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Cocrystals of a coumarin derivative: an efficient approach towards anti-leishmanial cocrystals against MIL-resistant Leishmania tropica 一种香豆素衍生物的共晶体:一种针对耐 MIL 的热带利什曼病的抗利什曼病共晶体的有效方法。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524001416
Muhammad Shahbaz , Saba Farooq , M. Iqbal Choudhary , Sammer Yousuf , L. R. MacGillivray (Editor)
{"title":"Cocrystals of a coumarin derivative: an efficient approach towards anti-leishmanial cocrystals against MIL-resistant Leishmania tropica","authors":"Muhammad Shahbaz , Saba Farooq , M. Iqbal Choudhary , Sammer Yousuf , L. R. MacGillivray (Editor)","doi":"10.1107/S2052252524001416","DOIUrl":"10.1107/S2052252524001416","url":null,"abstract":"<div><p>This study demonstrates the synthesis of non-cytotoxic active candidates (co-crystals) of coumarin-3-carb­oxy­lic acid with various coformers to target the MIL-resistant <em>Leishmania tropica</em>. These promising anti-leishmanial results indicate the importance of crystal engineering by highlighting that manipulation of supramolecular architecture in the solid state can impact the biological response.</p></div><div><p>Leishmaniasis is a neglected parasitic tropical disease with numerous clinical manifestations. One of the causative agents of cutaneous leishmaniasis (CL) is <em>Leishmania tropica</em> (<em>L. tropica</em>) known for causing ulcerative lesions on the skin. The adverse effects of the recommended available drugs, such as amphotericin B and pentavalent antimonial, and the emergence of drug resistance in parasites, mean the search for new safe and effective anti-leishmanial agents is crucial. Miltefosine (MIL) was the first recommended oral medication, but its use is now limited because of the rapid emergence of resistance. Pharmaceutical cocrystallization is an effective method to improve the physicochemical and biological properties of active pharmaceutical ingredients (APIs). Herein, we describe the cocrystallization of coumarin-3-carb­oxy­lic acid (<strong>CU</strong>, <strong>1a</strong>; 2-oxobenzo­pyrane-3-carb­oxy­lic acid, C<sub>10</sub>H<sub>6</sub>O<sub>4</sub>) with five coformers [2-amino-3-bromo­pyridine (<strong>1b</strong>), 2-amino-5-(tri­fluoro­methyl)-pyridine (<strong>1c</strong>), 2-amino-6-methyl­pyridine (<strong>1d</strong>), <em>p</em>-amino­benzoic acid (<strong>1e</strong>) and amitrole (<strong>1f</strong>)] in a 1:1 stoichiometric ratio via the neat grinding method. The cocrystals <strong>2</strong>–<strong>6</strong> obtained were characterized via single-crystal X-ray diffraction, powder X-ray diffraction, differential scanning calorimetry and thermogravimetric analysis, as well as Fourier transform infrared spectroscopy. Non-covalent interactions, such as van der Waals, hydrogen bonding, C—H⋯π and π⋯π interactions contribute significantly towards the packing of a crystal structure and alter the physicochemical and biological activity of <strong>CU</strong>. In this research, newly synthesized cocrystals were evaluated for their anti-leishmanial activity against the MIL-resistant <em>L. tropica</em> and cytotoxicity against the 3T3 (normal fibroblast) cell line. Among the non-cytotoxic cocrystals synthesized (<strong>2</strong>–<strong>6</strong>), <strong>CU</strong>:<strong>1b</strong> (<strong>2</strong>, IC<sub>50</sub> = 61.83 ± 0.59 µ<em>M</em>), <strong>CU</strong>:<strong>1c</strong> (<strong>3</strong>, 125.7 ± 1.15 µ<em>M</em>) and <strong>CU</strong>:<strong>1d</strong> (<strong>4</strong>, 48.71 ± 0.75 µ<em>M</em>) appeared to be potent anti-leishmanial agents and showed several-fold more anti-leishmanial potential than the tested standard drug (MIL, IC<sub>50</sub> = 169.55 ± 0.078 ","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 224-236"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural analysis of nanocrystals by pair distribution function combining electron diffraction with crystal tilting 通过电子衍射与晶体倾斜相结合的对分布函数分析纳米晶体的结构。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524001064
Linshuo Guo , Shitao Wu , Zhengyang Zhou , Yanhang Ma , M. Gemmi (Editor)
{"title":"Structural analysis of nanocrystals by pair distribution function combining electron diffraction with crystal tilting","authors":"Linshuo Guo ,&nbsp;Shitao Wu ,&nbsp;Zhengyang Zhou ,&nbsp;Yanhang Ma ,&nbsp;M. Gemmi (Editor)","doi":"10.1107/S2052252524001064","DOIUrl":"10.1107/S2052252524001064","url":null,"abstract":"<div><p>A new method is proposed to enhance the continuity of diffraction rings and improve the signal-to-noise ratio in electron diffraction data for electron pair distribution function (ePDF) analysis.</p></div><div><p>As an important characterization method, pair distribution function (PDF) has been extensively used in structural analysis of nanomaterials, providing key insights into the degree of crystallinity, atomic structure, local disorder <em>etc</em>. The collection of scattering signals with good statistics is necessary for a reliable structural analysis. However, current conventional electron diffraction experiments using PDF (ePDF) are limited in their ability to acquire continuous diffraction rings for large nanoparticles. Herein, a new method – tilt-ePDF – is proposed to improve the data quality and compatibility of ePDF by a combination of electron diffraction and specimen tilting. In the present work, a tilt-series of electron diffraction patterns was collected from gold nanoparticles with three different sizes and a standard sample polycrystalline aluminium film for ePDF analysis. The results show that tilt-ePDF can not only enhance the continuity of diffraction rings, but can also improve the signal-to-noise ratio in the high scattering angle range. As a result, compared with conventional ePDF data, tilt-ePDF data provide structure parameters with a better accuracy and lower residual factors in the refinement against the crystal structure. This method provides a new way of utilizing ePDF to obtain accurate local structure information from nanoparticles.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 202-209"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139741078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterizing self-assembled structures made with magnetic Janus nanoparticles 磁性 Janus 纳米粒子自组装结构的特征。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524001532
Elizabeth Blackburn
{"title":"Characterizing self-assembled structures made with magnetic Janus nanoparticles","authors":"Elizabeth Blackburn","doi":"10.1107/S2052252524001532","DOIUrl":"10.1107/S2052252524001532","url":null,"abstract":"<div><p>Small-angle X-ray scattering has revealed how magnetic Janus particles pair up in solutions in small and large magnetic fields.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 131-132"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Community recommendations on cryoEM data archiving and validation 关于低温电子显微镜数据存档和验证的社区建议。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524001246
Gerard J. Kleywegt , Paul D. Adams , Sarah J. Butcher , Catherine L. Lawson , Alexis Rohou , Peter B. Rosenthal , Sriram Subramaniam , Maya Topf , Sanja Abbott , Philip R. Baldwin , John M. Berrisford , Gérard Bricogne , Preeti Choudhary , Tristan I. Croll , Radostin Danev , Sai J. Ganesan , Timothy Grant , Aleksandras Gutmanas , Richard Henderson , J. Bernard Heymann , S. Raunser (Editor)
{"title":"Community recommendations on cryoEM data archiving and validation","authors":"Gerard J. Kleywegt ,&nbsp;Paul D. Adams ,&nbsp;Sarah J. Butcher ,&nbsp;Catherine L. Lawson ,&nbsp;Alexis Rohou ,&nbsp;Peter B. Rosenthal ,&nbsp;Sriram Subramaniam ,&nbsp;Maya Topf ,&nbsp;Sanja Abbott ,&nbsp;Philip R. Baldwin ,&nbsp;John M. Berrisford ,&nbsp;Gérard Bricogne ,&nbsp;Preeti Choudhary ,&nbsp;Tristan I. Croll ,&nbsp;Radostin Danev ,&nbsp;Sai J. Ganesan ,&nbsp;Timothy Grant ,&nbsp;Aleksandras Gutmanas ,&nbsp;Richard Henderson ,&nbsp;J. Bernard Heymann ,&nbsp;S. Raunser (Editor)","doi":"10.1107/S2052252524001246","DOIUrl":"10.1107/S2052252524001246","url":null,"abstract":"<div><p>This white paper describes recommendations to the wwPDB, EMDB and the cryoEM communities regarding archiving and validation of single-particle structures and volumes.</p></div><div><p>In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop’s motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 140-151"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139735235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion 将结构预测、分子置换和直接方法辅助模型完成相结合,解决蛋白质结构问题。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252523010291
Zengru Li , Haifu Fan , Wei Ding , Z.-J. Liu (Editor)
{"title":"Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion","authors":"Zengru Li ,&nbsp;Haifu Fan ,&nbsp;Wei Ding ,&nbsp;Z.-J. Liu (Editor)","doi":"10.1107/S2052252523010291","DOIUrl":"10.1107/S2052252523010291","url":null,"abstract":"<div><p>We propose a direct-methods-based dual-space iteration strategy for model completion of molecular replacement (MR) with predicted models. Direct methods has been demonstrated as a powerful tool for phase optimization in protein crystallography, whereas the dual-space iterative strategy is particularly suitable for solving crystallographic protein-complex structures starting from a small subunit. This combined approach provides a shortcut in simplifying the pre-processing steps of predicted models for MR and for final model completion.</p></div><div><p>Highly accurate protein structure prediction can generate accurate models of protein and protein–protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the more challenging cases such as multi-helical structures, multimeric structures and extremely large structures, both in the model preparation and in the completion steps, remains open for discussion. In this paper, a new strategy is proposed based on the framework of direct methods and dual-space iteration, which can greatly simplify the pre-processing steps of predicted models both in normal and in challenging cases. Following this strategy, full-length models or the conservative structural domains could be used directly as the starting model, and the phase error and the model bias between the starting model and the real structure would be modified in the direct-methods-based dual-space iteration. Many challenging cases (from CASP14) have been tested for the general applicability of this constructive strategy, and almost complete models have been generated with reasonable statistics. The hybrid strategy therefore provides a meaningful scheme for X-ray structure determination using a predicted model as the starting point.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 152-167"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139424780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Crystal structure of vancomycin bound to the resistance determinant d-alanine-d-serine 万古霉素与抗药性决定因子 D-丙氨酸-丝氨酸结合的晶体结构。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524000289
Jee Hoon Park , Rachel E. Reviello , Patrick J. Loll , E. N. Baker (Editor)
{"title":"Crystal structure of vancomycin bound to the resistance determinant d-alanine-d-serine","authors":"Jee Hoon Park ,&nbsp;Rachel E. Reviello ,&nbsp;Patrick J. Loll ,&nbsp;E. N. Baker (Editor)","doi":"10.1107/S2052252524000289","DOIUrl":"10.1107/S2052252524000289","url":null,"abstract":"<div><p>A structure is presented for vancomycin bound to the resistance-associated epitope <span>d</span>-Ala-<span>d</span>-Ser. This high-resolution view of the complex suggests that the reduced affinity of vancomycin for this epitope stems from a subtle size mismatch between the ligand and the antibiotic, in addition to potential unfavorable entropic effects.</p></div><div><p>Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a <span>d</span>-alanine-<span>d</span>-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either <span>d</span>-alanine-<span>d</span>-lactate or <span>d</span>-alanine-<span>d</span>-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude. The complex of vancomycin bound to <span>d</span>-alanine-<span>d</span>-serine has been crystallized, and its 1.20 Å X-ray crystal structure is presented here. This structure reveals that the <span>d</span>-alanine-<span>d</span>-serine ligand is bound in essentially the same position and same pose as the native <span>d</span>-alanine-<span>d</span>-alanine ligand. The serine-containing ligand appears to be slightly too large to be comfortably accommodated in this way, suggesting one possible contribution to the reduced binding affinity. In addition, two flexible hydroxyl groups – one from the serine side chain of the ligand, and the other from a glucose sugar on the antibiotic – are locked into single conformations in the complex, which is likely to contribute an unfavorable entropic component to the recognition of the serine-containing ligand.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 133-139"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139564096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The prediction of single-molecule magnet properties via deep learning 通过深度学习预测单分子磁特性。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524000770
Yuji Takiguchi , Daisuke Nakane , Takashiro Akitsu , C.-Y. Su (Editor)
{"title":"The prediction of single-molecule magnet properties via deep learning","authors":"Yuji Takiguchi ,&nbsp;Daisuke Nakane ,&nbsp;Takashiro Akitsu ,&nbsp;C.-Y. Su (Editor)","doi":"10.1107/S2052252524000770","DOIUrl":"10.1107/S2052252524000770","url":null,"abstract":"<div><p>This work involves extraction of salen metal complexes from the Cambridge Structural Database for deep learning to examine the 3D structural features that allow such complexes to act as single-molecule magnets. This research attempts to link a crystal structure database as big data with the molecular design of nanomaterials using artificial intelligence. The approach pioneers the future secondary use of similar crystal structure data.</p></div><div><p>This paper uses deep learning to present a proof-of-concept for data-driven chemistry in single-molecule magnets (SMMs). Previous discussions within SMM research have proposed links between molecular structures (crystal structures) and single-molecule magnetic properties; however, these have only interpreted the results. Therefore, this study introduces a data-driven approach to predict the properties of SMM structures using deep learning. The deep-learning model learns the structural features of the SMM molecules by extracting the single-molecule magnetic properties from the 3D coordinates presented in this paper. The model accurately determined whether a molecule was a single-molecule magnet, with an accuracy rate of approximately 70% in predicting the SMM properties. The deep-learning model found SMMs from 20 000 metal complexes extracted from the Cambridge Structural Database. Using deep-learning models for predicting SMM properties and guiding the design of novel molecules is promising.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 182-189"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The curious case of proton migration under pressure in the malonic acid and 4,4′-bi­pyridine cocrystal 丙二酸和 4,4'-联吡啶共晶体中质子在压力下迁移的奇特现象。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524000344
Ewa Patyk-Kaźmierczak , Fernando Izquierdo-Ruiz , Alvaro Lobato , Michał Kaźmierczak , Ida Moszczyńska , Anna Olejniczak , J. Manuel Recio , C.-Y. Su (Editor)
{"title":"The curious case of proton migration under pressure in the malonic acid and 4,4′-bi­pyridine cocrystal","authors":"Ewa Patyk-Kaźmierczak ,&nbsp;Fernando Izquierdo-Ruiz ,&nbsp;Alvaro Lobato ,&nbsp;Michał Kaźmierczak ,&nbsp;Ida Moszczyńska ,&nbsp;Anna Olejniczak ,&nbsp;J. Manuel Recio ,&nbsp;C.-Y. Su (Editor)","doi":"10.1107/S2052252524000344","DOIUrl":"10.1107/S2052252524000344","url":null,"abstract":"<div><p>Pressure was successfully used to induce single and double proton-transfer reactions in malonic acid and the 4,4′-bi­pyridine cocrystal. After contrasting with similar literature examples, an extended correlation between the Δp<em>K</em> <sub>a</sub> values of coformers and the pressure necessary to initiate proton-transfer reactions is unveiled.</p></div><div><p>In the search for new active pharmaceutical ingredients, the precise control of the chemistry of cocrystals becomes essential. One crucial step within this chemistry is proton migration between cocrystal coformers to form a salt, usually anticipated by the empirical Δp<em>K</em> <sub>a</sub> rule. Due to the effective role it plays in modifying intermolecular distances and interactions, pressure adds a new dimension to the Δp<em>K</em> <sub>a</sub> rule. Still, this variable has been scarcely applied to induce proton-transfer reactions within these systems. In our study, high-pressure X-ray diffraction and Raman spectroscopy experiments, supported by DFT calculations, reveal modifications to the protonation states of the 4,4′-bi­pyridine (BIPY) and malonic acid (MA) cocrystal (BIPYMA) that allow the conversion of the cocrystal phase into ionic salt polymorphs. On compression, neutral BIPYMA and monoprotonated (BIPYH<sup>+</sup>MA<sup>−</sup>) species coexist up to 3.1 GPa, where a phase transition to a structure of <em>P</em>2<sub>1</sub>/<em>c</em> symmetry occurs, induced by a double proton-transfer reaction forming BIPYH<sub>2</sub> <sup>2+</sup>MA<sup>2−</sup>. The low-pressure <em>C</em>2/<em>c</em> phase is recovered at 2.4 GPa on decompression, leading to a 0.7 GPa hysteresis pressure range. This is one of a few studies on proton transfer in multicomponent crystals that shows how susceptible the interconversion between differently charged species is to even slight pressure changes, and how the proton transfer can be a triggering factor leading to changes in the crystal symmetry. These new data, coupled with information from previous reports on proton-transfer reactions between coformers, extend the applicability of the Δp<em>K</em> <sub>a</sub> rule incorporating the pressure required to induce salt formation.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 168-181"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139564099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Persistence of atoms in molecules: there is room beyond electron densities 原子在分子中的存在:电子密度之外还有空间。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524000915
María Menéndez-Herrero , Ángel Martín Pendás , X. Zhang (Editor)
{"title":"Persistence of atoms in molecules: there is room beyond electron densities","authors":"María Menéndez-Herrero ,&nbsp;Ángel Martín Pendás ,&nbsp;X. Zhang (Editor)","doi":"10.1107/S2052252524000915","DOIUrl":"10.1107/S2052252524000915","url":null,"abstract":"<div><p>The 3<em>N</em>-dimensional maxima of the square of the wavefunction, the so-called Born maxima, show beyond doubt that the electronic structure of atoms persists in molecules, either in their original ground state or some low-lying excited state. The electron density is only a low-dimensional projection of this much richer landscape.</p></div><div><p>Evidence that the electronic structure of atoms persists in molecules to a much greater extent than has been usually admitted is presented. This is achieved by resorting to <em>N</em>-electron real-space descriptors instead of one- or at most two-particle projections like the electron or exchange-correlation densities. Here, the 3<em>N</em>-dimensional maxima of the square of the wavefunction, the so-called Born maxima, are used. Since this technique is relatively unknown to the crystallographic community, a case-based approach is taken, revisiting first the Born maxima of atoms in their ground state and then some of their excited states. It is shown how they survive in molecules and that, beyond any doubt, the distribution of electrons around an atom in a molecule can be recognized as that of its isolated, in many cases excited, counterpart, relating this fact with the concept of energetic promotion. Several other cases that exemplify the applicability of the technique to solve chemical bonding conflicts and to introduce predictability in real-space analyses are also examined.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 2","pages":"Pages 210-223"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139905681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Poetry in motion: catching molecules in action. 运动中的诗歌:捕捉行动中的分子。
IF 3.9 2区 材料科学
IUCrJ Pub Date : 2024-03-01 DOI: 10.1107/S2052252524002082
Edward N Baker
{"title":"Poetry in motion: catching molecules in action.","authors":"Edward N Baker","doi":"10.1107/S2052252524002082","DOIUrl":"10.1107/S2052252524002082","url":null,"abstract":"<p><p>Researchers have long sought to `see' proteins and other macromolecules in motion, to better understand their functions. Technological developments, notably advances in serial crystallography, are now making these dreams a reality, heralding a new era of kinetic crystallography.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 Pt 2","pages":"129-130"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10916286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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