Julio Marañon

Confined water in nanotube

Abstract In the present paper we show the properties of water confined in a hydrophobic and hydrophilic flexible prismatic network obtained in a molecular dynamics study. The confined water studied here produces very similar properties concerning density profile, water structure and ordering, and hydrogen bonds as a free water. In the hydrophilic simulation pressure and surface tension are larger than the hydrophobic ones. In the central region of the nanotube the mobility parallel to the surface is greater than the mobility of the corresponding bulk fluids.

A theoretical conformational analysis of morpholine

Abstract The CNDO and INDO methods were used for a theoretical conformational analysis of morpholine. The agreement between the methods is very satisfactory. Some results are also compared with the available experimental data.

Atomic orbitals of the nonrelativistic hydrogen atom in a four‐dimensional Riemann space through the path integral formalism

The Kustaanheimo–Stiefel transformation together with the well‐known expansion of the kernel of an isotropic harmonic oscillator is used to generate the atomic orbitals of the nonrelativistic hydrogen atom in a four‐dimensional Riemann space through the path integral formalism. Group theoretical implications of the present problem are briefly discussed.

Semiempirical CNDO/2 calculation of the electronic structure of the DNA molecule I. Ground state potential curves; Tunneling and tautomeric equilibrium in the NHN and OHN bonds of the adenine-thymine base pair

Abstract The ground electronic state structure of the double hydrogen bond in the adenine-thymine nucleotide base pair has been investigated in the semi-empirical CNDO/2 approximation. Potential curves are obtained for several nuclear configurations characterizing both, single and simultaneous tautomeric rearrangements of the NHN and NHO bonds. The results indicate two relative minima corresponding to the normal and tautomeric forms for the coupled motion of the two protons. For the single displacement, the bond energy analysis shows that W A-T (R, r) is repulsive in such a way that W A−T (R, r) + W A−H (R, r) -I- W T−H (R, r) shows only one minimum. These results are in agreement with earlier studies on the hydrogen bond in the guanine-cytosine base pair utilizing ab initio techniques. The atom-atom bond index curves for several pairs of atoms are given and some molecular orbitals have been correlated in the normal and tautomeric forms. Estimates are made within the WKB approximation of the tunneling rate and tunneling probability. The magnitude of the equilibrium distribution between the normal and tautomeric proton positions of minimum energy is consistent with the idea that simultaneous double proton tunneling in the ground state is not significant, thus ruling out a possibility for an error mechanism in the genetic code.

Feynman path integral and the Hückel model

The propagator of the Huckel model is obtained through the Feynman path integral formulation and the corresponding secular equations are generated via the saddle point approximation of the Gaussian integrals appearing in the path integral. The present formalism appears as a practical tool for the evaluation of thermodynamic and magnetic properties of molecular systems and constitutes an alternative method to those given previously using the Green’s function and Dyson equation to get self‐energies and reactivity indices.

Quantum fluctuations in molecules

Abstract The resonance phenomenon and the double hydrogen bonding of the adenine-thymine base pair are discussed in the light of non-linear wave equations. A link is established with bifurcation and catastrophe theory and a connection with vacuum state fluctuations is investigated.

Path-integral approach to a finite many-body problem

Abstract The Feynman path integral is used to show the equivalence between a finite many-body problem (Huckel model) for a nonrelativistic and nonspin molecular system of N electrons and N one-dimensional Ising models.

The hydrogen atom as a projection of an homogeneous space

The Kustaanheimo-Stiefel transformation as applied to the nonrelativistic hydrogen atom provides one of the rare examples of a free particle moving on a four-dimensional homogeneous space.

Molecular dynamics simulation with atomic partial charges update of erythtrol in water

Abstract A series of molecular dynamics simulations of erythrol in water was carried out with the purpose of analysing the influence of a change in molecular conformation on atomic partial charge and its consequences on the simulation. Three cases were considered: one in which the charge was kept constant, as is regularly done; in the other two cases the charge was updated every 1000 and every 100 steps, respectively. Charges were recalculated by a quantum-mechanical semiempirical method and converged to a stable value in a relatively short simulation time. The results are analysed in terms of conformation, atom-water oxygen radial distribution functions, and hydrogen-bonding network. Some properties are almost independent of the charge assignment but others show a distinct behaviour depending on whether the charges remain fixed or are updated. No significant differences were observed with respect to update frequency.

Adenine-thymine molecular dynamics simulation. Conformation, hydration and magnetic behaviour

Abstract In order to contribute to the knowledge of the properties of hydrogen bonds in macromolecular systems we performed molecular dynamics simulations of the pair adenine-thymine base pair in SPC/E water. Interaction parameters of adenine and thymine atoms are those corresponding to the GROMOS force field, except for atoms along the hydrogen bonds. In such cases the repulsion coefficient of the van der Wals components of the potential were taken as twice the regular coefficients. Atomic partial charges were calculated with the GAUSSIAN94 package including solvent effects. Simulations were done with the GROMOS86 simulation package working in the isothermal-isobaric ensemble at 30 K and 1 atm. Two torsional angles were selected to describe the twisting of the ring defined by the two hydrogen bonds and the atoms involved. The molecule was found to be mainly in two conformations, defined by the above-mentioned angles. Radial distribution functions of water oxygen atoms around different solute atoms suggest a non-polar behaviour but with little effect on the hydrogen bond network and the diffusion coefficient of bulk water. The adenine-thymine electrooptic and magnetic properties show slight changes during the overall run.