Spacer conformation in biologically active molecules

2004 ◽  
Vol 76 (5) ◽  
pp. 959-964 ◽  
Author(s):  
J. Karolak-Wojciechowska ◽  
A. Fruzinski
Keyword(s):  
Statistical Data ◽  
Population Analysis ◽  
Cambridge Structural Database ◽  
Biologically Active ◽  
Aliphatic Chain ◽  
X Ray ◽  
Flexible Spacer ◽  
Conformational Preferences ◽  
Structural Database ◽  
The One

Based on our contemporary studies on the structures of biologically active molecules, we focus our attention on the aliphatic chain and its conformation. That flexible spacer definitely influenced the balanced position of all pharmacophoric points in molecules of biological ligands. The one atomic linker and two or three atomic spacers with one heteroatom X =O, S, CH2, NH have been taken into account. The conformational preferences clearly depend on the heteroatom X. In the discussion, we utilize our own X-ray data, computation chemistry methods, population analysis, and statistical data from the Cambridge Structural Database (CSD).

scholarly journals SYNTHESIS AND STRUCTURE OF 3,5-DIAMINO-1,2,4-TRIAZOLIUM TETRACHLORO-GALLATE

2019 ◽  
Vol 62 (4) ◽  
pp. 121-127
Author(s):  
Tatyana V. Kudayarova ◽  
Elena A. Danilova ◽  
Yuliya A. Piteva ◽  
Kristina E. Mochalina ◽  
Maxim V. Dmitriev
Keyword(s):  
Complex Compound ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Cambridge Structural Database ◽  
X Ray Diffraction ◽  
Centrosymmetric Dimer ◽  
X Ray ◽  
Preferential Localization ◽  
Structural Database ◽  
Almost All

This paper discusses the synthesis and structure of a complex compound based on 3,5-diamino-1H-1,2,4-triazole (guanazole) with gallium ions, formed by the interaction of anhydrous gallium (III) chloride and guanazole in dried methanol. After distilling off the solvent under vacuum, the resulting product was washed with hexane, acetone. The target compound was extracted with acetonitrile, and slow evaporation of the latter at room temperature for three days resulted in beige-colored crystals, which were characterized by IR spectroscopy, elemental analysis, mass-spectrometry and X-ray diffraction analysis. The complex composition of gallate, C2H6N5+∙[GaCl4], exists as two crystallographically independent cations and two anions. The complex compound crystallizes in the centrosymmetric space group of the monoclinic syngony. The tetrachlorogallate anion is a slightly distorted tetrahedron, which is typical of structures of this type. 1,2,4-triazolium cations are selectively protonated on the N4 and N4A atoms, however, the site of the preferential localization of the positive charge is the N2 and N2A atoms. In addition to the electrostatic interaction of oppositely charged ions, a developed system of hydrogen bonds plays an important role in the stabilization of the crystal packing: almost all hydrogen and chlorine atoms are involved in its formation. Each of the crystallographically independent cations forms a centrosymmetric dimer due to the intermolecular hydrogen bond N2 – H2···N3 and N2A – H2A···N3A.  A full set of X-ray data is deposited into the Cambridge Structural Database of Compounds - the Cambridge Structural Database (Contributor CCDC 1894815) and it can be gotten from the site www.ccdc.cam.ac.uk/data_request/cif.

scholarly journals A Computational Study of Metallacycles Formed by Pyrazolate Ligands and the Coinage Metals M = Cu(I), Ag(I) and Au(I): (pzM)n for n = 2, 3, 4, 5 and 6. Comparison with Structures Reported in the Cambridge Crystallographic Data Center (CCDC)

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 5108
Author(s):  
José Elguero ◽  
Ibon Alkorta
Keyword(s):  
Data Center ◽  
Computational Study ◽  
Crystallographic Data ◽  
Cambridge Structural Database ◽  
X Ray ◽  
Cambridge Crystallographic Data Center ◽  
Coinage Metals ◽  
Structural Database

The structures reported in the Cambridge Structural Database (CSD) for neutral metallacycles formed by coinage metals in their valence (I) (cations) and pyrazolate anions were examined. Depending on the metal, dimers and trimers are the most common but some larger rings have also been reported, although some of the larger structures are not devoid of ambiguity. M06-2x calculations were carried out on simplified structures (without C-substituents on the pyrazolate rings) in order to facilitate a comparison with the reported X-ray structures (geometries and energies). The problems of stability of the different ring sizes were also analyzed.

Life-science applications of the Cambridge Structural Database

2002 ◽  
Vol 58 (6) ◽  
pp. 879-888 ◽  
Author(s):  
Robin Taylor
Keyword(s):  
Intermolecular Interactions ◽  
Life Science ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Crystallographic Data ◽  
Cambridge Structural Database ◽  
Biologically Active ◽  
Ligand Interaction ◽  
Chemical Structures ◽  
Structural Database

Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling ofin vivosituations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary toin vacuotheoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein–ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding `hot spots' on proteins, docking ligands into enzyme active sites,de novoligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules.

Non-aromatic endocyclic angle at the ring fusion with the aromatic ring in benzocyclopentene and -hexene, revisited

2004 ◽  
Vol 60 (3) ◽  
pp. 293-299
Author(s):  
Dirk J. A. De Ridder ◽  
Hans-Beat Bürgi
Keyword(s):  
Bond Length ◽  
Aromatic Ring ◽  
Cambridge Structural Database ◽  
Mirror Plane ◽  
Ring Size ◽  
Acta Cryst ◽  
Ring Fusion ◽  
X Ray ◽  
Fused Ring ◽  
Structural Database

X-ray geometries of monocycloalkenobenzenes with a fused-ring size of r = 5, 6 were obtained by the use of the Cambridge Structural Database. In contrast to Allen's study [Acta Cryst. (1981), B37, 900–906], the data were not averaged over exact or imposed m ad symmetry (m ad is the mirror plane going through the midpoint of the aromatic ring fusion bond and the aromatic bond parallel to it). The distribution of the non-aromatic endocyclic angle ∊ at the ring fusion clearly shows two and three, respectively, distinct curves for r = 5 and r = 6. The respective ranges are 104.3–112.6 and 104.4–123.2°. If one of the C atoms directly attached to the aromatic ring is sp 2 hybridized, the bond length e between the aromatic ring and this atom is shortened by some 0.044 (15) and 0.027 (12) Å for r = 5 and r = 6, respectively. However, for r = 5, e is only shortened by 0.030 (17) Å when both C atoms directly attached to the aromatic ring are sp 2 hybridized. For r = 5, the endocyclic angle ∊ is 1.2 (13)° smaller at the side involving the sp 2 hybridized C atom.

Kilobytes of kilopascals: high-pressure depositions of the Cambridge Structural Database

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Michal Kaźmierczak ◽  
Ewa Patyk-Kaźmierczak
Keyword(s):  
Data Mining ◽  
High Pressure ◽  
Organic Compounds ◽  
Statistical Data ◽  
Cambridge Structural Database ◽  
Depth Analysis ◽  
Metal Organic ◽  
Structural Database ◽  
Statistical Data Mining ◽  
High Pressure Crystallography

The Cambridge Structural Database (CSD) is the largest repository of crystal structures of organic and metal–organic compounds, containing over 1.1 million entries. Over 3300 of the deposits are structures determined under high pressure, with the number being strongly affected by the experimental requirements of the high-pressure techniques. Nevertheless, it still presents a population sufficiently representative for statistical data mining. In this work, an in-depth analysis of this population is presented, showing where contributors of high-pressure depositions come from, which journals high-pressure structures are published in, and also providing information on some trends in high-pressure crystallography and how they have changed over the years elucidated from data collected in the CSD. The ultimate goal of this article is to bring the high-pressure crystallography content in the CSD to a wider audience of scientists.

scholarly journals Gallic Acid Dimer As a Double π–Hole Donor: Evidence from X-ray, Theoretical Calculations, and Generalization from the Cambridge Structural Database

2019 ◽  
Vol 19 (7) ◽  
pp. 3989-3997 ◽  
Author(s):  
Rafel Prohens ◽  
Dafne de Sande ◽  
Mercè Font-Bardia ◽  
Antonio Franconetti ◽  
José F. González ◽  
...  
Keyword(s):  
Gallic Acid ◽  
Theoretical Calculations ◽  
Cambridge Structural Database ◽  
X Ray ◽  
Structural Database

From Experiments to Knowledge

2017 ◽  
Vol 39 (3) ◽  
Author(s):  
Ian Bruno
Keyword(s):  
Neutron Diffraction ◽  
Cambridge Structural Database ◽  
X Ray ◽  
Structural Database

AbstractThe Cambridge Structural Database (CSD) provides a platform for sharing data generated from X-ray and neutron diffraction experiments. [

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