Comparison of the Structures and Vibrational Modes of Carboxybiotin and N-Carboxy-2-imidazolidone

Abstract

The spontaneous decarboxylation of N-carboxy-2-imidazolidone (a model for carboxybiotin) and N(1‘)-carboxybiotin can be followed at high pH by Raman and FTIR spectroscopies. The major bands associated with vibrations of the carboxylate group have been assigned on the basis of quantum mechanical calculations of N-carboxy-2-imidazolidone and N(1‘)-carboxy-2-methylbiotin. The carboxylate modes are the asymmetric stretch, coupled to the ureido carbonyl stretch, near 1710 cm-1, the symmetric stretch near 1340 cm-1, and the −CO2 - scissoring motion near 830 cm-1. In the case of carboxybiotin, the last two modes are strongly coupled with biotin ring modes. All three carboxylate modes disappear as spontaneous decarboxylation occurs, to be replaced by features attributable to the noncarboxylated ring structures.The HF/6-31G* optimized structure of 2-methylbiotin revealed that the ureido ring portion is essentially planar, in accord with a number of X-ray crystallographic structures of biotin compounds. However, calculations at this level and at the B3LYP/6-31+G(d) level (using density functional theory) predict that the ureido ring in biotin puckers upon carboxylation. Comparison of the structures of carboxybiotin and carboxyimidazolidone, derived at the HF/6-31G* level, indicates that lengths of the ring-nitrogen-to-carboxylate bonds are equal and that the torsional angles about this linkage are very similar. This strong structural similarity provides a rationale for the observation that, at high pH, the spontaneous rates of decarboxylation of these two molecules are very similar.

Kinetics and Mechanism for CO2 Scrambling in a N-Carboxyimidazolidone Analogue for N1-Carboxybiotin

“…The carbonyl band at 1700 cm -1 remains nearly unchanged by isotope labeling at the carboxyl carbon, demonstrating the carboxylation does not directly involve the carbonyl group but rather occurs at the nitrogen center. These isotope-dependent vibrational assignments are consistent with those made by Clarkson and Carey 1 (a) Infrared spectra of 1 (dashed) and 2 (solid), showing appearance of the −CO 2 bands (*) at 1633 and 810 cm -1 .…”

Functionalized Surfaces of Mixed Alkanethiols on Gold as a Platform for Oligonucleotide Microarrays

“…However, the peak becomes broad and asymmetric with increasing X 1 sol , and the additional intensity (broadening) seen on the low-frequency side suggests that a part of the oligomer fold in a disordered, amorphous-like, conformation . The biotin moiety displays unique peaks at 1711, 1432, and 1267 cm -1 , respectively . The integrated areas of the 1711, 1432, and 1267 cm -1 peaks also can be used to follow the change in composition with increasing X 1 sol .…”

Characterization of the Carboxylate Delivery Module of Transcarboxylase: Following Spontaneous Decarboxylation of the 1.3S-CO2- Subunit by NMR and FTIR Spectroscopies

“…All the subunits have been cloned into and purified from Escherichia coli, and thus each half-reaction can be studied separately. In the present work, we continue our analysis of the smallest subunit of TC, the "carboxylate shuttle" 1.3S (2)(3)(4)(5). The biotinyl or 1.3S subunit is an 123-amino acid monomer (M r ∼ 12 600 Da), with its biotin cofactor covalently bound to the -amino group of Lys-89, which lies in the conserved sequence Ala-Met-Lys-Met (6).…”

“…In the present work, we continue our analysis of the smallest subunit of TC, the “carboxylate shuttle” 1.3S ( − ). The biotinyl or 1.3S subunit is an 123-amino acid monomer ( M r ∼ 12 600 Da), with its biotin cofactor covalently bound to the ε-amino group of Lys-89, which lies in the conserved sequence Ala−Met−Lys−Met ().…”