Topological representations of crystal structures: generation, analysis and implementation in the <i>TopCryst</i> system

Шевченко, А. П.; Shabalin, Aleksandr A.; Karpukhin, Igor Yu.; Блатов, В. А.

doi:10.1080/27660400.2022.2088041

Cited by 43 publications

(52 citation statements)

References 47 publications

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“…The creation of C from A is done through a modified and expanded version of the xyz2mol code developed by Jensen and coworkers based on previous work by Kim 42 . The use of C to define the molecular graph offers improved capabilities with respect to other codes based on A 29,30 . Lewis structures give access to q i and Q, and enable advanced substructural searches including specific bond patterns or functional groups.…”

Section: Resultsmentioning

confidence: 99%

“…While the adopted machinery offers a clear advantage, the number of possible C (i.e., Lewis structures) grows very fast with increasing the number of atoms, especially in conjugated backbones. For this reason, together with the difficulty to handle periodic connectivities, cell2mol cannot be applied to periodic structures, for which other approaches based on A are available 29 . However, the generation of C requires a known Q, which is precisely our unknown variable.…”

Section: Resultsmentioning

confidence: 99%

“…The only filters applied at this stage are the presence of the respective TM ion, and the absence of any socalled polymeric bond. Thus, periodic systems are discarded, for which other approaches offer excellent topological analysis tools, or the prediction of metal OS 25,26,29 . Overall, our databases cover molecular crystals of organometallic and coordination complexes.…”

Section: Performance Of Cell2molmentioning

confidence: 99%

“…Other approaches exist to extract more comprehensive information about crystallographic data [27][28][29][30] . On one hand, CSD editors interpret and curate the database entries using algorithms that assess not only Q M but also the molecular connectivity (C, i.e., the bond order network) and the formal atomic charges (q i ) 27 .…”

Section: Introductionmentioning

confidence: 99%

“…However, they are closed, the final C and Q M data are only accessible through the limited set of export options in the CCDC software, and have only been applied to few CSD entries, so their degree of automatization is unclear. On the other hand, a fully automatized topological analysis of crystals is available with the ToposPro package 30 at the TopCryst web interface 29 , which includes a simplified form of C based on geometry considerations. It is worth mentioning that both the CSD algorithms and ML models exploit statistics to make their predictions.…”

Section: Introductionmentioning

confidence: 99%

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cell2mol: encoding chemistry to interpret crystallographic data

et al. 2022

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The creation and maintenance of crystallographic data repositories is one of the greatest data-related achievements in chemistry. Platforms such as the Cambridge Structural Database host what is likely the most diverse collection of synthesizable molecules. If properly mined, they could be the basis for the large-scale exploration of new regions of the chemical space using quantum chemistry (QC). Yet, it is currently challenging to retrieve all the necessary information for QC codes based exclusively on the available structural data, especially for transition metal complexes. To overcome this limitation, we present cell2mol, a software that interprets crystallographic data and retrieves the connectivity and total charge of molecules, including the oxidation state (OS) of metal atoms. We demonstrate that cell2mol outperforms other popular methods at assigning the metal OS, while offering a comprehensive interpretation of the unit cell. The code is made available, as well as reliable QC-ready databases totaling 31k transition metal complexes and 13k ligands that contain incomparable chemical diversity.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Performance Of Cell2molmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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cell2mol: encoding chemistry to interpret crystallographic data

et al. 2022

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Super‐hard hybrid ene‐C₅, yne‐C₆, and ene‐yne‐C₇ allotropes from crystal engineering and first principles

Matar

2023

Zeitschrift anorg allge chemie

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Based on tetrahedral lonsdaleite‐like C4 inserted with C(sp2), C(sp1) and both C(sp2)‐ C(sp1) ultrahard hybrid allotropes ene‐C5, yne‐C6, and ene‐yne‐C7 were generated and identified from quantum density functional theory DFT calculations of ground states. The crystal density and the cohesive energy were found to decrease along the series C4‐C5‐C6‐C7 from the larger openness of the structures due to C insertions; such feature led to decrease the hardness throughout the series. The novel hybrid allotropes were found stable mechanically (elastic constants and their combinations) and dynamically (phonons band structures). From the electronic band structures, the inserted carbons were found to add up rigidly to the diamond‐like bands of C4 while being characterized by small band gap semi‐conductor to metallic‐like behavior. Modified diamonds such as the simple models herein considered exist (ex. nano‐diamond) and their investigations are of growing interest in materials sciences communities with applications as in electrochemistry.

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Synthesis, crystal structure, and spectroscopic characterization of aminoguanidinium thiosulfate, (CN₄H₇)₂S₂O₃

Charkin,

Banaru,

Ivanov

et al. 2023

Zeitschrift anorg allge chemie

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Aminoguanidinium thiosulfate, (CN4H7)2S2O3 (1), was prepared via an exchange route from barium thiosulfate and aminoguanidinium sulfate. The new compound is monoclinic, a=12.8344(6) Å, b=13.9134(6) Å, c=6.8757(3) Å, β=115.529(5)°, and crystallizes in a centrosymmetric C2/m space group. Its crystal structure can be considered either as pseudo‐columnar comprised of stacked [CN4H7]+ cations and isolated [S2O3]2− anions which are actively involved in hydrogen bonding, or as H‐bonded bilayers comprised of both [CN4H7]+ and [S2O3]2− of topologic type 3,6L60. The latter ones are H‐bound into a 4,8‐coordinated bearing framework of the type scu.

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Topological representations of crystal structures: generation, analysis and implementation in the TopCryst system

Cited by 43 publications

References 47 publications

cell2mol: encoding chemistry to interpret crystallographic data

cell2mol: encoding chemistry to interpret crystallographic data

Super‐hard hybrid ene‐C₅, yne‐C₆, and ene‐yne‐C₇ allotropes from crystal engineering and first principles

Synthesis, crystal structure, and spectroscopic characterization of aminoguanidinium thiosulfate, (CN₄H₇)₂S₂O₃

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Topological representations of crystal structures: generation, analysis and implementation in the TopCryst system

Cited by 43 publications

References 47 publications

cell2mol: encoding chemistry to interpret crystallographic data

cell2mol: encoding chemistry to interpret crystallographic data

Super‐hard hybrid ene‐C5, yne‐C6, and ene‐yne‐C7 allotropes from crystal engineering and first principles

Synthesis, crystal structure, and spectroscopic characterization of aminoguanidinium thiosulfate, (CN4H7)2S2O3

Contact Info

Product

Resources

About

Super‐hard hybrid ene‐C₅, yne‐C₆, and ene‐yne‐C₇ allotropes from crystal engineering and first principles

Synthesis, crystal structure, and spectroscopic characterization of aminoguanidinium thiosulfate, (CN₄H₇)₂S₂O₃