Exploring polymorphism of benzene and naphthalene with free energy based enhanced molecular dynamics

Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of semiconductors. Predicting the most stable crystalline form at a given temperature and pressure requires determining the crystalline form with the lowest relative Gibbs free energy. Effective computational prediction of the most stable polymorph could save significant time and effort in the design of novel molecular crystalline solids or predict their behavior under new conditions. In this study, we introduce a new approach using multistate reweighting to address the problem of determining solid-solid phase diagrams and apply this approach to the phase diagram of solid benzene. For this approach, we perform sampling at a selection of temperature and pressure states in the region of interest. We use multistate reweighting methods to determine the reduced free energy differences between T and P states within a given polymorph and validate this phase diagram using several measures. The relative stability of the polymorphs at the sampled states can be successively interpolated from these points to create the phase diagram by combining these reduced free energy differences with a reference Gibbs free energy difference between polymorphs. The method also allows for straightforward estimation of uncertainties in the phase boundary. We also find that when properly implemented, multistate reweighting for phase diagram determination scales better with the size of the system than previously estimated.

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“…9. The ordering of polymorphs as a function of pressure is consistent with the results of Schnieder et al 61…”

Section: A Full Molecular Dynamics Phase Diagram Of Benzenesupporting

confidence: 90%

Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams

Schieber

Dybeck

Shirts

2018

The Journal of Chemical Physics

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“…The space group is P42nm. Interestingly, as far as we know, the obtained unit cell structure is different from any other crystalline structures of benzene reported so far [1,[7][8][9][10][11][12][13][14][15][16][17][18] It is worth investigating the influence of pressure control on the melting behavior. In the above simulations, we used the isotropic pressure control, where the dimension of box was isotropically changed.…”

Section: Resultsmentioning

confidence: 64%

“…Regardless, its polymorphism [1][2][3] and local liquid structure [4][5][6] have been extensively explored until now. Five crystalline phases of pure benzene have been reported so far experimentally [7][8][9][10][11][12][13][14], and computational studies predicted many other potential crystalline structures [1,[15][16][17][18]. Although the phase diagram shows the most stable phase at a given condition, there can be rich intermediate phases on the transition pathway from the initial to the finally prevailed phase [19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Stepwise Homogeneous Melting of Benzene Phase I at High Pressure

Mahesta¹,

Mochizuki

2019

Crystals

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We investigate, using molecular dynamics simulations, the spontaneous homogeneous melting of benzene phase I under a high pressure of 1.0 GPa. We find an apparent stepwise transition via a metastable crystal phase, unlike the direct melting observed at ambient pressure. The transition to the metastable phase is achieved by rotational motions, without the diffusion of the center of mass of benzene. The metastable crystal completely occupies the whole space and maintains its structure for at least several picoseconds, so that the phase seems to have a local free energy minimum. The unit cell is found to be unique—no such crystalline structure has been reported so far. Furthermore, we discuss the influence of pressure control on the melting behavior.

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“…This was achieved by using supercell vectors or h ‐matrix elements as the CVs in a flexible‐cell NPT ensemble MD simulation. This approach was shown to be very efficient in sampling crystal structures, including organic crystals . In Figure , TAMD/d‐AFED trajectories exploring crystal structures of benzene at 100 K and 2 GPa are shown .…”

Section: Driven Afed and Temperature‐accelerated MDmentioning

confidence: 99%

Exploring high‐dimensional free energy landscapes of chemical reactions

Awasthi

Nair

2018

WIREs Comput Mol Sci

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Molecular dynamics (MD) techniques are widely used in computing free energy changes for conformational transitions and chemical reactions, mainly in condensed matter systems. Most of the MD-based approaches employ biased sampling of a priori selected coarse-grained coordinates or collective variables (CVs) and thereby accelerate otherwise infrequent transitions from one free energy basin to the other. A quick convergence in free energy estimations can be achieved by enhanced sampling of large number of CVs. Conventional enhanced sampling approaches become exponentially slower with increasing dimensionality of the CV space, and thus they turn out to be highly inefficient in sampling high-dimensional free energy landscapes. Here, we focus on some of the novel methods that are designed to overcome this limitation. In particular, we discuss four methods: biasexchange metadynamics, parallel-bias metadynamics, adiabatic free energy dynamics/temperature-accelerated MD, and temperature-accelerated sliced sampling. The basic idea behind these techniques is presented and applications using these techniques are illustrated. Advantages and disadvantages of these techniques are also delineated.adiabatic free energy dynamics, bias exchange metadyanmics, enhanced sampling, free energy calculations, parallel-bias metadynamics, temperatureaccelerated sliced sampling 1 | INTRODUCTION Free energy changes along the reaction coordinate of a chemical reaction manifests the feasibility of the process at a given temperature. Reaction coordinate, χ, on the other hand, can be an intricate function of nuclear coordinates even for a simple elementary reaction. To simplify, χ can be written as a linear combination of several coarse-grained coordinates or collective variables (CVs), S, as,

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Exploring polymorphism of benzene and naphthalene with free energy based enhanced molecular dynamics

Cited by 50 publications

References 51 publications

Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams

Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams

Stepwise Homogeneous Melting of Benzene Phase I at High Pressure

Exploring high‐dimensional free energy landscapes of chemical reactions

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