Simulating Water with the Self-Consistent-Charge Density Functional Tight Binding Method:  From Molecular Clusters to the Liquid State

Abstract

The recently developed self-consistent-charge density functional tight binding (SCCDFTB) method provides an accurate and inexpensive quantum mechanical solution to many molecular systems of interests. To examine the performance of the SCCDFTB method on (liquid) water, the most fundamental yet indispensable molecule in biological systems, we have reported here the simulation results of water in sizes ranging from molecular clusters to the liquid state. The latter simulation was achieved through the use of the linear scaling divide-and-conquer approach. The results of liquid water simulation indicated that the SCCDFTB method can describe the structural and energetics of liquid water in qualitative agreement with experiments, while the results of water clusters suggested potential future improvements that may apply to the SCCDFTB method.

Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method

“…The oxygen diffusion coefficients calculated here are slightly smaller than a previous study (1.11 ± 0.04 Å 2 /ps); 48 this result is likely due to the larger simulation box size used in Ref. 47 according to the analysis by Dünweg and Kremer. 56 However, in all cases, the calculated oxygen diffusion coefficients are much larger than the experimental value (0.23 Å 2 /ps).…”

“…Such differences between the experimental results and simulation results have been observed previoulsy. 47,48 Since DFT results do reproduce the experimental O-O RDF curve, 50, 54 the difference observed here reflects the deficiencies in the current implementation of SCC-DFTB. For O-H RDF curves in Fig.…”

“…In many studies, 47,48 10 −7 hartree has been used; this is also the default value in CHARMM. 49 Although such a value does not cause a large energy drift in the current simulation to C 2 F 4 , the energy drift continuously increases as the simulation time increase (i.e., the energy drift over 100 ps dynamics is about 5 Kcal/mol).…”

Density-functional expansion methods: Generalization of the auxiliary basis

“…By using this type of auxiliary basis, SCC-DFTB avoids the need for computing threeand four-center electron repulsion integrals, and Mulliken partitioning allows for the rapid construction of the auxiliary density from the atomic orbital (AO) density matrix through spline evaluation of the precomputed overlap matrices; however, this crude representation of the response density can have adverse effects on electrostatic interactions. 21 In general, accurate electrostatics are important for intermolecular 22,23 Variations of the SCC-DFTB method have been applied to water clusters, 24 liquid water, 24 and organic molecules, 6 and limitations in hydrogen bonding were noted in many cases, although it is difficult to directly attribute these deficiencies solely to the electrostatic description.…”

Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg2+-sensitive dye

“…It is a rigorous approach because its accuracy can be systematically controlled by increasing the buffer size for each fragment and hence decreasing the error in fragment truncation. The DC method has been used for many chemical applications by the Yang laboratory [29][30][31][32][33] and elsewhere. [34][35][36][37][38][39][40][41][42][43][44][45] There are also several approximate fragment approaches.…”