Extension of the fragment molecular orbital method to treat large open-shell systems in solution

Nakata, Hisao; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakamura, Shinichiro

doi:10.1016/j.cplett.2015.06.040

Cited by 13 publications

(8 citation statements)

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“…To describe systems with radical character in GAMESS-US, one can use restricted open-shell (RO) and unrestricted (U) methods, ROHF, 113,114 UHF, [115][116][117] UDFT, 118 ROMP2, 113 UMP2, 119 and ROCC. 113 Multiple open-shell fragments may be specified allowing for treating complex systems with multiple open-shell centers, which can be of interest to spintronics.…”

Section: Other Low-scaling Methods In Gamess-usmentioning

confidence: 99%

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Fedorov

2017

WIREs Comput Mol Sci

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The physical picture of the fragment molecular orbital (FMO) method is described on the basis of a many‐body expansion with terms describing the polarization of isolated fragments, charge transfer (CT), and exchange‐repulsion (EX) between them. Aspects of fragmentation are discussed in detail and FMO development in GAMESS‐US is summarized. Recent progress in method development and applications is reviewed, with a focus on studies of protein–ligand binding, excited states, and spectra of large molecular systems. WIREs Comput Mol Sci 2017, 7:e1322. doi: 10.1002/wcms.1322 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Ab Initio Electronic Structure Methods

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Section: Other Low-scaling Methods In Gamess-usmentioning

confidence: 99%

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Fedorov

2017

WIREs Comput Mol Sci

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128

122

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“…Recent work has been done with a divide-and-conquer inspired method, demonstrating successful fragmentation and recovery of open-shell species through the localization of fragment molecular orbitals . Additionally, the fragment molecular orbital fragmentation-based method has been extended to open-shell systems but has generally been restricted to monoradicals and the calculation of spin densities. , Here, we are interested not just in the behavior of a single radical site but in assessing the performance of an energy-based fragmentation scheme in computing coupling constants and the broken symmetry states of polyradicals.…”

Section: Introductionmentioning

confidence: 99%

Coupling Constants, High Spin, and Broken Symmetry States of Organic Radicals: an Assessment of the Molecules-in-Molecules Fragmentation-Based Method

Sadhukhan

Beckett

Thapa

et al. 2019

J. Chem. Theory Comput.

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We extend the application of our multilayer molecules-in-molecules (MIM) fragmentation-based method to the study of open-shell systems, particularly organic radicals. A test set of organic mono-, di- and polyradicals with a wide range in size, containing up to 360 atoms, was investigated. Total energies computed with MIM using density functional theory (DFT) were compared with full, unfragmented energies to assess the performance of MIM and to develop a systematic protocol for the treatment of large radical systems. More specifically, a two-layer (MIM2) model with a fragmentation scheme along the backbone involving covalently bonded dimers, trimers, or tetramers was considered, with DFT at a smaller basis set serving as the low level of theory. The MIM method was evaluated on the high-spin state and several possible broken-symmetry (BS) states for di- and polyradicals. When relevant spin–spin interactions were considered, the errors in total energies were less than 1 kcal mol–1. In addition, the applicability of MIM2 was extended to predict the intersite magnetic exchange coupling constants (J), which were compared with reference values. Further, since the energy levels derived from Hamiltonian diagonalization are physically more meaningful, the calculated J values estimated from the BS-DFT methodology were used to obtain the lower spin state energies of the polyradicals. The difference in calculated total energies of the lower spin state between full and MIM2 lie within 1 kcal mol–1 in the majority of these cases. Our rigorous, quantum chemical study demonstrates that MIM can be successfully applied to the study of large organic radicals reliably and accurately within the framework of BS-DFT.

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“…There are several variations of the original PCM model . Fedorov et al interfaced the conductor-like screening model (COSMO) with the FMO method, − and this approach has been applied to several biological and biochemical targets. ,− Furthermore, a practical definition of the fragment interaction energy in the PCM solvent has been suggested, and the electrostatic interactions are effectively reduced by solvent screening in their estimation.…”

Section: Introductionmentioning

confidence: 99%

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study

et al. 2018

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In this study, an ab initio fragment molecular orbital (FMO) methodology was developed to evaluate the solvent effects on electrostatic interactions, which make a significant contribution to the physical and chemical processes occurring in biological systems. Here, a fully polarizable solute consisting of the FMO electron density was electrostatically coupled with an implicit solvent based on the Poisson-Boltzmann (PB) equation; in addition, the nonpolar contributions empirically obtained from the molecular surface area (SA) were added. Interaction analysis considering solvent-screening and dispersion effects is now available as a powerful tool to determine the local stabilities inside solvated biomolecules. This methodology is applied to a deoxyribonucleic acid (DNA) duplex known as the Dickerson dodecamer. We found that excessively large electrostatic interactions inside the duplex are effectively damped by the screening, and the frontier molecular orbital energies are also successfully lowered. These observations indicate the stability of highly charged DNA duplexes in solution. Moreover, the solvation free energies in the implicit model show fairly good agreement with those in the explicit model while avoiding the costly statistical sampling of the electrolyte distribution. Consequently, our FMO-PBSA approach could yield new insights into biological phenomena and pharmacological problems via this ab initio methodology.

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Extension of the fragment molecular orbital method to treat large open-shell systems in solution

Cited by 13 publications

References 50 publications

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Coupling Constants, High Spin, and Broken Symmetry States of Organic Radicals: an Assessment of the Molecules-in-Molecules Fragmentation-Based Method

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study

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