Packing Of Molecules In Crystal Research Articles

Computational insight into the crystal structures of cubane and azacubanes.

Using quantum chemistry and atom-atom potential methods, the molecular and crystal structures of cubane 1 and all types of unsubstituted azacubanes 2-22 were calculated. Alternative possible polymorphs of cubane 1 have been proposed. The thermochemical properties of azacubanes in the gas and solid phases were assessed. Thermodynamic aspects of stability are considered, and a significant decrease in stability is revealed upon transition from cubane 1 to octaazacubane 22. It has been shown that the density and energetic properties of azacubanes depend nonlinearly on the number of nitrogen atoms in the structure and the density of octaazacubane 22 at room temperature is 1.546gcm-3, which is significantly lower than the previously given estimate. In this work, DFT calculations were conducted through the software Gaussian 09 using B3LYP functional with basis set aug-cc-PVDZ and the Grimme dispersion correction D2. For crystal structure optimization, the atom-atom potential methods with PMC (packing of molecules in crystal) program were used. Charges for molecular electrostatic potential were fitted by FitMEP, and enthalpies of formation in gas phase were assessed by G3B3.

Charge–Transfer Fluorescence and Room-Temperature Phosphorescence from a Bisamide-Based Derivative

The development of organic luminescent materials with bimodal emissions of both fluorescence and room-temperature phosphorescent (RTP) remains a challenge. The investigation of the relationship between fluorescence and RTP performance is especially rare. In this work, we obtained an organic luminescent molecule, 1,4-phenylenebis((9H-carbazol-9-yl)methanone) (PBCM), which exhibits bimodal emissions of cyan fluorescence and yellow RTP in its crystalline state through adopting an electron donor–acceptor–donor (D–A–D) structure. The charge–transfer (CT) effects in the bimodal luminescent properties of PBCM, as well as the single-crystal structures and thermal properties, were investigated. It was found that the CT effect in the singlet states effectively reduces the ∆Est and promotes the ISC processes, resulting in an efficient phosphorescence of PBCM at room temperature. In addition, many strong intermolecular interactions are formed between the donor and acceptor parts of adjacent molecules, leading to the rigid configurations and compact packing of molecules in crystals, which was also confirmed to facilitate the efficient bimodal emissions of PBCM.

Sublimation Enthalpies of Substituted Pyridine N-Oxides.

The enthalpies of sublimation of five substituted pyridine N-oxides were determined by the Knudsen effusion method with mass spectrometric control of the vapor composition within the framework of the second law of thermodynamics. The sublimation enthalpy of mono-substituted compounds 4-X-PyO depends on the nature of the substituent X and increases in the order CH3→NO2→OCH3. A difference is noted in the nature of dissociative ionization of disubstituted derivatives 2-CH3-4-NO2PyO and 3-CH3-4-NO2PyO. The relationship between the packing of molecules in crystals and the ΔH°subl values is considered.

Triphenylantimony(V) Catecholates of the Type (3-RS-4,6-DBCat)SbPh3-Catechol Thioether Derivatives: Structure, Electrochemical Properties, and Antiradical Activity.

A new series of triphenylantimony(V) 3-alkylthio/arylthio-substituted 4,6-di-tert-butylcatecholates of the type (3-RS-4,6-DBCat)SbPh3, where R = n-butyl (1), n-hexyl (2), n-octyl (3), cyclopentyl (4), cyclohexyl (5), benzyl (6), phenyl (7), and naphthyl-2 (8), were synthesized from the corresponding catechol thioethers and Ph3SbBr2 in the presence of a base. The crystal structures of 1, 2, 3, and 5 were determined by single-crystal X-ray analysis. The coordination polyhedron of 1–3 is better described as a tetragonal pyramid with a different degree of distortion, while that for 5- was a distorted trigonal bipyramid (τ = 0.014, 0.177, 0.26, 0.56, respectively). Complexes demonstrated different crystal packing of molecules. The electrochemical oxidation of the complexes involved the catecholate group as well as the thioether linker. The introduction of a thioether fragment into the aromatic ring of catechol ligand led to a shift in the potential of the “catechol/o-semiquinone” redox transition to the anodic region, which indicated the electron-withdrawing nature of the RS group. The radical scavenging activity of the complexes was determined in the reaction with DPPH radical.

Synthesis and crystal structures of 7,8-bromo (dibromo)-3-tert-butylpyrazolo[5,1-c][1,2,4]triazines.

Single crystal structures in a series of 7-bromo-, 8-bromo-, and 7,8-dibromo-3-tert-butylpyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones have been investigated by X-ray diffraction. Novel 7-bromo- and 7,8-dibromo-3-tert-butylpyrazolo[5,1-c][1,2,4]triazines were synthesized by reduction of triazine carbonyl with dehydrative aromatization in acidic media, and their XRD structural features were compared with that of the 4-oxo analogs. The lengths and bond angles and the packing of molecules in crystals have been considered. Non-valence interactions for some of the studied compounds were observed. Correlations between the presence of bromine atoms at different positions and structural features are determined.Graphical abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s11224-021-01768-0.

Introducing Students to Mechanochemistry via Environmentally Friendly Organic Synthesis Using a Solvent-Free Mechanochemical Preparation of the Antidiabetic Drug Tolbutamide

The implementation of environmentally friendly, solvent-free mechanochemical synthesis in an undergraduate chemistry teaching laboratory is described. As a model reaction, the experiment addresses the catalytic mechanochemical synthesis of a small library of sulfonylureas, including a known active pharmaceutical ingredient, tolbutamide. The experiment introduces students to mechanochemistry, and the use of automated ball milling as a solvent-free synthetic methodology with a choice of two instruments: a mixer mill and a planetary ball mill. The isolation and purification of final products is achieved simply by washing with water and characterization is performed through powder X-ray diffraction. As milling reactions under wet and dry conditions lead to the formation of two diverse polymorphs of tolbutamide, this experiment also provides an opportunity to discuss topics relevant to solid-state pharmaceutical materials science, such as crystal packing of molecules and polymorphism, and it is an illustration of the emergent field of medicinal mechanochemistry in an undergraduate teaching laboratory.

Weak Interactions: A Versatile Role in Aromatic Compounds

Aromatic interactions are essential for stabilizing the conformation and crystal packing of molecules. They also play a vital role in drug chemistry by mediating drug-receptor interactions. In the present review, we discuss the various fields in which aromatic interactions are important and the role of such interactions.

Crystal structures of 2-formyl-6-methyl- and 6-bromo-2-formylpyridine 4-phenylthiosemicarbazones

New thiosemicarbazones—2-formyl-6-methylpyridine 4-phenylthiosemicarbazone (I) and 6-bromo-2-formylpyridine 4-phenylthiosemicarbazone hydrate (II)—were synthesized and their structures were determined. Molecules I and II are nonplanar, the phenyl moiety at the terminal nitrogen atom being rotated by 19.9° and 39.5°, respectively. The water molecule is the main factor determining the crystal packing of molecules II.

Understanding Supramolecular Interactions Provides Clues for Building Molecules into Minerals and Materials: a Retrosynthetic Analysis of Copper-Based Solids

The influence of non-covalent interactions on the crystal packing of molecules is well documented in the literature. Unlike molecular solids, crystal engineering of non-molecular solids is difficult to interpret as aggregation is complicated by the presence of neutral as well as ionic species and a range of forces operating, from weak hydrogen bonding to strong covalent interactions. In this perspective, we demonstrate for the first time the role of non-bonding interactions in the occurrence of oxide, hydroxide, or chloride linkages in oxides, hydroxychlorides, and chlorides of copper-based minerals and coordination polymers in terms of a mechanistic approach based on supramolecular retrosynthesis. The model proposed here visualizes the crystal nucleus as a supramolecular analogue of a transition state wherein appropriate tectons (chemically reasonable molecules) aggregate through non-bonding forces that can be perceived through well-known supramolecular synthons. The mechanistic approach provides chemical insights into the occurrence of different topologies and solid-state phenomena like polymorphism.

Synthesis and structures of two novel indolo[3,2-b] carbazole derivatives

Indolocarbazole derivatives have already been reported to be good organic semiconductor candidates. The knowledge of the relationship between the structure and packing of molecules in crystal is indispensable in design of high performance organic semiconductor materials. Two new indolocarbazole derivatives, 2,8-dibromo-5,11-di-[4-(isoindole-1,3-dione-2-yl)butyl]indolo[3,2-b]carbazole (I) and 2,8,6,12-tetrabromo-5,11-di-(4-chlorobutyl)indolo[3,2-b]carbazole (II) have been synthesized and the crystal structures have been studied. The dichloromethane solvate of (I), C42H32Br2N4O4 · 2CH2Cl2, is monoclinic, space groups P21/n. Unit cell parameters are a = 11.6847(2), b = 12.6942(2), c = 13.7899(2) A, β = 91.8220(10)°. Unlike other indolo[3,2-b]carbazole derivatives, there is no any π–π stacking between the indolocarbazole backbone of two adjacent molecules in the crystal. Since the isoindole-1,3-dione-2-yl is introduced in 5- and 11-positions in the molecule, the intermolecular short contacts mainly localize in between the pendant groups of the neighboring indolocarbazole molecules. The compound (II) is also monoclinic with P21/c space groups. Unit cell parameters are a = 4.6427(9), b = 11.425(2), c = 24.511(4) A, β = 93.47(1)°. In contrast with compound (I), the molecules of (II) possess strong face-to-face π–π stacking. The crystal structures were studied in detail. It is concluded that linear pedant groups benefit to co-facial π–π interaction. Additionally, the molecule electronic spectra were studied by quantum chemistry theoretical calculation.

Intermolecular Embraces and Intermolecular Energies

ABSTRACT Control of the assembly of molecules in the crystalline state requires management of all possible intermolecular interactions, and their energies. Any one molecule is surrounded by and interacts with parts of the surface of several others, and it is the balance of all the intermolecular interaction energies that determines the lattice enthalpy, and therefore the product structure. In this context of competition between different intermolecular contacts, simplification occurs when intermolecular motifs operate in concert, as in multiple aryl embraces. Structural hierarchies of extended embrace motifs occur in crystals, analogous to the secondary ⇒ tertiary ⇒ quaternary construction of biological macromolecules. Some principles for the analysis and interpretation of intermolecular space in crystals are discussed. Richly abundant data on the packing of molecules in crystals provides the basis for the description of intermolecular motifs, but this data is only geometrical. A different property, intermolecular energy, is determinative in the assembly of molecules. In strong contrast to the abundance of geometrical data, there is a serious scarcity of experimental thermodynamic data about many types of intermolecular motifs, including embraces. However, intermolecular potentials for chemically diverse systems can be calculated efficiently by appropriate density functional methods. Key concepts relating intermolecular potentials, the van der Waals distance criterion, and distributions of intermolecular distances, are reiterated. Charged polyatomic molecules, prevalent in coordination chemistry, raise significant questions about the relative magnitudes and influences of the additional electrostatic components of intermolecular energy. Some of the issues and uncertainties in this, for instance in the multiple phenyl embraces that occur between homocharged molecules, are discussed.

Synthesis and Comparative Analysis of Molecular and Supramolecular Structures of 4,8-Disubstituted 1,5-Dichloro-2,6-dioxotricyclo[5.1.0.0 3,5 ]octanes

A series of 4,8-disubstituted 1,5-dichloro-2,6-dioxotricyclo-[5.1.0.03,5]octanes, synthesized by various methods, were studied by X-ray single crystal diffraction. The conformation (syn/anti) of the molecules does not depend on the method of preparation and nature of substituents. All the compounds crystallize in centrosymmetric space groups with half of the molecules in the asymmetric part of the unit cell. The main influence which the substituents render is on the packing of molecules in crystals and on the types of intermolecular interactions and supramolecular structures.

X-ray diffraction study of the first monomeric dioxygermylene Ge(OCH2CH2NMe 2)2 stabilized by two Ge ← N intramolecular coordination bonds: The influence of Ge ← N intramolecular coordination bonds on the structure and packing of molecules in crystals

The molecular and crystal structures of the first monomeric dioxygermylene Ge(OCH2CH2NMe 2)2 (I) stabilized by two Ge ← N intramolecular coordination bonds are determined by X-ray diffraction analysis. The Ge ← N bond lengths in two independent molecules are equal to 2.329(2), 2.337(2) and 2.324(2), 2.346(2) A, respectively. The central germanium atom plays the role of a spiro atom between two five-membered heterocycles in the envelope conformation and adopts a trigonal-bipyramidal configuration with a lone electron pair in the equatorial position. Compound I has two planar-chiral isomers which crystallize jointly. Molecules in the crystal have a layered packing (molecular layers are perpendicular to the [001] direction) composed of four translationally independent equivalent layers. These layers are spaced at 1/4c intervals and displaced with respect to each other by approximately +0.35a, −1/4b, −0.35a, and +1/4b, respectively. The characteristic displacement of the layers and their proper symmetry (pba2) that differs from the symmetry of the crystal (space group P212121) determine a large variety of pseudosymmetry operations.

Impact of Molecular Structure Change on the Hierarchy of Intermolecular Interactions Leading to Polar/Centrosymmetric Crystals

Perfectly polar packing of molecules in molecular crystals is of fundamental interest in applications based on the electro-optic effect and piezo, pyro, and ferroelectric effects. The packing of molecules in the crystals of VO(acac) 2 (DMAP) complex is investigated and analyzed in the context of the perfect polar packing reported earlier in VO(acac) 2 (MP) and Zn(acac) 2 (DMAP) complexes. The subtle modification of the ligand is found to effect a drastic change in the molecular geometry between trans and cis in the vanadyl complexes. This in turn affects the hierarchy of intermolecular interactions with dramatic impact on the molecular packing, causing the perfectly polar packing motif in VO(acac) 2 (MP) to change to a centrosymmetric one in VO(acac) 2 (DMAP).

Molecular and crystal structures of 1-methyl-2-Oxo-3-acetoxy-4-hydroxy-4-(Phenyl)piperidine, 1-ethyl-2-oxo-3,4-dihydroxy-4-(Pyridyl)piperidine, and 1-benzyl-2-oxo-3,4-dihydroxy-4-(Pyridyl)piperidine and the role of hydrogen bonds in molecular packing in crystals

The molecular and crystal structures of 1-methyl-2-oxo-3-acetoxy-4-hydroxy-4-(phenyl)hydropyridine, 1-ethyl-2-oxo-3,4-dihydroxy-4-(pyridyl)piperidine, and 1-benzyl-2-oxo-3,4-dihydroxy-4-(pyridyl)piperidine are determined by X-ray diffraction analysis. These three hydroxy derivatives of hydropyridine are the convenient model compounds in studies of the influence of intramolecular and intermolecular hydrogen bonds on the conformation and packing of molecules in crystals. The molecules of hydroxy derivatives possess a considerable conformational flexibility and can form an extended network of intramolecular and intermolecular hydrogen bonds. It is shown that these compounds more often than others form noncentrosymmetric and polysystem crystals. The role of the molecular association and the type of hydrogen-bonded associates (syntons) in crystal packing are discussed.

Structure of a metastable phase of piracetam from X-ray powder diffraction using the atom–atom potential method

The crystal structure of the room-temperature metastable phase of 2-oxo-1-pyrrolidineacetamide (piracetam), C 6 H 10 N 2 O 2 , has been solved using the atom-atom potential method and refined by Rietveld refinement from powder diffraction data collected with a curved position-sensitive detector (INEL CPS 120) using Debye-Scherrer diffraction geometry with monochromatic X-rays. In the first stage, the indexing of the powder pattern was performed by the successive dichotomy method from data collected with a high-resolution diffractometer using the Bragg-Brentano geometry. The lattice parameters are a = 6.747 (2), b = 13.418 (3), c = 8.090 (2) A, β = 99.01 (3)°, and the space group is P2 1 /n. The structure model was obtained from minimization of the crystal-lattice potential energy calculated with semi-empirical atom-atom potentials using the PMC [Packing of Molecules in Crystals; Dzyabchenko, Belsky & Zorkii (1979). Kristallografiya, 24, 221-226] program. The Rietveld refinement converged to the final crystal-structure model indicator R B = 0.04 and profile factors Rp = 0.03 and R wp = 0.04. The molecular packing is characterized by intermolecular hydrogen bonds (N-H...O). The structure consists of two types of perpendicular infinite chains of piracetam molecules, which build parallel layers containing rings. No cyclic dimers were found. For a description of the hydrogen-bond patterns, the method based on graph theory was employed

Solid-state photochemistry. Remarkable effects of the packing of molecules in crystals on the diastereoselectivity of the intramolecular 2 + 2 photocycloaddition of a 4-(3'-butenyl)-2,5-cyclohexadien-1-one

Solid-state photochemistry. Remarkable effects of the packing of molecules in crystals on the diastereoselectivity of the intramolecular 2 + 2 photocycloaddition of a 4-(3'-butenyl)-2,5-cyclohexadien-1-one