Molecular electrostatic potentials by systematic molecular fragmentation

Reid, David M.; Collins, Michael A.

doi:10.1063/1.4827020

Cited by 15 publications

(23 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1,2 Systematic Molecular Fragmentation by Annihilation (SMFA) is a general purpose program package which aims to approximate quantum chemistry calculations of molecular energies and properties for large organic, inorganic and biological molecules. The approximation employed, systematic molecular fragmentation by annihilation, [2][3][4][5][6][7][8][9][10] decomposes a molecule into relative small pieces (fragments), on which quantum chemistry calculations are carried out. The number of fragments is linearly proportional to the number of chemical functional groups in the molecule.…”

Section: This Article Is Categorized Undermentioning

confidence: 99%

See 1 more Smart Citation

The SMFA program for quantum chemistry calculations on large molecules

Kobayashi

Addicoat

Gilbert

et al. 2019

WIREs Comput Mol Sci

Self Cite

View full text Add to dashboard Cite

SMFA is a general program package for performing quantum chemistry calculations on large molecules, using an energy‐based fragmentation approach. The program can calculate electronic energies, energy gradients and second derivatives; perform geometry optimization; find first order saddle points (transition states); perform energy optimized scans along a user‐defined path; and evaluate various molecular properties. The program can use any of the following quantum chemistry packages: GAMESS(US), GAUSSIAN, NWChem and Q‐Chem. In addition, SMFA provides a number of utility programs that, inter alia, calculate vibrational frequencies and infrared spectra with isotopic substitutions, the electrostatic potential on the solvent‐accessible‐surface, and isodesmic and higher order near‐iso‐energetic reaction schemes. Calculations of the electronic energy and related properties can be carried out using a scheme that provides a computation time that is linearly dependent on the size of the molecule or, if the user has enough processing units available, in a walltime that is independent of the size of the molecule. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Structure and Mechanism > Computational Biochemistry and Biophysics

show abstract

Section: This Article Is Categorized Undermentioning

confidence: 99%

“…There are several papers in the literature which demonstrate the accuracy of SMFA for the calculation of the energy and other properties for moderately large molecules . Some details were included in the section on accuracy above.…”

Section: Examplesmentioning

confidence: 99%

The SMFA program for quantum chemistry calculations on large molecules

Kobayashi

Addicoat

Gilbert

et al. 2019

WIREs Comput Mol Sci

Self Cite

View full text Add to dashboard Cite

show abstract

“…As discussed in Appendix B for the current protocol, c mj is one or zero, although more complicated schemes have been considered. 46 Combining Eqs. (2.9) and (2.12), by the product rule, gives a contribution to the energy gradient with respect to the coordinates of atoms in groups represented by point charges, associated with the force on the point charges from the ab initio fragment charge distributions,…”

Section: Energy Gradientsmentioning

confidence: 99%

Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges

Collins

2014

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Some of these methods have already been successfully applied to evaluate the MEP of large molecular systems. 37,46,57 Also, a comprehensive discussion of fragmentation methods has recently been reviewed. 58 …”

Section: Introductionmentioning

confidence: 99%

MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex

Newcomer

Ragain

et al. 2014

J. Chem. Theory Comput.

View full text Add to dashboard Cite

A generalization of the Moving-Domain Quantum Mechanics/Molecular Mechanics (MoD-QM/MM) hybrid method [Gascon, J. A.; Leung, S. S. F.; Batista, E. R.; Batista, V. S. J. Chem. Theory Comput. 2006, 2, 175– 186] is introduced to provide a self-consistent computational protocol for structural refinement of extended systems. The method partitions the system into molecular domains that are iteratively optimized as quantum mechanical (QM) layers embedded in their surrounding molecular environment to obtain an ab initio quality description of the geometry and the molecular electrostatic potential of the extended system composed of those constituent fragments. The resulting methodology is benchmarked as applied to model systems that allow for full QM optimization as well as through refinement of the hydrogen bonding geometry in Oxytricha nova guanine quadruplex for which several studies have been reported, including the X-ray structure and NMR data. Calculations of 1H NMR chemical shifts based on the gauge independent atomic orbital (GIAO) method and direct comparisons with experiments show that solvated MoD-QM/MM structures, sampled from explicit solvent molecular dynamics simulations, allow for NMR simulations in much improved agreement with experimental data than models based on the X-ray structure or those optimized using classical molecular mechanics force fields.

show abstract

Molecular electrostatic potentials by systematic molecular fragmentation

Cited by 15 publications

References 53 publications

The SMFA program for quantum chemistry calculations on large molecules

The SMFA program for quantum chemistry calculations on large molecules

Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges

MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex

Contact Info

Product

Resources

About