Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches.

Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here, we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic time scale separation; the Franck-Condon method, which includes dynamical effects but generally only at the harmonic level; and the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.

[1]  M. Nooijen,et al.  Derivation and efficient implementation of a recursion formula to calculate harmonic Franck–Condon factors for polyatomic molecules , 2003 .

[2]  G. Scholes,et al.  Coherence Spectroscopy in the Condensed Phase: Insights into Molecular Structure, Environment, and Interactions. , 2017, Accounts of chemical research.

[3]  Christine M Isborn,et al.  Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent. , 2017, Journal of chemical theory and computation.

[4]  E. Condon A Theory of Intensity Distribution in Band Systems , 1926 .

[5]  D. Jacquemin,et al.  Going beyond the vertical approximation with time‐dependent density functional theory , 2016 .

[6]  J. P. Dahl,et al.  The Morse oscillator in position space, momentum space, and phase space , 1988 .

[7]  V. Barone,et al.  Effective method to compute Franck-Condon integrals for optical spectra of large molecules in solution. , 2007, The Journal of chemical physics.

[8]  Vladimir I. Man’ko,et al.  Dynamical symmetry of vibronic transitions in polyatomic molecules and the Franck-Condon principle , 1975 .

[9]  T J Zuehlsdorff,et al.  Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution. , 2017, The Journal of chemical physics.

[10]  L. Cederbaum,et al.  A many‐body approach to the vibrational structure in molecular electronic spectra. I. Theory , 1976 .

[11]  Tomoyuki Hayashi,et al.  Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges. , 2009, Angewandte Chemie.

[12]  Ivan S Ufimtsev,et al.  Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics. , 2009, Journal of chemical theory and computation.

[13]  D. Coker,et al.  Semiclassical Path Integral Dynamics: Photosynthetic Energy Transfer with Realistic Environment Interactions. , 2016, Annual review of physical chemistry.

[14]  M. Scully,et al.  Distribution functions in physics: Fundamentals , 1984 .

[15]  R. Hochstrasser,et al.  The 2D IR responses of amide and carbonyl modes in water cannot be described by Gaussian frequency fluctuations. , 2007, The journal of physical chemistry. B.

[16]  Benedetta Mennucci,et al.  Perspective: Polarizable continuum models for quantum-mechanical descriptions. , 2016, The Journal of chemical physics.

[17]  Joel S. Bader,et al.  Quantum and classical relaxation rates from classical simulations , 1994 .

[18]  S. Mukamel Fluorescence and absorption of large anharmonic molecules - spectroscopy without eigenstates , 1985 .

[19]  A. Aspuru‐Guzik,et al.  On the alternatives for bath correlators and spectral densities from mixed quantum-classical simulations. , 2012, The Journal of chemical physics.

[20]  Minhaeng Cho,et al.  Coherent two-dimensional optical spectroscopy. , 2008, Chemical reviews.

[21]  Marco Campetella,et al.  Classical Force Fields Tailored for QM Applications: Is It Really a Feasible Strategy? , 2017, Journal of chemical theory and computation.

[22]  R. Improta,et al.  Quantum-classical calculation of the absorption and emission spectral shapes of oligothiophenes at low and room temperature by first-principle calculations. , 2014, Chemphyschem : a European journal of chemical physics and physical chemistry.

[23]  Ian R. Craig,et al.  Quantum statistics and classical mechanics: real time correlation functions from ring polymer molecular dynamics. , 2004, The Journal of chemical physics.

[24]  J. Skinner,et al.  Quantum corrections in vibrational and electronic condensed phase spectroscopy: line shapes and echoes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M. Payne,et al.  Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red. , 2017, The Journal of chemical physics.

[26]  Qiang Shi,et al.  Vibrational energy relaxation in liquid oxygen from a semiclassical molecular dynamics simulation , 2003 .

[27]  J. Tomasi,et al.  Electronic excitation energies of molecules in solution: state specific and linear response methods for nonequilibrium continuum solvation models. , 2005, The Journal of chemical physics.

[28]  Frank Neese,et al.  On the theoretical prediction of fluorescence rates from first principles using the path integral approach. , 2018, The Journal of chemical physics.

[29]  Benedetta Mennucci,et al.  Polarizable continuum model , 2012 .

[30]  L. De Vico,et al.  Absorption and Fluorescence Lineshape Theory for Polynomial Potentials. , 2016, Journal of chemical theory and computation.

[31]  Vincenzo Barone,et al.  General Approach to Compute Vibrationally Resolved One-Photon Electronic Spectra , 2010 .

[32]  Todd J. Martínez,et al.  Generating Efficient Quantum Chemistry Codes for Novel Architectures. , 2013, Journal of chemical theory and computation.

[33]  Qiang Shi,et al.  Semiclassical Theory of Vibrational Energy Relaxation in the Condensed Phase , 2003 .

[34]  C. Pei,et al.  Exact evaluation of two-dimensional Franck—Condon integrals under the Duschinsky mixing effect , 1990 .

[35]  T. R. Faulkner,et al.  On the calculation of polyatomic Franck–Condon factors: Application to the 1A1g→1B2u absorption band of benzene , 1979 .

[36]  Donald G Truhlar,et al.  Electronic absorption spectra and solvatochromic shifts by the vertical excitation model: solvated clusters and molecular dynamics sampling. , 2015, The journal of physical chemistry. B.

[37]  Matthew C. Zwier,et al.  Hybrid molecular dynamics‐quantum mechanics simulations of solute spectral properties in the condensed phase: Evaluation of simulation parameters , 2007, J. Comput. Chem..

[38]  M. Roche On the polyatomic franck-condon factors , 1990 .

[39]  M. Menger,et al.  The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach , 2018, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[40]  Jeffrey A. Davis,et al.  Coherent multi-dimensional spectroscopy: Experimental considerations, direct comparisons and new capabilities , 2017 .

[41]  A. Aspuru‐Guzik,et al.  Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins. , 2015, The journal of physical chemistry. B.

[42]  D. Coker,et al.  Influence of site-dependent pigment-protein interactions on excitation energy transfer in photosynthetic light harvesting. , 2013, The journal of physical chemistry. B.

[43]  V. Barone,et al.  Computing the inhomogeneous broadening of electronic transitions in solution: a first-principle quantum mechanical approach. , 2011, Physical chemistry chemical physics : PCCP.

[44]  Lorenzo Cupellini,et al.  Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review , 2018, International Journal of Quantum Chemistry.

[45]  Christine M Isborn,et al.  Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models. , 2016, The journal of physical chemistry. B.

[46]  Benedetta Mennucci,et al.  Delocalized excitons in natural light-harvesting complexes , 2018, Reviews of Modern Physics.

[47]  Tim J. Zuehlsdorff,et al.  Modeling absorption spectra of molecules in solution , 2018, International Journal of Quantum Chemistry.

[48]  V. Barone,et al.  Effective method for the computation of optical spectra of large molecules at finite temperature including the Duschinsky and Herzberg-Teller effect: the Qx band of porphyrin as a case study. , 2008, The Journal of chemical physics.

[49]  Michele Ceriotti,et al.  i-PI: A Python interface for ab initio path integral molecular dynamics simulations , 2014, Comput. Phys. Commun..

[50]  C. Isborn,et al.  Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. , 2018, The Journal of chemical physics.

[51]  P. Rebentrost,et al.  Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex. , 2011, Biophysical journal.

[52]  M. Cho Two-Dimensional Optical Spectroscopy , 2009 .

[53]  N. Handy,et al.  A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP) , 2004 .

[54]  Benedetta Mennucci,et al.  Modeling absorption and fluorescence solvatochromism with QM/Classical approaches , 2015 .

[55]  Yu-Shan Lin,et al.  Vibrational Line Shapes, Spectral Diffusion, and Hydrogen Bonding in Liquid Water , 2008 .

[56]  J. Tomasi,et al.  Quantum mechanical continuum solvation models. , 2005, Chemical reviews.

[57]  D. M. Bishop,et al.  Calculation of Franck-Condon factors including anharmonicity: simulation of the C2H4+X2B3u<--C2H4X1A(g) band in the photoelectron spectrum of ethylene. , 2005, The Journal of chemical physics.

[58]  R. Berger,et al.  Vibronic transitions in large molecular systems: rigorous prescreening conditions for Franck-Condon factors. , 2007, The Journal of chemical physics.

[59]  M. Barbatti,et al.  Spectrum simulation and decomposition with nuclear ensemble: formal derivation and application to benzene, furan and 2-phenylfuran , 2012, Theoretical Chemistry Accounts.

[60]  H. Kupka,et al.  Multidimensional Franck–Condon integrals and Duschinsky mixing effects , 1986 .

[61]  Christine M Isborn,et al.  Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. , 2012, Journal of chemical theory and computation.

[62]  M. Biczysko,et al.  Aiming at an accurate prediction of vibrational and electronic spectra for medium‐to‐large molecules: An overview , 2016 .

[63]  S. Mukamel,et al.  Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations. , 2000, Annual review of physical chemistry.

[64]  S. Mukamel,et al.  Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. , 2017, Chemical reviews.

[65]  D. Jonas Two-dimensional femtosecond spectroscopy. , 2003, Annual review of physical chemistry.

[66]  S. Grimme,et al.  An efficient approach for the calculation of Franck-Condon integrals of large molecules. , 2005, The Journal of chemical physics.

[67]  E. Condon,et al.  Nuclear Motions Associated with Electron Transitions in Diatomic Molecules , 1928 .

[68]  Benjamin T. Miller,et al.  A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm–Dancoff approximation , 1999 .

[69]  R. Kubo A Stochastic Theory of Line Shape , 2007 .

[70]  T J Zuehlsdorff,et al.  Solvent Effects on Electronic Excitations of an Organic Chromophore. , 2016, Journal of chemical theory and computation.

[71]  Jacopo Tomasi,et al.  Formation and relaxation of excited states in solution: a new time dependent polarizable continuum model based on time dependent density functional theory. , 2006, The Journal of chemical physics.

[72]  P. Hamm,et al.  Three-point frequency fluctuation correlation functions of the OH stretch in liquid water. , 2008, The Journal of chemical physics.

[73]  M. Parrinello,et al.  Study of an F center in molten KCl , 1984 .

[74]  G. Prampolini,et al.  Modeling Solvent Broadening on the Vibronic Spectra of a Series of Coumarin Dyes. From Implicit to Explicit Solvent Models. , 2015, Journal of chemical theory and computation.

[75]  J. Skinner,et al.  Quantum Dynamics and Vibrational Relaxation , 1999 .

[76]  A. Toniolo,et al.  Efficient calculation of Franck–Condon factors and vibronic couplings in polyatomics , 2001, J. Comput. Chem..

[77]  J. Skinner,et al.  Vibrational spectroscopy as a probe of structure and dynamics in liquid water. , 2010, Chemical reviews.

[78]  P. T. Ruhoff Recursion relations for multi-dimensional Franck-Condon overlap integrals , 1994 .

[79]  Steven Vandenbrande,et al.  i-PI 2.0: A universal force engine for advanced molecular simulations , 2018, Comput. Phys. Commun..

[80]  Vincenzo Barone,et al.  General Time Dependent Approach to Vibronic Spectroscopy Including Franck-Condon, Herzberg-Teller, and Duschinsky Effects. , 2013, Journal of chemical theory and computation.

[81]  Fabrizio Santoro,et al.  Comparison of vertical and adiabatic harmonic approaches for the calculation of the vibrational structure of electronic spectra. , 2012, Physical chemistry chemical physics : PCCP.

[82]  V. Batista,et al.  Inclusion of nuclear quantum effects for simulations of nonlinear spectroscopy. , 2018, The Journal of chemical physics.

[83]  Lin,et al.  A New Expression for Multidimensional Franck-Condon Integrals. , 1999, Journal of molecular spectroscopy.

[84]  J. Saven,et al.  A molecular theory of the line shape : inhomogeneous and homogeneous electronic spectra of dilute chromophores in nonpolar fluids , 1993 .

[85]  Christine M. Isborn,et al.  Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units , 2011, Journal of chemical theory and computation.

[86]  M. Cho,et al.  Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: linear and nonlinear vibrational spectra. , 2004, The Journal of chemical physics.

[87]  Yingli Niu,et al.  Theory of excited state decays and optical spectra: application to polyatomic molecules. , 2010, The journal of physical chemistry. A.

[88]  D. Marx,et al.  Quantum corrections to classical time-correlation functions: hydrogen bonding and anharmonic floppy modes. , 2004, The Journal of chemical physics.

[89]  I. Timrov,et al.  Accurate and inexpensive prediction of the color optical properties of anthocyanins in solution. , 2015, The journal of physical chemistry. A.

[90]  M. Karplus,et al.  Vibrational structure of electronic transitions in conjugated molecules , 1972 .

[91]  C. Cramer,et al.  Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. , 1999, Chemical reviews.

[92]  T. H. Dunning Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[93]  M. Davari,et al.  The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part II: solution phase. , 2014, Chemphyschem : a European journal of chemical physics and physical chemistry.