Dynamic simulation of orientational disorder in organic crystals: methyl groups, trifluoromethyl groups and whole molecules

Gavezzotti, Angelo

doi:10.1107/s2052520621012191

Cited by 5 publications

(5 citation statements)

References 30 publications

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“…The addition of a second alcohol group in the case of 1,2-benzenediol prevents any rotation whatsoever (Table ). Although it has been noted before that benzene has rotational freedom in plastic crystals, , the simulations presented here provide detailed insight into time constants and energetics. By averaging the S 0 for three vectors (two in-plane and one out-of-plane), we get a value between 0 and 1 that is indicative of the type of motion.…”

Section: Resultsmentioning

confidence: 93%

Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

2022

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A profound understanding of the physicochemical properties of organic crystals is crucial for topics from material science to drug discovery. Using molecular dynamics (MD) simulations with a sufficiently accurate force field, microscopic insight into structure and dynamics can be obtained of materials, including liquids and biomolecules. They are a valuable complement to experimental investigations that are used routinely in drug design, but not very often for studies of organic crystals. Indeed, the often delicate interactions in organic crystals act as a sensitive probe to investigate the accuracy of force fields. Here, we study the structural, dynamic, and thermodynamic properties of 30 organic crystals using the popular general AMBER force field (GAFF). In particular, we investigate both solid–solid and solid–liquid phase transitions. Melting points were determined using extensive solid–liquid coexistence simulations. For many compounds, we detect a phase transition from an ordered to a plastic crystal in the simulations. Based on the translational and rotational dynamics of the compounds, we can rationalize the properties of the plastic crystal phase. MD simulations can therefore help to answer the important question of whether or not organic crystals have a plastic crystal phase, and if so, what are the underlying factors in the molecular structure determining that.

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Section: Resultsmentioning

confidence: 93%

Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

2022

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“…A further issue with simulations of crystals is that it may be cumbersome to evaluate many different crystals since it is nontrivial to assess whether a system is in the crystalline phase and, if so, what polymorph it is. In addition, some crystals are in a plastic crystal phase at certain conditions, that is the molecules occupy fixed lattice positions, with some more or less restrained degrees of freedom. , Some computational benchmarks based on organic crystals have been proposed (Table ). Reilly and Tkatchenko extended the C21 database to form the X23 database, both studying molecular crystals using DFT.…”

Section: Condensed Phasesmentioning

confidence: 99%

“…In addition, some crystals are in a plastic crystal phase at certain conditions, that is the molecules occupy fixed lattice positions, with some more or less restrained degrees of freedom. 241 , 242 Some computational benchmarks based on organic crystals have been proposed ( Table 5 ). Reilly and Tkatchenko extended the C21 database 243 to form the X23 database, 244 both studying molecular crystals using DFT.…”

Section: Condensed Phasesmentioning

confidence: 99%

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Kříž

Schmidt

Andersson

et al. 2023

J. Chem. Inf. Model.

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Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

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“…In addition, some crystals are in a plastic crystal phase at certain conditions, that is the molecules occupy fixed lattice positions, with some more or less restrained degrees of freedom. 208,209 Some computational benchmarks based on organic crystals have been proposed (Table 5). (a.u.…”

Section: Condensed Phases Organic Crystalsmentioning

confidence: 99%

An Imbalance in the Force: The Need for Standardised Benchmarks for Molecular Simulation

Kříž

Schmidt

Andersson

et al. 2022

Preprint

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Force fields (FF) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized datasets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are re-used to evaluate FFs and development teams rather use their own test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark datasets from quantum chemistry can in fact be re-used for evaluating FFs, but new gas phase data is still needed for compounds containing phosphor and sulfur. In addition, more non- equilibrium energies and forces are needed for compounds with halogens, P and S. For the condensed phases there is a large body of experimental data available and tools to utilise these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence would adopt a number of these datasets it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

show abstract

Dynamic simulation of orientational disorder in organic crystals: methyl groups, trifluoromethyl groups and whole molecules

Cited by 5 publications

References 30 publications

Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

An Imbalance in the Force: The Need for Standardised Benchmarks for Molecular Simulation

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