Vibrational solvatochromism of nitrile infrared probes: beyond the vibrational Stark dipole approach.

Systematic probing of local environments around biopolymers is important for understanding their functions. Therefore, there has been growing interest in in situ measurements of molecular granularity and heterogeneity through the systematic analysis of vibrational frequency shifts of carbonyl and nitrile infrared probes by vibrational Stark dipole theory. However, here we show that the nitrile vibrational frequency shift induced by its interaction with the surrounding molecules cannot be solely described by electric field-based theory because of the exchange-repulsion and dispersion interaction contributions. Considering a variety of molecular environments ranging from bulk solutions to protein environments, we explore the distinct scenarios of solute-environment contacts and their traces in vibrational frequency shifts. We believe that the present work could provide a set of clues that could be potentially used to design a rigorous theoretical model linking vibrational solvatochromism and molecular topology in complex heterogeneous environments.

[1]  W. DeGrado,et al.  Using nitrile-derivatized amino acids as infrared probes of local environment. , 2003, Journal of the American Chemical Society.

[2]  S. Boxer,et al.  Phosphate vibrations probe local electric fields and hydration in biomolecules. , 2011, Journal of the American Chemical Society.

[3]  Shinnosuke Saëki,et al.  Infrared intensities of acetonitrile , 1984 .

[4]  S. Benkovic,et al.  Perspectives on Electrostatics and Conformational Motions in Enzyme Catalysis , 2015, Accounts of chemical research.

[5]  D. Herschlag,et al.  Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. , 2010, Journal of the American Chemical Society.

[6]  Spencer R Pruitt,et al.  Fragmentation methods: a route to accurate calculations on large systems. , 2012, Chemical reviews.

[7]  Lauren J. Webb,et al.  Optimizing electrostatic field calculations with the adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces. I. Sampling and focusing. , 2013, The journal of physical chemistry. B.

[8]  Suman Chakrabarty,et al.  Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins. , 2016, The journal of physical chemistry. B.

[9]  M. Waegele,et al.  Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water. , 2010, The journal of physical chemistry letters.

[10]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[11]  J. Pople,et al.  Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions , 1980 .

[12]  L. Onsager.  Electric Moments of Molecules in Liquids , 1936 .

[13]  Vincenzo Barone,et al.  Anharmonic vibrational properties by a fully automated second-order perturbative approach. , 2005, The Journal of chemical physics.

[14]  I. Adamovic,et al.  Dynamic polarizability, dispersion coefficient C6 and dispersion energy in the effective fragment potential method , 2005 .

[15]  Minhaeng Cho,et al.  Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis. , 2008, The Journal of chemical physics.

[16]  J. Choi,et al.  Vibrational solvatochromism and electrochromism of infrared probe molecules containing C≡O, C≡N, C=O, or C-F vibrational chromophore. , 2011, The Journal of chemical physics.

[17]  Pengyu Y. Ren,et al.  Calculations of the electric fields in liquid solutions. , 2013, The journal of physical chemistry. B.

[18]  M. Cho,et al.  Vibrational solvatochromism: towards systematic approach to modeling solvation phenomena. , 2013, The Journal of chemical physics.

[19]  J. Choi,et al.  Nitrile and thiocyanate IR probes: molecular dynamics simulation studies. , 2008, The Journal of chemical physics.

[20]  C. Morales,et al.  Molecular-level mechanisms of vibrational frequency shifts in a polar liquid. , 2011, The journal of physical chemistry. B.

[21]  S. Boxer,et al.  Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins. , 2006, Journal of the American Chemical Society.

[22]  J. Reimers,et al.  The Solvation of Acetonitrile , 1999 .

[23]  M. Maienschein-Cline,et al.  The CN stretching band of aliphatic thiocyanate is sensitive to solvent dynamics and specific solvation. , 2007, The journal of physical chemistry. A.

[24]  I. Suzuki,et al.  Vibration—rotation spectrum of methyl cyanide— analyses of ν2 and ν3 + ν4 bands , 1977 .

[25]  S. Andrews,et al.  Vibrational Stark Effects of Nitriles II. Physical Origins of Stark Effects from Experiment and Perturbation Models , 2002 .

[26]  M. Szczęśniak,et al.  On the connection between the supermolecular Møller-Plesset treatment of the interaction energy and the perturbation theory of intermolecular forces , 1988 .

[27]  J. Choi,et al.  Vibrational solvatochromism and electrochromism. II. Multipole analysis. , 2012, The Journal of chemical physics.

[28]  P. Schultz,et al.  A genetically encoded infrared probe. , 2006, Journal of the American Chemical Society.

[29]  S. Boxer,et al.  Nitrile bonds as infrared probes of electrostatics in ribonuclease S. , 2010, The journal of physical chemistry. B.

[30]  N. Hush,et al.  Vibrational Stark Spectroscopy. 1. Basic Theory and Application to the CO Stretch , 1995 .

[31]  Jerzy Leszczynski,et al.  Intermolecular interactions in solution: elucidating the influence of the solvent. , 2004, The Journal of chemical physics.

[32]  S. Boxer,et al.  A solvatochromic model calibrates nitriles' vibrational frequencies to electrostatic fields. , 2012, Journal of the American Chemical Society.

[33]  Raymond A. Poirier,et al.  Cumulative atomic multipole representation of the molecular charge distribution and its basis set dependence , 1983 .

[34]  Feng Gai,et al.  C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency? , 2016, Physical chemistry chemical physics : PCCP.

[35]  W. Andrzej Sokalski,et al.  AN EFFICIENT PROCEDURE FOR DECOMPOSITION OF THE SCF INTERACTION ENERGY INTO COMPONENTS WITH REDUCED BASIS SET DEPENDENCE , 1988 .

[36]  S. Boxer,et al.  Measuring electric fields and noncovalent interactions using the vibrational stark effect. , 2015, Accounts of chemical research.

[37]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[38]  M. Cho,et al.  Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method. , 2014, The Journal of chemical physics.

[39]  M. Symons,et al.  Solvation of cyanoalkanes [CH3CN and (CH3)3CCN]. An infrared and nuclear magnetic resonance study , 1988 .

[40]  Robert Moszynski,et al.  On decomposition of second‐order Mo/ller–Plesset supermolecular interaction energy and basis set effects , 1990 .

[41]  Lauren J. Webb,et al.  Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations. , 2015, The journal of physical chemistry. B.

[42]  J. K. Blasie,et al.  Mechanism of interaction between the general anesthetic halothane and a model ion channel protein, III: Molecular dynamics simulation incorporating a cyanophenylalanine spectroscopic probe. , 2009, Biophysical journal.

[43]  R. Taft,et al.  The solvatochromic comparison method. 2. The .alpha.-scale of solvent hydrogen-bond donor (HBD) acidities , 1976 .

[44]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[45]  Paul G. Mezey,et al.  A fast intrinsic localization procedure applicable for ab initio and semiempirical linear combination of atomic orbital wave functions , 1989 .

[46]  M. Cho.  Correlation between electronic and molecular structure distortions and vibrational properties. I. Adiabatic approximations , 2003 .

[47]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[48]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[49]  Peter A. Kollman,et al.  Application of the RESP Methodology in the Parametrization of Organic Solvents , 1998 .

[50]  Lauren J. Webb,et al.  Role of electrostatics in differential binding of RalGDS to Rap mutations E30D and K31E investigated by vibrational spectroscopy of thiocyanate probes. , 2012, The journal of physical chemistry. B.

[51]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[52]  W. Fawcett,et al.  Solvent-induced frequency shifts in the infrared spectrum of acetonitrile in organic solvents , 1993 .

[53]  S. Boxer,et al.  Solvent-induced infrared frequency shifts in aromatic nitriles are quantitatively described by the vibrational Stark effect. , 2012, The journal of physical chemistry. B.

[54]  Lei Liu,et al.  On the physical origin of blue-shifted hydrogen bonds. , 2002, Journal of the American Chemical Society.

[55]  J. Kirkwood,et al.  Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions , 1934 .

[56]  P. Hobza,et al.  On differences between hydrogen bonding and improper blue-shifting hydrogen bonding. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[57]  M. Cho.  Vibrational solvatochromism and electrochromism: coarse-grained models and their relationships. , 2009, The Journal of chemical physics.

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

[59]  R. Taft,et al.  The solvatochromic comparison method. I. The .beta.-scale of solvent hydrogen-bond acceptor (HBA) basicities , 1976 .

[60]  Rossend Rey,et al.  Vibrational phase and energy relaxation of CN− in water , 1998 .

[61]  A. Buckingham.  Molecular quadrupole moments , 1959 .

[62]  S. Boxer,et al.  Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins. , 2003, Biochemistry.

[63]  D. Ensign,et al.  Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction. , 2010, The journal of physical chemistry. B.

[64]  A. H. Nielsen,et al.  The infrared absorption spectrum of methyl cyanide vapor , 1957 .

[65]  J. Stewart.  Optimization of parameters for semiempirical methods I. Method , 1989 .

[66]  P. Rodziewicz,et al.  Ab initio studies of electron acceptor-donor interactions with blue- and red-shifted hydrogen bonds. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[67]  Oliver Beckstein,et al.  MDAnalysis: A toolkit for the analysis of molecular dynamics simulations , 2011, J. Comput. Chem..

[68]  S. Andrews,et al.  Vibrational Stark Effects of Nitriles I. Methods and Experimental Results , 2000 .

[69]  Wei Zhang,et al.  A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..

[70]  M. Cho,et al.  Vibrational solvatochromism. III. Rigorous treatment of the dispersion interaction contribution. , 2015, The Journal of chemical physics.

[71]  M. Gordon,et al.  Gradients of the polarization energy in the effective fragment potential method. , 2006, The Journal of chemical physics.

[72]  D. Ben‐Amotz,et al.  Solvent and pressure‐induced perturbations of the vibrational potential surface of acetonitrile , 1992 .

[73]  D. Gautier,et al.  Infrared spectra of gaseous mononitriles: Application to the atmosphere of Titan , 1985 .

[74]  N. Hush,et al.  Vibrational Stark Spectroscopy. 2. Application to the CN Stretch in HCN and Acetonitrile , 1996 .

[75]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[76]  R. Skeel,et al.  Langevin stabilization of molecular dynamics , 2001 .

[77]  R. Taft,et al.  The solvatochromic comparison method. 6. The .pi.* scale of solvent polarities , 1977 .

[78]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[79]  J. Johansson,et al.  Mechanism of interaction between the general anesthetic halothane and a model ion channel protein, II: Fluorescence and vibrational spectroscopy using a cyanophenylalanine probe. , 2009, Biophysical Journal.

[80]  Clemens C. J. Roothaan,et al.  New Developments in Molecular Orbital Theory , 1951 .

[81]  S. Boxer,et al.  Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes. , 2013, Journal of the American Chemical Society.