A. Di Nola

Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency

From a specific definition of the roto-translational (external) and intramolecular (internal) coordinates, a constrained dynamics algorithm is derived for removing the roto-translational motions during molecular dynamics simulations, within the leap-frog integration scheme. In the paper the theoretical basis of this new method and its statistical mechanical consistency are reported, together with two applications.

An extended x‐ray absorption fine structure study of aqueous solutions by employing molecular dynamics simulations

Bromine–oxygen radial distribution functions [g(r)] have been calculated by means of molecular dynamics simulations for aqueous solutions of rubidium bromide, 2‐bromopropane and bromoethane. X‐ray absorption spectra at the bromine K edge have been recorded for these solutions. The water contribution to the extended x‐ray absorption fine structure spectra has been calculated starting from the gBr,O(r) distribution function. Fits of the x‐ray absorption spectra have been performed directly on the raw experimental data, allowing the reliability of the g(r) distribution functions to be verified. The agreement between theoretical and experimental spectra is satisfactory. A procedure to improve model g(r) functions on the basis of the short‐range structural information provided by extended x‐ray absorption fine structure data is proposed.

A first-principles method to model perturbed electronic wavefunctions : the effect of an external homogeneous electric field

In this Letter, we show that with the use of matrix notation to express the time-independent Schroedinger equation, it is possible to model perturbed electronic wavefunctions. Such a method makes use of first principles of the quantum mechanical theory and hence is rigorous within the only approximation due to the truncation of the perturbed Hamiltonian matrix used. Results show that for three different molecules in vacuo under an electric field, the proposed method provides reliable perturbed electronic wavefunctions at a low computational costs.

A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells

The dynamics of collective protein motions derived from Molecular Dynamics simulations have been studied for two small model proteins: initiation factor I and the B1 domain of Protein G. First, we compared the structural fluctuations, obtained by local harmonic approximations in different energy minima, with the ones revealed by large scale molecular dynamics (MD) simulations. It was found that a limited set of harmonic wells can be used to approximate the configurational fluctuations of these proteins, although any single harmonic approximation cannot properly describe their dynamics.

The essential dynamics of Cu, Zn superoxide dismutase : Suggestion of intersubunit communication

A 300-ps molecular dynamics simulation of the whole Cu, Zn superoxide dismutase dimer has been carried out in water, and the trajectory has been analyzed by the essential dynamics method. The results indicate that the motion is defined by few preferred directions identified by the first four to six eigenvectors and that the motion of the two monomers at each instant is not symmetrical. The vectors symmetrical to the eigenvectors are significantly sampled, suggesting that, on average, the motions of the two subunits will exchange. Large intra- and intersubunit motions involving different subdomains of the protein are observed. A mechanical coupling between the two subunits is also suggested, because displacements of the loops surrounding the active site in one monomer are correlated with the motion of parts of the second toward the intersubunit interface.

An extended x‐ray absorption fine structure study by employing molecular dynamics simulations: Bromide ion in methanolic solution

X‐ray absorption spectroscopy is widely employed in the structural analysis of disordered systems. In the standard extended x‐ray absorption fine structure (EXAFS) analysis the coordination of the photoabsorber is usually defined by means of Gaussian shells. It is known that this procedure can lead to significant errors in the determination of the coordination parameters for systems which present anharmonic thermal vibrations or interatomic asymmetric pair distribution functions. An efficient method has been recently employed in the study of the hydration shells of bromide and rubidium ions and brominated hydrocarbon molecules in diluted aqueous solutions. According to this method, pair distribution functions [g(r)] obtained from molecular dynamics simulations can be used as relevant models in the calculation of the EXAFS signals. Moreover, asymmetric shells modeled on the g(r) first peaks, have been employed in the EXAFS analysis and the parameters defining the asymmetric peaks have been optimized during...

Mixed Quantum-Classical Methods for Molecular Simulations of Biochemical Reactions With Microwave Fields: The Case Study of Myoglobin

Contradictory data in the huge literature on microwaves bio-effects may result from a poor understanding of the mechanisms of interaction between microwaves and biological systems. Molecular simulations of biochemical processes seem to be a promising tool to comprehend microwave induced bio-effects. Molecular simulations of classical and quantum events involved in relevant biochemical processes enable to follow the dynamic evolution of a biochemical reaction in the presence of microwave fields. In this paper, the action of a microwave signal (1 GHz) on the covalent binding process of a ligand (carbon monoxide) to a protein (myoglobin) has been studied. Our results indicate that microwave fields, with intensities much below the atomic/molecular electric interactions, cannot affect such biochemical process.

A pulsed low resolution NMR study on crystallization and melting processes of cocoa butter

Pulsed low resolution nuclear magnetic resonance (NMR) was employed to measure the «melting» curves of different series of cocoa butter samples. The samples were prepared from completely liquid phase by cooling and tempering them at different temperatures Tc for varying time Δt. The «melting» curves were measured while keeping the sample at a fixed temperature Tm. The complex shape of each curve was interpreted in terms of cocoa butter polymorphism, and the results were compared with data obtained by other techniques available in the literature. Using just two tempering temperatures (+7 C and −18C), we were able to distinguish four solid phases and identify them with the phases II, III, IV, and V described in literature. Our data are in full agreement with literature. Several novel results have been also found. These include the kinetic constants of the melting processes of phases II and III, the rate constants of solidification of phase V, the conversion of phase III into phase IV before melting at temperatures ≥30 C, and the growth of phase V out of phase II at −18 C (including the rate constant of this process). We are convinced that NMR may serve as a principal tool in fat polymorphism investigations, especially if it is combined with other techniques such as differential scanning calorimetry. Its advantage, apart from rapidity of measurement, is the fact that the measurement itself does not interfere with the melting or solidification process studied. On the other hand, it does not distinguish in a direct way between different solid phases present in the sample; this can be done only in inference from the behavior upon melting.

Oil and water determination in emulsions by pulsed low-resolution NMR

A pulsed, low-resolution nuclear magnetic resonance (NMR) technique has been used for the oil and water determination in O/W emulsions. The method is based on the analysis of the longitudinal magnetization decay curve, that, due to the different relaxation times of oil and water, consists of 2 recognizable components. Correlation of NMR results with fat content is described. A good correlation between the NMR response and fat content by weight has been found. The rapidity and accuracy of the measurements are comparable to those of other techniques.

Theoretical equations of state for temperature and electromagnetic field dependence of fluid systems, based on the quasi-Gaussian entropy theory

The quasi-Gaussian entropy (QGE) theory employs the fact that a free-energy change can be written as the moment-generating function of the appropriate probability distribution function of macroscopic fluctuations of an extensive property. By modeling this distribution, one obtains a model of free energy and resulting thermodynamics as a function of one state variable. In this paper the QGE theory has been extended towards theoretical models or equations of state (EOS’s) of the thermodynamics of semiclassical systems as a function of two state variables. Two “monovariate” QGE models are combined in the canonical ensemble: one based on fluctuations of the excess energy (the confined gamma state giving the temperature dependence) and the other based on fluctuations of the reduced electromagnetic moment [various models as derived in the preceding paper [Apol, Amadei, and Di Nola, J. Chem. Phys. 116, 4426 (2002)], giving the external field dependence]. This provides theoretical EOS’s for fluid systems as a function of both temperature and electromagnetic field. Special limits of these EOS’s are considered: the general weak-field EOS and the limit to a Curie’s law behavior. Based on experimental data of water and simulation data using the extended simple point charge (SPC/E) water model at 45.0 and 55.51 mol/dm3, the specific EOS based on a relatively simple combination of the confined gamma state model with a discrete uniform state field model accurately reproduces the dielectric properties of water at constant density, as the temperature dependence of the weak-field dielectric constant for gases and liquids, and the field dependence of the dielectric constant of liquids.