N-Methyl-4-(4-nitrophenyl)-N-nitroso-1,3-thiazol-2-amine
The title compound, C10H8N4O3S, is almost planar [dihedral angle between the rings = 2.2 (2)°; r.m.s. deviation for the non-H atoms = 0.050 Å]. In the crystal, C—H...O and C—H...N hydrogen bonds link the molecules into (10-2) layers.
DFT and experimental studies on structure and spectroscopic parameters of 3,6-diiodo-9-ethyl-9H-carbazole
The first report on crystal and molecular structure of 3,6-diiodo-9-ethyl-9H-carbazole is presented. Experimental room-temperature X-ray and 13C chemical shift studies were supported by advanced theoretical calculations using density functional theory (DFT). The 13C nuclear magnetic shieldings were predicted at the non-relativistic and relativistic level of theory using the zeroth-order regular approximation (ZORA). Theoretical relativistic calculations of chemical shifts of carbons C3 and C6, directly bonded to iodine atoms, produced a reasonable agreement with experiment (initial deviation from experiment of 44.3 dropped to 4.25 ppm). The changes in ring aromatic character via simple harm…
4,4,4′,4′,7,7′-Hexamethyl-2,2′-spirobichroman
The title compound, C23H28O2, was obtained from the reaction of acetone with meta-cresol. The molecular structure consists of two identical subunits which are nearly perpendicular to each other. The oxygen-containing rings are not planar and the molecule is chiral. The crystal structure consists of chains of molecules of the same chirality arranged along the [010] axis.
Triclinic conformational polymorph of N,N,N′,N′-tetrakis(2-cyanoethyl)-1,2-ethylenediamine (TCED)
Abstract The crystal and molecular structures of two polymorphs of N,N,N′,N′-tetrakis(2-cyanoethyl)-1,2-ethylenediamine have been characterized by X-ray diffraction along with density functional theory (DFT) studies. The molecules differ from each other by conformation. N,N,N′,N′-tetrakis(2-cyanoethyl)-1,2-ethylenediamine has been synthesized by cyanoethylation of ethylenediamine. Cyanoethylation of vicinal diamines is important for the synthesis of hyperbranched polymeric materials applied as catalysts, surfactants and encapsulating agents in drug delivery systems. The molecular geometry of N,N,N′,N′-tetracyanoethyl-1,2-ethylenediamine is similar to that of homologous compounds. DFT calcul…
Preparation and molecular structures of N′-(2-heteroarylmethylidene)-3-(3-pyridyl)acrylohydrazides
Abstract The crystal and molecular structures of N′-(2-furylmethylidene)-3-(3-pyridyl)acrylohydrazide and N′-(2-thienylmethylidene)-3-(3-pyridyl)acrylohydrazide are reported, and the influence of the type of the heteroatom on the aromaticity of the aromatic rings is discussed. Both molecules are nearly planar. The geometry of the acrylohydrazide arrangement is comparable to that of homologous compounds. Density functional theory (DFT) calculations were performed in order to analyze the changes in the geometry of the studied compounds in the crystalline state and for the isolated molecule. The most significant changes were observed in the values of the N–N and C–N bond lengths. The harmonic …
Tuning the Electronic Properties of the Dative N-B Bond with Associated O-B Interaction: Electron Localizability Indicator from X-Ray Wavefunction Refinement.
Despite the immense growth in interest in difluoroborate dyes, the nature of the interactions of the boron atom within the N-BF2 -O kernel is not yet fully understood. Herein, a set of real-space bonding indicators is used to quantify the electronic characteristics of the dative N-B bond in difluoroborate derivatives. The atoms-in-molecules (AIM) partitioning scheme is complemented by the electron localizability indicator (ELI-D) approach, and both were applied to experimental and theoretical electron-density distributions (X-ray constrained wavefunction fitting vs. DFT calculations). Additionally, Fermi orbital analysis was introduced for small DFT models to support and extend the findings…
5-Formyl-2-furanboronic acid at 100 K
The furan ring in the title compound, C5H5BO4, is planar and each of the formyl and boronic groups makes a dihedral angle of ca 3° with this ring. The geometry of the furan ring is somewhat different to that found for substituted and unsubstituted furan structures. The molecules are connected to each other in the bc plane by C—H⋯O and O—H⋯O hydrogen bonds.
Effect of conjugated system extension on structural features and electron-density distribution in charge–transfer difluoroborates
A comparative structural study of two related donor–acceptor pyridine-based BF2 complexes, namely, 3-(dimethylamino)-1,1-difluoro-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-ium-1-uide, C8H10BF2N3O (1), and 3-{(1E,3E)-4-[4-(dimethylamino)phenyl]buta-1,3-dien-1-yl}-1,1-difluoro-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-ium-1-uide, C18H18BF2N3O (2), containing a dimethylamino group and either the shortest (in 1) or the longest (in 2) charge-transfer path known until now in this family of compounds, is presented. Single-crystal X-ray diffraction analysis supported by computational investigations shed more light on these systems, indicating, among other aspects, the predominance of C—H...F cont…
3,5-diphenyl-1,2,4-triazin-6(1H)-one: synthesis, and X-ray and DFT-calculated structures.
The title compound, C15H11N3O, (I), was obtained by the air oxidation of 3,5-diphenyl-4,5-dihydro-1,2,4-triazin-6(1H)-one. In the crystal structure, (I) forms centrosymmetric hydrogen-bonded dimers through pairs of N—H...N hydrogen bonds. The molecular structure of (I) deviates somewhat from planarity in the crystalline state, whereas a density functional theory (DFT) study predicts a completely planar conformation (Cspoint-group symmetry) for the isolated molecule. The solid-state conformation of (I) is stabilized by intramolecular hydrogen bonds,viz.one C—H...O interaction, which forms a six-membered ring, and three C—H...N interactions that each form five-membered rings. To estimate the …
1,4-Dihydro-1-methyl-4-nitriminopyridine Dihydrate
Molecules of the title compound, C6H7N302.2H20, are almost planar with the NNO2 nitrimino group twisted 8 (1) ° out of the plane of the pyridine ring. The nitrimino group and CsN ring form a conju- gated 7r-electron system. These molecules together with water molecules are arranged in planes, They are con- nected with each other by O--H.-.O, O--H...N and weaker C--H..-O hydrogen bonds. Four water mol- ecules form a planar square (OH..-O--H)2 ring with O-..O distances equal to 2.741 (2) and 2.778(2)A. These rings join pairs of molecular planes into double layers, interacting otherwise by van der Waals forces.
Molecular balance forms of indium phthalocyanines in benzene and pyridine solution
Abstract The electronic absorption spectra of In2Pc3, InPc2 and InPcI solid compounds after dissolvation in one of the most commonly used solvents, i.e.: benzene and pyridine have been measured. In benzene, the molecules of the diindium tripledecker phthalocyanine, In2Pc3, undergoes transformation to ionic couples [InPc]+[InPc2]-, whereas when the InPc2 compound is dissolvated, the molecules of the indium sandwiches, InPc2, remain relatively stable in the solvent. When the In2Pc3 compound is dissolvated in py, the inner Pc(2-) ring of diindium tripledecker phthalocyanine molecule undergoes disjunction and rejection. In the results of it in the solution the couple of chromophores, being in t…
The enrichment ratio of atomic contacts in crystals, an indicator derived from the Hirshfeld surface analysis
An enrichment ratio is derived from the decomposition of the crystal contact surface between pairs of interacting chemical species. The propensity of different contact types to form is investigated.
Dimethyl 4,4′-(diazenediyl)dibenzoate at 100 K
In the asymmetric part of the unit cell of the title compound, C16H14N2O4, there are two chemically equivalent but crystallographic independent half molecules. The geometric centre of each complete molecule lies on a crystallographic inversion centre. Both molecules are almost planar [mean deviations of atoms in the two molecules are 0.032 (2) and 0.044 (2) Å] and their geometries are similar. In the crystal, molecules are arranged in columns along the a axis. There are no intermolecular donor–acceptor distances shorter than 3.4 Å.
ChemInform Abstract: 4,4,4′,4′,7,7′-Hexamethyl-2,2′-spirobichroman.
The title compound, C23H28O2, was obtained from the reaction of acetone with meta-cresol. The molecular structure consists of two identical subunits which are nearly perpendicular to each other. The oxygen-containing rings are not planar and the molecule is chiral. The crystal structure consists of chains of molecules of the same chirality arranged along the [010] axis.
Theoretical Multipolar Atom Model Transfer in Nitro-Derivatives of N-Methylaniline
The nitroanilines are an example of compounds in which the coexistence of electron-rich and electron-deficient substituents, connected through a conjugated π-electronic system, makes their molecular second-order hyperpolarizability and second-harmonic generation efficiency particularly high. This property makes them extremely interesting from the point of view of charge density distribution analysis. The electron density of three isomeric molecules, i.e., N-methyl-2-nitroaniline, N-methyl-3-nitroaniline, and N-methyl-4-nitroaniline, was calculated theoretically through the multipolar atom model transfer. Two types of refinement models, i.e., multipolar atom model (MAM) and independent atom …
Dependence of the Substituent Effect on Solvent Properties
The influence of a solvent on the substituent effect (SE) in 1,4-disubstituted derivatives of benzene (BEN), cyclohexa-1,3-diene (CHD), and bicyclo[2.2.2]octane (BCO) is studied by the use of polarizable continuum model method. In all X–R–Y systems for the functional group Y (NO2, COOH, OH, and NH2), the following substituents X have been chosen: NO2, CHO, H, OH, and NH2. The substituent effect is characterized by the charge of the substituent active region (cSAR(X)), substituent effect stabilization energy (SESE), and substituent constants σ or F descriptors, the functional groups by cSAR(Y), whereas π-electron delocalization of transmitting moieties (BEN and CHD) is characterized by a geo…
2-[4-(Dimethylamino)phenyl]-3,3-difluoro-3H-naphtho[1,2-e][1,3,2]oxazaborinin-2-ium-3-uide
In the title compound, C19H17BF2N2O, a twist about the N—C single bond is observed, making the cross conjugation not as efficient as in the case of a planar structure. The borone complex has tetrahedral geometry. In the crystal, molecules are conected by weak C—H...F hydrogen bonds.
π-Electron delocalization in 2-benzoyl-5-phenylpyrazolidin-3-one
Abstract The crystal and molecular structures of 2-benzoyl-5-phenylpyrazolidin-3-one have been characterized by X-ray diffraction along with density functional theory studies. Cinnamic acid chloride was reacted with benzhydrazide, yielding 2-benzoyl-5-phenylpyrazolidin-3-one. This product was formed in the transformation comprising the nucleophilic addition of benzhydrazide to the styryl fragment of the α,β-unsaturated arrangement and subsequent cyclization. The molecule contains two benzene rings and one five-membered heterocyclic ring with an N–N single bond. The five-membered ring is composed of three atoms of sp 3 hybridization and two atoms of sp 2 hybridization, which cause the flatte…
Tetrakis(tert-butylammonium) benzene-1,2,4,5-tetracarboxylate octahydrate
In the crystal structure of the title compound, 4C4H12N+·C10H2O8 4−·8H2O, there is a centre of symmetry at the centre of the benzene ring; the asymmetric unit comprises one half-anion, two cations and four water molecules. The pyromellitate tetraanion is nonplanar; it and the cations exhibit normal geometry. The two unique carboxylate groups are twisted out of the plane of the benzene ring by about 40 and 50°. The network formed by the ions and water molecules is based on eight O—H...O and six N—H...O strong hydrogen bonds.
Most of the field/inductive substituent effect works through the bonds
AbstractAn application of the quantum chemical modeling allowed to investigate the nature of the field/inductive substituent effect (SE). For this purpose, series of X-tert-butyl···tert-butane (TTX) complexes (where X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO) were studied. A starting distance between central carbon atoms in substituted and unsubstituted fragments of TTX, dC1–C4, was the same as the distance C1–C4 in X-substituted bicyclo[2.2.2]octane (BCO), where the SE acts both via bonds and via space. A strength of interaction between substituted and unsubstituted components of TTX was described by deformation and interaction energies. The substituent …
A vanadyl Schiff base complex: {2,2'-[1,1'-(o-phenylenedinitrilo)bis(ethan-1-yl-1-ylidene)]diphenolato}oxovanadium(IV).
The green crystals of the title compound, [V(C(22)H(18)N(2)O(2))O], represent a mononuclear oxovanadium complex. The central V(IV) centre has a distorted square-pyramidal coordination. Two N atoms and two O atoms of the Schiff base ligand define the base of the pyramid, and the oxide O atom is in the apical position. Density functional theory (DFT) calculations were performed to analyse the changes in the geometry of the ligand during the complex formation. The most significant changes are observed in the values of the torsion angles in the vicinity of the donor N atoms. The HOMA index (Harmonic Oscillator Model of Aromaticity) has been calculated to compare the aromaticity of the benzene r…
Bis(glycylglycinium) oxalate at 100 K.
The structure of the title compound, 2C(4)H(9)N(2)O(3)(+).C(2)O(4)(2-), which has been determined by X-ray diffraction, contains discrete glycylglycine (HGly-Gly)(+) cations in general positions and oxalate anions which lie across centres of inversion. Although the geometry of the (HGly-Gly)(+) cation is not significantly different compared with other structures containing this residue, a few changes in conformation are observed which indicate the presence of molecular interactions. The molecular network in the crystal consists of one nearly linear O-H...O, five N-H...O and two weak C-H.O hydrogen bonds.
Classical and reverse substituent effects in meta- and para-substituted nitrobenzene derivatives
Electron-accepting properties of the nitro group were studied in a series of meta- and para-X-substituted nitrobenzene derivatives (X = NMe2, NH2, OH, OMe, CH3, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, COCl, NO2, NO). For this purpose Hammett-like approaches were applied based on quantum chemistry modeling; the B3LYP/6-311++ G(d,p) method was used. The substituent effect (SE) was characterized by the mutually interrelated descriptors: the charge of the substituent active region, cSAR(X), and substituent effect stabilization energy, SESE, as well as substituent constants, σ. Classical SE is realized by dependences of the structural parameters of the nitro group (ONO angle and NO bond lengt…
N-(tert-butoxycarbonylglycyl-alpha,beta-dehydrophenylalanylglycylphenylalanyl)-4-nitroaniline.
In the crystal structure of the tetrapeptide Boc0–Gly1–ΔPhe2–Gly3–Phe4–p-NA (p-NA is para-nitroaniline), C33H36N6O8, there are two independent molecules differing in conformation in the asymmetric part of the unit cell. All the amino acids in the peptide are linked trans to each other. The torsion angles in the main chain of both molecules are close to the values of the type β-II turn. Two intramolecular and three intermolecular N—H⋯O hydrogen bonds stabilize the conformation of each of the molecules.
[5,10,15,20-Tetrakis(4-tert-butylphenyl)-porphyrinato-κ4N] zinc(II) toluene solvate
The structure of the title compound, [Zn(C60H60N4)]·C7H8, represents a typical clathrate containing a host molecule of [5,10,15,20-tetrakis(4-tert-butylphenyl)porphyrinato]zinc(II) and a toluene guest molecule. The Zn atom occupies an inversion center and exhibits ideal square-planar coordination, while the porphyrin group remains perfectly flat. The toluene molecule lies on an inversion center and is disordered.
Crystal structure of N-(tert-butoxycarbonyl)phenylalanyldehydroalanine isopropyl ester (Boc–Phe–ΔAla–OiPr)
In the crystal structure of the dehydrodipeptide (Boc-Phe-ΔAla-OiPr), the molecule has a trans configuration of the N-methylamide group. Its geometry is different from saturated peptides but is in excellent agreement with other dehydroalanine compounds. In the crystal, an N—H⋯O hydrogen bond links the molecules in a herringbone packing arrangement.
Study on the synthesis of novel 5-substituted 2-[2-(pyridyl)ethenyl]-1,3,4-oxadiazoles and their acid–base interactions
Abstract A series of novel 5-substituted 2-[2-(pyridyl)ethenyl]-1,3,4-oxadiazoles were efficiently synthesized by cyclocondensation of the appropriate 3-(pyridyl)acrylohydrazides with triethyl orthoesters in the presence of glacial acetic acid. The products were identified by means of spectroscopic methods and their pKA ionization constants were determined. The influence of substituents on the basicity of the pyridine system has been discussed. Graphical Abstract
Synthesis and electronic aspects of tetrahydrobenzothienopyrimidine derivatives
Abstract The chemistry of thiophenes, pyrimidines, triazolopyrimidines and benzothiophenes has drawn much attention because of their biological activities. Their interesting properties are connected with their complex π-electron delocalisation effects. Herein the synthesis, crystal and molecular structures at 100 K and DFT calculated structures of three tetrahydrobenzothienopyrimidine derivatives are reported i.e. 4-hydrazino-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidine which was a substrate for 2-phenyl-8,9,10,11-tetrahydro[1]benzothieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidine and 3-methyl-9,10,11,12-tetrahydro-2H-[1]benzothieno[2′,3′:4,5]pyrimido[1,6-b][1,2,4]triazin-2-one. Moreover t…
(2S,3S)-2-(N,N-dibenzylamino)butane-1,3-diol refined using a multipolar atom model.
The crystal structure of the title compound, C18H23NO2, was determined using the experimental library multipolar atom model. The refinement showed a significant improvement of crystallographic statistical indices when compared with a conventional spherical neutral atom refinement.
Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9H-carbazole
A combined experimental and theoretical study has been performed on 9-benzyl-3,6-diiodo-9H-carbazole. Experimental X-ray (100.0 K) and room-temperature 13C NMR studies were supported by advanced density functional theory (DFT) calculations. The non relativistic structure optimization was performed and the 13C nuclear magnetic shieldings were predicted at the relativistic level of theory using the Zeroth Order Regular Approximation (ZORA). The changes in the benzene and pyrrole rings compared to the unsubstituted carbazole or the parent molecules were discussed in terms of aromaticity changes using the harmonic oscillator model of aromaticity (HOMA) and the nucleus independent chemical shift…
A novel approach for obtaining α,β-diaminophosphonates bearing structurally diverse side chains and their interactions with transition metal ions studied by ITC
Aminophosphonates are an important group of building blocks in medicinal and pharmaceutical chemistry. Novel representatives of this class of compounds containing nontypical side chains are still needed. The aza-Michael-type addition of amines to phosphonodehydroalanine derivatives provides a simple and effective approach for synthesizing N′-substituted α,β-diaminoethylphosphonates and thus affords general access to aminophosphonates bearing structurally diverse side chains. Thermodynamic analysis of the chosen aminophosphonates at physiological pH proves that they serve as potent chelators for copper(II) ions and moderate chelators for nickel(II) ions.
Substituent effects of nitro group in cyclic compounds
AbstractNumerous studies on nitro group properties are associated with its high electron-withdrawing ability, by means of both resonance and inductive effect. The substituent effect of the nitro group may be well described using either traditional substituent constants or characteristics based on quantum chemistry, i.e., cSAR, SESE, and pEDA/sEDA models. Interestingly, the cSAR descriptor allows to describe the electron-attracting properties of the nitro group regardless of the position and the type of system. Analysis of classical and reverse substituent effects of the nitro group in various systems indicates strong pi-electron interactions with electron-donating substituents due to the re…
Novel 2,6-disubstituted phenylboronic compounds - Synthesis, crystal structures, solution behaviour and reactivity
Abstract 2,6-Diformylphenylboronic acid has been synthesized and characterized both in the solid state as well as in solution. In crystal, an unusual structural pattern has been found with the formation of intermolecular hydrogen bonds by B(OH) 2 and CHO groups as well as water molecules. In solution tautomeric equilibrium with the formation of oxaborole ring by one of the formyl groups was proved on the basis of multinuclear NMR spectroscopy. The title compound reacts with secondary mono- and diamines to form various types of substituted benzoxaboroles, which have been characterized by XRD and spectroscopic methods.
Diethylammonium hydrogen oxalate
The structure of the title compound, C4H12N+·C2HO4−, consists of discrete oxalate monoanions and diethylammonium cations. The N atom lies on a crystallographic twofold rotation axis and the oxalate ion is centrosymmetric. The oxalate monoanions are present as hydrogen-bonded linear chains. Conformationally extended diethylammonium cations link the linear chains through three–centre N–H⋯O hydrogen bonds.
Diethyl (1-benzyl-4-phenyl-3-trifluoromethyl-1H-pyrrol-2-yl)phosphonate
In the title compound, C22H23F3NO3P, the dihedral angles between the pyrrole ring and the benzyl and phenyl rings are 81.38 (7) and 46.21 (8)°, respectively. The ethyl phosphate groups present with P—O—C—C torsion angles of −178.47 (10) and 106.72 (16)°, and an intramolecular C—H...O hydrogen bond occurs. In the extended structure, molecules are linked by C—H...O and C—H...F hydrogen bonds to generate [001] chains.
3-Formyl-2-furanboronic acid: X-ray and DFT studies
The molecule of the title compound, C5H5BO4, is almost planar with the boronic acid group inclined to the furan ring by 3.7 (1)°. DFT (density functional theory) calculations at the B3LYP/6-311+G** level of theory (with no imaginary frequencies) were used to approximate the influence of hydrogen bonding on the molecular geometry and have confirmed the planarity of the molecule. No significant differences in geometrical parameters in the solid state and in the gas phase are associated with the presence of the O—H⋯O intermolecular hydrogen-bonding network. The crystal packing is characterized by O—H⋯O hydrogen-bonded dimers, which are additionally linked by O—H⋯O, as well as C—H⋯O interactio…
Structural and Molecular Characterization of meso-Substituted Zinc Porphyrins: A DFT Supported Study
Structural parameters of a range of over 100 meso-substituted zinc porphyrins were reviewed and compared to show how far the nature of the functional group may affect the interatomic distances and bond angles within the porphyrin core. It was proved that even despite evident deformations of the molecular structure, involving twisting of the porphyrin's central plane, the coupled π-bonding system remains flexible and stable. DFT calculations were applied to a number of selected porphyrins representative for the reviewed compounds to emphasize the relevance of theoretical methods in structural investigations of complex macrocyclic molecular systems. Experimental and DFT-simulated IR spectral …
Crystal structure of bis-(allyl-ammonium) oxalate.
The title salt, 2C3H8N+·C2O42−, crystallized with six independent allylammonium cations and three independent oxalate dianions in the asymmetric unit. One of the oxalate dianions is nearly planar [dihedral angle between CO2planes = 1.91 (19)°], while the other two are twisted with angles of 11.3 (3) and 26.09 (13)°. One cation has a synperiplanar (cis) conformation with an N—C—C—C torsion angle of 0.9 (3)°, whereas the five remaining cations are characterized bygauchearrangements, with the N—C—C—C torsion angles ranging from 115.9 (12) to 128.8 (3)°. One of the allylammonium cations is positionally disordered (fixed occupancy ratio = 0.45:0.55). In the crystal, the cations and anions are co…
Energetic study of bifurcated hydrogen bonds in secondary structures of salts composed with dicarboxylic acids and ethylamine
Abstract The nature of bifurcated hydrogen bonds prompted us to analyze the energy of supramolecular motifs on the example of new structures of carboxylic acids salts with amines, which guarantee a multitude of such interactions. Experimental and theoretical studies of four dicarboxylic salts with primary amine: ethylammonium succinate hydrate (1), tartrate hydrate (2) phthalate hydrate (3) and terephthalate (4) has been investigated along with study of the strength of interactions between the anions and cations. The complete topological analysis of the charge density for all new structures allowed designation of the estimated Cumulative Dissociation Energy (eCDE).
Disorder in the crystals of trans-4-fluoroazoxybenzene. Synthesis, spectral properties, crystal structures and DFT calculations
Abstract Two crystals of trans-4-fluoroazoxybenzene were obtained using two different methods. Oxidation of 4-fluoroazobenzene provided crystals of trans-4-fluoroazoxybenzene (I) consisting of two isomers; 51% α (ONN) and 49% β (NNO) isomer. From trans-amino-azoxybenzenes in Schiemann reaction it were obtained crystals of trans-4-fluoro-NNO-azoxybenzenes (II, β isomer) containing 4.7% of the α-isomer according to the HPLC analysis. The crystal structures of I and II were determined by the X-ray diffraction method. In the crystal I two nitrogen atoms of azoxy bridge and fluorine atom are disordered. In the crystal II, there are two independent molecules of trans-4-fluoroazoxybenzene; the mol…
Structural, electronic and energetic effects in heterocyclic fluorene derivatives fused with a fulvene unit
Abstract A set of 36 heterocyclic (B, N and O) fluorene (C) derivatives fused in nine ways with fulvene ring have been analyzed by means of different local aromaticity criteria. Molecular geometry of analyzed compounds were optimized at B3LYP/6-311++G(2d,2p) level of theory. The evaluation of the local aromaticity has been carried out through the use of the geometry-based harmonic oscillator model of aromaticity (HOMA) and the magnetism-based zz‐component of the nucleus independent chemical shifts calculated 1 A above the ring center (NICS1zz) indices as well as one aromaticity index derived from the Quantum Theory Atoms in Molecules (QTAIM), i.e. the para-delocalization index (PDI). Additi…
Ethylammonium 2,4,5-tricarboxybenzoate
9-Ethoxy-1,5,13-trimethyl-8,10-dioxatetracyclo[7.7.1.02,7.011,16]heptadeca-2,4,6,11,13,15-hexaene
The reaction of ethyl acetoacetate with meta-cresol in an acidic ionic liquid yielded a complex mixture of condensation products. 4,7-Dimethylcoumarin and the title compound, C20H22O3, were isolated. The title compound shows chemical but not crystallographic mirror symmetry. The two aromatic rings are inclined at an angle of 73.55 (6)°.
Temperature-dependent polymorphism of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide: experimental and theoretical studies on intermolecular interactions in the crystal state
X-ray analysis of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide reveals the temperature-dependent polymorphism associated with the crystallographic symmetry conversion. The observed crystal structure transformation corresponds to a symmetry reduction from I41 /a (I) to P43 (II) space groups. The phase transition mainly concerns the subtle but clearly noticeable reorganization of molecules in the crystal space, with the structure of individual molecules left almost unchanged. The Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, revealing graphically the differences in spatial arrangements of the molecule…
Substituent effects in trans-p,p'-disubstituted azobenzenes: X-ray structures at 100 K and DFT-calculated structures.
The crystal and molecular structures of twopara-substituted azobenzenes with π-electron-donating –NEt2and π-electron-withdrawing –COOEt groups are reported, along with the effects of the substituents on the aromaticity of the benzene ring. The deformation of the aromatic ring around the –NEt2group inN,N,N′,N′-tetraethyl-4,4′-(diazenediyl)dianiline, C20H28N4, (I), may be caused by steric hindrance and the π-electron-donating effects of the amine group. In this structure, one of the amine N atoms demonstrates clearsp2-hybridization and the other is slightly shifted from the plane of the surrounding atoms. The molecule of the second azobenzene, diethyl 4,4′-(diazenediyl)dibenzoate, C18H18N2O4,…
Symmetric Fluoroborate and its Boron Modification: Crystal and Electronic Structures
Four boron-carrying molecules were synthesized and purified. These were found to be (a) relatively neutral with respect to the parent BF derivative and (b) functionalized by donor&ndash
The conformation cis of N-acetyl-N-methyl-α,β-dehydroalanine N′-methylamide and saturated analogues
A series of three homologous amino acids derivatives: N-acetyl-N-methyl-α,β–dehydroalanine N′-methylamide (1), N-acetyl-N-methyl-L-alanine N′-methylamide (2), and N-acetyl-N-methyl-DL-alanine N′-methylamide have been synthesised. The racemic species undergoes spontaneous separation into L and D-enantiomers. From these two chiral forms, the structure of L-enantiomer (3) was analysed. The molecules of 1 – 3 adopt the cis arrangement of the N-terminal amide bond. The molecular conformations are similar for 1 (φ, ψ = 94.6(1)°, −1.7(1)°) and 3 (φ, ψ = 111.5(1)°, −23.8(1)°), and also 2 (φ, ψ = −114.8(2)°, 29.5(2)°), if inversion through the chiral C2 carbon is considered. They are stabilised by i…
Deduction of the oxidation degree of the group A15 elements at the phthalocyanines on the basis of the Q band
Ethyldimethylammonium oxalate
The title crystal structure, C4H12N+·C2HO4−, contains discrete ethyldimethylammonium cations and oxalate monoanions. Linear chains of oxalate monoanions are formed by strong O—H⋯O hydrogen bonds. These chains are further connected by N—H⋯O and C—H⋯O hydrogen bonds through ethyldimethylammonium cations, forming channels along the a axis.
Twotrans-4-aminoazoxybenzenes
Two isomeric trans-4-aminoazoxybenzenes, trans-1-(4-aminophenyl)-2-phenyldiazene 2-oxide (alpha, C(12)H(11)N(3)O) and trans-2-(4-aminophenyl)-1-phenyldiazene 2-oxide (beta, C(12)H(11)N(3)O), have been characterized by X-ray diffraction. The alpha isomer is almost planar, having torsion angles along the C(aryl)-N bonds of only 4.9 (2) and 8.0 (2) degrees. The relatively short C(aryl)-N bond to the non-oxidized site of the azoxy group [1.401 (2) A], together with the significant quinoid deformation of the respective phenyl ring, is evidence of conjugation between the aromatic sextet and the pi-electron system of the azoxy group. The geometry of the beta isomer is different. The non-substitute…
Toward the Physical Interpretation of Inductive and Resonance Substituent Effects and Reexamination Based on Quantum Chemical Modeling
An application of a charge of the substituent active region concept to 1-Y,4-X-disubstituted derivatives of bicyclo[2.2.2]octane (BCO) [where Y = NO2, COOH, OH, and NH2 and X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, and NO] provides a quantitative information on the inductive component of the substituent effect (SE). It is shown that the effect is highly additive but dependent on the kind of substituents. An application of the SE stabilization energy characteristics to 1,4-disubstituted derivatives of BCO and benzene allows the definition of inductive and resonance contributions to the overall SE. Good agreements with empirical approaches are found. All calc…
Substituent effects in nitro derivatives of carbazoles investigated by comparison of low-temperature crystallographic studies with density functional theory (DFT) calculations
The crystal structure of 9H-carbazole, C12H9N, (I), has been redetermined at low temperature for use as a reference structure in a comparative study with the structures of 1-nitro-9H-carbazole, C12H8N2O2, (II), and 9-nitrocarbazole, C12H8N2O2, (III). The molecule of (I) has crystallographically imposed mirror symmetry (Z′ = 0.5). All three solid-state structures are slightly nonplanar, the dihedral angles between the planes of the arene and pyrrole rings ranging from 0.40 (7)° in (III) to 1.82 (18)° in (II). Nevertheless, a density functional theory (DFT) study predicts completely planar conformations for the isolated molecules. To estimate the influence of nitro-group substitution on aroma…
The substituent effect of π-electron delocalization in N-methylamino-nitropyridine derivatives: crystal structure and DFT calculations
AbstractThe crystal and molecular structures of 3-(N-methylamino)-2-nitropyridine, 5-(N-methylamino)-2-nitropyridine and 2-(N-methylamino)-5-nitropyridine have been characterized by X-ray diffraction. To perform conformational analysis, the geometries of the compounds as well as their conformers and rotamers were optimized at the B3LYP/6-311++G(3df,3pd) level. The resulting data were used to analyze the π-electron delocalization effect in relation to the methylamino group rotation in ortho-, meta- and para-substitution positions. Quantitative aromaticity indices were calculated based on which we estimated the electronic structures of the analyzed compounds. The substituent effect of the met…
N-(Pyrazin-2-yl)adamantane-1-carboxamide
Molecules of the title compound, C15H19N3O, are composed of an adamantine unit and a pyrazine ring connected to each other through an amide bond. The H—N—C=O moiety is close to planar [C—N—C—O and C—N—C—C torsion angles of 4.7 (2) and −173.8 (1)°, respectively]. The N3—C5 bond has partial double-bond character [1.370 (1) Å]. The geometries of the pyrazine ring and the adamantane substituent are normal and in good agreement with closely related structures. In the crystal, molecules are connected by N—H...O hydrogen bonds, forming zigzag chains in the [001] direction and are arranged in a herringbone fashion.
Phosphorus mononitride: A difficult case for theory
Phosphorus nitride (PN) is the simplest molecule formed solely by phosphorus and nitrogen. It represents an interesting model for materials, where phosphorus is directly attached to nitrogen. Nevertheless, both theoretical and experimental studies often provide an incomplete picture on the structural, electronic, and spectral properties of PN. Theoretical predictions often suffer from insufficient level of theory, incomplete basis set, or from neglecting several effects, for example, zero‐point vibrational correction (ZPVC). Therefore, we performed an extensive benchmark study on structural, electronic, and spectral properties of PN at the Hartree‐Fock, density functional theory (DFT), or e…
Syntheses, spectroscopic and structural properties of phenoxysilyl compounds : X-ray structures, FT-IR and DFT calculations
Abstract The reaction of silicon disulfide with alkylphenols yields tetraphenoxysilane, cyclodisilthiane and silanethiol. The outcome of the reaction depends on the presence of the steric hindrance in the ortho position on the reacting phenol. New products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---π (X = C, S) whereas the intermolecular interactions are either very weak CH---π/CH---O contacts found in aryloxysilane or electrostatic dipole–dipole attraction in cyclodisilthiane and silanethiol. The S–H---π interactions in the obtained silanethiol ar…
4-Benzoyl-3,4-dihydro-2 H -1,4-benzoxazine-2-carbonitrile: refinement using a multipolar atom model
The structural model for the title compound, C(16)H(12)N(2)O(2), was refined using a multipolar atom model transferred from an experimental electron-density database. The refinement showed some improvements of crystallographic statistical indices when compared with a conventional spherical neutral-atom refinement. The title compound adopts a half-chair conformation. The amide N atom lies almost in the plane defined by the three neighbouring C atoms. In the crystal structure, molecules are linked by weak intermolecular C-H...O and C-H...pi hydrogen bonds.
9-Methyl-3-phenyldiazenyl-9H-carbazole: X-ray and DFT-calculated structures
The title compound, C19H15N3, was prepared by condensation of 3-nitrosocarbazole and aniline with subsequent methylation. The structure is built up of stacks of almost planar molecules. Density functional theory (DFT) calculations predict a completely planar conformation, different from that observed in the crystal lattice. HOMA (harmonic oscillator model of aromaticity) indices, calculated for three aromatic rings, demonstrate the small influence of the azo substituent on π electrons in the carbazole system.
Synthesis of 2-Aminothiazole Derivatives in Easy Two-Step, One-Pot Reaction
Proton tautomerism in 2-nitramino-C-nitropyridine derivatives - Experimental and quantum chemical study
Abstract The structures of 2-nitramino-3-nitropyridine and 2-nitramino-5-nitropyridine have been characterized by X-ray diffraction and Density Functional Theory (DFT) studies. In the crystals, both compounds exist as the imino forms. The DFT calculations were performed in order to explore the amino-imino tautomerism of the studied compounds in the gas phase and the influence of solvent polarity on the tautomeric equilibrium. The Harmonic Oscillator Model of Aromaticity index (HOMA) and Nucleus Independent Chemical Shift (NICS) calculated for the pyridine rings of the studied systems, demonstrated a noticeable decrease in aromaticity of the imino forms. This study showed also that the highe…
2,2-Difluoro-3-(4-fluorophenyl)-2H-benzo[e][1,3,2]oxazaborinin-3-ium-2-uide
There is one independent molecule in the asymmetric unit of the title compound, C13H9BF3NO, which crystallizes in the non-centrosymmetric space groupCc. In the molecular structure, the BF2-carrying ring is distorted from planarity and its mean plane makes a dihedral angle of 42.3 (1)° with the 4-fluorophenyl ring. F atoms are involved in all of the short intermolecular contacts of the crystal structure, which link molecules to form chains along [001] and [010].
Crystal structure of a novel bismuth phthalocyanine-bismuth iodide complex
Abstract A new phthalocyaninato complex of bismuth with formula [(BiPc) 4 (Bi 4 I 16 )] was obtained in the reaction of bismuth with 1,2-dicyanobenzene in iodine vapour. The crystal and molecular structure of the complex was determined by single crystal X-ray diffraction. The unit cell consists of four discrete (BiPc) + cations and (Bi 4 I 16 ) 4− anions. The (Bi 4 I 16 ) 4− complex anion is formed by four edge-sharing BiI 6 octahedra. The arrangement of molecules in the crystalline structure of the complex is mainly determined by ionic attraction between the (BiPc) + and (Bi 4 I 16 ) 4− moieties, i.e. each (Bi 4 I 16 ) 4− complex anion is encapsulated between four (BiPc) + cations. The str…
4-Chloro-N-methyl-N-nitroaniline
The molecular structure of (p-ClC 6 H 4 )(CH 3 )NNO 2 (or C 7 H 7 ClN 2 O 2 ) contains a planar NNO 2 nitroamino group which is twisted about the N-C phenyl bond by ca 68° from the plane of the aromatic ring. The structural data are in agreement with the spectral results and indicate that there is no conjugation between the aromatic sextet and the nitroamino group. There are no specific intermolecular interactions.
Tris(1,10-phenanthroline)zinc(II) dichromate tetrahydrate
The title compound, [Zn(C12H8N2)3][Cr2O7]·4H2O, was obtained by mixing 1,10-phenanthroline (phen), potassium chromate and zinc sulfate solutions. The asymmetric unit is composed of a [Zn(phen)3]2+ cation, a Cr2O72− anion and four water molecules. The ZnII ion is in a distorted octahedral environment, coordinated by six N atoms from three phen molecules. The cations are connected to anions by weak C—H⋯O hydrogen bonds, with shortest H⋯O distances of ca 2.27–2.33 A. The Cr2O72− anion is in a staggered conformation. Two of the four crystallographically independent water molecules are ordered, and two others are disordered, each over two sites.
Method and basis set dependence of the NICS indexes of aromaticity for benzene
The role of theory level in prediction of benzene magnetic indexes of aromaticity is analysed and compared with calculated nuclear magnetic shieldings of 3 He used as NMR probe. Three closely related nucleus-independent chemical shift (NICS) based indexes were calculated for benzene at SCF-HF, MP2, and DFT levels of theory and the impact of basis set on these quantities was studied. The changes of benzene NICS(0), NICS(1), and NICS(1)zz parameters calculated using SCF-HF, MP2 and several density functionals were within 1 to 3 ppm. Similar deviations between magnetic indexes of aromaticity were observed for values calculated with selected basis sets. Only very small effect of polar solvent o…
4-hydroxy-ONN-azoxybenzene
The oxidation of 4-hydroxyazobenzene provided a mixture of two azoxy compounds, which were separated by column chromatography. The isomer with the higher melting point appeared to belong to the α (ONN) series, as determined by X-ray diffraction. The molecule, C12H10N2O2, is almost planar. The benzene rings are twisted by 11.7 (2) (substituted) and 4.1 (1)° (unsubstituted) with respect to the ONN plane. The molecules are connected to one another by strong O—H⋯O hydrogen bonds forming chains extended along [001], which are bound by much weaker C—H⋯O hydrogen bonds forming layers in the bc plane.
The reaction of optically active α-aminocarboxylic acid hydrazides with triethyl orthoesters
New derivatives of 2-(1-amino-1-phenylmethyl)-1,3,4-oxadiazole and 1,2,4-triazin-6-one were synthesised in the reactions of optically active α-aminocarboxylic acid hydrazides and triethyl orthoesters in xylene. The electronic and steric effects of substituents at the α position influencing the formation of five- or six-membered products are discussed.
Evaluation of Cyclic Amides as Activating Groups in N-C Bond Cross-Coupling: Discovery of N-Acyl-δ-valerolactams as Effective Twisted Amide Precursors for Cross-Coupling Reactions
The development of efficient methods for facilitating N-C(O) bond activation in amides is an important objective in organic synthesis that permits the manipulation of the traditionally unreactive amide bonds. Herein, we report a comparative evaluation of a series of cyclic amides as activating groups in amide N-C(O) bond cross-coupling. Evaluation of N-acyl-imides, N-acyl-lactams, and N-acyl-oxazolidinones bearing five- and six-membered rings using Pd(II)-NHC and Pd-phosphine systems reveals the relative reactivity order of N-activating groups in Suzuki-Miyaura cross-coupling. The reactivity of activated phenolic esters and thioesters is evaluated for comparison in O-C(O) and S-C(O) cross-c…
Bis(tert-butylammonium) oxalate
The component species in the title compound, 2C4H12N2+·C2O42−, interact by way of N—H⋯O hydrogen bonds, resulting in a layered network. N and two C atoms of the cation possess site symmetry m and the C atom of the anion has site symmetry 2.
1-[(1-ethoxypropylidene)amino]-2-ethyl-4-(4-hydroxybenzyl)imidazol-5(4H)-one.
The racemic title compound, C17H23N3O3, isolated from the reaction of L-(−)-tyrosine hydrazide with triethyl orthopropionate in the presence of a catalytic quantity ofp-toluenesulfonic acid (p-TsOH), crystallizes withZ′ = 1 in a centrosymmetric monoclinic unit cell. The molecule contains two planar fragments,viz.the benzene and imidazole rings, linked by two C—C single bonds. The dihedral angle between the two planes is 59.54 (5)° and the molecule adopts a synclinal conformation. The HOMA (harmonic oscillator model of aromaticity) index, calculated for the benzene ring, demonstrates no substantial interaction between the two π-electron delocalization regions in the molecule. In the crystal …
The structural aspects of the transformation of 3-nitroisoxazoline-2-oxide to 1-aza-2,8-dioxabicyclo[3.3.0]octane derivatives: Experimental and MEDT theoretical study
Abstract Reaction of 3-nitroisoxazoline-2-oxide with monosubstituted ethenes, first time documented fifty years ago, have been reviewed. Structures of phenyl and cyano derivatives of 1-aza-2,8-dioxabicyclo[3.3.0]octane produced in [3 + 2] cycloaddition (32CA) between styrene and acrylonitrile with 3-nitroisoxazoline-2-oxide were determined through single crystal XRD analysis. The molecular mechanism of the title 32CA has been also analyzed within the Molecular Electron Density Theory (MEDT) based on the M06-2X(PCM)/6-311 + G(d,p) calculations.
X-ray, conformation and electronic structures of 1-nitropyrrolidine
Abstract The chemistry of pyrrolidine compounds has drawn much attention because of their biological activities. The crystal and molecular structure of 1-nitropyrrolidine (C4H8NNO2) at 150K, along with calculated structures (DFT and MP2), are reported herein. In the solid-state, the asymmetric part of the unit cell is composed of one quartermolecule at the position of two perpendicular mirror planes and the five-membered ring is disordered over a mirror plane, revealing the twisted conformation. Both geometries suggest slight sp3 hybridization of the amine nitrogen atom. The non-planar geometry suggests the lack of conjugation of the amine nitrogen lone pair with the nitro group, however th…
N′-(2-Fluorobenzoyl)benzohydrazide
In the crystal structure of the title compound, C(14)H(11)FN(2)O(2), the molecule is centrosymmetric. The F atom is disordered over four positions, on the two ortho positions of each ring, with occupancies of 0.287:0.213 (5). In the crystal structure, mol-ecules are linked by inter-molecular N-H⋯O and C-H⋯O hydrogen bonds.
5-(3,4-Dimethoxybenzyl)-7-isopropyl-1,3,5-triazepane-2,6-dione acetonitrile solvate refined using a multipolar atom model
International audience; The crystal structure of the title compound, C16H23N3O4·CH3CN, was refined using a multipolar atom model transferred from an experimental electron-density database. The refinement showed some improvement in crystallographic statistical indices compared with the independent atom model. The triazepane ring adopts a twist-boat conformation. In the crystal structure, the molecule forms intermolecular contacts with 14 different neighbours. There are two N-H...O and one C-H...O intermolecular hydrogen bond.
Halogen effect on structure and 13 C NMR chemical shift of 3,6-disubstituted-N -alkyl carbazoles
Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory, and their 13C nuclear magnetic resonance (NMR) isotropic shieldings were predicted using density functional theory (DFT). The model compounds contained 9H, N-methyl and N-ethyl derivatives. The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin–orbit zeroth-order regular approximation (ZORA) method. Significant heavy atom shielding effects for the carbon atom directly bonded with Br and I were observed (~−10 and ~−30 ppm while the other carbon shifts were practically unaffected). The decreasing electronegativity of the haloge…
Acetylhydroxamic acid
There is one independent molecule in the asymmetric unit of the title compound (alternatively namedN-hydroxyacetamide), C2H5NO2. It crystallizes in the noncentrosymmetric space groupP43. The structure is an anhydrous form of acetylhydroxamic acid with typical geometry that corresponds well with the hydrated structure described by Bracher & Small [Acta Cryst.(1970), B26, 1705–1709]. In the crystal, N—H...O and O—H...O hydrogen bonds connect the molecules into chains in thec-axis direction.
Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9<i>H</i>-carbazole
Tetrakis(methylammonium) benzene-1,2,4,5-tetracarboxylate dihydrate
In the title compound, 4CH6N+·C10H2O8 4−·2H2O, the complete C10H2O8 4− anion is generated by inversion; one of the unique carboxylate groups is almost coplanar with the benzene ring, perhaps as the result of intramolecular C—H...O interactions, and the other is almost perpendicular. A network of O—H...O and N—H...O hydrogen bonds helps to consolidate the crystal packing.
Relation between resonance energy and substituent resonance effect inP-phenols
Molecular geometries of phenol and its 17 p-substituted derivatives were optimized at the B3LYP/6–311 + G** level of theory. Three homodesmotic and three isodesmotic reaction schemes were used to estimate aromatic stabilization energies (ASE) and the substituent effect stabilization energy (SESE). Other descriptors of π-electron delocalization (HOMA and NICS, NICS(1) and NICS(1)zz) were also estimated. The SESE and ASE values correlated well with one another as well as with substituent constants. Much worse correlations with substituent constants were found for other aromaticity indices. The NICS(1)zz values are the most negative for unsubstituted phenol, indicating its highest aromaticity;…
Self-assembly mechanism based on charge density topological interaction energies
The packing interactions have been evaluated in the context of the self-assembly mechanism of crystal growth and also for its impacts on the aromaticity of the trimesate anion. The structure of ethylammonium trimesate hydrate (1) measured at 100 K and a charge density model, derived in part from theoretical structures, is reported. Theoretical structure factors were obtained from the geometry-optimized periodic wave function. The trimesic acid portion of 1 is fully deprotonated and participates in a variety hydrogen bonding motifs. Topological analysis of the charge density model reveals the most significant packing interactions and is then compared to a complementary analysis performed by …
Crystal structure ofN-(tert-butoxycarbonyl)glycyl-(Z)-β-bromodehydroalanine methyl ester [Boc–Gly–(β-Br)(Z)ΔAla–OMe]
In a dehydroamino acid with a C=C bond between the α- and β-C atoms, the amino acid residues are linked trans to each other and there are no strong intramolecular hydrogen bonds. The torsion angles indicate a non-helical conformation of the molecule.
How far the substituent effects in disubstituted cyclohexa-1,3-diene derivatives differ from those in bicyclo[2.2.2]octane and benzene?
Substituents effects in cyclic diene derivatives are studied using quantum chemical modeling and compared to the corresponding effects in aromatic (benzene) and fully saturated (bicyclo[2.2.2]octane) compounds. In particular, electronic properties of the fixed group Y in a series of 3- and 4-X-substituted cyclohexa-1,3-diene-Y derivatives (where Y = NO2, COOH, COO− OH, O−, NH2, and X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO) are examined using the B3LYP/6-311++G(d,p) method. For this purpose, quantum chemistry models of the substituent effect: cSAR (charge of the substituent active region) and SESE (substituent effect stabilization energy) as well as trad…
Conformation of tert-butoxycarbonylglycyl-dehydroalanyl-glycine methyl ester in the crystalline state and calculated in the gas phase.
tert-Butoxycarbonylglycyl-dehydroalanyl-glycine methyl ester (systematic name: methyl {2-[(tert-butoxycarbonylamino)acetamido]prop-2-enamido}acetate) (Boc0-Gly1-ΔAla2-Gly3-OMe), C13H21N3O6, has been structurally characterized by single-crystal X-ray diffraction and by density functional theory (DFT) calculations at the B3LYP/6–311+G** level. The peptide chain in both the solid-state and calculated structures adopts neither β nor γ turns. All amino acid residues in the tripeptide sequence are linked trans to each other. The bond lengths and valence angles of the amino acid units in the crystal structure and gas phase are comparable. However, the conformation of the third glycyl residue (…
Association of 2-acylaminopyridines and benzoic acids. Steric and electronic substituent effect studied by XRD, solution and solid-state NMR and calculations
Abstract Eight single crystal X-ray structures, solid-state NMR spectroscopic, and theoretical studies utilizing QTAIM methodology were used to characterize the 2-acyl (alkyl in acyl = methyl, ethyl, t-butyl, and 1-adamantyl) amino-6-R-pyridine/4-R′-benzoic acid (R,R′ = H or Me) cocrystals. As expected among alkyl groups 1-adamantyl due to its bulkiness has the most significant effect on the relative positions of molecules in cocrystals. In addition, the subtle electronic and steric effects by the methyl substituents were observed. The theoretical calculations with full geometry optimizations are in agreement with the experimental findings (geometry, energy of hydrogen bonds). Based on the …
N,N′-Bis(pyridin-2-yl)octanediamide
The complete molecule of the title compound, C18H22N4O2, is generated by crystallographic inversion symmetry. In the crystal, N—H...N hydrogen bonds connect the molecules into [010] chains, which featureR22(8) loops. The packing is consolidated by C—H...O interactions.
Crystal structure of allylammonium hydrogen succinate at 100 K
The asymmetric unit of the title compound, C2H8N+·C4H5O4−, consists of two allylammonium cations and two hydrogen succinate anions (Z′ = 2). One of the cations has a near-perfectsyn-periplanar (cis) conformation with an N—C—C—C torsion angle of 0.4 (3)°, while the other is characterized by agaucheconformation and a torsion angle of 102.5 (3)°. Regarding the anions, three out of four carboxilic groups are twisted with respect to the central C–CH2–CH2–C group [dihedral angles = 24.4 (2), 31.2 (2) and 40.4 (2)°], the remaining one being instead almost coplanar, with a dihedral angle of 4.0 (2)°. In the crystal, there are two very short, near linear O—H...O hydrogen bonds between anions, with t…
Substituent effect on the σ- and π-electron structure of the nitro group and the ring in meta- and para-substituted nitrobenzenes
An application of quantum chemical modeling allowed us to investigate a substituent effect on a σ and π electron structure of a ring and the nitro group in a series of meta- and para-X-substituted nitrobenzene derivatives (X = NMe2, NHMe, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, and NO). The obtained pEDA and sEDA parameters (the π- and σ-electron structure characteristics of a given planar fragment of the system obtained by the summation of π- and σ-orbital occupancies, respectively) of the NO2 group and the benzene ring allowed us to reveal the impact of the substituents on their mutual relations as well as to analyze them from the viewpoint of substituent charact…
Substituent effect of nitro group on aromaticity of carbazole rings
The molecular geometries of carbazole and its 17 nitro derivatives were optimized at the B3LYP/6-311++G(2d,2p) level of theory. The harmonic oscillator model of aromaticity and nucleus-independent chemical shift descriptors of π-electron delocalization were calculated to estimate the aromaticity of the carbazole five- and six-membered rings. The biggest changes in the value of both descriptors were observed for the pyrrole ring. The nitro group attached to 3 and/or 6 positions of the carbazole ring system exerts only a slight influence on the benzene ring aromaticity.
Crystal structure of isobutylammonium hydrogen oxalate hemihydrate
In the title hydrated molecular salt, C4H12N+·C2HO4−·0.5H2O, the O atom of the water molecule lies on a crystallographic twofold axis. The dihedral angle between the CO2and CO2H planes of the anion is 18.47 (8)°. In the crystal, the anions are connected to each other by strong near-linear O—H...O hydrogen bonds. The water molecules are located between the chains of anions and isobutylamine cations; their O atoms participate as donors and acceptors, respectively, in O—H...O and N—H...O hydrogen bonds, which form channels (dimensions = 4.615 and 3.387 Å) arranged parallel to [010].
Dimethyl 4,4'-(diazenedi-yl)dibenzoate at 100 K.
In the asymmetric part of the unit cell of the title compound, C16H14N2O4, there are two chemically equivalent but crystallographic independent half molecules. The geometric centre of each complete molecule lies on a crystallographic inversion centre. Both molecules are almost planar [mean deviations of atoms in the two molecules are 0.032 (2) and 0.044 (2) Å] and their geometries are similar. In the crystal, molecules are arranged in columns along theaaxis. There are no intermolecular donor–acceptor distances shorter than 3.4 Å.
2-Methyl-N-(pyrazin-2-yl)propanamide–1,2,4,5-tetrafluoro-3,6-diiodobenzene (2/1)
In the title compound, C8H11N3O·0.5C6F4I2, molecules ofiPr-substituted pyrazine are co-crystallized with 1,4-diiodo-2,3,5,6-tetrafluorobenzene. The complete molecule of 1,4-diiodo-2,3,5,6-tetrafluorobenzene is generated by an inversion centre at the middle of the aromatic ring. Both molecules have normal geometry and theiPr acylamine group is disordered over two sets of sites with an occupancy ratio of 0.51:0.49. In the crystal, the components are linked by I...N halogen bonds [2.830 (2) Å] and C—H...F interactions are observed.
trans-4-Bromo-ONN-azoxybenzene at 100 K.
The crystal structure of the alpha isomer of trans-4-bromoazoxybenzene [systematic name: trans-1-(bromophenyl)-2-phenyldiazene 2-oxide], C(12)H(9)BrN(2)O, has been determined by X-ray diffraction. The geometries of the two molecules in the asymmetric unit are slightly different and are within approximately 0.02 A for bond lengths, approximately 2 degrees for angles and approximately 3 degrees for torsion angles. The azoxy bridges in both molecules have the typical geometry observed for trans-azoxybenzenes. The crystal network contains two types of planar molecules arranged in columns. The torsion angles along the Ar-N bonds are only 7 (2) degrees, on either side of the azoxy group.
Orthorhombic polymorphs of twotrans-4-aminoazoxybenzenes
The two isomeric compounds 4-amino-ONN-azoxybenzene [or 1-(4-aminophenyl)-2-phenyldiazene 2-oxide], i.e. the alpha isomer, and 4-amino-NNO-azoxybenzene [or 2-(4-aminophenyl)-1-phenyldiazene 2-oxide], i.e. the beta isomer, both C(12)H(11)N(3)O, crystallized from a polar solvent in orthorhombic space groups, and their crystal and molecular structures have been determined using X-ray diffraction. There are no significant differences in the bond lengths and valence angles in the two isomers, in comparison with their monoclinic polymorphs. However, the conformations of the molecules are different due to rotation along the Ar-N bonds. In the alpha isomer, the benzene rings are twisted by 31.5 (2)…
Examples of UV–Vis profiles use as tool for evidence of the metallophthalocyanines transformation
Abstract The UV–Vis spectra for a set of MPcs (Mmetal, Pc = phthalocyanine ligand), i.e.: In(III)PcI (1), Hf(IV)PcI2Pht (Pht = phthalonitrile) (2), Sn(II)Pc (3), Sn(IV)PcI2 (4), and Ge(IV)PcI2 (5) have been examined in two solvents, O-donative acetylacetone, and non-coordinative benzene. The UV–Vis spectra in Hacac solution of 1,2 and 4,5 shows that the axially ligated iodine atoms are replaced by (acac)− anions of the solvent, whereas in 3 the oxygen donors of the solvent causing the auto-oxidation of Sn(II) to Sn(IV) ions and as a result the Sn(II)Pc is transformed into the Sn(IV)Pc(acac)2. The chloride complexes of the 1–5 compounds are formed at Hacac solution after acidification by hyd…
Allylammonium hydrogen oxalate hemihydrate
In the title hydrated molecular salt, C3H8N+·C2HO4−·0.5H2O, the water O atom lies on a crystallographic twofold axis. The C=C—C—N torsion angle in the cation is 2.8 (3)° and the dihedral angle between the CO2and CO2H planes in the anion is 1.0 (4)°. In the crystal, the hydrogen oxalate ions are linked by O—H...O hydrogen bonds, generating [010] chains. The allylammonium cations bond to the chains through N—H...O and N—H...(O,O) hydrogen bonds. The water molecule accepts two N—H...O hydrogen bonds and makes two O—H...O hydrogen bonds. Together, the hydrogen bonds generate (100) sheets.
X-ray and DFT-calculated structures of a vanadyl Schiff base complex: (methanol-κO)[2-methoxy-6-({2-[(2-oxido-3-methoxybenzylidene)amino]benzyl}iminomethyl)phenolato-κ4O1,N,N,O1′]oxidovanadium(IV) monohydrate
The central VVatom in the title mononuclear oxovanadium complex, [VO(C23H20N2O4)(CH3OH)]·H2O, has a distorted octahedral coordination. Two N atoms and two O atoms of the Schiff base define the base of the bipyramid and two O atoms are in the apical positions, one from vanadyl and the second from methanol. Density functional theory (DFT) calculations were performed for the title complex and its ligand to compare their geometry in the solid and gas phases. Additional analyses were made of the changes in the geometry of the ligand during complex formation. The HOMA (harmonic oscillator model of aromaticity) descriptor of π-electron delocalization was calculated to estimate the aromaticity of t…
Non-covalent interactions of N-phenyl-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide derivatives—a case of intramolecular N-oxide hydrogen bonds
The crystal structures of new N-phenyl-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide derivatives are reported. The results of X-ray diffraction showed the existence of intramolecular hydrogen bonding between carboxamide nitrogen donors and N-oxide oxygen acceptors. The use of Quantum Theory of Atoms in Molecules allowed its classification as a strong interaction, with energy about 10 kcal/mol, and of intermediate character between closed shell and shared bonds. Comparison of experimental data and quantum theoretical calculations indicated that a substituent attached to the phenyl ring in the para position influences the strength and geometry of the title hydrogen bonding. Stronger π-elect…
CCDC 917843: Experimental Crystal Structure Determination
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