A vibrational and conformational characterization of arginine at different pH values investigated using Raman spectroscopy combined with DFT calculations

Abstract

In the present study, the Raman spectra of an aqueous solution of arginine (Arg) at three different pH values (2.0, 9.0, and 10.5) were recorded in the spectral range 500-1800 cm À1 by using an excitation wavelength of 514 nm. The wavenumber position and intensity of the Raman bands lying in the spectral range 1000-1500 cm À1 changed with pH. The change in the peak parameters with pH was mainly attributed to the change of the molecular structure to zwitterionic (ZW), cationic zwitterionic (CATZW), or protonated (PRO) form. The presence of these conformers at a particular pH value is investigated by analyzing the experimental and theoretical Raman spectra. The structural, spectroscopic, and thermodynamical features of ZW, CATZW, and PRO conformers of Arg in the gas phase and the aqueous solution phase were investigated by using density functional theory (DFT) calculations at B3LYP/6-31 + G(d,p) and M062X/6-31 + G(d,p) levels of theory. The spectroscopic changes observed for the Arg-(water) 10 complex in the gas phase (explicit model) and in the bulk solvent water environment (implicit model) are explained in terms of the role that water molecules play in the stabilization or destabilization of the active sites of Arg. The structure of the most stable conformer of the ZW, CATZW, and PRO forms of Arg at the pH values of 2.0, 9.0, and 10.5 was determined by comparing the experimental and theoretical spectral features and performing a Boltzmann population analysis. The most stable conformer of Arg at a particular pH, as obtained by spectral analysis, is also well supported by the results obtained from a thermodynamical analysis.

Tracking the Amide I and αCOO− Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

“…The amide I vibration has been found to be heavily dependent on the formation of intramolecular hydrogen bonds in proteins, and hydrogen bonds, in turn, are integral in the stabilization of various protein secondary structures [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ]. As a result, vibrational spectroscopy combined with density functional theory (DFT) computations is commonly employed to investigate the molecular geometries, dynamics, and secondary structures of short peptide chains [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ]. Navarette and coworkers reported the Raman and IR vibrational spectra for l -glutamic acid [ 44 ], l -aspartic acid (D) [ 35 ], and the glutamic acid (EE) and aspartic acid (DD) dipeptides [ 35 ] in their seminal works and found that these molecules are zwitterio...…”

532‐nm‐excited hyper‐Raman spectroscopy of amino acids

“…Figure 3d illustrates the HR (thick) and Raman (dotted) spectra of Arg. Table 4 lists the band assignments, [ 51–53 ] and the name of each atom in the side chain is presented in Scheme 1b. The HR bands at 1,415 and 1,369 cm −1 are assignable to the modes including ν s (COO − ).…”

Raman Fingerprints of the SARS-CoV-2 Delta Variant and Mechanisms of Its Instantaneous Inactivation by Silicon Nitride Bioceramics

“…Arginine possesses two proton donor groups (OH and NH), six proton acceptor sites (N and O), and six or seven bonds enabling molecular rotations. Accordingly, a number of different tautomers and conformers, including hydrated, 98 , 99 protonated, 100 and alkali-cationized 101 , 102 structures, are possible upon stabilization by different intermolecular hydrogen bonds. 98 The present Raman experiments suggest that the 935 cm –1 (N–C–N symmetric stretching) Raman fingerprint of the guanidinium group can be taken as a marker for strain infectivity and viral inactivation upon deimination.…”