Molecular interactions in a homogeneous electric field: the (HF)2 complex

Alagona, Giuliano; Cammi, Roberto; Ghio, Caterina; Tomasi, Jacopo

doi:10.1007/bf01374586

Cited by 8 publications

(3 citation statements)

References 57 publications

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“…All the simulations were carried out with AMBER 5.0 22 employing the second generation force field, by Cornell et al 12. This choice was dictated by the fact that previous studies of ours 23, 24, as well as of other authors 13, showed a satisfactory performance of this force field in the evaluation of the stability of either H‐bonded or stacked complexes. Furthermore, the results obtained with AMBER turned out to be even better than those computed with other force fields 13, 24.…”

Section: Computational Detailsmentioning

confidence: 99%

5‐fluorouracil dimers in aqueous solution: molecular dynamics in water and continuum solvation*

Alagona¹,

Ghio²,

Monti³

2002

Int J of Quantum Chemistry

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ABSTRACT:The interactions established in aqueous solution by a variety of 5-fluorouracil (FU) dimers in water were examined to elucidate the strength of drug-solvent interactions. Molecular dynamics simulations for clusters made up of the FU dimer alone or embedded in 4, 12, and 100 waters at high temperature, followed by simulated annealing, allowed comparing the dimer structures in the different environments, the solute-solvent radial distribution functions and the cluster energetics. The statistics were consistent with those obtained from a 10 ns MD simulation in the NPT ensemble in 385 waters. Interestingly, the F atom was never preferred to O as H-bond acceptor either in the dimer or in water. The interactions within the dimers turned out to be remarkably affected by the presence of the solvent: stacked structures, unfavorable in the gas phase, prevailed even in the presence of four water molecules. The presence of real water molecules is thus of paramount importance to stabilize the system, using molecular dynamics or, alternatively, if affordable, the MP2 level. Geometry optimizations of the clusters at the B3LYP/6-31G * or HF/6-31G * level, in fact, though starting from a stacked hydrated arrangement of the FU dimer, produced almost exactly the same seashell structure. The polarizable continuum model is convenient to compute the solvation free energy of the dimers and clusters at the HF or MP2 level. Also, the partial charge distribution of the clusters can profitably be used to evaluate the solvent effect in the continuum framework.

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Section: Computational Detailsmentioning

confidence: 99%

5‐fluorouracil dimers in aqueous solution: molecular dynamics in water and continuum solvation*

Alagona¹,

Ghio²,

Monti³

2002

Int J of Quantum Chemistry

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“…This investigation, however, directly pertains to the vast literature, which we are not going to review, concerning the electronic and geometrical properties of bimolecular adducts and to the debate about stacked and T-shaped positions, in the gas phase , or in solution, , even inside a single molecule. − In addition, it constitutes a natural continuation of our previous studies on H-bonded dimers in the gas phase and in the presence of an external field . For these reasons, the highest level ab initio calculations compatible with the size of the complexes under scrutiny were used, and the counterpoise correction to the basis set superposition error (BSSE) was introduced for test cases in both the HF and MP2 correlated wave functions.…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Investigation of the Methylimidazole−Indole Complexes as Models of the Histidine−Tryptophan Pair

Alagona¹,

Ghio²,

Monti

1998

J. Phys. Chem. A

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Several histidine−tryptophan complexes, derived from the crystal structures available in the Brookhaven Protein Data Bank, have been examined with ab initio theoretical methods (using as model systems 5-methylimidazole and indole, respectively), in order to identify the most favorable arrangements of the two side chains, elucidating also the strength and the nature of the intermolecular interaction established between them. The equilibrium geometries of the isolated partners were optimized at the HF/6-31G* level and the interaction energy of the adducts was computed, employing the 6-31G* basis set with the d exponents reduced to 0.25, thus named 6-31G*(0.25), at the HF and MP2 (frozen-core approximation) levels. For a few typical orientations, the dependence of the interaction energy upon the intermolecular distance, as measured from the ring centroids, was then examined while keeping fixed reciprocal orientations and internal geometries of the partners. There is a fair linear correlation between the equilibrium distances (R eq) at the MP2 level and the experimental (R exp) ones and between the MP2 interaction energies at R eq and those computed at R exp. For three arrangements with a shallow or even repulsive HF interaction energy, the counterpoise correction to the basis set superposition error (BSSE) was introduced both at the HF and MP2 levels, using Pople's 6-31G* standard, 6-31G*(0.25), and Dunning's DZP basis sets, to test the reliability of the results obtained along the whole approaching path. This is made necessary by the noticeable displacement in the equilibrium distances usually found at the various levels. The DZP HF interaction energies turn out to be less affected by BSSEs than the 6-31G* and the 6-31G*(0.25) ones and are located in an intermediate position between them. As a general rule for these complexes, the counterpoise correction is larger at the correlated level; therefore the addition of the correlation effect to the counterpoise-corrected SCF energy produces a curve fairly close to the MP2 one that seems to represent a lower bound to the true interaction energy. Kitaura and Morokuma's decomposition analysis of the interaction energies was also carried out on these typical complexes.

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“…When a molecule is placed under the effect of an applied electric field, its electronic cloud is modified, its nuclear positions are changed, and its vibrational motion is perturbed. [14][15][16][17][18][19][20][21][22][23][24][25][26] All these induced changes can be explained in terms of different contributions to the electrical properties, namely, electronic (P el ), nuclear relaxation (P nr ) and vibrational (P vib ).…”

Section: Introductionmentioning

confidence: 99%

A systematic and feasible method for computing nuclear contributions to electrical properties of polyatomic molecules

Luis

Duran

Andrés

1997

The Journal of Chemical Physics

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An analytic method to evaluate nuclear contributions to electrical properties of polyatomic molecules is presented. Such contributions control changes induced by an electric field on equilibrium geometry ͑nuclear relaxation contribution͒ and vibrational motion ͑vibrational contribution͒ of a molecular system. Expressions to compute the nuclear contributions have been derived from a power series expansion of the potential energy. These contributions to the electrical properties are given in terms of energy derivatives with respect to normal coordinates, electric field intensity or both. Only one calculation of such derivatives at the field-free equilibrium geometry is required. To show the useful efficiency of the analytical evaluation of electrical properties ͑the so-called AEEP method͒, results for calculations on water and pyridine at the SCF/TZ2P and the MP2/TZ2P levels of theory are reported. The results obtained are compared with previous theoretical calculations and with experimental values.

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Molecular interactions in a homogeneous electric field: the (HF)2 complex

Abstract: Summary. The interaction energy of two HF molecules, subjected to a static external field, is analyzed. The analysis aims at the elaboration of simple expressions able to reproduce environmental and substitution effects on noncovalent molecular interactions.

Cited by 8 publications

References 57 publications

5‐fluorouracil dimers in aqueous solution: molecular dynamics in water and continuum solvation*

5‐fluorouracil dimers in aqueous solution: molecular dynamics in water and continuum solvation*

Ab Initio Investigation of the Methylimidazole−Indole Complexes as Models of the Histidine−Tryptophan Pair

A systematic and feasible method for computing nuclear contributions to electrical properties of polyatomic molecules

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