bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amino acid sequence specificities of an adhesive recognition signal
Authors: Yamada Kenneth M. , Kennedy Dorothy W. 
Published: December 2004

AbstractSynthetic 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

AbstractTwo 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

AbstractThe 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

AbstractPrevious 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

AbstractThe 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

AbstractThis 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

AbstractA 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

AbstractA 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

AbstractMINDO/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.
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

AbstractThe 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

AbstractCalculations 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

AbstractVE‐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

AbstractAb 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

AbstractCNDO/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

AbstractElectron 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

AbstractThe 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

AbstractPrediction 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

AbstractThe 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

AbstractAn 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.
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

AbstractEarlier 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

AbstractThe 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.