Charge assisted halogen and pnictogen bonds: insights from the Cambridge Structural Database and DFT calculations

CrystEngComm ◽  
2020 ◽  
Vol 22 (43) ◽  
pp. 7162-7169 ◽  
Author(s):  
Rosa M. Gomila ◽  
Antonio Frontera
Keyword(s):  
Dft Calculations ◽  
Cambridge Structural Database ◽  
Halogen Bonds ◽  
Structural Database

This manuscript combines a search in the Cambridge Structural Database and DFT calculations to analyse the existence and importance of charge assisted pnictogen and halogen bonds in halophosphonium salts.

scholarly journals N,N′-Bis(4-bromophenyl)-N,N′-dimethylurea

IUCrData ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Alexandre Pocinho ◽  
Sonia Mallet-Ladeira ◽  
Christelle Hureau ◽  
Emmanuel Gras
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Cambridge Structural Database ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Compound C ◽  
Structural Database

The structure of the title compound, C15H14Br2N2O, at 180 K has monoclinic (P21/n) symmetry. It was obtained unexpectedly from the decomposition of the parent 4-bromo-N-tert-butoxycarbonyl-N-methyl-aniline. It exhibits an `endo' conformation with angles between the two aromatic rings slightly lower than the average values found for similar compounds on the Cambridge Structural Database. In the crystal, C—H...O hydrogen bonds and short Br...Br halogen bonds [3.444 (1) Å] are observed.

Radical⋯radical chalcogen bonds: CSD analysis and DFT calculations

2020 ◽  
Vol 22 (22) ◽  
pp. 12757-12765
Author(s):  
Bartomeu Galmés ◽  
Jaume Adrover ◽  
Giancarlo Terraneo ◽  
Antonio Frontera ◽  
Giuseppe Resnati
Keyword(s):  
Dft Calculations ◽  
Theoretical Calculations ◽  
Substituent Effects ◽  
Cambridge Structural Database ◽  
Structural Database

A search in the Cambridge Structural Database and theoretical calculations (UPBE0-D3/def2-TZVP level of theory) show the existence and relevance of substituent effects on the strength of radical⋯radical chalcogen bonding interactions.

π-Hole Interactions with Various Nitro Compounds Relevant for Medicine: DFT Calculations and Surveys of the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB)

Synthesis ◽  
2019 ◽  
Vol 52 (04) ◽  
pp. 521-528 ◽  
Author(s):  
Jari M. Hoffmann ◽  
Akshay K. Sadhoe ◽  
Tiddo J. Mooibroek
Keyword(s):  
Dft Calculations ◽  
Protein Data Bank ◽  
Data Bank ◽  
Nitro Compounds ◽  
Cambridge Structural Database ◽  
Interaction Energies ◽  
Dft Computations ◽  
Structural Database

Model DFT computations and a thorough evaluation of the Cambridge structural database (CSD) and the protein data bank (PDB) were conducted to assess the occurrence and significance of intermolecular π-hole interactions with various nitro compounds relevant to medicine. DFT calculations indicate interaction energies between –3.9 to –6.5 kcal·mol–1, which is in the order of typical hydrogen- and halogen­-bonding interactions. Ample structural evidence for the occurrence of nitro π-hole interactions was found within the CSD and the PDB.

The structure of 1,2,4,4,6-pentaphenyl-1,4-dihydropyridine

1990 ◽  
Vol 55 (8) ◽  
pp. 2059-2065 ◽  
Author(s):  
Jaroslav Vojtěchovský ◽  
Jindřich Hašek ◽  
Jiří Ječný ◽  
Karel Huml
Keyword(s):  
Title Compound ◽  
Cambridge Structural Database ◽  
Boat Conformation ◽  
Planar Conformation ◽  
Structural Database ◽  
Independent Molecules ◽  
Dihydropyridine Ring

Title compound is triclinic, Mr = 461.60; P1, a = 9.158(1), b = 16.062(3), c = 19.472(3) Å, α = 110.69(1)°, β = 89.70(1)°, γ = 103.17(1)°, V = 2 600(1) Å3, Z = 4, Do = 1.15(3), Dc = 1.179(1) Mg m-3, λ(CuKα) = 1.5418 Å, μ = 0.509 mm-1, F(000) = 976 K, R = 0.040 for 8 059 unique observed reflections. Both symmetrically independent molecules show a different geometry of the 1,4-dihydropyridine ring: either the boat conformation with apexes C(sp3), N and boat angles 14.7(3)° and 10.3(2)° respectively, or the planar conformation. The conformation has been compared with similar dihydropyridines obtained from Cambridge Structural Database.

scholarly journals Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

Symmetry ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 766
Author(s):  
Barbara Bankiewicz ◽  
Marcin Palusiak
Keyword(s):  
Complex Formation ◽  
Hydrogen Bonds ◽  
Dft Calculations ◽  
Electrostatic Interactions ◽  
Dipole Moments ◽  
Main Role ◽  
Halogen Bonds ◽  
Topological Parameters ◽  
Leading Role ◽  
The Impact

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

scholarly journals Targeted classification of metal–organic frameworks in the Cambridge structural database (CSD)

2020 ◽  
Vol 11 (32) ◽  
pp. 8373-8387 ◽  
Author(s):  
Peyman Z. Moghadam ◽  
Aurelia Li ◽  
Xiao-Wei Liu ◽  
Rocio Bueno-Perez ◽  
Shu-Dong Wang ◽  
...  
Keyword(s):  
Surface Chemistry ◽  
Specific Surface ◽  
Large Scale ◽  
Metal Cluster ◽  
Metal Organic Frameworks ◽  
Cambridge Structural Database ◽  
Metal Organic ◽  
Structural Database

Large-scale targeted exploration of metal–organic frameworks (MOFs) with characteristics such as specific surface chemistry or metal-cluster family has not been investigated so far.

Applications of the Cambridge Structural Database to molecular inorganic chemistry

2002 ◽  
Vol 58 (3) ◽  
pp. 398-406 ◽  
Author(s):  
A. Guy Orpen
Keyword(s):  
Inorganic Chemistry ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
High Quality ◽  
Computational Data ◽  
Inorganic Complexes ◽  
Fundamental Research ◽  
Structural Database ◽  
Structure Correlation ◽  
Molecular Dimensions

Applications of the data in the Cambridge Structural Database (CSD) to knowledge acquisition and fundamental research in molecular inorganic chemistry are reviewed. Various classes of application are identified, including the derivation of typical molecular dimensions and their variability and transferability, the derivation and testing of theories of molecular structure and bonding, the identification of reaction paths and related conformational analyses based on the structure correlation hypothesis, and the identification of common and presumably energetically favourable intermolecular interactions. In many of these areas, the availability of plentiful structural data from the CSD is set against the emergence of high-quality computational data on the geometry and energy of inorganic complexes.

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).

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

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