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Title: Modeling absorption spectra of molecules in solution

Abstract

The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent configuration, explicit solute–solvent interactions are key to understanding solution-phase reactivity and spectroscopy, simulating accurate inhomogeneous broadening, and predicting absorption spectra. In this tutorial review, we give an overview of factors to consider when modeling excited states of molecules interacting with explicit solvent. We provide practical guidelines for sampling solute–solvent configurations, choosing a solvent model, performing the excited state electronic structure calculations, and computing spectral lineshapes. Furthermore, we introduce our recent results combining the vertical excitation energies computed from an ensemble of solute–solvent configurations with the vibronic spectra obtained from a small number of frozen solvent configurations, resulting in improved simulation of absorption spectra for molecules in solution.

Authors:
 [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) (SC-22)
OSTI Identifier:
1594842
Alternate Identifier(s):
OSTI ID: 1470594
Grant/Contract Number:  
[SC0014437]
Resource Type:
Accepted Manuscript
Journal Name:
International Journal of Quantum Chemistry
Additional Journal Information:
[ Journal Volume: 119; Journal Issue: 1]; Journal ID: ISSN 0020-7608
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; excited states; TDDFT; solvation; inhomogeneous broadening; absorption spectra

Citation Formats

Zuehlsdorff, Tim J., and Isborn, Christine M. Modeling absorption spectra of molecules in solution. United States: N. p., 2018. Web. doi:10.1002/qua.25719.
Zuehlsdorff, Tim J., & Isborn, Christine M. Modeling absorption spectra of molecules in solution. United States. doi:10.1002/qua.25719.
Zuehlsdorff, Tim J., and Isborn, Christine M. Thu . "Modeling absorption spectra of molecules in solution". United States. doi:10.1002/qua.25719. https://www.osti.gov/servlets/purl/1594842.
@article{osti_1594842,
title = {Modeling absorption spectra of molecules in solution},
author = {Zuehlsdorff, Tim J. and Isborn, Christine M.},
abstractNote = {The presence of solvent tunes many properties of a molecule, such as its ground and excited state geometry, dipole moment, excitation energy, and absorption spectrum. Because the energy of the system will vary depending on the solvent configuration, explicit solute–solvent interactions are key to understanding solution-phase reactivity and spectroscopy, simulating accurate inhomogeneous broadening, and predicting absorption spectra. In this tutorial review, we give an overview of factors to consider when modeling excited states of molecules interacting with explicit solvent. We provide practical guidelines for sampling solute–solvent configurations, choosing a solvent model, performing the excited state electronic structure calculations, and computing spectral lineshapes. Furthermore, we introduce our recent results combining the vertical excitation energies computed from an ensemble of solute–solvent configurations with the vibronic spectra obtained from a small number of frozen solvent configurations, resulting in improved simulation of absorption spectra for molecules in solution.},
doi = {10.1002/qua.25719},
journal = {International Journal of Quantum Chemistry},
number = [1],
volume = [119],
place = {United States},
year = {2018},
month = {9}
}

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Works referenced in this record:

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

Quantum Embedding Theories
journal, November 2016


A simple polarizable model of water based on classical Drude oscillators
journal, September 2003

  • Lamoureux, Guillaume; MacKerell, Alexander D.; Roux, Benoı̂t
  • The Journal of Chemical Physics, Vol. 119, Issue 10
  • DOI: 10.1063/1.1598191

Asymptotic correction of the exchange–correlation kernel of time-dependent density functional theory for long-range charge-transfer excitations
journal, July 2004

  • Gritsenko, Oleg; Baerends, Evert Jan
  • The Journal of Chemical Physics, Vol. 121, Issue 2
  • DOI: 10.1063/1.1759320

An EOM-CCSD-PCM Benchmark for Electronic Excitation Energies of Solvated Molecules
journal, December 2016

  • Ren, Sijin; Harms, Joseph; Caricato, Marco
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 1
  • DOI: 10.1021/acs.jctc.6b01053

Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules
journal, April 2015

  • Raghavachari, Krishnan; Saha, Arjun
  • Chemical Reviews, Vol. 115, Issue 12
  • DOI: 10.1021/cr500606e

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

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields
journal, January 2016

  • Kratz, Eric G.; Walker, Alice R.; Lagardère, Louis
  • Journal of Computational Chemistry, Vol. 37, Issue 11
  • DOI: 10.1002/jcc.24295

Size-dependent error of the density functional theory ionization potential in vacuum and solution
journal, December 2015

  • Sosa Vazquez, Xochitl A.; Isborn, Christine M.
  • The Journal of Chemical Physics, Vol. 143, Issue 24
  • DOI: 10.1063/1.4937417

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

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 Excitations in Solution: The Interplay between State Specific Approaches and a Time-Dependent Density Functional Theory Description
journal, November 2015

  • Guido, Ciro A.; Jacquemin, Denis; Adamo, Carlo
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 12
  • DOI: 10.1021/acs.jctc.5b00679

Electric Moments of Molecules in Liquids
journal, August 1936

  • Onsager, Lars
  • Journal of the American Chemical Society, Vol. 58, Issue 8
  • DOI: 10.1021/ja01299a050

Dielectric and Thermal Effects on the Optical Properties of Natural Dyes: A Case Study on Solvated Cyanin
journal, October 2011

  • Malcıoğlu, Osman Bariş; Calzolari, Arrigo; Gebauer, Ralph
  • Journal of the American Chemical Society, Vol. 133, Issue 39
  • DOI: 10.1021/ja201733v

Solvatochromism and solvent polarity scales
journal, July 1990

  • Buncel, Erwin; Rajagopal, Srinivasan
  • Accounts of Chemical Research, Vol. 23, Issue 7
  • DOI: 10.1021/ar00175a004

Exploring the Aqueous Vertical Ionization of Organic Molecules by Molecular Simulation and Liquid Microjet Photoelectron Spectroscopy
journal, December 2014

  • Tentscher, Peter R.; Seidel, Robert; Winter, Bernd
  • The Journal of Physical Chemistry B, Vol. 119, Issue 1
  • DOI: 10.1021/jp508053m

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

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

Assessment of range-separated functionals in the presence of implicit solvent: Computation of oxidation energy, reduction energy, and orbital energy
journal, April 2017

  • Boruah, Abhijit; Borpuzari, Manash Protim; Kawashima, Yukio
  • The Journal of Chemical Physics, Vol. 146, Issue 16
  • DOI: 10.1063/1.4981529

Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
journal, June 2011

  • Ufimtsev, Ivan S.; Luehr, Nathan; Martinez, Todd J.
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 14
  • DOI: 10.1021/jz200697c

Energy-Based Molecular Fragmentation Methods
journal, April 2015

  • Collins, Michael A.; Bettens, Ryan P. A.
  • Chemical Reviews, Vol. 115, Issue 12
  • DOI: 10.1021/cr500455b

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
journal, September 2016

  • Dziedzic, Jacek; Mao, Yuezhi; Shao, Yihan
  • The Journal of Chemical Physics, Vol. 145, Issue 12
  • DOI: 10.1063/1.4962909

A solvation model using a hybrid quantum mechanical/molecular mechanical potential with fluctuating solvent charges
journal, November 1997


Excited states in large molecular systems through polarizable embedding
journal, January 2016

  • List, Nanna Holmgaard; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 30
  • DOI: 10.1039/C6CP03834D

Role of Quantum Vibrations on the Structural, Electronic, and Optical Properties of 9-Methylguanine
journal, October 2015


Quantum Mechanical Continuum Solvation Models
journal, August 2005

  • Tomasi, Jacopo; Mennucci, Benedetta; Cammi, Roberto
  • Chemical Reviews, Vol. 105, Issue 8
  • DOI: 10.1021/cr9904009

The COSMO and COSMO-RS solvation models: The COSMO and COSMO-RS solvation models
journal, April 2011

  • Klamt, Andreas
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 5
  • DOI: 10.1002/wcms.56

Averaging Techniques for Reaction Barriers in QM/MM Simulations
journal, September 2014


Modeling Solvent Effects on Electronic Excited States
journal, August 2011

  • DeFusco, Albert; Minezawa, Noriyuki; Slipchenko, Lyudmila V.
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 17
  • DOI: 10.1021/jz200947j

Assessment of a Coulomb-attenuated exchange–correlation energy functional
journal, January 2006

  • Peach, Michael J. G.; Helgaker, Trygve; Sałek, Paweł
  • Phys. Chem. Chem. Phys., Vol. 8, Issue 5
  • DOI: 10.1039/B511865D

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

A long-range correction scheme for generalized-gradient-approximation exchange functionals
journal, August 2001

  • Iikura, Hisayoshi; Tsuneda, Takao; Yanai, Takeshi
  • The Journal of Chemical Physics, Vol. 115, Issue 8
  • DOI: 10.1063/1.1383587

Titrimetric and Equilibrium Studies Using Indicators Related to Nile Blue A.
journal, March 1966


Combining long-range configuration interaction with short-range density functionals
journal, August 1997


A discrete solvent reaction field model for calculating molecular linear response properties in solution
journal, August 2003

  • Jensen, Lasse; van Duijnen, Piet Th.; Snijders, Jaap G.
  • The Journal of Chemical Physics, Vol. 119, Issue 7
  • DOI: 10.1063/1.1590643

Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein
journal, September 2015

  • Daday, Csaba; Curutchet, Carles; Sinicropi, Adalgisa
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 10
  • DOI: 10.1021/acs.jctc.5b00650

Choosing a Functional for Computing Absorption and Fluorescence Band Shapes with TD-DFT
journal, May 2013

  • Charaf-Eddin, Azzam; Planchat, Aurélien; Mennucci, Benedetta
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 6
  • DOI: 10.1021/ct4000795

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

Simulation of volume polarization in reaction field theory
journal, April 1999

  • Chipman, Daniel M.
  • The Journal of Chemical Physics, Vol. 110, Issue 16
  • DOI: 10.1063/1.478729

Formation and relaxation of excited states in solution: A new time dependent polarizable continuum model based on time dependent density functional theory
journal, March 2006

  • Caricato, Marco; Mennucci, Benedetta; Tomasi, Jacopo
  • The Journal of Chemical Physics, Vol. 124, Issue 12
  • DOI: 10.1063/1.2183309

Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules
journal, March 2013


Derivation and efficient implementation of a recursion formula to calculate harmonic Franck-Condon factors for polyatomic molecules
journal, January 2003

  • Hazra, Anirban; Nooijen, Marcel
  • International Journal of Quantum Chemistry, Vol. 95, Issue 4-5
  • DOI: 10.1002/qua.10723

Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model
journal, March 1998

  • Barone, Vincenzo; Cossi, Maurizio
  • The Journal of Physical Chemistry A, Vol. 102, Issue 11
  • DOI: 10.1021/jp9716997

TD-DFT Assessment of Functionals for Optical 0–0 Transitions in Solvated Dyes
journal, June 2012

  • Jacquemin, Denis; Planchat, Aurélien; Adamo, Carlo
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 7
  • DOI: 10.1021/ct300326f

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

Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model
journal, October 2012

  • Boulanger, Eliot; Thiel, Walter
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 11
  • DOI: 10.1021/ct300722e

Charge transfer in time-dependent density functional theory
journal, September 2017


Erratum: “Effective method to compute Franck-Condon integrals for optical spectra of large molecules in solution” [J. Chem. Phys. 126, 084509 (2007)]
journal, April 2007

  • Santoro, Fabrizio; Improta, Roberto; Lami, Alessandro
  • The Journal of Chemical Physics, Vol. 126, Issue 16
  • DOI: 10.1063/1.2722259

Solvatochromic shift of phenol blue in water from a combined Car–Parrinello molecular dynamics hybrid quantum mechanics-molecular mechanics and ZINDO approach
journal, June 2010

  • Murugan, N. Arul; Jha, Prakash Chandra; Rinkevicius, Z.
  • The Journal of Chemical Physics, Vol. 132, Issue 23
  • DOI: 10.1063/1.3436516

Fragmentation Methods: A Route to Accurate Calculations on Large Systems
journal, August 2011

  • Gordon, Mark S.; Fedorov, Dmitri G.; Pruitt, Spencer R.
  • Chemical Reviews, Vol. 112, Issue 1
  • DOI: 10.1021/cr200093j

Tuned Range-Separated Hybrids in Density Functional Theory
journal, March 2010


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

Quantum-chemical embedding methods for treating local electronic excitations in complex chemical systems
journal, January 2012

  • Severo Pereira Gomes, André; Jacob, Christoph R.
  • Annual Reports Section "C" (Physical Chemistry), Vol. 108
  • DOI: 10.1039/c2pc90007f

Quantifying the Performances of DFT for Predicting Vibrationally Resolved Optical Spectra: Asymmetric Fluoroborate Dyes as Working Examples
journal, August 2017

  • Bednarska, Joanna; Zaleśny, Robert; Bartkowiak, Wojciech
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 9
  • DOI: 10.1021/acs.jctc.7b00469

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

The merits of the frozen-density embedding scheme to model solvatochromic shifts
journal, March 2005

  • Neugebauer, Johannes; Louwerse, Manuel J.; Baerends, Evert Jan
  • The Journal of Chemical Physics, Vol. 122, Issue 9
  • DOI: 10.1063/1.1858411

Tuned range separated hybrid functionals for solvated low bandgap oligomers
journal, July 2015

  • de Queiroz, Thiago B.; Kümmel, Stephan
  • The Journal of Chemical Physics, Vol. 143, Issue 3
  • DOI: 10.1063/1.4926468

Mechanism for the Enhanced Excited-State Lewis Acidity of Methyl Viologen
journal, January 2016

  • Hohenstein, Edward G.
  • Journal of the American Chemical Society, Vol. 138, Issue 6
  • DOI: 10.1021/jacs.5b08177

A long-range-corrected time-dependent density functional theory
journal, May 2004

  • Tawada, Yoshihiro; Tsuneda, Takao; Yanagisawa, Susumu
  • The Journal of Chemical Physics, Vol. 120, Issue 18
  • DOI: 10.1063/1.1688752

Quantum-Classical Calculation of the Absorption and Emission Spectral Shapes of Oligothiophenes at Low and Room Temperature by First-Principle Calculations
journal, August 2014

  • Improta, Roberto; Ferrer, Francisco J. Avila; Stendardo, Emiliano
  • ChemPhysChem, Vol. 15, Issue 15
  • DOI: 10.1002/cphc.201402323

Computation of accurate excitation energies for large organic molecules with double-hybrid density functionals
journal, January 2009

  • Goerigk, Lars; Moellmann, Jonas; Grimme, Stefan
  • Physical Chemistry Chemical Physics, Vol. 11, Issue 22
  • DOI: 10.1039/b902315a

Combining Explicit Quantum Solvent with a Polarizable Continuum Model
journal, October 2017

  • Provorse Long, Makenzie R.; Isborn, Christine M.
  • The Journal of Physical Chemistry B, Vol. 121, Issue 43
  • DOI: 10.1021/acs.jpcb.7b06693

Performance of an Optimally Tuned Range-Separated Hybrid Functional for 0–0 Electronic Excitation Energies
journal, March 2014

  • Jacquemin, Denis; Moore, Barry; Planchat, Aurélien
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 4
  • DOI: 10.1021/ct5000617

Modeling Solvent Broadening on the Vibronic Spectra of a Series of Coumarin Dyes. From Implicit to Explicit Solvent Models
journal, November 2015

  • Cerezo, Javier; Avila Ferrer, Francisco J.; Prampolini, Giacomo
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 12
  • DOI: 10.1021/acs.jctc.5b00870

The effect of dynamical fluctuations of hydration structures on the absorption spectra of oxyluciferin anions in an aqueous solution
journal, January 2017

  • Hiyama, Miyabi; Shiga, Motoyuki; Koga, Nobuaki
  • Physical Chemistry Chemical Physics, Vol. 19, Issue 15
  • DOI: 10.1039/C7CP01067B

Importance of Vibronic Effects in the UV–Vis Spectrum of the 7,7,8,8-Tetracyanoquinodimethane Anion
journal, September 2016

  • Tapavicza, Enrico; Furche, Filipp; Sundholm, Dage
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 10
  • DOI: 10.1021/acs.jctc.6b00720

Introducing QMC/MMpol: Quantum Monte Carlo in Polarizable Force Fields for Excited States
journal, March 2016

  • Guareschi, Riccardo; Zulfikri, Habiburrahman; Daday, Csaba
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 4
  • DOI: 10.1021/acs.jctc.6b00044

General Approach to Compute Vibrationally Resolved One-Photon Electronic Spectra
journal, March 2010

  • Bloino, Julien; Biczysko, Malgorzata; Santoro, Fabrizio
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 4
  • DOI: 10.1021/ct9006772

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

Generalization of the Kohn-Sham equations with constrained electron density formalism and its time-dependent response theory formulation
journal, January 2003

  • Casida, Mark E.; Weso?owski, Tomasz A.
  • International Journal of Quantum Chemistry, Vol. 96, Issue 6
  • DOI: 10.1002/qua.10744

Computing the inhomogeneous broadening of electronic transitions in solution: a first-principle quantum mechanical approach
journal, January 2011

  • Ferrer, Francisco José Avila; Improta, Roberto; Santoro, Fabrizio
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 38
  • DOI: 10.1039/c1cp22115a

Effects of different initial condition samplings on photodynamics and spectrum of pyrrole
journal, November 2015

  • Barbatti, Mario; Sen, Kakali
  • International Journal of Quantum Chemistry, Vol. 116, Issue 10
  • DOI: 10.1002/qua.25049

A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution
journal, August 2006

  • Improta, Roberto; Barone, Vincenzo; Scalmani, Giovanni
  • The Journal of Chemical Physics, Vol. 125, Issue 5
  • DOI: 10.1063/1.2222364

Effect of Solvation on the Vertical Ionization Energy of Thymine: From Microhydration to Bulk
journal, June 2011

  • Ghosh, Debashree; Isayev, Olexandr; Slipchenko, Lyudmila V.
  • The Journal of Physical Chemistry A, Vol. 115, Issue 23
  • DOI: 10.1021/jp110438c

Optimum Exchange for Calculation of Excitation Energies and Hyperpolarizabilities of Organic Electro-optic Chromophores
journal, August 2014

  • Garrett, Kerry; Sosa Vazquez, XochitlA; Egri, Shawn B.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 9
  • DOI: 10.1021/ct500528z

QM/MM Methods for Biomolecular Systems
journal, January 2009

  • Senn, Hans Martin; Thiel, Walter
  • Angewandte Chemie International Edition, Vol. 48, Issue 7
  • DOI: 10.1002/anie.200802019

Toward Fully Nonempirical Simulations of Optical Band Shapes of Molecules in Solution: A Case Study of Heterocyclic Ketoimine Difluoroborates
journal, December 2014

  • Zaleśny, Robert; Murugan, N. Arul; Gel’mukhanov, Faris
  • The Journal of Physical Chemistry A, Vol. 119, Issue 21
  • DOI: 10.1021/jp5094417

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

Reliable Prediction of Charge Transfer Excitations in Molecular Complexes Using Time-Dependent Density Functional Theory
journal, March 2009

  • Stein, Tamar; Kronik, Leeor; Baer, Roi
  • Journal of the American Chemical Society, Vol. 131, Issue 8
  • DOI: 10.1021/ja8087482

A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics
journal, August 1997

  • Cancès, E.; Mennucci, B.; Tomasi, J.
  • The Journal of Chemical Physics, Vol. 107, Issue 8
  • DOI: 10.1063/1.474659

The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein
journal, November 2017

  • Nåbo, Lina J.; Olsen, Jógvan Magnus Haugaard; Martínez, Todd J.
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 12
  • DOI: 10.1021/acs.jctc.7b00528

Planar vs. twisted intramolecular charge transfer mechanism in Nile Red: new hints from theory
journal, January 2010

  • Guido, Ciro A.; Mennucci, Benedetta; Jacquemin, Denis
  • Physical Chemistry Chemical Physics, Vol. 12, Issue 28
  • DOI: 10.1039/b927489h

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

Duschinsky, Herzberg–Teller, and Multiple Electronic Resonance Interferential Effects in Resonance Raman Spectra and Excitation Profiles. The Case of Pyrene
journal, July 2013

  • Avila Ferrer, Francisco J.; Barone, Vincenzo; Cappelli, Chiara
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 8
  • DOI: 10.1021/ct400197y

Solvatochromic Dyes as Solvent Polarity Indicators
journal, December 1994


QM/MM: what have we learned, where are we, and where do we go from here?
journal, July 2006


Absorption and Emission Spectra of a Flexible Dye in Solution: A Computational Time-Dependent Approach
journal, September 2013

  • De Mitri, Nicola; Monti, Susanna; Prampolini, Giacomo
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 10
  • DOI: 10.1021/ct4005799

Comparing classical approaches with empirical or quantum-mechanically derived force fields for the simulation electronic lineshapes: application to coumarin dyes
journal, May 2016

  • Cerezo, Javier; Santoro, Fabrizio; Prampolini, Giacomo
  • Theoretical Chemistry Accounts, Vol. 135, Issue 5
  • DOI: 10.1007/s00214-016-1888-7

Excitation Energies in Solution: The Fully Polarizable QM/MM/PCM Method
journal, March 2011

  • Steindal, Arnfinn Hykkerud; Ruud, Kenneth; Frediani, Luca
  • The Journal of Physical Chemistry B, Vol. 115, Issue 12
  • DOI: 10.1021/jp1101913

Effective Time-Independent Calculations of Vibrational Resonance Raman Spectra of Isolated and Solvated Molecules Including Duschinsky and Herzberg–Teller Effects
journal, April 2011

  • Santoro, Fabrizio; Cappelli, Chiara; Barone, Vincenzo
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 6
  • DOI: 10.1021/ct200054w

Simple Methods To Reduce Charge-Transfer Contamination in Time-Dependent Density-Functional Calculations of Clusters and Liquids
journal, August 2007

  • Lange, Adrian; Herbert, John M.
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 5
  • DOI: 10.1021/ct700125v

Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution
journal, May 2007

  • Santoro, Fabrizio; Lami, Alessandro; Improta, Roberto
  • The Journal of Chemical Physics, Vol. 126, Issue 18
  • DOI: 10.1063/1.2721539

Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water
journal, March 2018

  • García-Iriepa, Cristina; Gosset, Pauline; Berraud-Pache, Romain
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 4
  • DOI: 10.1021/acs.jctc.7b01240

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

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

Analytic energy gradient of excited electronic state within TDDFT/MMpol framework: Benchmark tests and parallel implementation
journal, October 2015

  • Zeng, Qiao; Liang, WanZhen
  • The Journal of Chemical Physics, Vol. 143, Issue 13
  • DOI: 10.1063/1.4931734

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

Pushing the Limits of EOM-CCSD with Projector-Based Embedding for Excitation Energies
journal, November 2017

  • Bennie, Simon J.; Curchod, Basile F. E.; Manby, Frederick R.
  • The Journal of Physical Chemistry Letters, Vol. 8, Issue 22
  • DOI: 10.1021/acs.jpclett.7b02500

Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: Acrolein in water
journal, January 2014

  • Floris, Franca Maria; Filippi, Claudia; Amovilli, Claudio
  • The Journal of Chemical Physics, Vol. 140, Issue 3
  • DOI: 10.1063/1.4861429

Modeling absorption and fluorescence solvatochromism with QM/Classical approaches
journal, February 2015

  • Mennucci, Benedetta
  • International Journal of Quantum Chemistry, Vol. 115, Issue 18
  • DOI: 10.1002/qua.24889

What is Solvatochromism?
journal, December 2010

  • Marini, Alberto; Muñoz-Losa, Aurora; Biancardi, Alessandro
  • The Journal of Physical Chemistry B, Vol. 114, Issue 51
  • DOI: 10.1021/jp1097487

Time dependent density functional theory study of charge-transfer and intramolecular electronic excitations in acetone–water systems
journal, December 2003

  • Bernasconi, Leonardo; Sprik, Michiel; Hutter, Jürg
  • The Journal of Chemical Physics, Vol. 119, Issue 23
  • DOI: 10.1063/1.1625633

Nuclear quantum effects enter the mainstream
journal, February 2018


Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings
journal, June 2012

  • Flaig, Denis; Beer, Matthias; Ochsenfeld, Christian
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 7
  • DOI: 10.1021/ct300036s

Computational Photophysics in the Presence of an Environment
journal, April 2018


Wavefunction in Density Functional Theory Embedding for Excited States: Which Wavefunctions, which Densities?
journal, October 2014

  • Daday, Csaba; König, Carolin; Neugebauer, Johannes
  • ChemPhysChem, Vol. 15, Issue 15
  • DOI: 10.1002/cphc.201402459

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

A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations
journal, July 2016

  • Loco, Daniele; Polack, Étienne; Caprasecca, Stefano
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 8
  • DOI: 10.1021/acs.jctc.6b00385

Optimal Tuning of Range-Separated Hybrids for Solvated Molecules with Time-Dependent Density Functional Theory
journal, September 2017

  • Rubešová, Martina; Muchová, Eva; Slavíček, Petr
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 10
  • DOI: 10.1021/acs.jctc.7b00675

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

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

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

Excited State Dipole Moments in Solution: Comparison between State-Specific and Linear-Response TD-DFT Values
journal, January 2018

  • Guido, Ciro Achille; Mennucci, Benedetta; Scalmani, Giovanni
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 3
  • DOI: 10.1021/acs.jctc.7b01230

Frozen density functional approach for ab initio calculations of solvated molecules
journal, July 1993

  • Wesolowski, Tomasz Adam; Warshel, Arieh
  • The Journal of Physical Chemistry, Vol. 97, Issue 30
  • DOI: 10.1021/j100132a040

Polarizable Force Fields and Polarizable Continuum Model: A Fluctuating Charges/PCM Approach. 1. Theory and Implementation
journal, September 2011

  • Lipparini, Filippo; Barone, Vincenzo
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 11
  • DOI: 10.1021/ct200376z

Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM
journal, May 2006

  • Vreven, Thom; Byun, K. Suzie; Komáromi, István
  • Journal of Chemical Theory and Computation, Vol. 2, Issue 3
  • DOI: 10.1021/ct050289g

Dynamical Discrete/Continuum Linear Response Shells Theory of Solvation: Convergence Test for NH 4 + and OH Ions in Water Solution Using DFT and DFTB Methods
journal, December 2010

  • de Lima, Guilherme Ferreira; Duarte, Hélio Anderson; Pliego, Josefredo R.
  • The Journal of Physical Chemistry B, Vol. 114, Issue 48
  • DOI: 10.1021/jp110202e

Implicit Solvation Models:  Equilibria, Structure, Spectra, and Dynamics
journal, August 1999

  • Cramer, Christopher J.; Truhlar, Donald G.
  • Chemical Reviews, Vol. 99, Issue 8
  • DOI: 10.1021/cr960149m

Solvatochromic probe in molecular solvents: implicit versus explicit solvent model
journal, July 2014


Long-range charge-transfer excited states in time-dependent density functional theory require non-local exchange
journal, August 2003

  • Dreuw, Andreas; Weisman, Jennifer L.; Head-Gordon, Martin
  • The Journal of Chemical Physics, Vol. 119, Issue 6
  • DOI: 10.1063/1.1590951

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

Excitation Gaps of Finite-Sized Systems from Optimally Tuned Range-Separated Hybrid Functionals
journal, April 2012

  • Kronik, Leeor; Stein, Tamar; Refaely-Abramson, Sivan
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 5
  • DOI: 10.1021/ct2009363

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

Organic Electronic Materials: Recent Advances in the DFT Description of the Ground and Excited States Using Tuned Range-Separated Hybrid Functionals
journal, April 2014

  • Körzdörfer, Thomas; Brédas, Jean-Luc
  • Accounts of Chemical Research, Vol. 47, Issue 11
  • DOI: 10.1021/ar500021t

Frozen-Density Embedding Strategy for Multilevel Simulations of Electronic Structure
journal, April 2015

  • Wesolowski, Tomasz A.; Shedge, Sapana; Zhou, Xiuwen
  • Chemical Reviews, Vol. 115, Issue 12
  • DOI: 10.1021/cr500502v

Charge-transfer excitations in low-gap systems under the influence of solvation and conformational disorder: Exploring range-separation tuning
journal, August 2014

  • de Queiroz, Thiago B.; Kümmel, Stephan
  • The Journal of Chemical Physics, Vol. 141, Issue 8
  • DOI: 10.1063/1.4892937

Vibronic transitions in large molecular systems: Rigorous prescreening conditions for Franck-Condon factors
journal, December 2007

  • Jankowiak, H. -C.; Stuber, J. L.; Berger, R.
  • The Journal of Chemical Physics, Vol. 127, Issue 23
  • DOI: 10.1063/1.2805398

    Works referencing / citing this record:

    QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra
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