Structural Chemistry最新文献

{"title":"Kinetic simulation of the reaction between N,N-dimethylazidoethylamine (DMAZ) and dinitrogen tetroxide (NTO) based on density functional theory","authors":"Jin Guofeng,&nbsp;Huang Zhiyong,&nbsp;Huang Yuanzheng,&nbsp;Gao Minna,&nbsp;Wang Yingying","doi":"10.1007/s11224-024-02401-6","DOIUrl":"10.1007/s11224-024-02401-6","url":null,"abstract":"<div><p>This study focuses on the application of N,N-dimethylazidoethylamine (DMAZ) as an alternative fuel to the traditional hydrazine fuel. Shortening ignition delay time is the key factor for the DMAZ application. In order to explore the ignition mechanism of DMAZ and NTO, the reaction mechanism between DMAZ and NO₂/NTO was studied based on density functional theory (DFT). The results showed that under the conditions of the gas phase and NTO liquid phase, the main path of the reaction is that NO₂ attacks the secondary hydrogen atom of DMAZ. The gas-phase reaction enthalpy is higher than that in the NTO liquid phase, indicating that the gas-phase reaction absorbs more energy and is not easy to proceed, while the NTO liquid-phase reaction is easier. The combustion mechanism of DMAZ and NTO was preliminarily obtained. It is speculated that under actual working conditions, DMAZ and NTO mainly undergo the liquid-phase reaction.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 3","pages":"807 - 815"},"PeriodicalIF":2.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fabrication and characterization of neodymium-macrocycle and its MDOPE composite antibacterial films","authors":"Kun Zhang,&nbsp;Daoxin Wang,&nbsp;Shuangquan Wu,&nbsp;Chengeng Wang,&nbsp;Zhengguang Yu,&nbsp;Lei Zhang","doi":"10.1007/s11224-024-02408-z","DOIUrl":"10.1007/s11224-024-02408-z","url":null,"abstract":"<div><p>This work aims to investigate relative effects of neodymium-macrocycle complex <b>Nd</b>-<b>2</b>_<b>f</b> as the antimicrobial agent on the microstructure, thermal stability, and antibacterial activity of <b>Nd</b>-<b>2</b>_<b>f</b>/MDOPE (machine direction orientation polyethylene) composite films. Under two different contents, 0.5 wt% and 5.0 wt% <b>Nd</b>-<b>2</b>_<b>f</b>/MDOPE composite films are designed and prepared by the extrusion blow molding technology. They are carefully characterized by Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM). It is shown that the low-content <b>Nd</b>-<b>2</b>_<b>f</b> can be uniformly mixed with MDOPE substrate. Compared with the pure MDOPE film, the incorporation of complex <b>Nd</b>-<b>2</b>_<b>f</b> will not affect the basic properties of MDOPE but greatly promote its antibacterial activity. When the content of complex <b>Nd</b>-<b>2</b>_<b>f</b> is 0.5 wt%, the <b>Nd</b>-<b>2</b>_<b>f</b>/MDOPE composite film shows optimal overall performance with excellent thermal stability and antibacterial activity, and it is thus referable for more polyethylene composite antibacterial films with high dispersibility and compatibility.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 2","pages":"745 - 753"},"PeriodicalIF":2.1,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143621822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, crystal structure, DNA studies, DFT calculation and luminescence properties of a new one dimensional copper(II) compound with 4,4′- trimethylenedipyridine and 2,2′-bipyridine","authors":"D. Parthiban,&nbsp;S. Baskaran,&nbsp;S. Rani,&nbsp;M. N. Arumugham,&nbsp;Rakesh Kumar,&nbsp;Sadegh Kaviani","doi":"10.1007/s11224-024-02388-0","DOIUrl":"10.1007/s11224-024-02388-0","url":null,"abstract":"<div><p>In the present work, a new ID polymeric Copper(II) coordination compound {[Cu(bpy)(tridipy)(NO₃)H₂O]·NO₃}_<b>n</b> has been synthesized using a bpy = 2,2′-bipyridine, tridipy = 4,4′- Trimethylenedipyridine) and it has been structurally characterized by elemental analysis, infrared (IR) spectroscopy, electronic paramagnetic resonance (EPR), ultraviolet-visible (UV-vis) spectroscopy and X-ray crystallography. The compound was crystallized in a monoclinic system with space group P 21/n, a = 16.1662(8) Å, b = 16.2604(8) Å, c = 19.1248(9) Å, α = 90°, β = 104.342(2) ° and γ = 90°. Single crystal X-ray structural characterization has revealed the distorted octahedral geometry of the metallic centers and a zipper like polymer structure. The geometry optimization of the title compound was carried using Density Functional Theory. Quantum theory of atoms in molecules (QTAIM) approach was applied to study the nature of interactions between the ligand and metal ion in the studied compound. By using UV-Vis absorption, fluorescence spectroscopy, and cyclic voltammetric techniques, the binding studies of Copper(II) compound with calf thymus DNA (CT-DNA) were investigated. Additionally, the method of gel electrophoresis was used to examine the cleavage of pBR322 DNA by coordination compound.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 3","pages":"797 - 806"},"PeriodicalIF":2.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the optoelectronic behavior of graphene—mordant red conjugate through DFT calculations and MD simulations","authors":"Naina,&nbsp;Madhur Babu Singh,&nbsp;Kumar Rakesh Ranjan,&nbsp;Sandeep Kumar Singh,&nbsp;Prashant Singh","doi":"10.1007/s11224-024-02399-x","DOIUrl":"10.1007/s11224-024-02399-x","url":null,"abstract":"<div><p>Recently, molecular photoswitches have garnered significant attention in the realm of research. The photochemistry of the azo (–N = N–) group due to its photodynamic features associated with the reversible (trans–cis-trans) isomerization cycle considers azo compounds as light-driven molecular devices. This research investigates the effect of mordant red and its derivatives as a photochromic molecule. The MRC1 and MRT1 showed valuable results among all. These derivatives are further explored with the graphene sheet. Density functional theory (DFT) computations were used to analyze the compounds’ and complexes’ structural and electrical characteristics. The garphene + MRC1 and graphene + MRT1 show 264,022.905 kJ/mol of change in energy which is much higher than the MRC1 and MRT1. These may show valuable results in effective photochromism. Furthermore, the interactions within the complexes were investigated through natural bond orbital (NBO) and noncovalent interactions (NCI) analysis. Moreover, the stability of the complexes was examined via molecular dynamics (MD) simulations using GROMACS. These were extensively and successfully employed in research on the structural and electrical characteristics of several azo-containing compounds. The research gives valuable results and might be useful for photoswitching molecules.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 3","pages":"783 - 796"},"PeriodicalIF":2.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning-integrated and fingerprint-based similarity search against immuno oncology library for identification of novel ERK2 inhibitors","authors":"Vikramsinh Sardarsinh Suryawanshi,&nbsp;Surbhi Pravin Pawar,&nbsp;Mahima Sudhir Kolpe,&nbsp;Heba Taha M. Abdelghani,&nbsp;Sonali Chikhale,&nbsp;Pritee Chunarkar Patil,&nbsp;Shovonlal Bhowmick","doi":"10.1007/s11224-024-02397-z","DOIUrl":"10.1007/s11224-024-02397-z","url":null,"abstract":"<div><p>The extracellular signal-regulated kinase 2 (ERK2) protein plays a pivotal role in regulating cell division cycles and signaling pathways essential for various biological processes. ERK2 inhibition is a promising therapeutic approach for diseases like cardiovascular deformities, neurodegenerative disorders, and other forms of cancers. The current study presents novel compounds potentially inhibiting ERK2 activity, thus disrupting its cellular functions. A thorough structural assessment of the available crystallographic information was undertaken. The protein’s active site was deciphered, and the experimental grid space of inhibitors interaction was allocated. The study proceeded further with a precise inhibitor search employing a “similarity search” algorithm based on the previously reported kinase inhibitors. Schematic virtual screening method combined with molecular docking steps were executed to enlist the probable hits. AI/ML-based pharmacokinetics properties helped streamline hits’ initial chemical space and select the most potent leads. Complexes formed by these compounds were analyzed for their stability by molecular dynamics (MD) simulations. Post dynamics statistical calculations, viz., protein backbone and ligand RMSD, the radius of gyration, and the constitutive amino acids fluctuations (RMSF), confirmed the protein–ligand association over a period of 300 ns. The magnitude of co-ordinations was estimated by intermolecular H-bond count and the MMGBSA calculations. The free energy landscape (FEL) and principal component analysis (PCA) demonstrated the thermodynamical feasibility of the complex formation with an affinity greater than the previously reported inhibitors. This study, thus, presents a promising avenue for advancing the drug discovery process by identifying novel ERK2 protein inhibitors with potential benefits for healthcare.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 2","pages":"681 - 700"},"PeriodicalIF":2.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anchoring of boron halides BX (X: F, Cl, and Br) on transition metal (M: Cr, Mo, W) carbonyl complexes M(CO)5 (M: Cr, Mo, W): structure, bonding, and energy decomposition studies based on theoretical calculations","authors":"Favour A. Nelson,&nbsp;Rawlings A. Timothy,&nbsp;Terkumbur E. Gber,&nbsp;Jisha M. Thomas,&nbsp;Thayalaraj Christopher Jeyakumar,&nbsp;Emmanuel Emmanuel","doi":"10.1007/s11224-024-02406-1","DOIUrl":"10.1007/s11224-024-02406-1","url":null,"abstract":"<div><p>This study investigates the structural and electronic properties of hexacarbonyl [M(CO)₆] (M = Cr, Mo, W) and haloborylene-substituted complexes [M(CO)₅BX] (X = F, Cl, Br) using the density functional theory (DFT) computation at the B3LYP-D3(BJ)/def2-SVP method. The M-C bond lengths are found to follow the order: W–C (2.090 Å in W(CO)₅BBr) &gt; Mo-C (2.055 Å) &gt; Cr-C (1.906 Å in Cr(CO)₅BCl). Substituting BX leads to a decrease in bond lengths and an increase in bond strength for Cr complexes, while Mo and W complexes show opposite trends. The M-B bond lengths increase from Cr (1.886 Å in Cr(CO)₅BBr) to W (2.115 Å in W(CO)₅BF), indicating a correlation with atomic radii and electronic interactions. Vibrational spectroscopy shows C-O stretching frequencies ranging from 2080 to 2210 cm⁻¹, with Cr(CO)₆ at 2208 cm⁻¹, while B-X stretching frequencies range from 1045 to 1456 cm⁻¹. The Wiberg bond order (WBO) analysis indicates strong bonding in Mo(CO)₅BCl (WBO = 1.234) and weaker bonds in bromide complexes, consistent with intrinsic bond strength values. A charge decomposition analysis reveals significant back-donation in Cr(CO)₅BBr, while Mo(CO)₆ favors σ-donation. Thermodynamic calculations show that bromide complexes exhibit high stability with negative entropy changes and elevated heat capacities. Quantum chemical parameters reveal that Cr(CO)₆ has the highest HOMO–LUMO gap (5.475 eV), whereas W(CO)₅BBr shows the smallest (4.372 eV), indicating greater reactivity. QTAIM analysis shows consistent electron density (ρ = 0.291–0.292 a.u.) and a Laplacian value of − 0.232, confirming similar electronic distributions. This comprehensive analysis elucidates the structural stability, bonding characteristics, and electronic properties of these complexes, providing insights into their potential catalytic applications.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 1","pages":"13 - 28"},"PeriodicalIF":2.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, structural characterization, computational studies, and in silico and in vitro biological activities of cyclodextrin inclusion complex with sulfonamide derived from L-valine as antimicrobial and anti-HIV-1 agents","authors":"Zineb Attou,&nbsp;Yamina Abdi,&nbsp;Yassamina Arbia,&nbsp;Belgacem Bezzina,&nbsp;Hadjer Merazka,&nbsp;Messaouda Mohamdi,&nbsp;Dhaouiya Siziani,&nbsp;Meziane Brahimi,&nbsp;Nadjia Bensouilah","doi":"10.1007/s11224-024-02393-3","DOIUrl":"10.1007/s11224-024-02393-3","url":null,"abstract":"<div><p>An inclusion complex of sulfonamide derived from L-valine (dimethyl 2, 2′- (sulfonylbis (azanediyl)) bis (3-methylbutanoate), (DSBM), with cyclodextrin has been synthesized and characterized using different spectroscopic techniques: FT-IR, ¹H NMR, ¹³C NMR, 2D NMR, and UV–Visible. The DFT/B3LYP method was utilized to perform theoretical calculations in order to examine vibrational properties, determine NBO (natural bond orbital) energies, and clarify the frontier molecular orbitals (FMOs). Time-dependent density functional theory TD-DFT calculations were realized for the optimized DSBM and its complex structures. To elucidate the different intermolecular interactions in the complex, a detailed analysis of the topological charge density based on the quantum theory of atoms in molecules (QTAIM) was performed. Moreover, the DHPS from <i>Staphylococcus aureus</i> (PDB code: 1AD4), HIV-1 reverse transcriptase (PDB code: 4KV8), and HIV-1 protease (PDB code: 4Q5M) were selected for molecular docking study. The in silico results indicate that the DSBM and β-CD inclusion complex can be used as a better inhibitor of DHPS enzyme from <i>Staphylococcus aureus</i> bacteria strain. The interaction between DSBM-β-CD inclusion complex and HIV-1 reverse transcriptase (RT) exhibits a higher binding energy (− 147.80 kcal/mol) than that of the drug reference nevirapine (− 103.43 kcal/mol) and DSBM (− 85.53 kcal/mol). The in silico evaluation against HIV-1 protease reveal that the inclusion complex presents antiviral properties better than the free ligand DSBM. Therefore, the in vitro antioxidant activity was evaluated using DPPH radical scavenging. The data show that the cyclodextrin inclusion complex displays an antioxidant activity better than the DSBM and ascorbic acid with inhibition concentration values of 472.71, 427.59, and 513.01 µg/mL for DSBM-β-CD complex, DSBM, and ascorbic acid, respectively. These values reveal that the complexation with β-CD enhances the antioxidant properties. The antimicrobial activity was realized against <i>Staphylococcus aureus</i> (ATCC 6538), <i>Escherichia coli</i> (ATCC 4157), and <i>Bacillus subtilis</i> (ATCC 9372) bacteria strains; <i>Candida albicans</i> (ATCC 24433) yeast strain; and <i>Aspergillus niger</i> (ATCC 16888) mold strain. The results show that the synthesized compounds are more active against <i>Aspergillus niger</i> with an inhibition zone diameter of 90 mm for both DSBM and its β-CD complex. These results indicate that the formed compounds can act as potent antifungal agents.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 2","pages":"637 - 660"},"PeriodicalIF":2.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A computational and spectral analysis of 2-arylhydrazone thiazolo[3,2-a]pyrimidine derivatives containing p-carboxyphenyl fragment","authors":"Victor L. Furer,&nbsp;Artem S. Agarkov,&nbsp;Alexandr E. Vandyukov,&nbsp;Elina R. Gabitova,&nbsp;Anna A. Nefedova,&nbsp;Svetlana E. Solovieva,&nbsp;Igor S. Antipin","doi":"10.1007/s11224-024-02404-3","DOIUrl":"10.1007/s11224-024-02404-3","url":null,"abstract":"<div><p>Experimental Raman and IR spectra of arylhydrazone thiazolo[3,2-<i>a</i>]pyrimidines containing a <i>p</i>-carboxyphenyl moiety are reproduced using <i>E-</i> and <i>Z</i>-conformational calculations. When the aryl group is rotated, two diastereomeric rotamers (<i>1</i>- and <i>2</i>-) can be made from the <i>E</i>- and <i>Z</i>-isomers of ortho-methoxyphenyl-substituted thiazolopyrimidine. Therefore, for compound 1, four isomers (<i>E1</i>, <i>E2</i>, <i>Z1</i>, and <i>Z2</i>) should be considered. For two distinct solvents, the conformations’ free energies and populations were computed. The experimental vibrational spectra of synthesized hydrazones have been analyzed and the bands categorized. Using infrared spectroscopy, the intermolecular H-bond between thiazolopyrimidines and dimethylformamide was studied. The thiazole and pirimidine rings of the obtained thiazolopyrimidine arylhydrazones molecules <b>1</b> and <b>2</b> are home to their HOMO and LUMO, which show a strong bond conjugation and an almost flat molecular skeleton. The molecule’s reactivity changes and there is a notable delocalization of charge with conformational changes. The thiazolopirimidines’ reactivity was described using descriptors. It was found that in terms of chemical potential, electrophilic index, ionization energy, and electron affinity, the <i>Z</i>-form was inferior to the <i>E</i>-form. The molecules are the same softness, but the <i>E</i>-form has a greater dipole moment.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 2","pages":"621 - 636"},"PeriodicalIF":2.1,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical study on the isomerization mechanism of azobenzene derivatives on graphene substrate","authors":"Yue Zhang,&nbsp;Jianqiang Zhao,&nbsp;Liqiang Sun,&nbsp;Xin Yan,&nbsp;Jiani Sun","doi":"10.1007/s11224-024-02405-2","DOIUrl":"10.1007/s11224-024-02405-2","url":null,"abstract":"<div><p>This article investigates the isomerization mechanism of 3,5-dimethoxy-4-phenyldiazenyl-aniline (DMA) and 3,5-dimethoxy-4-phenyldiazenyl-aniline on graphene (Gr) substrate (DMA-Gr) at B3LYP/def2-svp level. The similarities and differences between the isomerization of DMA and DMA on graphene with different grafting density were explored. According to DFT calculations, DMA has two inversion models: N1 and N2 inversion. N1 isomerization pathway is closely related to the substituents on the benzene ring connecting to N3 atom, and N2 isomerization pathway is closely related to the substituents on the benzene ring connecting to N2 atom. The transition states TS1 and TS2 of the isomerization reaction were found. The isomerization pathway of DMA is more favorable towards N1 inversion. In addition, the isomerization mechanism of a single molecular azobenzene derivative with a graphene substrate(s-DMA-Gr) is similar to that of DMA with s-TS1 and s-TS2 transition states. Interestingly, the isomerization pathway is more favorable towards N2 inversion, which is different from that of DMA. Due to two DMA molecules on graphene substrate, the isomerization pathway is different from that of DMA. The transition states FTS1, FTS2, STS1 and STS2 of the isomerization reaction of DMA-Gr were found. Among them, the isomerization path of the first DMA molecule functional group is more favorable to adopt the N1 inversion with the energy barrier of 34.62 kcal/mol, then the second DMA molecule functional group also adopts the N1 inversion model with the energy barrier of 35.95 kcal/mol. The energy barrier of isomerization of DMA-Gr is higher than that of DMA, corresponding to a longer lifetime for DMA-Gr as energy storage materials.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 2","pages":"661 - 671"},"PeriodicalIF":2.1,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The “reaction zone” concept in modeling solid-state transformations and predicting crystal structures","authors":"Ekaterina O. Bukhteeva,&nbsp;Vladislav A. Blatov","doi":"10.1007/s11224-024-02402-5","DOIUrl":"10.1007/s11224-024-02402-5","url":null,"abstract":"<div><p>We propose a new approach to determine a reaction zone in solid substances. The reaction zone of an origin atom A is defined as a region surrounded by the atoms, which can interact with A without forming self-crossings in the crystal structure network. The identification of this region is based on the topological characteristics of the free space and is essentially independent of its geometry which allows one to apply this model to different types of structures. The reaction zone can be determined by either constructing cages of the natural tiling, i.e., the partition of the crystal space by minimal cages, or analyzing the intersections of the smallest rings of connected atoms by potential interatomic contacts. The proposed approach enables one to determine the atoms to be available for interactions in a crystal structure, thus facilitating the analysis of mechanisms of solid-state transformations and the modeling of novel solid phases. We have applied this approach to generate two new sp³-hybridized carbon allotropes from 150 three-coordinated parent periodic nets. Our analysis of the natural tilings in these allotropes as well as in 1661 carbon allotropes from the SACADA database shows that the structures possessing an isohedral tiling and/or tiles with six-membered faces exhibit high hardness. The allotropes described by similar tilings demonstrate comparable mechanical properties.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 1","pages":"77 - 87"},"PeriodicalIF":2.1,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}