1
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Zhang Z, Le GNT, Ge Y, Tang X, Chen X, Ejim L, Bordeleau E, Wright GD, Burns DC, Tran S, Axerio-Cilies P, Wang YT, Dong M, Woolley GA. Isomerization of bioactive acylhydrazones triggered by light or thiols. Nat Chem 2023; 15:1285-1295. [PMID: 37308709 DOI: 10.1038/s41557-023-01239-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/12/2023] [Indexed: 06/14/2023]
Abstract
The acylhydrazone unit is well represented in screening databases used to find ligands for biological targets, and numerous bioactive acylhydrazones have been reported. However, potential E/Z isomerization of the C=N bond in these compounds is rarely examined when bioactivity is assayed. Here we analysed two ortho-hydroxylated acylhydrazones discovered in a virtual drug screen for modulators of N-methyl-D-aspartate receptors and other bioactive hydroxylated acylhydrazones with structurally defined targets reported in the Protein Data Bank. We found that ionized forms of these compounds, which are populated under laboratory conditions, photoisomerize readily and the isomeric forms have markedly different bioactivity. Furthermore, we show that glutathione, a tripeptide involved with cellular redox balance, catalyses dynamic E⇄Z isomerization of acylhydrazones. The ratio of E to Z isomers in cells is determined by the relative stabilities of the isomers regardless of which isomer was applied. We conclude that E/Z isomerization may be a common feature of the bioactivity observed with acylhydrazones and should be routinely analysed.
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Affiliation(s)
- Zhiwei Zhang
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Giang N T Le
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yang Ge
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiaowen Tang
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Xin Chen
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Linda Ejim
- David Braley Centre for Antibiotics Discovery M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Emily Bordeleau
- David Braley Centre for Antibiotics Discovery M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D Wright
- David Braley Centre for Antibiotics Discovery M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Darcy C Burns
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Susannah Tran
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Peter Axerio-Cilies
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Yu Tian Wang
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Mingxin Dong
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China.
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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2
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Alam B, Jiang H, Zimmerman PM, Herbert JM. State-specific solvation for restricted active space spin-flip (RAS-SF) wave functions based on the polarizable continuum formalism. J Chem Phys 2022; 156:194110. [PMID: 35597663 DOI: 10.1063/5.0091636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The restricted active space spin-flip (RAS-SF) formalism is a particular form of single-reference configuration interaction that can describe some forms of strong correlation at a relatively low cost and which has recently been formulated for the description of charge-transfer excited states. Here, we introduce both equilibrium and nonequilibrium versions of a state-specific solvation correction for vertical transition energies computed using RAS-SF wave functions, based on the framework of a polarizable continuum model (PCM). Ground-state polarization is described using the solvent's static dielectric constant and in the nonequilibrium solvation approach that polarization is modified upon vertical excitation using the solvent's optical dielectric constant. Benchmark calculations are reported for well-studied models of photo-induced charge transfer, including naphthalene dimer, C2H4⋯C2F4, pentacene dimer, and perylene diimide (PDI) dimer, several of which are important in organic photovoltaic applications. For the PDI dimer, we demonstrate that the charge-transfer character of the excited states is enhanced in the presence of a low-dielectric medium (static dielectric constant ɛ0 = 3) as compared to a gas-phase calculation (ɛ0 = 1). This stabilizes mechanistic traps for singlet fission and helps to explain experimental singlet fission rates. We also examine the effects of nonequilibrium solvation on charge-separated states in an intramolecular singlet fission chromophore, where we demonstrate that the energetic ordering of the states changes as a function of solvent polarity. The RAS-SF + PCM methodology that is reported here provides a framework to study charge-separated states in solution and in photovoltaic materials.
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Affiliation(s)
- Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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3
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Ringe S, Hörmann NG, Oberhofer H, Reuter K. Implicit Solvation Methods for Catalysis at Electrified Interfaces. Chem Rev 2021; 122:10777-10820. [PMID: 34928131 PMCID: PMC9227731 DOI: 10.1021/acs.chemrev.1c00675] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Implicit solvation
is an effective, highly coarse-grained approach
in atomic-scale simulations to account for a surrounding liquid electrolyte
on the level of a continuous polarizable medium. Originating in molecular
chemistry with finite solutes, implicit solvation techniques are now
increasingly used in the context of first-principles modeling of electrochemistry
and electrocatalysis at extended (often metallic) electrodes. The
prevalent ansatz to model the latter electrodes and the reactive surface
chemistry at them through slabs in periodic boundary condition supercells
brings its specific challenges. Foremost this concerns the difficulty
of describing the entire double layer forming at the electrified solid–liquid
interface (SLI) within supercell sizes tractable by commonly employed
density functional theory (DFT). We review liquid solvation methodology
from this specific application angle, highlighting in particular its
use in the widespread ab initio thermodynamics approach
to surface catalysis. Notably, implicit solvation can be employed
to mimic a polarization of the electrode’s electronic density
under the applied potential and the concomitant capacitive charging
of the entire double layer beyond the limitations of the employed
DFT supercell. Most critical for continuing advances of this effective
methodology for the SLI context is the lack of pertinent (experimental
or high-level theoretical) reference data needed for parametrization.
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Affiliation(s)
- Stefan Ringe
- Department of Energy Science and Engineering, Daegu Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea.,Energy Science & Engineering Research Center, Daegu Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Nicolas G Hörmann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany.,Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstraße 4, D-85747 Garching, Germany.,Chair for Theoretical Physics VII and Bavarian Center for Battery Technology (BayBatt), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Karsten Reuter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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4
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Morales-Guevara R, Fuentes JA, Paez-Hernández D, Carreño A. The role of substituted pyridine Schiff bases as ancillary ligands in the optical properties of a new series of fac-rhenium(i) tricarbonyl complexes: a theoretical view. RSC Adv 2021; 11:37181-37193. [PMID: 35496390 PMCID: PMC9043815 DOI: 10.1039/d1ra05737e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/01/2021] [Accepted: 11/01/2021] [Indexed: 11/21/2022] Open
Abstract
Over the last few years, luminescent Re(i) tricarbonyl complexes have been increasingly proposed as fluorophores suitable for fluorescence microscopy to visualize biological structures and cells. In this sense, incorporating an asymmetrical pyridine Schiff base (PSB) as the ancillary ligand strongly modifies the staining and luminescent properties of Re(i) tricarbonyl complexes. In this work, we analyzed two series of Re(i) tricarbonyl complexes with their respective PSB ligands: (1) fac-[Re(CO)3(2,2'-bpy)(PSB)]1+ and (2) fac-[Re(CO)3(4,4'-bis(ethoxycarbonyl)-2,2'-bpy)(PSB)]1+, where the PSB exhibits substitutions at positions 4 or 6 in the phenolic ring with methyl or halogen substituents. Thus, we performed computational relativistic DFT and TDDFT studies to determine their optical properties. The ten complexes analyzed showed absorption in the visible light range. Furthermore, our analyses, including zero-field splitting (ZFS), allowed us to determine that the low-lying excited state locates below the 3LLCT states. Interestingly, seven of the ten analyzed complexes, whose corresponding PSB harbors an intramolecular hydrogen bond (IHB), exhibited luminescent emission that could be suitable for biological purposes: large Stokes shift, emission in the range 600-700 nm and τ in the order of 10-2 to 10-3 s. Conversely, the three complexes lacking the IHB due to two halogen substituents in the corresponding PSB showed a predicted emission with the lowest triplet excited state energy entering the NIR region. The main differences in the complexes' photophysical behavior have been explained by the energy gap law and time-resolved luminescence. These results emphasize the importance of choosing suitable substituents at the 4 and 6 positions in the phenolic ring of the PSB, which determine the presence of the IHB since they modulate the luminescence properties of the Re(i) core. Therefore, this study could predict Re(i) tricarbonyl complexes' properties, considering the desired emission features for biological and other applications.
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Affiliation(s)
- Rosaly Morales-Guevara
- Universidad Andres Bello, Programa de Doctorado en Físicoquímica Molecular, Facultad de Ciencias Exactas Santiago Chile
- Laboratory of Organometallic Synthesis, Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello República 330 Santiago Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andres Bello República 330 Santiago Chile
| | - Dayán Paez-Hernández
- Universidad Andres Bello, Programa de Doctorado en Físicoquímica Molecular, Facultad de Ciencias Exactas Santiago Chile
- Laboratory of Organometallic Synthesis, Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello República 330 Santiago Chile
| | - Alexander Carreño
- Universidad Andres Bello, Programa de Doctorado en Físicoquímica Molecular, Facultad de Ciencias Exactas Santiago Chile
- Laboratory of Organometallic Synthesis, Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello República 330 Santiago Chile
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5
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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6
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Vogler S, Dietschreit JCB, Peters LDM, Ochsenfeld C. Important components for accurate hyperfine coupling constants: electron correlation, dynamic contributions, and solvation effects. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1772515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Sigurd Vogler
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | | | - Laurens D. M. Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
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7
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Stein CJ, Herbert JM, Head-Gordon M. The Poisson–Boltzmann model for implicit solvation of electrolyte solutions: Quantum chemical implementation and assessment via Sechenov coefficients. J Chem Phys 2019; 151:224111. [DOI: 10.1063/1.5131020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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8
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Lange AW, Herbert JM, Albrecht BJ, You ZQ. Intrinsically smooth discretisation of Connolly's solvent-excluded molecular surface. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1644384] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Benjamin J. Albrecht
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Zhi-Qiang You
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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9
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Fedorov DG, Brekhov A, Mironov V, Alexeev Y. Molecular Electrostatic Potential and Electron Density of Large Systems in Solution Computed with the Fragment Molecular Orbital Method. J Phys Chem A 2019; 123:6281-6290. [DOI: 10.1021/acs.jpca.9b04936] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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
| | - Anton Brekhov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Yuri Alexeev
- Argonne Leadership Computing Facility and Computational Science Division, Argonne National Laboratory, Argonne, Illinois, 60439, United States
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10
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Pohl MN, Muchová E, Seidel R, Ali H, Sršeň Š, Wilkinson I, Winter B, Slavíček P. Do water's electrons care about electrolytes? Chem Sci 2019; 10:848-865. [PMID: 30774880 PMCID: PMC6346409 DOI: 10.1039/c8sc03381a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/01/2018] [Indexed: 01/01/2023] Open
Abstract
Ions have a profound effect on the geometrical structure of liquid water and an aqueous environment is known to change the electronic structure of ions. Here we combine photoelectron spectroscopy measurements from liquid microjets with molecular dynamical and quantum chemical calculations to address the reverse question, to what extent do ions affect the electronic structure of liquid water? We study aqueous solutions of sodium iodide (NaI) over a wide concentration range, from nearly pure water to 8 M solutions, recording spectra in the 5 to 60 eV binding energy range to include all water valence and the solute Na+ 2p, I- 4d, and I- 5p orbital ionization peaks. We observe that the electron binding energies of the solute ions change only slightly as a function of electrolyte concentration, less than 150 ± 60 meV over an ∼8 M range. Furthermore, the photoelectron spectrum of liquid water is surprisingly mildly affected as we transform the sample from a dilute aqueous salt solution to a viscous, crystalline-like phase. The most noticeable spectral changes are a negative binding energy shift of the water 1b2 ionizing transition (up to -370 ± 60 meV) and a narrowing of the flat-top shape water 3a1 ionization feature (up to 450 ± 90 meV). A novel computationally efficient technique is introduced to calculate liquid-state photoemission spectra using small clusters from molecular dynamics (MD) simulations embedded in dielectric continuum. This theoretical treatment captured the characteristic positions and structures of the aqueous photoemission peaks, reproducing the experimentally observed narrowing of the water 3a1 feature and weak sensitivity of the water binding energies to electrolyte concentration. The calculations allowed us to attribute the small binding energy shifts to ion-induced disruptions of intermolecular electronic interactions. Furthermore, they demonstrate the importance of considering concentration-dependent screening lengths for a correct description of the electronic structure of solvated systems. Accounting for electronic screening, the calculations highlight the minimal effect of electrolyte concentration on the 1b1 binding energy reference, in accord with the experiments. This leads us to a key finding that the isolated, lowest-binding-energy, 1b1, photoemission feature of liquid water is a robust energetic reference for aqueous liquid microjet photoemission studies.
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Affiliation(s)
- Marvin N Pohl
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , D-14195 Berlin , Germany .
- Fachbereich Physik , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
| | - Eva Muchová
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic .
| | - Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner-Platz 1 , D-14109 Berlin , Germany .
- Humboldt-Universität zu Berlin , Department of Chemistry , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany
| | - Hebatallah Ali
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , D-14195 Berlin , Germany .
- Fachbereich Physik , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
| | - Štěpán Sršeň
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic .
| | - Iain Wilkinson
- Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner-Platz 1 , D-14109 Berlin , Germany .
| | - Bernd Winter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , D-14195 Berlin , Germany .
| | - Petr Slavíček
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic .
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11
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Sun Q, Klaseboer E, Chan DYC. A robust and accurate formulation of molecular and colloidal electrostatics. J Chem Phys 2016; 145:054106. [DOI: 10.1063/1.4960033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qiang Sun
- Particulate Fluids Processing Center, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville VIC 3010, Australia
| | - Evert Klaseboer
- Institute of High Performance Computing, 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Derek Y. C. Chan
- Particulate Fluids Processing Center, School of Mathematics and Statistics, The University of Melbourne, Parkville VIC 3010, Australia and Department of Chemistry and Biochemistry, Swinburne University of Technology, Hawthorn VIC 3122, Australia
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12
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Yamagishi J, Okimoto N, Morimoto G, Taiji M. A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model. J Comput Chem 2014; 35:2132-9. [PMID: 25220475 PMCID: PMC4263261 DOI: 10.1002/jcc.23728] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/04/2014] [Accepted: 08/20/2014] [Indexed: 01/16/2023]
Abstract
The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N- and C-terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.
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Affiliation(s)
- Junya Yamagishi
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Noriaki Okimoto
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Gentaro Morimoto
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Makoto Taiji
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
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13
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Abstract
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects.
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14
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Lee S, Cho KH, Acree WE, No KT. Development of Surface-SFED Models for Polar Solvents. J Chem Inf Model 2012; 52:440-8. [DOI: 10.1021/ci2004913] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Sehan Lee
- Department of Biotechnology,
Yonsei University, Seoul, 120-749, Korea
| | - Kwang-Hwi Cho
- Department of Bioinformatics,
Soongsil University, Seoul, 156-743, Korea
| | - William E. Acree
- Department of Chemistry, University
of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76230-5017,
United
States
| | - Kyoung Tai No
- Department of Biotechnology,
Yonsei University, Seoul, 120-749, Korea
- Bioinformatics and
Molecular
Design Research Center, Seoul, 120-749, Korea
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