bluuebunny/crossref_metadata_2025_split huggingface dataset:
MM2' calculations on methylenecyclohexane, methylenecyclopentane, and cyclopentane. Pitfalls in the two‐bond drive technique: How large should the ring be?
Authors: Jaime Carlos 
Published: January 2005

AbstractMolecular mechanics calculations (MM2') are reported on methylenecyclohexane, 1, methylenecyclopentane, 2, and cyclopentane itself, 3. The calculated torsional energy barrier for the chair/chair interconversion of 1 if 8.7 kcal/mol (experimental ΔH ≠ = 8.4 ±0.1 kcal/mol); compounds 2 and 3 have virtually free pseudorotational pathways (calculated ΔH ≠ = 2.33 and 0.008 kcal/mol, respectively).
Molecular modeling studies of novel heteroarotinoids
Authors: Welsh William J. , Cody Vivian 
Published: January 2005

AbstractThe molecular structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem‐X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles ϕ1 and ϕ2 in closest agreement with the crystal structure, and all three computational methods yield values of ϕ1 and ϕ2 within about 10° of that found in the crystal structures. All three computational methods locate a minimum‐energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans‐stilbene. The calculated heteroring geometries also reproduce the twist‐sofa conformation observed for the crystal structure. Calculated conformational energies versus ϕ1 and ϕ2 indicate broad energy wells about the minimum‐energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur‐containing bond lengths and bond angles. The C‐S bonds found in these thio heteroarotinoids may possess more double‐bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur‐related force‐field parameters adopted for these calculations may require further refinement.
Overestimation of the coupling component in the CP technique. Application of the indirect counterpoise correction to the H2OHF hydrogen‐bonded system
Authors: Tolosa S. , Esperilla J. J. , del Valle F. J. Olivares 
Published: January 2005

AbstractAn extension of the Indirect Counterpoise (ICP) method, proposed in previous work, has been applied to the H2OHF hydrogen‐bonded system. The new version, which introduces important numerical changes is called EICP (Extended Indirect Counterpoise method). In their framework, the nonnegligible overestimation of the Counterpoise correction (CP) of Boys and Bernardi in the coupling component (MIX) of the interaction energy, computed via the Kitaura and Morokuma method is studied. Several basis sets, BS, were used to describe the oxygen, fluorine and hydrogen atoms that constitute the complex. The EICP results leads to more coherent values with the uncorrected energy than with the CP correction, which seems to be significantly affected by the size and type of the basis set used (especially for minimal basis sets).
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
Authors: Field Martin J. , Bash Paul A. , Karplus Martin 
Published: January 2005

AbstractA combined quantum mechanical (QM) and molecular mechanical (MM) potential has been developed for the study of reactions in condensed phases. For the quantum mechanical calculations semiempirical methods of the MNDO and AM1 type are used, while the molecular mechanics part is treated with the CHARMM force field. Specific prescriptions are given for the interactions between the QM and MM portions of the system; cases in which the QM and MM methodology is applied to parts of the same molecule or to different molecules are considered. The details of the method and a range of test calculations, including comparisons with ab initio and experimental results, are given. It is found that in many cases satisfactory results are obtained. However, there are limitations to this type of approach, some of which arise from the AM1 or MNDO methods themselves and others from the present QM/MM implementation. This suggests that it is important to test the applicability of the method to each particular case prior to its use. Possible areas of improvement in the methodology are discussed.
Design and application of a molecular mechanics force field for alkyl iodides including an electrostatic polarization model
Authors: Carballeira L. , Pereiras A. J. , Rios M. A. 
Published: January 2005

AbstractWe describe a force field extending Boyd and Kesner's molecule mechanics treatment of alkyl chlorides, fluorides and bromides to alkyl iodides: accordingly, as well as parameters for the potential energy of bond stretching and bending and for interactions between nonbonded atoms, the field includes parameters taking into account permanent and induced C‐I dipoles, whose values have been estimated by fitting the model to experimental dipole moment data. The results of applying this force field to 22 organic iodides comprising several substitution series are reported, and the structural and energy trends in the various series are discussed. These results agree satisfactorily with available experimental data and with those obtained by A. Y. Meyer using a different kind of force field.
The anomeric effect: Ab‐initio studies on molecules of the type XCH2OCH3
Authors: Krol Maarten C. , Huige Cornelis J. M. , Altona Cornelis 
Published: January 2005

AbstractThe anomeric effect of the functional groups X = CN, CCH, COOH, COO−, OCH3, NH2, and NH+3 has been studied with ab initio techniques. Geometry effects upon rotation around the central CO bond in XCH2OCH3 have been compared in the various compounds. The energy differences between the conformers with a gauche and trans (XCOC) arrangement were calculated at the 6‐31G* level in the fully optimized 4‐21G geometries. Energy differences calculated at the 4‐21G level appeared not to be reliable, especially for the groups X that contain non‐sp3 hybridized atoms. The 6‐31G* energy differences indicate a normal anomeric effect for X = COO−, OCH3, and NH2(g+) (ca. 13 kJ/mol) and a small anomeric effect for X = COOH, CN, and CCH (ca. 6 kJ/mol). For X = NH2(t) and NH+3 a reverse anomeric effect occurs. These observations are in line with experimental results and evidence is given for a competition among various stereoelectronic interactions that occur at the same anomeric center. Geometry variations can be understood in terms of simple rules associated with anomeric orbital interactions. Trends followed when the group X is varied cannot be related in a straightforward way to the energy differences between the trans and the gauche forms in these compounds. Only the variation in the gauche torsion angle XCOC follows roughly the same trend.
Computer generation of distance polynomials of graphs
Authors: Balasubramanian K. 
Published: January 2005

AbstractA computer program is developed to compute distance polynomials of graphs containing up to 200 vertices. The code also computes the eigenvalues and the eigenvectors of the distance matrix. It requires as input only the neighborhood information from which the program constructs the distance matrix. The eigenvalues and eigenvectors are computed using the Givens‐Householder method while the characteristic polynomials of the distance matrix are constructed using the codes developed by the author before. The newly developed codes are tested out on many graphs containing large numbers of vertices. It is shown that some cyclic isospectral graphs are differentiated by their distance polynomials although distance polynomials themselves are in general not unique structural invariants.
MM2 study of 20‐hydroxy‐4,7,13,16‐tetraoxa‐1,10‐diazabicyclo [8,8,3] heneicosane and its formation controlled by hydrogen bonding
Authors: Stibor Ivan , Holý Petr , Hobza Pavel , Čársky Petr 
Published: January 2005

AbstractA van der Waals‐type parameter set has been developed for hydrogen bonding in the MM2(85) force field to reproduce the structures and binding energies of complexes (H2O)2, (CH3OH)2, H3N …︁ H2O, H3N …︁ HOCH3, (CH3)3N …︁ H2O, and HCONH2 …︁ H2O reported in the literature. The MM2(85) force field modified in this way was then applied to the title compound to explain its unexpected stability, unusual properties of its hydroxyl group, and solvent effect on the reaction mechanism in the condensation of Kryptofix 22 ® with epichlorohydrine.
PRODEN: A new program for calculating integrated projected populations
Authors: Agrafiotis Dimitris K. , Tansy Brian , Streitwieser Andrew 
Published: January 2005

AbstractTwo new computational methods for the evaluation and partitioning of projected, planar, and averaged slab electron densities, implemented in the program PRODEN, are presented. The new algorithms for the projection, demarcation, and integration of electron densities are described and evaluated in terms of speed and numerical accuracy. Integrated Projected Populations are analyzed and some of the advantages and limitations of the methods are discussed.
Theoretical studies on the intramolecular cyclization of alkyl halide anions
Authors: Lee Ikchoon , Kim Chang Kon 
Published: January 2005

AbstractThe intramolecular cyclization reactions of alkyl fluoride and chloride anions1 were investigated theoretically using the AM1 method. Formation of five‐membered ring was the most reactive and that of three‐membered ring was the least reactive process in both series. For the fluoride series the reactivity order of n = 5 > 6 > 7 > 4 > 3 was dictated by the enthalpy (ΔH≠) effect while for the chloride series the entropy (ΔS≠) effect was found to play somewhat greater role due to the much better leaving ability of the chloride anion leading to the reactivity order of n = 5 > 6 > 4 > 7 > 3. For both series, BEP principle held and the degree of bond formation was greater with the fluoride series owing to the poor electron acceptor ability of the cleaving bond.
A cautionary note on the use of the frozen‐core approximation for correlation energy calculations involving alkali metals
Authors: Hofmann Heinz , Hünsele Elke , Clark Timothy 
Published: January 2005

AbstractTest calculations have shown that correlation energies calculated using the frozen‐core approximation in programs, such as the Gaussian series, that assume the lowest MOs to be the core orbitals may be significantly in error. Some valence orbitals in systems involving the heavier alkali metals and electronegative elements have lower energies than the highest core orbitals of the metal and are therefore erroneously omitted from the correlation energy calculation. Some examples are discussed.
A space‐saving modification of Davidson's eigenvector algorithm
Authors: van Lenthe Johan H. , Pulay Peter 
Published: January 2005

AbstractA modification of Davidson's eigenvalue algorithm, based on the conjugate gradient method, is described. This method needs storage only for a few vectors (five to seven, depending on the implementation), making it practical for very large problems where disk storage is the limiting factor, without the necessity of restarting or discarding some expansion vectors. The convergence characteristics of the modified method are essentially identical with those of the original Davidson method if all expansion vectors are retained in the latter.
Compact contracted basis sets for third‐row atoms: Ga–Kr
Authors: Binning R. C. , Curtiss L. A. 
Published: January 2005

AbstractThe (14s11p5d) primitive basis set of Dunning for the third‐row main group atoms Ga‐Kr has been contracted [6s4p1d]. The core functions have been relatively highly contracted while those which represent the valence region have been left uncontracted to maintain flexibility. Calculations with the [6s4p1d] contraction are reported for a variety of molecules involving third‐row atoms. This basis set is found to satisfactorily reproduce experimental properties such as geometric configurations, dipole moments, and vibrational frequencies for a range of molecules. Comparisons are made with the performance of the uncontracted basis set. Polarization functions for the contracted basis set are reported and performance of the basis set with and without polarization functions is examined. A relaxation of the [6s4p1d] contraction to [9s6p2d] for higher level evergy calculations is also presented.
Comparison of semiempirical MO methods applied to large molecules
Authors: Scano P. , Thomson C. 
Published: January 2005

AbstractThe heats of formation for 19 molecules have been calculated with PM3 and AM1 semiempirical methods. The values obtained have been compared with experimental heats of formation. With PM3 and AM1 the average differences between calculated and experimental heats of formation are 8.45 and 12.34 kcal mol−1 respectively. There are significant differences when large molecules are considered: this suggests that the parameterization should be done including larger molecules.
Towards the truly nonempirical computation of hyperfine interactions: A contribution to the debate on the t‐butyl radical
Authors: Overill Richard E. 
Published: January 2005

AbstractCarefully calibrated large‐scale nonempirical CI computations have been performed for the isotropic hyperfine splittings of the t‐butyl radical. The results have been used to interpret the effects of out‐of‐plane vibration of the radical center, with and without coupling to methyl rotations, on the observed splitting at the radical center. In particular, the value computed under rotation‐inversion is 39 G, in good agreement with the ESR result of 45 G.
Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi
Authors: Stewart James J. P. 
Published: January 2005

AbstractUsing a recently developed procedure for optimizing parameters for semiempirical methods,1 PM3 has been extended to a total of 28 elements. Average ΔHf errors for the newly parameterized elements are Be: 8.6, Mg: 8.4, Zn: 5.8, Ga: 14.9, Ge: 11.4, As: 8.5, Se: 11.1, Cd: 2.6, In: 11.3, Sn: 9.0, Sb: 13.7, Te: 11.3, Hg: 6.8, Tl: 6.5, Pb: 7.4, and Bi: 10.9 kcal/mol. For some elements the paucity of data has resulted in a method, which, while highly accurate, is likely to be only poorly predictive.
Applications of simulated annealing to the conformational analysis of flexible molecules
Authors: Wilson Stephen R. , Cui Weili , Moskowitz Jules W. , Schmidt Kevin E. 
Published: January 2005

AbstractWe describe in this article our solution to the global minimum problem which uses the simulated annealing algorithm of Kirkpatrick. This method is a Metropolis (e‐ΔE/kT) Monte Carlo sampling of conformation space with simultaneous constraint of the search by lowering the temperature T so that the search converges on the global minimum. The Anneal‐Conformer program has been extensively tested with peptides and organic molecules using either the Amber or MM2 force fields. A history file of the simulated annealing process allows reconstruction of the random walk in conformation space for subsequent examination. Thus plots of distance and dihedral angle changes during the search for the global minimum can be examined to deduce molecular shape and flexibility. A separate program Conf‐Gen reads the history file and extracts all low energy conformations visited during the run.
Correlation of singlet‐triplet gaps for aryl carbenes calculated by MINDO/3, MNDO, AM1, and PM3 with Hammett‐type substituent constants
Authors: Karaman Rafik , Huang Jun‐Tsu Luke , Fry James L. 
Published: January 2005

AbstractHeats of formation, atomic charges, and geometries of some 110 structures involving substituted singlet and triplet phenyl and 4,4‐dimethyl‐1,4‐dihydronaphthalene carbenes and the corresponding diazomethanes were calculated by MINDO/3, MNDO, AM1, and PM3 semiempirical molecular orbital methods. The singlet‐triplet gaps for AM1 and PM3 calculations for the para derivatives in both systems have been successfully correlated with Brown σ+ constants. Good correlations with σ+ were found for the charges on the carbenic centers of the singlets as well as with the energy barrier for rotation of the aryl group about the C‐C single bond in substituted singlet phenylcarbenes. Comparisons of these results with experimental data indicate that AM1 and PM3 are much better than MNDO and MINDO/3 in predicting the intrinsic substituent effects in singlet carbenes.
Conformational preferences of XONO2 systems (X = H, F, Cl, CH3) from ab initio techniques
Authors: Smith Brian J. , Marsden Colin J. 
Published: January 2005

AbstractAb initio SCF and MP2 methods have been used to calculate the geometries and relative energies of both planar and nonplanar rotamers of several nitrates with a DZP basis set. The planar arrangement of atoms is found to be the lower energy configuration in all cases. The interconversion between rotamers is analyzed by partitioning the contributions to the total SCF energy in a variety of ways.
Searching for conformers of nine‐ to twelve‐ring hydrocarbons on the MM2 and MM3 energy surfaces: Stochastic search for interconversion pathways
Authors: Saunders Martin 
Published: January 2005

AbstractThe stochastic search method was employed to find as many conformers on the MM2 and MM3 energy surfaces as possible for cyclic saturated hydrocarbons with ring sizes from 9 through 12. The number found was 8 MM2 (8 MM3) for 9 rings, 18 MM2 (16 MM3) for 10 rings, 40 MM2 (29 MM3) for 11 rings, and 111 MM2 (90 MM3) for 12 rings. A measure of similarity between pairs of conformers of a compound, called conformational distance, is described. It was used to correlate similar MM2 and MM3 conformers. It was discovered that some conformers on each energy surface are not close to minima on the other surface in rings larger than 9. On refinement with the other optimizer, they changed considerably—going downhill to other previously found minima on the other energy surface or (in a few cases) going to minima which had not been found by direct searches. Conformational distance was also employed as an indication of which pairs of MM2 (or MM3) conformers are likely to interconvert rapidly. A new stochastic procedure of using small kicks was used to search for the most likely interconversion processes among the conformers. There is fairly good agreement between the most facile pathways located by it and unusually short conformational distances. Several additional 12‐ring conformers (not found with previous methods) were located through application of this small kick procedure.
A topological analysis of molecular electrostatic potential on van der Waals surfaces for histamine and 4‐substituted derivatives as H2‐receptor agonists
Authors: Arteca Gustavo A. , Hernández‐Laguna Alfonso , Rández Juan J. , Smeyers Yves G. , Mezey Paul G. 
Published: January 2005

AbstractThe molecular electrostatic potential is an important property for characterizing chemical reactivity and the interactions between biomolecules. A joint description of the molecular electrostatics and the molecular shape in 3‐space is more complete than the one provided by only the electrostatics. The characterization of the interrelations between the shape features of a formal “molecular surface” and electrostatic potential is of importance in assessing the degree of similarity within a family of molecules. In this work, we have applied a recently developed topological technique to characterize these aspects of the molecular shape. The approach allows one to calculate simple and concise shape codes which can be used for rationalizing structure‐activity correlations. These shape codes are related to topological invariants which characterize the topological structure given to the molecular surface by the electrostatic potential. In this work the molecules of interest are a series of four agonists of the H2‐receptor of histamine with very different pharmacological activities. We have analyzed the electrostatics on the fused‐sphere (van der Waals) surfaces of these compounds for a number of conformations. Some structural properties and the shape descriptions have been found to correlate with the activity. The results are discussed in the context of the current H2‐receptor models.
An alternative self‐interaction correction in the generalized exchange local‐density functional theory
Authors: Guo Yufei , Whitehead M. A. 
Published: January 2005

AbstractThe local‐density functional (LDF) theory does not accurately predict the total energy and the orbital energy of an atom, because of the incomplete cancellation of the self‐interaction in the Coulomb integral by that in the exchange integral. Recent investigations showed that the agreement of the total energy and one‐electron eigenvalue of an atom in the LDF and Hartree–Fock (HF) theories are remarkably improved by introducing a self‐interaction correction in the LDF theory. An alternative self‐interaction correction (ASIC) in the generalized exchange local‐density functional (GX‐LSD) theory is developed by equalizing the one‐electron eigenvalue with the ionization potential of the corresponding orbital. The ASIC is subsequently applied to some closed‐shell atoms and shown to give numerically better results than both the self‐interaction corrected (SIC) exchange‐only local‐spin‐density functional theory (SIC‐XO‐LSD) and the self‐interaction corrected GX‐LSD theory (SIC‐GX‐LSD).
Development of an internal searching algorithm for parameterization of the MM2/MM3 force fields
Authors: Schnur Dora M. , Grieshaber Mark V. , Bowen J. Phillip 
Published: January 2005

AbstractApplication of Allinger's MM2/MM3 force fields to molecules of real interest is frequently hindered by the lack of parameters for various heterocyclic systems and for poly‐functionalized molecules. A common approach to this problem is to manually choose missing parameters “by analogy” with those that are part of the force field's internal parameter set. Naturally, this is generally attempted only by those possessing extensive experience with force fields. In order to use the MM2/MM3 force fields to study herbicides, an algorithm has been developed to automate this process for the non MM2 specialist. Using a set of “relative cost” criteria for atom type replacement, the algorithm searches the force field parameter set and selects the most appropriate parameters for a given molecule whose MM2 output file contains “missing parameter” errors. The program selects parameter error messages from a standard MM2 output file, finds analogous parameters, asks the user to verify their appropriateness and creates a standard MM2 parameter deck for the molecule of interest.
Detection of cavities in a set of interpenetrating spheres
Authors: Alard Philippe , Wodak Shoshana J. 
Published: January 2005

AbstractA general topological procedure is described that is able to detect cavities of all shapes and sizes in a system of interpenetrating spheres. The procedure is coupled to an analytic algorithm for computing surface areas and volumes, but as such, involves only logical operations and is therefore not subject to numerical imprecision. Its application to the identification of internal cavities in molecular systems is illustrated.