Journal of Computational Chemistry

Russo, Nino; Toscano, Marirosa; Grand, André; Jolibois, Franck

doi: 10.1002/(SICI)1096-987X(19980715)19:9<989::AID-JCC1>3.0.CO;2-Fpmid: N/A

Gradient‐corrected density functional computations with triple‐zeta‐type basis sets were performed to determine the preferred protonation site and the absolute gas‐phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero‐point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998

Lii, Jenn‐Huei; Allinger, Norman L.

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1001::AID-JCC2>3.0.CO;2-Upmid: N/A

Extensive calculations on hydrogen bonded systems were carried out using the improved MM3 directional hydrogen bond potential. The resulting total function was reoptimized. Comparisons of the hydrogen bonding potential function from ab initio calculations (MP2/6‐31G**); the original MM3(89); and the reoptimized MM3 force field MM3(96), for a variety of C, N, O, and Cl systems including the formamide dimer and formamide–water complex, are described herein. Hydrogen bonding is shown to be a far more complicated and ubiquitous phenomenon than is generally recognized. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1001–1016, 1998

Chasman, David; Beachy, Michael D.; Wang, Limin; Friesner, Richard A.

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1017::AID-JCC3>3.0.CO;2-Tpmid: N/A

We present an outline of the parallel implementation of our pseudospectral electronic structure program, Jaguar, including the algorithm and timings for the Hartree–Fock and analytic gradient portions of the program. We also present the parallel algorithm and timings for our Lanczos eigenvector refinement code and demonstrate that its performance is superior to the ScaLAPACK diagonalization routines. The overall efficiency of our code increases as the size of the calculation is increased, demonstrating actual as well as theoretical scalability. For our largest test system, alanine pentapeptide (818 basis functions in the cc‐pVTZ(‐f) basis set), our Fock matrix assembly procedure has an efficiency of nearly 90% on a 16‐processor SP2 partition. The SCF portion for this case (including eigenvector refinement) has an overall efficiency of 87% on a partition of 8 processors and 74% on a partition of 16 processors. Finally, our parallel gradient calculations have a parallel efficiency of 84% on 8 processors for porphine (430 basis functions). © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1017–1029, 1998

Beachy, Michael D.; Chasman, David; Friesner, Richard A.; Murphy, Robert B.

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1030::AID-JCC4>3.0.CO;2-Rpmid: N/A

We have developed a parallel version of our pseudospectral localized Møller–Plesset electronic structure code. We present timings for molecules up to 1010 basis functions and parallel speedup for molecules in the range of 260–658 basis functions. We demonstrate that the code is scalable; that is, a larger number of nodes can be efficiently utilized as the size of the molecule increases. By taking advantage of the available distributed memory and disk space of a scalable parallel computer, the parallel code can calculate LMP2 energies of molecules too large to be done on workstations. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1030–1038, 1998

Duncan, Wendell T.; Bell, Robert L.; Truong, Thanh N.

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1039::AID-JCC5>3.0.CO;2-Rpmid: N/A

We introduce TheRate (THEoretical RATEs), a complete application program with a graphical user interface (GUI) for calculating rate constants from first principles. It is based on canonical variational transition‐state theory (CVT) augmented by multidimensional semiclassical zero and small curvature tunneling approximations. Conventional transition‐state theory (TST) with one‐dimensional Wigner or Eckart tunneling corrections is also available. Potential energy information needed for the rate calculations are obtained from ab initio molecular orbital and/or density functional electronic structure theory. Vibrational‐state‐selected rate constants may be calculated using a diabetic model. TheRate also introduces several technical advancements, namely the focusing technique and energy interpolation procedure. The focusing technique minimizes the number of Hessian calculations required by distributing more Hessian grid points in regions that are critical to the CVT and tunneling calculations and fewer Hessian grid points elsewhere. The energy interpolation procedure allows the use of a computationally less demanding electronic structure theory such as DFT to calculate the Hessians and geometries, while the energetics can be improved by performing a small number of single‐point energy calculations along the MEP at a more accurate level of theory. The CH4+H↔CH3+H2 reaction is used as a model to demonstrate usage of the program, and the convergence of the rate constants with respect to the number of electronic structure calculations. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1039–1052, 1998

Sosa, C. P.; Ochterski, J.; Carpenter, J.; Frisch, M. J.

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1053::AID-JCC6>3.0.CO;2-Ppmid: N/A

Gaussian‐94 is the series of electronic structure programs. It is an integrated system to model a broad range of molecular systems under a variety of conditions, performing its calculations from the basic laws of quantum chemistry. This new version includes methods and algorithms for scalable massively parallel systems such as the Cray T3E supercomputer. In this study, we discuss the performance of Gaussian using large number of processors. In particular, we analyze the scalability of methods such as Hartree–Fock and density functional theory (DFT), including first and second derivatives. In addition, we explore scalability for CIS, MP2, and MCSCF calculations. Scalability and speedups were investigated for most of the examples with up to 64 process elements. A single‐point energy calculation (B3‐LYP/6‐311++G3df,3p) was tested with up to 512 process elements. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1053–1063, 1998

Freeman, Fillmore; Lee, Choonsun; Po, Henry N.; Hehre, Warren J.

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1064::AID-JCC7>3.0.CO;2-Opmid: N/A

Optimized geometries and energies for 3,4‐dihydro‐1,2‐dithiin (1), 3,6‐dihydro‐1,2‐dithiin (2), 4H‐1,3‐dithiin (3), and 2,3‐dihydro‐1,4‐dithiin (4) were calculated using ab initio 6‐31G* and MP2/6‐31G*//6‐31G* methods. At the MP2/6‐31G*//6‐31G* level, the half‐chair conformer of 4 is more stable than those of 1, 2, and 3 by 2.5, 3.5, and 3.6 kcal/mol, respectively. The half‐chair conformers of 1, 2, 3, and 4 are 2.9, 7.1, 2.0, and 5.6 kcal/mol, respectively, more stable than their boat conformers. The calculated half‐chair structures of 1–4 are compared with the calculated chair conformer of cyclohexane and the half‐chair structures for cyclohexene, 3,4‐dihydro‐1,2‐dioxin (5), 3,6‐dihydro‐1,2‐dioxin (6), 4H‐1,3‐dioxin (7), and 2,3‐dihydro‐1,4‐dioxin (8). © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1064–1071, 1998

Alcamí, M.; Mó, O.; Yáñez, M.

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1072::AID-JCC8>3.0.CO;2-Npmid: N/A

G2 ab initio calculations on all ABX three‐membered rings (TMRs) that can be derived from cyclopropane by systematic substitution of the (SINGLE BOND)CH2 groups by (SINGLE BOND)NH or (SINGLE BOND)O groups have been performed. Our results show that the decrease in the A(SINGLE BOND)B bond length as the electronegativity of X increases is significantly larger than that found for the corresponding acyclic analogs. In general, a systematic substitution of the (SINGLE BOND)CH2 groups of cyclopropane by (SINGLE BOND)NH or (SINGLE BOND)O groups implies significant geometric changes that are not reflected in a parallel change of the corresponding conventional ring strain energy (CRSE). When the electronegativity of the groups forming the TMR increases the effect on the CRSE of the system is small, although the charge delocalization inside the ring decreases. The near constancy of the CRSE along the series can be explained in terms of the charge redistribution of the system where the (SINGLE BOND)CH2 groups play a crucial role. There are, however, significant changes in the hydrogenation energies of the TMR investigated; our results show that, when in an ABX three‐membered ring, the electronegativity of X increases the hydrogenation energy of A(SINGLE BOND)B bond decreases and vice versa. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1072–1086, 1998

Quapp, Wolfgang; Hirsch, Michael; Imig, Olaf; Heidrich, Dietmar

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1087::AID-JCC9>3.0.CO;2-Mpmid: N/A

The old coordinate driving procedure to find transition structures in chemical systems is revisited. The well‐known gradient criterion, ∇E(x)=0, which defines the stationary points of the potential energy surface (PES), is reduced by one equation corresponding to one search direction. In this manner, abstract curves can be defined connecting stationary points of the PES. Starting at a given minimum, one follows a well‐selected coordinate to reach the saddle of interest. Usually, but not necessarily, this coordinate will be related to the reaction progress. The method, called reduced gradient following (RGF), locally has an explicit analytical definition. We present a predictor–corrector method for tracing such curves. RGF uses the gradient and the Hessian matrix or updates of the latter at every curve point. For the purpose of testing a whole surface, the six‐dimensional PES of formaldehyde, H2CO, was explored by RGF using the restricted Hartree–Fock (RHF) method and the STO‐3G basis set. Forty‐nine minima and saddle points of different indices were found. At least seven stationary points representing bonded structures were detected in addition to those located using another search algorithm on the same level of theory. Further examples are the localization of the saddle for the HCN⇌CNH isomerization (used for steplength tests) and for the ring closure of azidoazomethine to 1H‐tetrazole. The results show that following the reduced gradient may represent a serious alternative to other methods used to locate saddle points in quantum chemistry. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1087–1100, 1998

Pan, Wei; Lee, Tai‐Sung; Yang, Weitao

doi: 10.1002/(SICI)1096-987X(19980715)19:9<1101::AID-JCC10>3.0.CO;2-8pmid: N/A

We have implemented a parallel divide‐and‐conquer method for semiempirical quantum mechanical calculations. The standard message passing library, the message passing interface (MPI), was used. In this parallel version, the memory needed to store the Fock and density matrix elements is distributed among the processors. This memory distribution solves the problem of demanding requirement of memory for very large molecules. While the parallel calculation for construction of matrix elements is straightforward, the parallel calculation of Fock matrix diagonalization is achieved via the divide‐and‐conquer method. Geometry optimization is also implemented with parallel gradient calculations. The code has been tested on a Cray T3E parallel computer, and impressive speedup of calculations has been achieved. Our results indicate that the divide‐and‐conquer method is efficient for parallel implementation. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1101–1109, 1998