Crystal Packing Forces Research Articles

A Direct Route to closo-SBnCln Thiaboranes from Simple Electron-Precise Synthons: The Different Role of Chalcogen Bonding in SB5Cl5 and SB11Cl11 Crystals.

Six-vertex closo-SB5Cl5 (1) and ten-vertex closo-1-SB9Cl9 (2) thiaboranes have been prepared, besides the already known 12-vertex closo-SB11Cl11 (3), from the co-pyrolysis reaction of B2Cl4 with S2Cl2 at 280 °C in vacuo. The compounds are sublimable, off-white solids. Their elemental composition has been determined by high-resolution mass spectrometry. They were further characterized by one- and two-dimensional 11B NMR spectroscopy and X-ray structure determination for 1 and 3. Ab initio/GIAO/NMR computations support octahedral, bicapped square-antiprismatic, and icosahedral geometries for 1, 2 and 3, respectively, as expected based on their closo-electron counts. 1 is the first isolated example of a neutral polyhedral closo-thiaborane with a cluster size smaller than ten vertices. The solid-state structure of 3 is one of the rare examples of a single-crystal X-ray structure determination of an icosahedral heteroborane reported. The corresponding crystal-packing forces show the different role of chalcogen bonding in these octahedral and icosahedral crystals. In addition, there is a mass-spectrometry evidence for the recurrent formation of further thiaborane homologs of closo-SBnCln with n=4, 6, 10, and supra-icosahedral 12.

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein.

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.

Poly[[μ-1,3-bis-(pyridin-3-yl)urea]bis-(μ4-succinato)dicopper(II)], a ribbon-like coordination polymer.

In the title com-pound, [Cu2(C4H4O4)2(C11H10N4O)]n, mono-periodic coordination polymer ribbons are held into the crystal structure by means of N-H⋯O hydrogen bonding and crystal packing forces.

Catena-Poly[[di-aqua-bis-(1,3-di-hydro-3-oxo-isobenzo-furan-1-acetato)-copper(II)]-μ-N,N'-(ethane-1,2-di-yl)dinicotinamide

The title compound, {[Cu(C10H7O4)2(C14H14N4O2)(H2O)2]n, contains octa-hed-rally coordinated CuII ions ligated by two bis-(1,3-di-hydro-3-oxo-1-isobenzo-furan-acetate (dibf) ligands and two trans water mol-ecules, linked by N,N'-(ethane-1,2-di-yl)dinicotinamide (edn) ligands into mono-periodic coordination polymer chains. The dibf ligands exhibit a pseudo-mirror positional disorder over two positions in a 89.2 (3)/10.8 (3) ratio; the central amide groups of the edn ligands are disordered pseudo-rotationally in the same ratio. These mono-periodic chain motifs are held into supra-molecular di-periodic supra-molecular layers by means of N-H⋯O hydrogen bonding between edn amide groups and unligated dibf carboxyl-ate O atoms. In turn, the supra-molecular layers are held by crystal packing forces into the full crystal structure of the title compound.

Structure and Conformation of Novel BODIPY Ugi Adducts.

Two novel BODIPY‐Ugi (boron dipyrromethene) adducts exhibit peculiar room temperature (T=20 °C) H‐1 NMR spectra in that several protons located at the aromatic aniline‐type ring are lost in the baseline. This observation revealed the existence of a dynamic conformational process where rotation around the C−N bond is hindered. Variable‐temperature H‐1 and C‐13 NMR spectroscopic analysis confirmed this conclusion; that is, low‐temperature spectra show distinct signals for all four aromatic protons below coalescence, whereas average signals are recorded above coalescence (T=+120 °C). Particularly interesting was the rather large difference in chemical shifts for the ortho protons below coalescence, Δδ=1.45 ppm, which was explained based on DFT computational analysis. Indeed, the calculated lowest‐energy gas‐phase conformation of the BODIPY Ugi adducts locates one half of the aniline‐type ring in the shielding anisotropic cone of the bridge phenyl ring in the BODIPY segment. This is in contrast to the solid‐state conformation established by X‐ray diffraction analysis that shows a nearly parallel arrangement of the aromatic rings, probably induced by crystal packing forces.

Control of Molecular Conformation and Crystal Packing of Biphenyl Derivatives.

This Review presents a discussion of the conformation of biphenyl derivatives in different chemical environments. The interplay between aromatic stabilization and steric repulsion, normally considered to explain the conformation of the molecule, is contrasted with the interpretation provided by models not based on molecular orbitals. The electronic control of conformation by means of appropriate hydrogen substitution is discussed by examples taken from chemistry and molecular electronics. Supramolecular synthons involving biphenyl are critically analyzed in terms of the molecular conformation, crystal packing and intermolecular forces. Some directions for future research on the control of the conformation of biphenyls are also presented.

Nonsteroidal Anti-Inflammatory Drugs–1-Phenylethylamine Diastereomeric Salts: A Systematic Solid-State Investigation

The solid-state investigation of the diastereomeric salts (S)-ibuprofen (S-Ibu), (S)-naproxen, (S-Nap), and (S)-ketoprofen (S-Ket) with (R)-(+)- and (S)-(−)-1-phenylethylamine, R-PEA, and S-PEA respectively, has been carried out by using a combination of experimental and in-silico tools. The focus was on their crystal packing and on the stability/transformation of their solid forms under different experimental conditions with the final aim of extracting useful information on the forces/features which could be exploited for the chiral separation of the corresponding racemic compounds. All the salts are 21-column crystals, each column consisting of API and 1-phenylethylamine ions assembled via the 1-phenylethylammonium-carboxylate supramolecular heterosynthon which originates a R43 (10) pattern, the intercolumns contacts being definitely weaker. In spite of an overall similarity in the crystal packing forces and motifs of the anhydrous salts, the temperature stability range suggests that the homochiral species are the most stable. The fact that the homochiral salt of S-Ket (S-Ket_S-PEA) is stable toward the hydration, at variance with the heterochiral one (S-Ket_R-PEA), further confirms this hypothesis. On the other hand, preliminary sorption tests show that S-Ket and S-Ibu preferentially capture the homochiral PEA (S-Nap is not selective). This behavior has been correlated to the almost planar boundary surfaces which characterize and differentiate the 21 sheets in S-Ket_S-PEA and S-Ibu_S-PEA salts with respect to the corresponding heterochiral ones.

Crystallographic and Theoretical Evidences of Anion⋅⋅⋅Anion Interaction

Planar (HgCl3 )- anions are stacked fairly closely together in a slipped parallel arrangement within several crystal structures. Quantum chemical analysis shows evidence of strong noncovalent spodium bonds between the Hg π-hole of one unit and the Cl atom of an adjacent unit. Anion⋅⋅⋅anion spodium bonds work in tandem with crystal packing forces.

Synthesis, Characterization and Sorptive Removal of Heavy metals on Nano-Structured Agglomerates of Iron (III)-Cerium (IV) Bimetal Mixed Oxide (NICMO): Search For An Efficient, Low Cost Decontamination Technique

Nano particles usually exhibit remarkable physical properties, rapid chemical reactivity, and high sorption capacity for inorganic compounds. Studies of the fate and transport of nano particles were largely concerned with their properties and behavioral change over time, whether they would interact with toxic contaminants after being released into the environment. Keeping in line with the above facts, here, we aim to develop an efficient material by eco-friendly green synthetic route that was further characterized to be crystalline ranging in nano-dimension for filtering heavy metals containing groundwater. The average particle size was found to be approximately 3.56 nm calculated from the Gaussian fit of the distinct peaks and then computing its modeled data into Scherrer’s equation. The thermal stability of iron(III)-cerium(IV) mixed oxide nanoparticle agglomerates (NICMO) was well established from the consistent particle size at different temperature and also, from differential thermal. The bimetal mixed oxide contained agglomerated crystalline nano-particles of dimension 10-20 nm held together by crystal packing forces and, its corresponding empirical composition FeCe1.1O7.6. Appearance of weak band at 534 cm-1 in the FTIR spectrum of NICMO is presumed for the presence of hetero- metal bonding via oxygen linkage (i.e, Fe-O-Ce). Scanning electron microscopic (SEM) image of NICMO established the agglomerated surface morphology with irregular shape that was unevenly dispersed over a base matrix of oxide surface almost covering up its porous nature. Decreasing sharpness of inflexion points of NICMO in BET isotherm indicates porosity arising out of channels of the template framework but surely with non uniformity in pore size distribution.The positive change in entropy (△S°) values of both Pb(II) and Cd(II) species with NICMO in the systems investigated conclude that the reactions were entropy driven, occurring with increase of randomness at solid-liquid interface owing to the release of water molecules when hydrated Pb(II) and Cd(II) species binds on to the solid surface

Crystal structure, Hirshfeld surface analysis and DFT studies of 5-(adamantan-1-yl)-3-[(4-chlorobenzyl)sulfanyl]-4-methyl-4H-1,2,4-triazole, a potential 11\u03b2-HSD1 inhibitor

5-(Adamantan-1-yl)-3-[(4-chlorobenzyl)sulfanyl]-4-methyl-4H-1,2,4-triazole (4) was identified as a potential 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) inhibitor and this paper describes the in-depth structural analysis thereof. Compound 4 was synthesized in a 92% yield and its 3D-structure confirmed by single-crystal X-ray diffraction. Hirshfeld surface analysis indicated that H…H, C-H…C, C-H…Cl and especially C-H…N hydrogen bond interactions are the primary contributors to the intermolecular stabilisation in the crystal. In order to explore the properties of 4, free from the influence of the crystal field, density functional theory (DFT) calculations were conducted. Results indicated that the DFT optimized geometry of 4 produced a conformer (4a) that is significantly different from the crystal structure. Further experiments confirmed that the crystal structure is not the absolute minimum conformation. This indicated that the crystal packing forces has significantly influenced the conformation thereof. Frontier molecular orbital energies and net atomic charges were also calculated to elucidate the electronic properties of 4a. These results provided insight into areas of the molecule that may present with the ability to form binding interactions at the 11β-HSD1 active site. Molecular docking experiments revealed important intermolecular interactions between 4a and 11β-HSD1. These results indicate that 4 may be considered for further drug design endeavors.

Structure of Diferrocenyl Thioketone: From Molecule to Crystal.

Ferrocenyl-functionalized thioketones have recently been recognized as useful building blocks for sulfur-containing compounds with potential applications in materials chemistry. This work is devoted to a single representative of such thioketones, namely diferrocenyl thioketone (Fc2CS), whose structure has been determined here for the first time. Both X-ray crystallography and a wide variety of quantum-chemical methods were used to explore the structure of Fc2CS. In addition to the X-ray structure determination, intermolecular interactions occurring in the crystal structure of Fc2CS were examined in detail by quantum-chemical methods. These methods were also an invaluable tool in studying the molecular structure of Fc2CS, from the gas phase to solutions and to its crystal. Intramolecular interactions governing the conformational behavior of an isolated Fc2CS molecule were deduced from quantum-chemical analyses carried out in orbital space and real space. Our experimental and theoretical results indicate that the main structural features of an isolated Fc2CS molecule in its lowest-energy geometry are retained both upon solvation and in the crystal. The tilt of ferrocenyl groups is only slightly affected by crystal packing forces that are dominated by dispersion. Nonetheless, a network of intermolecular interactions, such as H···H, C···H and S···H, was detected in the Fc2CS crystal but each of them is fairly weak.

Solvent Dependent Prototropic Tautomerism in a Schiff Base Derived from o‐Vanillin and 2‐Aminobenzylalcohol

AbstractThe Schiff base H2L, namely 2‐(3‐methoxysalicylidene‐amino)‐benzyl‐alcohol, 1 and its two pseudo‐polymorphs H2L⋅CH3OH 2 and H2L⋅H2O 3, have been synthesized by the condensation reaction of 2‐aminobenzyl alcohol and o‐vanillin in different solvents. X‐ray crystallographic analysis revealed that the keto‐enol tautomerism of H2L in solid state exists as a complex system of three different enol, keto and zwitterionic forms in equilibrium, dependent on crystal packing forces and the crystallization solvent. The enol, keto and mixed enol‐zwitterionic (roughly 1:1) forms were observed in the crystal structures of 1, 2 and 3, respectively. The crystallographic results are supported by FTIR and DFT calculations. Photophysical properties were determined in acetonitrile solution and solid state and were supported by TD‐DFT studies.

Dimethylphenylphosphine oxide coordinated trivalent rhenium featuring pyridylbenzazole chelation: Oxygen atom transfer kinetics, isomer preference, metal oxidation and computational analysis

The present work embodies outward oxygen atom transfer (OAT) reaction from pyridylbenzoxazole (L1) chelated oxorhenium(V) complex of type [ReOCl3(L1)], 1 towards oxophilic PMe2Ph resulting in the formation of reduced Re(III) derivative [Re(OPMe2Ph)Cl3(L1)], 4 containing oxidised phosphine trans to azole nitrogen. Another possible isomer (4a) having oxidised phosphine trans to pyridyl nitrogen has not been isolated. Structural elucidation of 4 reveals meridional disposition of three Cl atoms around the metal featuring distorted octahedral geometry. DFT analysis of isomers of type [Re(OPMe2Ph)Cl3(L1)] (4 and 4a) confirms isoenergetic nature in gas phase, however, stereospecific binding of L1 to Re(III) centre affording 4 as exclusive product is attributed to crystal packing force. 1 → 4 redox transformation has also been attended with the change in singlet → triplet spin state of the metal. Triplet state of 4 is more stable by ca. 15 kcal mol−1 compared to the singlet state in gas phase. Two electron paramagnetic nature (2.13 μB) in solid state affirms triplet ground state characterised with strong orbital coupling. Kinetic data for 1 → 4 transformation suggests associative pathway (ΔS≠ = ∼−36 J/K/mol) with no major structural reorganisation in the primary coordination sphere of the substrate and the reagent (ΔH≠ = ∼+10 kcal mol−1) to reach the transition state. Pyridylbenzthiazole (L2) chelated oxorhenium(V) complex of type [ReOCl3(L2)], 1b also reacts with PMe2Ph in a same manner to from [Re(OPMe2Ph)Cl3(L2)], 4b where the pyridyl nitrogen lies trans to phosphineoxide moiety unlike 4. The second order rate constants of OAT to PMe2Ph for [ReOCl3(L1)] are nearly two times higher than that of [ReOCl3(L2)] at all recorded temperatures due to difference in azole heteroatom electronegativity, ReVO bond length and ReVI/ReV reduction potential.

Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes.

The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography have provided many important insights into the gating mechanisms of thermoTRPV channels. Interestingly, crystallographic studies of ligand-dependent TRPV2 gating have shown that the TRPV2 channel adopts two-fold symmetric arrangements during the gating cycle. However, it was unclear if crystal packing forces played a role in stabilizing the two-fold symmetric arrangement of the channel. Here, we employ cryo-EM to elucidate the structure of full-length rabbit TRPV2 in complex with the agonist resiniferatoxin (RTx) in nanodiscs and amphipol. We show that RTx induces two-fold symmetric conformations of TRPV2 in both environments. However, the two-fold symmetry is more pronounced in the native-like lipid environment of the nanodiscs. Our data offers insights into a gating pathway in TRPV2 involving symmetry transitions.

Dicyclopenta[ghi,pqr]perylene as a Structural Motif for Bowl-Shaped Hydrocarbons: Synthetic and Conformational Studies.

Dicyclopenta[ghi,pqr]perylene (DCPP) is a substructural fragment on the surface of C70 yet not on C60. Unlike its intensely investigated buckybowl cousins, corannulene and sumanene, DCPP is largely ignored due to the lack of synthetic accessibility. This communication describes the first preparation of a DCPP derivative from bay substituted perylene bis(4-(trifluoromethyl)phenyl)methanol as the key cyclization precursor. Further incorporation of indeno substitutions at peri positions was accomplished through Suzuki-Heck benzannulation. DCPP derivatives 4 adopts a planar structure in crystal. On the contrary, indeno DCPP 5 and bis-indeno DCPP 6 adopt the bowl-shaped conformation in both the solid state and solution. Density functional theory (DFT) calculation reveals that the lowest-energy conformations of 4, 5, and 6 are all bowl-shaped. Nevertheless, small bowl-to-bowl inversion barrier for 4 (3.4 kcal/mol) is overcome by the crystal packing force, which leads to its observed planar structure. However, the bowl-shaped structures of 5 and 6 are affirmed by DFT calculation with intermediate and high bowl-to-bowl inversion barriers (10.4 and 18.5 kcal/mol, respectively).

Stereochemistry of polypeptoid chain configurations.

Like polypeptides, peptoids, or N-substituted glycine oligomers, have intrinsic conformational preferences due to their amide backbones and close spacing of side chain substituents. However, the conformations that peptoids adopt are distinct from polypeptides due to several structural differences: the peptoid backbone is composed of tertiary amide bonds that have trans and cis conformers similar in energy, they lack a backbone hydrogen bond donor, and have an N-substituent. To better understand how these differences manifest in actual peptoid structures, we analyzed 46 high quality, experimentally determined peptoid structures reported in the literature to extract their backbone conformational preferences. One hundred thirty-two monomer dihedral angle pairs were compared to the calculated energy landscape for the peptoid Ramachandran plot, and were found to fall within the expected minima. Interestingly, only two regions of the backbone dihedral angles ϕ and ψ were found to be populated that are mirror images of each other. Furthermore, these two conformers are present in both cis and trans forms. Thus, there are four primary conformers that are sufficient to describe almost all known backbone conformations for peptoid oligomers, despite conformational constraints imposed by a variety of side chains, macrocyclization, or crystal packing forces. Because these conformers are predominant in peptoid structure, and are distinct from those found in protein secondary structures, we propose a simple naming system to aid in the description and classification of peptoid structure.

Supramolecular polymers derived from the PtII and PdII schiff base complexes via C(sp2)–H … Hal hydrogen bonding: Combined experimental and theoretical study

A synthesis of the PdII and PtIIN,N-diaryldiazabutadiene complexes and their self-assembly into infinite 1-dimensional chains in the solid state via rare C (sp2)–H … Hal hydrogen bonding is reported. All the new compounds were characterized using elemental analyses (C, H, N), ESI-MS, IR, 1H and 13C NMR techniques and X-ray diffraction analysis. The nature and energies of intermolecular non-covalent interactions, which are responsible for the supramolecular polymerization, were studied theoretically using DFT calculations and topological analysis of the electron density distribution within the formalism of Bader's theory (QTAIM method). While chloro-complexes, which feature a relatively stronger C (sp2)–H … Hal hydrogen bonding, form supramolecular polymers, the iodo-derivative does not self-assemble into 1-D chains due to the dominance of other crystal packing forces over the potential H⋯I contacts. Thus, the C (sp2)–H … Hal HB can dictate a packing preference in the solid state and serve as a useful tool for supramolecular engineers.

Unveiling the n\u2192\u03c0* interactions in dipeptides

Numerous studies have suggested that the n→π* interactions between carbonyls could contribute significantly to the stability of proteins. Nevertheless, their evaluation is challenging because of the solvent environment or crystal packing forces in solids. Here we study the rotational spectrum of HGlyProOH dipeptide, a very common sequence found in collagen, the most abundant protein in vertebrates, in isolated conditions. Three different structures are unequivocally characterized in the gas phase. Interestingly, the most abundant structure is stabilized by an n→π* interaction and adopts the same conformation as is found in crystalline collagen. This observation serves to support the importance of the n→π* interactions between carbonyl groups.

Poly[(μ5-cis-cyclohex-4-ene-1,2-dicarboxylato)(μ3-cis-cyclohex-4-ene-1,2-dicarboxylato)dicadmium(II)

The title compound, [Cd2(C8H8O4)2] n , crystallizes in the centrosymmetric monoclinic P21/n space group. Via cis-cyclohex-4-ene-1,2-dicarboxylate ligands in two different binding modes, square pyramidally and pentagonal bipyramidally coordinated Cd atoms are connected into coordination polymer layer motifs oriented parallel to the ab plane. These layered motifs are aggregated into the three-dimensional supramolecular crystal structure of the title compound by means of crystal packing forces.

1-Deoxy-1-(N-methyl-4-fluorophenylamino)-D-arabino-hexulose

The title compound, C13H18FNO5, consists of D-fructose with an aromatic amine. The carbohydrate chain is in the acyclic keto form and has the zigzag conformation, while the solid-state NMR data suggests a conformational dimorphism at the aromatic amine group. The carbohydrate portion is involved in extensive O—H...O hydrogen bonding, which forms a two-dimensional network parallel to (001) and organized into fused homodromic ring patterns. The Hirshfeld surface fingerprint plots reveal a major contribution of the non-polar H...H and C...H interactions to the crystal packing forces.