The chloro-methyl exchange rule and its violations in the packing of organic molecular solids

Since chloro and methyl groups have nearly the same volume, they may be interchanged in a molecule without altering the crystal structure. Such isostructural behaviour is found when crystal stabilization is mainly through dispersive and repulsive interactions. Violations of this rule are, however, observed when directional forces or weak bonds are involved and the failure of complete chloro-methyl exchange in a substance like hexachlorobenzene, points to the importance of weakly attractive Cl…Cl interactions

Bis[5-oxo-4,5-dihydro-8H-2-azonia-4,8,9-trizabicyclo[4.3.0]nona-2,6,9(1)-triene] sulfate

In the crystal structure of the title compound, 2C5H5N4O+·SO4 2−, N—H⋯O hydrogen bonds assemble the mol­ecules into a two-dimensional network structure parallel to the cb plane. The S atom of the sulfate ion lies on a special position on a twofold axis

Design of an SHG-active crystal, 4-iodo-4'-nitrobiphenyl: therole of supramolecular synthons

The crystal structure of 4-iodo-4'-nitrobiphenyl has been determined with packing calculations and the presence of polar and parallel iodo···nitro supramolecular synthons leads to non-centrosymmetry and measurable SHG activity

Norfloxacin sesquihydrate

In the crystal structure of the title compound [systematic name: 1-ethyl-6-fluoro-4-oxo-7-(piperazin-4-ium-1-yl)-1,4-dihydro­quinoline-3-carboxyl­ate sesquihydrate], C16H18FN3O3·1.42H2O, N—H⋯O and O—H⋯O hydrogen bonds assemble the mol­ecules in a two-dimensional layered corrugated sheet structure parallel to the b axis. The water mol­ecules are disordered [occupancies 0.741 (11) and 0.259 (11)]

Solid state nuclear bromination with N-bromosuccinimide. Part 2. Experimental and theoretical studies of reactions with some substituted benzaldehydes

N-Bromosuccinimide reacts with aromatic aldehydes in the solid state to yield exclusively nuclear brominated products while a similar reaction in the solution phase produces a number of products under varied conditions. The reactivity and regioselectivity have been studied in terms of the energies of HOMO, HOMO–LUMO difference, reaction free energy, reaction conditions and crystal packing. Single crystal X-ray structural analysis of 3,4-dihydroxybenzaldehyde has been carried out. Crystal packing energies of some of the reactive and unreactive benzaldehydes indicate the importance of molecular bromine diffusion in the solid state

Annotated chemical patent corpus: A gold standard for text mining

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, t

The role of Cl···Cl and C-H···O interactions in the crystal engineering of 4Å short-axis structures

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C-H···O interactions and the adoption of 4 Å short-axis crystal structures by oxygenated aromatic compounds

Oxygen atoms, pendant as substituents or occurring within the ring systems of planar aromatic molecules, have a pronounced tendency to direct crystallisation patterns of such compounds to the β -structure, characterised by a 4 Åshort axis. They seem to perform this function by stabilising a critical number of hydrogen atoms, covalently bonded to carbon, through short and directionally specific intermolecular C-H···O hydrogen bonds. Consequently, the number of free hydrogen atoms which contribute to crystal stabilisation through non-β steering C H interactions is reduced. Both these factors result in the formation of C-H…O stabilised two-dimensional entities such as sheets and ribbons. Such entities may be stacked at 4 Å translational separation to generate the entire structure. These concepts are illustrated for some methylenedioxy and alkoxy aromatic systems, quinones, and heterocycles. However, both intra- and inter-sheet C-H…O interactions may sometimes be present and the unusual crystal structure of 7-acetoxycoumarin (5) shows how a significantly non-planar molecule may still adopt the β-structure if it is particularly well suited for the formation of C-H···O bonds. Yet 4-acetoxycinnamic acid (6), the crystal structure of which was determined in this work and which has almost the same C:H:O ratio as (5), adopts a non-β structure because the number of oxygen atoms available for C-H···O bond formation is greatly reduced. The crucial role of the number of such available oxygen atoms and H-bonded and free(C-)H atoms vis-à-vis the carbon content is exemplified by the β-steering behaviour of oxygen in some large fused-ring quinones and heterocycles. These trends may also be extended to nitrogen and sulphur heterocycles

The novel 1:1 donor-acceptor complex, 3,4-dimethoxycinnamic acid-2,4-dinitrocinnamic acid. Crystal engineering, structure, and anomalous lack of solid-state topochemical reactivity

Donor-acceptor interactions have been exploited to engineer a crystal structure of a 1:1 molecular complex (2a) of the title acids (1a) and (1d), where solid-state topochemical 2 + 2 photoaddition to yield pseudo-symmetrical cyclobutanes is permitted. Orange crystals of (2a) are triclinic, P, a= 8.857(5), b= 13.872(8), c= 8.578(4)Å, α = 101.41(4), β = 100.98(4), γ = 95.98(4)° , Z= 2, R= 0.054 on 1 315 non-zero reflections. The crystal structure consists of interleaving donor and acceptor molecules in the stack with two unequal separations of 3.80 and 4.97 Å with the former overlap relating potentially reactive double bonds. Contrary to expectation, complex (2a) is photostable. This inertness is shared by several other aromatic nitro compounds and some mechanistic possibilities are discussed. A classification of solid-state 2 + 2 cycloaddition reactions is attempted on the basis of how far topochemical predictions match with observed photochemical behaviour

Molecular discrimination in the formation of mixed crystals of some substituted chlorocinnamic acids

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