The need for a new generation of substructure searching software

2021 ◽  
Vol 77 (5) ◽  
Author(s):  
Paul R. Raithby ◽  
Robin Taylor
Keyword(s):  
Three Dimensional ◽  
Molecular Fragments ◽  
Complex Molecules ◽  
Substructure Search ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structural Database ◽  
Mechanical Bonds ◽  
New Generation ◽  
Chemistry Community

Advances in synthetic chemistry mean that the molecules now synthesized include increasingly complex entities with mechanical bonds or extensive frameworks. For these complex molecular and supramolecular species, single-crystal X-ray crystallography has proved to be the optimal technique for determining full three-dimensional structures in the solid state. These structures are curated and placed in structural databases, the most comprehensive of which (for organic and metallo–organic structures) is the Cambridge Structural Database. A question of increasing importance is how users can search such databases effectively for these structures. Here some of the classes of complex molecules and supramolecules and the challenges associated with searching for them are highlighted. The idea of substructure searches that involve topological searches as well as searches for molecular fragments is developed, and significant enhancements are proposed to substructure search programs that are both achievable and highly beneficial for both the database user community and the broader chemistry community.

scholarly journals DSR- A tool for disorder refinements with SHELXL

2014 ◽  
Vol 70 (a1) ◽  
pp. C1788-C1788
Author(s):  
Daniel Kratzert ◽  
Ingo Krossing
Keyword(s):  
Crystal Structures ◽  
Structure Refinement ◽  
Coordination Complexes ◽  
Free Variable ◽  
Molecular Fragments ◽  
X Ray ◽  
X Ray Crystallography ◽  
Disordered Structures ◽  
Structural Database

X-ray crystallography as a method used for identifying the atomic and molecular structure of a crystal has led to a better understanding of chemical bonds. It is an essential tool to determine the absolute configuration of molecules, has been important for the characterization of coordination complexes, as well as identifying supramolecular assemblies in biology and material science. Being so successful, one of the remaining problems in practical crystallography is the description of disorder in crystal structures. The Cambridge Structural Database includes 23% of disordered structures in its collection of nearly 700000.[1] The program described here is able to simplify many aspects of disorder modelling. The modelling of disorder with SHELXL is possible since its early stages. SHELXL is able to treat almost every possible kind of disorder but with a lot of manual work. It needs a free variable and a part number in combination of displacement parameters and bond length restraints. DSR (Disordered Structure Refinement) transfers a molecular fragment from a database of molecular fragments to the desired position in the unit cell automatically and generates restraints to stabilize the model (Figure 1). In practice, the user writes a command line into the SHELXL .res file, which subsequently is interpreted by DSR. The command line's main purpose is to tell DSR, which source atom of the fragment should go on which target coordinates in the .res file. The user has to choose a minimum of three atoms from the database fragment (source atoms) and the same amount of target positions (target atoms) where the fitting fragment should be placed on. Molecular fragments can be either imported directly from the GRADE server of Globalphasing Ltd.[4], from existing crystal structures or from ab initio calculations. DSR offers several more options available to make disorder modelling a convenient process. DSR can be obtained from http://goo.gl/BL6wP1.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

scholarly journals Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography

2015 ◽  
Vol 48 (4) ◽  
pp. 1072-1079 ◽  
Author(s):  
Geoffrey K. Feld ◽  
Michael Heymann ◽  
W. Henry Benner ◽  
Tommaso Pardini ◽  
Ching-Ju Tsai ◽  
...  
Keyword(s):  
Protective Antigen ◽  
Three Dimensional ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Linac Coherent Light Source ◽  
Efficient Alternative

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

scholarly journals Serial Electron Diffraction Data Processing With diffractem and CrystFEL

2021 ◽  
Vol 8 ◽  
Author(s):  
Robert Bücker ◽  
Pascal Hogan-Lamarre ◽  
R. J. Dwayne Miller
Keyword(s):  
Electron Diffraction ◽  
Data Processing ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
New Techniques ◽  
X Ray ◽  
X Ray Crystallography ◽  
Level Of Automation ◽  
Rotation Method ◽  
High Level

Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.

scholarly journals An Unexpected Trinuclear Cobalt(II) Complex Based on a Half-Salamo-Like Ligand: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, Antimicrobial and Fluorescent Properties

Crystals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 408 ◽  
Author(s):  
Ruo-Yan Li ◽  
Xiao-Xin An ◽  
Juan-Li Wu ◽  
You-Peng Zhang ◽  
Wen-Kui Dong
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Antimicrobial Activities ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Fluorescent Properties ◽  
X Ray ◽  
X Ray Crystallography ◽  
Elemental Analyses

An unexpected trinuclear Co(II) complex, [Co3(L2)2(μ-OAc)2(CH3OH)2]·2CH3OH (H2L2 = 4,4′-dibromo-2,2′-[ethylenedioxybis(nitrilomethylidyne)]diphenol) constructed from a half-Salamo-based ligand (HL1 = 2-[O-(1-ethyloxyamide)]oxime-4-bromophenol) and Co(OAc)2·4H2O, has been synthesized and characterized by elemental analyses, infrared spectra (IR), UV-Vis spectra, X-ray crystallography and Hirshfeld surface analysis. The Co(II) complex contains three Co(II) atoms, two completely deprotonated (L2)2− units, two bridged acetate molecules, two coordinated methanol molecules and two crystalline methanol molecules, and finally, a three-dimensional supramolecular structure with infinite extension was formed. Interestingly, during the formation of the Co(II) complex, the ligand changed from half-Salamo-like to a symmetrical single Salamo-like ligand due to the bonding interactions of the molecules. In addition, the antimicrobial activities of HL1 and its Co(II) complex were also investigated.

scholarly journals Molecular Recognition in Proton-Transfer Compounds of Brucine with Achiral Substituted Salicylic Acid Analogues

2006 ◽  
Vol 59 (5) ◽  
pp. 320 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth ◽  
Peter C. Healy ◽  
Jonathan M. White
Keyword(s):  
Proton Transfer ◽  
Three Dimensional ◽  
Water Molecules ◽  
Sulfosalicylic Acid ◽  
X Ray ◽  
X Ray Crystallography ◽  
Guest Species ◽  
Substituted Benzoic Acids ◽  
Proton Transfer Compounds ◽  
Hydrogen Bonded

The 1:1 proton-transfer brucinium compounds from the reaction of the alkaloid brucine with 5-nitrosalicylic acid, 3,5-dinitrosalicylic acid, and 5-sulfosalicylic acid, namely anhydrous brucinium 5-nitrosalicylate (1), brucinium 3,5-dinitrosalicylate monohydrate (2), and brucinium 5-sulfosalicylate trihydrate (3) have been prepared and their crystal structures determined by X-ray crystallography. All structures further demonstrate the selectivity of brucine for meta-substituted benzoic acids and comprise three-dimensional hydrogen-bonded framework polymers. Two of the compounds (1 and 3) have the previously described undulating brucine sheet host-substructures which incorporate interstitially hydrogen-bonded salicylate anion guest species and additionally in 3 the water molecules of solvation. The structure of 2 differs in having a three-centre brucinium–salicylate anion bidentate N+–H···O(carboxyl) hydrogen-bonding association linking the species through interstitial associations involving also the water molecules of solvation. A review of the crystallographic structural literature on strychnine and brucine is also given.

Teflon tape for laboratory teaching of three-dimensional x-ray crystallography

2018 ◽  
Vol 39 (5) ◽  
pp. 055502 ◽  
Author(s):  
Aitor Larrañaga ◽  
Nestor Goikoetxea ◽  
Mikel Iturrate ◽  
Erlantz Lizundia
Keyword(s):  
Three Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Laboratory Teaching

Introduction

1986 ◽  
Vol 317 (1540) ◽  
pp. 293-294 ◽  
Keyword(s):  
Direct Method ◽  
Hydrolytic Enzyme ◽  
Hydrolytic Enzymes ◽  
Three Dimensional ◽  
X Ray ◽  
Enzyme Active Site ◽  
X Ray Crystallography ◽  
Protein Molecules ◽  
Biological Catalysis ◽  
The 1960S

Our understanding of the function of protein molecules was revolutionized in the 1960s by the use of X-ray crystallography to give a three-dimensional picture of their structures at atomic resolution. The structure of myoglobin was rapidly followed by the structure of several hydrolytic enzymes such as lysozyme, carboxypeptidase, ribonuclease, chymotrypsin, and subtilisin; and, not long after, by the much more complicated structure of haemoglobin, composed of four myoglobin-like molecules interacting with each other. The first hydrolytic enzyme structures showed us how enzymes perform biological catalysis by immobilizing their substrates at the enzyme active site, and gave us definite ideas about the specific functions of different parts of the protein molecules. These ideas had to be treated as hypotheses, because there was no direct method to check them. A few particular points could be proved by cunning but tedious experiments.

Sign in / Sign up

Export Citation Format

Share Document