Luis A. Montero

OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach

Density functional theory (B3LYP and BHandHLYP) and unrestricted second‐order Møller–Plesset (MP2) calculations have been performed using 3‐21G, 6‐31G(d,p), and 6‐311 G(2d,2p) basis sets, to study the OH hydrogen abstraction reaction from alanine and glycine. The structures of the different stationary points are discussed. Ring‐like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and very low or negative net energy barriers are obtained depending on the method and on the reacting site. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for B3LYP activation energies are included. A complex mechanism involving the formation of a prereactive complex is proposed, and the rate coefficients for the overall reactions are calculated using classical transition state theory. The predicted values of the rate coefficients are 3.54×108 L⋅mol−1⋅s−1 for glycine and 1.38×109 L⋅mol−1⋅s−1 for alanine.

Multiple Minima Hypersurfaces of Water Clusters for Calculations of Association Energy

Multiple minima of water cluster hypersurfaces are explored to find thermodynamic properties by means of the corresponding partition functions of their canonical distributions. The combination of semiempirical quantum chemical procedures for calculating the cluster energies in local minima of supermolecules and the statistical thermodynamics approach for both the evaluation of macroscopic association energies and the possible reduction by average of absolute errors intrinsic to the parametrized Hamiltonian are shown to provide an appropriate model for comparison between experimental and theoretical results. The method can explicitly take into account environmental effects due to intermolecular interaction. Water trimer and tetramer association energies of 10.9 and 14.1 kJ/mol obtained from virial coefficient calculations compare very well to the values of 10.5 and 16.4 kJ/mol, respectively, found for the theoretical association energies in this paper. c 2000 John Wiley & Sons, Inc. Int J Quantum Chem 79: 8-16, 2000

Basis set superposition error in MP2 and density-functional theory: A case of methane-nitric oxide association

A systematic study of basis set superposition error (BSSE) behavior in H(3)C-H[ellipsis (horizontal)][NO] complexes for both -H...N- and -H...O- orientations were carried out using MP2 and density-functional theory with Poples [6-31G(d,p),6-311++G(nd,nd), where n=1,2,3, and 6-311++G(3df,3pd)] and Dunnings augmented correlation consistent basis sets [aug-cc-pVXZ (X=D and T)]. Corrected and uncorrected counterpoise potential-energy surfaces (PESs) were explored and differences obtained between them indicate that reliable optimizations of these molecular interactions must be carried out in a PES free of BSSE, even in the case of large basis sets and popularly used functionals such as B3LYP. Although all basis used could be always considered within a margin of approximation for representing molecular orbitals and show important values of BSSE, 6-311++G(2d,2p) basis set shows the best results in uncorrected PES with respect to the corrected ones. B3LYP functional produces erratic results: complexes appear repulsive and the intermolecular distances are always large, evidencing the lack of a correct dispersive forces treatment in the original parameterization. According to the MP2 results, the -H...N- interactions appear as slightly more stable than those of the -H...O- orientation.

Clinoptilolite–heulandite polymorphism: structural features from computer simulation

Static lattice computer modelling techniques are applied to investigate the framework and extra-framework cation distribution in clinoptilolite/heulandite zeolitic materials. The results emphasise the close coupling between the framework Al distribution and the location of the extra-framework cations. In the majority of the polymorphs, Al is predicted to be preferentially localised at the T2 and T3 crystallographic sites. Extra-framework cation distributions are often controlled by a strong driving force for the location of Ca2+ close to Al-rich regions. Cation–cation repulsion also play a substantial role in controlling the position of extra-framework cations. We find significant differences in both the distribution of Al in the framework and in the location and distribution of the extra-framework cations depending on the exact composition of the heulandite-structured material considered.

Understanding rhodopsin mutations linked to the retinitis pigmentosa disease: a QM/MM and DFT/MRCI study.

Retinitis pigmentosa (RP) is a pathological condition associated with blindness due to progressive retinal degeneration. RP-linked mutations lead to changes at the retinal binding pocket and in the absorption spectra. Here, we evaluate the geometries, electronic effects, and vertical excitation energies in the dark state of mutated human rhodopsins carrying the abnormal substitutions M207R or S186W at the retinal binding pocket. Two models are used, the solvated protein and the protein in a solvated POPC lipid bilayer. We apply homology modeling, classical molecular dynamics simulations, density functional theory (DFT), and quantum mechanical/molecular mechanical (QM/MM) methods. Our results for the wild type bovine and human rhodopsins, used as a reference, are in good agreement with experiment. For the mutants, we find less twisted QM/MM ground-state chromophore geometries around the C(11)-C(12) double bond and substantial blue shifts in the lowest vertical DFT excitation energies. An analysis of the QM energies shows that the chromophore-counterion region is less stable in the mutants compared to the wild type, consistent with recent protein folding studies. The influence of the mutations near the chromophore is discussed in detail to gain more insight into the properties of these mutants. The spectral tuning is mainly associated with counterion effects and structural features of the retinal chain in the case of the hM207R mutant, and with the presence of a neutral chromophore with deprotonated Lys296 in the case of the hS186W mutant.

Silicon–aluminium distribution in dehydrated calcium heulandite

The distribution of aluminium within the lattice of a model calcium heulandite is considered. Significant segregation of Al to particular sites is noted with T2 being preferentially occupied whereas T4 has a low Al occupancy. T5 is also occupied, in contrast to earlier work on Na-clinoptilolite. The resulting distributions are also significantly different to previous work on Na-clinoptilolite, demonstrating the influence of the Si/Al ratio and cation species on the spatial arrangement of Si and Al in the framework.

Patterns of retinal light absorption related to retinitis pigmentosa mutants from in silico model structures of rhodopsin

Changes induced by mutations in rhodopsin that are associated with the degenerative visual disease retinitis pigmentosa result in an altered pattern of light absorption according to quantum mechanical simulations and reference experimental works. Eleven single‐point mutations associated with retinitis pigmentosa at and in the proximity to the retinal binding pocket of rhodopsin have been modeled in silico and their spectra calculated with the NDOL (Neglect of Differential Overlap accounting L azimuthal quantum number) a priori method. The altered pattern of absorption found would lead to cumulative consequences in energy dissipation with aging. Different energy balances in the case of mutants at the very molecular level, compared to native nonmutated rhodopsin, can cause permanent cellular stress and would play a role in the progression of the retine degenerative process. It could explain the worsening of the pathological condition mostly in adults and suggests the probable beneficial effects of using quenching drugs and protection devices against excess of light in the early stages of life for avoiding or reducing potential damage. Proteins 2004.

Bond order weighted graphs in molecules as structure-property indices

A new topological index is defined. This index can be used in the presence of multiple bonds, considering molecules as weighted graphs, where the elements of the edge set are substituted by bond orders between the connected atoms in the molecule calculated by both empirical and semi-empirical quantum mechanical methods. Good correlations are found between the boiling points of alkenes and the proposed Ω index,which permits one to differentiate between alkenes with different branching, position of the double bonds and geometrical disposition of the groups. Indexes calculated using two different methods (EHT and MNDO without geometry optimization) do not show appreciable differences in regression parameters. Deviations of predicted values in cases where methyl groups are linked to double bonds can be treated with a two-variable regression.

The Bardeen-Cooper-Schrieffer approach to electron correlation in the density matrix formalism

A generalization of the reduced density matrix theory when the number of particles is not fixed is given here. The first and second order reduced density matrices are defined with respect to a Bardeen–Cooper–Schrieffer ground state for molecules with an even number of electrons. This formalism is extended to molecules with an odd number of electrons. Valatin’s generalized Hartree-Fock method is applied to the functional of energy. A new one-particle operator, Vq, is thus obtained. This operator has two new terms. It takes into account all the correlation effects mainly through a new non-local potential Lq — the Exchange and Time Inversion Potential. The operator Vq thus correlates the motion of two particles with anti-parallel spins and determines a new set of spin-orbitals. The new set of equations is established and solved by using the MO-LCAO approximation. The method was tested for several molecules with good results. The calculated vertical ionization potentials compare satisfactorily with the exp...

Theoretical model of internal rotation in monosubstituted derivatives of furfural

The present work explores the effect of substitution in all free positions of furfural on conformational preferences of formyl group by using ab‐initio calculations at the MP2/6‐31G(p,d) level of theory. Theoretical modeling was made in vacuo. The selected substituents were CH3, NH2, NO2 and F groups in 3, 4, 5 and ipso carbonyl positions. Geometries of all derivatives were analyzed and it is ascertained that substitution has not important consequences on furan ring geometry. Differences of energy between OO‐cis and trans conformers and energy barriers between them are described and extreme cases are explained. Interesting features appear in the cases of NH2 and NO2 groups, and particularly when the 3 and ipso carbonyl positions are substituted. Variations in energy barriers are correlated with variations in C2‐C6 distances for the transition states and planar forms. Substitution effect on Mülliken charges are analyzed and related with internal rotation energy barriers and differences between conformers.