The Experts below are selected from a list of 273 Experts worldwide ranked by ideXlab platform
Dmitri G Fedorov - One of the best experts on this subject based on the ideXlab platform.
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The fragment Molecular Orbital Method combined with density-functional tight-binding and periodic boundary conditions.
The Journal of chemical physics, 2021Co-Authors: Yoshio Nishimoto, Dmitri G FedorovAbstract:The density-functional tight-binding (DFTB) formulation of the fragment Molecular Orbital Method is combined with periodic boundary conditions. Long-range electrostatics and dispersion are evaluated with the Ewald summation technique. The first analytic derivatives of the energy with respect to atomic coordinates and lattice parameters are formulated. The accuracy of the Method is established in comparison to numerical gradients and DFTB without fragmentation. The largest elementary cell in this work has 1631 atoms. The Method is applied to elucidate the polarization, charge transfer, and interactions in the solution.
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Three-Body Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method
The journal of physical chemistry. A, 2020Co-Authors: Dmitri G FedorovAbstract:An energy decomposition analysis is developed for the three-body expansion of the fragment Molecular Orbital Method at the level of density functional theory, density-functional tight-binding, coup...
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Analytic First and Second Derivatives for the Fragment Molecular Orbital Method Combined with Molecular Mechanics
2020Co-Authors: Hiroya Nakata, Dmitri G FedorovAbstract:Analytic first and second derivatives of the energy are developed for the fragment Molecular Orbital Method interfaced with Molecular mechanics in the electrostatic embedding scheme at the level of Hartree-Fock and density functional theory. The importance of the Orbital response terms is demonstrated. The role of the electrostatic embedding upon Molecular vibrations is analyzed, comparing force field and quantum-mechanical treatments for an ionic liquid and a solvated protein. The Method is applied for 100 protein conformations sampled in MD to take into account the complexity of a flexible protein structure in solution, and a good agreement to experimental data is obtained: frequencies from an experimental IR spectrum are reproduced within 17 cm$^{-1}$.
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Analyzing Interactions with the Fragment Molecular Orbital Method.
Methods in molecular biology (Clifton N.J.), 2020Co-Authors: Dmitri G FedorovAbstract:Basic concepts in the analysis of binding using the fragment Molecular Orbital Method are discussed at length: polarization, desolvation, and interaction. The components in the pair interaction energy decomposition analysis are introduced, and the analysis is illustrated for a water dimer and a protein-ligand complex.
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Molecular Electrostatic Potential and Electron Density of Large Systems in Solution Computed with the Fragment Molecular Orbital Method.
The journal of physical chemistry. A, 2019Co-Authors: Dmitri G Fedorov, Anton Brekhov, Vladimir Mironov, Yuri AlexeevAbstract:A solvent screening model for the Molecular electrostatic potential is developed for the fragment Molecular Orbital Method combined with the polarizable continuum model at the Hartree-Fock and density functional theory levels. The accuracy of the generated potentials is established in comparison to calculations without fragmentation. Solvent effects upon the Molecular electrostatic potential and electron density of solute are discussed. The Method is applied to two proteins: chignolin (PDB: 1UAO ) and ovine prostaglandin H(2) synthase-1 ( 1EQG ).
Kazuo Kitaura - One of the best experts on this subject based on the ideXlab platform.
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Many-body expansion of the Fock matrix in the fragment Molecular Orbital Method.
The Journal of chemical physics, 2017Co-Authors: Dmitri G Fedorov, Kazuo KitauraAbstract:A many-body expansion of the Fock matrix in the fragment Molecular Orbital Method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic Orbital basis and compared to the expansion in the basis of fragment Molecular Orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed Methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon. The physical nature of metallicity is discussed, and it is shown what kinds of metallic systems can be treated by fragment-based Methods. The density of states is calculated for a fully closed and a partially open nano-ring of boron nitride with a diameter of 105 nm.
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Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.
Journal of chemical theory and computation, 2016Co-Authors: Spencer R. Pruitt, Yuri Alexeev, Kazuo Kitaura, Dmitri G Fedorov, Hiroya Nakata, Takeshi Nagata, Graham D. Fletcher, Maricris L. Mayes, Mark S GordonAbstract:The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment Molecular Orbital (FMO) Method. The gradient has been derived and implemented for restricted second-order Moller–Plesset perturbation theory, as well as for both restricted and unrestricted Hartree–Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO Method during Molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment Molecular Orbital Method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262 144 CPU cores are also discussed.
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analytic second derivative of the energy for density functional theory based on the three body fragment Molecular Orbital Method
Journal of Chemical Physics, 2015Co-Authors: Hiroya Nakata, Kazuo Kitaura, Dmitri G Fedorov, Mark S Gordon, Federico Zahariev, Michael W Schmidt, Shinichiro NakamuraAbstract:Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment Molecular Orbital Method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT Method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.
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Simulations of Raman Spectra Using the Fragment Molecular Orbital Method.
Journal of chemical theory and computation, 2014Co-Authors: Hiroya Nakata, Kazuo Kitaura, Dmitri G Fedorov, Satoshi Yokojima, Shinichiro NakamuraAbstract:We developed an approach to calculate normal Raman activities based on the fragment Molecular Orbital Method. For this purpose, we derived the FMO gradient and coupled-perturbed Hartree-Fock equations in the presence of the static electric field. The accuracy is evaluated in comparison with full ab initio calculations for a set of closed-shell and radical systems. We applied the Method to calculate Raman and IR spectra of a polystyrene oligomer and crambin (PDB: 1CRN ) and performed an assignment of peaks based on localized normal modes. The computational timings demonstrate the efficiency of the Method.
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An Efficient Method to Evaluate InterMolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method
The journal of physical chemistry letters, 2012Co-Authors: Naoya Asada, Kazuo Kitaura, Dmitri G Fedorov, Isao Nakanishi, Kenneth M. MerzAbstract:We propose an approach based on the overlapping multicenter ONIOM to evaluate interMolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the interMolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment Molecular Orbital Method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed Method is shown to be efficient and accurate in the evaluation of the protein–ligand interaction energies.
Hiroya Nakata - One of the best experts on this subject based on the ideXlab platform.
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Analytic First and Second Derivatives for the Fragment Molecular Orbital Method Combined with Molecular Mechanics
2020Co-Authors: Hiroya Nakata, Dmitri G FedorovAbstract:Analytic first and second derivatives of the energy are developed for the fragment Molecular Orbital Method interfaced with Molecular mechanics in the electrostatic embedding scheme at the level of Hartree-Fock and density functional theory. The importance of the Orbital response terms is demonstrated. The role of the electrostatic embedding upon Molecular vibrations is analyzed, comparing force field and quantum-mechanical treatments for an ionic liquid and a solvated protein. The Method is applied for 100 protein conformations sampled in MD to take into account the complexity of a flexible protein structure in solution, and a good agreement to experimental data is obtained: frequencies from an experimental IR spectrum are reproduced within 17 cm$^{-1}$.
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Simulations of infrared and Raman spectra in solution using the fragment Molecular Orbital Method
Physical chemistry chemical physics : PCCP, 2019Co-Authors: Hiroya Nakata, Dmitri G FedorovAbstract:Analytic second derivatives of the energy with respect to nuclear coordinates are derived for the fragment Molecular Orbital Method combined with the polarizable continuum model. Harmonic frequencies, infrared intensities and normal Raman activities of large Molecular systems in solution can be evaluated. Periodic trends on SN2 chemical reactions are elucidated. The accuracy of the developed Method is established in comparison to full calculations without fragmentation. The Method is applied to ionic liquids and crambin (PDB: 1CRN). Solvent effects on the vibrational frequencies are discussed.
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Analytic second derivatives for the efficient electrostatic embedding in the fragment Molecular Orbital Method.
Journal of computational chemistry, 2018Co-Authors: Hiroya Nakata, Dmitri G FedorovAbstract:The analytic second derivatives of the energy with respect to nuclear coordinates are developed for restricted Hartree-Fock and density functional theory, based on the two-body fragment Molecular Orbital Method (FMO) and combined with the electrostatic embedding potential, self-consistently determined by point charges for far separated fragments and electron densities for near fragments. The accuracy of the Method is established with respect to FMO using the exact embedding potential based on electron densities and to full calculations without fragmentation. The computational efficiency of parallelization is measured on the K supercomputer and the Method is applied to simulate infrared spectra of two proteins, Trp-cage (PDB: 1L2Y) and crambin (1CRN). The nature of the vibrations in the Amide I peak of crambin and the Tyr symmetric stretch peak in Trp-cage are analyzed in terms of localized vibrations. © 2018 Wiley Periodicals, Inc.
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Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.
Journal of chemical theory and computation, 2016Co-Authors: Spencer R. Pruitt, Yuri Alexeev, Kazuo Kitaura, Dmitri G Fedorov, Hiroya Nakata, Takeshi Nagata, Graham D. Fletcher, Maricris L. Mayes, Mark S GordonAbstract:The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment Molecular Orbital (FMO) Method. The gradient has been derived and implemented for restricted second-order Moller–Plesset perturbation theory, as well as for both restricted and unrestricted Hartree–Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO Method during Molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment Molecular Orbital Method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262 144 CPU cores are also discussed.
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Radical damage in lipids investigated with the fragment Molecular Orbital Method
Chemical Physics Letters, 2016Co-Authors: Mandy C. Green, Dmitri G Fedorov, Hiroya Nakata, Lyudmila V. SlipchenkoAbstract:Abstract To quantify the thermodynamics for hydrogen abstraction lipids, the fragment Molecular Orbital Method (FMO) is used to calculate structures and energies of the reactants and products. The analytic second derivative is developed for the open-shell Hartree–Fock formulation of FMO and used to calculate zero point energy corrections. The accuracy of FMO is evaluated for a lipid model and the errors in reaction energies are found not to exceed 0.5 kcal/mol. The reaction energies determined for multiple sites in two lipids are used to discuss likely sites and pathways of radical initiation in membranes.
Mark S Gordon - One of the best experts on this subject based on the ideXlab platform.
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analytic gradients for the effective fragment Molecular Orbital Method
Journal of Chemical Theory and Computation, 2016Co-Authors: Colleen Bertoni, Mark S GordonAbstract:The analytic gradient for the Coulomb, polarization, exchange-repulsion, and dispersion terms of the fully integrated effective fragment Molecular Orbital (EFMO) Method is derived and the implementation is discussed. The derivation of the EFMO analytic gradient is more complicated than that for the effective fragment potential (EFP) gradient, because the geometry of each EFP fragment is flexible (not rigid) in the EFMO approach. The accuracy of the gradient is demonstrated by comparing the EFMO analytic gradient with the numeric gradient for several systems, and by assessing the energy conservation during an EFMO NVE ensemble Molecular dynamics simulation of water molecules. In addition to facilitating accurate EFMO geometry optimizations, this allows calculations with flexible EFP fragments to be performed.
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Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.
Journal of chemical theory and computation, 2016Co-Authors: Spencer R. Pruitt, Yuri Alexeev, Kazuo Kitaura, Dmitri G Fedorov, Hiroya Nakata, Takeshi Nagata, Graham D. Fletcher, Maricris L. Mayes, Mark S GordonAbstract:The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment Molecular Orbital (FMO) Method. The gradient has been derived and implemented for restricted second-order Moller–Plesset perturbation theory, as well as for both restricted and unrestricted Hartree–Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO Method during Molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment Molecular Orbital Method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262 144 CPU cores are also discussed.
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analytic second derivative of the energy for density functional theory based on the three body fragment Molecular Orbital Method
Journal of Chemical Physics, 2015Co-Authors: Hiroya Nakata, Kazuo Kitaura, Dmitri G Fedorov, Mark S Gordon, Federico Zahariev, Michael W Schmidt, Shinichiro NakamuraAbstract:Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment Molecular Orbital Method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT Method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.
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fully integrated effective fragment Molecular Orbital Method
Journal of Chemical Theory and Computation, 2013Co-Authors: Spencer R. Pruitt, Casper Steinmann, Jan H. Jensen, Mark S GordonAbstract:In this work, the effective fragment potential (EFP) Method is fully integrated (FI) into the fragment Molecular Orbital (FMO) Method to produce an effective fragment Molecular Orbital (EFMO) Method that is able to account for all of the fundamental types of both bonded and interMolecular interactions, including many-body effects, in an accurate and efficient manner. The accuracy of the Method is tested and compared to both the standard FMO Method as well as to fully ab initio Methods. It is shown that the FIEFMO Method provides significant reductions in error while at the same time reducing the computational cost associated with standard FMO calculations by up to 96%.
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Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method.
Journal of chemical theory and computation, 2011Co-Authors: Graham D. Fletcher, Spencer R. Pruitt, Dmitri G Fedorov, Theresa L. Windus, Mark S GordonAbstract:Benchmark timings are presented for the fragment Molecular Orbital Method on a Blue Gene/P computer. Algorithmic modifications that lead to enhanced performance on the Blue Gene/P architecture include strategies for the storage of fragment density matrices by process subgroups in the global address space. The computation of the atomic forces for a system with more than 3000 atoms and 44 000 basis functions, using second order perturbation theory and an augmented and polarized double-ζ basis set, takes ∼7 min on 131 072 cores.
Jan H. Jensen - One of the best experts on this subject based on the ideXlab platform.
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Hybrid RHF/MP2 geometry optimizations with the effective fragment Molecular Orbital Method.
PloS one, 2014Co-Authors: Anders S. Christensen, Dmitri G Fedorov, Casper Steinmann, Jan H. JensenAbstract:The frozen domain effective fragment Molecular Orbital Method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.
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hybrid rhf mp2 geometry optimizations with the effective fragment Molecular Orbital Method
PLOS ONE, 2014Co-Authors: Anders S. Christensen, Dmitri G Fedorov, Casper Steinmann, Jan H. JensenAbstract:The frozen domain effective fragment Molecular Orbital Method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.
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fully integrated effective fragment Molecular Orbital Method
Journal of Chemical Theory and Computation, 2013Co-Authors: Spencer R. Pruitt, Casper Steinmann, Jan H. Jensen, Mark S GordonAbstract:In this work, the effective fragment potential (EFP) Method is fully integrated (FI) into the fragment Molecular Orbital (FMO) Method to produce an effective fragment Molecular Orbital (EFMO) Method that is able to account for all of the fundamental types of both bonded and interMolecular interactions, including many-body effects, in an accurate and efficient manner. The accuracy of the Method is tested and compared to both the standard FMO Method as well as to fully ab initio Methods. It is shown that the FIEFMO Method provides significant reductions in error while at the same time reducing the computational cost associated with standard FMO calculations by up to 96%.
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The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds
PloS one, 2012Co-Authors: Casper Steinmann, Dmitri G Fedorov, Jan H. JensenAbstract:We extend the effective fragment Molecular Orbital Method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure Methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 A for RHF and MP2, respectively.
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Analytic gradient for the adaptive frozen Orbital bond detachment in the fragment Molecular Orbital Method
Chemical Physics Letters, 2009Co-Authors: Dmitri G Fedorov, Jan H. Jensen, Pavel V. Avramov, Kazuo KitauraAbstract:We have developed and implemented the analytic energy gradient for the bond detachment scheme in the fragment Molecular Orbital Method (FMO) suitable to describe solids, and applied it to the geometry optimization of a silicon nanowire at several levels of theory. In addition, we have examined in detail the effects of the particular choice of the fragmentation upon the accuracy and introduced a number of numerical criteria to characterize the errors. The established route is expected to provide guidance for future applications of FMO to surfaces, solids and nanosystems.