A New Algorithm for Molecular Fragmentation in Quantum Chemical Calculations

Bettens, Ryan P. A.; Lee, Adrian M.

doi:10.1021/jp062104n

Cited by 118 publications

(143 citation statements)

References 54 publications

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“…52 This strategy of subsystem formation has been adopted following the connectivity-based hierarchy (CBH) defined by Ramabhadran and Raghavachari, 55,56 and is related to prior work by Deev and Collins 31 and by Bettens and Lee. 57 As mentioned in our original MOB report, 52 successful execution of MOB essentially needs two parameters denoted as MOBα.β (where α denotes the order of MOB expansion and β denotes the monomer degree). In this work, we have consistently used the MOB2.3 model that uses two-body interactions using a monomer degree of 3 (each heavy atom bond has the same environment as in the parent system).…”

Section: Methodsmentioning

confidence: 99%

Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor

Saha

Raghavachari

2015

J. Chem. Theory Comput.

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We have investigated the performance of two classes of fragmentation methods developed in our group (Molecules-in-Molecules (MIM) and Many-Overlapping-Body (MOB) expansion), to reproduce the unfragmented MP2 energies on a test set composed of 10 small to large biomolecules. They have also been assessed to recover the relative energies of different motifs of the acetyl(ala)18NH2 system. Performance of different bond-cutting environments and the use of Hartree-Fock and different density functionals (as a low level of theory) in conjunction with the fragmentation strategies have been analyzed. Our investigation shows that while a low level of theory (for recovering long-range interactions) may not be necessary for small peptides, it provides a very effective strategy to accurately reproduce the total and relative energies of larger peptides such as the different motifs of the acetyl(ala)18NH2 system. Employing M06-2X as the low level of theory, the calculated mean total energy deviation (maximum deviation) in the total MP2 energies for the 10 molecules in the test set at MIM(d=3.5Å), MIM(η=9), and MOB(d=5Å) are 1.16 (2.31), 0.72 (1.87), and 0.43 (2.02) kcal/mol, respectively. The excellent performance suggests that such fragment-based methods should be of general use for the computation of accurate energies of large biomolecular systems.

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Section: Methodsmentioning

confidence: 99%

Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor

Saha

Raghavachari

2015

J. Chem. Theory Comput.

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“…In the recent years, a significant amount of effort has been devoted towards this goal. Various molecular fragmentation approaches, [16][17][18][19][20][21][22][23][24][25][26][27][28] and localized normal mode analyses [16][17][18][19][20][21][22][23][24][25][26][27][28] have been introduced for approximately obtaining the equilibrium geometries and vibrational spectra of large molecules. Subsequent Hessian calculations, through the estimation of analytic second order derivatives and vibrational frequency calculations, have been implemented only within very few of these methods.…”

Section: Introductionmentioning

confidence: 99%

Accurate vibrational spectra via molecular tailoring approach: A case study of water clusters at MP2 level

Sahu

Gadre

2015

The Journal of Chemical Physics

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In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm(-1) with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.

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“…33–35 Energy-based fragmentation methods include the molecular tailoring approach (MTA), 36,37 the kernel energy method, 38,39 the molecular fractionation with conjugate caps (MFCC) method, 40,41 the generalized energy-based fragmentation method, 42 and systematic fragmentation methods. 43–48 Other related approaches include the effective fragment potential method, 49–51 as well as the explicit polarization (X-Pol) potential, 52–56 which are essentially electronic structure based force fields. Some of these methods have already been successfully applied to evaluate the MEP of large molecular systems.…”

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.

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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.

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A New Algorithm for Molecular Fragmentation in Quantum Chemical Calculations

Cited by 118 publications

References 54 publications

Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor

Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor

Accurate vibrational spectra via molecular tailoring approach: A case study of water clusters at MP2 level

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

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