bluuebunny/crossref_metadata_2025_split huggingface dataset:
A theoretical study of the rotational isomers of nitrosomethanol by semiempirical (AM1) and ab initio methods
Authors: Higgins Derek , Thomson Colin 
Published: January 2005

AbstractThe 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

AbstractAn 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

AbstractAn 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

AbstractA 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

AbstractA 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

AbstractApproximate 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

AbstractAcidities 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

AbstractA 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

AbstractEmpirical 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

AbstractAn 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

AbstractExpressions 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

AbstractThe 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

AbstractNormal 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

AbstractThe 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

AbstractThe 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

AbstractAb 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

AbstractA 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

AbstractMolecular 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

AbstractA 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

AbstractThe 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

AbstractIn 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

AbstractA 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

AbstractAn 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

AbstractThe 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

AbstractA 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

AbstractA 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.