bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular orbital theory of the hydrogen bond. 26. The hydration of uracil
Authors: Bene Janet E. Del 
Published: December 2004

AbstractAb initio SCF calculations with the STO‐3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen‐bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water–water interactions and nonadditivity effects are also significant.
MNDO calculations for compounds containing aluminum and boron
Authors: Davis L. P. , Guidry R. M. , Williams J. R. , Dewar M. J. S. , Rzepa H. S. 
Published: December 2004

AbstractParametrization of MNDO for aluminum and comparisons of calculated molecular properties with experimental values indicate the general usefulness of MNDO to study aluminum‐containing compounds. Although results are not as good as for molecules containing only C, H, N, and O, they are nevertheless accurate enough to be useful, especially when predictive biases noted in this article are considered. Inclusion of the d orbital in the MNDO scheme may improve the aluminum results. Results for boron‐containing molecules not previously reported are also reported in this article.
Selectivity effects and hydrocarbon‐chain growth during Fischer–Tropsch synthesis
Authors: Collis F. P. , Schwarz J. A. 
Published: December 2004

AbstractIt is well known that if the formation of hydrocarbons during Fischer–Tropsch synthesis occurs via the condensation polymerization mechanism, there is little hope for selectivity enhancement in the desired range of products. Recent data on low surface area model catalysts, where readsorption is unlikely, have shown that at low conversions, the product distribution obeys the condensation polymerization mechanism and the distribution of products is shifted to lower‐molecular‐weight hydrocarbons. We have used a computer simulation of the growth of hydrocarbon chains to obtain a picture of the catalyst surface under synthesis conditions. Such an approach could prove useful in distinguishing between various theoretical models. We have applied the simulation to compare the changes in selectivity when readsorption occurs and when it does not. The dynamic behavior of the reacting system which is obtained from the computer results has shown that selectivity to lower‐molecular‐weight hydrocarbons is a stronger function of the extent of reaction than the incorporation of readsorption into the chain growth mechanism.
Thermochemical data from ab initio calculations. II. Total correlation energies, Schrödinger energies, and theoretical heats of formation
Authors: Cremer Dieter 
Published: December 2004

AbstractBond correlation energies ϵ(XY) have been derived by partitioning second‐order Rayleigh–Schrödinger–Møller–Plesset (RSMP) correlation energies. Values of ϵ(XY) depend on the type of bonding between atoms X and Y. They can be considered as comprising correlation energies of bond, lone, and inner‐shell electron pairs of the group XY. Once a set of appropriate increments ϵ(XY) has been obtained, it is possible to estimate unknown RSMP energies of larger molecules. This concept also can be used when estimating total correlation energies E(CORR). For this purpose e(XY) values have been derived from known E(CORR) energies of small molecules. It is shown that ∣ϵ(XY)∣ increments increase linearly with the number n of electron pairs of the group XY. The function ϵ(n) becomes zero for n = 1/2 (one uncorrelated electron) and passes through −0.042 for n = 1, which is approximately the correlation energy of the bonding electron pair of H2 or a 1s inner‐shell pair. With the aid of estimated E(CORR) and HF limit energies, Schrödinger energies and theoretical heats of formation of relatively large molecules are obtained.
Configuration interaction (CI): Approximate inclusion of fourfold and threefold excitations, an application of knowledge engineering
Authors: Wenzel Klaus B. 
Published: December 2004

AbstractIt is shown that even the CPMET approximation for the contributions of fourfold excitations can be replaced by a more sophisticated method. Furthermore, an approximation is presented for the contributions of threefold excitations which are neglected in CPMET. Finally, it is described how the advantages of different CEPA methods can be united in a single CEPA scheme (called CEPA‐U). The various approximations are discussed in terms of Slater determinants, and it is shown how the relatively large amount of details can be handled with the help of computer programs, i.e., how knowledge engineering can be successfully applied here.
Optimization of equilibrium geometries and transition structures
Authors: Schlegel H. Bernhard 
Published: December 2004

AbstractA modified conjugate gradient algorithm for geometry optimization is outlined for use with ab initio MO methods. Since the computation time for analytical energy gradients is approximately the same as for the energy, the optimization algorithm evaluates and utilizes the gradients each time the energy is computed. The second derivative matrix, rather than its inverse, is updated employing the gradients. At each step, a one‐dimensional minimization using a quartic polynomial is carried out, followed by an n‐dimensional search using the second derivative matrix. By suitably controlling the number of negative eigenvalues of the second derivative matrix, the algorithm can also be used to locate transition structures. Representative timing data for optimizations of equilibrium geometries and transition structures are reported for ab initio SCF–MO calculations.
Effect of electron correlation on theoretical vibrational frequencies
Authors: Hout Robert F. , Levi Beverly A. , Hehre Warren J. 
Published: December 2004

AbstractTheoretical HF/6‐31G* (Hartree–Fock, 6‐31G* basis set) and MP2/6‐31G* (second‐order Møller–Plesset, 6‐31G* basis set) vibrational frequencies based on complete quadratic force fields have been obtained for a set of 36 one‐ and two‐heavy‐atom molecules comprising first‐row elements for which experimental spectroscopic data are available. Frequencies calculated at the HF/6‐31G* level are an average of 12.6% higher than experimental values. Partial treatment of electron correlation via the perturbation method of Møller and Plesset, terminated at second order, leads to a significant reduction in this error, although theoretical MP2/6‐31G* frequencies are still larger than the experimental quantities by 7.3%. Part of the difference may be traced to the restriction of quadratic force fields, as comparison with experimental harmonic frequencies shows deviations of only 9.5% and 4.7% for the two levels, respectively. The calculated frequencies are used in conjunction with the corresponding theoretical equilibrium structures to obtain absolute molecular entropies, which may in turn be used to yield entropies of reaction. These latter quantities are generally in good accord with entropies derived using experimental structures and frequencies.
The calculated structures of the C4H8NO+ cations resulting from the unimolecular gas‐phase dissociation (CH3)2NCOCH2X·+ → C4H8NO+ + X· (X  CL, NO2)
Authors: Frenking Gernot , Schwarz Helmut 
Published: December 2004

AbstractThe structures and rearrangements of various cyclic and acyclic C4H8NO+ cations resulting from the title reaction have been investigated by means of semiempirical (MNDO) and ab initio (4‐31G) calculations.
An ab initio study of the geometry, energy, and selected force constants for the three planar conformers of carbonic acid, and the bicarbonate ion; and of the energy for the reaction H2O + CO2 → H2CO3
Authors: George Philip , Bock Charles W. , Trachtman Mendel 
Published: December 2004

AbstractAb initio calculations using the unscaled 4‐31G basis set have been carried out on the cc, tc, and tt conformers of carbonic acid and the bicarbonate ion, with full geometry optimization assuming the structures to be planar. The complete harmonic force field is reported for the (most stable) tt conformer and for the bicarbonate ion, also selected quadratic force constants for the cc and tc conformers. The changes in certain bond lengths and stretching force constants in the cc → tc, tc → tt, and cc → tt conformer conversion reactions are indicative of intramolecular hydrogen bonding, CO…HO and HO…HO, which is examined in greater detail by partitioning the overall conformer conversion energy into distortion and bonding energy components. The fundamental vibration frequencies for the tt conformer and the bicarbonate ion are calculated from the force constant matrices, and hence, using a scaling factor based on a comparison of calculated and experimental values for the bicarbonate ion and trans‐formic acid, a value is predicted for the zero‐point energy of the tt conformer. A new estimate of ΔH˚ for the hydration reaction, H2O + CO2 → H2CO3, at 298 K in the gas phase; is made from thermochemical data, +20.2 ± 3.4 kJ mol−1, which, together with estimates of (H298˚ – H0˚) and the zero‐point energy for H2CO3, gives +8.1 ± 7.0 kJ mol−1 for ΔET(expt). ΔET calculated from the 4‐31G basis set data is ‐29.1 kJ mol−1. Comparison of the experimental value, the Hartree–Fock limit value, and values calculated with a variety of basis sets for the bond separation reaction, CO2 + CH4 → 2H2CO, suggests that the differences, ΔET(expt) minus ΔET(SCF), are due mainly to basis set limitations and not substantial correlation energy contributions.
An ab initio study of the relationship between the OH bond length and the harmonic and anharmonic stretching force constants for planar molecules containing COH, NOH, and OOH groups
Authors: Bock Charles W. , Trachtman Mendel , George Philip 
Published: December 2004

AbstractThe OH bond length and the quadratic, cubic, and quartic stretching force constants, calculated ab initio using the unscaled 4‐31G basis set with full geometry optimization, are reported for 30 planar conformers of ten molecules contaning either the COH, NOH, or OOH group. The data are analyzed in terms of the general form of Clark's equation, and the power functions and exponential functions proposed by Herschbach and Laurie. In the case of the quadratic constants, significant trends are found in the values of the parameters depending on whether the OH group is bonded to carbon, nitrogen, or oxygen, and whether it is non‐hydrogen‐bonded or involved in intramolecular hydrogen bond formation in four‐, five‐, or six‐membered rings. Using data for diatomic molecules, OH, and CH bonds, and the CO and CC bonds in planar monosubstituted carbonyl compounds, the parameter dij in the power function equation for quadratic constants, which can be regarded as the distance of closest approach of the two nuclei, is shown to increase progressively along the series (i) diatomic molecule; (ii) similar bond in a polyatomic environment with one of the two atoms covalently bonded to a neighboring atom; (iii) as in (ii) but with the second atom hydrogen bonded; and (iv) with both atoms covalently bonded to neighboring atoms.
Localized molecular orbital energies within the CNDO/BW formulation
Authors: Tseng T. J. , Whitehead M. A. 
Published: December 2004

AbstractLocalized molecular orbital (LMO) energies obtained from the canonical molecular orbital (CMO) energies and unitary transformation or from the matrix of the Fock operator and the LMOs are described. The results for water and ethylene are given, and compared with earlier work of Wilhite and Whitten.
A molecular packing analysis of some ferrous porphyrin complexes
Authors: Hall David , Barry Sexton K. 
Published: December 2004

AbstractAn analysis has been made of the applicability of various sets of nonbonded interaction potential parameters which do not consider hydrogen atoms explicitly, to represent molecular packing interactions in crystals of ferrous porphyrin complexes, which are models for deoxyhemoglobin. Ordered regions of the structures are well described, but disordered solvent or ligands cause difficulty.
Ground states of molecules. 56. MNDO calculations for molecules containing sulfur
Authors: Dewar Michael J. S. , McKee Michael L. 
Published: December 2004

AbstractMNDO has been extended to sulfur, but without inclusion of 3d AOs. Calculations are reported for heats of formation, geometries, dipole moments, and ionization energies of a variety of sulfur‐containing molecules. The average discrepancy between calculated and observed heats of formation is larger than for compounds of other elements, a difference probably due, at least partly, to the lower accuracy of the thermochemical data for sulfur compounds. The calculated dipole moments agree well with experiment as do the calculated ionization energies, except for those corresponding to ionization from sulfur “lone‐pair” orbitals which are too high by ca. 1 eV, probably as a result of the neglect in NDDO of interactions between inner and valence shell orbitals. As in the case of other third‐period elements, the calculated heats of formation of compounds of sulfur in its higher valence states (SIV, SVI) were too positive by large amounts, due presumably to the neglect of 3d AOs.
On the general transformation from molecular geometric parameters to cartesian coordinates
Authors: Essén Hanno 
Published: December 2004

AbstractThis article presents a general method and accurate algorithm for calculating the Cartesian coordinates (xa, ya, za) from an arbitrary triple of distances r(a,i), angles, θ(a,j,k), or dihedral angles ϕ(a,l,m,n), specifying the position of the nucleus a relative to nuclei i, ⃜, n with known Cartesian coordinates. There is a brief discussion of the requirements on the 3N‐6 geometric parameters in order for them to determine the shape of an N‐atomic molecule.
Molecular orbital theory of the properties of inorganic and organometallic compounds. 3. STO‐3G basis sets for first‐ and second‐row transition metals
Authors: Pietro William J. , Hehre Warren J. 
Published: December 2004

AbstractSTO‐3G minimal basis sets for first‐ and second‐row transition metals have been formulated and applied to the calculation of equilibrium geometries for a variety of inorganic systems, metal carbonyls, and organometallic compounds. While the overall level of agreement with experiment is not as good as that previously noted for main‐group compounds, most trends and many subtle features in geometries are reproduced.
Electronic optical activity of (−)‐α‐phellandrene
Authors: Palmieri P. , Poggi G. , Vrbancich J. 
Published: December 2004

AbstractMolecular orbital computations on the sign and magnitude of the Cotton effect of (−)‐α‐phellandrene (a conjugated diene) and the separate twisted butadiene chromophore were performed using configuration interaction (CI) and the random phase approximation (RPA) methods with a standard minimal basis set of STO/3G orbitals. The relative contributions to the rotatory strength of (−)‐α‐phellandrene which arise from a twist in the diene unit, the allylic axial bond, and nonplanarity of either one or both of the CC double bonds were determined by examining various molecular geometries. This theoretical study confirms that the allylic axial substituent/bond provides the largest contribution to the longwavelength Cotton effect. It is found that the rotatory strength arising from distortion of the planar geometry of the double bonds tends to cancel the rotatory strength arising from the sense of twist of the diene unit. The computed energies suggest that molecular geometries where the trisubstituted bond is kept planar, and where twisting is allowed about the cis double bond, may be favored over geometries where torsion is allowed about both double bonds.
Molecular mechanics with an array processor
Authors: Berens Peter H. , Wilson Kent R. 
Published: December 2004

AbstractComputer simulation of the mechanics of molecular systems is a popular and powerful method for understanding chemical processes. The complexity of modeled chemical systems has advanced from hard spheres and rare gases to liquid solutions and biomolecules. Such simulations are computationally intensive and thus are limited by the speed of available computers. This article describes the use of specialized hardware, a high‐speed floating‐point array processor (AP), to dramatically speed up molecular mechanics, in other words molecular dynamics, Monte Carlo, and energy‐minimization calculations. Although the array processor is a cost effective solution for computationally intensive problems in terms of hardware (full‐time AP usage is equivalent to 2–8 h/day of Cray‐1 time), its full speed comes at the expense of programming in a relatively difficult parallel assembly language. Since the architecture of the machine is dramatically different from conventional computers and utilizing its fast speed necessitates using this architecture on the assembly language level, the proper design and implementation of algorithms is critical. The molecular mechanics software design discussed here, consisting of 12,000 lines of C and 7000 lines of AP assembly language code, is quite general and has been used to study systems ranging from rare gases to biomolecules. This implementation yields effective speeds approximately 35 times faster than a dedicated DEC VAX 11/780 computer with floating‐point accelerator and optimized VMS FORTRAN, thus allowing simulations to be run in one and a half weeks on the AP which would require a year of dedicated VAX time. The flexibility of the UNIX operating system, whose source code is accessible and can be modified to optimize performance, combined with the modern features of the C language, have made this implementation much easier by providing a convenient and powerful environment in which to imbed the hand‐coded AP assembly language modules. Applications to date range from the molecular‐dynamic calculation of infrared, Raman, and electronic spectra in gas and liquid solutions to the calculation of thermodynamic quantities for water and the simulation of the molecular dynamics of solution reactions and polypeptides.
Energetics of the neighbor exclusion model of intercalation
Authors: Sawaryn Andrezej , Leps Bernd , Bradaczek Hans 
Published: December 2004

AbstractThe nearest‐neighbor exclusion model for intercalation was studied using an energetical approach. It was shown that creation of the intercalation site in the exclusion model corresponds to the same energetical destabilization of the structure as in the standard model of intercalation. The stability of the intercalation complex formed in the case of the exclusion model is lower by 68 kcal/mol as compared with the standard model, but geometrical structures of both complexes are very similar. The electrostatic molecular potential method was also used to further characterize the intercalation site formed within both models of intercalation.
Multicollinearity and some applications in biological chemistry
Authors: Sanjeevi R. , Nagarajan R. , Ram V. Sri 
Published: December 2004

AbstractThe relationship between various parameters characterizing a particular system are established using various techniques. In some specific cases, ordinary multiple regression is resorted to for relating one variable to various other variables. However, in such problems there is a high probability of an interrelationship among different variables giving rise to multicollinearity, thereby making it infeasible to place much reliability on ordinary regression techniques. This problem can be circumvented using ridge regression techniques. In this preent investigation an attempt has been made to study the multicollinear problems in biology.
Faster finite‐difference calculations of molecular properties
Authors: Mullally D. J. , McIver J. W. 
Published: December 2004

AbstractA very simple yet effective device for reducing the number of self‐consistent‐field (SCF) cycles in central finite‐difference calculations of molecular properties is presented. The efficiency of this is demonstrated by MINDO/2 calculations of the force constants of a variety of molecules. The device consists of using information about the wavefunction at two values of a perturbation parameter to provide an estimate of the wavefunction at a third. This estimate is then used as an initial guess in an SCF procedure. The underlying theory is discussed and applications to other problems are suggested.
Quantum chemistry with an attached processor
Authors: Bair Raymond A. , Dunning Thomas H. 
Published: December 2004

AbstractThe Floating Point Systems, Inc. Model 164 Attached Processor (FPS‐164) is a high‐speed, pipelined, parallel processor designed for large‐scale scientific computation. Benchmark studies of operations common in quantum chemistry codes are discussed and the performance of the FPS‐164 is compared with other commonly available computers. A complete system of electronic structure codes has been implemented on the FPS‐164 using the Fortran‐77 cross‐compiler and calls to optimized vector and matrix routines. The conversion of a generalized valence bond (GVB) code illustrates the strategy adopted to adapt Fortran codes to the FPS‐164. A typical production example, a large scale (GVB) and configuration interaction calculation on the vinyl radical, shows a net throughput equivalent to nearly nine VAX 11/780 computers.
Electron correlation and relative energetic characteristics of complex hydrides of light elements. I. Beryllohydrides
Authors: Cimiraglia R. , Persico M. , Tomasi J. , Charkin O. P. 
Published: December 2004

AbstractThe effect of correlation energy on the relative stability of different structures and dissociation products of complex lithium beryllohydrides has been investigated. The adequacy of the method employed (third‐order Möller–Plesset perturbation theory) and the basis set dependence have been assessed. Trends of the correlation energy according to the molecular structure have been discussed, and the validity of an additive scheme based on electron pair contributions has been tested.
Conformational analysis by scaled energy embedding
Authors: Crippen Gordon M. 
Published: December 2004

AbstractDistance geometry has been used for some years to find conformations of molecules consistent with given bounds on the interatomic distances. A recent extension of the method, called energy embedding, enforces the geometric constraints as before, but also biases the results toward low‐energy structures. Now a significant improvement on energy embedding is presented, which is less dependent on local optimization for satisfying the geometric constraints. Tests on very small systems with well understood energy functions show that the global minimum energy value is often attained, and geometric constraints are always satisfied.
Approaches to charge calculations in molecular mechanics. 2 Resonance effects in conjugated systems
Authors: Abraham Raymond J. , Hudson Brian 
Published: December 2004

AbstractA previously published scheme of estimating atomic charges in haloalkanes is extended to include olefines, alcohols amines, acids, ethers, and amides. In the conjugated systems the effects of mesomeric transfer of charge are explicitly included. Generally good agreement with the observed dipole moments of these compounds and their substituted derivatives is found. The atomic charges so obtained are compared with those of other semiempirical and quantum‐mechanical calculations for the amide group. The charges so obtained fall within the range of values obtained by these other schemes, supporting the general validity of this approach.