Computing molecular electrostatic potentials with the PRISM algorithm

Abstract

The PRISM integral algorithm has been applied to the computation of the ab initio molecular electrostatic potential and its derivatives. Implementational details which are relevant to the additional efficiency ofthe algorithm in the electrostatic case are discuksed. On a range of machines, CPU timings of the PRISM electrostatic properties program, which is included in the GAUSSIAN 92 quantum chemistry package, rcvcal a dramatic performance incnasc (in some casts more than two orders of magnitude) over other commonly used electrostatic programs (GAUSSIAN 90, GAMES& MOPAC ESP, CHELPG). In addition, timings are reported for a particularly large electrostatic potential evaluation job on the six base-pair oligonucleotide CI'CGAG (%&sN~G6sPt8-).

A fast algorithm to compute atomic charges based on the topology of the electron density

“…The electron density of a free molecule occupies all space and hence integrals occurring in derived properties such as the electric ®eld have in®nite boundaries, which are much easier to tackle than ®nite boundaries. Moreover, recent advances in integral evaluation [16] justi®es the computational overhead generated by the electric ®eld compared to that of the electron density. In view of the ®nite boundaries of the integrals a completely analytical integration of an atomic property is prohibitive [7].…”

Charge Transfer Mechanism in Titanium-Doped Microporous Silica for Photocatalytic Water-Splitting Applications

“…As portrayed in Figure 1B, the unit cell may be replicated and then translated in the x, y, or z directions. The potential is not affected by this replication and subsequent movement along a translation vector, á t , and therefore, the potential experienced by the electrons [29,30] of the original unit cell is equivalent to any replica as given by Equation (1) u´á r¯" u´á r`k¨á a x`l¨á a y`m¨á a z¯" u´á r`á t¯ (1) with component vectors (2) where the first term corresponds to kinetic energy, T, and includes a symbol for the gradient…”

“…Molecular dynamics (MD) [30] was used to simulate the change of the positions of the atoms after the cluster is "heated" at a given temperature for a given amount of time. The kinetic energy of the model should remain constant, so the velocities of all the atoms were rescaled to mimic a constant temperature during the MD process according to Equation (9) [20,31] were computed along the nuclear trajectory t á R I ptqu by Equation (11).…”

Theoretical Study on Current-Voltage Characteristics of Oxygen Reduction Reaction near Platinum Surfaces

“…Separately optimized Pt n clusters (n = 6, 8, 10, and 12) were frozen and located on the xy-plane to additionally adsorb an O 2 molecule on it. The O-O bond lengths above Pt 6 , Pt 8 , Pt 10 , and Pt 12 clusters resulted in 1.39, 1.33, 1.28, and 1.23 Å, respectively. Comparing to the natural bond length of O-O in gas phase, 1.21 Å [13], the bond length is elongated in all configurations.…”

“…As a consequence, the voltage drop, ∆V, is evaluated by the averaged potential difference between the Pt cluster and O 2 molecule. It can be expressed as follows [10]:…”