arXiv subjects

Nathan S. Abraham

Publications and source records attributed to Nathan S. Abraham.

4 recordsLinked to original sources

arXiv2020

Probing the force field sensitivity of entropy and enthalpy differences in organic polymorphs using classical potentials

We evaluate the effectiveness of different classical potentials to predict the thermodynamics of a number of organic solid form polymorphs relative to experimentally reported values using the quasi-harmonic approximation. Using the polarizable potential AMOEBA we are able to predict the correct sign of the enthalpy difference for 71+/-12 % of the polymorphs. Alternatively, all point charge potentials perform on par with random chance of correcting the correct sign (50%) for enthalpy. We find that the entropy is less sensitive to the accuracy of the potential with all force fields, excluding CGenFF, reporting the correct sign of the entropy for 64+/-13 - 75+/-11 % of the systems. Predicting the correct sign of the enthalpy and entropy differences can help indicate the low and high temperature stability of the polymorphs, unfortunately the error relative to experiment in these predicted values can be as large as 1 - 2.5 kcal/mol at the transition temperature.

cond-mat.mtrl-sci↗

arXiv2020

Statistical mechanical approximations to more efficiently determine polymorph free energy differences for small organic molecules

Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include use of static lattice phonons, quasi-harmonic approximation (QHA), and computing the full thermodynamic cycle using replica exchange molecular dynamics (REMD). We found that 13 out of the 29 systems minimized from experiment restructured to a lower energy minima when heated using REMD, a phenomena that QHA cannot capture. Here, we present a series of methods that are intermediate in accuracy and expense between QHA and computing the full thermodynamic cycle which can save 42-80% of the computational cost and introduces, on this benchmark, a relatively small (0.16 +/- 0.04 kcal/mol) error relative to the full pseudosupercritical path approach. In particular, a method that Boltzmann weights the harmonic free energy of the trajectory of an REMD replica appears to be an appropriate intermediate between QHA and full thermodynamic cycle using MD when screening crystal polymorph stability.

cond-mat.mtrl-sci↗

arXiv2019

Adding anisotropy to the standard quasi-harmonic approximation still fails in several ways to capture organic crystal thermodynamics

We evaluate the accuracy of varying thermal expansion models for the quasi-harmonic approximation (QHA) relative to molecular dynamics (MD) for 10 sets of enantiotropic organic polymorphs. Relative to experiment we find that MD, using an off-the-shelf point charge potential gets the sign of the enthalpic contributions correct for 6 of the 10 pairs of polymorphs and the sign of the entropic contributions correct for all pairs. We find that anisotropic QHA provides little improvement to the error in free energy differences from MD relative to isotropic QHA, but does a better job capturing the thermal expansion of the crystals. A form of entropy-enthalpy compensation allows the free energy differences of QHA to deviate less than 0.1 kcal/mol from MD for most polymorphic pairs, despite errors up to 0.4 kcal/mol in the entropy and enthalpy. Much of the error previously found between QHA and MD for these flexible molecules is reduced when QHA is run from a lattice minimum consistent with the same basin as MD, rather than the energy-minimized experimental crystal structure. Specifically, performing anisotropic QHA on lattice minimum quenched from low-temperature replica exchange simulations reduced the error previously found by 0.2 kcal/mol on average. However, these conformationally flexible molecules can have many low-temperature conformational minima, and the choice of an inconsistent minima causes free energies estimated from QHA to deviate from MD at temperatures as low as 10 K. The errors between MD and experiment are 1-2 orders of magnitude larger than those seen between QHA and MD, so the quality of the force field used is still of primary concern, but this study illustrates a number of other important factors that must be considered to obtain quantitative organic crystal thermodynamics.

cond-mat.mtrl-sci↗

arXiv2018

A Thermal Gradient Approach for the Quasi-Harmonic Approximation and its Application to Improved Treatment of Anisotropic Expansion

We present a novel approach to efficiently implement thermal expansion in the quasi-harmonic approximation (QHA) for both isotropic and more importantly, anisotropic expansion. In this approach, we rapidly determine a crystal's equilibrium volume and shape at a given temperature by integrating along the gradient of expansion from zero Kelvin up to the desired temperature. We compare our approach to previous isotropic methods that rely on a brute-force grid search to determine the free energy minimum, which is infeasible to carry out for anisotropic expansion, as well as quasi-anisotropic approaches that take into account the contributions to anisotropic expansion from the lattice energy. We compare these methods for experimentally known polymorphs of piracetam and resorcinol and show that both isotropic methods agree to within error up to 300 K. Using the Grüneisen parameter causes up to 0.04 kcal/mol deviation in the Gibbs free energy, but for polymorph free energy differences there is a cancellation in error with all isotropic methods within 0.025 kcal/mol at 300 K. Anisotropic expansion allows the crystals to relax into lattice geometries 0.01-0.23 kcal/mol lower in energy at 300 K relative to isotropic expansion. For polymorph free energy differences all QHA methods produced results within 0.02 kcal/mol of each other for resorcinol and 0.12 kcal/mol for piracetam, the two molecules tested here, demonstrating a cancellation of error for isotropic methods. We also find that when expanding in more than a single volume variable, there is a non-negligible rate of failure of the basic approximations of QHA. Specifically, while expanding into new harmonic modes as the box vectors are increased, the system often falls into alternate, structurally distinct harmonic modes unrelated by continuous deformation from the original harmonic mode.

cond-mat.mtrl-sci↗