Systematic Name Research Articles

Rac-N-(4-Eth-oxy-phen-yl)-3-hy-droxy-butanamide.

In the title compound, racemic bucetin [systematic name: N-(4-eth-oxy-phen-yl)-3-hydroxy-butanamide], C12H17NO3, the mol-ecule is in an extended conformation as illustrated by the C-O-C-C torsion angle [170.14 (15)°] in the eth-oxy group and the subsequent C-N-C-C [-177.24 (16)°], N-C-C-C [170.08 (15)°] and C-C-C-C [171.41 (15)°] torsion angles in the butanamide chain. In the crystal, the O-H group donates an inter-molecular O-H⋯O hydrogen bond to the amide carbonyl oxygen atom and also accepts an inter-molecular N-H⋯O hydrogen bond from an adjacent N-H group. The former forms 12-membered dimeric rings about inversion centers, and the latter form chains in the [001] direction. The overall hydrogen-bonded network is two-dimensional, with no propagation in the [100] direction.

Synthesis and structure of 4-hy-droxy-N-iso-propyl-tryptamine (4-HO-NiPT) and its precursors.

The title compound, 4-hy-droxy-N-iso-propyl-tryptamine (4) or 4-HO-NiPT (systematic name: 3-{2-[(propan-2-yl)amino]-eth-yl}-1H-indol-4-ol), C13H18N2O, was synthesized in three steps from 4-benzyl-oxyindole (1) (systematic name: 4-phen-oxy-1H-indole), C15H13NO. (1) was treated with oxalyl chloride and iso-propyl-amine to produce N-isopropyl-4-benz-yloxy-3-indole-glyoxyl-amide (2) {systematic name: 2-[4-(benz-yloxy)-1H-indol-3-yl]-2-oxo-N-(propan-2-yl)acet-amide}, C20H20N2O3. (2) was reduced to generate 4-benz-yloxy-N-iso-propyl-tryptamine (3) or 4-HO-NiPT, which was characterized as its chloride salt 4-benz-yloxy-N-iso-propyl-tryptammonium chloride (3a) (systematic name: {2-[4-(benz-yloxy)-1H-indol-3-yl]eth-yl}(propan-2-yl)aza-nium chloride), C20H25N2O·Cl. Finally the benzyl group of (3) was removed via hydrogenation to generate 4-HO-NiPT. The crystal structures of the title compound and all three synthetic precursors are presented.

Meloxicam hydro-chloride.

The title salt, C14H14N3O4S2 +·Cl- [systematic name: 2-(4-hy-droxy-2-methyl-1,1-dioxo-1,2-benzo-thia-zine-3-amido)-5-methyl-1,3-thia-zol-3-ium chloride] is the hydro-chloride derivative of meloxicam, a drug used to treat pain and inflammation in rheumatic disorders and osteoarthritis. Although its mol-ecular structure is similar to that previously reported for the hydro-bromide analogue, both salts are not isomorphous. Different crystal structures originate from a conformational modification, arising from a degree of rotational freedom for the thia-zolium ring in the cations. By taking as a reference the conformation of meloxicam, the thia-zolium ring is twisted by 10.96 and -16.70° in the hydro-chloride and hydro-bromide salts, while the 1,2-benzo-thia-zine core is a rigid scaffold. This behaviour could explain why meloxicam is a polymorphous compound.

Co-crystal of nadifloxacin with oxalic acid.

The 2:1 co-crystal of nadifloxacin [systematic name: 9-fluoro-8-(4-hy-droxy-piperidin-1-yl)-5-methyl-1-oxo-6,7-di-hydro-1H,5H-pyrido[3,2,1-ij]quinoline-2-carb-oxy-lic acid] with oxalic acid, C19H21FN2O4·0.5C2H2O4, was prepared by slow evaporation from a chloro-form:acetone solvent system. Nadifloxacin belongs to the group of anti-bacterial drugs. The co-crystal is stabilized through an intra-molecular O-H⋯O bond and inter-molecular hydrogen bonds. It was studied by FT-IR spectroscopy, differential scanning calorimetry and X-ray diffraction. Hirshfeld surface analysis indicated that the major contribution to the packing is from O⋯H/H⋯O inter-actions.

A new copper(II) complex containing triclopyr: one-pot crystallization, structure, conformation and Hirshfeld surface analyses

Abstract A new copper(II) complex [Cu(3,5,6-tcpa)(2,2′-bipy)Cl] (1) has been obtained through the one-pot hydrothermal reaction of copper chloride dihydrate with triclopyr (systematic name 2-((3,5,6-trichloropyridin-2-yl)oxy)acetic acid, abbreviation 3,5,6-Htcpa) and 2,2′-bipyridine (2,2′-bipy) coligands. 1 has crystallized in triclinic crystal system, P 1 ‾ $\overline{1}$ space group. The central copper(II) ion displayed a distorted square–pyramidal geometry and was connected by one chlorido co-ligand (Clˉ), one 3,5,6-tcpa anionic chelator and one chelating 2,2’-bipy ligand to afford a mononuclear structure. 1 is further extended into a 3D network by the non-covalent interactions of H⋯Cl, H⋯O hydrogen bonds, aromatic π⋯π stacking together with Cl⋯Cl halogen bond interactions. The co-crystallization process, the crystal structure of 1 as well as the Hirshfeld surface analysis for 1 have been analyzed and described. In addition, the flexible conformation of phenoxy methylene group among 1, triclopyr acid and its previously reported co-crystallized compound also have been carefully compared and discussed.

Synthesis, crystal structure and Hirshfeld surface analysis of the ortho-rhom-bic polymorph of 4-bromo-N-(4-bromo-benzyl-idene)aniline.

The crystal structure of the title compound, C13H9Br2N [systematic name: (E)-N,1-bis-(4-bromo-phen-yl)methanimine], is a second polymorph (Form II) crystallizing in the ortho-rhom-bic space group Pccn. The first polymorph (Form I) crystallizes in the monoclinic space group P21/c [Bernstein & Izak (1975 ▸). J. Cryst. Mol. Struct. 5, 257-266; Marin et al. (2013 ▸). J. Mol. Struct. 1049, 377-385]. The mol-ecule is disordered about an inversion center situated in the middle of the C=N bond, similar to the situation in the monoclinic polymorph: the C=N bond length is 1.243 (7) Å. In the crystal, mol-ecules stack along the b-axis direction and are linked by C-H⋯π inter-actions. The inter-atomic contacts in the crystal for both polymorphs were studied by Hirshfeld surface analysis and have notable differences. The solid-state fluorescence spectrum of Form II shows an emission peak at ca 469 nm. The two-photon absorption coefficient measured from the open aperture Z-scan technique is 1.3 × 10 -11 m W-1, hence, Form II shows optical limiting behaviour.

High-resolution structural study on pyridin-3-yl ebselen and its N-methylated tosylate and iodide derivatives.

The crystal structure of the pyridine-substituted benzisoselenazolinone 2-(pyridin-3-yl)-2,3-dihydro-1,2-benzoselenazol-3-one (C12H8N2OSe, 2), related to the antioxidant ebselen [systematic name: 2-phenyl-1,2-benzoselenazol-3(2H)-one, 1], is characterized by strong intermolecular N...Se(-N) chalcogen bonding, where the N...Se distance of 2.3831 (6) Å is well within the sum of the van der Waals radii for N and Se (3.34 Å). This strong interaction results in significant lengthening of the internal N-Se distance, consistent with significant population of the Se-N σ* antibonding orbital. Much weaker intermolecular O...Se chalcogen bonding occurs between the amide-like O atom in 2 and the less polarized C-Se bond in this structure. Charge density analysis of 2 using multipole refinement of high-resolution data allowed the electrostatic surface potential for 2 to be mapped, and clearly reveals the σ-hole at the extension of the Se-N bond as an area of positive electrostatic potential. Topological analysis of the electron-density distribution in 2 was carried out within the Quantum Theory of Atoms in Molecules (QTAIM) framework and revealed bond paths and (3,-1) bond critical points (BCPs) for the N...Se-N moiety consistent with a closed-shell interaction; however, the potential energy term is suggestive of electron sharing. Analysis of the electron localization function (ELF) for the strong N...Se and the weak O...Se chalcogen-bonding interactions in the structure of 2 suggest significant electron sharing in the former interaction, and a largely electrostatic interaction in the latter. Conversion of 2 to its N-methylated derivatives by reaction with methyl iodide [1-methyl-3-(3-oxo-2,3-dihydro-1,2-benzoselenazol-2-yl)pyridin-1-ium iodide, C13H11N2OSe+·I-] and methyl tosylate [1-methyl-3-(3-oxo-2,3-dihydro-1,2-benzoselenazol-2-yl)pyridin-1-ium toluenesulfonate trihydrate, C13H11N2OSe+·C7H7O3S-·3H2O] removes the possibility of N...Se chalcogen bonding and instead structures are obtained where the iodide and tosylate counter-ions fulfill the role of chalcogen-bond acceptors, with a strong I-...Se interaction in the iodide salt and a weaker p-Tol-SO3-...Se interaction in the tosylate salt.

Aqua-tri-fluorido-boron-1,3-dioxolan-2-one (1/2).

The crystal structure of the co-crystal of aqua-tri-fluorido-boron with two ethyl-ene carbonate (systematic name: 1,3-dioxolan-2-one) mol-ecules, BF3H2O·2OC(OCH2)2, was determined by low-temperature single-crystal X-ray diffraction. The co-crystal crystallizes in the ortho-rhom-bic space group P212121 with four formula units per unit cell. The asymmetric unit consists of an aqua-tri-fluorido-boron mol-ecule and two ethyl-ene carbonate mol-ecules, connected by O-H⋯O=C hydrogen bonds. This crystal structure is an inter-esting example of a superacidic BF3H2O species co-crystallized with an organic carbonate.

Crystal structure of the insecticide ethiprole (C13H9Cl2F3N4OS): a case study of whole-mol-ecule configurational disorder.

The crystal structure of ethiprole {systematic name: 5-amino-1-[2,6-di-chloro-4-(tri-fluoro-meth-yl)phen-yl]-4-ethane-sulfinyl-1H-imidazole-3-carbo-nitrile}, C13H9Cl2F3N4OS, a phenyl-pyrazole-based insecticide, is presented. The pyrazole ring carries four substituents: an N-bound 2,6-di-chloro-4-tri-fluoro-methyl-phenyl ring and C-bound amine, ethane-sulfinyl, and cyano groups. The sulfur atom of the ethane-sulfinyl group is trigonal-pyramidal and stereogenic. The structure exhibits whole-mol-ecule configurational disorder due to superposition of enanti-omers. The crystal packing is dominated by strong N-H⋯O and N-H⋯N hydrogen bonds, which form R 4 4(18) and R 2 2(12) ring motifs. Since the ethiprole mol-ecule is quite small, and structure solution and refinement were straightforward, the structure presents a convenient instructional example for modelling whole-body disorder of a non-rigid mol-ecule. To this end, a step-by-step overview of the model-building and refinement process is also given. The structure could form the basis of a useful classroom, practical, or workshop-style example.

A standalone editing protein deacylates mischarged canavanyl-tRNAArg to prevent canavanine incorporation into proteins.

Error-free translation of the genetic code into proteins is vitally important for all organisms. Therefore, it is crucial that the correct amino acids are loaded onto their corresponding tRNAs. This process is highly challenging when aminoacyl-tRNA-synthetases encounter structural analogues to the native substrate like the arginine antimetabolite canavanine. To circumvent deleterious incorporation due to tRNA mischarging, editing mechanisms have evolved. However, only for half of the tRNA synthetases, editing activity is known and only few specific standalone editing proteins have been described. Understanding the diverse mechanisms resulting in error-free protein synthesis is of great importance. Here, we report the discovery of a protein that is upregulated upon canavanine stimulation in bacteria that live associated with canavanine-producing plants. We demonstrate that it acts as standalone editing protein specifically deacylating canavanylated tRNAArg. We therefore propose canavanyl-tRNAArgdeacylase (CtdA) as systematic name. Knockout strains show severe growth defects in canavanine-containing media and incorporate high amounts of canavanine into the proteome. CtdA is frequently found under control of guanidine riboswitches, revealing a functional connection of canavanine and guanidine metabolisms. Our results are the first to show editing activity towards mischarged tRNAArg and add to the puzzle of how faithful translation is ensured in nature.

Zwitterionic versus neutral molecules of fluoroquinolones: crystal structure of danofloxacin dihydrate.

The crystal structure of danofloxacin (DFX) as a zwitterionic dihydrate [systematic name: (1S,4S)-5-(3-carboxylato-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)-2-methyl-2,5-diazabicyclo[2.2.1]heptan-2-ium dihydrate], C19H20FN3O3·2H2O, has been determined for the first time. The stability of the crystal structure is ensured by N-H...O and O-H...O hydrogen bonds, some of which are assisted by charge. The zwitterionic molecules of DFX are packed in stacks and this structural motif can be defined as a basic one from a supramolecular and energetic point of view. Hirshfeld surface analysis was used for an additional interpretation of the close contacts. The nature of the intermolecular interactions was evaluated in a pairwise manner. Destabilizing interactions were also discussed. In the context of our study on danofloxacin, we addressed the question: how common is a zwitterionic form for fluoroquinolones (FQ) in the crystalline state? A survey of the Cambridge Structural Database limited to anhydrous/hydrated/solvated forms of the most typical FQs revealed that neutral molecules are preferred, while zwitterions are less common.

Ethidium tetra-phenyl-borate aceto-nitrile disolvate.

In the title solvated salt, (C21H20N3){B(C6H5)4}·2CH3CN (systematic name 3,8-di-amino-5-ethyl-6-phenyl-phenanthridin-5-ium tetra-phenyl-borate aceto-nitrile disolvate), the dihedral angle between the tricyclic fused ring system (r.m.s. deviation = 0.021 Å) and the pendant phenyl group of the ethidium cation is 84.91 (7)°. The {B(C6H5)4}- anion has a typical tetra-hedral structure. The aceto-nitrile solvent mol-ecules do not accept hydrogen bonds from the -NH2 groups of the ethidium ions.

Crystal structure of the monoglycidyl ether of isoeugenol.

The title compound, C13H16O3 [GE-isoEu; systematic name: 2-({2-meth-oxy-4-[(E)-1-propen-1-yl]phen-oxy}meth-yl)oxirane], which crystallizes in the triclinic P space group, was synthesized in one step from iso-eugenol, a bio-based phenyl-propanoid, with an excess of epi-chloro-hydrin. Colourless prismatic crystals suitable for X-ray diffraction were obtained from a mixture of ethyl acetate and cyclo-hexane, during purification by column chromatography on silica gel. GE-isoEu, which corresponds to the trans isomer of the monoglycidyl ether of iso-eugenol, is based on a 1,2,4-tris-ubstituted benzene ring by diglycidyl ether, meth-oxy and 1-(E)-propenyl groups, respectively. In the crystal, mol-ecules are organized through offset π-stacking inter-actions. Chemically, GE-isoEu constitutes an inter-mediate in the synthesis protocol of 2-[3-meth-oxy-4-(2-oxiranylmeth-oxy)phen-yl]-3-methyl-oxirane (GEEp-isoEu), a di-epoxy-dized monomer used in the manufacturing of thermosetting resins and intended for the elaboration of bio-composites.

Bis(4-hy-droxy-phen-yl) 1,4-phenyl-enebiscarbamate.

The title compound, C20H16N2O6 (systematic name: 4-hy-droxy-phenyl N-{4-[(4-hy-droxy-phen-oxy-carbon-yl)amino]-phen-yl}carbamate), contains two urethane groups substituting the central benzene ring in para positions. The mol-ecule is centrosymmetric, and displays a twisted conformation for the three aromatic rings [the dihedral angle between central benzene ring and the urethane group is 33.4 (6)°, and that between the latter and the terminal ring is 65.1 (1)°]. In the crystal, a three-dimensional framework is formed through O-H⋯O and N-H⋯O hydrogen bonds involving the hy-droxy and urethane functional groups, respectively.

Ethidium hepta-fluoro-butyrate.

In the title compound (systematic name: 3,8-diamino-5-ethyl-6-phenylphenanthridin-5-ium 2,2,3,3,4,4,4-heptafluorobutyrate), C21H20N3 +·C4F7O2 -, two ethidium ions, C21H20N3 + form a dimerized structure due to π-π inter-actions, even though they are positively charged. The hepta-fluoro-butyrate anions are connected to neighbouring cation dimers via hydrogen-bonding inter-actions, the hydrogen-bonding donor sites of the -NH2 groups of the ethidium ions connecting to the hydrogen-bonding acceptor sites of the -COO- groups of the hepta-fluoro-butyrate anions.

Synthesis and crystal structure of topiramate azido-sulfate at 90 K and 298 K.

The low (90 K) and room (298 K) temperature crystal structures of topiramate azido-sulfate [systematic name 2,3:4,5-bis-O-(1-methyl-ethyl-idene)-β-d-fructo-pyran-ose azido-sulfate], C12H19N3O8S, an inter-mediate in the synthesis of the anti-convulsant drug topiramate, are described. Topiramate azido-sulfate (I) finds use as a reference impurity standard for topiramate. A modified synthesis and some spectroscopic details are also presented.

Crystal structure, PIXEL calculations of inter-molecular inter-action energies and solid-state characterization of the herbicide isoxaflutole.

In the isoxaflutole mol-ecule {systematic name: (5-cyclo-propyl-1,2-oxazol-4-yl)[2-(methyl-sulfon-yl)-4-(tri-fluoro-meth-yl)phen-yl]methanone; C15H12F3NO4S}, the 1,2-oxazole and methanone fragments form an almost coplanar unit, whereas the methanone and phenyl mean planes are inclined by an angle of more than 60°. This conformation differs fundamentally from all other known examples of the 1,2-oxazol-4-yl(phen-yl)methanone fragment and is ascribed to the presence of the bulky methyl-sulfonyl para substituent at the phenyl ring. PIXEL calculations reveal that the largest contributions to the stabilization of the crystal persist within a columnar arrangement of mol-ecules along the twofold screw axis and in inter-actions between adjacent columns related by an inversion operation. Both these intra-column and inter-column motifs are dominated by the dispersion energy term but also display additional significant stabilization effects as a result of three short inter-molecular C-H⋯O contacts involving the methane-sulfonyl-O atoms.

Synthesis and crystal structure of ebastinium hydrogen fumarate.

The structure of ebastinium hydrogen fumarate {systematic name: 1-[4-(4-tert-butyl-phen-yl)-4-oxobut-yl]-4-(di-phenyl-meth-oxy)piperidin-1-ium (E)-3-carb-oxy-1-hy-droxy-prop-2-en-1-olate}, C32H40NO2 +·C4H3O4 -, a 1:1 salt formed in the reaction between ebastine and fumaric acid is presented. All examined crystals were found to be twinned by pseudo-merohedry. The structure is extensively disordered, with over half (20 out of 35) its non-hydrogen atoms modelled as lying over two sets of sites. In the crystal, cation-anion pairs are linked by a strong N-H⋯O hydrogen bond [N⋯O = 2.697 (11) Å]. These units inter-act via weaker C-H⋯O and C-H⋯π contacts to form layers lying parallel to the bc plane. The hydrogen fumarate anions are linked by a very short O-H⋯O hydrogen bond [O⋯O = 2.5402 (17) Å], augmented by weak C-H⋯O contacts into pairs of R 2 2(6) ring motifs to form chains that extend parallel to the b-axis direction. Comparisons to similar crystal structures are presented.

Synthetic cannabinoids and their semi-systematic naming developed in Europe – Overview of the chemical diversity and practical guidelines

A nomenclature for the naming of synthetic cannabinoids (SC) notified to the EMCDDA was developed. The harmonized names shall convey the structural features of SCs accurately and consistently without the need for a complex systematic name. SCs are the largest group of new psychoactive substances monitored by the EMCDDA and are heterogeneous in their structural makeup. Consistent, concise, and informative naming of SCs has been an ongoing challenge. Over time, several naming conventions have been employed to refer to SCs to avoid the complex but unambiguous systematic IUPAC name, which gives clear hints at the molecular features. Each naming approach aims to make SCs accessible to and recognizable by non-chemists/non-experts/regulators. However, ease of pronunciation and simplicity comes at the cost of detailed information on the structure accessible through the assigned name. All compounds classified as cannabinoids monitored by the EMCDDA were analyzed, and the four building blocks in each SC were identified and abbreviated using consistent letter codes. Inconsistencies in the formerly used names were reviewed and included in developing new consistent letter codes. Rules of the nomenclature and an expanded syntax that combines the letter codes abbreviating the structural features, were developed. The developed nomenclature enables the consistent naming of SCs, which is easy to understand and can be applied by the forensic community, researchers, clinical practitioners, and policy-makers alike. The framework is presented with hands-on guidelines and examples. The chemical diversity of SCs is visualized and made accessible through an electronic data file on all 227 SCs covered. The nomenclature was built on the established letter code system for the molecular building blocks (core, linker, linked group, and tail) implemented by the EMCDDA in 2011 and was expanded to incorporate more structural features through substitution. The main principle of the nomenclature is to reuse previously assigned letter codes, making it easier to recognize the molecular structures. The overall vocabulary is limited by sharing abbreviations of common features across building blocks. Whenever a letter code has to be derived for a new moiety, all previous building blocks and the derived letter codes are taken into account to maximize consistency and minimize complexity. The time of notification of an SC significantly impacts the letter code assigned to the molecular structure. Because of this, the scope of application for the nomenclature has intentionally been limited to SCs which have emerged on the drug market. The developed nomenclature streamlines the process of assigning letter codes to SCs. The nomenclature has already been used to assign names to the most recent SCs detected in the EU. The formerly used name (common name) will continue to be available for reference purposes.

Crystal structure of 4-(2-meth-oxy-phen-yl)piper-azin-1-ium 3,5-dintrosalicylate.

The title salt [systematic name: 4-(2-methoxyphenyl)piperazin-1-ium 2-carboxy-4,6-dinitrophenolate], C11H17N2O+·C7H3N2O7 -, exhibits secondary nitro-gen atoms (N-H) in the 2-meth-oxy-phenyl-piperazine (2MeOPP) cation, which is protonated with a phenolic hydrogen atom of 3,5-di-nitro-salicylic acid (DNSA). One of the oxygen atoms of the nitro group in the 3,5-di-nitro-salicylate anion is disordered over two orientations with occupancy factors of 0.65 (7) and 0.35 (7) . The 2-meth--oxy-phenyl-piperazinium cation and 3,5-di-nitro-salicylate anion are linked in the asymmetric unit by a bifurcated N-H⋯O hydrogen bond, which formed is between the H atom in the protonated piperazinium unit of the cation and the carb-oxy-lic acid group in the anion. The piperazine ring adopts a chair conformation. The crystal structure features N-H⋯O and C-H⋯O hydrogen bonds inter-actions, which lead to the formation of a sandwich-like arrangement. Hirshfeld surface analysis was used to determine the relative contributions of various inter-molecular inter-actions, indicating that that H⋯O/O⋯H (38. 3%) and H⋯H (31. 8%) contacts are the major contributors.