bluuebunny/crossref_metadata_2025 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

Molecular 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

The 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

An 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

A 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

We 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

The 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

A 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

A 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

Two 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

The 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

Test 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

A 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

The (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

The 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

Carefully 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

Using 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

We 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

Heats 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

Ab 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

The 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

The 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

The 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

Application 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

A 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.
GEPOL: An improved description of molecular surfaces II. Computing the molecular area and volume
Authors: Silla Estanislao , Tuñón Iñaki , Pascual‐Ahuir Juan Luis
Published: January 2005

The algorithm used by the program GEPOL for a finer description of molecular surface (for a fast calculation of molecular area and volume and for an efficient selection of sampling points) is presented in detail. Different types of surfaces such as van der Waals and Richard's molecular surfaces can be computed. As we described in the first article (J.L. Pascual‐Ahuir and E. Silla, J. Comp. Chem., 11, 1047(1990)), GEPOL begins by building a set of spherical surfaces which fill the space which is not solvent accessible. In this second article, a triangular tessellation approach to select the parts of these spherical surfaces which form the molecular surface is described. By using a data coded generic pentakisdodecahedron, each spherical surface is divided in triangular tesserae. A simple method is used to eliminate all triangles found at the intersection volume of the spheres. The center coordinates and the surface of the remaining triangles are used in order to calculate the molecular area and volume and as starting point of the graphic representation of scalar and vector properties. We study the behavior of the method, presenting several examples of application. Special attention is given to the accuracy, spatial invariance and computer efficiency measured by CPU time. Some models of aligned spheres whose area and volume can be found exactly allow us to do a comparative study with a well‐known method, analyzing their behavior in line with their respective graining parameters. A fragment of protein is used as an example of the application of the method for characterizing biomolecular surfaces. Aqueous solubility of organic compounds is studied as an example of the experimental property that depends on the molecular area obtaining a good correlation between the logarithm of the solubility and the area calculated using GEPOL.
An SCF study of 10‐vertex and 12‐vertex boranes and heteroboranes
Authors: Zahradník Rudolf , Balaji V. , Michl Josef
Published: January 2005

For symmetry‐constrained boranes B10H, B12H, and their valence isoelectronic analogues containing a single hetero atom, completely optimized geometries were obtained using Hartree–Fock SCF calculations with the 3‐21G and 6‐31G* basis sets. For the anionic and dianionic species, the geometry optimization was also carried out using the 6‐31 + G* basis set. Harmonic vibrational frequencies were obtained at HF/3‐21G level. The results compare well with experiment where available.
Variable atomic radii based on some approximate configurational invariance and transferability properties of the electron density
Authors: Arteca Gustavo A. , Grant Naomi D. , Mezey Paul G.
Published: January 2005

The purpose of this study is to design a technique that generates a variable van der Waals‐like surface for any desired charge density value of a molecule. The method is based on the recognition that for each fixed density value, within a wide range, certain shape features of the electron density contours are approximately invariant under configuration rearrangements, such as bending and stretchings in polyatomic molecules. These invariants appear in the form of spherical regions in space around the nuclei, where no density contours of a given level set value enter. These regions, the so‐called invariant cores, behave as approximately transferable quasi‐atomic spherical surfaces. We have evaluated these cores in molecules, and also approximated them in terms of the electron density of isolated atoms. The properties of these quasi‐atomic surfaces allow one to design a scale of variable atomic radii based on the size of the transferable isodensity spheres. In this work we provide a detailed description of the dependence of the diameters of these spheres on the electron density values. We show that, by using this scale of radii, it is possible to design fused‐sphere molecular models that closely mimic isodensity surfaces for a whole range of density values. The results discussed here allow one to relate molecular size with charge density. We propose the use of these scales for the construction of more realistic van der Waals model surfaces when studying molecular shape in the context of computer‐assisted molecular modeling.
Reactivity of biologically important reduced pyridines. VIII. A semiempirical (AM1) study of the oxidation of 3‐substituted‐1‐methyl‐1,4‐dihydropyridines
Authors: Brewster Marcus E. , Huang Ming‐Ju , Kaminski James J. , Pop Emil , Bodor Nicholas
Published: January 2005

Significant linear correlations were observed between AM1‐derived adiabatic, but not vertical, ionization potentials and the log of ferricyanide‐mediated oxidation of 3‐substituted‐1‐methyl‐1,4‐dihydropyridines. This result is consistent with a rate‐determining electron loss in the reaction sequence and suggests molecular relaxation subsequent to the initial electron transfer. In addition, useful relationships were generated between oxidation rate and absolute electronegativity, a parameter derived from hard‐soft acid‐base theory.
Reliability of atomic natural orbital basis sets in calculations involving pseudopotentials
Authors: Sousa C. , Rubio J. , Illas F.
Published: January 2005

The performance of Atomic Natural Orbital (ANO) basis sets for calculations involving nonempirical core pseudopotentials has been studied by comparing the results for atomic and molecular nitrogen obtained using contracted ANO basis sets with those obtained using both the primitive set and a segmented one. The primitive set has been optimized at the SCF level for atomic N treated as a five‐electron pseudo‐atom, and consists of 7s and 7p primitive GTOs supplemented by 2d and 1f GTOs optimized at the CI level. From this primitive set three contracted [3s 3p 2d 1f] sets have been obtained. The first one has been derived from the ANOs of the neutral atom, the second has been obtained from an averaged density matrix and the third one is a segmented set. For the atom, the segmented set gives a zero contraction error at the SCF level as it must be in valence‐only calculations. The ANO basis sets show some small contraction error at the SCF level but perform better in CI calculations. However, for the diatomic N2 molecule the ANO basis sets exhibit a rather large contraction error in the calculated SCF energy. A detailed analysis of the origin of this error is reported, which shows that the conventional strategy used to derive ANO basis sets does not work very well when pseudopotentials are involved.
New realization of loop driven direct CI
Authors: Wang Yubin , Wen Zhenyi , Zhang Zhiyong , Du Quishi
Published: January 2005

In this article we report a newly developed direct CI program and its preliminary applications. This program is based mainly on the relationship between direct and exchange type loops and the rederivation of the external loop shapes.
Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies
Authors: Luzhkov V. , Warshel A.
Published: January 2005

Our previously developed approaches for integrating quantum mechanical molecular orbital methods with microscopic solvent models are refined and examined. These approaches consider the nonlinear solute–solvent coupling in a self‐consistent way by incorporating the potential from the solvent dipoles in the solute Hamiltonian, while considering the polarization of the solvent by the potential from the solute charges. The solvent models used include the simplified Langevin Dipoles (LD) model and the much more expensive surface constrained All Atom Solvent (SCAAS) model, which is combined with a free energy pertubation (FEP) approach. Both methods are effectively integrated with the quantum mechanical AMPAC package and can be easily combined with other quantum mechanical programs. The advantages of the present approaches and their earlier versions over macroscopic reaction field models and supermolecular approaches are considered. A LD/MNDO study of solvated organic ions demonstrates that this model can yield reliable solvation energies, provided the quantum mechanical charges are scaled to have similar magnitudes to those obtained by high level ab initio methods. The incorporation of a field‐dependent hydrophobic term in the LD free energy makes the present approach capable of evaluating the free energy of transfer of polar molecules from non polar solvents to aqueous solutions. The reliability of the LD approach is examined not only by evaluating a rather standard set of solvation energies of organic ions and polar molecules, but also by considering the stringent test case of sterically hindered hydrophobic ions. In this case, we compare the LD/MNDO solvation energies to the more rigorous FEP/SCAAS/MNDO solvation energies. Both methods are found to give similar results even in this challenging test case. The FEP/SCAAS/AMPAC method is incorporated into the current version of the program ENZYMIX. This option allows one to study chemical reactions in enzymes and in solutions using the MNDO and AM1 approximations. A special procedure that uses the EVB method as a reference potential for SCF MO calculations should help in improving the reliability of such studies.
The optimized ellisoidal cavity and its application to the self‐consistent reaction field calculation of hydration energies of cations and neutral molecules
Authors: Ford George P. , Wang Bingze
Published: January 2005

An optimized ellipsoidal cavity has been defined for use in self‐consistent reaction field (SCRF) calculations for the incorporation of aqueous medium effects. The location, size, and orientation of the cavity is obtained by minimizing the average interaction between the solute and a simplified water molecule over the surface of the cavity. The calculated hydration energies of organic cations and neutral molecules using this cavity and the SCRF method of Rinaldi and Rivail with the AM1 wave function led to surprisingly good agreement with the experimental data. The optimized cavities are discussed in relation to those based on van der Waals' volumes and on polarizability criteria.
Pauli repulsion in the open shell species BeH and Co+
Authors: Chang T.C.
Published: January 2005

Using the natural bond orbital method, one may associate the valence bond configuration and Lewis structure concepts to wave functions consisting of molecular orbitals and thus gain intuitive insight into the molecular potential energy curves. Natural bond orbital analysis of the restricted open shell Hartree–Fock and unrestricted Hartree–Fock wave functions for the BeH ground state provides an intuitive model to help understand the nature of the bonding in this open shell species. The contrasting behavior of the bonding orbitals for different spins can be attributed to differences in the Pauli repulsive interactions with the lonepair orbitals. Such behavior occurs in BeH(2Σ) but does not in CO+(2Π) because the Pauli repulsion depends on the orbital overlap.
Standard‐geometry chains fitted to X‐ray derived structures: Validation of the rigid‐geometry approximation. II. Systematic searches for short loops in proteins: Applications to bovine pancreatic ribonuclease A and human lysozyme
Authors: Palmer Kathleen A. , Scheraga Harold A.
Published: January 2005

A rigid‐geometry approach to protein conformational searches has been used to calculate stable structures for localized regions of the molecules bovine pancreatic ribonuclease A and human lysozyme. The search method is essentially an application of the local deformation algorithm of Gō and Scheraga [Macromolecules, 3, 178–187 (1970)]. A series of local chain deformations is produced in the polypeptide chain. The deformations are screened to eliminate structures having serious atomic overlaps or energetically unreasonable backbone dihedral angles. The remaining structures are refined by energy minimization and the rms deviations of the energy‐minimized structures, relative to the native structures, are calculated. The correlation between low rms deviation and low energy is reasonably good, indicating that this method should be useful in generating a small number of candidate structures for further energy refinement. Further applications to proteins with an unknown structure, such as homology‐based modeling applications, should now be amenable to this type of procedure.
Kramers' restricted hartree—fock method for polyatomic molecules using ab initio relativistic effective core potentials with spin—orbit operators
Authors: Lee Sang Yeon , Lee Yoon Sup
Published: January 2005

A two‐component Kramers' restricted Hartree–Fock method (KRHF) has been developed for the polyatomic molecules with closed shell configurations. The present KRHF program utilizes the relativistic effective core potentials with spin–orbit operators at the Hartree–Fock (HF) level and produces molecular spinors obeying the double group symmetry. The KRHF program enables the variational calculation of spin–orbit interactions at the HF level. KRHF calculations have been performed for the HX, X2, XY(X, Y = I, Br), and CH3I molecules. It is demonstrated that the orbital energies from KRHF calculations are useful for the interpretation of spin‐orbit splittings in photoelectron spectra. In all molecules studied, bond lengths are only slightly expanded, harmonic vibrational frequencies are reduced, and bond energies are significantly decreased by the spin–orbit interactions.
Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water
Authors: Mezei Mihaly
Published: January 2005

The polynomial path is introduced for the calculation of liquid state free energies. The well‐characterized SPC, TIP4P, and MCY water models were used to demonstrate its efficiency, as well as its range of applicability in conjunction with Monte Carlo computer simulations using thermodynamic integration based on Gaussian quadratures. The technique employed is compared with the slow‐growth method (another variant of thermodynamic integration), the perturbation method, and the use of the grand‐canonical ensemble.
Fast geometry optimizationin self‐cosistent reaction field computations on solvated molecules
Authors: Rinaldi Daniel , Rivail Jean‐Louis , Rguini Noureddine
Published: January 2005

The free energy gradient or Hessian of a molecule interacting with a liquid represented by a dielectric continuum is derived in the self‐consistent reaction field formalism. An ellipsoidal approximation of the cavity is proposed with an algorithm to automatically define the ellipsoid from the nuclear coordinates of the atoms. With this approximation, geometry optimization of the solvated molecule becomes very fast. This method has been implemented in some standard ab initio or semiempirical computational codes. As a first test of the method, full geometry optimization of formamide in a high dielectric constant medium reveals that the CPU time needed for one optimization cycle is less than 3% longer for a solvated species than for the corresponding free molecule.
DMC: A multifunctional hybrid dynamics/Monte Carlo simulation algorithm for the evaluation of conformational space
Authors: Morley S.D. , Jackson D.E. , Saunders M.R. , Vinter J.G.
Published: January 2005

A hybrid conformational search algorithm (DMC) is described that combines a modified form of molecular dynamics with Metropolis Monte Carlo sampling, using the COSMIC(90) force field. Trial configurations are generated by short bursts of high‐temperature dynamics in which the initial kinetic energy is focused into single bond rotations or alternatively into “corner‐flapping” motions in ring systems. Constant temperature and simulated annealing search protocols have been applied to the conformational analysis of several model hydrocarbons (cyclopentane, cyclohexane, cycloheptane, cyclooctane, cycloheptadecane, decane, and tetradecane), and the performance compared with conventional molecular dynamics and Monte Carlo sampling methods. Optimum Metropolis sampling temperatures have been determined and range from 1000–2000 K for acyclic molecules to 3000 K for cyclic systems. Simulated annealing runs are most successful at locating the global minimum when cooling slowing from these optimum temperatures.
Torsional energy levels and wave functions
Authors: Chung‐Phillips Alice
Published: January 2005

A numerical method for solving the approximate Schrödinger equation (SE) for a single internal motion is presented. In the SE the reduced moment of inertia I(ϕ) and potential energy V(ϕ) are expressed as functions of the torsional angle ϕ. Molecular examples include ethane, chloroethane, and 1,2‐dichloroethane for which I(ϕ) and V(ϕ) have been derived from the HF/6‐31G* optimized geometries and energies at ϕ increments of 30°. The resulting potential energy curves, energy levels, and wave functions are shown graphically. The calculated fundamental torsional frequencies are found to fall within 10 cm−1 of the experimental values. Approximations for the off‐diagonal energy matrix elements, and numerical accuracy of torsional energy levels, are shown to be satisfactory. Attention is called to the computer programs developed for this work and their applications to torsional studies in relevant areas of spectroscopy, thermodynamics, and reaction rates. © 1992 by John Wiley & Sons, Inc.
Theoretical studies of [n]paracyclophanes and their valence isomers. I. Geometries, strain energies, and enthalpies of the inter‐conversions of [n]paracyclophanes and their Dewar benzee isomers
Authors: Bockisch F. , Rayez J.C. , Liotard D. , Duguay B.
Published: January 2005

Four semiempirical methods (AM1, MNDO, PM3, and MINDO/3) are used to calculate the deformation angles of [n]paracyclophanes and their Dewar benzene isomers for n = 3… 10. The results obtained by all these methods are in good agreement with data from X‐ray studies. We have determined the strain energies that, in both series of compounds, are due to two components: (1) the strain energy of deformation of the cycle (aromatic or Dewar Benzene skeletons) and (2) the strain energy of the oligomethylene chain. In [6]paracyclophane, the strain energy [SEring(MNDO) ≈︁ 32.9 kcal/mol] almost compensates the resonance energy (Eresonance ≈ 36 kcal/mol) so that its chemical properties are closer to alkenes than to benzenic compounds. To better reproduce the enthalpy of the valence isomerization [n]Dewar bezene → [n]paracyclophane, which is poorly calculated with these methods, a correction is proposed and the reaction enthalpy of [6]paracyclophane is estimated to be about ΔHr ≈ 15 ± 15 kcal/mol. It is found that MNDO and MINDO/3 need the smallest corrections, but MNDO leads to better geometries than MINDO/3. In conclusion, MNDO seems to be the best technique for further studies of these compounds. © 1992 by John Wiley & Sons, Inc.
PM3‐SM3: A general parameterization for including aqueous solvation effects in the PM3 molecular orbital model
Authors: Cramer Christopher J. , Truhlar Donald G.
Published: January 2005

Our recently proposed scheme for including aqueous solvation free energies in parameterized NDDO SCF models is extended to the Parameterized Model 3 semiempirical Hamiltonian. The solvation model takes accurate account of the hydrophobic effect for hydrocarbons, as well as electric polarization of the solvent, the free energy of cavitation, and dispersion interactions. Eight heteroatoms are included (along with H and C), and the new model is parameterized accurately for the water molecule itself, which allows meaningful treatments of specifically hydrogen bonded water molecules. The unphysical partial charges on nitrogen atoms predicted by the Parameterized Model 3 Hamiltonian limit the accuracy of the predicted solvation energies for some compounds containing nitrogen, but the model may be very useful for other systems, especially those for which PM3 is preferred over AM1 for the solute properties of the particular system under study. © 1992 by John Wiley & Sons, Inc.
Molecular mechanics studies of ketene derivatives and related structures
Authors: Stewart Eugene L. , Bowen J. Phillip
Published: January 2005

The MM2 and MM3 force fields have now been parameterized for ketene and its various derivatives. With the addition of the Csp  O bond stretching and CCspO bond bending parameters, calculations were performed on ketene and six substituted ketene compounds. The MM2 results are quite good with only minimal errors in the calculation of CH bond lengths and H‐C‐H bond angles. Additionally, CF bond parameters in MM2 have been re‐adjusted to give better results in monofluorinated species, but, unfortunately, resulting in greater error in the polyfluorinated compounds. The results of geometry calculations by MM3 are similar to those obtained by MM2 with the exception of a significant improvement in the geometry of dimethylketene. The MM3 vibrational frequencies calculated in this study are also in good agreement with available experimental and ab initio results with the exception of a few low frequency in‐and out‐of‐plane bending modes. © 1992 by John Wiley & Sons, Inc.
From linear combinations to integrals: A new approach to the basis function problem
Authors: Flores Jesús R.
Published: January 2005

A new formalism is presented, based upon the finite element method, that permits a dual representation of orbitals in terms of exponential or Gaussian functions as both an integral over the space of exponential parameters and as a linear combination of basis functions. The method has been implemented for the atomic Hartree–Fock problem using exponential functions and test calculations made for atoms ranging from B to Cl. Accurate and consistent results can be obtained for a variety of atoms in a simple way using computational schemes that are systematic and hierarchic in nature. The new formalism is promising for any method where the calculation of integrals is not a major problem, such as some approaches of the density functional method and the pseudospectral formulation of ab initio methods. © 1992 by John Wiley & Sons, Inc.
Vector processing algorithm for electron repulsion integrals in Ab Initio HF calculation based upon the PK supermatrix
Authors: Yahiro Shuichi , Gondo Yasuhiko
Published: January 2005

An efficient vector processing algorithm generating PK supermatrices has been developed, in particular aiming at calculations on large molecules. The algorithm utilizes the recurrence relations for electron repulsion integrals. The PK supermatrices are listed in a nearly canonical order so that the Fock matrix generation is efficiently vectorized, no temporary ERI and PK files being used. This is effected by partition of the basis set (atomic orbitals) into subsets of certain appropriate sizes, and the partition approach is named as the three‐dimensional partial space method. A high‐speed Hartree–Fock calculation including integrals and SCF procedures is achieved. © 1992 by John Wiley & Sons, Inc.
Optimal use of the recurrence relations for the evaluation of molecular integrals over Cartesian Gaussian basis functions
Authors: Ryu Ungsik , Kim Myeongcheol , Lee Yoon Sup
Published: January 2005

We consider the tree search problem for the recurrence relation that appears in the evaluation of molecular integrals over Cartesian Gaussian basis functions. A systematic way of performing tree search is shown. By applying the result of tree searching to the LRL2 method of Lindh, Ryu, and Liu (LRL) (J. Chem. Phys., 95, 5889 1991), which is an auxiliary function‐based method, we obtain significant reductions of the floating point operations (FLOPS) counts in the K4 region. The resulting FLOPS counts in the K4 region are comparable up to [dd|dd] angular momentum cases to the LRL1 method of LRL, currently the method requiring least FLOPS for [dd|dd] and higher angular momentum basis functions. For [ff|ff], [gg|gg], [hh|hh], and [ii|ii] cases, the required FLOPS are 24, 40, 51, and 59%, respectively, less than the LRL1 method in the K4 region. These are the best FLOPS counts available in the literature for high angular momentum cases. Also, there will be no overhead in either the K2 or K0 region in implementing the present scheme. This should lead to more efficient codes of integral evaluations for higher angular momentum cases than any other existing codes. © 1993 John Wiley & Sons, Inc.