Research applications of the Cambridge Structural Database (CSD)

Crystal structure data are of fundamental importance in a wide spectrum of scientific activities. This tutorial review summarises the principal application areas, so far, for the data from more than 300,000 crystal structures of small organic and metal-organic compounds that are stored in the Cambridge Structural Database (CSD). Direct use of the accumulated data is valuable in establishing standard molecular dimensions, determining conformational preferences and in the study of intermolecular interactions, all of which are crucial in structural chemistry and rational drug design. More recently, information derived from the CSD has been used to construct two dynamic libraries of structural knowledge: Mogul, which stores intramolecular information, and IsoStar, which stores information about intermolecular interactions. These electronic libraries provide information "at the touch of a button". In their turn, the libraries also serve as sources of structural knowledge for applications software that address specific problems in small-molecule and biological chemistry.     

The Cambridge Structural Database in Retrospect and Prospect

The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal–organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700 000 structures and is a comprehensive and fully retrospective historical archive of small‐molecule crystallography. Nearly 40 000 new structures are added each year. As X‐ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self‐financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC’s funding model in relation to open access and open data paradigms.     

英国剑桥晶体结构数据系统及中国区中心

简介了英国剑桥晶体结构数据系统及建立在中国科学院化工冶金所计算机化学开放实验室该系统的中国区中心（ＮａｔｉｏｎａｌＡｆｆｉｌｉａｔｅｄＣｅｎｔｒｅｏｆＣｈｉｎａ）。     

Vaporization of Molecular Coordination Organotitanium Compounds: Development of the Structure-Thermochemical Approach with Programmed Use of the Cambridge Structural Database

The structure-thermochemical approach to analysis and prediction of vaporization parameters of volatile organometallic compounds was modified and software-implemented on the basis of the concept of Voronoi–Dirichlet molecular polyhedra. The TOPOS program package was employed to analyze the intermolecular contacts and to calculate the vaporization enthalpies for 570 organotitanium molecular complexes selected from the Cambridge Structural Database. In the case of titanium hydrocarbon complexes, the results of semiempirical calculation are in satisfactory agreement with experimental data. In other cases, the quantitative thermochemical parameters obtained allow one to estimate the unknown cooperative contributions for various functional groups.     

Prediction of H-Bonding Motifs for Pyrazoles and Oximes Using the Cambridge Structural Database

H-bonding motifs for pyrazoles and oximes have been examined in the Cambridge Structural Database. The accessible surface of the N atoms has been found to be useful as a discriminator to divide structures into dimer and catemer motifs for both pyrazoles and oximes. Low accessibility favors dimers and tetramers and high values favor catemers and trimers. Total molecular volume shows some correlation for oximes, while high values favor dimers. Empirical rules were successfully applied to predict the motifs of eight new structures in the subsequent release of the CSD.     

Identifying porous cage subsets in the Cambridge Structural Database using topological data analysis

As rationally designable materials, the variety and number of synthesised metal–organic cages (MOCs) and organic cages (OCs) are expected to grow in the Cambridge Structural Database (CSD). In this regard, two of the most important questions are, which structures are already present in the CSD and how can they be identified? Here, we present a cage mining methodology based on topological data analysis and a combination of supervised and unsupervised learning that led to the derivation of – to the best of our knowledge – the first and only MOC dataset of 1839 structures and the largest experimental OC dataset of 7736 cages, as of March 2022. We illustrate the use of such datasets with a high-throughput screening of MOCs and OCs for xenon/krypton separation, important gases in multiple industries, including healthcare.

We mined the Cambridge Structural Database for porous cages using topological data analysis, which resulted in the first and only dataset of metal-organic cages and the largest dataset of organic cages.     

Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses

The metal coordination number (CN) is a key determinant of the structure and properties of metal complexes. It also plays an important role in metal selectivity in certain metalloproteins. Despite its central role, the preferred CN for several metal cations remains ambiguous, and the factors determining the metal CN are not fully understood. Here, we evaluate how the CN depends on (1) the metal's size, charge, and charge-accepting ability for a given set of ligands, and (2) the ligand's size, charge, charge-donating ability, and denticity for a given metal by analyzing the Cambridge Structural Database (CSD) structures of metal ions in the periodic table. The results show that for a given ligand type, the metal's size seems to affect its CN more than its charge, especially if the ligand is neutral, whereas, for a given metal type, the ligand's charge and charge-donating ability appear to affect the metal CN more than the ligand's size. Interestingly, all 98 metal cations surveyed could adopt more than than one CN, and most of them show an apparent preference toward even rather than odd CNs. Furthermore, as compared to the preferred metal CNs observed in the CSD, those in protein binding sites generally remain the same. This implies that the protein matrix (excluding amino acid residues in the metal's first and second coordination shell) does not impose severe geometrical restrictions on the bound metal cation.     

Automated site-directed drug design: Searches of the Cambridge Structural Database for bond lengths in molecular fragments to be used for automated structure assembly

Summary In this paper a database of small frequently occurring molecular fragments is used for the determination of fragment bond lengths from the Cambridge Structural Database. A large number of bond types are described that have not been reported previously.     

不含手性碳的手性化合物及其绝对构型——剑桥结构数据库实例分析

利用英国剑桥结构数据库中的实例并结合相关三维可视化软件,介绍了含有氮/磷等手性杂原子、轴手性、平面手性、螺旋手性、超分子手性等手性因素的手性化合物及其绝对构型,以加深对手性概念的认识和理解。     

利用《CA on CD》光盘数据库查找信息资源

1　《ＣＡｏｎＣＤ》光盘数据库简介　　《ＣＡｏｎＣＤ》光盘数据库由美国化学会制作 ,文摘内容与书本式《化学文摘》相对应 ,收录了世界范围内有关化学及化工方面的大量科技文献 ,年文献量达 77.3万条 ,其中约 1 2 .3万条专利。数据库文献内容及索引信息按月更新。2　《ＣＡｏｎＣＤ》的检索方法　　《ＣＡｏｎＣＤ》提供下面 4种基本检索途径 :　　 ( 1 )词条检索 (ＷｏｒｄＳｅａｒｃｈ)　　在检索菜单窗口 ,点击Ｓｅａｒｃｈ键或在Ｓｅａｒｃｈ命令菜单中选择ＷｏｒｄＳｅａｒｃｈ命令 ,在检索词对话框中输入检索词 ,用鼠标点击Ｓｅａ…     

Structural Diversity of Metal-Organic Hydrates: A Crystallographic Structural Database Study

Different hydrogen bonding configurations (0+1, 1+0, 1+2, 2+0, 2+1, 2+2) of lattice water molecules are identified through the crystal database mining. The reported patterns help propagate the discrete molecular complexes into 1D, 2D, and 3D metal-organic architectures.     

Use of isotopes in search of Lost River

Ample evidence exists from ancient Indian texts, geomorphology and sedimentology that a mighty river that once originated in the Himalayas flowed in the North-west India during 7000-3000 BP and disappeared in the sands of the Rajasthan desert. Remote sensing combined with ground search identified part of the buried channel of the ancient river in the Jaisalmer region of Rajasthan. Isotope study showed that the fresh groundwater in that region was indeed ancient and slowly moving southwest and probably had headwater connection in the lower ranges of Himalayas, but not to any glacier. The isotope data (²H, ¹⁸O, ³H and ¹⁴C) compare well with the data in a similar study on another branch of the buried channel in the Cholistan part of the Thar Desert in Pakistan.     

Crystal structures of four δ‐keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ‐keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2‐cyano‐5‐oxo‐5‐phenyl‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₂N₂O₃, (1), ethyl 2‐cyano‐5‐(4‐methoxyphenyl)‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₂₀H₂₄N₂O₄, (2), ethyl 5‐(4‐chlorophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁ClN₂O₃, (3), and the previously published ethyl 5‐(4‐bromophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁BrN₂O₃, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3 , 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53 , 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple‐bond]C interaction (X = F, Cl, Br or I), viz. the N...X distance and the C—X...N and C—N...X angles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.     

Use of an automated image processing program to quantify recombinant adenovirus particles.

Electron microscopy has a pivotal role as an analytical tool in pharmaceutical research. However, digital image data have proven to be too large for efficient quantitative analysis. We describe here the development and application of an automated image processing (AIP) program that rapidly quantifies shape measurements of recombinant adenovirus (rAd) obtained from digitized field emission scanning electron microscope (FESEM) images. The program was written using the macro-recording features within Image-Pro Plus software. The macro program, which is linked to a Microsoft Excel spreadsheet, consists of a series of subroutines designed to automatically measure rAd vector objects from the FESEM images. The application and utility of this macro program has enabled us to rapidly and efficiently analyze very large data sets of rAd samples while minimizing operator time.     

Use of Structural Descriptors to Predict the RM Values of m- and p-Alkoxyphenols in RP TLC

JPC – Journal of Planar Chromatography – Modern TLC - Selected meta- and para-alkoxyphenols have been separated by RP TLC on cellulose impregnated with ethyl oleate, with ethanol-water,...     

Structural Similarity and IR Spectrum Modeling Using the Spectrum–Fragment Composition Database

It is shown on numerous examples that IR spectra of organic compounds may be modeled by using the spectra of the structural analogs selected from the database. This paper presents a technique for model construction and the results of modeling along with some examples of model and experimental spectra. The applicability of this approach to modern and traditional methods of spectral analysis is discussed.     

Interplay between Cation–π and Coinage‐Metal–Oxygen Interactions: An Ab Initio Study and Cambridge Structural Database Survey

The interplay between cation–π and coinage‐metal–oxygen interactions are investigated in the ternary systems N???PhCCM???O (N=Li⁺, Na⁺, Mg²⁺; M=Ag, Au; O=water, methanol, ethanol). A synergetic effect is observed when cation–π and coinage‐metal–oxygen interactions coexist in the same complex. The cation–π interaction in most triads has a greater enhancing effect on the coinage‐metal–oxygen interaction. This effect is analyzed in terms of the binding distance, interaction energy, and electrostatic potential in the complexes. Furthermore, the formation, strength, and nature of both the cation–π and coinage‐metal–oxygen interactions can be understood in terms of electrostatic potential and energy decomposition. In addition, experimental evidence for the coexistence of both interactions is obtained from the Cambridge Structural Database (CSD).