Molecular dynamics simulations in condensed phase
- Details
- Category: Research
In parallel with an ever growing availability of microscopic analysis techniques, there is presently an ever growing interest in chemical objects of nanometer dimensions, both on the theoretical and applicative side. For example, nanocluster science is an essential part of the development of functional nanoparticles, mostly made of salts or metals, but also organic molecular aggregates are important in many sectors of applied chemistry and physics such as, to quote just one example, atmospheric pollution. Molecular clusters are interesting also as precursors of crystal nucleation and growth mechanisms.
We study both equilibrium and non-equilibrium phenomena in condensed phase by means of classical Monte Carlo and Molecular Dynamics methods. Our software is now part of the MiCMoS package, which can be downloaded (registered users only) for free for academic users and non-profit organizations.
If you want more information on this topic, you can have a look on the MiCMoS users' manual. Some Tutorials are available on this site to help new users getting acquainted with the program and I/O handling. A library of ready-to-use Topologies for the simulation of various liquids and solids is also available.
Relevant publications:
Macetti, Sironi & Lo Presti, Classical molecular dynamics simulation of molecular crystals and materials: old lessons and new perspectives, in "Comprehensive Computational Chemistry" Elsevier, Book series in Theoretical and Computational Chemistry nº21, 2023; https://doi.org/10.1016/B978-0-12-821978-2.00107-0
Sironi, Rizzato & Lo Presti, Why Is alpha-D-Glucose Monomorphic? Insights from Accurate Experimental Charge Density at 90 K. Cryst. Growth Des. 2022, 22, 11, 6627-6638; DOI: 10.1021/acs.cgd.2c00846
Gavezzotti, Lo Presti & Rizzato, Molecular dynamics simulation of organic materials: structure, potentials and the MiCMoS computer platform. CrystEngComm, 2022,24, 922-930 DOI: 10.1039/D1CE01360B
Lo Presti, Rizzato & Gavezzotti, Kinetic-Bias Model for the Dynamic Simulation of Molecular Aggregation. The Liquid, Solute, Solvated-Nanodrop, and Solvated-Nanocrystal States of Benzoic Acid. Crystal Growth Des. 2022, 22 1857–1866, DOI: 10.1021/acs.cgd.1c01410
Destro et al., Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T= 23 K. Molecules 2021, 26(11), 3075; DOI: 10.3390/molecules26113075
Gavezzotti & Lo Presti, Dynamic simulation of liquid molecular nanoclusters: structure, stability and quantification of internal (pseudo)symmetries. New J. Chem. 2019, 43, 2077-2084. DOI: 10.1039/c8nj05825c
Gavezzotti, Lo Presti & Rizzato, Mining the Cambridge Database for theoretical chemistry. Mi-LJC: a new set of Lennard-Jones–Coulomb atom–atom potentials for the computer simulation of organic condensed matter. CrystEngComm 2020, 22, 7350-7360, DOI: 10.1039/D0CE00334D
Rizzato, Gavezzotti & Lo Presti, Molecular Dynamics Simulation of Molecular Crystals under Anisotropic Compression: Bulk and Directional Effects in Anthracene and Paracetamol. Crystal Growth Des. 2020, 20,7421–7428, DOI: 10.1021/acs.cgd.0c01098
Gavezzotti & Lo Presti, Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment. J. Appl. Cryst. 2019, 52, 1253-1263. DOI: 10.1107/S1600576719012238