ALBERT

Notes: The affinity of a ligand for a receptor is usually expressed in terms of the dissociation constant (Ki) of the drug-receptor complex, conveniently measured by the inhibition of radioligand binding. However, a ligand can be an antagonist, a partial agonist, or a full agonist, a property largely independent of its receptor affinity. This property can be quantitated as intrinsic activity (1A), which can range from 0 for a full antagonist to 1 for a full agonist. Although quantitative structure-activity relationship (QSAR) methods have been applied to the prediction of receptor affinity with considerable success, the prediction of IA, even qualitatively, has rarely been attempted. Because most traditional QSAR methods are limited to congeneric series, and there are often major structural differences between agonists and antagonists, this lack of success in predicting IA is understandable. To overcome this limitation, we used the method of comparative molecular field analysis (CoMFA), which, unlike traditional Hansch analysis, permits the inclusion of structurally dissimilar compounds in a single QSAR model. A structurally diverse set of 5-hydroxytryptamine1A (5-HT1A) receptor ligands, with literature IA data (determined by the inhibition of 5-HT sensitive forskolin-stimulated adenylate cyclase), was used to develop a 3-D QSAR model correlating intrinsic activity with molecular structure properties of 5HT1A receptor ligands. This CoMFA model had a crossvalidated r2 of 0.481, five components and final conventional r2 of 0.943. The receptor model suggests that agonist and antagonist ligands can share parts of a common binding site on the receptor, with a primary agonist binding region that is also occupied by antagonists and a secondary binding site accommodating the excess bulk present in the sidechains of many antagonists and partial agonists. The CoMFA steric field graph clearly shows that agonists tend to be “flatter” (more coplanar) than antagonists, consistent with the difference between the 5-HT1A agonist and antagonist pharmacophores proposed by Hibert and coworkers. The CoMFA electrostatic field graph suggests that, in the region surrounding the essential protonated aliphatic amino group, the positive molecular electrostatic potential may be weaker in antagonists as compared to agonists. Together, the steric and electrostatic maps suggest that in the secondary binding site region increased hydrophobic binding may enhance antagonist activity. These results demonstrate that CoMFA is capable of generating a statistically crossvalidated 3-D QSAR model that can successfully distinguish between agonist and antagonist 5-HT1A ligands. To the best of our knowledge, this is the first time this or any other QSAR method has been successfully applied to the correlation of structure with IA rather than potency or affinity. The analysis has suggested various structural features associated with agonist and antagonist behaviors of 5-HT1A ligands and thus should assist in the future design of drugs that act via 5-HT1A receptors. © 1993 John Wiley & Sons, Inc.

Notes: We consider the tree search problem for the recurrence relation that appears in the evaluation of molecular integrals over Cartesian Gaussian basis functions. A systematic way of performing tree search is shown. By applying the result of tree searching to the LRL2 method of Lindh, Ryu, and Liu (LRL) (J. Chem. Phys., 95, 5889 1991), which is an auxiliary function-based method, we obtain significant reductions of the floating point operations (FLOPS) counts in the K4 region. The resulting FLOPS counts in the K4 region are comparable up to [dd|dd] angular momentum cases to the LRL1 method of LRL, currently the method requiring least FLOPS for [dd|dd] and higher angular momentum basis functions. For [ff|ff], [gg|gg], [hh|hh], and [ii|ii] cases, the required FLOPS are 24, 40, 51, and 59%, respectively, less than the LRL1 method in the K4 region. These are the best FLOPS counts available in the literature for high angular momentum cases. Also, there will be no overhead in either the K2 or K0 region in implementing the present scheme. This should lead to more efficient codes of integral evaluations for higher angular momentum cases than any other existing codes. © 1993 John Wiley & Sons, Inc.

Notes: A method is proposed to perform computer simulations of protein dynamics in the long-time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 106 scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End-to-end distance autocorrelation functions decay to 1/e of its initial value in about 103-104 scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.

Notes: The antitumor drug cis-diamminedichloroplatinum(II) (cisplatin) binds preferentially to GpG and ApG sequences of DNA, forming N7,N7 intrastrand chelates. Molecular modeling of the intrastrand adducts have been handicapped, so far, by the lack of force-field data describing the Pt-guanine and Pt-adenine binding. We used ab initio calculations with relativistic pseudopotentials to evaluate three important parameters for the platinum-adenine model complex [Pt(NH3)3(Ade)]2+: (1) the force constant for the Pt—N7 bond bending out of the adenine plane; (2) the energy profile for the torsion about Pt—N7; (3) a set of fractional atomic charges that reproduce the ab initio potential for a number of space points placed around the adduct. A population analysis and comparative study on the tetrammine complex [Pt(NH3)4]2+ have shown that for platinum adenine is a better σ-donor than NH3, but its capacity as a π-acceptor is weak. © 1993 John Wiley & Sons, Inc.

Notes: A procedure is reported for the prediction of dense crystal structures of C-, H-, N-, O-, and F-containing organic compounds in the primitive triclinic, monoclinic, and orthorhombic space groups with Z ≤ 4. The crystal environments of molecules in 242 crystal structures have been analyzed to determine the common coordination sphere pattens. This led to the development of the MOLPAK (MOLecular PAcKing) program, which uses a rigid-body molecular structure probe to build packing arrangements (possible crystal structures) in the various space groups. A MOLPAK search, which involves the investigation of all unique orientations of a central molecule and the construction of the appropriate coordination patterns about the central molecule, provides a 3-D map of minimum unit cell volume as a function of the orientation of the central molecule. MOLPAK uses a repulsion-only potential and a preset threshold to place molecules in contact with each other. The 5-10 smallest volume packing arrangements from a search are subjected to a lattice energy minimization refinement with the WMIN program to yield possible crystal structures. The results are described from the analyses of several known compounds starting with the crystal molecular structures as the MOLPAK search probes in the P1, P21, P21/c, and P212121 space groups. In addition, several examples are given in which the search probes were created by AM1 geometry optimization of preliminary molecular models. More extensive data are given in supplementary tables. © 1993 John Wiley & Sons, Inc.

Notes: A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long-range nonbonded Coulomb and Lennard-Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1-4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed-memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen-containing bonds but also all heavy-atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time-step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.

Notes: We report the development of a new approximate method of calculating molecular surface areas. Our technique is based upon the method of Sharake and Rupley but incorporates several major advances. First, we represent the state of surface points as bits in a bit string so we can utilize Boolean operations to simultaneously turn off multiple test points in one Boolean AND operation. Second, we use a series of Boolean mask look-up tables to reduce the time complexity of the calculation of molecular surface area down to the same magnitude as doing a potential energy evaluation. When we use a 256 surface point sphere for all of the atoms in BPTI, a 454 nonhydrogen atom protein, and a 1.4-Å solvent probe, we in general underestimate the total solvent-accessible surface area (SASA) by approximately 1.25% with a correlation coefficient of 0.9990 over a wide range of conformations. The average CPU time required to calculate the SASA of a BPTI conformer is 0.58 s on an SGI 4D/220 workstation. We also describe a method by which we can calculate an approximate finite difference SASA gradient for BPTI in 0.79 of CPU time. © 1993 John Wiley & Sons, Inc.

Notes: A method is proposed for calculating the forces in path integral theory and tested on semiclassic systems. It takes the range of the classic and quantum interactions into account and uses a second table within the neighbors table for the nearest neighbors. This method is found to be much more efficient than either the standard direct method or the traditional neighbors table, the efficiency increasing with the size of the system. The method can also be applied to clusters whose interaction centers are much farther apart than the distances between two consecutive members of the cluster. © 1993 John Wiley & Sons, Inc.

Notes: Parallelization of the SCF method for closed-shell molecules on the highly parallel transputer-based system PARAM is described. The parallelization has been implemented on three different hardware and software environments: (1) a network of bare 64 transputers; (2) configuration 1 plus a back-end file system (BFS); and (3) configuration 2 with one INTEL i860 processor. The evaluation of electron repulsion integrals (ERIs) and setting up of the Fock matrix is carried out in parallel on 64 nodes using minimal communication strategies. A good load balance is achieved for ERI evaluation with the help of bounds, local symmetry features, and the shell concept, as well as a data randomization technique, resulting into almost linear speedup (for ERI evaluation). In configurations 2 and 3, BFS is used for parallel storage and retrieval of ERIs. Further, in 3 matrix operations are implemented as remote procedure calls on the i860 processor. Routine techniques of level shifting and extrapolation are used for accelerating SCF convergence. The resulting package, INDMOL, has been tested for some randomly selected molecules having up to 255 contractions. Using configuration 3, a factor of 2 to 5 in computation time is obtained over 1, for the systems for which the ERIs cannot be stored in the distributed core memory. In summary, a heterogeneous system, as in configuration 3, can indeed be optimally exploited for programming peculiar diverse requirements of the SCF procedure. © 1993 John Wiley & Sons, Inc.

Notes: One of the features of the polypeptide backbone is that it represents a flexible chain that contains almost rigid CO—NH peptide bonds. One may try to substitute one or more such bonds by another relatively rigid unit to maintain the overall conformational properties of the backbone and at the same time modify some other properties of the molecule (“pseudopeptide”), such as the ability to form hydrogen bonds. By a detailed conformational analysis, it is shown that the carbon—carbon double bond is quite isosteric with the peptide bond and for this reason suitable for such a substitution. This is accomplished by applying molecular mechanics in calculation of the φ, ψ maps for pseudopeptide analogs of the N-acetyl-Ala-NHMe molecule. © 1993 John Wiley & Sons, Inc.

Notes: We present analytical expressions to calculate the gradient of the water-accessible surface area of proteins with respect to Cartesian coordinates and dihedral angles. A detailed mathematical analysis leads to corrected equations for the gradient calculation used previously in the ANAREA program. To study the hydrophobic effect of solvent-protein interactions, our expressions have been implemented to further improve the program package FANTOM. We used this version of FANTOM to minimize the ECEPP/2 and the hydrophobic energy of tendamistat. © 1993 John Wiley & Sons, Inc.

Notes: The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.

Notes: We describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling-relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all-atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA-type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence-Jones). © 1993 John Wiley & Sons, Inc.

Notes: A new index suitable for computing molecular similarity based upon the similarity of molecular properties such as electrostatic potentials or electrostatic fields is presented in two forms. For one form of the present index, general conditions are established for which a linear measure of similarity is obtained. An illustrative example is provided in which the electrostatic field and electrostatic potential of guanine obtained from different wave functions are compared. © 1993 John Wiley & Sons, Inc.

Notes: Using the MM2-87 program and parameter set, conformational analyses have been performed on cocaine (1), the potent analog 2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT, 2), and a group of dopamine reuptake blockers that contain two phenyl rings. The latter includes LU 19-005 (3), a 1-amino-4-phenyltetralin (4), a hexahydropyrrolo[2,1-a]isoquinoline (5), diclofensine (6), and a hexahydro[1,2-b]pyridine (7). Using different values for the dielectric constant, the global minimum of 1 and 2 is a conformer in which there is a favorable electrostatic interaction between the ammonium hydrogen and the carbonyl of the carbomethoxy group. The N-methyl groups in 1 and 2 are found to strongly prefer the equatorial position of the piperidine ring. These results were also related to four crystal structures of 1 and its close derivatives. Compounds 3-7 are found to have a common conformation that was used to define the pharmacophore for dopamine reuptake blockers including the required orientation of the ammonium hydrogen. The pharmacophore provides an explanation for why the tertiary amine analogs of 3 and 4 are less potent than the secondary amines because the added N-methyl group occupies the position required for the ammonium hydrogen. This explanation, however, does not work for 7, in which the tertiary amine is again less active than the secondary amine. However, this last series appears to have a number of anomalous features. Superposition of 2 with the pharmacophore suggests that its carbomethoxy may occupy the same region of the receptor as the second phenyl ring in compounds 3-7. © 1993 John Wiley & Sons, Inc.

Notes: The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N′-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed. © 1993 John Wiley & Sons, Inc.

Notes: The program AQUARIUS2 calculates probable positions for water molecules within the first hydration shell of any protein for which atomic coordinates are known. Like its predecessor, AQUARIUS, it uses a knowledge of water molecules sites from crystallographically determined protein structures. Energy calculations are not employed. It differs substantially from the original program in that a 3-D probability map (for solvent sites) is generated around the surface of the protein instead of the previously used discrete points. The accuracy of the program has been gauged by comparison with experimentally derived water molecule positions for proteins not used in the knowledge base of the program. It has also been tested by combining the probability density maps with crystallographically determined electron density maps for the protein porphobilinogen deaminase. This procedure filters the most likely solvent electron density peaks from the background noise and has been used in the determination of the solvent structure around the protein nerve growth factor. © John Wiley & Sons, Inc.

Notes: Net atomic charges are derived from a least-squares fitting to electrostatic potentials at atomic sites. The method treats atoms in the molecule as having spherically averaged Hartree-Fock densities, the atomic densities overlapping with one another. The method has the advantage of best reproducing the electrostatic potentials at the atomic nuclei and avoiding the arbitrariness in choosing the points used in the fitting. We have written a FORTRAN program, CHELPN92 (Z. Su, Chemistry Department, SUNY at Buffalo, Buffalo, NY, 1992), based on the method and applied it to deuterated benzene, l-alanine, d,l-histidine, 2-methyl-4-nitroaniline, and deuterated pyridinium-1-dicyanomethylide using the molecular geometry and electrostatic potentials from analysis of accurate X-ray diffraction data. The derived charges are used to calculate the molecular dipole moments. While the charges from this method are in general significantly different from those from the kappa refinement [P. Coppens, T.N. Guru Row, P. Leung, E.D. Stevens, P.J. Becker, and Y.W. Yang, Acta Cryst. A, 35, 63 (1979)], the dipole moments obtained with the new method agree well with those from the kappa refinement. © John Wiley & Sons, Inc.

Notes: Several methods are available in the literature for the conformational analysis of small molecules. Each of these methods has some advantages and some disadvantages. Also, each of these methods may be expected to perform better or worse on different types of molecules. There is no clear calibration of each of these methods against a “standardized” set of molecules available in the literature. Such a reference work would be useful to the community because it would allow the choice of methods to be based on some facts. We attempted to provide a start to such a calibration in this article with an examination of the SYBYL SEARCH method. Methods for evaluating the performance of this method are described in detail and will be applied to all other available conformational analysis methods in future papers. © John Wiley & Sons, Inc.

Notes: The problem of quantifying similarity between crystal structures is transformed into the problem of comparing the associated X-ray powder diagrams. A smooth similarity measure between two powder diagrams, termed a “fold,” is defined. In contrast to conventional comparison methods, the introduced method is still applicable when the peaks of the spectra to be compared have no overlap. The main areas of application of the method are the construction of a molecular crystal structure when only the experimental powder diagram is available and the analysis of possible crystal packings predicted on the basis of molecular information only. A suitable empirical parameterization of the fold has been derived from a large set of experimental and force-field-generated crystals. The analysis of the outcome of an ab initio packing of a flexible molecule is given as an example. The algorithmic details of the method are given as a FORTRAN 77 code. © John Wiley & Sons, Inc.

Notes: We describe a new method for de novo design of molecules that bind to protein active sites. The method, CONCEPTS (Creation of Novel Compounds by Evaluation of Particles at Target Sites), places a group of atom-like particles in the site. The particles are free to move within the site to improve binding to the protein. A key innovation of this technique is that covalent connections are made among the particles in a stochastic and dynamically reversible manner. These changes in the topology are either accepted or rejected depending on their ability to improve the total energy of the enzyme-inhibitor complex. The method is applied to two test systems: The FK506 binding protein (FKBP-12) and HIV-1 aspartyl protease. In both cases, we are able to predict, de novo, drugs that have striking similarities to known potent inhibitors and that can successfully be used to generate “hits” of the known inhibitors from a data base. © John Wiley & Sons, Inc.

Notes: The separation of the short- and long-range terms in the potentials generated by pairs of Slater functions is reformulated in the context of the Gauss transform method. Analytic expressions of the long-range potentials (in closed form) are derived for equal exponents and generalized (as expansion series) for different exponents. Additionally, the representation of these potentials from small sets of charges or lowest-order multipoles is examined, paying special attention to their values and optimal positions. Finally, numerical tests of the formal developments are presented. It is concluded that the long-range three- and four-center integrals can be calculated with high accuracy in a simple and relatively inexpensive manner. © John Wiley & Sons, Inc.

Notes: To compare the GROMOS force field with one designed by Ha et al., molecular dynamics simulations of α-D-glucose anhydrate and monohydrate crystals were performed. Also, the long-range interactions were calculated both with a cutoff approximation and with Ewald summations. The results are compared with results obtained experimentally by neutron and X-ray diffraction. The force-field parameters had been optimized with the cutoff approximation; this apparently led to worse results when the Ewald summations were used. However, in all simulations the symmetry was roughly preserved and the mean atomic coordinates and thermal parameters, bond angles, and dihedrals without hydrogen atoms were rather well reproduced. The dihedrals with hydrogen atoms exhibited conformational transitions, which resulted in a disordered hydrogen bonding scheme. In general, the GROMOS force field performed better than the Ha force field. © John Wiley & Sons, Inc.

Notes: Lithium parameters have been optimized for Stewart's standard PM3 method. The average deviation of the heats of formation calculated for 18 reference compounds is 6.2 kcal/mol from the experimental or high-level ab initio data; the average deviation with Li/MNDO is 18.9 kcal/mol. The average error in bond lengths is also reduced by a factor of two to three. Ionization potentials and dipole moments are reproduced with comparable accuracy than Li/MNDO. However, the mean deviation for the heats of formation of both methods increases when being applied to other systems, especially to small inorgnic molecules. The applicability of the new parameter set is demonstrated further for various compounds not included in the reference set, for the calculation of the activation barriers of several lithiation reactions, as well as for the estimation of oligomerization energies of methyl lithium (including the tetramer). Li/PM3 gives reliable results even for large dimeric complexes, like [{4-(CH3CR)C5H4N}Li]2, containing TMEDA or THF as coligands and reproduces the haptotropic interaction between Li+ and π-systems (e.g., in benzyl lithium) as well as the relative energies and structural features of compounds with “hypervalent” atoms (e.g., in lithiated sulfones). © John Wiley & Sons, Inc.

Notes: We apply a recently developed method, the multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, metenkephalin is studied and the ergodicity problem, or multiple-minima problem, is shown to be overcome by this algorithm. The lowest-energy conformation obtained agrees with that determined by other efficient methods such as Monte Carlo simulated annealing. The superiority of the present method to simulated annealing lies in the fact that the relationship to the canonical ensemble remains exactly controlled. Once the multicanonical parameters are determined, only one simulation run is necessary to obtain the lowest-energy conformation and further the results of this one run can be used to calculate various thermodynamic quantities at any temperature. The latter point is demonstrated by the calculation of the average potential energy and specific heat as functions of temperature. © John Wiley & Sons, Inc.

Notes: Optimized geometries and total energies for the conformers of 3,6-dihydro-1,2-dithiin (2) and 3,6-dihydro-1,2-dioxin (3) were calculated at several ab initio MO levels: RHF/3-21G(*), RHF/6-31G*, MP2/6-31G*, and MP2/6-31G*/ /RHF/3-21G(*). For the dioxin, in addition to the above levels the corresponding nonextended basis sets ab initio methods were also carried out. The dithiin results are compared with those of simple disulfanes, HSSH and (CH3)2S2, whose optimized geometries agree closely with the observed structures, which is the gauche (C2 symmetry). For the disulfanes, the gauche geometries from RHF/3-21G(*) are in good agreement with the observed structure while the RHF/3-21G results best fit the dioxin. Pertinent structural data at the RHF/3-21G(*) for the half-chair (C2) dithiin are: bond lengths, —SS—, —CS—, —CC=, and —C=C—, 2.050, 1.817, 1.515, and 1.317 Å, respectively; bond angles, CSS, =CCS, and C=CS, 98.0, 114.2, and 127.8°, respectively; CSSC dihedral angle of 63.2°; and twist angle of 36.5°. The total energy for half-chair dithiin at MP2/6-31G*//RHF/3-21G(*) is less than the planar (C2v) and the half-boat (Cs) structures by 69.67 and 29.05 kJ/mol, respectively. The calculated structural data (vs. observed) at RHF/3-21G for the half-chair dioxin are: bond lengths, —OO—, —CO—, —CC=, and C=C, 1.464 (1.463), 1.454, 1.509, and 1.313 Å (1.338 Å), respectively; bond angles, COO, =CCO, and C=CO, 105.0, 109.8 (110.3), and 120.7° (119.9°), respectively; COOC dihedral angle of 79.7° (80 ± 2°); and twist angle of 39.0 (38.3°). The total energy for half-chair dioxin at MP2/6-31G//RHF/3-21G is less than the planar and the half-boat structures by 70.35 and 42.85 kJ/mol, respectively. The total energies calculated at the extended basis sets (*) ab initio levels for the C2 symmetry dioxin are much lower than those of the nonextended basis sets. © John Wiley & Sons, Inc.

Notes: A common problem in the solution of the Poisson-Boltzmann equation using finite difference methods is the self-energy of the system, also known as the grid energy. Because atoms are typically modeled as a point charge, the infinite self-energy of a point charge is likewise modeled. In this article, a simple, alternate treatment of atomic charge is described where each atom is represented as a sphere of uniform charge. Unlike the point charge model, this method converges as the grid spacing is reduced. The uniform charge model generates the same electrostatic field outside the atoms. In addition, the use of fine grids reduces the variations in the potential due to variations in the position of atoms relative to the grid. Calculations of Born ion solvation energies, small-molecule solvation energies, and the electrostatic field of superoxide dismutase are used to demonstrate that this method yields the same results as the point charge model. © John Wiley & Sons, Inc.

Notes: An algorithm is introduced that tests whether a proposed elementary reaction can be realized within a specified number of cleavages and formations of covalent bonds. This is related to the problem of computing the minimum chemical distance of a given stoichiometry, but differs from it in important ways that are exploited in the algorithm design. One application of the algorithm is as a filter in MECHEM - a computer aid for the elucidation of reaction pathways. In that application, reaction steps implying more changes to covalent bonds than a given threshold are ruled implausible, and in practice such tests need to be carried out many thousands of times. Future applications of the algorithm can be expected because the question addressed is a fundamental one: What elementary reactions can occur? © 1993 by John Wiley & Sons, Inc.

Notes: Computer methods for analytic surface calculations of molecular systems suffer from numerical instabilities and are CPU time consuming. In this article, we present proposals toward the solution of both problems. Singularities arise when nearly collinear triples of neighboring atoms or multiple vertices are encountered during the calculation. Topological decisions in analytic surface calculation algorithms (accessibility of vertices and arcs) are based upon the comparison of distances or angles. If two such numbers are nearly equal, then currently used computer programs may not resolve this ambiguity correctly and can subsequently fail. In this article, modifications in the analytic surface calculation algorithm are described that recognize singularities automatically and treat them appropriately without restarting parts of the computation. The computing time required to execute these alterations is minimal. The basic modification consists in defining an accuracy limit within which two values may be assumed as equal. The search algorithm has been reformulated to reduce the computational effort. A new set of formulas makes it possible to avoid mostly the extraction of square roots. Tests for small-and medium-sized intersection circles and for pairs of vertices with small vertex height help recognize fully buried circles and vertex pairs at an early stage. The new program can compute the complete topology of the surface and accessible surface area of the protein crambin in 1.50-4.29 s (on a single R3000 processor of an SGI 4D/480) depending on the compactness of the conformation where the limits correspond to the fully extended or fully folded chain, respectively. The algorithm, implemented in a computer program, will be made available on request. © John Wiley & Sons, Inc.

Notes: The problem of the representation of the RKR (or IPA) diatomic potential by a simple analytic function is considered. This old problem has for a fairly good solution the Coxon-Hajigeorgiou function U(x) = D[1 - exp-fn(x)]2 with fn(x) = Σm = 1n amxm. The problem of the determination of the disposable parameters a1 … an [in order that U(r) fits the given RKR potential] is reduced to that of a set of linear equations in am where a standard least-squares technique is used. The application to several states (ground or excited) of several molecules shows that a fairly “good” fit is obtained for n ∼ 10, even for the state XOg - I2 bounded by 109 vibrational levels, for which the RKR potential is defined by the coordinates of 219 points. It is shown that the percentage deviation |U(r)RKR - U(r)| throughout the range of r values is about 0.04% for XΣ—Li2, 0.0005% for XΣ—HCl, 0.06% for XOg—I2, and 0.05% for BOu—I2 (as examples). This approach shows the same success for deep and shallow potentials. The comparison of the computed Ev (vibrational energy) and Bv (rotational constant) with their corresponding experimental values shows that a good agreement is reached even for high vibrational levels close to the dissociation. © John Wiley & Sons, Inc.

Notes: A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.

Notes: The nonbonded portion of a force field for lecithins was characterized by application to the study of the crystal packing geometry and energetics of eight different molecules. The molecules were either lecithin fragments or chosen to isolate particular intermolecular features to test the accuracy of the force field specifically for those interactions. In particular, the hydrocarbon interactions, hydrogen bonding, electrostatics, and phosphate interactions were critiqued. The results support previous findings that indicated that this force field is reasonably accurate for lecithins. For all molecules, a minimum was found near the experimentally determined crystal structure. Using D-glucitol as an example, it is shown that the structural effect of hydrogen bonding is better represented by a nonelectrostatic force-field model than by a purely electrostatic model. Results obtained with glycerylphosphocholine and four smaller organic phosphate molecules suggest that further study of nonbonded interactions of phosphate groups is needed. © John Wiley & Sons, Inc.

Notes: An algorithm is presented within the context of the calculation of the time-relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time-relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325-ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefix operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time. © John Wiley & Sons, Inc.

Notes: The recently developed parallel coupled-cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett., 194, 84 (1992)] is extended to allow four-indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed-memory parallel processors. Quantities such as the double-excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2-hydroxypyridine/2-pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed-memory supercomputers. The largest coupled-cluster calculations contained over 2 million double-excitation amplitudes. © John Wiley & Sons, Inc.

Notes: A method for the estimation of pKa from empirically calculated atomic charges has been developed and tested on a diverse set of organic oxyacids. The approach involves a comparison of the atomic charges calculated for both the acid and the negative ion that is formed after loss of the acidic proton. These charges have been used in conjunction with the familiar concepts of induction and resonance to develop an accurate formula to predict pKa. Results for a set of 135 compounds, including alcohols, phenols, and carboxylic acids, yielded a fit of pKa with r = 0.993 and an rms error of 0.455. © John Wiley & Sons, Inc.

Notes: A justification of Berlin's theorem that concerns the binding force concept in diatomic molecules is presented based on the Hellmann-Feynman theorem and its electrostatic interpretations. The concepts of binding and the binding region first derived by Berlin for diatomic molecules are extended to polyatomic molecules; the virial of forces necessary to hold the nuclei in a molecule fixed is proved to be an exact description of the total binding effect in the molecule. The partition of molecular space into binding and antibinding regions based on the binding function, which is defined in this paper, is proposed for polyatomic molecules. The binding diagrams for some planar molecules are developed as simple applications of our theoretical considerations. © 1993 John Wiley & Sons, Inc.

Notes: Earlier experimental data by Friedrich et al. found out, from time-of-flight experiments of collisions between H+ and HF molecules, that most of the available relative energy becomes transferred into internal rotations of the target and that vibrational excitation only begins to be noticeable around and above 30 eV of relative collision energy. The present theoretical and computational model starts from the potential energy function presented in the preceding paper and carries out quantum calculations that explicitly include the coupling of vibrational target states. The results indeed show very few vibrational excitations and rather large rotational energy transfers as the collision energy is increased up to 50 eV. Microscopic features of both the interaction and the dynamics are found to be responsible for such behavior, which brings the present calculations in agreement with experimental findings. © 1993 John Wiley & Sons, Inc.

Notes: The various structures and geometries of the cation FH2+ (fluoronium ion) have been investigated over a broad range of relative orientations between the proton and the HF molecule using ab initio, correlated wave functions and focusing on the lowest-energy channel that can lead to the production of vibrationally excited HF in the collisions with near-thermal H+ atoms. Various quality controls have been carried out on the accuracy of the target molecule description and a reliable, overall structure of the vibrational-rotational potential energy surface is obtained, for the first time extensively enough, to carry out scattering calculations in the direct excitation channels for the rotovibrational modes. © 1993 John Wiley & Sons, Inc.

Notes: A general formula to decompose the p-power of irreducible representations of an arbitrary space group into sum of sets of irreducible representations of such a group, having identical permutational symmetry, is presented. Its proof is based upon a straightforward application of the properties of the generalized projection (shift) operators. © 1993 John Wiley & Sons, Inc.

Notes: This contribution analyzes the changes in the intrinsic reaction coordinate (IRC) and in the potential energy profiles (PEP) caused by application of a uniform electric field evaluated using standard ab initio MO methods. Two typical organic processes have been studied, namely, the Friedel-Crafts and the Walden inversion reactions, which are modeled by suitable simple systems. The results for the Walden inversion reaction show that the IRC for the field-free and that for perturbed processes are almost coincident; in this case, using the field-free IRC to compute the perturbed energy profile is a very good approximation. On the contrary, for the Friedel-Crafts model reaction, the two IRCs differ slightly, so the energy profiles using the perturbed and the unperturbed IRCs are somewhat different. © 1993 John Wiley & Sons, Inc.

Notes: The formulation of a combinatorial theory of the structure of the class-algebra of the symmetric group is pursued. Recurrence relations for reduced class-coefficients involving imbedded cycles are presented. It is pointed out that for bridging cycles one can obtain elimination rules that involve symmetrization over sets of reduced class-coefficients with common cycle-structures but inequivalent index distributions. Consequently, some of these reduced class-coefficients remain individually inaccessible. © 1993 John Wiley & Sons, Inc.

Notes: General theory of the long-range intermolecular potentials, resulting from the use of the Rayleigh-Schrödinger perturbation theory at the multipole approximation level and the irreducible tensor formalism, is applied to describe the three-body induction effects in a system composed of two atoms and a linear molecule. Explicit expressions for the leading van der Waals coefficients are derived by employing the symbolic computation language MAPLE. Both the general geometry and the special case of the isosceles triangular configuration are considered. Final equations are presented using the interface between MAPLE and the typesetting language LATEX. Some technical aspects associated with the use of MAPLE in theory of long-range intermolecular potentials are briefly discussed. Explicit expressions obtained in this article should be useful in determination of the nonadditive induction effects in van der Waals clusters composed of two atoms and a diatomic molecule. In particular, they may be helpful in explaining the discrepancies between experiment and theory that are observed in high-resolution microwave studies of the complex Ar⃛Ar⃛HCl. © 1993 John Wiley & Sons, Inc.

Notes: The concept of the electronic-phase transition of the Hartree-Fock solution has been applied to an arbitrarily doped polyacetylene (PA) chain to examine the structural change of the polymer skeletons under such doping regimes. It has been found that the n-doped PA chain tends to suppress the generation of the charge-density wave (CDW) phase, whereas the p-doped PA favors the CDW phase leading to the charged-soliton shape. © 1993 John Wiley & Sons, Inc.

Notes: The interaction of Al+ (1S) ions with H2 on the lowest electronic energy surface is studied using ab initio electronic structure methods. A Cs symmetry transition state is located and found to have the geometry of a product AlH+ ion loosely bound to a H atom, consistent with the Hammond postulate for this endothermic reaction. Locating this transition state, beginning at geometries that characterize vibrationally cold H2 and translationally hot Al+, posed special challenges to the commonly used “hill-climbing” algorithm because of regions of geometrical instability along the path thus generated. This instability was found to be a result of second-order Jahn-Teller coupling with a low-lying 1B2 electronic state. In addition to these primary findings, a weakly bound T-shaped Al+  -  -  -  H2 C2v van der Waals complex is found that lies only 242 cm-1 below the Al+ and H2 asymptote, with H—H internuclear separation only slightly distorted from the equilibrium bond distance of H2 and Al—H distance (3.5 Å) much longer than the covalent bond length in AlH+ (1.6 Å). The locally stable but thermodynamically unstable linear HAlH+ (1∑g+) species and, of course, the H + AlH+(2∑+) reaction products have also been identified as critical points on the ground-state surface. Where known, the geometries and energies that we calculte agree well with experimental data. © 1993 John Wiley & Sons, Inc.

Notes: We here report the AM1 and PM3 evaluation of proton affinities for phosphorus compounds. The substituent effects, the preferred site of protonation, and the geometry changes produced upon protonation are discussed in terms of the present semiempirical calculations that are compared with experimental data and previous ab initio results. © 1993 John Wiley & Sons, Inc.

Notes: Molecular calculations are presented using “space-restricted basis functions,” i.e., basis functions that are nonzero only in selected regions of space. The nature of the calculations their justification, and their possible utility to quantum chemistry are described. © 1993 John Wiley & Sons, Inc.

Notes: Structural features of benzocyclobutenes, benzocyclobutadienes, and some of their fluoroderivatives are studied at the HF/SCF niveau employing a 6-31G* basis set. A Mills-Nixon-type of distortion (lengthening of the annelated bonds with concomitant shortening of the adjacent bonds in the benzene moiety) is found in all molecules, with the exception of polyannelated benzocyclobutenes with perflouro-substituted methylene groups. The latter compounds exhibit a weak anti-Mills-Nixon effect. Peripheral double bonds in benzocyclobutadienes enhance the double-bond localization in the benzene ring, but the main effect originates from angular deformations of the σ-skeleton. Salient structural features are rationalized by rehybridization at the carbon junction atoms and variation of Coulson's π-bond orders. Finally, several scales for quantifying the Mills-Nixon effect are briefly discussed. © 1993 John Wiley & Sons, Inc.

Notes: The geometry and electronic structure of peroxynitrous acid (O=NOOH) and peroxynitrite ion (O=NOO-) were studied at the 6-31G** level. The cis-configuration of peroxynitrous acid was found to be more stable by 3.9 kJ/mol than the trans-form, whereas peroxynitrite is more stable by 4.6 kJ/mol in the trans-form. Calculations of the skew forms, which are as defined by an angle of 90° between the ONO/NOO planes, yield energies larger than those of the most stable forms of the acid or anion by 51.4 and 68.1 kJ/mol, respectively, thus providing an estimate of the gas-phase energy barrier. The electronic structure is discussed from the point of view of the reactivities and transformation processes of ONOOH and ONOO-. © 1993 John Wiley & Sons, Inc.

Notes: The carbon dioxide (CO2) to methylamine (CH3NH2) addition reaction is investigated using an ab initio MO method with the aim of obtaining an insight into the relation between transition-state structure and reactivity. The complete potential energy hypersurface was explored and the stationary points representing reactants, transition state, and product were localized. To establish the relevance of different basis sets, calculations were carried out at different levels of theory: STO-3G, 3-21G, 4-21G, 4-31G, 6-31G, 6-311G, 6-31G*, and MP2/6-31G*//HF/6-31G*. A reaction analysis done by correlation of bond-order indices using the More O'Ferrall-Jencks diagram reveals the reaction mechanism as an asynchronous process. The transition state can be described as a four-membered ring. The lone nitrogen electron pair of the amine appears as the driving force of the reaction, where a positive hydrogen rather than a radical is more likely to be transferred. © 1993 John Wiley & Sons, Inc.

Notes: A number of established nonlinear convergence acceleration methods are presented. It is discussed how these methods, and also some new algorithms, can be applied successfully to Fourier series. Some of the new accelerators are tailored for these-series. Others are also useful for other types of series and sequences, and not only for convergence acceleration, but also for extrapolation or summation problems. Applications to the numerical inversion of the Laplace transform and to a Fourier series arising in the Matsubara formalism are presented. © 1993 John Wiley & Sons, Inc.

Notes: We shall start with very small systems like H2 and H3, computed with very accurate methods (Hylleraas-CI) or atomic systems up to Zn with accurate methods (CI), then move to more complex ones, like C60, but now with somewhat less accurate methods, specifically Hartree-Fock with density functionals, the latter for the correlation energy but not for the exchange energy. For even more complex tasks like geometry optimization of C60, we have resorted to even simpler and parametrized methods, like local density functionals. Then, we could use quantum mechanics either to provide interaction potentials for classical molecular dynamics or to directly solve dynamical systems, in a quantum molecular dynamics approximation. Having demonstrated that we can use the computational output from small systems as input to larger ones, we discuss in detail a new model for liquid water, which is borne out entirely from ab initio methods and nicely links spectroscopic, thermodynamics, and other physicochemical data. Concerning time scales, we use classical molecular dynamics to determine friction coefficients, and with these we perform stochastic dynamic simulations. The use of simulation results from smaller systems to provide inputs for larger system simulations is the “global simulation” approach, which, today, with the easily available computers, is becoming more and more feasible. Projections on simulations in the 1996-1998 period are discussed, new computational areas are outlined, and a N4 complexity algorithm is compared to density functional approaches. © 1993 John Wiley & Sons, Inc.

Notes: A review is presented of our recent work which deals with some aspects of the inclusion of connected triple excitations in single reference coupled-cluster theory. We first consider basic aspects of the theory and computational cost, noting the need for accurate and economical approximations to the complete coupled-cluster single, double and triple excitation method (CCSDT). Several such approximations are now available, including the CCSD + T(CCSD) and CCSD(T) methods. We have now efficiently implemented analytical derivative methods for these and related methods for open-shell reference determinants, including restricted open-shell Hartree-Fock for CCSD(T). Some results with large basis sets are presented for the HCO radical which further demonstrate the reliability of these methods for the spectroscopic characterization of small open-shell species. The remainder of this article deals with several applications of the complete CCSDT method, a new implementation of which we have recently completed. Like our previous work, this is for general single reference determinants, although we have now incorporated Abelian symmetry. We present a comparison with full configuration interaction data for CH3; a study of the N2 potential curve using restricted and unrestricted Hartree-Fock references; a comparison of the dipole moments and polarizabilities of BeO; and a study of the harmonic force field of 2Σu+ C3+. These studies also provide assessments of the accuracy of the approximate schemes for including T3. Finally, we present some timing data for some CCSDT calculations with out new implementation. © 1993 John Wiley & Sons, Inc.

Notes: Solutions of Hartree-Fock equations expressed as Gaussian functions are studied in various spaces: position, momentum, and position-momentum spaces. The use of the wavelet transform allows one to visualize position and momentum characteristics of atomic orbitals on the same drawing. A complementary viewpoint is then obtained on top of usual position and momentum representations. Applications to Gaussian “atomic” orbitals modeled as one-dimensional functions are performed. © 1993 John Wiley & Sons, Inc.

Notes: Multiconfigurational second-order perturbation theory is tested for the calculation of molecular structure and binding energies. The scheme is based on the Complete Active Space (CAS) SCF method, which gives a proper description of the major features in the electronic structure, independent of its complexity, accounts for all near degeneracy effects, and includes full orbital relaxation. Remaining dynamic electron correlation effects are in a subsequent step added using second-order perturbation theory with the CASSCF wave function as the reference state (CASPT2). The approach is applied to the calculation of equilibrium geometry and atomization energies for 27 benchmark molecules containing first-row atoms (the “G1” test). Large atomic natural orbital (ANO)-type basis sets are applied (5s4p3d2f for Li—F and 3s2p1d for H). It is shown that the CASSCF/CASPT2 approach is able to predict the equilibrium geometry with an accuracy better than 0.01 Å for bond distances and 0°-2° for bond angles. Calculated atomization energies are underestimated with between 3 and 6 kcal/mol times the number of extra electron pairs formed. The error in the heat of reaction for a number of isogyric reaction (no difference in number of pairs) varies between -2.5 and +1.0 kcal/mol. The same type of accuracy is obtained in calculations for excited states. The molecules B2, C2, FO, FOO, and FOOF have also been studied. Results for the first three molecules are in accordance with those of the benchmark molecules. The FO bond distance in FOO is predicted to be 0.02 Å longer than experiment. The heat of formation for FOO is computed to be 2.9 kcal/mol with an uncertainty of ±3 kcal/mol. Preliminary results for FOOF (obtained with a smaller basis set) indicate that the approach yields a somewhat too long FO bond distance (1.64 Å compared to 1.58 Å experimentally). © 1993 John Wiley & Sons, Inc.

Notes: A method using the Svartholm iterative procedure to solve atomic Hartree-Fock equations in momentum space is defined and applied to the ground states of Be and B+. The calculated atomic orbital properties follow a monotonic and stable convergence, but with rates of convergence depending on each property. The evolution of the orbitals during the iterations is explained by the combined actions of the variational principle, the Svartholm iterative procedure, and the momentum space representation. © 1993 John Wiley & Sons, Inc.

Notes: In our previous work, the stopping properties of metallic and covalent films were investigated. Here we consider an ionically bound film. The energy loss of a proton in an LiF monolayer (LiF-1L) is calculated in orbital fashion, based on kinetic theory. The required momentum density and mean excitation energy are obtained from the local density approximation and local plasma approximation respectively. For comparison, the LiF molecule is treated by use of a large intermolecular distance in the film. We find the stopping cross section of the LiF molecule to be only slightly larger than that for the LiF-1L. The Bragg rule (additivity of stopping for the corresponding atoms) is not valid for the ionically bound molecule nor the corresponding extended system, but may be valid if additivity of stopping of atomic ions is assumed. © 1993 John Wiley & Sons, Inc.

Notes: We evaluate binding energies, ionization energies, and second-order energy differences as functions of valence electron number for small spherical clusters of stabilized jellium, using the Kohn-Sham equations with the local-spin-density (LSD) approximation. Cohesive energies are also reported. A comparison is made with semiclassical formulas (liquid drop model and Padé approximant, with surface and curvature coefficients derived from first principles). These formulas nicely average the shell-structure oscillations of the energy, which are found to be almost the same as for ordinary jellium. Spherical clusters with 1, 7, and 9 electrons have binding energies very close to those of the semiclassical predictions. © 1993 John Wiley & Sons, Inc.

Notes: The equilibrium geometries, excitation energies, force constants, and vibrational frequencies for four low-lying electronic states X 2A1, 2B1, 2B2, and 2A2 of the BF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated excitation energy for X2A1 → 2B1 is in agreement with available experimental data. The electronic transition dipole moments, oscillator strengths for the 2B1 → X2A1 and 2B2 → X2A1 transitions, radiative lifetimes for the 2B1 and 2B2 states, and the spin properties for the X2A1 state are calculated based on the MRSDCI wave functions, predicting results in reasonable agreement with available experimental data. © 1993 John Wiley & Sons, Inc.

Notes: The bands of orbital energies for several polymeric species of alternant hydrocarbon are calculated. From these, the densities of states are graphed. By integration over the bands, the slope of the asymptotic line for the energy is calculated and compared with the energies of members of the same series calculated directly. For some series, the second, constant, term in the asymptotic line can also be calculated theoretically and compared with that derived from the molecular energies. The results for some related series indicate that for long molecules the number of Kekulé structures does not influence the major term in the energy. The extension of the argument to twodimensional arrays of hexagons is indicated and some results reported. © 1993 John Wiley & Sons, Inc.

Notes: The electrostatic potential (EP) and the polarization correction (PL) on the (EP) were calculated for four aromatic compounds: benzene, chlorobenzene, phenol, and benzoic amide, at the ab initio SCF level within two basis sets: 6-31G** and MINI-1. One calculation was performed using the polarized MINI-1** basis set. The quantity total interaction energy (TEH) defined as -EP + PL can be used as an indicator of the nucleophilic attack preferential position. By reference to 6-31G**, MINI-1 provides very satisfactory results. Moreover, the MINI-1** results are very similar to the MINI-1 ones. It appears that -EP does not provide a reliable tool to study the nucleophilic attack susceptibility, whereas TEH seems to be very well adapted for this kind of approach. © 1993 John Wiley & Sons, Inc.

Notes: Silicon analogs of aromatic monocyclic ions, (SiH)3+ (4), (SiH)42+ (5), and (SiH)5- (6) have been studied ab initio at MP2(full)/6-31G*. The D3h structure of Si3H3+ is the global minimum, whereas other two ions are nonplanar. The D2d structure of (SiH)42+ is less folded than the carbon analog and possesses a higher stabilization energy. Stabilization energies for the monocharged ions are diminished with respect to the corresponding carbons © 1993 John Wiley & Sons, Inc.

Notes: All-electron ab initio Hartree-Fock (RHF) calculations have been carried out to investigate the keto/enol equilibrium of phloroglucinol. The calculations predict that the enol form of phloroglucinol, 1,3,5-benzenetriol, is by far the most stable of the two. This is confirmed by NMR spectra taken on phloroglucinol. A comparison of the keto enol form transformation of phloroglucinol with that of the phenol system shows that the keto form of phloroglucinol, 1,3,5-cyclohexanetrion, is more abundant in the phloroglucinol system, and the keto form of phenol, 2,4-cyclohexadien-1-on, in the phenol system. © 1993 John Wiley & Sons, Inc.

Notes: In the present work, we present results of all-electron ab initio CASSCF calculations of nine electronic states of the molecule YN. Also reported are the spectroscopic constants derived on the basis of the calculated potential energies. The predicted electronic ground state is 1∑+, and this state is found to be separated from the excited states 3∑+, 3Π, and 1Π by 5177, 9290, and 9915 cm-1, respectively. The chemical bond in the YN molecule is polar with charge transfer from Y to N, giving rise to a dipole moment of 8.19 Debye at 3.3 au in the 1∑+ ground state is basically a double bond composed of two π bonds. The dissociation energy of the YN molecule has been derived as 4.59 eV. © 1993 John Wiley & Sons, Inc.

Notes: 3-21G RHF calculations on (CF3)2O and (CF3)2OH+ molecules are carried out to assess the changes induced in the molecular properties of ether links in poly (perfluoro ethers) interacting with acid sites at contact surfaces. Geometry of the species, vibrational frequencies, proton affinity, and energetics of the (CF3)2OH+ fragmentation provide a preliminary basis to understand problems raised by lubricant degradation. © 1993 John Wiley & Sons, Inc.

Notes: Glycine receptor substrates are molecules potentially involved in tautomerism phenomena. This study is expected to provide information that might help understand their intrinsic reactivities; such physicochemical data would allow us to establish predictive models in a search for better antagonists. Ab initio molecular orbital studies, using 3-21G and 6-31G* basis sets, are reported for the tautomeric equilibrium of 2-pyridone · H2O/2-hydroxypyridine · H2O. The geometry of the transition state has also been optimized. The results show the important effect of the water molecule through the formation of hydrogen bonds. This system will be used as a prototype for the design of antagonists of the glycine receptor, a potential site for the action of new antiepileptic drugs and compounds preventing ischemic brain damage. © 1993 John Wiley & Sons, Inc.

Notes: Gound-state electronic properties of porphine, phthalocyanine, and their derivatives, photosensitizers with potential use in the photodynamic therapy of tumors, were studied by semiempirical (MNDO) molecular orbital calculations. Geometry, bond orders, electron populations, and net atomic charges were analyzed. The obtained models were applied to study the intermolecular interactions of these molecules utilizing a classical mechanics approach. The dimerization characteristics of different derivatives were obtained by a separate evaluation of the contribution of electrostatic and steric factors. © 1993 John Wiley & Sons, Inc.

Notes: By means of ab initio calculations, the rotational constants and dipole moments of HnC3N (n = 1, 3, 5, 7, and 9) species have been calculated at the HF / 6-31G* level of theory. Selected cases have been also calculated at the MP2/6-31G* level and the influence of calculation level on rotational constant values is briefly discussed. Some of these species were discovered in the interstellar medium, while others have still not been detected there, although their existence is very probable. The results given here could help in their detection. © 1993 John Wiley & Sons, Inc.

Notes: Conformational analyses of large molecules as fatty acids and triglycerides are usually amenable by molecular mechanics. A correct evaluation of the electrostatic energy term is thus crucial in determining reliable results. In this contribution, we have considered the most abundant fatty acids in biomembranes, i.e., lauric, stearic, oleic, and elaidic acid, and the corresponding triglycerides, i.e., trilaurin, tristearin, triolein, and trielaidin, and estimated the Mulliken and potential-derived charges both at the semiempirical AM1 and ab initio HF MO STO-3G level. Atomic charges obtained by the Mulliken population analysis do not take into account the full geometry of the molecule. On the contrary, the change of conformation, due to different chains length or the presence of a trans or cis double bond, greatly influences the repartition of the potential-derived charges. A systematic comparative analysis shows that charges calculated by AM 1 are not suitable because as they do not reproduce potential-derived charges obtained by ab initio. © 1993 John Wiley & Sons, Inc.

Notes: A potential-derived atomic multipole method called the cumulative potential-derived atomic multipole method is developed, with which electrostatic atomic multipole moments are derived by fitting the molecular electric potential in a cumulative way. It is applied to the hydrides of N, O, F, S, Cl, and methanol and the hydrogen-bonded dimers formed between them. The relationship between atomic multipole moments and molecular charge distributions is found. The structures calculated with Buckingham's electrostatic model are in good agreement with experiments. The phenomena of nonlinear structures of most H-bonded complexes - the deviations of symmetry axes of electron donors from H bonds - and correct distinguishing between two alternative structures are attributed to atomic dipole and quadrupole moments. Compared with other methods, this method has a quantitative and qualitative advantage and simple algorithm. The main conclusion is that the atomic multipole moments play a substantial role, although a potential-derived charge model was deemed sufficient previously. © 1993 John Wiley & Sons, Inc.

Notes: The spatial symmetries of the harmonic oscillator and the recently found irreducible tensors constructed from the associated annihilation and creation operators are exploited to obtain new expressions for the elements of the matrix representatives of several examples of vibrational operators. Since all vibrational operators are expressible in terms of the irreducible tensors, their matrix elements reflect the angular momentum symmetry inherent in them, for the results derived here are in terms of the Clebsch-Gordan coefficients and the isoscalar factors that arise from the couplinig rule of the irreducible tensors. Familiarity with the mathematical properties of these quantities derived from the elementary theory of angular momentum facilitates the evaluation of many vibrational operators that may be of importance in the study of potentials in this basis. In particular, it is shown that the nonvanishing of matrix elements is governed by a law of conservation of angular momentum along the axis of quantization of the nondegenerate harmonic oscillator. © 1993 John Wiley & Sons, Inc.

Notes: A recently developed self-consistent crystal field (SCCF) method is applied to two suggested crystal structures of solid hydrogen fluoride, polar and nonpolar, respectively. Constrained geometry optimizations are performed and the results are compared with experiment and previous theoretical studies. Comparisons are also made with a previous SCCF study on hydrogen cyanide. The Pauli repulsion, dispersion, and “classical” crystal field contributions to the lattice energy are calculated. © 1993 John Wiley & Sons, Inc.

Notes: An SCF analysis has been carried for ensembles that simulate the CuO2 conduction layer in the tetragonal layer crystal T′ - Nd2CuO4 (Fig. 1). In this work, the CuO2 layer is described by a planar macromolecule, (CuO2)n, subject to the crystal field produced by the point charges in the ionic layers of D4h symmetry The computations were carried out using the KGNMOL, HONDO, and KGNGRAF codes in MOTECC -91. The computations were carried out with different oxygen and copper basis sets and energy convergence to less than 10-8 Hartrees. The purpose of the SCF computation was to estimate the cohesive energy of the ensembles, the electron density for the individual molecular orbitals, and the excess correlation energy, to ascertain the nature of the Cu—O bond in the conduction layer. The results indicate the following: (1) The cohesive energy of the ensembles (measured by the SCF energy plus the correlation energy, above the atomic values): ΔUc ≡ ΔESCF + ΔEC = -4.35 to -4.17 Hartrees per CuO bond as n increases from 4 to 9. Further insight was obtained by considering the electrostatic energy contributions to ΔUc; Eelectrostatic (ensemble) → EModeling (infinite lattice) were evaluated by replacing the oxygen and copper atoms by point charges determined by a Mullion population analysis. The larger oxygen basis set (13, 8/5,3) gave consistent results for the different ensembles of ΔEcovalent ≡ ΔUc - Eelectrostatic = -1.1 Hartrees per CuO bond. (ii) The electron density indicates that covalent bonds are formed and that the oxygen atoms play an important role in the structure stability. The covalent bonds formed indicate that nominal ionic valences do not apply. Mulliken population analyses gave valences of the order of one at the copper and oxygen atoms. The CuO bond orders are 0.47 between neighboring atoms and 0.048 for those separated by two atoms. (iv) The covalent nature of the CuO bonds in (CuO2)n was compared to that for the H2 molecule using as a measure the electron density and the excess correlation energy. The excess correlation energy per CuO bond above the atomic values is one order of magnitude lower that that for the H2 molecule and that for the C=C bond in alternant hydrocarbons. © 1993 John Wiley & Sons, Inc.

Notes: A brute-force numerical investigation has been carried out on the hopping of excitons in a three-dimensional molecular aggregate. Possibilities of vibronic decay, rapid chemical reactions of saturated species, radiative decay of overpopulated molecules, and cooperative chemical reactions involving saturated exciton populations on traps of two different types have been considered. Investigation have been performed with two types of initial distribution of excitons - facial and random - and for 10,000 or, sometimes, for 20,000 time steps each of duration 1ps. Several interesting observations have been made from this computer experiment: (1) The total number of occurrences of fast reactions depends upon the initial distribution of excitons. (2) It decreases if other exciton depleting processes are at work. (3) It also depends on the pattern of placement of traps. (4) The location of impurities also affects the rate of occurrence of these reactions. Thus, more reactions occur when the excitons are initially concentrated on one face and traps are suitably located on the path of flow of these excitons. A random initial distribution tends to equilibrate the excitons quickly over all the lattice points, thus giving rise to fewer reactions. (5) The number of reactions need not necessarily increase with the number of reaction centers; in fact, it decreases as more centers are added when the supply of excitons is severely limited. (6) A Complicated dynamics results when different types of additional processes, viz., enhanced fluorescence, radiative emissions, and cooperative chemical reactions are simultaneously allowed. The cooperative process has been clearly found to dominate. A first-order rate constant of about 108 s-1 has been calculated for the occurrence of the cooperative process. This rate is affected when other nonconserving processes are switched on. Observations (1), (4), and (5) are the most important conclusions of our work. They lie outside the scope of traditional models such as the random walk model, the diffusion model, and the lattice model for the migration of excitons in a molecular aggregate. © 1993 John Wiley & Sons, Inc.

Notes: The Complex Coordinate Scattering Theory is reformulated for the general case of a time-independent Hamiltonian. It is applied to scattering of He atoms from a Cu(115) crystal surface by constracting the Green operator for the T-matrix from the eigenvectors of both the complex scaled Hamiltonian and its transposed (“right” and “left” eigenvectors), which are different in this case. The weakly asymmetric corrugation function describing the (115) face of Cu is shown to cause a strong dependence of the calculated diffraction intensities upon the direction of the incident atomic beam. The calculated transition probabilities are in excellent agreement with the experimentally measured ones, previously obtained by Perreau and Lapujoulade. We show that additional information about the gas atom/surface physisorption interaction potential can be obtained if the incident angle of the atomic beam (the angles between the beam and the surface normal) is changed from γ to -γ. © 1993 John Wiley & Sons, Inc.

Notes: An implementation of the complex coordinate method is demonstrated that exploits a new technique for obtaining the matrix representation of the complex dilated Hamiltonian. The purpose is to make the complex coordinate method applicable together with standard numerical ab initio codes designed for large-scale calculations on many-electron atoms and/or molecules. No complex intergrals have to be calculated, and no changes of the standard codes are required even in the common case where the kinetic and potential energy components are not stored separately. Instead, two standard (real) CI calculations are used to generate the dilated (complex) CI matrix representation. The performance of the procedure is demonstrated in the context of the GAMESS program and applied to obtain the resonant structure of the Bethe surface pertinent to the absorption spectrum of the helium atom. © 1993 John Wiley & Sons, Inc.

Notes: Approximate conditions determining the complex energy resonances of a one-dimensional model potential, originally discussed by Moiseyev et al., are derived within a multiple-transition-point WKB treatment. It is shown that an erroneous energy spectrum is generated if too few transition points are considered. The numerical results of a correct semiclassical treatment of the problem, where several transition points are included, agree well with the, presumably exact, results of Rittby, Elander, and Brändas. © 1993 John Wiley & Sons, Inc.

Notes: It is proved that for a certain class of potentials dilation operators used in the method of complex scaling (CSM) represent a special case of Lyapunov converters. The time evolution of quantum systems is investigated from the viewpoint of this result, with special emphasis on the time evolution of resonant functions. © 1993 John Wiley & Sons, Inc.

Notes: Complex scaling of the Schrödinger equation on the halfaxis with a nontrivial boundary condition at the origin is investigated. A self-adjoint dilation of the corresponding dissipative operator is constructed. The relations between the scattering problems for the operator and it's dilation are clarified. © 1993 John Wiley & Sons, Inc.

Notes: The relations between the Schrödinger and wave evolutions are investigated. A generalization of the Lax-Phillips scattering theory for the case of the Schrödinger equation is constructed. An analog of the wave decay operator is obtained. The general ideas are illustrated by an explicitly solvable model of multichannel scattering on the halfaxis. A Lax-Phillips scattering theory is developed for the model operator obtained by a self-adjoint perturbation of the background operator. © 1993 John Wiley & Sons, Int.

Notes: Expansions of STO orbitals with GTOs for the first-row atoms have been obtained by the method of the distance between subspaces. The expansion coefficients and exponential parameters were simultaneously varied when the distance between subspaces, which are generated from STO and GTO functions, is minimized. The ζ; exponents (or scale factors) for the atomic orbitals that are optimized for these atoms are also shown to be almost independent of the number of Gaussian functions. Comparisons carried out with Stewart's least-squares method produce equivalent results when exponents for 2s and 2p functions are different. Some examples and applications for several atomic properties of the first-row atoms are included: energies and expectation values of ri and pi for the several expansions. These new minimal basis sets were tested for diatomic and polyatomic molecules containing these atoms. © 1993 John Wiley & Sons, Inc.

Notes: We describe a simple expansion of the Krylov type for the estimation of the electronic correlation energy of the ground state of closed-shell systems and show its relationship with Brillouin-Wigner perturbation theory. We demonstrate the Brillouin-Wigner perturbation theory can be quickly solved in a noniterative fashion. Examples are presented using the intermediate neglect of the differential overlap model Hamiltonian (INDO/1), which indicates that this scheme captures well over 95% of the configuration interaction over double excitations method (CID) in a fraction of the computational effort. © 1993 John Wiley & Sons, Inc.