Correlation between the Hydrogen-Bond Structures and the C═O Stretching Frequencies of Carboxylic Acids as Studied by Density Functional Theory Calculations: Theoretical Basis for Interpretation of Infrared Bands of Carboxylic Groups in Proteins

Abstract

Carboxylic groups (COOH) of Asp and Glu side chains often function as key components in enzymatic reactions, and identifying their H-bond structures in the active sites is essential for understanding the reaction mechanisms. In this study, the correlation between the H-bond structures and the C=O stretching (nuC=O) frequencies of COOH groups was studied using density functional theory calculations. The nuC=O frequencies and their shifts upon OH deuteration were calculated for model complexes of acetic acid and propionic acid H bonded at different sites with various compounds. Calculation results together with some experimental data showed that, upon direct H bonding at the C=O group, the nuC=O frequencies downshift from the free value (1770-1780 cm(-1) in an Ar matrix) to 1745-1760 cm(-1), while H bonding at the OH hydrogen induce even larger downshifts to provide the frequencies at 1720-1745 cm(-1). In contrast, when the COH oxygen is H-bonded, the nuC=O frequencies upshift to 1785-1800 cm(-1). In double and multiple H-bond forms, H-bonding effects at individual sites are basically additive, and complexes in which the C=O and the OH hydrogen are simultaneously H bonded exhibit significantly low nuC=O frequencies at 1725-1700 cm(-1), while complexes H bonded at the oxygen of the COH in addition to either at the C=O or the OH hydrogen exhibit medium frequencies of 1740-1765 cm(-1). The nuC=O frequencies linearly correlate with the C=O lengths, which are changed by H bonding at different sites. Upon OH deuteration, all the complexes showed nuC=O downshifts mostly by approximately 10 cm(-1) and in some cases as large as approximately 20 cm(-1), and hence deuteration-induced downshifts can be a good indicator, irrespective of H-bond forms, for assignments of the nuC=O bands of carboxylic groups. The results in this study provide the criteria for determining the H-bond structures of Asp and Glu side chains in proteins using their nuC=O bands in Fourier transform infrared spectra.

Theoretical Characterization of Hydrogen Bonding Interactions between RCHO (R = H, CN, CF3, OCH3, NH2) and HOR′(R′ = H, Cl, CH3, NH2, C(O)H, C6H5)

“…Consistent with bond elongation of C=O group, the stretching frequency is red shifted and the values, υ range between 12.57 to 94.68 cm −1 (table S22). The red shift of C=O stretching frequencies has also been reported by Takei et al in their DFT study on hydrogen bonded carboxylic acid· · · H-OR complexes 90. For example, when acetic acid accepts a proton from water or ethanol, its C=O bond length was lengthened by 0.007 Å and the shift of frequency was by −27 cm −1 from the free acetic acid.…”

Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating

“…For such low vibrational energy to occur, the C=O group must interact with an H-bonding donor and the O-H group must be H-bonded to a strong acceptor (29,30). νC=O frequencies lower than 1,700 cm −1 have been reported for carboxylic groups only when the H-bonding donor is the NH 3 + group from a lysine (29, 30) or when the H-bond acceptor is a COO − group (43).…”

“…The groups accepting and donating the proton from and to the SB are yet unknown, but prime candidates are the terminal carboxylic groups of aspartate or glutamate residues and their corresponding acids as in other well-characterized rhodopsins. IR difference spectroscopy is particularly suited for the identification of protonation changes (26)(27)(28) because the C=O stretching vibration (νC=O) of protonated carboxylic groups appears in the 1,780 to 1,690 cm −1 frequency range (29,30). The vibrational bands in the carboxylic region of the four intermediate states exhibit significant spectral overlap ( ) bands were resolved (Fig.…”

Fourier transform infrared spectroscopy of special pair bacteriochlorophylls in homodimeric reaction centers of heliobacteria and green sulfur bacteria

“…In contrast, the former signal showed that almost no dichroism, indicative of a nearly parallel orientation of the C=O bond. Assignment to COOH vibrations that show C=O bands in the similar region (Takei et al 2008) was dismissed by the observation of only minor downshifts (\2 cm -1 ) upon deuteration (Noguchi et al 1997) in comparison with an expected downshift by *10 cm -1 for a COOH group. From the significant difference in hydrogen bonding interactions and orientations between these two 13 2 -ester C=O groups, it was suggested that one of the signals originates from the 13 2 -ester C=O groups of P798, while the other is attributed to the ester C=O group of an adjacent pigment (Noguchi et al 1997).…”