Synthesis,characterization, X-ray diffraction studies and biological evaluation of tert-butyl 4-(2-ethoxy-2-oxoethyl)-piperazine-1-carboxylate and tert-butyl 4-(2-hydrazino-2-oxoethyl)piperazine-1-carboxylate

Two derivatives of N-Boc piperazine, an ester derivative, i.e., tert-butyl 4-(2-ethoxy-2-oxoethyl)-piperazine-1-carboxylate (1), and, a hydrazide derivative tert-butyl 4-(2-hydrazino-2-oxoethyl)piperazine-1-carboxylate (2) were synthesized and were characterized by FT-IR, ¹H & ¹³C NMR and LCMS spectroscopic studies. The structures of both 1 and 2 were further confirmed by single crystal X-ray diffraction analysis. The molecule of 1 is linear in shape with the ethyl acetate moiety adopting fully extended conformation, while the molecule of 2 is L-shaped with the molecule being twisted at the C10 atom. The crystal structure of 1 adopts a two-dimensional zig-zag architecture featuring C–H…O intermolecular interactions, while that of 2 features strong N–H…O hydrogen bonds and intermolecular interactions of the type N–H…N and C–H…N, resulting in a two-dimensional structure. Furthermore, a detailed analysis of the intermolecular interactions and crystal packing of 1 and 2 via Hirshfeld surface analysis and fingerprint plots was performed. The antibacterial and antifungal activities of both the compounds have been studied against several microorganisms, and were found to be moderately active.     

Self‐inclusion structure of 5,11,17,23‐tetrakis(azidomethyl)‐25,26,27,28‐tetrahydroxycalix[4]arene,and 5,11,17,23‐tetra‐tert‐butyl‐25,27‐bis(chloroacetoxy)‐26,28‐bis(2‐pyridylmethoxy)calix[4]arene

In the structures of the two title calix[4]arene derivatives, C₃₂H₂₈N₁₂O₄, (I), and C₆₀H₆₈Cl₂N₂O₆, (II), compound (I) adopts an open‐cone conformation in which there are four intramolecular O—H...O hydrogen bonds, while compound (II) adopts a distorted chalice conformation where the two pendant pyridyl rings, one of which is disordered, are almost mutually perpendicular, with an interplanar angle of 79.2 (2) or 71.4 (2)°. The dihedral angles between the virtual plane defined by the four bridging methylene C atoms and the phenol rings are 120.27 (7), 124.03 (6), 120.14 (8) and 128.25 (7)° for (I), and 95.99 (8), 135.93 (7), 97.21 (8) and 126.10 (8)° for (II). In the supramolecular structure of (I), pairs of molecules associate by self‐inclusion, where one azide group of the molecule is inserted into the cavity of the inversion‐related molecule, and the association is stabilized by weak intermolecular C—H...N hydrogen bonds and π(N₃)–π(aromatic) interactions. The molecular pairs are linked into a two‐dimensional network by a combination of weak intermolecular C—H...N contacts. Each network is further connected to its neighbor to produce a three‐dimensional framework via intersheet C—H...N hydrogen bonds. In the crystal packing of (II), the molecular components are linked into an infinite chain by intermolecular C—H...O hydrogen bonds. This study demonstrates the ability of calix[4]arene derivatives to form self‐inclusion structures.     

3‐(p‐Chloro­phenyl)‐4‐phenyl‐4,5‐di­hydro­isoxazole‐5‐spiro‐2′‐1′,2′,3′,4′‐tetra­hydro­naphthalen‐1′‐one

In the title compound, C₂₄H₁₈ClNO₂, the phenyl ring and the tetralone moiety are approximately orthogonal to the isoxazoline ring. The isoxazoline ring adopts an envelope conformation, while the cyclo­hexenone ring of the tetralone moiety has an intermediate sofa/half‐chair conformation. In this structure, one C—H?N intermolecular and two C—H?O intramolecular hydrogen bonds occur; the H?A distances are 2.60, and 2.35 and 2.57 Å, respectively. The mol­ecules are held together by an intermolecular C—H?N hydrogen bond, forming a one‐dimensional chain along the [100] direction.     

4‐[(2‐Chloro­phenyl)­diazenyl]‐6‐methoxy‐2‐{[tris­(hydroxy­methyl)­methyl]­amino­methyl­ene}cyclo­hexa‐3,5‐dien‐1(2H)‐one

The structure of the title compound, C₁₈H₂₀ClN₃O₅, displays the characteristic features of azo­benzene derivatives. Intramolecular N—H⋯O, weak intramolecular C—H⋯O, and intermolecular O—H⋯O and C—H⋯O interactions influence the conformation of the mol­ecules and the crystal packing. Intermolecular hydrogen bonds link the mol­ecules into infinite chains, and the title compound adopts the keto–amine tautomeric form. The azo­benzene moiety of the mol­ecule has a trans configuration. The mol­ecule is not planar, and the dihedral angle between the two phenyl rings is 35.6 (2)°.     

Transformations of griseofulvin in strong acidic conditions--crystal structures of 2'-demethylgriseofulvin and dimerized griseofulvin

The structure of griseofulvic acid, C16H15ClO6, at 100 K has orthorhombic (P2(1)2(1)2) symmetry. It is of interest with respect to biological activity. The structure displays intermolecular O-H...O, C-H...O hydrogen bonding as well as week C-H...pi and pi...pi interactions. In strong acidic conditions the griseofulvin undergoes dimerization. The structure of dimerized griseofulvin, C34H32C12O12 x C2H6O x H2O, at 100 K has monoclinic (P2(1)) symmetry. The molecule crystallized as a solvate with one ethanol and one water molecule. The dimeric molecules form intermolecular O-H...O hydrogen bonds to solvents molecules only but they interact via week C-H...O, C-H...pi, C-Cl...pi and pi...pi interactions with other dimerized molecules.     

Intramolecular Interactions of Trityl Groups

Trityl group, Tr, is a molecular dynamic rotor of which the conformation and helicity depend on other groups in the close vicinity. Interactions with another covalently linked Tr group and with other substituents are analyzed in terms of transfer of chirality to the trityl group. Two trityl groups in a molecule can mutually interact at a distance of two, three, or five bonds. Despite its size, a Tr group attached to a cyclohexane or cyclopentane ring through an oxygen or nitrogen atom adopts either an axial or equatorial position, depending on additional stabilizing interactions, such as hydrogen bonding.     

Hydrogen‐bonded networks in 1‐(4‐methoxyphenyl)‐2,2‐dimethylpropan‐1‐ol

The asymmetric unit of the title compound, C₁₂H₁₈O₂, contains two independent molecules. They differ only slightly in conformation but form completely different intermolecular hydrogen‐bonded arrays. One molecule exhibits disorder in the hydroxy group region, but this does not influence the formation of hydrogen bonds. The bulky tert‐butyl group on one side of the carbinol C atom and the benzene ring on the other side promote the formation of discrete dimeric motifs via hydrogen‐bridged hydroxy groups. Dimers are further joined by strong hydroxy–methoxy O—H...O bonds to form chains with dangling alcohol groups. Weaker intermolecular C—H...O interactions mediate the formation of a two‐dimensional network.     

Structure ofN S-butyl-N O-phenyl(thiooxamide)

The molecular and crystal structure of N^S-butyl-N^O-phenyl(thiooxamide) (1) has been established by X-ray structural analysis. The thiooxamide fragment and the phenyl ring are coplanar. The conformation of 1 is stabilized by NH...O and NH...S hydrogen bonds. No conjugation between the thioamide and the oxamide fragments of the molecule occurs. In the crystal, the centrosymmetrically related molecules 1 are linked in dimers through NH ... O' intermolecular hydrogen bonds.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 485–487, February, 1996     

N‐(3‐tert‐Butyl‐1‐phenyl‐1H‐pyrazol‐5‐yl)‐N‐(4‐methoxybenzyl)acetamide: a hydrogen‐bonded chain of centrosymmetric rings

The molecule of the title compound, C₂₃H₂₇N₃O₂, adopts a conformation having no internal symmetry so that the compound exhibits conformational chirality. The molecules are linked by a combination of C—H...O and C—H...π(arene) hydrogen bonds into a chain of rings in which two types of centrosymmetric ring alternate.     

Structures of N—（2,3,4,6—Tetra—O—acetyl—β—D—glycosyl） thiocarbamic Benzoyl Hydrazine

The crystal structure of N-(2,3,4,6-tetra-O-acetyl-β-D-gly-cosyl)-thiocarbamic benzoyl hydrazine(C22H27N3O9S) was determined by X-ray diffracton method.The hexopyranosyl ring adopts a chair conformation.All the ring substituents are in the equatorial positions.The acetoxyl-methyl group is in synclinal conformation.The S atom is in synperiplanar conformation while the benzoyl hydrazine moiety is anti-periplanar.The thiocarbamic moiety is almost companar with the benzoyl hydrazine group.There are two intramolecular hydrogen bonds and one intermolecular hydrogen bond for each molecule in the crystal structure.The molecules form a network structure through intermolecular hydrogen bonds.     

Structural studies of model peptides containing beta-, gamma- and delta-amino acids

The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-betaGly-NHMe (2), Piv-Pro-betaGly-OMe (3), Piv-Pro-deltaAva-OMe (4) and Boc-Pro-gammaAbu-OH (5) are described (Piv: pivaloyl; NHMe: N-methylamide; betaGly: beta-glycine; OMe: O-methyl ester; deltaAva: delta-aminovaleric acid; gammaAbu: gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-betaGly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the deltaAva residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H...O hydrogen bond.     

N‐Methyl‐N‐phenylaminomethyl 2‐naphthyl ketone: an X‐ray diffraction and density functional theory study

The crystallographically observed molecular structure of the title compound, C₁₉H₁₇NO, and its inverted counterpart are compared with that calculated by density functional theory (DFT) at the B3LYP/6‐311++G(d,p) level. The results from both methods suggest that the observed molecular conformation of the title compound is primarily determined by intermolecular interactions in the crystal structure. The periodic organization of the molecules is stabilized by weak C—H...O and C—H...π hydrogen bonds and thus a two‐dimensional puckered network consisting of R₄⁴(22) and R₄⁴(38) ring motifs is established. The title molecule has a (+)‐antiperiplanar conformation about the C—C bond in the aminoacetone bridge. The pyramidal geometry observed around the vertex N atom is flattened by the presence of bulky phenyl and naphthylethanone fragments.     

(E)‐Methyl 2‐anilinomethylene‐3‐oxobutanoate: X‐ray and density functional theory studies

Molecules of the title compound, C₁₂H₁₃NO₃, are not planar and are stabilized by electrostatic interactions, as the dipole moment of the molecule is 3.76 D. They are also stabilized by intramolecular hydrogen bonds of N...O and C...O types, and by a complicated network of weak intermolecular hydrogen bonds of the C...O type. This paper also reports the theoretical investigation of the hydrogen bonding and electronic structure of the title compound using natural bond orbital (NBO) analysis.     

Bis(5‐tert‐butyl‐2‐hydroxy‐3‐methylbenzyl)(6‐hydroxyhexyl)ammonium chloride monohydrate,an anion receptor complex

In the title compound, C₃₀H₄₈NO₃⁺·Cl⁻·H₂O, the cation acts with a water molecule as a chloride ion receptor. The chloride ion forms three strong intramolecular hydrogen bonds. The water molecule forms both an intramolecular bridge between one phenol H atom and the chloride ion, and an intermolecular link to the aliphatic alcohol O atom. Weak intermolecular C—H...Cl and C—H ...O hydrogen bonds provide additional packing interactions.     

3,6‐Bis­(4‐hydroxy­benzyl)­piperazine‐2,5‐dione

In the title compound, C₁₈H₁₆N₂O₄, the piperidine ring adopts a chair conformation, lying on an inversion centre. The 4‐hydroxy­benzyl groups are in quasi‐axial positions. A two‐dimensional network is formed through N—H?O and O—H?O intermolecular hydrogen bonds and C—H?O interactions.     

On the interplay between CH...O and OH...O interactions in determining crystal packing and molecular conformation: an experimental and theoretical charge density study of the fungal secondary metabolite austdiol (C12H12O5)

The total experimental electron density rho(r), its Laplacian inverted delta(2)rho(r), the molecular dipole moment, the electrostatic potential phi(r), and the intermolecular interaction energies have been obtained from an extensive set of single-crystal X-ray diffracted intensities, collected at T = 70(1) K, for the fungal metabolite austdiol (1). The experimental results have been compared with theoretical densities from DFT calculations on the isolated molecule and with fully periodic calculations. The crystal structure of (1) consists of zigzag ribbons extended along one cell axis and formed by molecules connected by both OH...O and CH...O interactions, while in a perpendicular direction, adjacent molecules are linked by short CH...O intermolecular contacts. An extensive, quantitative study of all the intra- and intermolecular H...O interactions, based not only on geometrical criteria, but also on the topological analysis of rho(r), as well as on the evaluation of the pertinent energetics, allowed us (i) to assess the mutual role of OH...O and CH...O interactions in determining molecular conformation and crystal packing; (ii) to identify those CH...O contacts which are true hydrogen bonds (HBs); (iii) to determine the relative hydrogen bond strengths. An experimental, quantitative evidence is given that CH...O HBs are very similar to the conventional OH...O HBs, albeit generally weaker. The comparison between experimental and theoretical electric dipole moments indicates that a noticeable charge rearrangement occurs upon crystallization and shows the effects of the mutual cooperation of HBs in the crystal. The total intermolecular interaction energies and the electrostatic energy contribution obtained through different theoretical methods are reported and compared with the experimental results. It is found that the new approach proposed by Spackman, based on the use of the promolecular charge density to approximate the penetration contribution to intermolecular electrostatic energies, predicts the correct relative electrostatic interaction energies in most of the cases.     

Understanding the structural properties of a homologous series of bis-diphenylphosphine oxides

A homologous series of bis-diphenylphosphine oxides (C6H5)2PO(CH2)(n)PO(C6H5)2 (with n = 2-8; denoted 2-8] have been investigated to explore the effects of a range of competing and cooperative intermolecular and intramolecular interactions on the structural properties in the solid state. The important factors influencing the structural properties include intramolecular aspects such as the conformation of the aliphatic chain and the intramolecular interaction between the two P=O dipoles in the molecule, and intermolecular aspects such as long-range electrostatic interactions (dominated by the arrangement of the P=O dipoles), C-H...O interactions, C-H...pi interactions and pi...pi interactions. Compounds 3 and 5 could be crystallized only as solvate co-crystals (3 water and 5 x (toluene)2], whereas the crystal structures of all the other compounds contain only the bis-diphenylphosphine oxide molecule. The crystal structures have been determined from single-crystal X-ray diffraction data, with the exception of 7 (which has been determined here from powder X-ray diffraction data) and 4 (which was known previously). The compounds with even n represent a systematic structural series, exhibiting characteristic, essentially linear P=O...P=O...P=O dipolar arrays, together with C-H...O and C-H...pi interactions. For the compounds with odd n, on the other hand, uniform structural behaviour is not observed across the series, although certain aspects of these crystal structures contribute in a general sense to our understanding of the structural properties of bis-diphenylphosphine oxides. Importantly, for the compounds with odd n, there is "frustration" with regard to the molecular conformation, as the preferred all-anti conformation of the aliphatic chain gives rise to an unfavourable parallel alignment of the two P=O dipoles within the molecule. Clearly the importance of avoiding a parallel alignment of the P=O dipoles becomes greater as n decreases. Local structural aspects (investigated by high-resolution solid-state 31P NMR spectroscopy) and thermal properties of the bis-diphenylphosphine oxide materials are also reported.     

Solution and solid-state spectra of quinacridone derivatives as viewed from the intermolecular hydrogen bond

Quinacridones are industrially important hydrogen-bonded pigments. The color in the solid state is vivid red, while it is pale yellow in solution, indicating evidently the involvement of intermolecular interactions in the solid state. The electronic structure has therefore been investigated with special attention to the role of intermolecular NH...O hydrogen bonds for three representative quinacridone compounds with different hydrogen-bond forming characteristics: unsubstituted gamma-quinacridone (gamma-QA) with two NH groups, mono-N-methylquinacridone (MMQA) with one NH and one CH(3), and N,N'-dimethyl-quinacridone (DMQA) with two CH(3) groups. The number of the NH...O hydrogen bonds per molecule is four, two, and zero for gamma-QA, MMQA, and DMQA, respectively. In solution, no significant difference in absorption maximum is recognized between gamma-QA, MMQA, and DMQA. However, in the solid state, the absorption maximum of gamma-QA appears at the longest wavelength, followed by MMQA and then DMQA, depending on the number of NH...O intermolecular hydrogen bonds. The role of the hydrogen bond is found to align transition dipoles in a "head-to-tail" fashion and to displace the absorption band toward longer wavelengths due to excitonic interactions. The extent of the spectral shift increases with increasing number of hydrogen bonds per molecule.     

Guest-induced supramolecular isomerism in inclusion complexes of T-shaped host 4,4-bis(4'-hydroxyphenyl)cyclohexanone

The T-shaped host molecule 4,4-bis(4'-hydroxyphenyl)cyclohexanone (1) has an equatorial phenol group and a cyclohexanone group along the arms and an axial phenol ring as the stem. The equatorial phenyl ring adopts a "shut" or "open" conformation, like a windowpane, depending on the size of the guest (phenol or o/m-cresol), for the rectangular voids of the hydrogen-bonded ladder host framework. The adaptable cavity of host 1 expands to 11x15-18 A through the inclusion of water with the larger cresol and halophenol guests (o-cresol, m-cresol, o-chlorophenol, and m-bromophenol) compared with a size of 10x13 A for phenol and aniline inclusion. The ladder host framework of 1 is chiral (P2(1)) with phenol, whereas the inclusion of isosteric o- and m-fluorophenol results in a novel polar brick-wall assembly (7x11 A voids) as a result of auxiliary C-H...F interactions. The conformational flexibility of strong O-H...O hydrogen-bonding groups (host 1, phenol guest), the role of guest size (phenol versus cresol), and weak but specific intermolecular interactions (herringbone T-motif, C-H...F interactions) drive the crystallization of T-host 1 towards 1D ladder and 2D brick-wall structures, that is, supramolecular isomerism. Host 1 exhibits selectivity for the inclusion of aniline in preference to phenol as confirmed by X-ray diffraction, 1H NMR spectroscopy, and thermogravimetry-infrared (TG-IR) analysis. The T(onset) value (140 degrees C) of aniline in the TGA is higher than those of phenol and the higher-boiling cresol guests (T(onset)=90-110 degrees C) because the former structure has more O-H...N/N-H...O hydrogen bonds than the clathrate of 1 with phenol which has O-H...O hydrogen bonds. Guest-binding selectivity for same-sized phenol/aniline molecules as a result of differences in hydrogen-bonding motifs is a notable property of host 1. Host-guest clathrates of 1 provide an example of spontaneous chirality evolution during crystallization and a two-in-one host-guest crystal (phenol and aniline), and show how weak C-H...F interactions (o- and m-fluorophenol) can change the molecular arrangement in strongly hydrogen-bonded crystal structures.