Parag Acharya

Computational and NMR study of quaternary ammonium ion conformations in solution

Conformations around C–N bonds at the quaternary centre in tetraalkylammonium ions in water solution are investigated. Structures of Me4N+, Et4N+, n-Pr4N+, n-Bu4N+, and n-Pe4N+ are calculated using quantum mechanical HF and DFT methods together with the PCM solvent model. Relative solvation free energies of tetraalkylammonium ions are further estimated from microscopic molecular dynamics free energy perturbation simulations using the Gromos-87 and Amber-95 force fields. The predicted free energy difference in solution between two stable conformations of Et4N+, D2d and S4, is 0.6–1.0 kcal mol−1 (in favour of D2d), which is in quantitative agreement with the recent Raman spectroscopy results. The energies of the g+g− conformations of Et4N+ are 3.6–4.0 kcal mol−1 higher. The ions with longer hydrocarbon chains show quite similar energy gap between D2d and S4. The torsion barrier for a two-step interconversion between the D2d and S4 structures is 9.5 kcal mol−1 (HF/6-31G(d) calculations). The computational results are augmented by NMR measurements of the Et4N+–I− salt in aqueous solution, which predict a symmetric structure of Et4N+ in water. However, the D2d and S4 conformers are not discernible due to presumably high similarity of chemical shifts. The calculated conformational energetics in solution together with previously observed D2d, S4 and high-energy g+g−-type structures of Et4N+, n-Pr4N+, and n-Bu4N+ in the solid state indicate that the carbon chain conformations at the quaternary ammonium centre sensitively depend on the actual microenvironment.

MOLECULAR MODELLING OF 2′-OH MEDIATED HYDROGEN BONDING IN RIBONUCLEOS(T)IDES BY NMR CONSTRAINED AM1 AND MMX CALCULATIONS

The intra- and intermolecular hydrogen bonding (ΔGº298K ≈ 2, kcal mol−1) of 2′-OH in nucleos(t)ides has been reported by the temperature- and concentration-dependent NMR study in conjunction with dihedral dependence of the NMR derived both endo (3 J H,H)- and exocyclic (3 JH,OH) coupling constants, nOe contacts and lineshape analyses of hydroxyl protons for EtpA (1), 3′-dA (2), rA (3), 2′-dA (4) [Fig. 1] in DMSO-d 6 at 500 MHz. Figure 1. The schematic representation of the bias of the dymanic two-state pseudorotational equilibrium between the North-type (N, C2′-exo -C3′-endo) and the South-type (S, C3′-exo-C2′-endo) [3a] pseudorotamers of the sugar moeity for EtpA (1), 3′-dA (2), rA (3), 2′-dA (4) and torsion (Φ) around C2′/3′-O bond viz. Φ1 = ΦH2′‒C2′‒O‒H and Φ2 = ΦH3′‒C3′‒O‒H except in 1 where the torsion across C3′-O3′ bond is actually ϵ− [C4′-C3′-O3′-P].

DO THE 16 MER, 5′-GUGGUCUGAUGAGGCC-3′ AND THE 25 MER, 5′-GGCCGAAACUCGUAAGAGUCACCAC-3′, FORM A HAMMERHEAD RIBOZYME STRUCTURE IN PHYSIOLOGICAL CONDITIONS? AN NMR AND UV THERMODYNAMIC STUDY

In a wide range of salt concentrations, 10–30 mM phosphate buffer containing up to 0.5 M Li2SO4 and 300 mM NaCl, 7.5 mM Mg2+, pH 5.5–7.5, a mixture of the 16 mer and the 25 mer RNA strands does not form a hammerhead in any amount detectable by NMR at 600 MHz. The imino-, amino-, aromatic- and anomeric protons in the NMR spectra of both the 16 mer and the 25 mer RNA have been assigned separately. Both the 16 mer and the 25 mer RNA both take up very stable hairpin structures, and when mixed together there is no major change of conformation in neither oligo-RNA.

AN ENERGETIC CORRELATION OF AB INITIO AND NMR STUDIES OF THE 3′-GAUCHE EFFECT IN 3′-SUBSTITUTED THYMIDINES

A straightforward correlation of our experimental NMR findings on 3′-substituted thymidine derivatives with that of the ab initio calculations shows that (i) the ΔG of N ← S equilibrium in nucleoside can be predicted from the ab initio calculated ΔE S-N obtained from 6-311++G** level of theory; (ii) the substituent-dependent steric and stereoelectronic effects on the bias of the two-state N ← S equilibrium in nucleosides can also be predicted from the ab initio calculations with sufficiently large basis functions, and (iii) the necessity of mimicking the solvation behaviour of the experimental NMR measurement condition in the ab initio calculations of biomolecules is also emphasized.