Biomedical subjects

Massimo Mella

Publications and source records attributed to Massimo Mella.

6 recordsLinked to original sources

PubMed2006

Study of the structure, energetics, and vibrational properties of small ammonia clusters (NH3)n (n = 2-5) using correlated ab initio methods.

Equilibrium geometries, interaction energies, and harmonic frequencies of (NH3)n isomers (n = 2-5) have been computed using correlated calculations (MP2) in conjunction with Dunning's aug-cc-pVXZ (X = D, T, Q) basis sets and the Counterpoise procedure. Whenever available, literature values for the binding energy and geometry of dimers and trimers agree well with our data. Low lying isomers for (NH3)4 and (NH3)5 have been found to have similar binding energies (roughly 16 and 20 kcal/mol for the tetramer and pentamer, respectively), perhaps suggesting the presence of a very smooth energy landscape. Using BSSE corrected forces or freezing the monomer structure to its gas phase geometry have been found to have only a weak impact on the energetic and structural properties of the clusters. The effect of zero-point energy (ZPE) on the relative stability of the clusters has been estimated using harmonic frequencies. The latter also highlighted the presence of vibrational fingerprints for the presence of double acceptor ammonia molecules. Many-body effects for (NH3)n isomers (n = 2-4) have been investigated to explore the possibility of building a pairwise interaction model for ammonia. In the frame of the work presented, we have found the 3-body effect to account for 10-15% of the total interaction energy, whereas the 4-body effects may be neglected as first approximation.

Ammonia↗

PubMed2006

Alternative low-energy mechanisms for isotopic exchange in gas-phase D2O-H+(H2O)n reactions.

Molecular-dynamics (MD) trajectories and high-level ab initio methods have been used to study the low-energy mechanism for D(2)O-H(+)(H(2)O)(n) reactions. At low collisional energies, MD simulations show that the collisional complexes are long-lived and undergo fast monomolecular isomerization, converting between different isomers within 50-500 ps. Such processes, primarily involving water-molecule shifts along a water chain, require the surmounting of very-low-energy barriers and present sizable non- Rice-Ramsperger-Kassel-Marcus (RRKM) effects, which are interpreted as a lack of randomization of the internal kinetic energy. Interestingly, the rate of water shifts was found to increase upon increasing the size of the cluster. Based on these findings, we propose to incorporate the following steps into the mechanism for low-energy isotopic scrambling these D(2)O-H(+)(H(2)O)(n) reactions: a) formation of the collisional complex [H(+)(H(2)O)(n)D(2)O]* in a vibro-rotational excited state; b) incorporation of the heavy-water molecule in the cluster core as HD(2)O(+) by means of isomerization involving molecular shifts; c) displacement of solvation molecules from the first shell of HD(2)O(+) inducing de-deuteration (shift of a D(+) to a neighbor water molecule); d) reorganization of the clusters and/or expulsion of one of the isotopic variants of water (H(2)O, HDO or D(2)O) from the periphery of the complex.

Journal Article↗

PubMed2006

Efficient calculation of low energy statistical rates for gas phase dissociation using umbrella sampling.

Monte Carlo (MC) simulations can be used to compute microcanonical statistical rates of gas phase dissociation reactions. Unfortunately, the MC approach may suffer from a slow convergence and large statistical errors for energies just above the dissociation threshold. In this work, umbrella sampling is proposed as a device to reduce the statistical error of MC rate constants. The method is tested by computing the classical dissociation rate for the reaction [H5O2+]* --> H2O + H3O(+) over the range of internal energy 38 < E < or = 100 kcal/mol. Comparing with other literature methods, it is found that umbrella sampling reduces the computational effort by up to two orders of magnitude when used in conjunction with a careful choice of sampling distributions. The comparison between MC rate constants and classical Rice-Ramsperberg-Kassel harmonic theory shows that anharmonicity plays an important role in the dissociation process of the Zundel cation (H5O2+) at all energies.

Journal Article↗

PubMed2005

Predicting atomic dopant solvation in helium clusters: the MgHe(n) case.

We present a quantum Monte Carlo study of the solvation and spectroscopic properties of the Mg-doped helium clusters MgHe(n) with n=2-50. Three high-level [MP4, CCSD(T), and CCSDT] MgHe interaction potentials have been used to study the sensitivity of the dopant location on the shape of the pair interaction. Despite the similar MgHe well depth, the pair distribution functions obtained in the diffusion Monte Carlo simulations markedly differ for the three pair potentials, therefore indicating different solubility properties for Mg in He(n). Moreover, we found interesting size effects for the behavior of the Mg impurity. As a sensitive probe of the solvation properties, the Mg excitation spectra have been simulated for various cluster sizes and compared with the available experimental results. The interaction between the excited 1P Mg atom and the He moiety has been approximated using the diatomics-in-molecules method and the two excited 1pi and 1sigma MgHe potentials. The shape of the simulated MgHe50 spectra shows a substantial dependency on the location of the Mg impurity, and hence on the MgHe pair interaction employed. To unravel the dependency of the solvation behavior on the shape of the computed potentials, exact density-functional theory has been adapted to the case of doped He(n) and various energy distributions have been computed. The results indicate the shape of the repulsive part of the MgHe potential as an important cause of the different behaviors.

Journal Article↗

PubMed2005

Electronic quantum Monte Carlo calculations of atomic forces, vibrations, and anharmonicities.

Atomic forces are calculated for first-row monohydrides and carbon monoxide within electronic quantum Monte Carlo (QMC). Accurate and efficient forces are achieved by using an improved method for moving variational parameters in variational QMC. Newton's method with singular value decomposition (SVD) is combined with steepest-descent (SD) updates along directions rejected by the SVD, after initial SD steps. Dissociation energies in variational and diffusion QMC agree well with the experiment. The atomic forces agree quantitatively with potential-energy surfaces, demonstrating the accuracy of this force procedure. The harmonic vibrational frequencies and anharmonicity constants, derived from the QMC energies and atomic forces, also agree well with the experimental values.

Journal Article↗

PubMed2005

Improved importance sampling distribution for rate constant calculation.

An efficient method to compute the thermal rate constant for rare events within the correlation function C(t) approach is presented. This method, which is based on a modification of the sampling function used to evaluate the dynamical correlation function C(t), can be applied to high-dimensional systems having a rough energy landscape without previous knowledge on the transition states location. In this work, the sampling of a Boltzmann-like distribution for the linear momenta with a lower inverse temperature (beta(*)=1/kT(*)) than the correct one (beta=1/kT) is proposed as a way to increase the number of reactive trajectories. The mismatch between the beta(*) and beta distributions is then corrected by a reweighting procedure which allows one to obtain the exact correlation function C(t). The efficiency of this scheme in computing the rate of a particle jumping across the barrier of a simple 2D double well potential is improved by a factor 4-25 depending on the relative value of the original beta and modified beta(*) temperatures. When merged with the "puddle potential" method [S. A. Corcelli, J. A. Rohman, and J. C. Tully, J. Chem. Phys., 118, 1085 (2003)], the new importance sampling function improves the efficiency of the correlation function approach by a factor 16-800 with respect to the unbiased sampling. To test the method in a more challenging case, the previous model system was extended by adding six harmonically restrained particles, each one interacting with the diffusing particle. This model introduces both the possibility of energy exchange and a rougher energy landscape. The new sampling function alone is found to produce an improvement in efficiency of, at least, an order of magnitude when compared with the unbiased case; when merged with the puddle potential method, a 400-fold saving in computer time is found.

Journal Article↗