A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy

Abstract

Link to publication in University of Groningen/UMCG research database Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. A method for modeling infrared solvent shifts using the electrostatic field generated by the solvent is presented. The method is applied to the amide I vibration of N-methyl acetamide. Using ab initio calculations the fundamental frequency, anharmonicity, and the transition dipoles between the three lowest vibrational states are parametrized in terms of the electrostatic field. The generated map, which takes into account the electric field and its gradients at four molecular positions, is tested in a number of common solvents. Agreement of solvent shift and linewidths with experimental Fourier transform infrared ͑FTIR͒ data is found to within seven and four wave numbers, respectively, for polar solvents. This shows that in these solvents electrostatic contributions dominate solvation effects and the map is transferable between these types of solvents. The effect of motional narrowing arising from the fast solvent fluctuations is found to be substantial for the FTIR spectra. Also the two-dimensional infrared ͑2DIR͒ spectra, simulated using the constructed map, reproduce experimental results very well. The effect of anharmonicity fluctuations on the 2DIR spectra was found to be negligible.

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

“…27 Both the magnitude and direction parameters of the TDM were subject to optimization, however, not the position. Different positions have been proposed in literature, 11,66 but as the position is not readily observable, there is little guidance as to the possible range.…”

“…A computationally inexpensive way of including solvent effects on the amide I frequencies is to parametrize ab initio calculations of N-methylacetamide (NMA) and water clusters. [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] This method exploits the linear correlation found between the C=O bond length, stretching frequency and electrostatic potential at the atoms of NMA, 18,31,32 which provides a link between perturbation of molecular (and electronic) structure by the electric field of the solvent and the resulting shift of the vibrational frequency. Parametrized electrostatic calculations using the building block approach have been used in protein amide I sim-ulations of ubiquitin, 10,33 other proteins 34 as well as polypeptides in membrane environment.…”

Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment

“…Clear experimental evidence in support of either model has been difficult to obtain, however, and a surprising degree of variability has grown up surrounding the choice of both electrostatic components and map sites for parameterization, ranging from the two-site/field model of Skinner and co-workers 12 to the seven-site/potential model of Watson and Hirst 18 or the four-site/four-component (field/gradient) model of Jansen and Knoester. 24 Unfortunately, amide I computational maps still have limited accuracy and are usually specialized to specific systems or force fields. Although useful for qualitative interpretation, comparison with experimental data is generally limited (at best) to peak shapes and must be assisted by the application of arbitrary frequency shifts to simulated spectra.…”

“…11,18,26 In parameterizing the expansion coefficients c i in Eq. (2), generally either the field 12,19,24,26 or the potential 13,14,17,18,25 is chosen to have non-zero coefficients, but not both. The theoretical arguments behind each choice have been discussed in detail by Cho.…”

“…9 Although simple in form, the accurate structure-based parameterization of this Hamiltonian is non-trivial and has been the subject of numerous computational studies. [11][12][13][14][15][16][17][18][19][22][23][24][25][26] Siteto-site coupling constants are generally extracted by a combination of electrostatic models (e.g., dipole-dipole 22,27 or transition charge coupling 11,13,15,28 ) and DFT-parameterized dihedral maps for nearest-neighbor interactions. 11,13,18,22,26 Site energy maps are based on the observation that electrostatic interactions (particularly hydrogen bonding) between a solvated molecule and its environment are the primary predictors of local vibrational frequencies.…”