Marta B. Ferraro

Significant progress in predicting the crystal structures of small organic molecules – a report on the fourth blind test

We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.

Report on the sixth blind test of organic crystal structure prediction methods

The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.

Modified genetic algorithm to model crystal structures. I. Benzene, naphthalene and anthracene

This paper describes a new computational scheme to model crystal structures of organic compounds employing a modified genetic algorithm. The method uses real-valued Cartesian coordinates and Euler angles between molecules in a crystal block as variables identifying the genetic parameters, i.e., genes. The model does not make any assumption on the crystallographic group at which the compound belongs nor to the number of molecules in the unit cell. The method has been implemented in the computer package MGAC (Modified Genetic Algorithm for Crystal and Cluster structures) that allows for optimizations using any arbitrary selection function. The examples presented here for the crystalline structures of benzene, naphthalene and anthracene, using an empirical potential energy function as the selection function, show excellent agreement with the experimental ones. While these examples use the “rigid molecule approximation,” the method is quite general and can be extended to take into account any number of intram...

On the theoretical determination of the static dipole polarizability of intermediate size silicon clusters

The B3PW91 method of the density functional theory has been applied to the study of the dipole polarizability of medium size silicon clusters employing pseudopotential on all of them. All electron calculations have been performed for those clusters with less than nine atoms. In addition, we have optimized the structures of the clusters with less than ten atoms. On using the modified genetic algorithm, fourteen conformers of silicon isomers with nine atoms have been determined. The corresponding geometry of these clusters was optimized and their relative stability determined. The calculated polarizabilities are compared with experimental data and previous theoretical results.

Modeling NMR chemical shifts: A comparison of charge models for solid state effects on 15N chemical shift tensors

This paper presents results from applying different point charge models to take into account intermolecular interactions to model the solid state effects on the 15N NMR chemical shifts tensors. The DFT approach with the BLYP gradient corrected exchange correlation functional has been used because it can include electron correlation effects at a reasonable cost and is able to reproduce 15N NMR chemical shifts with reasonable accuracy. The results obtained with the point charge models are compared with the experimental data and with results obtained using the cluster model, which includes explicitly neighboring molecular fragments. The results show that the point charge models can take into account solid state effects at a cost much lower than the cluster methods.

A general framework to understand parallel performance in heterogeneous clusters: analysis of a new adaptive parallel genetic algorithm

This paper presents a general model to define, measure and predict the efficiency of applications running on heterogeneous parallel computer systems. Using this framework, it is possible to understand the influence that the heterogeneity of the hardware has on the efficiency of an algorithm. This methodology is used to compare an existing parallel genetic algorithm with a new adaptive parallel model. All the performance measurements were taken in a loosely coupled cluster of processors.

Calculation of Molecular Magnetic-properties Within the Landau Gauge In Hydrogen-fluoride, Ammonia, and Methane Molecules

The magnetic susceptibility and the nuclear magnetic shielding tensors of HF, NH3, and CH4 molecules in the presence of a spatially uniform time‐independent magnetic field have been calculated within the Landau gauge for the vector potential. The random‐phase approximation has been used, adopting flexible Gaussian basis sets of large size. Magnetic susceptibilities are quite harder to evaluate accurately in the Landau gauge than in Coulomb gauge. Calculated nuclear magnetic shieldings are close to the Hartree–Fock limit. Sum rules for charge conservation and origin independence of magnetic susceptibility and nuclear magnetic shieldings are fairly well satisfied by basis sets of extended size.

Modeling NMR chemical shifts: surface charge representation of the electrostatic embedding potential modeling of crystalline intermolecular effects in 19F solid state NMR chemical shifts

Abstract This contribution compares the results obtained using two different charge models with those of the cluster model, when they are used to take into account the crystalline intermolecular interactions in the calculation of 19 F chemical shifts tensors. The density functional theory (DFT) approach, with the B3LYP gradient corrected exchange correlation functional, was used in the calculations. This method includes electron correlation effects at a reasonable cost and is able to reproduce chemical shifts for a great variety of nuclei with reasonable accuracy. The two charge models used here, GRID and SCREEP, differ in the method applied to determine the point charge distribution that mimics the crystal field in the shielding calculations. The results show that the point charge models offer similar accuracy to the cluster model with a much lower computational cost.

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecules force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.