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Vos, R. J.; Hendriks, R.; Van Duijneveldt, F. B.
doi: 10.1002/jcc.540110102pmid: N/A
Counterpoise corrected ab initio calculations are reported for (H2O)2 and H2O‐H2CO. Geometry searches were done in the moment‐optimized basis DZP' at the SCF, MP2, and CEPA‐1 levels of theory, followed by more accurate single‐point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are −4.7 ±0.3 kcal/mol for a near‐linear (H2O)2 structure and −4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH2 structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C2h) and bifurcated (C2v) transition structures for (H2O)2 are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA‐1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.
doi: 10.1002/jcc.540110103pmid: N/A
We have performed “High Temperature Annealed Molecular Dynamics Simulations” (HTAMDS) on the bicyclic 222 cryptand, and on model M+/222 cryptates with different representations of M+. The analysis of four sets of 500 structures allows assessment of the ability of HTAMDS to: (1) interconvert experimentally known conformers starting from one of them, (2) locate the energy minima, (3) generate new conformers of low energy, and (4) account for the average structure observed on the NMR time scale. In view of the ionophoric behavior of 222, structures are also analyzed in terms of the “in/out” orientation of the binding sites. It is found that simulations on the free molecule, although widely sampling the conformational space, do not give structures adequate for cation inclusion. They generate however the lowest energy structure known experimentally and other new closely related ones. Inclusion of the substrate in the simulation (either as a purely electrostatic “driver,” or as a charged sphere) is required to generate conformations found in several complexes. These results suggest that in the field of drug design, conformation of drugs suitable for binding to a given receptor may not be found when the simulations are performed on the isolated drug or substrate.
Facelli, Julio C.; Grant, David M.; Bouman, Thomas D.; Hansen, Aage E.
doi: 10.1002/jcc.540110104pmid: N/A
The individual gauge for localized orbitals (IGLO) and localized orbital/local origin (LORG) methods for the calculation of chemical shieldings are compared from their theoretical and computational viewpoints. A detailed analysis of the fluorine α‐substituent effect in a series of fluoromethanes is given in terms of the IGLO and LORG bond contributions. The performance of both methods is discussed for molecular systems of fairly different sizes.
doi: 10.1002/jcc.540110105pmid: N/A
A data compression method is presented that is generally applicable to first‐order convergent iterative procedures that employ subspace expansions or extrapolations based on successive correction vectors. This method is based on the truncation of insignificant information in successive correction vectors. Although the correction vectors themselves may be severely truncated with the proposed approach, the final solution vector may be represented to arbitrary accuracy. A feature of the proposed method is that more slowly convergent iterative procedures allow the correction vectors to be more severely truncated without affecting the overall convergence rate. The method is implemented and applied to the iterative Davidson diagonalization method. If the compressed representation of the expansion vectors can be held in main computer memory, then a significant reduction in the I/O requirements is achieved.
Stanton, John F.; Bernholdt, David E.
doi: 10.1002/jcc.540110106pmid: N/A
A simple extension of the Newton–Raphson method is proposed that approximately accounts for anharmonicity in bond‐stretching coordinates. By modeling each bonded distance in a polyatomic molecule as a Morse oscillator with no anharmonic stretch‐stretch or stretch‐bend coupling, a multiplicative correction factor to the Newton–Raphson step is derived. Representative examples suggest that the rate of convergence of the proposed scheme is typically faster than that of the standard Newton–Raphson method.
doi: 10.1002/jcc.540110108pmid: N/A
By examining the displacement coordinate metric three modes of constrained optimization for large molecules and clusters are suggested. The first method corresponds to a conventional optimization using internal coordinates. The second mode has applications with respect to both internal and cartesian coordinates. The final mode is particularly interesting because it can result in computational savings. A mixture of both internal and cartesian coordinates is specified where these coordinates are usually a subset of the molecules or clusters total coordinate set. In the optimization only a subset of the energy derivatives need be evaluated reducing the computational effort associated with the gradient calculation.
Saito, Minoru; Nakamura, Haruki
doi: 10.1002/jcc.540110109pmid: N/A
The hydration energy difference between the alanine and glycine zwitter ions was calculated by both the free energy perturbation method and the acceptance ratio method. The calculations were carried out by using different increments of the mutation parameter λ, δλ = − 0.05, −0.10, and −0.20. The free energy difference calculated by the acceptance ratio method was found to be approximately the same as an average of the two free energy differences in the forward and the backward directions calculated by the perturbation method. The results by the perturbation method were significantly affected by large δλ as compared with that by the acceptance ratio method. The statistical error caused by decreasing the simulation time for sampling equilibrium configurations is discussed.
Kurtz, Henry A.; Stewart, James J. P.; Dieter, Kenneth M.
doi: 10.1002/jcc.540110110pmid: N/A
A finite‐field method for the calculation of polarizabilities and hyperpolarizabilities is developed based on both an energy expansion and a dipole moment expansion. This procedure is implemented in the MOPAC semiempirical program. Values and components of the dipole moment (μ), polarizability (α), first hyperpolarizability (β), and second hyperpolarizability (γ) are calculated as an extension of the usual MOPAC run. Applications to benzene and substituted benzenes are shown as test cases utilizing both MNDO and AM1 Hamiltonians.
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