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1. Contact map based crystal structure prediction using global optimization

   https://doi.org/10.1039/D0CE01714K  

   Hu, Jianjun ; Yang, Wenhui ; Dong, Rongzhi ; Li, Yuxin ; Li, Xiang ; Li, Shaobo ; Siriwardane, Edirisuriya M. ( March 2021 , CrystEngComm)

   null (Ed.)

   Crystal structure prediction is now playing an increasingly important role in the discovery of new materials or crystal engineering. Global optimization methods such as genetic algorithms (GAs) and particle swarm optimization have been combined with first-principles free energy calculations to predict crystal structures given the composition or only a chemical system. While these approaches can exploit certain crystal patterns such as symmetry and periodicity in their search process, they usually do not exploit the large amount of implicit rules and constraints of atom configurations embodied in the large number of known crystal structures. They currently can only handle crystal structure prediction of relatively small systems. Inspired by the knowledge-rich protein structure prediction approach, herein we explore whether known geometric constraints such as the atomic contact map of a target crystal material can help predict its structure given its space group information. We propose a global optimization-based algorithm, CMCrystal, for crystal structure (atomic coordinates) reconstruction based on atomic contact maps. Based on extensive experiments using six global optimization algorithms, we show that it is viable to reconstruct the crystal structure given the atomic contact map for some crystal materials, but more geometric or physicochemical constraints are needed to achieve the successful reconstruction of other materials. 

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2. Overcoming the difficulties of predicting conformational polymorph energetics in molecular crystals via correlated wavefunction methods

   https://doi.org/10.1039/C9SC05689K  

   Greenwell, Chandler ; McKinley, Jessica L. ; Zhang, Peiyu ; Zeng, Qun ; Sun, Guangxu ; Li, Bochen ; Wen, Shuhao ; Beran, Gregory J. ( February 2020 , Chemical Science)

   Molecular crystal structure prediction is increasingly being applied to study the solid form landscapes of larger, more flexible pharmaceutical molecules. Despite many successes in crystal structure prediction, van der Waals-inclusive density functional theory (DFT) methods exhibit serious failures predicting the polymorph stabilities for a number of systems exhibiting conformational polymorphism, where changes in intramolecular conformation lead to different intermolecular crystal packings. Here, the stabilities of the conformational polymorphs of o -acetamidobenzamide, ROY, and oxalyl dihydrazide are examined in detail. DFT functionals that have previously been very successful in crystal structure prediction perform poorly in all three systems, due primarily to the poor intramolecular conformational energies, but also due to the intermolecular description in oxalyl dihydrazide. In all three cases, a fragment-based dispersion-corrected second-order Møller–Plesset perturbation theory (MP2D) treatment of the crystals overcomes these difficulties and predicts conformational polymorph stabilities in good agreement with experiment. These results highlight the need for methods which go beyond current-generation DFT functionals to make crystal polymorph stability predictions truly reliable. 

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3. Structurally Constrained Evolutionary Algorithm for the Discovery and Design of Metastable Phases

   https://doi.org/10.1021/acs.jctc.3c00594  

   Wang, Busheng ; Hilleke, Katerina P ; Hajinazar, Samad ; Frapper, Gilles ; Zurek, Eva ( November 2023 , Journal of Chemical Theory and Computation)

   Metastable materials are abundant in nature and technology, showcasing remarkable properties that inspire innovative materials design. However, traditional crystal structure prediction methods, which rely solely on energetic factors to determine a structure’s fitness, are not suitable for predicting the vast number of potentially synthesizable phases that represent a local minimum corresponding to a state in thermodynamic equilibrium. Here, we present a new approach for the prediction of metastable phases with specific structural features and interface this method with the XTALOPT evolutionary algorithm. Our method relies on structural features that include the local crystalline order (e.g, the coordination number or chemical environment), and symmetry (e.g, Bravais lattice and space group) to filter the breeding pool of an evolutionary crystal structure search. The effectiveness of this approach is benchmarked on three known metastable systems: XeN8, with a two-dimensional polymeric nitrogen sublattice, brookite TiO2, and a high pressure BaH4 phase, which was recently characterized. Additionally, a newly predicted metastable melaminate salt, P1̅ WC3N6, was found to possess an energy that is lower than that of two phases proposed in a recent computational study. The method presented here could help in identifying the structures of compounds that have already been synthesized, and in developing new synthesis targets with desired properties. 

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4. Intraspecific variation in group structure arises due to environmentally‐mediated directional dispersal in a cooperative breeder

   https://doi.org/10.1111/1365-2656.14162  

   Shah, Shailee_S ; Rubenstein, Dustin_R ( August 2024 , Journal of Animal Ecology)

   Many cooperatively breeding species live in groups with complex structure—large group sizes, low and variable kin structure, and multiple breeding pairs. Since these mixed‐kin groups typically form because of immigration of unrelated individuals of both sexes in addition to limited offspring dispersal, differences in patterns of dispersal can generate variation in group structure, even within the same species or population.

   Here, we examine how environmentally mediated dispersal patterns influence variation in group structure in the plural breeding superb starling (Lamprotornis superbus), an avian cooperative breeder that inhabits a spatiotemporally variable savanna environment and forms mixed‐kin groups with variable group sizes and more than one breeding pair per group.

   Using 4068 genome‐wide polymorphic loci and fine‐scale, remotely sensed ecological data from 22 groups sampled across a nearly 200 km²environmental gradient in central Kenya, we find evidence of not only frequent and long‐distance dispersal in both sexes (low isolation‐by‐distance and weak genetic structure), but also directional dispersal from small groups in lower quality habitat with low normalised difference vegetation index (NDVI) to large groups in higher quality habitat with high NDVI.

   Additionally, we find stronger genetic structure among groups in lower quality habitat, and higher genetic diversity and lower relatedness of groups in higher quality habitat. Previous work using long‐term data from groups in the same population has shown that groups with lower relatedness are larger and have more breeding pairs.

   Long‐distance, directional dispersal to maximise individual fitness can thus lead to smaller and simpler kin‐based social groups in lower quality habitat, but larger and more complex mixed‐kin groups in higher quality habitat.

   Such intraspecific, within‐population variation in group structure, including variation in kin structure of social groups, could have profound implications for the relative importance of the evolutionary mechanisms (i.e. direct vs. indirect fitness benefits) underlying the formation of cooperative societies.

    

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5. MAISE: Construction of neural network interatomic models and evolutionary structure optimization

   https://doi.org/10.17632/vfzgt2gnsh.1  

   Hajinazar, S. ; Thorn, A. ; Sandoval, E.D. ; Kharabadze, S. ; Kolmogorov, A.N. ( October 2020 , Computer physics communications)

   null (Ed.)

   Module for ab initio structure evolution (MAISE) is an open-source package for materials modeling and prediction. The code’s main feature is an automated generation of neural network (NN) interatomic potentials for use in global structure searches. The systematic construction of Behler–Parrinello-type NN models approximating ab initio energy and forces relies on two approaches introduced in our recent studies. An evolutionary sampling scheme for generating reference structures improves the NNs’ mapping of regions visited in unconstrained searches, while a stratified training approach enables the creation of standardized NN models for multiple elements. A more flexible NN architecture proposed here expands the applicability of the stratified scheme for an arbitrary number of elements. The full workflow in the NN development is managed with a customizable ‘MAISE-NET’ wrapper written in Python. The global structure optimization capability in MAISE is based on an evolutionary algorithm applicable for nanoparticles, films, and bulk crystals. A multitribe extension of the algorithm allows for an efficient simultaneous optimization of nanoparticles in a given size range. Implemented structure analysis functions include fingerprinting with radial distribution functions and finding space groups with the SPGLIB tool. This work overviews MAISE’s available features, constructed models, and confirmed predictions. 

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