Ab initio Hartree-Fock Investigation of 2-Methylindole-3-acetic Acid

The potential energy surface (PES) of 2-methylindole-3-acetic acid (2-Me-IAA) has been investigated via RHF/6-31G* and RHF/6-31++G** calculations. With both basis sets, only three symmetry unique local minima with syn orientation of the COOH group are contained in the PES. A network of reaction paths connects these energy minima. One symmetry unique energy minimum has an extremely low barrier to the adjacent global minimum. Comparison with unsubstituted IAA and its alkylated as well as halogenated derivatives substituted at positions 4, 5, 6, and 7 shows that the PES of 2-Me-IAA is quite different. This is in accord with its significantly lower auxin activity and weaker binding to auxin binding protein 1 (ABP1)

Combined Ab initio SCF and Molecular Mechanics Studies of Propionic and Isobutyric Acids and Their Indole Derivatives Related to the Phytohormone Auxin (Indole-3-acetic Acid)

Detailed conformational analyses of propionic and isobutyric acids were performed to contribute to a better understanding of the stereochemical characteristics of biologically active indole-3-aliphatic acids. The studies are based on ab initio SCF (RHF/6-31G*) and molecular mechanics (force fields used: MM2, MM3, CFF91, AMBER, CVFF, ESFF) methods. The results obtained with the CFF91 and MM3 force fields revealed the best agreement with the experimental values and those from ab initio calculations. Normal mode frequencies in the harmonic oscillator approximation were calculated for the geometry optimized conformers with Cs symmetry of these compounds as well as of indole-3-acetic acid (IAA) and some of its biologically important derivatives (4-Cl-IAA, 6-Cl-IAA, 7-Cl-IAA, 4-Me-IAA) and indole-3-isobutyric acid (IIBA). The influence of the indole ring on the C=O and O–H stretching frequencies was analyzed. A small decrease of the C=O frequency was determined in the indole-3-acetic acid derivatives and a larger one in indole-3-isobutyric acid

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed