bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractFor 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

AbstractThe 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

AbstractSignificant 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

AbstractThe 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.
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

AbstractOur 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

AbstractAn 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

AbstractUsing 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

AbstractA 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

AbstractA 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

AbstractThe 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

AbstractThe 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

AbstractA 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

AbstractA 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

AbstractFour 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

AbstractOur 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

AbstractThe 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

AbstractA 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

AbstractAn 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.