bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular mechanics and molecular shape. V. on the computation of the bare surface area of molecules
Authors: Meyer A. Y.
Published: January 2005

This article examines the numerical estimation of molecular surface areas within the model of overlapping atomic spheres. One has the choice of either basing the estimate on all elements that contribute to the surface, or of ignoring systematically some elements in the interatomic clefts. It is argued that the second choice, even though more approximate, implicitly improves on the model and is to be preferred. Since surface areas are not measurable, the demonstration is unavoidably roundabout, relying mostly on correlation analysis. Among the regressors occur two compounded parameters. One, ratio of the surface area of the equivalent sphere to the surface area, is interpreted as a measure of molecular globularity. It reflects the molecular axis‐ratio and surface convolution. The other, ratio of the surface area to the volume, is interpreted as a measure of the global congestion of a chemical residue. Together with a measure of the local congestion at the point of attachment, it affects the steric hindrance that a residue offers. The relation between the surface area and the number of valence electrons is also discussed.
Application of SINDO1 to silicon, aluminum, and magnesium compounds
Authors: Jug Karl , Iffert Rüdiger
Published: January 2005

SINDO1 calculations are presented for ground state geometries, heats of formation, ionization potentials and dipole moments of silicon, aluminum and magnesium compounds. These calculations are based on a new parametrization of SINDO1 for second‐row elements. Important features are the inclusion of 3d orbitals and the explicit evaluation of zero point energies. A comparison with MNDO data is presented.
Explorations on the multidimensional potential energy surface of a chiral stationary phase
Authors: Lipkowitz Kenny B. , Demeter David A. , Landwer Jo. M. , Parish Carol A. , Darden Thomas
Published: January 2005

The multidimensional potential energy surface for a soluble analog of a chiral phase is computed with MM2 and MNDO. Minimum energy conformations are located. The minimum energy reaction pathway between these forms is located, and the templating ability of these phases is described.
The rigorous computation of the molecular electric potential
Authors: Zauhar R. J. , Morgan R. S.
Published: January 2005

A method is presented for the rigorous computation of the electric potential of molecules of arbitrary shape, under the assumption of continuous linear dielectric media. The computational technique involves finding the distribution of induced polarization charge on the molecular surface, and proceeds by an application of the method of boundary elements. The surface, which separates the molecular interior (of low dielectric constant) from the highly polar solvent, is given a piece‐wise analytic representation as a collection of curvilinear elements. Given a set of internal fixed charges, the distribution of polarization‐charge is found as a continuous function over the surface elements, and the electric potential (including all polarization effects) is then easily computed at any point. The method is applied to a spherical interface, and to several small molecules of biological interest, including a hexapeptide. The resulting potentials show good convergence in all cases. The future application of the method to macromolecules is discussed.
A theoretical study of the rotational isomers of nitrosomethanol by semiempirical (AM1) and ab initio methods
Authors: Higgins Derek , Thomson Colin
Published: January 2005

The conformational potential energy surface as a function of the two internal torsion angles in C‐nitrosomethanol has been obtained using the semiempirical AM1 method. Optimized geometries are reported for the local minima on this surface and also for the corresponding points on the HF/6‐31G, 6‐31G*, and 6‐31G** surfaces. All methods predict cis and trans minima which occur in degenerate pairs, each pair being connected by a transition state of Cs symmetry. The AM1 structures are found to compare well with the corresponding ab initio structures. Ab initio HF/6‐31G and HF/6‐31G* harmonic vibrational frequencies are reported for the cis and trans forms of nitrosomethanol. When scaled appropriately the calculated frequencies are found to compare well with experimental frequencies. The ab initio calculations predict the energy barrier for cis → trans isomerization to be between 5.8 and 6.5 kcal/mol with the trans → cis isomerization barrier lying between 2.3 and 6.5 kcal/mol. The corresponding AM1 energy barriers are around 1 kcal/mol lower in energy. The ab initio calculations predict the barrier to conversion between the two cis rotamers to be very small with the AM1 value being around 1 kcal/mol. Both AM1 and ab initio calculations predict interconversion between trans rotamers to require between 1.2 and 1.4 kcal/mol.
Application of finite‐element method to the two‐dimensional Schrödinger equation
Authors: Sato Nobuyuki , Iwata Suehiro
Published: January 2005

An algorithm to solve the two‐dimensional Schrödinger equation based on the finite‐element method is proposed. In our scheme, the molecular Hamiltonian with any arbitrary internal coordinate system can be solved as easily as with the Cartesian coordinate system. The efficient computer program based on the algorithm was developed on the HITAC S‐810 supercomputer. The performance of the program is examined in the following test problems; (1) free particle in a box, (2) linear triatomic molecule with two equal force constants, (3) coupled Morse oscillators, (4) Henon‐Heiles potential, (5) H3O+ symmetric vibrational modes. The algorithm is demonstrated to be very suited for the vector‐type supercomputer.
An efficient algorithm for solving eigenvalue problems of the type HC = SCe or FC = SCe
Authors: Masamura M.
Published: January 2005

An efficient algorithm for solving eigenvalue problems of type HC = SCe or FC = SCe is described. This algorithm is generally faster than conventional algorithms. That is to say, this algorithm is more than 1.8 times faster than Gram‐Schmidt orthogonalization and about 8 times faster than Löwdin's S−1/2 method. This algorithm is beneficial for large molecules and molecules having a high degree of symmetry. In addition, this algorithm is more compact than conventional algorithms.
Pattern recognition in the prediction of protein structure. III. An importance‐sampling minimization procedure
Authors: Lambert Millard H. , Scheraga Harold A.
Published: January 2005

A procedure that generates random conformations of a protein chain, and then applies energy minimization to find the structure of lowest energy, is described. Single‐residue conformations are represented in terms of four conformational states, α, ϵ, α*, and ϵ*. Each state corresponds to a rectangular region in the ϕ, ψ map. The conformation of an entire chain is then represented by a sequence of single‐residue conformational states. The distinct “chain‐states” in this representation correspond to multidimensional rectangular regions in the conformational space of the whole protein. A set of highly‐probable chain‐states can be predicted from the amino acid sequence using the pattern recognition procedure developed in the first two articles of this series. The importance‐sampling minimization procedure of the present article is then used to explore the regions of conformational space corresponding to each of these chain‐states. The importance‐sampling procedure generates a number of random conformations within a particular multidimensional rectangular region, sampling most densely from the most probable, or “important,” sections of the ϕ, ψ map. All values of ϕ and ψ are allowed, but the less‐probable values are sampled less often. To achieve this, the random values of ϕ and Φ are generated from bivariate gaussian distributions that are determined from known X‐ray structures. Separate gaussian distributions are used for proline residues in the α and ϵ states, for glycine residues in the α, ϵ, α*, and ϵ* states, and for ordinary residues involved in 29 different tripeptide conformations. Energy minimization is then applied to the randomly‐generated structures to optimize interactions and to improve packing. The final energy values are used to select the best structures. The importance‐sampling minimization procedure is tested on the avian pancreatic polypeptide, using chain‐states predicted from the amino acid sequence. The conformation having the lowest energy is very similar to the X‐ray conformation.
A theoretical study of solvation energies of FCH2COO−, FCH2COOH, and F2CHCOO−
Authors: Jain Duli C. , De Gale Denyse , Sapse Anne‐Marie
Published: January 2005

A continuum and a discrete‐continuum models are used to determine the solvation energies of FCH2COO−, FCH2COOH, and F2CHCOO−. For the anions, the continuum model provides results closer to the experiment, while for the acid, the addition of one water molecule improves the continuum‐only energy.
Calculation of Langevin‐type capture rate constants for rotating molecules with arbitrary interaction potentials
Authors: Phillips Leon F.
Published: January 2005

Approximate classical trajectory calculations of capture rates are performed for collisions occurring under the influence of a combination of angle‐dependent and isotropic potentials. Results calculated for a wide range of temperatures are in good accord with existing data for ion‐dipole (H3+ + HCN), ionquadrupole (OH− + C2H2), dipole‐dipole (BH + NO), and dipole‐quadrupole (CN + O2) reactions.
Hydrocarbon acidities calculated with MINDO/3, MNDO, and AM1
Authors: Kass Steven R.
Published: January 2005

Acidities of 32 hydrocarbons have been calculated using MINDO/3, MNDO, and AM1. All three semiempirical procedures have systematic errors and reproduce experimental acidities poorly. A linear correlation, however, does exist between the calculated and experimental results. Correction of the AM1 or MNDO acidities leads to good agreement with literature values even for acids, such as methane and ethylene, whose conjugate bases are small localized anions. Predictions for several hydrocarbons are given.
On the validity of polarization and correlation additivity in ab initio molecular orbital calculations
Authors: Dewar Michael J. S. , Holder Andrew J.
Published: January 2005

A common approximation used in ab initio molecular orbital calculations assumes that the changes in energy due to use of a larger basis set (as in the inclusion of polarization orbitals) and to allowance for electron correlation are additives. Thus, small basis sets may be used for correlated ab initio calculations, resulting in a great savings in time. While this approach has been shown to perform acceptably in some cases, a systematic study has not been published. We examined 35 species and computed the heats of reaction for 15 processes at the 6‐31G level of theory using polarization and correlation correction up to the MP4 level. The same items were then treated by an additive procedure to attain the same level of theory. We also examined the conrotrary ring opening of cyclobutene. Our results indicate that the errors do cancel to some extent but that the uncertainty associated with open shell species is significantly larger than closed shell systems. This calls into question the use of the procedure in predicting the properties of transition states.
Molecular mechanics criterion for metal complex formation
Authors: Yoshikawa Yuzo
Published: January 2005

Empirical force‐field calculations were carried out before and after metal‐complex formation for a cobalt(III)‐complex system with a series of aliphatic amines. The limit of the strain‐energy differences in metal‐complex formation is evaluated by comparing the calculated data with experimental results. A criterion for the synthesizability of unknown metal complexes was derived from these findings. The strain energy of the ion pair was also calculated for some of the complexes. The results suggest that the ion‐pair formation effectively contributes to their stabilization.
Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics
Authors: Mohamadi Fariborz , Richards Nigel G. J. , Guida Wayne C. , Liskamp Rob , Lipton Mark , Caufield Craig , Chang George , Hendrickson Thomas , Still W. Clark
Published: January 2005

An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom‐based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state‐of‐the‐art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.
Dynamics of peptides with fixed geometry: Kinetic energy terms and potential energy derivatives as functions of dihedral angles
Authors: Gibson Kenneth D. , Scheraga Harold A.
Published: January 2005

Expressions are derived for computing the kinetic energy of a peptide with fixed geometry, in terms of dihedral angles as generalized coordinates; other expressions required for the solution of Lagrange's equations are also presented. The peptide is regarded as held stationary at one end. We also outline the computations that are needed in calculating the components of the third derivative of a potential energy function that consists of a sum of pairwise interatomic interactions.
Theoretical studies on the alkaline hydrolysis of N‐Methylcarbamates
Authors: Katagi Toshiyuki
Published: January 2005

The reaction mechanisms of the alkaline hydrolysis of N‐methylcarbamates were studied using the AM1 method by assuming two possible pathways: (1) nucleophilic attack of hydroxide ion on the carbonyl carbon to give a tetrahedral complex followed by its breakdown to carbamic acid (BAC2); and (2) proton abstraction by hydroxide ion at the nitrogen atom followed by elimination of the alkoxide ion to form N‐methyl isocyanate (E1cB). Reaction coordinate analysis showed that the reaction mechanism is determined by both the stability of an intermediate and the energy barrier for elimination.
A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K
Authors: Derreumaux Philippe , Vergoten Gérard , Lagant Philippe
Published: January 2005

Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey–Bradley–Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm–1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the CN bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen‐bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.
Electronic structure and hypolipidemic activity of phthalimide and related compounds. A QSAR study
Authors: Ramos Mozart N. , de B. Neto Benício
Published: January 2005

The hypolipidemic activities of phthalimide and seven related compounds are subjected to a QSAR analysis based on results from AM1 molecular orbital calculations. Least‐squares fits show a correlation of the activities with LUMO energies and carbonyl polarities and predict enhanced activities for two new phthalimide derivatives.
Molecular mechanics. The MM3 force field for alkenes
Authors: Allinger Norman L. , Li Fanbing , Yan Liqun
Published: January 2005

The MM3 force field has been extended to include alkenes. Forty‐five compounds were examined, and structures, conformational equilibria, heats of formation, and rotational barriers, were calculated. For a smaller representative group, the vibrational spectra and entropies were also calculated. In general, these quantities, except for the vibrational spectra, agree with available data to approximately within experimental error. The vibrational frequencies for a set of eight well‐assigned structures were calculated to a root‐mean‐square error of 47 cm−1.
The theoretical reaction path for the cation radical vinylcyclobutane rearrangement: A concerted SR path
Authors: Bauld Nathan L.
Published: January 2005

Ab initio reaction path calculations for the cation radical vinylcyclobutane rearrangement at the MP2/ 6‐31G*//3‐21G level reveal a concerted, sr reaction path with an activation energy of 9.4 kcal/mol. The vinylcyclobutane cation radical itself, at both the MP2 and MP3 levels of theory has predominant olefin cation radical character but with modest stretching of one of the adjacent ring carbon—carbon bonds.
Concise, open‐ended implementation of Rys polynomial evaluation of two‐Electron integrals
Authors: Augspurger Joseph D. , Bernholdt David E. , Dykstra Clifford E.
Published: January 2005

A quadrature‐point‐driven implementation of the standard Rys polynomial method for computing two‐electron repulsion integrals of gaussian basis functions has been found to be both concise and openended with respect to the angular momentum of the gaussian functions (i.e., s,p,d,f,g,…). These are important features in certain applications, such as molecular properties and property gradients.
Hydration of superoxide studied by molecular dynamics simulation
Authors: Shen Jian , Wong Chung F. , McCammon J. Andrew
Published: January 2005

Molecular dynamics was used to study the hydration of superoxide (O). The Helmholtz free energy of hydration of O was estimated by the thermodynamic integration method. The diffusion of O and the water structure around O were also studied. Two water models were used in the calculations and the results were compared to experiments.
Molecular mechanics calculations of several lanthanide complexes: An application of the random incremental pulse search
Authors: Ferguson David M. , Raber Douglas J.
Published: January 2005

A new method for the evaluation of metal complexes with molecular mechanics calculations is described. The method has been employed to determine the global minimum energy conformations of three seven‐coordinate lanthanide complexes. The method searches the potential energy surface of the metal complexes for the global minimum structure using the recently reported Random Incremental Pulse Search (RIPS). The molecular mechanics calculations were performed using the MM2 metal‐extended force field (MM2MX). This force field excludes 1‐3 bending terms about the metal center and, instead, explicitly includes 1‐3 nonbonded van der Waals interactions. This affords a model based mainly on steric interactions about the ligating atoms, and removes the necessity of specifying ligand‐metal‐ligand bond angles for seven‐coordinate and higher metal complexes in which no preferred bond angle can be proficiently determined. The calculated minimum‐energy structures were well known seven‐coordinate conformations in all cases, and a comparison with X‐ray crystallographic is presented.
MRD‐CI calculations of proton affinity within the ab initio method for approximation of the frozen molecular fragment
Authors: Roszak S. , Hariharan P. C. , Kaufman Joyce J. , Koski W. S.
Published: January 2005

The method of approximation of the frozen molecular fragment (FMF) we derived has been applied to calculations of proton affinities. Results are in good agreement with experimental data and extended basis set calculations.
A general approach for atom‐type assignment and the interconversion of molecular structure files
Authors: O'Donnell T. J. , Rao Shashidhar N. , Koehler Konrad , Martin Yvonne C. , Eccles Beverly
Published: January 2005

In molecular modeling projects which require use of several different computer programs, one encounters problems in sharing data between programs. One difficult problem is the conversion of atom types from one program's definition to another. A second problem is the conversion of a polymer, such as a protein or polynucleotide molecule, from a “general” program, which understands molecules as a collection of atoms, to a “polymer” program, which understands molecules as a collection of molecular fragments stored in some library. We describe here a new method by which atom types are deduced from the environment of each atom. We use the Daylight Chemical Information Systems library of programs to deduce the atom types based only on the atomic symbol, connectivity and formal charge of each atom in the molecule. We also describe a method by which the polypeptide nature and sequence of a molecule can be deduced from minimal information about the atoms in the molecule. We have written a computer program which demonstrates this method. This program deduces atom types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will also produce input files for the AMBER/PREP fragment library preparation program.
Two‐electron integral evaluation for uncontracted geometrical‐type Gaussian functions
Authors: Wong M. W. , Corongiu G. , Clementi E.
Published: January 2005

A new algorithm for efficient evaluation of two‐electron repulsion integrals (ERIs) using uncontracted geometrical‐type Gaussian basis functions is presented. Integrals are evaluated by the Habitz and Clementi method. The use of uncontracted geometrical basis sets allows grouping of basis functions into shells (s, sp, spd, or spdf) and processing of integrals in blocks (shell quartets). By utilizing information common to a block of integrals, this method achieves high efficiency. This technique has been incorporated into the KGNMOL molecular interaction program. Representative timings for a number of molecules with different basis sets are presented. The new code is found to be significantly faster than the previous program. For ERIs involving only s and p functions, the new algorithm is a factor of two faster than previously. The new program is also found to be competitive when compared with other standard molecular packages, such as HONDO‐8 and Gaussian 86.
On the determination of the minimum on the crossing seam of two potential energy surfaces
Authors: Farazdel Abbas , Dupuis Michel
Published: January 2005

An improved gradient‐based algorithm is presented for the determination of the minimum energy point on the crossing seam hypersurface between two arbitrary potential energy hypersurfaces. The Hessian matrix is updated employing the gradient information. The method is demonstrated in a study of some representative cases including charge‐transfer states of a typical molecular‐device molecule (a rigid spiro π – σ – π molecular cation) with, as well as without, an external electric field.
Hydration of small anions: Calculations by the AM1 semiempirical method
Authors: Davis Larry P. , Burggraf Larry W. , Storch Donn M.
Published: January 2005

The AM1 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite‐sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.
Projection operator method for geometry optimization with constraints
Authors: Lu Da‐Hong , Zhao Meishan , Truhlar Donald G.
Published: January 2005

A new approach is presented for performing geometry optimization for stationary points on potential energy hypersurfaces with equality constraints on the internal coordinates of a polyatomic system. The working equations are the same as for unconstrained Newton–Raphson optimization in Cartesian coordinates except that projection operators are applied to the gradient and Hessian to enforce the constraints. Two reactive systems with different kinds of constraints are treated as examples: OH + H2 → OH → H2O + H with one constrained OH bond distance and CH3 + H2 → CH → CH4 + H with one constrained HCH bond angle in the CH3 group or with one constrained bond distance and one simultaneously constrained bond angle. In each case we optimized all reactants and products as well as the saddle point, all subject to the constraints.
Comparison of semiempirical calculations for silicon compounds
Authors: Verwoerd W. S. , Weimer K.
Published: January 2005

A comparison is made of the performance of the MINDO/3, MNDO, AM1, and PM3 methods in calculating the nature of the dimer reconstruction observed on the silicon (100) crystal surface. Based on this case study we conclude that MINDO/3 gives the most realistic results, with PM3 calculations being quite similar but both MNDO and AM1 missing some key features of this system and giving rather unrealistic charge distributions. Hence use of PM3 is recommended for Si containing molecules where a lack of parameters or other restrictions prevent the use of MINDO/3.
Ab initio calculations on CO4 centers in silicon dioxide
Authors: McEachern R. J. , Rao P. S. , Weil J. A.
Published: January 2005

Ab initio SCF‐MO Hartree–Fock calculations were performed using the STO‐3G, 6‐31G, and 6‐31G* basis sets to model hypothetical substitutional carbon impurities in silicon dioxide. We utilized nine‐atom clusters, [C(OH)4]qt, with charge number qt = 0 and + 1. The positions of the C and O atoms were varied to achieve minimum total energies, while the fixed protons served to simulate the rigid crystal surroundings. In the optimized configuration of the neutral cluster, the CO bond lengths are appreciably longer than typical CO bonds, indicating relatively weak bonds for a carbon impurity at a silicon site. For comparison, the relative positions of all nine atoms in the [C(OH)4]0 model were allowed to vary. This unconstrained model yielded more normal bond lengths and was lower in energy than the fixed‐proton model by 6.80 eV with the 6‐31G* basis set. The free‐H model compared favorably with the x‐ray diffraction data for an analogous orthocarbonate. Our results are in concert with the lack of reports of any substitutional carbon impurity in α‐quartz. In the fixed‐H models, the twofold local symmetry was found to be retained when qt is 0 but not when qt is + 1. For the latter ion, the unrestricted H‐F calculations indicate that this paramagnetic center has its spin population almost entirely on one oxygen ion and is high in energy (5.31 eV with 6‐31G) compared to the diamagnetic neutral one. Conclusions reached with the nine‐atom clusters were confirmed by a series of calculations on the extended model [C(OSiH3)4]0.
Standard‐geometry chains fitted to X‐ray derived structures: Validation of the rigid‐geometry approximation. I. Chain closure through a limited search of “loop” conformations
Authors: Palmer Kathleen A. , Scheraga Harold A.
Published: January 2005

The Gō–Scheraga algorithm to produce rigid‐geometry chain closures for polypeptide chains (N. Gō and H.A. Scheraga, Macromolecules, 3, 178, 1970) has been updated to allow each residue in the chain to adopt different bond lengths or bond angles. A treatment of five‐residue local chain deformations is presented in detail. For chain sections shorter than five residues in length, it is shown that satisfactory closures may be obtained by direct fitting, indicating that the rigid‐geometry approximation is adequate to model even short sections of chains having perturbed local geometry. The new implementation of the algorithm has been applied to several problems in protein structure determination and molecular modeling. The first of these is the problem of finding standard‐geometry closures for short regions of chains having irregular geometry. It is shown that standard‐geometry closures which superimpose well upon the coordinates of the irregular structures may be obtained routinely for chain sections that are five amino acid residues or more in length. Another application of the algorithm is to generate a large number of closures for a short segment of a protein chain, as a method to search the conformational space of this segment. The latter application should prove useful in studies in which the conformation of some region of a given protein has not been determined experimentally. Such applications include the modeling of proteins which have a sequence homology to a crystallized protein, and modeling regions of crystallized proteins which are not well‐defined in electron density maps.
The Hylleraas‐CI method in molecular calculations. III. Implementation and numerical verification of a three‐electron many‐center theory
Authors: Frye D. , Preiskorn A. , Clementi E.
Published: January 2005

The general theory of three‐electron Hylleraas‐Configuration‐Interaction method using linear correlation factors of the form rij has been implemented for molecular systems using cartesian Gaussians as basis sets. A brief review of the theory and the form of the three‐electron integrals is presented. Additionally, a table of numerical values of some selected three‐electron integrals is given. Results from test calculations on H3 using the full form of the theory are presented for some simple basis sets. A discussion of the computational problems that need to be overcome before this approach is competitive with traditional methods is included.
Geometry optimization in cartesian coordinates: The end of the Z‐matrix?
Authors: Baker Jon , Hehre Warren J.
Published: January 2005

Geometry optimization directly in Cartesian coordinates using the EF and GDIIS algorithms with standard Hessian updating techniques is compared and contrasted with optimization in internal coordinates utilizing the well known Z‐matrix formalism. Results on a test set of 20 molecules show that, with an appropriate initial Hessian, optimization in Cartesians is just as efficient as optimization in internals, thus rendering it unnecessary to construct a Z‐matrix in situations where Cartesians are readily available, for example from structural databases or graphical model builders.
PM3 study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase
Authors: Szafran Miroslaw , Koput Jacek
Published: January 2005

Heats of formation (ΔHf) and proton affinities (PA) of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase are calculated using the AM1 and PM3 semiempirical methods. The following substitutents are considered: NO2, CN, CF3, CHO, F, Cl, COCH3, H, CH3, OCH3, SCH3, NH2, and N(CH3)2. The results are compared with the experimental data. Both methods reproduce the ΔHf with comparble accuracy; the rms deviations are 4.1 (AM1) and 4.5 kcal/mol (PM3) for the free bases and 9.5 (AM1) and 9.7 kcal/mol (PM3) for their conjugated acids. The PA are systematically underestimated by both methods, but AM1 appears to be clearly better than PM3 for reproducing the experimental values. The rms deviations for AM1 and PM3 are 5.1 and 9.6 kcal/mol, respectively. This is due to a cancellation of systematic errors in the calculated ΔHf in the AM1 case and to a summation of the errors in the PM3 case. Both methods correctly reproduce conformations of the molecules under consideration.
The use of ultraviolet resonance Raman intensities to test proposed molecular force fields for nucleic acid bases
Authors: Lagant Philippe , Derreumaux Philippe , Vergoten Gerard , Peticolas Warner
Published: January 2005

The harmonic molecular force fields for the nucleic acid bases, cytosine, and guanine, that have been previously published by several investigators are tested by the calculation of the relative intensities of the in‐plane modes in the ultraviolet resonance Raman (UVRR) effect from the two lowest lying absorption bands using a theoretical approach devised previously.1–3 Since only a fraction of the 2N – 3 in‐plane vibrations of a molecule are active in the UVRR, the two criteria that are taken for the adjustment of the force constant are: (1) the closest possible agreement between the observed and calculated frequencies of the 2N – 3 in‐plane vibrations, and (2) the closest possible agreement between the calculated and observed intensities of those few vibrations that are strongly active in the ultraviolet resonance Raman effect. In particular it is necessary that the force constants be adjusted to avoid the calculation of intense Raman lines with frequencies that are not observed in the UVRR spectrum. Using this criteria, a new force field has been developed that appears to give better agreement with the observed UVRR intensities than previously published ones. It is suggested that this calculation of the UVRR intensities can be used to refine molecular force fields in combination with other methods such as isotopic replacement currently in use to refine force constants.
Grid‐search molecular accessible surface algorithm for solving the protein docking problem
Authors: Wang Huajun
Published: January 2005

An algorithm for solving the protein docking problem is presented. Many tentative dockings are first generated by requiring a hole on the surface of one protein to match a knob on the surface of the other. All the tentative dockings are then applied. The initial configurations thus generated are further optimized. The optimization is facilitated by giving a discrete representation to the protein interior and a double‐layer discrete representation to the protein surface. The algorithm presented correctly predicts the association of trypsin with its inhibitor as well as that of the α and β subunits in hemoglobin.
Parallel algorithm for the computation of characteristic polynomials of chemical graphs
Authors: Venuvanalingam P. , Thangavel P.
Published: January 2005

A parallel algorithm is developed for the first time based on Frame's method to compute the characteristic polynomials of chemical graphs. This algorithm can handle all types of graphs: ordinary, weighted, directed, and signed. Our algorithm takes only linear time in the CRCW PRAM model with O(n3) processors whereas the sequential algorithm takes O(n4) time. Especially when the number of vertices of the graph is large this method will be more efficient than the recently developed vectorized Frame and Givens–Householder methods.
Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation
Authors: Floris F. M. , Tomasi J. , Ahuir J. L. Pascual
Published: January 2005

A computational method for the evaluation of dispersion and repulsion contributions to the solvation energy is here presented in a formulation which makes use of a continuous distribution of the solvent, without introducing additional assumptions (e.g., local isotropy in the solvent distribution). The analysis is addressed to compare the relative importance of the various components of the dispersion energy (n = 6, 8, 10) and of the repulsion term, to compare several molecular indicators (molecular surface and volume, number of electrons) which may be put in relation to the dispersion‐repulsion energy, and to define simplified computational strategies. The numerical examples refer to saturated hydrocarbons in water, treated with the homogeneous approximation of the distribution function which for this type of solution appears to be acceptable.
A molecular orbital study of amiloride
Authors: Venanzi Carol A. , Plant Christopher , Venanzi Thomas J.
Published: January 2005

Molecular orbital calculations with geometry optimization in the 3‐21G(*) basis set were carried out for the acylimino (A, 1a) and the isoimino (E, 1b) tautomers of the free base form of amiloride, and for the protonated form (F, 1c) of amiloride. The results showed the E1 tautomer to be 16.8 kcal/mol higher in energy than the A conformer of lowest energy, A1. The protonation energy of the A1 species was found to be 269.4 kcal/mol. Similar results were obtained using the AM1 method. These results are in agreement with the NMR results of Smith et al. which show the A and F species to be predominant in solution. The 3‐21G(*) rotational barrier for the acylimino tautomer was found to be 19.0 kcal/mol, with the A4 conformer 2.50 kcal/mol higher in energy than the A1.
Conformational studies of 2‐methylbutyronitrile and 3‐methyl‐1‐pentyne by vibrational spectroscopy and molecular mechanics
Authors: Crowder G. A. , Carlisle G. O.
Published: January 2005

Vibrational spectra were obtained for the structurally similar compounds 2‐methylbutyronitrile and 3‐methyl‐1‐pentyne, and vibrational assignments were made with the aid of normal coordinate calculations. Molecular mechanics calculations were also made, and each compound was shown to exist as a mixture of three conformers, with the most stable conformer being the one with the two methyl groups trans to each other. Results of the calculations are given.
Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence
Authors: Davis Malcolm E. , McCammon J. Andrew
Published: January 2005

Finite difference methods are becoming very popular for calculating electrostatic fields around molecules. Due to the large amount of computer memory required, grid spacings cannot be made extremely small in relation to the size of the van der Waals radii of the atoms. As a result, the calculations make a rather crude approximation to the molecular surface by defining grid line midpoints discontinuously as either interior or exterior. We present a method which “smoothes” the boundary, but more accurately models the potential from the analytic solution of the discontinuous dielectric problem and improves convergence in electrostatic energy calculations. In addition, a small improvement in convergence rate is observed.
Molecular geometries and heats of formation of C60 and C70 as computed by MM2‐87
Authors: Froimowitz Mark
Published: January 2005

MM2‐87 calculations have been performed on C60 (buckminsterfullerence; footballene) and C70 with full energy minimization. The steric energies for C60 and C70 were computed to be 179.9 and 177.9 kcal/mol, respectively. The heats of formation for C60 is found to be more stable than C60. The two bond lengths for C60 were computed to be 1.393 and 1.444 Å. Eight different bond lengths were found for C70 ranging from 1.386 to 1.452 Å. Bond angles, dihedral angles, and moments of inertia are also reported for the compounds.
Approximate STO functions for the first‐row transition metal atoms
Authors: de la Vega J. M. García , Miguel B.
Published: January 2005

Slater type orbital (STO) basis sets for the atoms Sc‐Zn have been derived using a technique based on the distance between subspaces. The accuracy for several properties of these basis sets has been tested. Basis sets studied are of both single‐ and double‐zeta sizes, although this technique can be generalized for any size. Uniform quality criteria through the series of atoms Sc‐Zn are difficulty to establish due to the varying number of d electrons. A comparative study at the atomic level of the quality of STO basis sets (both the two new basis sets and Clementi's basis sets) for the first‐row transition elements has been carried out. Results show that the new basis sets provide better simulation for several properties. Molecular calculations on compounds with these atoms using a Gaussian expansion fitted according to the new values of optimized STOs are also included. The results obtained are similar to those reported when STO‐3G basis set is used.
The graph isomorphism problem
Authors: Liu X. , Klein D. J.
Published: January 2005

A chemically and graph‐theoretically relevant problem is that of determining whether a pair of graphs G and G′ are isomorphic. A two‐stage computational test is developed. In the first stage an “eigenvalue‐eigenprojector” tabular graph‐theoretic invariant is computed, whence if the two tables differ, G and G′ must be nonisomorphic. The second stage, utilizing the tables of the first stage, orders the vertices, thereby leading to a special labeling for them, whence if the associated adjacency matrices for G and G′ are equal, it must be that G and G′ are isomorphic. The computational implementation, and testing of the algorithm is described.
Extension of SINDO1 to transition metal compounds
Authors: Li Jian , De Mello Paulo Correa , Jug Karl
Published: January 2005

The semiempirical MO method SINDO1, originally suitable for first‐ and second‐row atoms, is extended to transition metals from scandium to zinc. The core Hamiltonian elements in a symmetrically orthogonalized atomic orbital (OAO) basis set are modified and the parameters are optimized to reproduce the experimental geometries, heats of formation, and ionization potentials. An application of the method to a selected number of molecules, as well as a comparison between calculated and experimental data is reported.
Analysis of an intermediate in a 1,3‐dipolar cycloaddition of methylsulfonyl azide
Authors: Sustmann Reiner , Sicking Willi , Quast Helmut
Published: January 2005

MNDO‐PM3 calculations, carried out on an experimentally determined structure of an intermediate in the cycloaddition of an electrophilic azide and a nucleophilic 1,3‐dipolarophile, show that the semiempirical MO scheme models this structure closely. Transition structures for formation of the intermediate and ring closure of the latter are described.
Charge distributions of phosphorylcholine and its derivatives
Authors: Schaumberger M. , Köhler J.
Published: January 2005

Hartree–Fock self‐consistent field calculations on the 3‐21G(*) level of approximation have been performed to phosphorylcholine and its derivatives in a geometry close to an X‐ray structure of an antibody/antigen complex. Wave functions have been analyzed using different methods for derivation of atomic charges used as Coulomb charges in empirical force fields for molecular dynamics simulations. Among the three applied methods—Mulliken population analysis, natural population analysis, and electrostatical fit—the natural population analysis seems to give best results for these molecules.
A conformational analysis of 3′‐azido‐3′‐deoxythymidine
Authors: Sabio Michael , Topiol Sid
Published: January 2005

An extensive conformational analysis of 3′‐azido‐3′‐deoxythymidine (AZT) was performed at the semiempirical AM1 level with full relaxation of all geometric parameters and careful consideration of furan puckering and the rotational states of the thymine—furan, furan—azide, furan—methylene, and methylene—hydroxyl bonds. The search located 70 conformers, 21 of which have relative energies within 2.5 kcal/mol of the global minimum. Several geometric features, including various forms of hydrogen bonding, within this selected lowenergy subset were examined in terms of their relative contributions to the conformational states of AZT. Hydrogen bonding of thymine's position 2 carbonyl oxygen atom to the hydroxymethyl group (O2;HO), which until recently has not been mentioned in the literature, is observed in a few low‐energy AM1 conformations; however, this form is less favored at the AM1 level than the usually depicted modes involving the thymine moiety with the oxygen atoms of the hydroxyl and furan groups (H6;OH and H6Ofur, as observed in the two crystallographically independent structures), as well as that involving the hydroxyl hydrogen and furan oxygen atoms (OHOfur, which also has not been mentioned for AZT in the literature until recently). The AM1‐optimized geometries agree more closely with nuclear magnetic resonance data than with crystallographic structures and bear little resemblance to molecular mechanics results. The present study shows no evidence of a single dominant conformation or single structural parameter that determines AZT's conformational states. In contrast to our previous analogous study of cGMP, this computational study of AZT does not show strong evidence of a syn conformation with hydrogen bonding involving the base.
Automated docking with grid‐based energy evaluation
Authors: Meng Elaine C. , Shoichet Brian K. , Kuntz Irwin D.
Published: January 2005

The ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor‐dependent terms in the potential function at points on a three‐dimensional grid. In four test cases where the components of crystallographically determined complexes are redocked, the “force field” score correctly identifies the family of orientations closest to the experimental binding geometry. Scoring functions that consider only steric factors or only electrostatic factors are less successful. The force field function will play an important role in our efforts to search databases for potential lead compounds.
Pathways for ring inversion in 9, 10‐dihydroanthracene, 9, 10‐dihydrophenanthrene, and 7, 12‐dihydropleiadene: Combined molecular orbital and molecular mechanics study
Authors: Sygula Andrzej , Rabideau Peter W.
Published: January 2005

The combined semiempirical AM1 and MM2 study of the ring inversion processes in 9, 10‐dihydroanthracene (1), 9, 10‐dihydrophenanthrene (2), and 7, 12‐dihydropleiadene (3) predicts planar transition states for 1 and 2, in accord with earlier assumptions. In the case of 3, however, a nonplanar, chair‐like transition state is located on the potential energy surface in contrast with previous conclusions. Implications of the nonplanar TS on the rationalization of available experimental data are discussed. The calculated barriers for ring inversion in 1–3 are in reasonable agreement with both experiment and previous theoretical results. In general, AM1 is found to slightly underestimate the barriers as compared to the MM2 calculations.
Theoretical study of some nitriles: Intramolecular hydrogen bonds and anomeric effect
Authors: Fernández Berta , Vázquez Saulo A. , Ríos Miguel A.
Published: January 2005

An ab initio study of 3‐chloro‐, 3‐hydroxy‐, 3‐mercapto‐, and 3‐amino‐propanenitrile and 4‐chloro‐bu‐ tanenitrile was carried out at several levels of theory. The calculated stabilities and geometrical trends are interpreted in terms of the effects of intramolecular hydrogen bonds and anomeric interactions, and compared with available experimental data.