Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystal structure and Hirshfeld surface analysis of lapachol acetate 80 years after its first synthesis.

ABSTRACT: Lapachol acetate [systematic name: 3-(3-methyl-but-2-en-yl)-1,4-dioxonaph-thalen-2-yl acetate], C₁₇H₁₆O₄, was prepared using a modified high-yield procedure and its crystal structure is reported for the first time 80 years after its first synthesis. The full spectroscopic characterization of the mol-ecule is reported. The mol-ecular conformation shows little difference with other lapachol derivatives and lapachol itself. The packing is directed by inter-molecular ?-? and C-H?O inter-actions, as described by Hirshfeld surface analysis. The former inter-actions make the largest contributions to the total packing energy in a ratio of 2:1 with respect to the latter.

SUBMITTER: Martinez-Cabrera MA

PROVIDER: S-EPMC6727062 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystal structure and Hirshfeld surface analysis of lapachol acetate 80 years after its first synthesis.

Martínez-Cabrera Miguel A MA Macías Mario A MA Ferreira Francisco F Pandolfi Enrique E Barúa Javier J Suescun Leopoldo L

Acta crystallographica. Section E, Crystallographic communications 20190819 Pt 9

Lapachol acetate [systematic name: 3-(3-methyl-but-2-en-yl)-1,4-dioxonaph-thalen-2-yl acetate], C17H16O4, was prepared using a modified high-yield procedure and its crystal structure is reported for the first time 80 years after its first synthesis. The full spectroscopic characterization of the mol-ecule is reported. The mol-ecular conformation shows little difference with other lapachol derivatives and lapachol itself. The packing is directed by inter-molecular ...[more]

PMID: 31523467

Similar Datasets

Racemic mefloquinium chloro-difluoro-acetate: crystal structure and Hirshfeld surface analysis.

Project description:In the racemic title mol-ecular salt, C17H17F6N2O+·C2ClF2O3- (systematic name: 2-{[2,8-bis-(tri-fluoro-meth-yl)quinolin-4-yl](hy-droxy)meth-yl}piperidin-1-ium chloro-difluoro-acetate), the cation, which is protonated at the piperidine N atom, has the shape of the letter, L, with the piperidin-1-ium group being approximately orthogonal to the quinolinyl residue [the Cq-Cm-Cm-Na (q = quinolinyl; m = methine; a = ammonium) torsion angle is 177.79?(18)°]. An intra-molecular, charge-assisted ammonium-N-H?O(hydrox-yl) hydrogen bond ensures the hy-droxy-O and ammonium-N atoms lie to the same side of the mol-ecule [Oh-Cm-Cm-Na (h = hydrox-yl) = -59.7?(2)°]. In the crystal, charge-assisted hydroxyl-O-H?O-(carboxyl-ate) and ammonium-N+-H?O-(carboxyl-ate) hydrogen bonds generate a supra-molecular chain along [010]; the chain is consolidated by C-H?O inter-actions. Links between chains to form supra-molecular layers are of the type C-Cl??(quinolinyl-C6) and the layers thus formed stack along the a-axis direction without directional inter-actions between them. The analysis of the calculated Hirshfeld surface points to the dominance of F?H contacts to the surface (40.8%) with significant contributions from F?F (10.5%) and C?F (7.0%) contacts.

| S-EPMC6038619 | biostudies-literature

Synthesis, crystal structure and Hirshfeld surface analysis of sodium bis(malonato)borate monohydrate

Project description: Not available

| S-EPMC10848979 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of 2-(1H-indol-3-yl)ethanaminium acetate hemihydrate.

Project description:The title mol-ecular salt, C10H13N2 +·C2H3O2 -·0.5H2O, crystallized with four 2-(1H-indol-3-yl)ethanaminium cations (A, B, C and D) and four acetate anions in the asymmetric unit, together with two water mol-ecules of crystallization. Each cation is linked to an anion by a C-H⋯π inter-action. The alkyl-aminium side chains have folded conformations, with N-C-C-C torsion angles of -58.5 (3), 59.5 (3), -64.6 (3) and -56.0 (3)° for cations A, B, C and D, respectively. In the crystal, the cations and anions are liked by N-H⋯O and C-H⋯O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by the water mol-ecules via Owater-H⋯O and N-H⋯Owater hydrogen bonds, forming layers lying parallel to the bc plane. The overall inter-molecular inter-actions were investigated using Hirshfeld surfaces analysis.

| S-EPMC6509690 | biostudies-literature

m-Xylylenediaminium sulfate: crystal structure and Hirshfeld surface analysis.

Project description:The crystal structure of the title salt {systematic name: [1,3-phenyl-enebis(methyl-ene)]bis-(aza-nium) sulfate}, C8H14N2 (2+)·SO4 (2-), consists of infinite (100) sheets of alternating organic and inorganic entities The m-xylylenediaminium cations are linked to the sulfate anions by N-H?O and asymmetric bifurcated N-H?(O,O) hydrogen bonds, generating a three-dimensional network. A weak C-H?O inter-action also occurs. The Hirshfeld surface analysis and the two-dimensional fingerprint maps indicate that the packing is dominated by H?O/O?H and H?H contacts.

| S-EPMC4908557 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of 1,3-diethynyladamantane.

Project description:The title compound, C14H16, exhibits exceptionally weak inter-molecular C-H⋯π hydrogen bonding of the ethynyl groups, with the corresponding H⋯π separations [2.91 (2) and 3.12 (2) Å] exceeding normal vdW distances. This bonding complements distal contacts of the CH (aliphatic)⋯π type [H⋯π = 3.12 (2)-3.14 (2) Å] to sustain supra-molecular layers. Hirshfeld surface analysis of the title compound suggests a relatively limited significance of the C⋯H/H⋯C contacts to the crystal packing (24.6%) and a major contribution from H⋯H contacts accounting 74.9% to the entire surface.

| S-EPMC7273986 | biostudies-literature

Crystal structure and Hirshfeld surface analysis of pulcherrin J.

Project description:The title compound, C29H36O4 [systematic name (4aR,5R,6aS,7R,11aS,11bR)-4a-hydroxy-4,4,7,11b-tetramethyl-1,2,3,4,4a,5,6,6a,7,11,11a,11b-dodecahydrophen-anthro[3,2-b]furan-5-yl cinnamate], a natural diterpene known as pulcherrin J, was isolated from stem barks of medicinally important Caesalpinia pulcherrima (L.). The crystal structure of pulcherrin J shows it to be composed of a central core of three trans-fused cyclo-hexane rings and a near planar five-membered furan ring, along with an axially oriented cinnamate moiety and an -hydroxy substituent attached at positions 4a and 5 of the steroid ring system, respectively. The absolute structure was established with the use of Cu Kα radiation. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds to generate [100] C(8) chains. Hirshfeld surface analysis indicates that the most significant contacts in packing are H⋯H (67.5%), followed by C⋯H (19.6%) and H⋯O (12.9%).

| S-EPMC5730321 | biostudies-literature

Synthesis, crystal structure, Hirshfeld surface analysis, energy frameworks and computational studies of Schiff base derivative.

Project description:The compound (E)-ethyl 3-(2-(2,4-dinitrophenyl)hydrazono)butanoate (3) was synthesised and crystallized using ethanol as a solvent. The compound was characterized by 1H NMR, and single crystal X-ray diffraction. The compound crystallizes in the monoclinic crystal system with the space group P21/c. The intermolecular interactions and the interaction energies responsible for the stabilization of the molecules were determined by Hirshfeld surface analysis and energy framework calculations. The structure of the compound was optimized by Density Functional Theory calculations and HOMO-LUMO energy gap was calculated. The non-covalent interactions were revealed by reduced density gradient analysis. The Mulliken atomic charges and natural atomic charges were calculated by density functional theory calculations. The reactive sites present in the molecule are shown by molecular electrostatic potential map. The inter and intra molecular charge transfer were investigated by NBO analysis.

| S-EPMC9434054 | biostudies-literature

[4-(2-Aminoethyl)morpholine-κ2N,N′]dibromidocadmium(II): synthesis, crystal structure and Hirshfeld surface analysis

Project description: Not available

| S-EPMC10915673 | biostudies-literature

Synthesis, crystal structure and Hirshfeld surface of bis-(2-amino-pyridinium) hexa-chlorido-stannate(IV).

Project description:In the title mol-ecular salt, (C5H7N2)2[SnCl6], the cation is protonated at the pyridine N atom and the complete dianion is generated by a crystallographic centre of symmetry. In the crystal, N-H⋯Cl hydrogen bonds link the components into a three-dimensional network built up from the stacking of alternate cationic and anionic layers. The nature of the inter-molecular inter-actions has been analysed in terms of the Hirshfeld surfaces of the cations and the anions. The thermal behaviour and the Raman spectrum of the title compound are reported.

| S-EPMC7405591 | biostudies-literature

Ethyl 2-(4-benzyl-3-methyl-6-oxo-1,6-dihydropyridazin-1-yl)acetate: crystal structure and Hirshfeld surface analysis.

Project description:The title compound, C16H18N2O3, is constructed about a central oxopyridazinyl ring (r.m.s. deviation = 0.0047 Å), which is connected to an ethyl-acetate group at the N atom closest to the carbonyl group, and benzyl and methyl groups second furthest and furthest from the carbonyl group, respectively. An approximately orthogonal relationship exists between the oxopyridazinyl ring and the best plane through the ethyl-acetate group [dihedral angle = 77.48 (3)°]; the latter lies to one side of the central plane [the Nr-Nr-Cm-Cc (r = ring, m = methyl-ene, c = carbon-yl) torsion angle being 104.34 (9)°]. In the crystal, both H atoms of the N-bound methyl-ene group form methyl-ene-C-H⋯O(ring carbon-yl) or N(pyridazin-yl) inter-actions, resulting in the formation of a supra-molecular tape along the a-axis direction. The tapes are assembled into a three-dimensional architecture by methyl- and phenyl-C-H⋯O(ring carbon-yl) and phenyl-C-H⋯O(ester carbon-yl) inter-actions. The analysis of the calculated Hirshfeld surface indicates the dominance of H⋯H contacts to the overall surface (i.e. 52.2%). Reflecting other identified points of contact between mol-ecules noted above, O⋯H/H⋯O (23.3%), C⋯H/H⋯C (14.7%) and N⋯H/H⋯N (6.6%) contacts also make significant contributions to the surface.

| S-EPMC6399698 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data