共 77 条
An enhanced sampling QM/AMOEBA approach: The case of the excited state intramolecular proton transfer in solvated 3-hydroxyflavone
被引:14
作者:

Nottoli, Michele
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy

Bondanza, Mattia
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy

Lipparini, Filippo
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy

论文数: 引用数:
h-index:
机构:
机构:
[1] Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy
基金:
欧洲研究理事会;
关键词:
MOLECULAR-DYNAMICS;
QM/MM METHODS;
COMPLEX-SYSTEMS;
SOLVENT;
SPECTROSCOPY;
FLUORESCENCE;
SIMULATIONS;
QUANTUM;
ESIPT;
ENERGIES;
D O I:
10.1063/5.0046844
中图分类号:
O64 [物理化学(理论化学)、化学物理学];
学科分类号:
070304 ;
081704 ;
摘要:
We present an extension of the polarizable quantum mechanical (QM)/AMOEBA approach to enhanced sampling techniques. This is achieved by connecting the enhanced sampling PLUMED library to the machinery based on the interface of Gaussian and Tinker to perform QM/AMOEBA molecular dynamics. As an application, we study the excited state intramolecular proton transfer of 3-hydroxyflavone in two solvents: methanol and methylcyclohexane. By using a combination of molecular dynamics and umbrella sampling, we find an ultrafast component of the transfer, which is common to the two solvents, and a much slower component, which is active in the protic solvent only. The mechanisms of the two components are explained in terms of intramolecular vibrational redistribution and intermolecular hydrogen-bonding, respectively. Ground and excited state free energies along an effective reaction coordinate are finally obtained allowing for a detailed analysis of the solvent mediated mechanism.
引用
收藏
页数:10
相关论文
共 77 条
[1]
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
[J].
Abrams, Cameron
;
Bussi, Giovanni
.
ENTROPY,
2014, 16 (01)
:163-199

Abrams, Cameron
论文数: 0 引用数: 0
h-index: 0
机构:
Drexel Univ, Dept Chem & Biol Engn, Philadelphia, PA 19104 USA Drexel Univ, Dept Chem & Biol Engn, Philadelphia, PA 19104 USA

Bussi, Giovanni
论文数: 0 引用数: 0
h-index: 0
机构:
SISSA, I-34136 Trieste, Italy Drexel Univ, Dept Chem & Biol Engn, Philadelphia, PA 19104 USA
[2]
Ultrafast measurements of excited state intramolecular proton transfer (ESIPT) in room temperature solutions of 3-hydroxyflavone and derivatives
[J].
Ameer-Beg, S
;
Ormson, SM
;
Brown, RG
;
Matousek, P
;
Towrie, M
;
Nibbering, ETJ
;
Foggi, P
;
Neuwahl, FVR
.
JOURNAL OF PHYSICAL CHEMISTRY A,
2001, 105 (15)
:3709-3718

论文数: 引用数:
h-index:
机构:

Ormson, SM
论文数: 0 引用数: 0
h-index: 0
机构: Univ Cent Lancashire, Ctr Photochem, Preston PR1 2HE, Lancs, England

Brown, RG
论文数: 0 引用数: 0
h-index: 0
机构: Univ Cent Lancashire, Ctr Photochem, Preston PR1 2HE, Lancs, England

Matousek, P
论文数: 0 引用数: 0
h-index: 0
机构: Univ Cent Lancashire, Ctr Photochem, Preston PR1 2HE, Lancs, England

Towrie, M
论文数: 0 引用数: 0
h-index: 0
机构: Univ Cent Lancashire, Ctr Photochem, Preston PR1 2HE, Lancs, England

Nibbering, ETJ
论文数: 0 引用数: 0
h-index: 0
机构: Univ Cent Lancashire, Ctr Photochem, Preston PR1 2HE, Lancs, England

Foggi, P
论文数: 0 引用数: 0
h-index: 0
机构: Univ Cent Lancashire, Ctr Photochem, Preston PR1 2HE, Lancs, England

Neuwahl, FVR
论文数: 0 引用数: 0
h-index: 0
机构: Univ Cent Lancashire, Ctr Photochem, Preston PR1 2HE, Lancs, England
[3]
Excited state and ground state proton transfer rates of 3-hydroxyflavone and its derivatives studied by shpol'skii spectroscopy: The influence of redistribution of electron density
[J].
Bader, AN
;
Pivovarenko, VG
;
Demchenko, AP
;
Ariese, F
;
Gooijer, C
.
JOURNAL OF PHYSICAL CHEMISTRY B,
2004, 108 (29)
:10589-10595

Bader, AN
论文数: 0 引用数: 0
h-index: 0
机构: Free Univ Amsterdam, Dept Analyt Chem & Appl Spect, Ctr Laser, NL-1081 HV Amsterdam, Netherlands

Pivovarenko, VG
论文数: 0 引用数: 0
h-index: 0
机构: Free Univ Amsterdam, Dept Analyt Chem & Appl Spect, Ctr Laser, NL-1081 HV Amsterdam, Netherlands

Demchenko, AP
论文数: 0 引用数: 0
h-index: 0
机构: Free Univ Amsterdam, Dept Analyt Chem & Appl Spect, Ctr Laser, NL-1081 HV Amsterdam, Netherlands

Ariese, F
论文数: 0 引用数: 0
h-index: 0
机构: Free Univ Amsterdam, Dept Analyt Chem & Appl Spect, Ctr Laser, NL-1081 HV Amsterdam, Netherlands

Gooijer, C
论文数: 0 引用数: 0
h-index: 0
机构: Free Univ Amsterdam, Dept Analyt Chem & Appl Spect, Ctr Laser, NL-1081 HV Amsterdam, Netherlands
[4]
Molecular dynamics of excited state intramolecular proton transfer: 3-hydroxyflavone in solution
[J].
Bellucci, Michael A.
;
Coker, David F.
.
JOURNAL OF CHEMICAL PHYSICS,
2012, 136 (19)

Bellucci, Michael A.
论文数: 0 引用数: 0
h-index: 0
机构:
Boston Univ, Dept Chem, Boston, MA 02215 USA Boston Univ, Dept Chem, Boston, MA 02215 USA

Coker, David F.
论文数: 0 引用数: 0
h-index: 0
机构:
Boston Univ, Dept Chem, Boston, MA 02215 USA
Univ Coll Dublin, Sch Phys, Dublin 4, Ireland
Univ Coll Dublin, Complex Adapt Syst Lab, Dublin 4, Ireland Boston Univ, Dept Chem, Boston, MA 02215 USA
[5]
Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?
[J].
Bondanza, Mattia
;
Nottoli, Michele
;
Cupellini, Lorenzo
;
Lipparini, Filippo
;
Mennucci, Benedetta
.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
2020, 22 (26)
:14433-14448

Bondanza, Mattia
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy

Nottoli, Michele
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy

论文数: 引用数:
h-index:
机构:

Lipparini, Filippo
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, Via G Moruzzi 13, I-56124 Pisa, Italy

论文数: 引用数:
h-index:
机构:
[6]
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
[J].
Bonomi, Massimiliano
;
Branduardi, Davide
;
Bussi, Giovanni
;
Camilloni, Carlo
;
Provasi, Davide
;
Raiteri, Paolo
;
Donadio, Davide
;
Marinelli, Fabrizio
;
Pietrucci, Fabio
;
Broglia, Ricardo A.
;
Parrinello, Michele
.
COMPUTER PHYSICS COMMUNICATIONS,
2009, 180 (10)
:1961-1972

Bonomi, Massimiliano
论文数: 0 引用数: 0
h-index: 0
机构:
Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Branduardi, Davide
论文数: 0 引用数: 0
h-index: 0
机构:
Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Bussi, Giovanni
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Modena & Reggio Emilia, I-41100 Modena, Italy
INFM CNR S3, I-41100 Modena, Italy Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Camilloni, Carlo
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Milan, Dept Phys, I-20133 Milan, Italy
Ist Nazl Fis Nucl, Sez Milano, I-20133 Milan, Italy Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Provasi, Davide
论文数: 0 引用数: 0
h-index: 0
机构:
Mt Sinai Sch Med, Dept Struct & Chem Biol, New York, NY 10029 USA Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Raiteri, Paolo
论文数: 0 引用数: 0
h-index: 0
机构:
NRI, Perth, WA 6845, Australia
Dept Appl Chem, Perth, WA 6845, Australia Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Donadio, Davide
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Calif Davis, Dept Chem, Davis, CA 95616 USA Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Marinelli, Fabrizio
论文数: 0 引用数: 0
h-index: 0
机构:
SISSA, Int Sch Adv Studies, I-34014 Trieste, Italy Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Pietrucci, Fabio
论文数: 0 引用数: 0
h-index: 0
机构:
SISSA, Int Sch Adv Studies, I-34014 Trieste, Italy Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Broglia, Ricardo A.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Milan, Dept Phys, I-20133 Milan, Italy
Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

Parrinello, Michele
论文数: 0 引用数: 0
h-index: 0
机构:
Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland
[7]
QM/MM methods for free energies and photochemistry
[J].
Boulanger, Eliot
;
Harvey, Jeremy N.
.
CURRENT OPINION IN STRUCTURAL BIOLOGY,
2018, 49
:72-76

Boulanger, Eliot
论文数: 0 引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium

Harvey, Jeremy N.
论文数: 0 引用数: 0
h-index: 0
机构:
Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium
[8]
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
[J].
Brunk, Elizabeth
;
Rothlisberger, Ursula
.
CHEMICAL REVIEWS,
2015, 115 (12)
:6217-6263

Brunk, Elizabeth
论文数: 0 引用数: 0
h-index: 0
机构:
Ecole Polytech Fed Lausanne, Lab Computat Chem & Biochem, CH-1015 Lausanne, Switzerland
Lawrence Berkeley Natl Lab, Joint BioEnergy Inst, Emeryville, CA 94618 USA Ecole Polytech Fed Lausanne, Lab Computat Chem & Biochem, CH-1015 Lausanne, Switzerland

Rothlisberger, Ursula
论文数: 0 引用数: 0
h-index: 0
机构:
Ecole Polytech Fed Lausanne, Lab Computat Chem & Biochem, CH-1015 Lausanne, Switzerland
Natl Competence Ctr Res NCCR MARVEL Mat Revolut C, CH-1015 Lausanne, Switzerland Ecole Polytech Fed Lausanne, Lab Computat Chem & Biochem, CH-1015 Lausanne, Switzerland
[9]
Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding
[J].
Caprasecca, Stefano
;
Jurinovich, Sandro
;
Lagardere, Louis
;
Stamm, Benjamin
;
Lipparini, Filippo
.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION,
2015, 11 (02)
:694-704

Caprasecca, Stefano
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, I-56124 Pisa, Italy

Jurinovich, Sandro
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Pisa, Dipartimento Chim & Chim Ind, I-56124 Pisa, Italy Univ Pisa, Dipartimento Chim & Chim Ind, I-56124 Pisa, Italy

Lagardere, Louis
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Paris 06, Sorbonne Univ, Inst Calcul & Simulat, F-75005 Paris, France Univ Pisa, Dipartimento Chim & Chim Ind, I-56124 Pisa, Italy

Stamm, Benjamin
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Paris 06, Sorbonne Univ, Lab Jacques Louis Lions, UMR 7598, F-75005 Paris, France
CNRS, UMR 7598, F-75005 Paris, France
CNRS, UMR 7616, F-75005 Paris, France Univ Pisa, Dipartimento Chim & Chim Ind, I-56124 Pisa, Italy

Lipparini, Filippo
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Paris 06, Sorbonne Univ, Inst Calcul & Simulat, F-75005 Paris, France
Univ Paris 06, Sorbonne Univ, Lab Jacques Louis Lions, UMR 7598, F-75005 Paris, France
Univ Paris 06, Sorbonne Univ, Chim Theor Lab, UMR 7616, F-75005 Paris, France Univ Pisa, Dipartimento Chim & Chim Ind, I-56124 Pisa, Italy
[10]
On the intramolecular proton transfer of 3-hydroxyflavone in the first singlet excited state:: A theoretical study
[J].
Casadesus, Ricard
;
Vendrell, Oriol
;
Moreno, Miquel
;
Lluch, Jose M.
;
Morokuma, Keiji
.
CHEMICAL PHYSICS,
2006, 325 (02)
:243-250

Casadesus, Ricard
论文数: 0 引用数: 0
h-index: 0
机构: Univ Autonoma Barcelona, Dept Quim, E-08193 Barcelona, Spain

Vendrell, Oriol
论文数: 0 引用数: 0
h-index: 0
机构: Univ Autonoma Barcelona, Dept Quim, E-08193 Barcelona, Spain

Moreno, Miquel
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Autonoma Barcelona, Dept Quim, E-08193 Barcelona, Spain Univ Autonoma Barcelona, Dept Quim, E-08193 Barcelona, Spain

Lluch, Jose M.
论文数: 0 引用数: 0
h-index: 0
机构: Univ Autonoma Barcelona, Dept Quim, E-08193 Barcelona, Spain

Morokuma, Keiji
论文数: 0 引用数: 0
h-index: 0
机构: Univ Autonoma Barcelona, Dept Quim, E-08193 Barcelona, Spain