Alberte Pullman

N- versus O-proton affinities of the amide group: Ab initio electrostatic molecular potentials

Abstract The electrostatic molecular potentials arising from ab initio LCAO SCF wavefunctions with two different gaussian basis sets are used to discuss the protonation of formamide. Oxygen protonation is clearly favoured.

Success of the PCILO method and failure of the CNDO/2 method for predicting conformations in some conjugated systems

Abstract Contrary to the CNDO/2 method, the PCILO method accounts correctly for the preferred conformation of glyoxal, butadiene, benzaldehyde, benzoic acid, biphenyl and 2,2′-difluorobiphenyl.

Ab initio investigation of the energy and electronic evolution upon progressive solvation of ammonium ions

Abstract The evolution of the energies of stepwise addition of n = 1 to 5 molecules of NH 3 or H 2 O to NH 4 + , computed in an STO 3G basis set, are shown to reproduce all the qualitative features of the corresponding experimental data and the numerical error in the energy values is shown to decrease with increasing n . The evolution of the structure of the solvated ion upon increasing solvation is followed. The reasons for the initial preference of NH 4 + for NH 3 over H 2 O and the crossing-over of the preferential affinities in the second shell are shown to reside in the crossing-over of the order of the values of the Coulomb component of the binding energies.

Ab initio molecular electrostatic potentials

The ab initio isopotential map of guanine is given and compared to that of adenine.It shows that in contrast to the situation in adenine, the most basic site of guanine is N7 with a secondary potential minimum at O6. These results as well as those concerning the secondary out-of-plane attractive regions over the NH2 group and C8 H bonds of the two molecules are discussed in connection with the available experimental knowledge concerning the bonding of alkylating carcinogens and mutagens.

SCF AB initio study of the protonation of the peptide bond

Abstract The polarization (energy lowering, electronic displacements and induced dipoles) and charge-transfer effects are separately computed for the approach of a proton in various directions towards formamide, and the further effect of the geometrical deformations of the attacked molecule is established. None of these effects appears capable to reverse the prediction made on the basis of electrostatic potentials pointing to the oxygen atom as the primary protonation site.

Cation binding to “crown” ethers: An ab initio model study

Abstract An STO/3G study of the binding of alkali cations to dimethylether is performed. The study of the conformation of free 12-crown-4 and of its Li + complex indicates that a modification of the conformation of the polyether accompanies the complexation.

The gramicidin A channel

The inclusion of the presence and flexibility of the CH2CH2OH end chain in the computation of the energy profile for single occupancy by Na+ of the gramicidin A channel modifies substantially the profile obtained without that chain. The binding site (deepest minimum) in the profile is situated at 10.5 Å from the center of the channel, in satisfactory agreement with the conclusions based on 13C‐NMR studies. The existence of an external minimum at the mouth is confirmed.

A new theoretical index of biochemical reactivity combining steric and electrostatic factors: An application to yeast tRNAPhe

A new theoretical index of the chemical reactivity of sites within macromolecules is developed, which combines both steric and electrostatic factors. It is applied to the study of yeast tRNAPhe and the results obtained are compared with known experimental reactivities. A comparison indicates the superiority of the new index over the sole use of the surface accessibility.

The gramicidin A channel: the energy profile for single and double occupancy in a head-to-head β6.33,3-helical dimer backbone

The energy profile for Na+ in the channel formed by the gramicidin A β‐helical dimer backbone was computed introducing all the terms in the theory of intermolecular interactions. The effect of allowing the ion to reach its successive optimal positions shows the presence of a series of energy minima associated with different carbonyls. The presence of a second ion lowers the central barrier for the first one and facilitates its progression and exit. The energy profile for double occupancy indicates the presence of two symmetrical minima at about 13 Å from the center.

The gramicidin A channel: comparison of the energy profiles of Na+, K+ and Cs+: Influence of the flexibility of the ethanolamine end chain on the profiles

Energy profile Gramicidin A Ethanolamine end Caesium Potassium Sodium Energy barrier Theoretical computation