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Title: Influence of Electronic Polarization on the Spectral Density

Abstract

Accurate spectral densities are necessary for computing realistic exciton dynamics and nonlinear optical spectra of chromophores in condensed-phase environments, including multichromophore pigment–protein systems. However, due to the significant computational cost of computing spectral densities from first principles, requiring many thousands of excited-state calculations, most simulations of realistic systems rely on treating the environment as fixed-point charges. In this work, using a number of representative systems ranging from solvated chromophores to the photoactive yellow protein (PYP), we demonstrate that the quantum mechanical (QM) electronic polarization of the environment is key to obtaining accurate spectral densities and line shapes within the cumulant framework. We show that the QM environment can enhance or depress the coupling of fast chromophore degrees of freedom to the energy gap, altering the electronic–vibrational coupling and the resulting vibronic progressions in the absorption spectrum. In analyzing the physical origin of peaks in the spectral density, we identify vibrational modes that couple the electron and the hole as being particularly sensitive to the QM screening of the environment. For PYP, we reveal the need for careful determination of the appropriate QM region to obtain reliable spectral densities. Our findings suggest that the QM polarization of the environment can bemore » crucial not just for excitation energies but also for electronic–vibrational coupling in complex systems with implications for the correct modeling of linear and nonlinear optical spectroscopy in the condensed phase as well as energy transfer in pigment–protein complexes.« less

Authors:
 [1];  [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Univ. of California, Merced, CA (United States)
Publication Date:
Research Org.:
Univ. of California, Merced, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1594844
Grant/Contract Number:  
SC0019053
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 124; Journal Issue: 3; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Zuehlsdorff, Tim J., Hong, Hanbo, Shi, Liang, and Isborn, Christine M. Influence of Electronic Polarization on the Spectral Density. United States: N. p., 2019. Web. doi:10.1021/acs.jpcb.9b10250.
Zuehlsdorff, Tim J., Hong, Hanbo, Shi, Liang, & Isborn, Christine M. Influence of Electronic Polarization on the Spectral Density. United States. https://doi.org/10.1021/acs.jpcb.9b10250
Zuehlsdorff, Tim J., Hong, Hanbo, Shi, Liang, and Isborn, Christine M. Fri . "Influence of Electronic Polarization on the Spectral Density". United States. https://doi.org/10.1021/acs.jpcb.9b10250. https://www.osti.gov/servlets/purl/1594844.
@article{osti_1594844,
title = {Influence of Electronic Polarization on the Spectral Density},
author = {Zuehlsdorff, Tim J. and Hong, Hanbo and Shi, Liang and Isborn, Christine M.},
abstractNote = {Accurate spectral densities are necessary for computing realistic exciton dynamics and nonlinear optical spectra of chromophores in condensed-phase environments, including multichromophore pigment–protein systems. However, due to the significant computational cost of computing spectral densities from first principles, requiring many thousands of excited-state calculations, most simulations of realistic systems rely on treating the environment as fixed-point charges. In this work, using a number of representative systems ranging from solvated chromophores to the photoactive yellow protein (PYP), we demonstrate that the quantum mechanical (QM) electronic polarization of the environment is key to obtaining accurate spectral densities and line shapes within the cumulant framework. We show that the QM environment can enhance or depress the coupling of fast chromophore degrees of freedom to the energy gap, altering the electronic–vibrational coupling and the resulting vibronic progressions in the absorption spectrum. In analyzing the physical origin of peaks in the spectral density, we identify vibrational modes that couple the electron and the hole as being particularly sensitive to the QM screening of the environment. For PYP, we reveal the need for careful determination of the appropriate QM region to obtain reliable spectral densities. Our findings suggest that the QM polarization of the environment can be crucial not just for excitation energies but also for electronic–vibrational coupling in complex systems with implications for the correct modeling of linear and nonlinear optical spectroscopy in the condensed phase as well as energy transfer in pigment–protein complexes.},
doi = {10.1021/acs.jpcb.9b10250},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 3,
volume = 124,
place = {United States},
year = {2019},
month = {12}
}

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Works referenced in this record:

The quantitative relationship between structure and polarized spectroscopy in the FMO complex of Prosthecochloris aestuarii: refining experiments and simulations
journal, January 2002

  • Wendling, Markus; Przyjalgowski, Milosz A.; Gülen, Demet
  • Photosynthesis Research, Vol. 71, Issue 1/2, p. 99-123
  • DOI: 10.1023/A:1014947732165

How Proteins Trigger Excitation Energy Transfer in the FMO Complex of Green Sulfur Bacteria
journal, October 2006


Theory and Simulation of the Environmental Effects on FMO Electronic Transitions
journal, June 2011

  • Olbrich, Carsten; Strümpfer, Johan; Schulten, Klaus
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 14
  • DOI: 10.1021/jz2007676

Long-Lived Electronic Coherence in Dissipative Exciton Dynamics of Light-Harvesting Complexes
journal, September 2012

  • Kreisbeck, Christoph; Kramer, Tobias
  • The Journal of Physical Chemistry Letters, Vol. 3, Issue 19
  • DOI: 10.1021/jz3012029

Atomistic Study of the Long-Lived Quantum Coherences in the Fenna-Matthews-Olson Complex
journal, February 2012

  • Shim, Sangwoo; Rebentrost, Patrick; Valleau, Stéphanie
  • Biophysical Journal, Vol. 102, Issue 3
  • DOI: 10.1016/j.bpj.2011.12.021

Toward Ab Initio Optical Spectroscopy of the Fenna–Matthews–Olson Complex
journal, November 2013

  • Cole, Daniel J.; Chin, Alex W.; Hine, Nicholas D. M.
  • The Journal of Physical Chemistry Letters, Vol. 4, Issue 24
  • DOI: 10.1021/jz402000c

Molecular basis of the exciton–phonon interactions in the PE545 light-harvesting complex
journal, January 2014

  • Viani, Lucas; Corbella, Marina; Curutchet, Carles
  • Phys. Chem. Chem. Phys., Vol. 16, Issue 30
  • DOI: 10.1039/C4CP01477D

Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins
journal, July 2015

  • Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie
  • The Journal of Physical Chemistry B, Vol. 119, Issue 31
  • DOI: 10.1021/acs.jpcb.5b03654

Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes
journal, August 2016


Semiclassical Path Integral Dynamics: Photosynthetic Energy Transfer with Realistic Environment Interactions
journal, May 2016


First-Principles Models for Biological Light-Harvesting: Phycobiliprotein Complexes from Cryptophyte Algae
journal, June 2017

  • Lee, Mi Kyung; Bravaya, Ksenia B.; Coker, David F.
  • Journal of the American Chemical Society, Vol. 139, Issue 23
  • DOI: 10.1021/jacs.7b01780

Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport
journal, March 2018

  • Blau, Samuel M.; Bennett, Doran I. G.; Kreisbeck, Christoph
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 15
  • DOI: 10.1073/pnas.1800370115

Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations
journal, November 2018


Delocalized excitons in natural light-harvesting complexes
journal, August 2018


Coherence Spectroscopy in the Condensed Phase: Insights into Molecular Structure, Environment, and Interactions
journal, October 2017


Using coherence to enhance function in chemical and biophysical systems
journal, March 2017

  • Scholes, Gregory D.; Fleming, Graham R.; Chen, Lin X.
  • Nature, Vol. 543, Issue 7647
  • DOI: 10.1038/nature21425

Environment-assisted quantum transport
journal, March 2009


Highly efficient energy excitation transfer in light-harvesting complexes: The fundamental role of noise-assisted transport
journal, January 2009

  • Caruso, F.; Chin, A. W.; Datta, A.
  • The Journal of Chemical Physics, Vol. 131, Issue 10
  • DOI: 10.1063/1.3223548

Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein
journal, September 2012

  • Isborn, Christine M.; Götz, Andreas W.; Clark, Matthew A.
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 12
  • DOI: 10.1021/ct3006826

Spectrum simulation and decomposition with nuclear ensemble: formal derivation and application to benzene, furan and 2-phenylfuran
journal, June 2012


Accurate and Inexpensive Prediction of the Color Optical Properties of Anthocyanins in Solution
journal, April 2015

  • Ge, Xiaochuan; Timrov, Iurii; Binnie, Simon
  • The Journal of Physical Chemistry A, Vol. 119, Issue 16
  • DOI: 10.1021/acs.jpca.5b01272

Electronic Absorption Spectra and Solvatochromic Shifts by the Vertical Excitation Model: Solvated Clusters and Molecular Dynamics Sampling
journal, August 2014

  • Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
  • The Journal of Physical Chemistry B, Vol. 119, Issue 3
  • DOI: 10.1021/jp506293w

Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red
journal, March 2017

  • Zuehlsdorff, T. J.; Haynes, P. D.; Payne, M. C.
  • The Journal of Chemical Physics, Vol. 146, Issue 12
  • DOI: 10.1063/1.4979196

Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent
journal, April 2017

  • Milanese, Joel M.; Provorse, Makenzie R.; Alameda, Enrique
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 5
  • DOI: 10.1021/acs.jctc.7b00159

Vibrational structure of electronic transitions in conjugated molecules
journal, November 1972


A many‐body approach to the vibrational structure in molecular electronic spectra. I. Theory
journal, January 1976

  • Cederbaum, L. S.; Domcke, W.
  • The Journal of Chemical Physics, Vol. 64, Issue 2
  • DOI: 10.1063/1.432250

Recursion relations for multi-dimensional Franck-Condon overlap integrals
journal, September 1994


An efficient approach for the calculation of Franck–Condon integrals of large molecules
journal, June 2005

  • Dierksen, Marc; Grimme, Stefan
  • The Journal of Chemical Physics, Vol. 122, Issue 24
  • DOI: 10.1063/1.1924389

General Time Dependent Approach to Vibronic Spectroscopy Including Franck–Condon, Herzberg–Teller, and Duschinsky Effects
journal, August 2013

  • Baiardi, Alberto; Bloino, Julien; Barone, Vincenzo
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 9
  • DOI: 10.1021/ct400450k

Going beyond the vertical approximation with time-dependent density functional theory: Going beyond the vertical approximation with TD-DFT
journal, April 2016

  • Santoro, Fabrizio; Jacquemin, Denis
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 6, Issue 5
  • DOI: 10.1002/wcms.1260

Electronic excitation energies of molecules in solution: State specific and linear response methods for nonequilibrium continuum solvation models
journal, March 2005

  • Cammi, R.; Corni, S.; Mennucci, B.
  • The Journal of Chemical Physics, Vol. 122, Issue 10
  • DOI: 10.1063/1.1867373

Polarizable continuum model: Polarizable continuum model
journal, January 2012

  • Mennucci, Benedetta
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 3
  • DOI: 10.1002/wcms.1086

Perspective: Polarizable continuum models for quantum-mechanical descriptions
journal, April 2016

  • Lipparini, Filippo; Mennucci, Benedetta
  • The Journal of Chemical Physics, Vol. 144, Issue 16
  • DOI: 10.1063/1.4947236

Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution
journal, January 2018

  • Zuehlsdorff, T. J.; Isborn, C. M.
  • The Journal of Chemical Physics, Vol. 148, Issue 2
  • DOI: 10.1063/1.5006043

Modeling absorption spectra of molecules in solution
journal, September 2018

  • Zuehlsdorff, Tim J.; Isborn, Christine M.
  • International Journal of Quantum Chemistry, Vol. 119, Issue 1
  • DOI: 10.1002/qua.25719

Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches
journal, August 2019

  • Zuehlsdorff, Tim J.; Montoya-Castillo, Andrés; Napoli, Joseph A.
  • The Journal of Chemical Physics, Vol. 151, Issue 7
  • DOI: 10.1063/1.5114818

The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach
journal, January 2018

  • Loco, Daniele; Jurinovich, Sandro; Cupellini, Lorenzo
  • Photochemical & Photobiological Sciences, Vol. 17, Issue 5
  • DOI: 10.1039/C8PP00033F

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review
journal, September 2018

  • Loco, Daniele; Cupellini, Lorenzo
  • International Journal of Quantum Chemistry, Vol. 119, Issue 1
  • DOI: 10.1002/qua.25726

Solvent Effects on Ground and Excited Electronic State Structures of the Push-Pull Chromophore Julolidinyl- n - N , N ‘-diethylthiobarbituric Acid
journal, November 2001

  • Moran, Andrew M.; Delbecque, Claire; Kelley, Anne Myers
  • The Journal of Physical Chemistry A, Vol. 105, Issue 45
  • DOI: 10.1021/jp011662t

Solvent effects on ground and excited electronic state structures of p -nitroaniline
journal, July 2001

  • Moran, Andrew M.; Kelley, Anne Myers
  • The Journal of Chemical Physics, Vol. 115, Issue 2
  • DOI: 10.1063/1.1378319

Vibronic effects on solvent dependent linear and nonlinear optical properties of push-pull chromophores: Julolidinemalononitrile
journal, February 2002

  • Moran, Andrew M.; Egolf, Debra S.; Blanchard-Desce, Mireille
  • The Journal of Chemical Physics, Vol. 116, Issue 6
  • DOI: 10.1063/1.1433966

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units
journal, May 2011

  • Isborn, Christine M.; Luehr, Nathan; Ufimtsev, Ivan S.
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 6
  • DOI: 10.1021/ct200030k

Linear-scaling time-dependent density-functional theory in the linear response formalism
journal, August 2013

  • Zuehlsdorff, T. J.; Hine, N. D. M.; Spencer, J. S.
  • The Journal of Chemical Physics, Vol. 139, Issue 6
  • DOI: 10.1063/1.4817330

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals
journal, November 2015

  • Zuehlsdorff, T. J.; Hine, N. D. M.; Payne, M. C.
  • The Journal of Chemical Physics, Vol. 143, Issue 20
  • DOI: 10.1063/1.4936280

Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II
journal, July 2013

  • Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 8
  • DOI: 10.1021/ct400477j

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls
journal, April 2013

  • Valsson, Omar; Campomanes, Pablo; Tavernelli, Ivano
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 5
  • DOI: 10.1021/ct3010408

Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models
journal, November 2016

  • Provorse, Makenzie R.; Peev, Thomas; Xiong, Chou
  • The Journal of Physical Chemistry B, Vol. 120, Issue 47
  • DOI: 10.1021/acs.jpcb.6b09176

Solvent Effects on Electronic Excitations of an Organic Chromophore
journal, March 2016

  • Zuehlsdorff, T. J.; Haynes, P. D.; Hanke, F.
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 4
  • DOI: 10.1021/acs.jctc.5b01014

A Theory of Intensity Distribution in Band Systems
journal, December 1926


Nuclear Motions Associated with Electron Transitions in Diatomic Molecules
journal, December 1928


Fluorescence and absorption of large anharmonic molecules - spectroscopy without eigenstates
journal, March 1985


Quantum and classical relaxation rates from classical simulations
journal, June 1994

  • Bader, Joel S.; Berne, B. J.
  • The Journal of Chemical Physics, Vol. 100, Issue 11
  • DOI: 10.1063/1.466780

Evaluation of Quantum Correlation Functions from Classical Data
journal, August 2002

  • Kim, Hyojoon; Rossky, Peter J.
  • The Journal of Physical Chemistry B, Vol. 106, Issue 33
  • DOI: 10.1021/jp020669n

Quantum Dynamics and Vibrational Relaxation
journal, November 1999

  • Egorov, S. A.; Everitt, K. F.; Skinner, J. L.
  • The Journal of Physical Chemistry A, Vol. 103, Issue 47
  • DOI: 10.1021/jp9919314

Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics
journal, August 2004

  • Craig, Ian R.; Manolopoulos, David E.
  • The Journal of Chemical Physics, Vol. 121, Issue 8
  • DOI: 10.1063/1.1777575

Quantum corrections to classical time-correlation functions: Hydrogen bonding and anharmonic floppy modes
journal, September 2004

  • Ramı́rez, Rafael; López-Ciudad, Telesforo; Kumar P., Padma
  • The Journal of Chemical Physics, Vol. 121, Issue 9
  • DOI: 10.1063/1.1774986

On the alternatives for bath correlators and spectral densities from mixed quantum-classical simulations
journal, December 2012

  • Valleau, Stéphanie; Eisfeld, Alexander; Aspuru-Guzik, Alán
  • The Journal of Chemical Physics, Vol. 137, Issue 22
  • DOI: 10.1063/1.4769079

Low-lying electronic excitations of the green fluorescent protein chromophore
journal, July 2000


Absorption Spectrum of the Green Fluorescent Protein Chromophore Anion In Vacuo
journal, November 2001


Absorption Spectra of Photoactive Yellow Protein Chromophores in Vacuum
journal, October 2005


On the Photodetachment from the Green Fluorescent Protein Chromophore
journal, May 2013

  • Bravaya, Ksenia B.; Krylov, Anna I.
  • The Journal of Physical Chemistry A, Vol. 117, Issue 46
  • DOI: 10.1021/jp4028904

The Lineshape of the Electronic Spectrum of the Green Fluorescent Protein Chromophore, Part II: Solution Phase
journal, September 2014

  • Avila Ferrer, Francisco J.; Davari, Mehdi D.; Morozov, Dmitry
  • ChemPhysChem, Vol. 15, Issue 15
  • DOI: 10.1002/cphc.201402485

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water
journal, July 2018

  • Zuehlsdorff, Tim J.; Napoli, Joseph A.; Milanese, Joel M.
  • The Journal of Chemical Physics, Vol. 149, Issue 2
  • DOI: 10.1063/1.5025517

Development and testing of a general amber force field
journal, January 2004

  • Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
  • Journal of Computational Chemistry, Vol. 25, Issue 9
  • DOI: 10.1002/jcc.20035

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation
journal, July 2003

  • Getzoff, Elizabeth D.; Gutwin, Karl N.; Genick, Ulrich K.
  • Nature Structural & Molecular Biology, Vol. 10, Issue 8
  • DOI: 10.1038/nsb958

The implementation of a fast and accurate QM/MM potential method in Amber
journal, January 2008

  • Walker, Ross C.; Crowley, Michael F.; Case, David A.
  • Journal of Computational Chemistry, Vol. 29, Issue 7
  • DOI: 10.1002/jcc.20857

Fragment Quantum Mechanical Calculation of Proteins and Its Applications
journal, May 2014

  • He, Xiao; Zhu, Tong; Wang, Xianwei
  • Accounts of Chemical Research, Vol. 47, Issue 9
  • DOI: 10.1021/ar500077t

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O -Methyltransferase
journal, October 2016

  • Kulik, Heather J.; Zhang, Jianyu; Klinman, Judith P.
  • The Journal of Physical Chemistry B, Vol. 120, Issue 44
  • DOI: 10.1021/acs.jpcb.6b07814

Systematic Quantum Mechanical Region Determination in QM/MM Simulation
journal, January 2017

  • Karelina, Maria; Kulik, Heather J.
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 2
  • DOI: 10.1021/acs.jctc.6b01049

Time-dependent density functional theory within the Tamm–Dancoff approximation
journal, December 1999


A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)
journal, July 2004

  • Yanai, Takeshi; Tew, David P.; Handy, Nicholas C.
  • Chemical Physics Letters, Vol. 393, Issue 1-3, p. 51-57
  • DOI: 10.1016/j.cplett.2004.06.011

Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen
journal, January 1989

  • Dunning, Thom H.
  • The Journal of Chemical Physics, Vol. 90, Issue 2
  • DOI: 10.1063/1.456153

Effect of Chromophore Potential Model on the Description of Exciton–Phonon Interactions
journal, July 2015

  • Kim, Chang Woo; Park, Jae Woo; Rhee, Young Min
  • The Journal of Physical Chemistry Letters, Vol. 6, Issue 15
  • DOI: 10.1021/acs.jpclett.5b01141

Classical Force Fields Tailored for QM Applications: Is It Really a Feasible Strategy?
journal, September 2017

  • Andreussi, Oliviero; Prandi, Ingrid G.; Campetella, Marco
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 10
  • DOI: 10.1021/acs.jctc.7b00777

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics
journal, January 2019

  • Horton, Joshua T.; Allen, Alice E. A.; Dodda, Leela S.
  • Journal of Chemical Information and Modeling, Vol. 59, Issue 4
  • DOI: 10.1021/acs.jcim.8b00767

Photosynthetic Light-Harvesting Is Tuned by the Heterogeneous Polarizable Environment of the Protein
journal, March 2011

  • Curutchet, Carles; Kongsted, Jacob; Muñoz-Losa, Aurora
  • Journal of the American Chemical Society, Vol. 133, Issue 9
  • DOI: 10.1021/ja110053y

Energy Flow in the Cryptophyte PE545 Antenna Is Directed by Bilin Pigment Conformation
journal, October 2012

  • Curutchet, Carles; Novoderezhkin, Vladimir I.; Kongsted, Jacob
  • The Journal of Physical Chemistry B, Vol. 117, Issue 16
  • DOI: 10.1021/jp305033d

Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II
journal, January 2015

  • Jurinovich, Sandro; Viani, Lucas; Prandi, Ingrid G.
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 22
  • DOI: 10.1039/C4CP05647G

Impact of Electronic Fluctuations and Their Description on the Exciton Dynamics in the Light-Harvesting Complex PE545
journal, February 2017

  • Aghtar, Mortaza; Kleinekathöfer, Ulrich; Curutchet, Carles
  • The Journal of Physical Chemistry B, Vol. 121, Issue 6
  • DOI: 10.1021/acs.jpcb.6b10772

A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
journal, April 2002

  • Laio, Alessandro; VandeVondele, Joost; Rothlisberger, Ursula
  • The Journal of Chemical Physics, Vol. 116, Issue 16
  • DOI: 10.1063/1.1462041

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method
journal, December 2002

  • Das, Debananda; Eurenius, Kirsten P.; Billings, Eric M.
  • The Journal of Chemical Physics, Vol. 117, Issue 23
  • DOI: 10.1063/1.1520134

Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds
journal, September 2008

  • Senthilkumar, Kittusamy; Mujika, Jon I.; Ranaghan, Kara E.
  • Journal of The Royal Society Interface, Vol. 5, Issue suppl_3
  • DOI: 10.1098/rsif.2008.0243.focus

A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations
journal, May 2011

  • Beierlein, Frank R.; Michel, Julien; Essex, Jonathan W.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 17
  • DOI: 10.1021/jp109054j

The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules
journal, October 2013

  • Isborn, Christine M.; Mar, Brendan D.; Curchod, Basile F. E.
  • The Journal of Physical Chemistry B, Vol. 117, Issue 40
  • DOI: 10.1021/jp4058274

Sensitive Circular Dichroism Marker for the Chromophore Environment of Photoactive Yellow Protein: Assignment of the 307 and 318 nm Bands to the n → π* Transition of the Carbonyl
journal, January 2005

  • Borucki, Berthold; Otto, Harald; Meyer, Terrance E.
  • The Journal of Physical Chemistry B, Vol. 109, Issue 1
  • DOI: 10.1021/jp046515k

Proton Disorder in Ice Ih and Inhomogeneous Broadening in Two-Dimensional Infrared Spectroscopy
journal, August 2013

  • Shi, L.; Skinner, J. L.
  • The Journal of Physical Chemistry B, Vol. 117, Issue 49
  • DOI: 10.1021/jp405860u

Low-barrier hydrogen bond in photoactive yellow protein
journal, January 2009

  • Yamaguchi, S.; Kamikubo, H.; Kurihara, K.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 2
  • DOI: 10.1073/pnas.0811882106