‐based importance sampling minimization.
Polypentapeptide of elastin: Damping of internal chain dynamics on extension
Authors: Chang D. K. , Urry D. W.
Published: January 2005

Molecular dynamics simulations out to 100 ps have been carried out at 300 K in vacuo on the repeating pentapeptide, (VPGVG), of the elastin fiber. The structure employed in the simulation is a β‐spiral (helical structure) with 2.7 pentamers per turn and with a 9.45 Å rise per turn and 21.6 Å rise per turn in the relaxed and extended states, respectively. Large amplitude backbone torsion angle fluctuations are observed in the relaxed state, and significant damping is observed upon extension, particularly in the suspended segments of the β‐spiral structure. Accordingly the entropy change an extension was computed and found to be a substantial −1.1 entropy units per residue. The various energy components are compared for relaxed and extended states and the relevance of the results to the molecular mechanism of entropic elasticity is discussed.
Calculations of a list of neighbors in Molecular Dynamics simulations
Authors: Yip Virginia , Elber Ron
Published: January 2005

A new algorithm is proposed for the evaluation of nonbonded interactions in Molecular Dynamics simulations. The algorithm is based on a grid search and on partitioning of the atoms into boxes rather than on calculations of distances. The effort associated with the generation of the box list grows only linearly with the number of atoms. The algorithm is particularly advantageous for solvated systems. Test calculations show significant savings in CPU time and storage compared to commonly used algorithms for systems containing in excess of ca. 600 atoms.
A concept of charge and valence for ab initio wave functions
Authors: Jug Karl , Fasold Eckhard , Gopinathan M. S.
Published: January 2005

A modified scheme of a previously developed concept of atomic valence numbers in molecules is presented. The relation to population analysis is demonstrated. The scheme is suitable for ab initio wave functions with extended basis sets. The procedure involved a combination of symmetric orthogonalization and contraction of the basis set. The method is used for a systematic investigation of a series of compounds with first‐row atoms from Li to F. The predicted atomic charges and valence numbers are in line with results from infrared spectroscopy and multipole moment analysis.
Molecular dynamics simulations of polymers: Methods for optimal Fortran programming
Authors: Noid D. W. , Sumpter B. G. , Wunderlich B. , Pfeffer G. A.
Published: January 2005

The structure of the general classical trajectory FORTRAN code is discussed for use in molecular dynamics simulations of polymer processes. Substantial reductions in the number of mathematical operations in the code are achieved by using statement functions, modifying the ususal chain rule derivatives, applying appropriate vector identities, and using closure relationships among the required derivatives of the potential.
Theoretical study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted phenolate ions in the gas phase by means of MINDO/3, MNDO, and AM1
Authors: Voets R. , Fraņois J.‐P. , Martin J. M. L. , Mullens J. , Yperman J. , Van Poucke L. C.
Published: January 2005

Proton affinities (PAs) of 2‐, 3‐, and 4‐monosubstituted phenolates in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: H, F, Cl (only MNDO and AM1), CN, CH3, OH, NO2, OCH3, COOH, and NH2. The results are compared with experimental values (high‐pressure mass spectroscopy) at 600 K. The MINDO/3 method overestimates the experimental PAs with a mean percentual error of ca. 4.3%. The MNDO results agree much better with the experimental values and are only ca. 1.3% too high. However, the best agreement is observed for the AM1 method, where the mean percentual error is only ca. 0.69% (in absolute value). The greatest disagreement is found for 2‐hydroxyphenolate (ca. +2.0%) and 2‐carboxyphenolate (ca. +2.7%). The PA of 2‐nitrophenolate is underestimated by ca. 1.6%. Correlations between the calculated proton affinities on the one hand, charge densities on the acid H atom of the phenols, charges on the O atom in the phenolate ions, and substituent parameters on the other hand are studied. Particularly good linear relationships are found for the 3‐ and 4‐monosubstituted compounds within the AM1 formlism. For the 2‐substituted phenolates, only the AM1 method is satifactory. As a general conclusion, the AM1 method appears to be distinctly superior to MNDO for the calculation of PAs, and definitely superior to MINDO/3.
Theoretical study of adsorption of hydrocarbons on graphite
Authors: Sordo T. L. , Sordo J. A. , Flórez R.
Published: January 2005

The adsorption of methane, ethane, propane, n‐butane, ethylene, propene, 1‐butene, 1,3‐butadiene, acetylene, benzene, toluene, naphthalene, anthracene, and pyrene on the basal plane of graphite has been studied by means of a semiempirical method proposed by Fraga based on a 1/R expansion of atom‐atom pair potentials. The energies of interaction obtained agree reasonably well with experimental data and statistical calculations. The orientation of the adsorbed molecules relative to the graphite surface rendered by Fraga's method improves the picture provided by other calculations with empirical potentials. These results display Fraga's method as an economical alternative for the study of physisorption of hydrocarbons on the graphite surface.
First and second derivative matrix elements for linear and out‐of‐plane bending motion
Authors: Miller Kenneth J.
Published: January 2005

Simplified formulas for first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for linear and out‐of‐plane bending motion. They are expressed in a local coordinate system and then rotated to a space‐fixed Cartesian coordinate system. For linear motion the important points are: (1) the invariance of the energy with respect to translational and rotational coordinate transformations and (2) the presentation of derivatives of the energy in terms of (α − π)2 rather than (α − π), where α is the bond angle, to avoid indeterminant forms. By factoring the second derivatives of the energy with respect to (α − π) and sinα, analysis in this local coordinate system avoids division by sinα as α → π. The formulas describe linear systems without the need to project the motion onto two perpendicular planes. When the angle is exactly π two degenerate directions arise, and the coordinate axes perpendicular to the axis of the linear sequence of atoms may be chosen arbitrarily. Further refinements and clarifications of methods reported previously to obtain matrix elements for linear and out‐of‐plane motion are presented.
Force field calculation of equilibrium thermodynamic properties: Diels–Alder reaction of 1,3‐butadiene and ethylene and Diels–Alder dimerization of 1,3‐butadiene
Authors: Lenz Terry G. , Vaughan John D.
Published: January 2005

ΔH0, ΔS0, and Kp have been calculated by force field methods for two prototype Diels–Alder reactions, the condensation of 1,3‐butadiene and ethylene, and the dimerization of 1,3‐butadiene. Three force field programs were employed, Allinger's MMP2, Warshel and Karplus' CFF/PI, and Boyd's MOLBD3 (with Anet and Yavari diene parameters). MMP2 and CFF/PI were combined to calculate reactant and product ΔH (by MMP2) and thermodynamic functions S0, C, and (H − H) by use of CFF/PI molecular geometry and vibrational frequencies. MOLBD3 was used separately to calculate these properties. The combined MMP2, CFF/PI calculations exhibited excellent agreement with available experimental equilibrium data for both reactions, despite uncertainties in the number and energies of adduct conformers in the dimerization reaction. The MOLBD3 results were less satisfying, particularly for the dimerization reaction, because the entropy of 1,3‐butadiene was overestimated by 2.5 cal mol−1 K−1.
Calculating electrostatic forces from grid‐calculated potentials
Authors: Davis M. E. , McCammon J. A.
Published: January 2005

The accurate calculation of forces from finite difference potentials is very important, especially in the area of Brownian dynamics simulations. Test charge methods are typically used to calculate these forces. In these methods, the potential is calculated with one group of charges present, then the force on a second set of charges is calculated as the negative of the gradient of the potential times the charge. The test charge methods for calculating forces between solute molecules have been compared with more accurate methods and then regions of validity of the test charge methods explored. The test charge methods neglect certain reaction field effects. It is found for the simple charged systems studied that beyond a center‐to‐center separation of about twice the sum of the molecular radii the test charge approximations can be quite good. For polar molecules with no net charges, however, the corrections can be significant to even longer ranges.