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Fedorov DG. Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method. J Comput Chem 2024; 45:1540-1551. [PMID: 38490813 DOI: 10.1002/jcc.27345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
An auxiliary polarization formulation of the fragment molecular orbital (FMO) method is developed, combining a basis set correction computed for capped isolated fragments with a polarization obtained from uncapped fragments. For a set of organic and inorganic test systems, it is shown that the total energy and atomic charges are accurately reproduced with respect to full unfragmented calculations. It is demonstrated that the method is accurate for computing electronic excited states. The developed approach is applied to rank the isomers of chignolin from experimental NMR data (PDB: 1UAO) according to their relative energy. Contributions of polarization and basis set effects to pair interactions between fragments are elucidated.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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2
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Fedorov DG. Partition analysis of dipole moments in solution applied to functional groups in polypeptide motifs. Phys Chem Chem Phys 2024. [PMID: 38919134 DOI: 10.1039/d4cp01654h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
A partition analysis based on segments is developed for density functional theory defining solute dipole moments of functional groups, and the corresponding induced solvent dipoles representing solvent screening. The accuracy of dipoles from the fragment molecular orbital method is evaluated in comparison to unfragmented values. The analysis is applied to evaluate dipole moments of side chains, amino and carbonyl groups in common polypeptide motifs, α-helixes, β-turns, and random coils in solution. The membrane domain of the ATP synthase (1B9U) is analyzed, revealing the effect of the bend splitting of the α-helix into two pieces.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
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3
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Fedorov DG. The Peptide Bond: Resonance Increases Bond Order and Complicates Fragmentation. Chemphyschem 2024:e202400170. [PMID: 38749916 DOI: 10.1002/cphc.202400170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/15/2024] [Indexed: 06/28/2024]
Abstract
The enhancement of the peptide bond order by a resonance in the lone pair of N and the π-bond of CO is analyzed. A decomposition of the bond order in terms of localized molecular orbitals is developed and applied to the peptide bond. A combination of two rotations of hybrid orbitals is proposed to improve the boundary treatment in the fragment molecular orbital method. The developed approach is applied to peptide bonds, and it is found crucial to retain the π orbital in the variational space of both fragments across the boundary. The interaction energies between conventional amino acid residues in Trp-cage (1L2Y) are discussed.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
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Matsuoka S, Sakakura K, Akinaga Y, Akisawa K, Okuwaki K, Doi H, Mochizuki Y. Enhancement of energy decomposition analysis in fragment molecular orbital calculations. J Comput Chem 2024; 45:898-902. [PMID: 38158621 DOI: 10.1002/jcc.27297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Energy decomposition analysis is one of the most attractive features of fragment molecular orbital (FMO) calculations from the point of view of practical applications. Here we report some enhancements for PIEDA in the ABINIT-MP program. One is a separation of the dispersion-type stabilization from the electron correlation energy, traditionally referred to as the "dispersion interaction" (DI). Another is an alternative evaluation of the electrostatic (ES) interaction using the restrained electrostatic potential (RESP) charges. The GA:CT stacked base pair and the Trp-Cage miniprotein were used as illustrative examples.
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Affiliation(s)
- Sota Matsuoka
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | | | | | - Kazuki Akisawa
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | - Koji Okuwaki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
- JSOL Corp., Kudan-Kaikan Terrace, Tokyo, Japan
| | - Hideo Doi
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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Fedorov DG. Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization. J Phys Chem A 2024; 128:1154-1162. [PMID: 38302431 DOI: 10.1021/acs.jpca.3c06293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
An excitonic coupling model is developed based on an equation-of-motion coupled cluster combined with the fragment molecular orbital method. The effects of polarization and excitonic coupling on the splitting of quasi-degenerate levels in systems containing multiple chromophores are elucidated on dimers of formaldehyde, water, formic acid, hydrogen fluoride, and carbon monoxide. It is shown that the level structure is mainly determined by the mutual polarization of chromophores and to a lesser extent by the excitonic coupling. The role of symmetry in excitonic coupling in dimers is discussed. The excitonic coupling between all residues in the photoactive yellow protein (PDB: 2PHY) is analyzed.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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Paciotti R, Marrone A. A computational insight on the aromatic amino acids conjugation with [Cp*Rh(H 2O) 3] 2+ by using the meta-dynamics/FMO3 approach. J Mol Model 2023; 30:4. [PMID: 38082186 PMCID: PMC10713709 DOI: 10.1007/s00894-023-05794-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023]
Abstract
CONTEXT Rh(III) complexes demonstrated to exert promising pharmacological effects with potential applications as anti-cancer, anti-bacterial, and antimicrobial agents. One important Rh(III)-ligand is the pentamethylcyclopentadienyl (Cp*) group forming in water the [Cp*Rh(H2O)3]2+ complex. Among of its attractive chemical properties is the ability to react specifically with Tyr amino acid side chain of G-protein-coupled receptor (GPCR) peptides by means of highly chemoselective bioconjugation reaction, at room temperature and at pH 5-6. In this computational work, in order to deepen the mechanism of this chemoselective conjugation, we study the ligand exchange reaction between [Cp*Rh(H2O)3]2+ and three small molecules, namely p-cresol, 3-methylimidazole, and toluene, selected as mimetic of aromatic side chains of tyrosine (Tyr), tryptophan (Trp) and phenylalanine (Phe), respectively. Our outcomes suggest that the high selectivity for Tyr side chain might be related to OH group able to affect both thermodynamic and kinetic of ligand exchange reaction, due to its ability to act as both H bond acceptor and donor. These mechanistic aspects can be used to design new metal drugs containing the [Cp*Rh]2+ scaffold targeting specifically Tyr residues involved in biological/pathological processes such as phosphorylation by means of Tyr-kinase enzyme and protein-protein interactions. METHODS The geometry of three encounter complexes and product adducts were optimized at the B3LYP//CPCM/ωB97X-D level of theory, adopting the 6-311+G(d,p) basis set for all non-metal atoms and the LANL2DZ pseudopotential for the Rh atom. Meta-dynamics RMSD (MTD(RMSD)) calculations at GFN2-xTB level of theory were performed in NVT conditions at 298.15 K to investigate the bioconjugation reactions (simulation time: 100 ps; integration step 2.0; implicit solvent model: GBSA). The MTD(RMSD) simulation was performed in two replicates for each encounter complex. Final representative subsets of 100 structures for each run were gained with a sampling rate of 1 ps and analyzed by performing single point calculations using the FMO3 method at RI-MP2/6-311G//PCM[1] level of theory, adopting the MCP-TZP core potential for Rh atom.
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Affiliation(s)
- Roberto Paciotti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, I-66100, Chieti, Italy.
| | - Alessandro Marrone
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, I-66100, Chieti, Italy
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Paciotti R, Marrone A, Coletti C, Re N. Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals. J Comput Aided Mol Des 2023; 37:707-719. [PMID: 37743428 PMCID: PMC10618332 DOI: 10.1007/s10822-023-00532-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
Polarization and charge transfer strongly characterize the ligand-receptor interaction when metal atoms are present, as for the Au(I)-biscarbene/DNA G-quadruplex complexes. In a previous work (J Comput Aided Mol Des2022, 36, 851-866) we used the ab initio FMO2 method at the RI-MP2/6-31G* level of theory with the PCM [1] solvation approach to calculate the binding energy (ΔEFMO) of two Au(I)-biscarbene derivatives, [Au(9-methylcaffein-8-ylidene)2]+ and [Au(1,3-dimethylbenzimidazole-2-ylidene)2]+, able to interact with DNA G-quadruplex motif. We found that ΔEFMO and ligand-receptor pair interaction energies (EINT) show very large negative values making the direct comparison with experimental data difficult and related this issue to the overestimation of the embedded charge transfer energy between fragments containing metal atoms. In this work, to improve the accuracy of the FMO method for predicting the binding affinity of metal-based ligands interacting with DNA G-quadruplex (Gq), we assess the effect of the following computational features: (i) the electron correlation, considering the Hartree-Fock (HF) and a post-HF method, namely RI-MP2; (ii) the two (FMO2) and three-body (FMO3) approaches; (iii) the basis set size (polarization functions and double-ζ vs. triple-ζ) and (iv) the embedding electrostatic potential (ESP). Moreover, the partial screening method was systematically adopted to simulate the solvent screening effect for each calculation. We found that the use of the ESP computed using the screened point charges for all atoms (ESP-SPTC) has a critical impact on the accuracy of both ΔEFMO and EINT, eliminating the overestimation of charge transfer energy and leading to energy values with magnitude comparable with typical experimental binding energies. With this computational approach, EINT values describe the binding efficiency of metal-based binders to DNA Gq more accurately than ΔEFMO. Therefore, to study the binding process of metal containing systems with the FMO method, the adoption of partial screening solvent method combined with ESP-SPCT should be considered. This computational protocol is suggested for FMO calculations on biological systems containing metals, especially when the adoption of the default ESP treatment leads to questionable results.
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Affiliation(s)
- R Paciotti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy.
| | - A Marrone
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - C Coletti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - N Re
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
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Corinti D, Paciotti R, Coletti C, Re N, Chiavarino B, Frison G, Crestoni ME, Fornarini S. IRMPD spectroscopy and quantum-chemical simulations of the reaction products of cisplatin with the dipeptide CysGly. J Inorg Biochem 2023; 247:112342. [PMID: 37536163 DOI: 10.1016/j.jinorgbio.2023.112342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023]
Abstract
The inorganic antineoplastic drug cisplatin was made to react in solution with the dipeptide cysteinylglycine (CysGly), chosen as a functional model of glutathione, and the reaction products were analyzed using electrospray ionization mass spectrometry (ESI-MS). Selected complexes, i.e., the primary substitution product cis-[PtCl(NH3)2(CysGly)]+ and the chelate cis-[PtCl(NH3)(CysGly)]+, were submitted to IR multiple photon dissociation (IRMPD) spectroscopy obtaining their vibrational features. The experimental IR ion spectra were compared with the calculated IR absorptions of different plausible isomeric families, finding CysGly to bind preferentially platinum(II) via its deprotonated thiolic group in the monovalent complex, cis-[PtCl(NH3)2(CysGly)]+, and to evolve in the S,N-bound chelate structure cis-[PtCl(NH3)(CysGly)]+ through the SH and NH2 functionality of the cysteine residue. Moreover, our findings indicate that the platination reaction does not affect the CysGly peptide bond, which remains in its trans configuration. These results provide additional insights into the reactivity of Pt(II)-complexes with glutathione which is involved in cellular cisplatin resistance.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy.
| | - Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy.
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Gilles Frison
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, F-75005 Paris, France
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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Nakata H, Fedorov DG. Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2023; 19:1276-1285. [PMID: 36753486 DOI: 10.1021/acs.jctc.2c01177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).
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Affiliation(s)
- Hiroya Nakata
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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Fedorov DG. Parametrized quantum-mechanical approaches combined with the fragment molecular orbital method. J Chem Phys 2022; 157:231001. [PMID: 36550057 DOI: 10.1063/5.0131256] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Fast parameterized methods such as density-functional tight-binding (DFTB) facilitate realistic calculations of large molecular systems, which can be accelerated by the fragment molecular orbital (FMO) method. Fragmentation facilitates interaction analyses between functional parts of molecular systems. In addition to DFTB, other parameterized methods combined with FMO are also described. Applications of FMO methods to biochemical and inorganic systems are reviewed.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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Paciotti R, Coletti C, Marrone A, Re N. The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study. J Comput Aided Mol Des 2022; 36:851-866. [PMID: 36318393 DOI: 10.1007/s10822-022-00484-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/16/2022] [Indexed: 11/24/2022]
Abstract
In this work, the ab initio fragment molecular orbital (FMO) method was applied to calculate and analyze the binding energy of two biscarbene-Au(I) derivatives, [Au(9-methylcaffein-8-ylidene)2]+ and [Au(1,3-dimethylbenzimidazol-2-ylidene)2]+, to the DNA G-Quadruplex structure. The FMO2 binding energy considers the ligand-receptor complex as well as the isolated forms of energy-minimum state of ligand and receptor, providing a better description of ligand-receptor affinity compared with simple pair interaction energies (PIE). Our results highlight important features of the binding process of biscarbene-Au(I) derivatives to DNA G-Quadruplex, indicating that the total deformation-polarization energy and desolvation penalty of the ligands are the main terms destabilizing the binding. The pair interaction energy decomposition analysis (PIEDA) between ligand and nucleobases suggest that the main interaction terms are electrostatic and charge-transfer energies supporting the hypothesis that Au(I) ion can be involved in π-cation interactions further stabilizing the ligand-receptor complex. Moreover, the presence of polar groups on the carbene ring, as C = O, can improve the charge-transfer interaction with K+ ion. These findings can be employed to design new powerful biscarbene-Au(I) DNA-G quadruplex binders as promising anticancer drugs. The procedure described in this work can be applied to investigate any ligand-receptor system and is particularly useful when the binding process is strongly characterized by polarization, charge-transfer and dispersion interactions, properly evaluated by ab initio methods.
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Affiliation(s)
- Roberto Paciotti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy.
| | - Cecilia Coletti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - Alessandro Marrone
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - Nazzareno Re
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
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12
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Fedorov DG. Polarization energies in the fragment molecular orbital method. J Comput Chem 2022; 43:1094-1103. [PMID: 35446441 DOI: 10.1002/jcc.26869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/25/2022] [Accepted: 04/05/2022] [Indexed: 12/23/2022]
Abstract
Using isolated and polarized states of fragments, a method for computing the polarization energies in density functional theory (DFT) and density-functional tight-binding (DFTB) is developed in the framework of the fragment molecular orbital method. For DFTB, the method is extended into the use of periodic boundary conditions (PBC), for which a new component, a periodic self-polarization energy, is derived. The couplings of the polarization to other components in the pair interaction energy analysis (PIEDA) are derived for DFT and DFTB, and compared to Hartree-Fock and second-order Møller-Plesset perturbation theory (MP2). The effect of the self-consistent (DFT) and perturbative (MP2) treatment of the electron correlation on the polarization is discussed. The difference in the polarization in the bulk (PBC) and micro (cluster) solvation is elucidated.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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13
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Nakamura T, Yokaichiya T, Fedorov DG. Analysis of Guest Adsorption on Crystal Surfaces Based on the Fragment Molecular Orbital Method. J Phys Chem A 2022; 126:957-969. [PMID: 35080391 DOI: 10.1021/acs.jpca.1c10229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For gaining insights into interactions in periodic systems, an analysis is developed based on the fragment molecular orbital method combined with periodic boundary conditions. The adsorption energy is decomposed into guest and surface polarization and deformation energy, guest-surface and guest-guest interactions, and the vibrational free energy. The analysis is applied to the adsorption of guest molecules to Ih (001) ice surface. The cooperativity effects result in a non-linear change in the adsorption energy with coverage due to many-body effects. The role of dispersion is found to be dominant for guests with long hydrophobic tails. A rule is proposed relating the length of the alkyl tail with the formation of the guest layer. The computed binding enthalpies are in good agreement with experimental values. For high coverage, adsorbed molecules can form an ordered layer known as self-assembled monolayer.
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Affiliation(s)
- Taiji Nakamura
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Tomoko Yokaichiya
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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14
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Electron density from the fragment molecular orbital method combined with density-functional tight-binding. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Takaya D, Watanabe C, Nagase S, Kamisaka K, Okiyama Y, Moriwaki H, Yuki H, Sato T, Kurita N, Yagi Y, Takagi T, Kawashita N, Takaba K, Ozawa T, Takimoto-Kamimura M, Tanaka S, Fukuzawa K, Honma T. FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. J Chem Inf Model 2021; 61:777-794. [PMID: 33511845 DOI: 10.1021/acs.jcim.0c01062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.
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Affiliation(s)
- Daisuke Takaya
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shunpei Nagase
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kikuko Kamisaka
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshio Okiyama
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Sato
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Yoichiro Yagi
- Graduate School of Engineering, Okayama University of Science, Okayama, 1-1 Ridai-cho, Okayama 700-0005, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norihito Kawashita
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Kenichiro Takaba
- Pharmaceutical Research Center, Laboratory for Medicinal Chemistry, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Tomonaga Ozawa
- Kissei Pharmaceutical Co., LTD., Frontier Technology Research Lab., Research Div. 4365-1 Hotaka Kashiwabara, Azumino, Nagano 399-8304, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Biomedical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Kobe, Hyogo 657-8501, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan.,Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Sendai, Miyagi 980-8579, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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16
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Abstract
High-order charge transfer is incorporated into the fragment molecular orbital (FMO) method using a charge transfer state with fractional charges. This state is used for a partition analysis of properties based on segments that may be different from fragments in FMO. The partition analysis is also formulated for calculations without fragmentation. All development in this work is limited to density-functional tight-binding. The analysis is applied to a water cluster, crambin (PDB: 1CBN), and two complexes of Trp-cage (1L2Y) with ligands. The contributions of functional groups in ligands are obtained, providing useful information for drug discovery.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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