Amedeo Palma

Effect of the potential well on low temperature pressure broadening in CO-He

Previously reported low temperature pressure broadening calculations for CO–He interacting via an SCF‐CI potential are compared with new calculations in which the attractive part of the potential is (1) reduced by half and (2) eliminated entirely. Results demonstrate that the attractive well is responsible for low temperature enhancement of pressure broadening cross sections and suggest that agreement with recent experimental values at 4 K can be obtained by a modest reduction, probably within the expected uncertainty, in the attractive part of the SCF‐CI potential.

Theoretical modeling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase.

In this paper, by using the perturbed matrix method (PMM) in combination with basic statistical mechanical relations both based on nanosecond time-scale molecular dynamics (MD) simulations, we quantitatively address the thermodynamics of compound 0 (Cpd 0) formation in horseradish peroxidase (HRP) enzyme. Our results, in the same trend of low-temperature experimental data, obtained in cryoenzymology studies indicate that such a reaction can be described essentially as a stepwise spontaneous process: a first step mechanically constrained, strongly exothermic proton transfer from the heme-H2O2 complex to the conserved His42, followed by a solvent-protein relaxation involving a large entropy increase. Critical evaluation of PMM/MD data also reveals the crucial role played by specific residues in the reaction pocket and, more in general, by the conformational fluctuations of the overall environment in physiological conditions.

Collisional excitation of interstellar water.

Rates for rotational excitation of water molecules in collisions with He atoms have been obtained from a new, accurate theoretical interaction potential. Rates among the lowest 40 ortho levels are given for kinetic temperatures to 1400 K and among the lowest 29 para levels for kinetic temperatures to 800 K.

Molecular and solid-state (8-hydroxy-quinoline)aluminum interaction with magnesium: A first-principles study

The interaction between Mg and (8-hydroxyquinoline)aluminum, Alq3, is investigated via ab initio molecular dynamics based on density-functional theory. We model the Alq3 thin film both with a single Alq3 molecule in vacuo (as is usually done in the literature) and with an Alq3 crystalline structure. Comparing the results from these two models, we show that bulk calculations provide a better description of the chemical processes involved, allowing the Mg atom to react with two neighboring Alq3 molecules, as was alluded to in a previous publication [S. Meloni, A. Palma, A. Kahn, J. Schwartz, and R. Car, J. Am. Chem. Soc. 125, 7808 (2003)]. Moreover, core-level shift calculations are in good agreement with experimental measurements only when using the solid phase approach. We also propose a different interpretation of the Al(2p) experimental core level presented in a previous work [C. Shen, A. Kahn, and J. Schwartz, J. Appl. Phys. 89, 449 (2001)].

Cu++ and Li+ interaction with polyethylene oxide by ab initio molecular dynamics

Equilibrium positions on the Li+–PEO and on the Cu++–PEO ground state potential energy surfaces have been determined by ab initio molecular dynamics. Our results confirm the previously proposed jump mechanism for ion diffusion in polymer electrolytes. The energy barriers for Li+ and Cu++ ionic diffusion along the PEO chain have been estimated.

Collisional excitation of an asymmetric rotor, silicon dicarbide

Rotational excitation rates have been computed for the asymmetric top molecule SiC/sub 2/ in collisions with low-energy He atoms. The intermolecular forces were obtained from an electron gas model, and collision dynamics were treated within the infinite-order sudden approximation. Total excitation rates, i.e., summed over final levels, are expected to be accurate to about 50 percent, and the larger state-to-state rates are likely to be within a factor of about 2 of the correct values, although some of the smaller (and less important) rates may be less accurate. These rates are also thought to reflect, within this level of accuracy, rates for excitation by collisions with H/sub 2/ molecules. 18 references.

Computational study on compound I redox-active species in horseradish peroxydase enzyme: conformational fluctuations and solvation effects.

Molecular dynamics simulations for the compound I species in horseradish peroxidase were carried out over a nanoseconds time-scale. Results indicate that the supramolecular assembly composed of compound I in interaction with highly conserved distal residues (His42 and Arg38) exists in two well-defined conformations basically differing in the local position of the distal histidine (i.e., His42). Furthermore, we observe the presence of a biological channel in the distal side of the heme cavity, between Arg38 and Pro139 residues, that represents a direct link connecting the compound I (CpdI) species to bulk molecules. Our investigation supports the idea that when CpdI is formed, the biological machinery relaxes the local electrostatic forces, opening a structural channel through which an exchange of water molecules with the bulk solvent takes place without any significant kinetic barrier. Interestingly, we also show that the combined effect of enzyme and solvent, modulated by thermal fluctuations, affects the order and the energy difference between the lowest doublet and quartet magnetic states of the CpdI-His42-Arg38 complex. Consequently, when passing from the gas phase to the biological environment, the doublet spin state becomes slightly more stable than the higher spin multiplicity state. The distribution of the perturbed low-lying states energy variation, induced by surrounding fluctuations, yields results rather close to that obtained by other state of the art quantum-mechanics/molecular mechanics calculations, and still in line with previous polarizable continuum calculations.

On the catalytic role of structural fluctuations in enzyme reactions: computational evidence on the formation of compound 0 in horseradish peroxidase

In this study the question as to whether and to what extent horseradish peroxidase (HRP) enzyme structural flexibility affects the free energy barrier for the formation of the key intermediate compound 0 (Cpd0) is addressed by the use of a combined application of molecular dynamics simulations and perturbed matrix method calculations. Results are intriguing and indicate that, within the simulated conditions, free energy profiles are substantially affected by structural fluctuations of the whole surrounding biological environment (i.e. HRP enzyme and solvent). In this respect our results show that the combined effect of enzyme and solvent provides a substantial lowering of the free energy barrier to the formation of Cpd0, with respect to both gas-phase and QM/MM results carried out at a comparable level of theory. A careful inspection of such observations and their general implications in currently employed methodological approaches to the modelling of enzyme reactions, is also discussed.

In Silico Characterization of a Fourfold Magnesium Organometallic Compound in PTCDA Thin Films

In this contribution, using first principles calculations within a density functional theory framework, we report, for the first time, evidence for the formation of a fourfold magnesium organometallic compound upon metal deposition on perylene-3,4,9,10-tetracarboxyl dianhydride (PTCDA) organic semiconductor. Current investigation clearly indicates that in the bulk of the organic crystallographic structure the magnesium atom mainly interacts with three PTCDA molecules. The reactive metal is bound both to carboxylic oxygen atoms of the anhydride-end moieties and to a perylene carbon atom which changes its hybridization state, from sp(2) to sp(3), in the presence of metal impurities. In turn, the analysis of the electronic structure of the reacted system prevalently reveals the formation of four covalent bonds, as a consequence of a weak charge transfer toward the organic material. Such a result confirms the capability of the PTCDA thin films to host metal atoms providing, inside their structural empty channels, a rather accessible and soft chemical environment. Interestingly, in the light of these findings and of previous works, a relationship between first ionization potential of the doping metal and the character of the newly formed chemical bonds is confirmed.

STRUCTURAL AND ELECTRONIC PROPERTIES OF METAL-DOPED ORGANIC SEMICONDUCTORS

Interaction of metal atoms with organic thin films is a fundamental issue in the optimization performances of novel devices. The computational investigations, based on density functional theory, reveal that a realistic description of the reactive processes is obtained when the organic thin film is modeled by its crystallographic structure. In this case, the metal atoms can react with multiple organic molecules present in the solid forming complexes where they are bound both to O atoms and to aromatic C atoms of the molecules. Calculated band gap states, induced by chemical reaction upon deposition, reproduce quite well the measured density of states as a function of the metal concentration in the solid. Simulated core level shift spectra for N(1s), O(1s) and Al (2p) in doped systems are in good agreement with experimental spectra and the electronic structure analysis provides a microscopic description of reaction processes. Interestingly, K atoms in PTCDA solid are ionically bound to anhydride O atoms and...