Journal of Computational Chemistry

Jin, A. Y.; Leung, F. Y.; Weaver, D. F.

doi: 10.1002/(SICI)1096-987X(199910)20:13<1329::AID-JCC1>3.0.CO;2-Hpmid: N/A

Three genetic algorithm programs, GAP 1.0, 2.0, and 3.0, were used in conjunction with the ECEPP/2 force field to search the conformation space of (Met)‐enkephalin. Each program was proficient at quickly finding many diverse low‐energy conformers. Conformer populations displayed a variety of secondary structure motifs including those likely to bind to the μ‐opioid receptor. Limitations in the program's sampling behavior are discussed and method improvements are suggested. Although still in a developmental stage, the GAP programs represent a useful addition to conformational search techniques when no a priori structural information is available. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1329–1342, 1999

Gilardoni, F.; Weber, J.; Hauser, A.; Daul, C.

doi: 10.1002/(SICI)1096-987X(199910)20:13<1343::AID-JCC2>3.0.CO;2-Upmid: N/A

The ground‐ and excited‐state properties of both (Ru(bz)2)2+ and crystalline bis(η6‐benzene)ruthenium(II) p‐toluenesulfonate are investigated using the density functional theory. A symmetry‐based technique is employed to calculate the energies of the multiplet structure splitting of the singly excited triplet states. For the crystalline system, a Buckingham potential is introduced to describe the intermolecular interactions between the (Ru(bz)2)2+ system and its first shell of neighbor molecules. The overall agreement between experimental and calculated ground‐ and excited‐state properties is good, as far as the absolute transition energies, the Stokes shift, and the geometry of the excited states are concerned. The calculated d‐d excitation energies of the isolated cluster are typically 1000–2000 cm−1 too low. An energy lowering is obtained in a1g→e1g(3E1g) excited state when the geometry of (Ru(bz)2)2+ is bent along the e1u Renner–Teller active coordinate. It vanishes as the crystal packing is taken into account. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1343–1353, 1999

Klepeis, J. L.; Floudas, C. A.; Morikis, D.; Lambris, J. D.

doi: 10.1002/(SICI)1096-987X(199910)20:13<1354::AID-JCC3>3.0.CO;2-Npmid: N/A

The ability to analyze large molecular structures by NMR techniques requires efficient methods for structure calculation. Currently, there are several widely available methods for tackling these problems, which, in general, rely on the optimization of penalty‐type target functions to satisfy the conformational restraints. Typically, these methods combine simulated annealing protocols with molecular dynamics and local minimization, either in distance or torsional angle space. In this work, both a novel formulation and algorithmic procedure for the solution of the NMR structure prediction problem is outlined. First, the unconstrained, penalty‐type structure prediction problem is reformulated using nonlinear constraints, which can be individually enumerated for all, or subsets, of the distance restraints. In this way, the violation can be controlled as a constraint, in contrast to the usual penalty‐type restraints. In addition, the customary simplified objective function is replaced by a full atom force field in the torsional angle space. This guarantees a better description of atomic interactions, which dictate the native structure of the molecule along with the distance restraints. The second novel portion of this work involves the solution method. Rather than pursue the typical simulated annealing procedure, this work relies on a deterministic method, which theoretically guarantees that the global solution can be located. This branch and bound technique, based on the αBB algorithm, has already been successfully applied to the identification of global minimum energy structures of peptides modeled by full atom force fields. Finally, the approach is applied to the Compstatin structure prediction, and it is found to possess some important merits when compared to existing techniques. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1354–1370, 1999

Lewin, Anita H.; Sorensen, Jennifer B.; Dustman, John A.; Bowen, J. Phillip

doi: 10.1002/(SICI)1096-987X(199910)20:13<1371::AID-JCC4>3.0.CO;2-Rpmid: N/A

A comparative study has been performed to evaluate the ability of a range of computational theories to predict the relative basicity and the conformations of diamine systems. Specifically, molecular mechanics (MM3), semiempirical (AM1), and ab initio (Hartree–Fock) methods have been used in the conformational analyses of unprotonated, monoprotonated, and diprotonated 3‐aminotropanes, a pair of isomeric 1,3‐diamines. Use of the molecular mechanics force field, with the recently determined parameter set for protonated amines, affords results that are in agreement with experimental data, when corrected for water solvent (by setting the dielectric constant to 80). Ab initio and semiempirical calculations, in contrast, give inconsistent and incorrect results. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1371–1378, 1999

Tiraboschi, Gilles; Roques, Bernard‐Pierre; Gresh, Nohad

doi: 10.1002/(SICI)1096-987X(199910)20:13<1379::AID-JCC5>3.0.CO;2-0pmid: N/A

In order to gain an understanding of the energetics of polycoordinated Zn2+ binding to the formate anion (the end side chain of the Asp and Glu residues of proteins), we compare three competing binding modes in the presence of five and six water molecules: a, bidentate binding of Zn2+ to both formate oxygens; b, monodentate binding of Zn2+ to one formate oxygen; and c, through‐water binding of Zn2+ to formate, in which the cation remains bound to its first‐hydration shell waters and interacts with both formate oxygens through three water molecules. We also investigate a complex d, which is similar to c, in which formate is protonated into formic acid and one water molecule is deprotonated. The computations are carried out using the ab initio self‐consistent field/MP2 with three basis sets of increasing size density functional theory, semiempirical AM1 and PM3, and the sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics procedures. The summed energies of the isolated molecules making up the complexes disfavor tautomer d compared to a–c. On the other hand, the ab initio computations give the ordering of intermolecular interaction energies as d formic acid tautomer >b monodentate >a bidentate >c through‐water. Whereas the first‐order energy E1 favors both inner‐shell Zn2+ complexes with formate over the outer‐shell complex, the polarization and the charge‐transfer components of the second‐order energy E2 both favor the outer‐shell complex over the inner‐shell one, despite the increased separation between the cation and the highly polarizable formate ion. Energy balances including continuum solvation enthalpies produce an equilibration of complexes a–d. The preference favoring the monodentate complex over the bidentate one is consistent with other ab initio results for formate binding by a fully coordinated Zn2+ cation and with structural results from X‐ray crystallography. The SIBFA results are consistent with the ab initio results, and the computed interaction energy values match the ab initio ones to within 3%. The effects of nonadditivity are analyzed in the ab initio, SIBFA, and semiempirical computations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1379–1390, 1999

Ruiz, Eliseo; Cano, Joan; Alvarez, Santiago; Alemany, Pere

doi: 10.1002/(SICI)1096-987X(199910)20:13<1391::AID-JCC6>3.0.CO;2-Jpmid: N/A

The application of broken symmetry density functional calculations to homobinuclear and heterobinuclear transition metal complexes produces good estimates of the exchange coupling constants as compared to experimental data. The accuracy of different hybrid density functional theory methods was tested. A discussion is presented of the different methodological approaches that apply when a broken symmetry wave function is used with either Hartree–Fock or density functional calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1391–1400, 1999

Pitarch, Jesús; Pascual–Ahuir, Juan‐Luis; Silla, Estanislao; Tuñón, Iñaki; Ruiz–López, Manuel F.

doi: 10.1002/(SICI)1096-987X(199910)20:13<1401::AID-JCC7>3.0.CO;2-Mpmid: N/A

In this article, we have carried out a series of theoretical computations intended to analyze the interactions of β‐lactam compounds in aqueous solution. The final aim is to rationalize the influence of the medium on β‐lactam antibiotics reactivity. In particular, the hydrolysis reaction has been studied because of the considerable interest due to its relationship with resistance mechanisms developed by bacteria. The study is extended to the simplest β‐lactam molecule, propiolactam or 2‐azetidinone, and to the corresponding hydroxylated complex (resulting from the addition of a hydroxyl anion to the carbonyl group) that plays a crucial role in hydrolysis processes. Molecular Dynamics simulations have been carried out using a hybrid quantum mechanics–molecular mechanics potential: the solute is described using the density functional theory, whereas water solvent molecules are treated classically. This represents a sophisticated computational level which, compared to usual force‐field simulations, has the advantage of allowing a detailed analysis of solute's electronic properties. The discussion of results is focused on the role played by solute–solvent hydrogen bonds and solvent fluctuations on solute's structure. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1401–1411, 1999

Ferrer, Santiago Melchor; Molina, Jose Molina

doi: 10.1002/(SICI)1096-987X(199910)20:13<1412::AID-JCC8>3.0.CO;2-Fpmid: N/A

Density Functional Theory (DFT) calculations at the B3LYP/6‐31G* level have been performed on four bowl‐shaped polyaromatic hydrocarbons of C30H12 molecular formula (1–4) showing C3 (1), C2v (2 and 4), and C2h (3) symmetries. The geometrical and electronic properties of the compounds studied have been analyzed to explain their relative stability. NMR chemical shifts parameters for the atoms and Nucleus Independent Chemical Shifts (NICSs) for the rings were calculated using the GIAO method. The 13C and 1H chemical shifts calculated are in very good agreement with the experimental data. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1412–1421, 1999

Forés, Marta; Adamowicz, Ludwik

doi: 10.1002/(SICI)1096-987X(199910)20:13<1422::AID-JCC9>3.0.CO;2-Bpmid: N/A

In this work we analyze how the choice of the active space in the CASSCF (the complete‐active‐space multiconfiguration self‐consistent‐field method) and CASPT2 (the second‐order perturbation theory based on the CASSCF reference wave function) calculations affects the computed potential energy curves (PECs) for the intramolecular proton transfer reaction in the ground state and the two lowest lying singlet excited states of 1‐amino‐3‐propenal. As anticipated, the results revealed that, qualitatively, the proton transfer in the different states can be correctly described even by minimal active spaces, which include the orbitals involved in the electronic excitation of the considered state and the antibonding sigma orbital corresponding to the bond formed by the molecule with the migrating hydrogen atom. However, quantitatively, the relative energies of the two tautomers and the energy barriers computed at the CASSCF level change when the active space is increased, indicating importance of the dynamic electron correlation. Introducing the dynamic correlation effects via CASPT2 makes the calculated energy parameters more uniform among the different active spaces. The analysis suggested certain optimal active spaces for studying proton transfer reactions in systems similar to 1‐amino‐3‐propenal. The PEC calculations for excited states showed that the results are sensitive to the molecular geometries used in the calculations, particularly near the transition point. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1422–1431 (1999)

López, R.; Del Río, E.; Menéndez, M. I.; Sordo, T. L.

doi: 10.1002/(SICI)1096-987X(199910)20:13<1432::AID-JCC10>3.0.CO;2-Opmid: N/A

An MP4(full,SDTQ)/6‐311++G(d,p)//MP2(full)/6‐311++G(d,p) ab initio study was performed of the reactions of formyl and isoformyl cations with H2O and NH3, which play an important role in flame and interstellar chemistries. Two different confluent channels were located leading to CO+H3O+/NH 4+. The first one corresponds to the approach of the neutral molecule to the carbon atom of the cations. The second one leads to the direct proton transfer from the cations to the neutrals. At 900 K the separate products CO+H3O+/NH 4+ are the most stable species along the Gibbs energy profiles for the processes. For the reaction with H2O the reaction channel leading to HC(OH) 2+ (protonated formic acid) is disfavored with respect to the two CO+H3O+ channels in agreement with the experimental evidence that H3O+ is the major ion observed in hydrocarbon flames. According to our calculations, NH 4++H2O are considerably more stable in Gibbs energy than NH3+H3O+;NH 4+ will predominate in the reaction zone when ammonia is added to CH4+Ar diffusion flame, as experimentally observed. At 100 K the most stable structures are the intermediate complexes CO…HOH 2+/HNH 3+. Particularly the CO…HOH 2+ complex has a lifetime large enough to be detected and, therefore, could play a certain role in interstellar chemistry. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1432–1443, 1999