Riccardo Chelli

A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle

A polarizable electrostatic potential model for classical molecular mechanics is presented. Based on the chemical potential equalization (CPE) principle, the model is developed starting from the original formulation of Mortier, Ghosh, and Shankar [J. Am. Chem. Soc. 108, 4315 (1986)]. Following York and Yang [J. Chem. Phys. 104, 159 (1996)] we present an SP-basis CPE parametrization to describe realistically any sort of molecular system. By fitting ab initio electronic properties, such as dipole moment, polarizability and global molecular hardness of a restricted set of organic molecules, we derive atomic parameters to be applied to a more vast target set of compounds. We show, indeed, that the atomic CPE parameters calculated for the learning set of molecules give reliable values for several electronic properties of various compounds not included in the learning set. The multipole moments obtained by using the proposed CPE parametrization are compared to the results of a fixed charge parametrization like ...

Electrical response in chemical potential equalization schemes

In this paper we compare the polarization response given by two different chemical potential equalization schemes to be applied to molecular dynamics simulations: the standard fluctuating point charge model (FQ) and the atom–atom charge transfer model (AACT). We have tested the transferability of FQ and AACT parameters, fitted to the polarizability of small size alkanes and polyenes, to large size homologues. We show that the FQ scheme is not adequate for the n-alkanes as it strongly overestimates the polarizability tensor components as the number of carbon atoms increases. The FQ approach has been found more predictive for highly conjugated systems like polyenes, although still unsatisfactory. The AACT parameters tuned on ethane are instead perfectly transferable to alkanes of any length and conformation. The AACT scheme satisfactorily reproduces the polarization response also for highly conjugated systems.

Glycerol condensed phases Part II.A molecular dynamics study of the conformational structure and hydrogen bonding

An analysis of the conformational properties and hydrogen bonding in the condensed phases of glycerol is reported using the same model as adopted in Part I (Phys. Chem. Chem. Phys., 1999, 1, 871). Structural properties of the liquid and glassy states are analyzed in relation to the molecular backbone conformation of the glycerol molecule. The effects of hydrogen bonding and of temperature on the conformational distribution are analyzed. The structural and dynamical properties of hydrogen bonding in glycerol are also investigated. The results are consistent with available experimental observations and clarify many important and interrelated aspects of the microscopic structure of liquid, glassy and crystalline phases of glycerol.

The nature of intermolecular interactions between aromatic amino acid residues

The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single‐point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic–aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures. Proteins 2002;48:117–125.

Calculation of optical spectra in liquid methanol using molecular dynamics and the chemical potential equalization method

We apply the chemical potential equalization (CPE) method to the calculation of the optical spectra in liquid methanol at 298 K and normal pressure. The configurations of the liquid are obtained by conventional molecular dynamics (MD) using a completely flexible all-atoms model. The infrared and Raman spectra are computed a posteriori using a CPE parametrization of methanol calibrated to reproduce the electronic properties of the isolated molecule evaluated with accurate ab initio calculations. The MD/CPE method reproduces correctly the optical spectra in the region of the intermolecular motions. The spectra are discussed and interpreted on the basis of hydrogen bonding structure and dynamics.

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open‐source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac.

Glycerol condensed phases Part I. A molecular dynamics study

Using a model potential function we have performed a molecular dynamics simulation of several static and dynamical properties of glycerol in the crystal, glass and liquid phases. Comparison with available experimental data shows an excellent agreeent and proves the validity of the potential model used. For the calculation of the molar specific heat of the liquid and of the glass we have developed a theoretical approach which takes into account the contributions of the conformational structure energy and of the vibrational energy computed using the Bose–Einstein statistics.

Simulated structure, dynamics, and vibrational spectra of liquid benzene

A classical molecular dynamics simulation of liquid benzene is performed, using a potential model which allows for full molecular flexibility. The short range intermolecular radial distribution function is on average reminiscent of the crystalline structure, although practically no preferential orientation can be found for the molecules in the first coordination shell. The average cage lifetime and its vibrational dynamics are obtained from appropriate time correlation functions. The intramolecular vibrations are investigated by calculating the vibrational density of states and the infrared and Raman spectra, achieving an excellent agreement with the experimental data. Finally, the dephasing of the ν1(A1g) ring breathing mode and of the ν6(E2g) in-plane bending mode is analyzed on the basis of the Kubo dephasing function. For ν1 mode the Kubo correlation time of 516 fs agrees with the experimental value, and is consistent with a relaxation mechanism involving the cage reorganization. In contrast, ν6 has a...

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)], originally derived for microscopically reversible Markovian systems, relates the work done on a system during an irreversible transformation to the free energy difference between the final and the initial state of the transformation. In the present work we provide a theoretical proof of the Crooks equation in the context of constant volume, constant temperature steered molecular dynamics simulations of systems thermostated by means of the Nosé-Hoover method (and its variant using a chain of thermostats). As a numerical test we use the folding and unfolding processes of decaalanine in vacuo at finite temperature. We show that the distribution of the irreversible work for the folding process is markedly non-Gaussian thereby implying, according to Crooks equation, that also the work distribution of the unfolding process must be inherently non-Gaussian. The clearly asymmetric behavior of the forward and backward irreversible work distributions is a signature of a non-Markovian regime for the folding/unfolding of decaalanine.

A study on the anisole–water complex by molecular beam–electronic spectroscopy and molecular mechanics calculations

An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy.