How Accurate Can Crystal Structure Predictions Be for High-Energy Molecular Crystals?

Molecules

Department of Civil, Materials and Environmental Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA.

Published: May 2023

Molecular crystals have shallow potential energy landscapes, with multiple local minima separated by very small differences in total energy. Predicting molecular packing and molecular conformation in the crystal generally requires ab initio methods of high accuracy, especially when polymorphs are involved. We used dispersion-corrected density functional theory (DFT-D) to assess the capabilities of an evolutionary algorithm (EA) for the crystal structure prediction (CSP) of well-known but challenging high-energy molecular crystals (HMX, RDX, CL-20, and FOX-7). While providing the EA with the experimental conformation of the molecule quickly re-discovers the experimental packing, it is more realistic to start instead from a naïve, flat, or neutral initial conformation, which reflects the limited experimental knowledge we generally have in the computational design of molecular crystals. By doing so, and using fully flexible molecules in fully variable unit cells, we show that the experimental structures can be predicted in fewer than 20 generations. Nonetheless, one must be aware that some molecular crystals have naturally hindered evolutions, requiring as many attempts as there are space groups of interest to predict their structures, and some may require the accuracy of all-electron calculations to discriminate between closely ranked structures. To save resources in this computationally demanding process, we showed that a hybrid xTB/DFT-D approach could be considered in a subsequent study to push the limits of CSP beyond 200+ atoms and for cocrystals.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10254755PMC
http://dx.doi.org/10.3390/molecules28114471DOI Listing

Publication Analysis

Top Keywords

molecular crystals
16
crystal structure
8
high-energy molecular
8
molecular
7
accurate crystal
4
structure predictions
4
predictions high-energy
4
molecular crystals?
4
crystals? molecular
4
crystals
4

Similar Publications

The structure of His15 acetamide-modified hen egg-white lysozyme: a nice surprise from an old friend.

Acta Crystallogr F Struct Biol Commun

February 2025

Department of Chemistry `Ugo Schiff', Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.

Hen egg-white lysozyme (HEWL) is a small polycationic protein which is highly soluble and stable. This has led to it becoming a `molecular laboratory' where chemical biological operations and structural techniques are tested. To date, HEWL accounts for 1233 PDB entries, roughly 0.

View Article and Find Full Text PDF

Drug Property Optimization: Design, Synthesis, and Characterization of Novel Pharmaceutical Salts and Cocrystal-Salt of Lumefantrine.

Mol Pharm

January 2025

Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.

Lumefantrine (LMF) is a low-solubility antimalarial drug that cures acute, uncomplicated malaria. It exerts its pharmacological effects against erythrocytic stages of spp. and prevents malaria pathogens from producing nucleic acid and protein, thereby eliminating the parasites.

View Article and Find Full Text PDF

Peptidomics & Molecular Simulation-Based Specific Screening of Antifreeze Peptides from Scale and the Action Mechanism.

J Agric Food Chem

January 2025

College of Chemical Engineering, College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, P.R.China.

This study aims to explore the cryoprotective mechanisms of food-derived hydrolyzed peptides and develop novel cryoprotectants to enhance the quality of frozen foods. scale antifreeze peptides (Ej-AFP) were prepared using enzymatic hydrolysis, which had a 4-fold increase in protection efficiency for surimi compared to traditional cryoprotectants. Furthermore, Ej-AFP was able to control 63.

View Article and Find Full Text PDF

A challenging aspect in the synthesis of covalent organic frameworks (COFs) that goes beyond the framework's structure and topology is interpenetration, where two or more independent frameworks are mechanically interlocked with each other. Such interpenetrated or interlocked frameworks are commonly found in three-dimensional (3D) COFs with large pores. However, interlocked two-dimensional (2D) COFs are rarely seen in the literature, as 2D COF layers typically crystallize in stacks that maximize stabilization through π-stacking.

View Article and Find Full Text PDF

Citronellol (CT) is a naturally occurring lipophilic monoterpenoid which has shown anticancer effects in numerous cancerous cell lines. This study was, therefore, designed to examine CT's potential as an anticancer agent against glioblastoma (GBM). Network pharmacology analysis was employed to identify potential anticancer targets of CT.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!