Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

The UV–vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV–vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua‐p‐Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV–vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical–computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.

[1]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

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

[3]  A. Amadei,et al.  Theoretical characterization of electronic states in interacting chemical systems. , 2009, The Journal of chemical physics.

[4]  Vincenzo Barone,et al.  Fully Integrated Approach to Compute Vibrationally Resolved Optical Spectra: From Small Molecules to Macrosystems. , 2009, Journal of chemical theory and computation.

[5]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[6]  Ian Barnes,et al.  Gas-phase absorption cross sections of 24 monocyclic aromatic hydrocarbons in the UV and IR spectral ranges , 1999 .

[7]  D. Shepard A two-dimensional interpolation function for irregularly-spaced data , 1968, ACM National Conference.

[8]  D. Wetlaufer,et al.  Ultraviolet difference spectra of tyrosine groups in proteins and amino acids. , 1958, The Journal of biological chemistry.

[9]  G. Scuseria,et al.  Gaussian 03, Revision E.01. , 2007 .

[10]  H. Berendsen,et al.  Essential dynamics of proteins , 1993, Proteins.

[11]  J. Antosiewicz,et al.  UV–Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications , 2016, Biophysical Reviews.

[12]  P. Bouř,et al.  Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions. , 2014, Physical chemistry chemical physics : PCCP.

[13]  A. Amadei,et al.  STATISTICAL MECHANICAL MODELING OF CHEMICAL REACTIONS IN CONDENSED PHASE SYSTEMS , 2008 .

[14]  Vincenzo Barone,et al.  Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data. , 2013, Physical chemistry chemical physics : PCCP.

[15]  Luca Frediani,et al.  The Dalton quantum chemistry program system , 2013, Wiley interdisciplinary reviews. Computational molecular science.

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

[17]  Alessandro Laio,et al.  Clustering by fast search and find of density peaks , 2014, Science.

[18]  J. Olsen,et al.  Quadratic response functions for a multiconfigurational self‐consistent field wave function , 1992 .

[19]  Donald G Truhlar,et al.  Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases. , 2012, Journal of chemical theory and computation.

[20]  A. Amadei,et al.  In silico characterization of protein partial molecular volumes and hydration shells. , 2015, Physical chemistry chemical physics : PCCP.

[21]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[22]  David Creed,et al.  THE PHOTOPHYSICS AND PHOTOCHEMISTRY OF THE NEAR‐UV ABSORBING AMINO ACIDS–I. TRYPTOPHAN AND ITS SIMPLE DERIVATIVES , 1984 .

[23]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[24]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[25]  R. Ahlrichs,et al.  Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory , 1996 .

[26]  V. Barone,et al.  Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model , 1998 .

[27]  Ivo Cacelli,et al.  Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations. , 2007, Journal of chemical theory and computation.

[28]  Vincenzo Barone,et al.  Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. , 2017, Journal of chemical theory and computation.

[29]  U. Platt,et al.  UV-absorption cross sections of a series of monocyclic aromatic compounds , 1997 .

[30]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[31]  Sara Del Galdo,et al.  In silico characterization of bimolecular electron transfer reactions: The ferrocene–ferrocenium reaction as a test case , 2016 .

[32]  Giovanni Scalmani,et al.  Energies, structures, and electronic properties of molecules in solution with the C‐PCM solvation model , 2003, J. Comput. Chem..

[33]  C. Shepard,et al.  Cell Walls from Mycobacterium tuberculosis (BCG) as Vaccine Against Mycobacterium leprae Infections in Mice , 1968, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[34]  A. Amadei,et al.  Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: the vertical transition approximation. , 2013, The Journal of chemical physics.

[35]  A. Amadei,et al.  The unfolding effects on the protein hydration shell and partial molar volume: a computational study. , 2016, Physical chemistry chemical physics : PCCP.

[36]  V. Barone,et al.  Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model. , 2016, Physical chemistry chemical physics : PCCP.

[37]  B. Nordén,et al.  UV transition moments of tyrosine. , 2014, The journal of physical chemistry. B.

[38]  Robert J. Renka,et al.  Algorithm 790: CSHEP2D: cubic Shepard method for bivariate interpolation of scattered data , 1988, TOMS.

[39]  Andrea Amadei,et al.  Essential dynamics: foundation and applications , 2012 .

[40]  A. Amadei,et al.  Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: explicit treatment of the vibronic transitions. , 2014, The Journal of chemical physics.

[41]  J. Antosiewicz,et al.  UV–Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 1: basic principles and properties of tyrosine chromophore , 2016, Biophysical Reviews.

[42]  A. Amadei,et al.  Statistical Mechanical Modeling of Chemical Reactions in Complex Systems: The Reaction Free Energy Surface , 2004 .

[43]  M. Petersilka,et al.  DENSITY FUNCTIONAL THEORY OF TIME-DEPENDENT PHENOMENA , 1996 .

[44]  William L. Jorgensen,et al.  OPLS all‐atom force field for carbohydrates , 1997 .

[45]  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.

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

[47]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[48]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997 .

[49]  Jeppe Olsen,et al.  Linear response calculations for large scale multiconfiguration self‐consistent field wave functions , 1988 .

[50]  R. Franke Scattered data interpolation: tests of some methods , 1982 .