Page 1. ORAC Manual and Guide Piero Procacci and Massimo Marchi† A Molecular Dynamics Program to ... more Page 1. ORAC Manual and Guide Piero Procacci and Massimo Marchi† A Molecular Dynamics Program to Simulate Complex Molecular Systems at the atomistic level Dipartimento di Chimica, Polo Scientifico dell'Universitá ...
Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations
We present a new computational strategy for calculating the absolute binding free energy for prot... more We present a new computational strategy for calculating the absolute binding free energy for protein ligand association in the context of atomistic simulation in explicit solvent. The method is based on an appropriate definition of a solute tempering scheme enforced via Hamilton replica exchange method (HREM). The definition of "solute" includes both the ligand and the active site, with the remainder of the systems defined as "solvent". The hydrophilicity of the solute and the solute torsional plus nonbonded intrasolute interactions are increased and decreased, respectively, along the replica progression, thus favoring the extrusion of the drug form the active site in the scaled states of the generalized ensemble. The proposed technique, named "Energy Driven Undocking" (EDU-HREM), completely bypasses the need for defining and/or identifying the relevant reaction coordinates in a ligand receptor interactions and allows the calculation of the absolute binding free energy in one single generalized simulation of the drug-receptor system. The methodology is applied, with encouraging results, to the calculation of the absolute binding free energy of some FK506-related ligands of the peptidyl prolyl cis-trans isomerase protein (FKBP12) with known dissociation constants. Aspects of the binding/inhibition mechanism in FKBP12 are also analyzed and discussed.
A review of the recent theoretical and computational activity at the Chemistry Department of the ... more A review of the recent theoretical and computational activity at the Chemistry Department of the University of Firenze in the field of molecular simulations of condensed phases is reported. The topics considered include quantitative methods for accurate free energy calculations, molecular dynamics of liquids and ionic solutions, chemical reactions in solutions, phase transformations and polymerization reactions at high pressures.
In this paper we discuss an algorithm for calculation of the temperature-dependent anharmonic cor... more In this paper we discuss an algorithm for calculation of the temperature-dependent anharmonic correction to the phonon spectrum in atomic and molecular crystals. We show how the equation of motion method can be used to compute corrections of arbitrary perturbation order to the phonon self-energy. Complete analytical expressions up to order λ 6 are obtained as an application of the method.
We present the results of the parametrization of the AMBER molecular mechanical force ®eld for si... more We present the results of the parametrization of the AMBER molecular mechanical force ®eld for simulating Bacteriochlorophylls (BChls) and Bacteriopheophytins (BPhs). Ab initio Density Functional Theory (DFT) calculations on fragments and the entire chromophores in their gas-phase have been used to obtain a new set of force ®eld parameters which are able to reproduce static properties and vibrational frequencies of the chromophores. Molecular dynamics (MD) simulations of crystalline BPh and BChl have been performed to test our intramolecular parameterization as well as the non-bonded parameters. Ó : S 0 9 2 7 -0 2 5 6 ( 0 0 ) 0 0 1 8 9 -0
The Raman spectrum of a single SO2 crystal in various polarization geometries has been measured a... more The Raman spectrum of a single SO2 crystal in various polarization geometries has been measured at 20 K and discussed in terms of LO and TO components of polar crystal modes. Lattice phonons have been assigned on the basis of their behaviour with polarization. Lattice dynamical calculations on both the internal and lattice phonons are in good agreement with experimental data. Using gas-phase transition dipole moments and a dipole-dipole intermolecular potential the angular dispersion of fundamental vibrons has been calculated. For lattice phonons, a combination of atom-atom and electrostatic potential reproduces not only the phonon frequencies but, for polar phonons, also their LO-TO splitting.
We present non equilibrium molecular dynamics experiments of the unfolding and refolding of an al... more We present non equilibrium molecular dynamics experiments of the unfolding and refolding of an alanine decapeptide in vacuo subject to a Nosé thermostat. Forward (unfolding) and reverse (refolding) work distribution are numerically calculated for various duration times of the non equilibrium experiments. Crooks theorem is accurately verified for all non equilibrium regimes and the time asymmetry of the process is measured using the recently proposed Jensen-Shannon divergence [E.H. Fend, G. Crooks Phys. Rev. Lett, 101, 090602] . Results on the alanine decapeptide are found similar to recent experimental data on m-RNA molecule, thus evidencing the universal character of the Jensen-Shannon divergence. The patent non markovianity of the process is rationalized by assuming that the observed forward and reverse distributions can be each described by a combination of two normal distributions satisfying the Crooks theorem, representative of two mutually exclusive linear events. Such bimodal approach reproduce with surprising accuracy the observed non Markovian work distributions.
The far-infrared spectrum of crystalline fullerene C60
The Journal of Physical Chemistry, 1993
The infrared spectrum of crystalline C[sub 60] has been measured in the frequency range 500-20 cm... more The infrared spectrum of crystalline C[sub 60] has been measured in the frequency range 500-20 cm[sup [minus]1] at various temperatures between 300 and 10 K. Since no dipole-allowed intramolecular vibration is active below 500 cm[sup [minus]1], the infrared absorption is determined by crystal and quadrupolar interactions. Davydov splittings of several intramolecular vibrations have been observed. The infrared activity of H[sub
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Papers by Piero Procacci