R. Santamaria

Vibrational spectra of nucleic acid bases and their Watson–Crick pair complexes

The vibrational spectra of the nucleic acid bases adenine, thymine, guanine, and cytosine are calculated in the frame of density functional theory (DFT). In particular we use the Kohn–Sham scheme with gradient corrections for exchange and correlation to determine normal modes, frequencies, and intensities. The DFT results are found to be in good agreement with the experiment. Our computations provide assignments for IR, Raman, and neutron inelastic scattering spectroscopies; yield characteristic vibrational fingerprints of each compound for its identification in larger systems; and show general vibrational trends of nucleic acids. The Kohn–Sham scheme is further applied to obtain the spectra of the Watson–Crick pairs adenine‐thymine and guanine‐cytosine. A large number of monomeric vibrations are recognized in dimers; characteristic vibrations of pairs, which are mainly attributed to hydrogen bridges, are quantified according to changes in normal modes and frequency shifts. Binding and zero‐point vibrational energies are analyzed to establish the stability of the complexes and discuss the quality of the energetic calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 511–530, 1999

A comparative theoretical study of stable geometries and energetic properties of small silver clusters

Abstract The systematic quantum-mechanical investigation of the stable geometries and some energetic characteristics of neutral silver clusters up to the hexamer is performed by the all-electron spin density approach with non-local corrections included. We compare these results with experimental data and with previous calculations on anionic silver clusters. We find that for the hexamer the ground-state geometry of the neutral cluster differs from the geometry of the anionic. For the neutral silver clusters Ag n the transition from a 2D conformation to a 3D occurs at n > 6. The size effects for the atomic fragmentation energy yield opposite alternations for neutral and anionic clusters.

Structural and electronic property changes of the nucleic acid bases upon base pair formation

A systematic study of structures and electronic properties has been carried out for the nucleic acid bases adenine, guanine, thymine, and cytosine and for the base pairs adenine–thymine and guanine–cytosine. We focus our attention on these properties, which experience significant changes when single nucleic bases join to form base pairs. Such properties are expected to play an important role during the formation of the DNA molecule in its B conformation. All‐electron calculations with inclusion of correlation effects were performed according to the local and nonlocal density functional approaches. We compare our results with previous ab initio and semiempirical values and with available experimental data. Advantages and disadvantages for these density functional‐based methods are discussed. We conclude that applications of such models to investigate larger compounds of a similar nature are promising.

Non-additive forces in atomic clusters: The case of Ag n

The closed recurrence formula which expresses the energy of m-body interactions through the energies of 2-, 3- and (m - 1)-body ones is obtained. The m-body contributions to the interaction energy of silver clusters are calculated by the all-electron non-local spin density method. The importance of not only 3- but also 4- and 5-body forces for cluster stability has been revealed. The stable geometry of planar and spatial silver clusters is determined by the competition of attractive additive forces and repulsive non-additive forces. The larger magnitude of non-additive forces for three-dimensional conformations in comparison with two-dimensional ones is the reason that for Ag n with n = 4-6 the most stable geometries are planar.

MOLECULAR DYNAMICS STUDY OF THE AG6 CLUSTER USING AN AB INITIO MANY-BODY MODEL POTENTIAL

A general approach to construct a model potential with parameters fitted to ab initio energy surfaces, including many-body nonadditive effects, developed in our previous works is applied to the Ag6 cluster. A molecular dynamics study of structural and dynamical properties of this cluster is performed using such a potential. Two new stable two-dimensional isomers with C2v and C2h symmetries are identified as local minima of the potential surface using the simulated quenching technique. An analysis of the thermal stability as a function of the cluster temperature reveals interesting features in the meltinglike transition of Ag6. A two-step isomerization phenomenon is observed: at temperatures around 300 K, the cluster structures fluctuate among two-dimensional isomers, at higher temperatures (500 K), fast transitions occur between two- and three-dimensional cluster configurations. The simulation was extended up to the cluster fragmentation which is observed through dimer evaporation.

Molecular electrostatic potentials and Mulliken charge populations of DNA mini-sequences

Abstract Molecular electrostatic potentials (MEPs) are used to investigate the biochemical reactivity of DNA nucleic acid bases (NABs). As a complementary scheme, a Mulliken population analysis is performed to determine internal charge distribution changes when nucleic acids take part in pair complexes and DNA mini-sequences. From the fact that MEPs are capable enough for predicting the formation of different hydrogen bonded pairs among NABs, it is inferred that for these compounds the electrostatic force plays a dominant role. Particular attention is paid to Watson–Crick dimers as they exhibit different preferred sites for an electrophilic attack to these of single nucleic acids. Finally, from the mini-sequences studied here, it is concluded that recognition of DNA segments proceeds at relatively short distances as a result of a poor influence of NABs on sugar and phosphate fragments. All quantum mechanical computations are performed within the density functional formulation.

DFT Study of the Interaction of the HZSM-5 Zeolite with the Benzene Molecule

We have performed density functional theory (DFT) calculations to describe the interaction of an active site of the HZSM-5 zeolite with a benzene molecule. We used a ring of ten SiO4 tetrahedral (10T) units to represent the structure of the HZSM-5 zeolite. The calculations were of the all-electron type, the exchange-correlation contributions were taken into account by means of the BLYP density functional, and orbital basis sets of double numerical polarization quality were employed for all atoms. Starting from the silicalite 10T ring, with silicon atoms at each site, we found the most energetically favored site for the substitution of an aluminum atom by a silicon atom to produce an HZSM-5 ring model, with a Si/Al ratio of 9. In order to simulate the adsorbed state of benzene onto the zeolite, the geometry of the aromatic molecule was fully optimized in its interaction with the zeolite model, while keeping the ring frozen. The electronic structure of the benzene-HZSM-5 complex was then analyzed and discussed. Our results account for a significant interaction between the acid proton from the HZSM-5 cavity with benzene, shown by changes of the-bond cloud of benzene, which would lead to an active carbocationic moiety. c 2000 John Wiley & Sons, Inc. Int J Quantum Chem 80: 125-132, 2000

Vibrational circular dichroism and IR absorption spectra of amino acids: a density functional study.

With density functional theory, vibrational circular dichroism (VCD) and infrared absorption (IR) spectra are obtained at the B3LYP/CC-pVTZ level of theory for 20 alpha-amino acids. The contribution of different vibration modes to the IR and VCD spectra is analyzed. Overall agreement between calculated results for amino acids in gas phase with the available experimental VCD data for matrix-assisted amino acid films is found. The analysis of the calculated IR and VCD spectra indicates that the functional groups in the backbones and side chains of amino acids contribute differently to the spectra line shape. It is obtained that molecular torsions are the characteristic vibrations of the amino acids at the low-frequency regime, whereas the bending of bond angles, the out-of-plane wagging of individual atoms, and some stretching modes dominate the intermediate frequency range. Specific modes like NH(2) scissoring, CO bond stretching, and the (symmetric and asymmetric) stretching of the hydrogen atoms in the NH(2) and OH groups characterize the high-frequency regime. A general trend emerging from these calculations indicates that the rho(OH) rocking and nu(C=O) stretching modes have the highest intensity in the VCD spectra of most amino acids.

STRUCTURES AND ENERGETIC PROPERTIES OF B-DNA NUCLEOTIDES

Abstract A density functional study is carried out for the B-DNA nucleotides adenine, thymine, cytosine, and guanine and some of their modifications (tautomeric and methylated forms). The local spin density method is applied to find gas-phase structures. Gradient corrections for exchange and correlation terms are included to compute energetic features such as total, nonlocal, interaction, and reorganization energies. Special attention is paid to the relative stabilities among naturally occurring nucleotides and some tautomeric forms. Structural stability and flexibility in terms of reorganization and interaction energies, of concern in selective and mutation processes, is also discussed for nucleic acid bases of different nucleotides.

Pressure and size effects in endohedrally confined hydrogen clusters

Density functional theory is used to carry out a systematic study of zero-temperature structural and energy properties of endohedrally confined hydrogen clusters as a function of pressure and the cluster size. At low pressures, the most stable structural forms of (H(2))(n) possess rotational symmetry that changes from C(4) through C(5) to C(6) as the cluster grows in size from n=8 through n=12 to n=15. The equilibrium configurational energy of the clusters increases with an increase of the pressure. The rate of this increase, however, as gauged on the per atom basis is different for different clusters sizes. As a consequence, the size dependencies of the configurational energies per atom at different fixed values of pressure are nonmonotonic functions. At high pressures, the molecular (H(2))(n) clusters gradually become atomic or dominantly atomic. The pressure-induced changes in the HOMO-LUMO gap of the clusters indicate a finite-size analog of the pressure-driven metallization of the bulk hydrogen. The ionization potentials of the clusters decrease with the increase of pressure on them.