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X-ray Crystallography Based Study on Molecular Structure

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Structure".

Deadline for manuscript submissions: closed (15 March 2024) | Viewed by 7664

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Dr. Kam-Hung Low

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Guest Editor

X-ray Crystallography Laboratory, Department of Chemistry, University of Hong Kong, Hong Kong, China
Interests: crystal structure determination; single-crystal diffraction; powder diffraction; pharmaceutical cocrystals; functional materials

Special Issue Information

Dear Colleagues,

The discovery of X-ray crystallography a century ago by Sirs William and Lawrence Bragg began a flourishing era of studies on molecular structures. The three-dimensional structure of molecules holds an essential key to understanding and, in some particular cases, predicting their chemical and physical properties, which is the foundation of diverse research fields in modern science, including drug discovery, materials design, structural biology, and quantum mechanics. Accurate atom connectivity with high bond precision (generally better than 0.01 Angstrom) can be achieved in contemporary chemical single-crystal X-ray diffractometers conveniently. X-ray crystallography is advantageous over other structure determination methods, such as cryogenic electron microscopy, in terms of simple sample preparation, user-friendly instrument setup, and low operating expense.

This Special Issue aims to present an overview of the most recent advances in applying X-ray crystallography to a molecular structure. Contributions, including original research manuscripts and reviews, which reveal the studies involving molecular structure determination by X-ray crystallography, are welcome. Studies concerning biologically active small molecules, novel functional materials, and crystallographic data analysis by machine learning will be particularly appreciated.

Dr. Kam-Hung Low
Guest Editor

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Keywords

crystal structure determination
single crystal diffraction
powder diffraction
non-ambient conditions
charge density
structure prediction
non-covalent frameworks
absolute structure and configuration
drug design
computational crystallography

Published Papers (5 papers)

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Research

17 pages, 7240 KiB

Open AccessArticle

New Cocrystals of Ligustrazine: Enhancing Hygroscopicity and Stability

by Yifei Xie, Lixiang Gong, Yue Tao, Baoxi Zhang, Li Zhang, Shiying Yang, Dezhi Yang, Yang Lu and Guanhua Du

Molecules 2024, 29(10), 2208; https://doi.org/10.3390/molecules29102208 - 8 May 2024

Viewed by 567

Abstract

Ligustrazine (TMP) is the main active ingredient extracted from Rhizoma Chuanxiong, which is used in the treatment of cardiovascular and cerebrovascular diseases, with the drawback of being unstable and readily sublimated. Cocrystal technology is an effective method to improve the stability of TMP. Three benzoic acid compounds including P-aminobenzoic acid (PABA), 3-Aminobenzoic acid (MABA), and 3,5-Dinitrobenzoic acid (DNBA) were chosen for co-crystallization with TMP. Three novel cocrystals were obtained, including TMP-PABA (1:2), TMP-MABA (1.5:1), and TMP-DNBA (0.5:1). Hygroscopicity was characterized by the dynamic vapor sorption (DVS) method. Three cocrystals significantly improved the hygroscopicity stability, and the mass change in TMP decreased from 25% to 1.64% (TMP-PABA), 0.12% (TMP-MABA), and 0.03% (TMP-DNBA) at 90% relative humidity. The melting points of the three cocrystals were all higher than TMP, among which the TMP-DNBA cocrystal had the highest melting point and showed the best stability in reducing hygroscopicity. Crystal structure analysis shows that the mesh-like structure formed by the O-H⋯N hydrogen bond in the TMP-DNBA cocrystal was the reason for improving the stability of TMP. Full article

(This article belongs to the Special Issue X-ray Crystallography Based Study on Molecular Structure)

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13 pages, 4296 KiB

Open AccessArticle

Crystal Structures and Physicochemical Properties of 3-Chloro-4-hydroxyphenylacetic Acid Salts with Amines

by Remi Rolland Ngoma Tchibouanga and Ayesha Jacobs

Molecules 2023, 28(19), 6965; https://doi.org/10.3390/molecules28196965 - 7 Oct 2023

Viewed by 1074

Abstract

3-chloro-4-hydroxyphenylacetic acid (CHPAA) is a fungal metabolite. It is a small molecule that is useful in crystal engineering studies due to the functional groups present. Six amines were selected to form salts with CHPAA. Linear derivatives included diethylamine (DEA) and di-N-butylamine (DBM). The aromatic compounds chosen were 2-aminopyridine (A2MP), 2-amino-4-methylpyridine (A24MP), 2-amino-6-methylpyridine (A26MP) and 4-dimethylaminopyridine (DMAP). The salts were characterised using single-crystal X-ray diffraction, thermal analysis, FTIR spectroscopy and Hirshfeld surface analysis. For all the crystal structures, N-H···O and C-H···Cl contacts were present. O-H···O contacts were found in all the crystal structures except for (

C H P A A^{2 -}) (2 D E A^{+})

, which was also the only structure that displayed a Cl···Cl contact. Furthermore, C-H···O contacts were found in all the crystal structures except for

(C H P A A^{-}) (D B M^{+}) .

The thermal stability trend showed that the DBM salt was more stable than the DEA salt. For the aromatic co-formers, the thermal stability trend showed the following:

(C H P A A^{-}) (D M A P^{+})

(C H P A A^{-}) (A 2 M P^{+}) > (2 C H P A A^{-}) (2 A 26 M P^{+}) > (C H P A A^{-}) (A 24 M P^{+})

. Full article

(This article belongs to the Special Issue X-ray Crystallography Based Study on Molecular Structure)

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18 pages, 4620 KiB

Open AccessArticle

Global Analysis of Plasmodium falciparum Dihydropteroate Synthase Variants Associated with Sulfadoxine Resistance Reveals Variant Distribution and Mechanisms of Resistance: A Computational-Based Study

by Rita Afriyie Boateng, James L. Myers-Hansen, Nigel N. O. Dolling, Benedicta A. Mensah, Elia Brodsky, Mohit Mazumder and Anita Ghansah

Molecules 2023, 28(1), 145; https://doi.org/10.3390/molecules28010145 - 24 Dec 2022

Viewed by 2897

Abstract

The continual rise in sulfadoxine (SDX) resistance affects the therapeutic efficacy of sulfadoxine-pyrimethamine; therefore, careful monitoring will help guide its prolonged usage. Mutations in Plasmodium falciparum dihydropteroate synthase (Pfdhps) are being surveilled, based on their link with SDX resistance. However, there is a lack of continuous analyses and data on the potential effect of molecular markers on the Pfdhps structure and function. This study explored single-nucleotide polymorphisms (SNPs) in Pfdhps that were isolated in Africa and other countries, highlighting the regional distribution and its link with structure. In total, 6336 genomic sequences from 13 countries were subjected to SNPs, haplotypes, and structure-based analyses. The SNP analysis revealed that the key SDX resistance marker, A437G, was nearing fixation in all countries, peaking in Malawi. The mutation A613S was rare except in isolates from the Democratic Republic of Congo and Malawi. Molecular docking revealed a general loss of interactions when comparing mutant proteins to the wild-type protein. During MD simulations, SDX was released from the active site in mutants A581G and A613S before the end of run-time, whereas an unstable binding of SDX to mutant A613S and haplotype A437A/A581G/A613S was observed. Conformational changes in mutant A581G and the haplotypes A581G/A613S, A437G/A581G, and A437G/A581G/A613S were seen. The radius of gyration revealed an unfolding behavior for the A613S, K540E/A581G, and A437G/A581G systems. Overall, tracking such mutations by the continuous analysis of Pfdhps SNPs is encouraged. SNPs on the Pfdhps structure may cause protein–drug function loss, which could affect the applicability of SDX in preventing malaria in pregnant women and children. Full article

(This article belongs to the Special Issue X-ray Crystallography Based Study on Molecular Structure)

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12 pages, 3384 KiB

Open AccessArticle

The Influence of Alkali Metals on the Doping of Poly(p-phenylene) Oligomers

by Laura Oliveira Péres, Rebeca da Rochas Rodrigues and Guy Louarn

Molecules 2022, 27(24), 8699; https://doi.org/10.3390/molecules27248699 - 8 Dec 2022

Viewed by 1003

Abstract

In this study, we report on crystallographic studies that were performed on Na- and K-doped terphenyl and quaterphenyl. The data obtained via X-ray scattering and transmission electron diffraction show that, for both K-doped terphenyl and quaterphenyl samples, there is an increase in the c parameter. However, in regard to Na-doped terphenyl, there is a c parameter decrease along with an a parameter increase, which may be accounted for by the polymerization of this oligomer. Moreover, in order to complete the crystallographic study, a Raman analysis was conducted to describe the localization of the radical anions and the local distortions induced by the electric charges during the doping process. Full article

(This article belongs to the Special Issue X-ray Crystallography Based Study on Molecular Structure)

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19 pages, 5763 KiB

Open AccessArticle

The First Noncovalent-Bonded Supramolecular Frameworks of (Benzylthio)Acetic Acid with Proline Compounds, Isonicotinamide and Tryptamine

by Justyna Sienkiewicz-Gromiuk and Aleksandra Drzewiecka-Antonik

Molecules 2022, 27(23), 8203; https://doi.org/10.3390/molecules27238203 - 24 Nov 2022

Cited by 3 | Viewed by 1349

Abstract

The co-crystallization of (benzylthio)acetic acid (HBTA) with L-proline (L-PRO), D-proline (D-PRO), DL-proline (DL-PRO), isonicotinamide (INA) and tryptamine (TPA) led to the formation of five novel crystalline compounds: L-PRO^±·HBTA (1), D-PRO^±·HBTA (2), DL-PRO^±·HBTA (3), INA·HBTA (4) and TPA⁺·BTA⁻ (5). The prepared supramolecular assemblies were characterized by single crystal X-ray diffraction, an elemental analysis, FT-IR spectroscopy and a thermal analysis based on thermogravimetry (TG) combined with differential scanning calorimetry (DSC). Additionally, their melting points through TG/DSC measurements were established. All fabricated adducts demonstrated the same stoichiometry, displayed as 1:1. The integration of HBTA with selected N-containing co-formers yielded different forms of multi-component crystalline phases: zwitterionic co-crystals (1–3), true co-crystal (4) or true salt (5). In the asymmetric units of 1–4, the acidic ingredient is protonated, whereas the corresponding N-containing entities take either the zwitterionic form (1–3) or remain in the original neutral figure (4). The molecular structure of complex 5 is occupied by the real ionic forms of both components, namely the (benzylthio)acetate anion (BTA⁻) and the tryptaminium cation (TPA⁺). In crystals 1–5, the respective molecular residues are permanently bound to each other via strong H-bonds provided by the following pairs of donor···acceptor: O_carboxylic···O_carboxylate and N_{pyrrolidinium}···O_carboxylate in 1–3, O_carboxylic···N_pyridine and N_amine···O_carboxylic in 4 as well as N_indole···O_carboxylate and N_aminium···O_carboxylate in 5. The crystal structures of conglomerates 1–5 are also stabilized by numerous weaker intermolecular contacts, including C–H···O (1–3, 5), C–H···S (1, 2, 5), C–H···N (5), C–H···C (5), C–H···π (1–5) as well as π···π (4) interactions. The different courses of registered FT-IR spectral traces and thermal profiles for materials 1–5 in relation to their counterparts, gained for the pure molecular ingredients, also clearly confirm the formation of new crystalline phases. Full article

(This article belongs to the Special Issue X-ray Crystallography Based Study on Molecular Structure)

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