bluuebunny/crossref_metadata_2025 huggingface dataset:
The remarkably invariant interaction energies of lithium first‐row compounds with water and with ammonia
Authors: Kaufmann Elmar , Tidor Bruce , Schleyer Paul Von Ragué
Published: January 2005

Solvation energies of lithium first‐row compounds LiX (X  H, Li, BeH, BH2, CH3, NH2, OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito (MP2/6‐31 + G*//6‐31G* with zero‐point vibrational energy corrections at 3‐21G//3‐21G). The solvation energies are found to be remarkably constant: −18.0 ± 1.2 and −21.5 ± 1.3 kcal/mol for the hydrates and ammonia solvates, respectively. This independence on the nature of X is due largely to the ionic character of the LiX compounds (dipole moments 4.7–6.6 debye). The unexpectedly high solvation energies of the lithium molecule (−14.3 and −17.8 kcal/mol, respectively) are due to the polarizability of Li2. At the same level, the lithium cation has interaction energies with H2O and NH3 of −34.1 and −39.7 kcal/mol, respectively. For the hydrates of LiOH and LiF cyclic structures with hydrogen bonds and somewhat increased solvation energies also are described.
The evaluation of molecular electron affinities
Authors: Baker Jon , Nobes Ross H. , Radom Leo
Published: January 2005

The performance of a variety of levels of theory in evaluating molecular electron affinities (EAs) has been systematically examined. Calculations have been carried out for six different basis sets and for nine theoretical procedures including unrestricted (UHF) and restricted (RHF) Hartree‐Fock theory, Møler‐Plesset perturbation theory (UMP2, UMP3, UMP4), configuration interaction (UCISD, RCISD, RCISD(Q)) and equations‐of‐motion (EOM) approaches. Electron affinities were evaluated for CH3, NH2, OH, F, C2H, CN, BO, N3, OCN, and NO2. Very poor results are generally obtained unless diffuse functions are included in the basis set and electron correlation is incorporated. Even with the largest basis set used in the present study (6‐311 + + G(2d, 2p)), there are still residual errors greater than 0.2 eV (UMP4) or 0.6 eV (CISD) in the absolute EAs. However, better results are obtained under certain circumstances for relative EAs. The results appear to be significantly affected by spin contamination in the UHF wave‐functions. For those systems for which spin contamination is small, best absolute values of the EAs generally come from the EOM and UMP2 calculations, whereas the most constant errors (thereby allowing systematic correction) are found at the UMP4, CISD, and RCISD(Q) levels. For the systems for which spin contamination is larger, best results are obtained with the CI‐based procedures (CISD and RCISD(Q)). The errors in calculated EAs for the molecules with differing electronic characteristics can vary quite widely. Caution must therefore be exercised before applying schemes which rely on a constancy of errors to estimate electron affinities. The UMP procedures appear particularly suspect in this regard if spin contamination is significant. The RCISD(Q) approach is recommended under such circumstances.
An algorithm for the location of transition states
Authors: Baker Jon
Published: January 2005

An algorithm for locating transition states designed for use in the ab initio program package GAUSSIAN 82 is presented. It is capable of locating transition states even if started in the wrong region of the energy surface, and, by incorporating the ideas on hessian mode following due to Cerjan and Miller, can locate transition states for alternative rearrangement/dissociation reactions from the same initial starting point. It can also be used to locate minima.
Theoretical Investigations on Fluorine‐Substituted Ethylene Dications C2HnF4‐n2+(n = 0–4)
Authors: Frenking Gernot , Koch Wolfram , Schwarz Helmut
Published: January 2005

The optimized geometries and energies of fluorine‐substituted ethylene dications C2HnF4‐n 2+ (n = 0–4) have been investigated by means of ab initio methods. At the MP3/6‐31G**//6‐31G* + zero‐point energy level of theory, the results predict that C2F42+ and C2HF32+ are planar, while C2H42+, C2H3F2+ and 1,1—C2H2F22+ prefer a perpendicular geometry. For 1,2—C2H2F22+ an energy difference of only 0.3 kcal/mol is found between the (trans) planar and perpendicular structure. The stabilizations attributed to hyperconjugation, fluorine lone‐pair donation, and (CF) double‐bond conjugation are discussed. A comparison is made for the CC and CF stretching frequencies determined at 6‐31G*//6‐31G* between the neutral and dicationic species. The theoretically determined ionization energies for the vertical process N+ → N2+ at the MP3/6‐31G*//3‐21G level are compared with experimental Qmin values.
A New Method for Molecular Mechanics
Authors: Saunders Martin , Jarret Ronald M.
Published: January 2005

A promising new method for optimizing molecular structures is described. In place of the terms involving bond angles and torsion angles, used in the force fields of conventional molecular mechanics, two‐body central forces between atoms are used exclusively, resulting in a considerable computational advantage. The program STRFIT, using this method has been tested by comparing geometries obtained with those found using the popular molecular mechanics program MM2 (Allinger) for a variety of cyclic and acyclic molecules. For unstrained molecules, the difference in steric energy between geometries refined by STRFIT and MM2 is only a few tenths of a kilocalorie and up to about a kilocalorie for strained molecules. Geometry optimization with STRFIT, to a structure that is slightly higher in energy than the structure arrived at by MM2 starting from the same initial starting geometry, is three to eight times faster. A complete new package of programs for conveniently and rapidly doing molecular mechanics calculations is described. It includes a convenient algorithm for the input of approximate molecular structures, a rapid structure‐optimizing module using a pure Central force‐field approach, and a drawing program designed for use with a dot‐matrix printer or a laser printer.
Optimized Structures and Relative Stabilities of the Carboranes from Ab Initio Calculations
Authors: Ott Jane J. , Gimarc Benjamin M.
Published: January 2005

Ab initio calculations at the STO‐3G level were performed on almost all of the possible isomers for the entire series of closo‐carboranes, C2Bn‐2Hn, 5 ⩽ n ⩽ 12. Geometry optimizations using the gradient method were also included in all calculations. We report here the relative energies obtained for the various isomers as well as the optimized structures. These calculations confirm our previous predictions of relative stabilities obtained from topological charge stabilization. Comparisons of our structures with those from experimental data provide us with a measure of reliability for bond distances obtained using ab initio SCF MO calculations at the STO‐3G level. Results from the geometry optimization substantiated the experimentally known fluxional behavior of the 8 and 11 atom polyhedra.
Calculations of first‐ and second‐order nonlinear molecular hyperpolarizabilities by perturbation methods: I. An efficient method for evaluating time‐independent hyperpolarizabilities
Authors: Fripiat J. G. , Barbier C. , Bodart V. P. , André J. M.
Published: January 2005

From a suitable reorganisation of the sum‐over‐states (SOS) equations of the usual time‐independent perturbation theory, recurrent expressions for static polarizability (α) and second‐ (beta;) and third‐(γ) order hyperpolarizabilities are obtained. These expressions are given in a well‐adapted way for computer implementation and lead to an efficient algorithm reducing the computing time by a factor of 50 with respect to a “brute‐force” translation of the standard SOS equations.
Molecular modeling of polymers: I. Correct and efficient enumeration of intrachain conformational energetics
Authors: Orchard B. J. , Tripathy S. K. , Pearlstein R. A. , Hopfinger A. J.
Published: January 2005

Polymer conformational analyses can require being able to model the intramolecular energetics of a very long (infinite) chain employing calculations carried out on a relatively short chain sequence. A method to meet this need, based upon symmetry considerations and molecular mechanics energetics, has been developed. Given N equivalent degrees of freedom in a linear polymer chain, N unique molecular groups are determined within the chain. A molecular unit is defined as a group of atoms containing backbone rotational degrees of conformational freedom on each of its ends. The interaction of these N molecular groups, each with a finite number of nearest neighbors, properly describe the intramolecular energetics of a long (infinite) polymer chain. Thus, conformational energetics arising from arbitrarily distant neighbor interactions can be included in the estimation of statistical and thermodynamic properties of a linear polymeric system. This approach is called the polymer reduced interaction matrix method (PRIMM) and the results of applying it to isotactic polystyrene (I‐PS) are presented by way of example.
Coupled equations approach to multiphoton molecular processes
Authors: Bandrauk André D. , Gélinas Nadia
Published: January 2005

Using the dressed molecule picture of molecule radiation interactions (A.D. Bandrauk et al., J. Chem. Phys., 79, 3256; 80, 4926; 83, 2840) one can deduce multiphoton processes (absorption, scattering, nonlinear optical properties, etc.) amplitudes from coupled second‐order differential equations with electronic surfaces and transition moments as input data obtainable from quantum chemical calculations. The present approach enables one to include in the calculation bound and continuum states simultaneously by the use of appropriate boundary conditions for the numerical solutions of these coupled equations. In the case of weak radiative couplings, one recovers the usual Fermi‐Golden rule expressions for electronic absorption, raman scattering, etc. The method is thus quite general, bridging the weak field (traditional photochemistry) and the strong field (laser chemistry) regimes which are attainable with today's lasers. The numerical solutions of the coupled equations give us the stationary states of the molecule + radiation system, called dressed molecule. Preparation of the initial state can be mimicked in the coupled equations by an artificial channel method for processes involving a final‐state dissociation. Examples of such calculations will be presented in the diatomic Cl2 for which several ab initio electronic states and transition moments were available.
Simulation studies of branched polymer molecules
Authors: Lipson J. E. G.
Published: January 2005

Monte Carlo simulation results are presented for lattice models of uniform stars (one branch point of functionality f = 3), combs (two branch points, ƒ = 3,3) and brushes (two branch points ƒ = 3,4 and ƒ = 3,5). We estimate the critical exponent γ(ƒ), the ratio g(ƒ) = 〈S(ƒ)〉/〈S(1)〉 (where 〈S(ƒ)〉 is the mean‐square radius of gyration of a structure having ƒ branches and N monomers), and the meansquare end‐to‐end branch lengths, as a function of the number and arrangement of branches. Comparisons with theoretical predictions and experimental data are made where possible, leading to a test of some predictions, and a suggestion concerning future experiments.
Computational aspects of master equation transformation in terms of moments
Authors: Gidiotis Grigorios , Forst Wendell
Published: January 2005

The master equation describing the temporal evolution of a gaseous system in contact with a heat bath can be transformed into a system of linear, constant‐coefficient, first‐order differential equations of moments of the population distribution. While it has the advantage that populations are obtained directly from observables (moments), this system of equations is not too well‐conditioned and unless precautions are taken, unsurmountable numerical problems appear. These are principally associated with manipulations (inversion and taking the exponential of a matrix) involving slightly modified Vandermonde matrices whose elements span a very wide range of orders of magnitude. This article discusses ways to avoid these pitfalls which consist principally of a suitable matrix normalization.
Open‐shell coupled‐cluster method: Electron affinities of Li and Na
Authors: Kaldor Uzi
Published: January 2005

The open‐shell coupled‐cluster method and the diagrams needed for its implementation are described. The method is applied to the electron affinities of Li and Na, which are calculated in two ways: as the ionization potential of the anions or as the energy of adding the second electron to the cations. The two schemes give essentially the same results, in very good agreement (<0.02 eV) with experiment. Three‐body effects are negligible.
Molecular dynamics simulation of the 1:1 enzyme‐ligand complex between porcine pancreatic elastase and acetyl‐alanine‐proline‐alanine
Authors: Fujita T. , Meyer E. F.
Published: January 2005

A 31.5 picosecond (ps) MD calculation has been completed for the 1:1 enzyme‐ligand complex between porcine pancreatic elastase (PPE) and acetyl‐alanine‐proline‐alanine (APA). The 1:2 complex studied crystallographically at product saturation conditions precludes the study of a 1:1 complex (PPE and APA1); this objective has been achieved by computational methods described here. The acetyl group of the ligand was found to occupy two neighboring sites, one within the primary specificity site and the other out into solution. The primary change of the ligand structure is ψ1 torsion angle being 171.5°. Supported by an interactive graphic display, the dynamical fluctuations of a smaller ligand compared with the width of the active site as PPE were observed by the MD simulation, although the complex has not been detected by any spectroscopic method.
Fast matrix multiplication
Authors: Bunge Carlos F. , Cisneros Gerardo
Published: January 2005

Several implementations of matrix multiplication (MMUL) in Fortran and VAX assembly language are discussed. On a VAX‐11/780 computer, the most efficient MMUL is achieved through vector‐scalar‐multiply‐and‐add (VSMA) operations, rather than by means of dot products. We also discuss optimal MMUL algorithms for use in virtual memory machines when the data overflow the working set.
Gaussian basis sets for the fifth row elements, Mo‐Cd, and the sixth row elements W‐RN
Authors: Gropen Odd
Published: January 2005

Gaussian basis sets, consisting of 17 s‐type, 12 p‐type, and 8 d‐type functions, for the fifth row elements, MoCd, and 19 s‐type, 14 p‐type (16 p‐type), 10 d‐type and 5 f‐type functions for the sixth row elements, WRn, are presented. The basis sets are of double zeta quality, and are optimized to .002 a.u. in the energy. The energies are compared with D.Z. STO basis sets.
Benzene‐benzene (phenyl‐phenyl) interactions in MM2/MMP2 molecular mechanics calculations
Authors: Pettersson Ingrid , Liljefors Tommy
Published: January 2005

The MM2/MMP2 force‐field gives an incorrect description of benzene‐benzene interactions. This deficiency may be overcome by the addition of electrostatic interactions. Using point charges of −0.15 on carbon and +0.15 on hydrogen, a good agreement between benzene dimer potentials calculated by MMP2 and ab initio SCF CI potentials is obtained. The influence of the addition of point charges on calculated structures and conformational energies has been studied. Examples are given in which the addition of electrostatic interactions between phenyl groups substantially improves calculated conformational energies.
An analysis of the structural and energetic properties of deoxyribose by potential energy methods
Authors: Schlick Tamar , Peskin Charles , Broyde Suse , Overton Michael
Published: January 2005

We discuss the three fundamental issues of a computational approach in structure prediction by potential energy minimization, and analyze them for the nucleic acid component deoxyribose. Predicting the conformation of deoxyribose is important not only because of the molecule's central conformational role in the nucleotide backbone, but also because energetic and geometric discrepancies from experimental data have exposed some underlying uncertainties in potential energy calculations. The three fundamental issues examined here are: (i) choice of coordinate system to represent the molecular conformation; (ii) construction of the potential energy function; and (iii) choice of the minimization technique. For our study, we use the following combination. First, the molecular conformation is represented in cartesian coordinate space with the full set of degrees of freedom. This provides an opportunity for comparison with the pseudorotation approximation. Second, the potential energy function is constructed so that all the interactions other than the nonbonded terms are represented bypolynomialsof the coordinate variables. Third, two powerful Newton methods that are globally and quadratically convergent are implemented: Gill and Murray's Modified Newton method and a Truncated Newton method, specifically developed for potential energy minimization. These strategies have produced the two experimentally‐observed structures of deoxyribose with geometric data (bond angles and dihedral angles) in very good agreement with experiment. More generally, the application of these modeling and minimization techniques to potential energy investigations is promising. The use of cartesian variables and polynomial representation of bond length, bond angle and torsional potentials promotes efficient second‐derivative computation and, hence, application of Newton methods. The truncated Newton, in particular, is ideally suited for potential energy minimization not only because the storage and computational requirements of Newton methods are made manageable, but also because it contains an important algorithmic adaptive feature: the minimization search is diverted from regions where the function is nonconvex and is directed quickly toward physically interesting regions.
Molecular mechanics parameters for organosilicon compounds calculated from ab initio computations
Authors: Grigoras Stelian , Lane Thomas H.
Published: January 2005

Molecular structures of 26 organosilicon compounds have been optimized using ab initio calculations at the 3‐21G* (modified) level. From these optimized structures, the internal coordinates have been deformed and the variation of the total molecular energy has been studied. Parameters for stretching and bending deformations are reported herein. The bending potential for the SiOSi bond which has an unusual flexibility is also included. Nonbonding interactions are described in terms of steric and electrostatic potentials. For systems which do not include bond resonance effects, torsional behavior is well described by steric potentials with van der Waals radii 20% larger than the previous values and simple electrostatic potential (monopole‐monopole) with net atomic charges obtained from ab initio or Extended Huckel Theory calculations. The nonbonding potentials, as defined in this study, have an advantage in that they allow for the computation of torsional barriers without torsional potentials, in the case of single bonds where no additional electronic effects interfere. As an example, it is shown that no torsional potentials are necessary to estimate the torsional barriers in the case of ethane. The newly defined potentials are used to study the torsional barrier in hexamethyldisiloxane and the conformation of octamethylcyclotetrasiloxane (D4). The most stable calculated conformation of D4, coincides with the experimentally determined structure. This study shows that the most stable conformation is determined by the steric repulsion of methyl groups.
A conformational study of a biologically active conjugated syn‐oxime
Authors: Venanzi Thomas J. , Venanzi Carol A.
Published: January 2005

The conjugated system (E)‐tiglaldoxime is the simplest example of a perillartine analog which exhibits sweetness with a taste potency greater than sucrose with almost no bitter aftertaste. In previous studies, the structure of this biologically active compound has been assumed to be planar with the CC double bond trans to the CN bond of the oxime moiety. In this article a conformational analysis of this molecule is reported. The results indicate that, although the trans conformer of the planar molecule is indeed the global minimum, other conformers lie within a few kilocalories of this minimum. Hence, other accessible conformations may be available for interaction with the receptor and, therefore, may be biologically active. The structural parameters obtained for this conjugated syn‐oxime are nearly identical to those of (E)‐acetaldoxime. This fact has implications for the transferability of these parameters to the more complicated perillartine analogs.
Ab initio vibrational transition dipole moments and intensities of formaldehyde
Authors: Hsieh Hsiuchin C. , Ermler Walter C.
Published: January 2005

Vibrational transition dipole moments and absorption band intensities for the ground state of formaldehyde, including the deuterated isotopic forms, are calculated. The analysis is based on ab initio SCF and CI potential energy and dipole moment surfaces. The formalism derives from second‐order perturbation theory and involves the expansion of the dipole moment in terms of normal coordinates, as well as the incorporation of point group symmetry in the selection of the dipole moment components for the allowed transitions. Dipole moment expansion coefficients for the three molecule‐fixed Cartesian coordinates of formaldehyde are calculated for internal and normal coordinate representations. Transition dipole moments and absorption band intensities of the fundamental, first overtone, combination, and second overtone transitions are reported. The calculated intensities and dipole moment derivatives are compared to experiment and discussed in the context of molecular orbital and bond polarization theory.
Contraction of the well‐tempered Gaussian basis sets: The first‐row diatomic molecules
Authors: Dingle T. W. , Huzinaga S. , Klobukowski M.
Published: January 2005

The well‐tempered Gaussian basis sets (14s 10p) for atoms from lithium to neon were contracted and used in restricted Hartree–Fock calculations on 13 systems: Li2(Σ), B2(Σ), C2(Σ), N2(Σ), O2(Σ), F2(Σ), Ne2(Σ), LiF(Σ), BeO(Σ), BF(Σ), CN−(Σ), CO(Σ), and NO+(Σ). Spectroscopic constants (Re, ωe, ωexe, Be, αe, and ke) and one‐electron properties (dipole, quadrupole, and octupole moments at the center of mass and electric field, electric field gradient, potential, and electron density at the nuclei) were evaluated and compared with the Hartree–Fock results. The largest contracted basis set (7s6p3d) gives results very close to the Hartree–Fock values; the remaining differences are attributed to the absence of the f functions in the present basis sets. For Ne2, the interaction energy was calculated; the magnitude of the basis‐set superposition error was found to be very small (less than 3 μEh at 2.8 a0 and less than 2 μEh at 5.0 a0).
Chlorosilanes: Development and application of MM2 force field parameters
Authors: Cho Soo Gyeong , Unwalla Rayomand J. , Cartledge Frank K. , Profeta Salvatore
Published: January 2005

The geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3–21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.
Molecular mechanics conformational analysis of cyclononane using the RIPS method and comparison with quantum‐mechanical calculations
Authors: Ferguson David M. , Glauser William A. , Raber Douglas J.
Published: January 2005

The recently reported Random Incremental Pulse Search (RIPS) technique has been used to probe the conformational energy surface of cyclononane. The stochastic method permits searching of the potential energy surface for all minimum‐energy conformations. The search located all previously reported structures together with three additional conformations that were not found by earlier, primitive searching techniques. Two of these structures are high‐nergy skew forms, and the third is a low‐energy conformer that should contribute significantly to the overall equilibrium set of cyclononane conformations. The global minimum has been found to be the D3 symmetrical twist chair‐boat (TBC) form in accordance with previous studies. The newly discovered low‐energy structure, which lies only 2.2 kcal/mol above the global minimum, has been designated twist chair‐twist chair (TCTC). The two higher energy conformers are skewed chair‐chair (SCC) and skewed boat‐boat (SBB) forms that are 5.7 kcal/mol and 10.4 kcal/mol above the global minimum, respectively. The seven reported conformations were reanalyzed quantum mechanically (AM1), and a comparison between MM2 and AM1 results is presented.
Coupled cluster method with first‐order correlation orbitals versus multireference configuration interaction method. Accurate calculations for HF, H2O, and NH3
Authors: Adamowicz Ludwik
Published: January 2005

This article shows that with our Hylleras‐functional based method1 for generating correlation orbitals, we can determine electronic structures for small polyatomic systems very accurately. The procedure is ab initio, uses conventional Gaussian basis sets, and solves the electronic Schrödinger equation with the coupled cluster method. A comparison is made with MRCI results obtained in equivalent basis sets for the HF, H2O, and NH3 molecules.
Characters for symmetric and antisymmetric higher powers of representations: Application to the number of anharmonic force constants in symmetrical molecules
Authors: Zhou Xue‐Feng , Pulay Peter
Published: January 2005

Explicit formulas are given for the characters of symmetric and antisymmetric powers of an arbitrary representation up to the sixth, and a general method for obtaining the higher ones is described. The results allow, among others, the determination of nonvanishing higher force constants in symmetrical molecules. The benzene molecule, for instance, has 237 nonvanishing cubic and 1890 quartic force constants. Other potential applications are a general method for the symmetry species of vibrational overtones, the determination of the number of independent centrifugal distortion constants, and the symmetry classification of vibrational multiplets.
A recipe for evaluating and differentiating cos ϕ expressions
Authors: Schlick Tamar
Published: January 2005

We present a simple recipe for calculating and differentiating cosine of bond angle and dihedral angle expressions. The resulting formulas can be incorporated in a straightforward manner into the bond angle and dihedral angle components of potential energy functions. These formulas rely only on expressions and derivatives of dot products, and, in particular, they avoid cross products as well as excessive Fortran function references. Consequently, the expressions derived in this article can be written compactly and evaluated rapidly.
The dynamics of gallamine: A potent neuromuscular blocker. A determination by quantum mechanics and molecular dynamics (i) in vacuo studies
Authors: Saldanha José W. , Howlin Brendan , Toit Louis Du , Palmer Rex A.
Published: January 2005

The potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.
Validation of the general purpose tripos 5.2 force field
Authors: Clark Matthew , Cramer Richard D. , Van Opdenbosch Nicole
Published: January 2005

A molecular mechanics force field implemented in the Sybyl program is described along with a statistical evaluation of its efficiency on a variety of compounds by analysis of internal coordinates and thermodynamic barriers. The goal of the force field is to provide good quality geometries and relative energies for a large variety of organic molecules by energy minimization. Performance in protein modeling was tested by minimizations starting from crystallographic coordinates for three cyclic hexapeptides in the crystal lattice with rms movements of 0.019 angstroms, 2.06 degrees, and 6.82 degrees for bond lengths, angles, and torsions, respectively, and an rms movement of 0.16 angstroms for heavy atoms. Isolated crambin was also analyzed with rms movements of 0.025 angstroms, 2.97 degrees, and 13.0 degrees for bond lengths, angles, and torsions respectively, and an rms movement of 0.42 angstroms for heavy atoms. Accuracy in calculating thermodynamic barriers was tested for 17 energy differences between conformers, 12 stereoisomers, and 15 torsional barriers. The rms errors were 0.8, 1.7, and 1.13 kcal/mol, respectively, for the three tests. Performance in general purpose applications was assessed by minimizing 76 diverse complex organic crystal structures, with and without randomization by coordinate truncation, with rms movements of 0.025 angstroms, 2.50 degrees, and 9.54 degrees for bond lengths, angles and torsions respectively, and an average rms movement of 0.192 angstroms for heavy atoms.
Computational chemistry applied to the design of chiral stationary phases for enantiomeric separation
Authors: Däppen Richard , Karfunkel Heinrich R. , Leusen Frank J. J.
Published: January 2005

A general computational scheme for the rational design of chiral stationary phases for the chromatographic separation of enantiomers has been established. The developed scheme was based on applying different interaction models (force field methods versus semi empirical quantum chemical methods), different docking algorithms (systematic grid search methods versus interactive methods guided by rules based on binding modes) and different levels of approximations (rigid versus flexible docking) to a representative test problem containing the 3,5‐dinitrobenzoyl group. The computational methods in use covered the most sophisticated methods which could presently be applied to problems of such a size (about 80 atoms). It has been shown that the current computational approaches using rigid body approximations for the docked molecules and simple molecular mechanics (not taking pi‐“effects” into account) are invalid in view of the required predictive precision of about 1–2 Kcal/mole for the differential binding energy. Another surprising result was the failure of the commonly used systematic search methods in determining the most favorable binding modes. Based on our calculations on the representative test problem we propose a new arrangement for the most stable complexes without parallel stacking of the aromatic pi‐donor and the 3,5‐dinitrobenzoyl pi‐acceptor systems.
η5‐P‐ or η4‐P‐Coordination in apically oxygenated phosphoranes? An ab initio study of PH4O−, PH4O− · E (E = Li+, NH4+, and HF) and related fluorinated oxyphosphoranes
Authors: Glaser Rainer , Streitwieser Andrew
Published: January 2005

Structural optimizations of the apically substituted isomer of PH4O− and the diapically substituted isomer of PH3FO− with diffuse‐function augmented 3–21G* basis sets and with the 6–31 + G* and 6–31 + + G* basis sets result in P‐η4‐coordination in these anions. The structures obtained are those of a hydride or fluoride ion “solvated” by or complexed with phosphine oxide, rather than phosphoranes. In contrast, 3–21G* basis sets without diffuse functions on the atom in the trans‐apical position with regard to the oxy‐substituent yield P‐η5‐phosphorane structures that appear to be computational artifacts of the small basis set; the formation of the P‐η4‐geometries is curtailed by the insufficient functional description of the potential trans‐apical nucleophilic leaving group. The overall neutral apical isomers of PH4O− · E(E = Li+, NH4+), the diapical isomer of PH3FO−Li+, as well as the model‐solvated apical isomer of PH4O− · HF favor P‐η5‐phosphorane geometries at all of these computational levels. The mechanism by which the E‐group alters the electronic structures within PH4Oa− is discussed based on the geometries, the molecular orbitals, and electron density analysis techniques.
Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase
Authors: Shen Jian , Wong Chung F. , Subramaniam Shankar , Albright Thomas A. , McCammon J. Andrew
Published: January 2005

Atomic partial charges for three model systems that mimic the metal‐ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction
Authors: Luque F. J. , Illas F. , Orozco M.
Published: January 2005

A systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first‐order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO‐3G, 4‐31G, 6‐31G, 4‐31G*, 6‐31G*, and 6‐31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split‐valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6‐31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.
A structural approach to calculate physical properties of pure organic substances: The critical temperature, critical volume and related properties
Authors: Grigoras Stelian
Published: January 2005

A new approach based on computation of the molecular surface interactions (MSI) to estimate several physical properties of pure organic substances is described. MSI are derived from molecular structural data and consist of total molecular surface area, electrostatic molecular surface interactions, and a hydrogen bonding term. This new approach estimates the critical temperature and the molar critical volume of pure organic substances with molecular weights in the range of 40–500 a.u‥ In addition, the following properties can be calculated: the critical pressure, the boiling temperature, the molar volume in liquid state at normal pressure and temperature. The method can be used to predict physical properties of compounds having flexible or rigid, symmetric or asymmetric, polar or nonpolar molecular structures, and compounds with or without hydrogen bonding groups.
H/He Molecules in strong electric fields
Authors: Gründler W. , Steinke T. , Walther P.
Published: January 2005

Floating spherical Gaussian orbitals are used within a split‐shell description to calculate the properties of H, He, He+, H2, H+2, HeH+, and H+3 in a strong uniform electric field. Accurate polarizabilities including their field strength dependence are obtained with two basis functions at most. Critical field strengths for ionization and deprotonation are determined for different orientations of molecules. Electron tunneling is described within the time dependent approach using floating Gaussian orbitals also.
Solvent effect and librational entropy calculations on N‐acetylalanylglycine amide
Authors: Sapse Anne‐Marie , Jain Duli C. , De Gale Denyse , Wu T. C.
Published: January 2005

Entropy and solvent effects are calculated for some conformations of Ala‐Gly. The inclusion of these effects in energy calculations show the βII type structure to be the most stable.
Computer generation of character tables of generalized wreath product groups
Authors: Liu Xiaoyu , Balasubramanian K.
Published: January 2005

Algorithms and computer codes in FORTRAN 77 are developed for the computation of characters of generalized wreath product groups through generating function methods. Characters of generalized wreath product groups of symmetric groups are computed in terms of the characters of much smaller composing groups using plethysms of S‐functions. The developed codes were tested for many generalized wreath product groups. The character tables of generalized wreath products, S2[S3, S2, S2] (NMR group of hexane) and S4[S3] containing 576 and 31,104 elements, respectively, were constructed as examples.
Effect of basic set quality and electron correlation on the scale factors of a harmonic force field
Authors: Bock C. W. , Panchenko Y. N. , Pupyshev V. I.
Published: January 2005

The completely optimized structure and harmonic force field of s‐trans‐buta‐1,3‐diene are reported at the MP2/6‐31G and MP2/6‐31G* levels of computation. Sets of empirical scale factors for the calculated force fields are derived and compared with the corresponding values computed at the RHF/4‐31G and RHF/6‐31G levels. Changes in the scale factors for this series of force fields are discussed. The vibrational frequencies are also reported for thirteen isotopomers of s‐trans‐buta‐1,3‐diene using the MP2/6‐31G* force field. Some characteristics of the gauche and cis forms of buta‐1,3‐diene are also given.
A new method for the calculation of atomic and local hardness
Authors: Baumer Luca , Sala Giordano , Sello Guido
Published: January 2005

The relationships between atomic hardness, atomic electronegativity, and electronic energy are considered and emphasized. A new method for calculating atomic hardness is described. The concept of local hardness is quantified through the calculation of a new variable named alfahardness. Atomic hardness and alfahardness are used for the calculation of both the mean molecular and local properties. The results obtained are discussed and a comparison made with the analogous quantities presented by Pearson. An algorithm has been realized and transformed into a computer routine for use within a CAOS program.
Pepto: An expert system for automatic peak assignment of two‐dimensional nuclear magnetic resonance spectra of proteins
Authors: Catasti Paolo , Carrara Enrico , Nicolini Claudio
Published: January 2005

Two‐dimensional Nuclear Magnetic Resonance (2DFTNMR) is presently the most powerful tool to determine protein structures in solution. Peak assignment (an interpretation of the two‐dimensional spectra that leads to the individuation of pairs of Hydrogen atoms that are involved in an NOE peak) is a cornerstone of such use of 2DFTNMR. Manual peak assignment of a protein often requires months of work by a specialized equipe. An automation of this task could speed up the protein study process, or alternatively allow to study previously unmanageable proteins. This article describes PEPTO, an expert system for the interpretation of sets of 2DFTNMR spectra on proteins. The present version of the program deals with spectra obtained from NOESY and COSY experiments. Tests of PEPTO on simulated spectra of five proteins with known assignments are also described and dicussed.
Combined application of pair potentials and the MM2 force field for the modeling of ionophores
Authors: Badertscher Martin , Musso Stefano , Welti Martin , Pretsch Ernö , Maruizumi Takuya , Ha Tae‐kyu
Published: January 2005

Complexes of alkali and alkaline earth cations with organic compounds are modeled by describing ionligand interaction energies with pair potentials and intraligand as well as interligand energies with the MM2 potential. New pair potentials for the interaction of Li+, Na+, K+, Mg2+, and Ca2+ ions are derived on the basis of 30,000 ab initio interaction energy values with 70 selected model ligand molecules. Various problems of the combination of these two basically different potentials are discussed. An application for the K+ complex of 18‐crown‐6 is presented. For more flexible ligands the introduction of three‐body correction terms of the pair potentials seems necessary.
Molecular mechanics (MM3) calculations on conjugated hydrocarbons
Authors: Allinger Norman L. , Li Fanbing , Yan Liqun , Tai Julia C.
Published: January 2005

The MM3 molecular mechanics program has been extended to conjugated systems. A VESCF method is applied to the pi‐system to calculate bond orders, from which various stretching and torsional parameters are obtained. The procedure gives somewhat better results than the analogous MM2 calculations. It has been applied to a study of 81 compounds of aromatic and other conjugated hydrocarbons, as well as 45 alkenes and unconjugated polyenes. The structures calculated are generally in good agreement with experiment, and the heats of formation of these compounds can be calculated with a rms value of 0.62 kcal/mol, which may be compared with the average experimental error of 0.61 kcal/mol. In addition, vibrational frequencies for five representative conjugated model structures are calculated, with an rms value of 46 cm−1, and from these, other properties such as entropy can be calculated.
Monte Carlo simulations of liquid alkyl ethers with the OPLS potential functions
Authors: Briggs James M. , Matsui Tooru , Jorgensen William L.
Published: January 2005

Intermolecular potential functions have been developed for use in computer simulations of alkyl ethers. The simple OPLS model was adopted and parameterized to yield good descriptions of bimolecular and ion‐molecule complexes as well as to reproduce experimental thermodynamic properties of liquid ethers. The principal testing featured Monte Carlo statistical mechanics simulations for liquid dimethyl ether (DME), ethyl methyl ether (EME), diethyl ether (DEE), and tetrahydrofuran (THF). Average errors of 1–3% are obtained for the computed densities and heats of vaporization including results for THF at pressures up to 5000 atm. The torsional motion about the central CO bonds in EME and DEE was included in the simulations using rotational potential functions fit to results of molecular mechanics (MM2) calculations. The liquid‐state environment is found to have negligible effect on the conformational equilibria.
Partial charges by multipole constraint. Application to the amino acids
Authors: Gruschus James M. , Kuki Atsuo
Published: January 2005

Atom‐centered partial charges which exactly reproduce the lowest several multipoles of a molecule's charge distribution can be obtained in a straightforward and convenient manner from the output of existing electronic structure calculations. The multipole constraint method is demonstrated by a computation of partial charges for the twenty common amino acids. The electron density employed here, derived from a semiempirical MNDO calculation, incorporates Slater‐type orbitals which imbue it with the exponential fall‐off vital to electronic tunneling calculations. In addition, a procedure based on these charges is described which divides the original electron density into two components, a large component with a simple electrostatic potential, and a much smaller residual whose several lowest multipoles vanish.
Correlation of the acidity of substituted phenols, anilines, and benzoic acids calculated by 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 and net atomic charges of some 120 structures involving substituted phenols, anilines, and benzoic acids and the corresponding anions were calculated by MNDO, AM1, and PM3 semiempirical methods. The gas phase acidities of substituted phenols and anilines and the net atomic charges on the anionic heteroatoms of the corresponding anions have been successfully correlated with σ− constants. Moreover, good correlations with σ were found for the charges on the acidic hydrogens of substituted phenols and anilines. In contrast, the gas phase acidities of substituted benzoic acids and the charges on the anionic oxygens of the corresponding anions are better correlated with Taft σ° constants. Comparisons of these results with experimental data and ab initio theoretical calculations indicate that AM1 and PM3 methods are much better than MNDO in predicting the acidity of aromatic compounds.
Theoretical analysis of the electronic spectrum of GeH4 from ab initio CI calculations
Authors: Sanz Javier Fernändez , Dargelos Alain
Published: January 2005

Ab initio CI calculations using pseudopotentials to describe germanium inner electrons are carried out on the low‐lying excited singlet states (T2) of GeH4. A theoretical analysis of these states in terms of Mulliken population of Rydberg orbitals for each state and oscillator strengths allow us to reinterpret its experimental Vacuum UV electronic spectrum.
Pseudopotential calculations for methyl compounds of zinc and magnesium
Authors: Kaupp M. , Stoll H. , Preuss H.
Published: January 2005

Pseudopotentials and valence basis sets to be used in calculations for organometallic compounds of zinc and magnesium have been tested in calculations for the M(CH3)n (M = Zn, Mg; n = 1,2) molecules. Valence correlation effects are treated at the SDCI and CEPA levels. The capability of a polarization potential on zinc to account for the valence shell contracting effect of core valence correlation is studied. Properties considered are geometries, force constants, Mulliken populations, ionization potentials, atomization, and binding energies. Differences in bonding between the two dimethyl compounds are discussed.
GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set
Authors: Pascual‐Ahuir Juan Luis , Silla Estanislao
Published: January 2005

The algorithm used by the program GEPOL to compute the Molecular Surface (MS), as defined by Richards, is presented in detail. GEPOL starts like other algorithms from a set of spheres with van der Waals radii, centered on the atoms or group of atoms of the molecule. GEPOL computes the MS by first searching the spaces inaccessible to the solvent and consequently filling them with a new set of spheres. Here we study the behavior of the method with its parameters, presenting several examples of application.