Molecular Sheets Research Articles

Quantitative investigation on the intermolecular interactions present in 8-(4-ethoxyphenyl)-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione with insight from interaction energies, energy framework, electrostatic potential map and fingerprint analysis

In this study, we have performed a detailed quantitative analysis of the different intermolecular interactions present in 8-(4-ethoxyphenyl)-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione (I). The molecule crystallizes in the P-1 space group with one molecule in the asymmetric unit. The molecule had a layered crystal packing wherein the molecular sheets are primarily formed by hydrogen bonds and the stabilization is dominated via the electrostatic energy contribution. This molecular sheet is then interconnected to other similar sheets via different stacking motifs with significant contribution from dispersion energy components. The quantitative investigation of intermolecular interactions in a xanthine derivative reveals that there is an anisotropic distribution of interaction energies (coulombic and dispersion) along different directions, indicating possible applications of this class of molecules in the design of new materials.

Crystal structure of a new polymorph of 3-acetyl-8-meth-oxy-2H-chromen-2-one.

A new polymorphic form of the title compound, C12H10O4, is described in the ortho-rhom-bic space group Pbca and Z = 8, as compared to polymorph I, which crystallizes in the monoclinic space group C2/c and Z = 8 [Li et al. (2012). Chin. J. Struct. Chem. 31, 1003-1007.]. In polymorph II, the coumarin ring system is almost planar (r.m.s. deviation = 0.00129 Å). In the crystal, mol-ecules are connected by Csp 3-H⋯O and Car-H⋯O hydrogen bonds, forming mol-ecular sheets linked into zigzag shaped layers along the b-axis direction. The three-dimensional lattice is assembled through stacking of the zigzag layers by π-π inter-actions with a centroid-to-centroid distance of 3.600 (9) Å and anti-parallel C=O⋯C=O inter-actions with a distance of 3.1986 (17) Å, which give rise to a helical supra-molecular architecture.

Improving Cytotoxicity by Changing a Linker from Diphenylether to Diphenylmethane and now to Phenylene in Binuclear Dithiocarbamate Complexes: Synthesis and Cytotoxicity Study

Abstractα‐chloroamide 1,3‐bis(2‐chloroacetamido)phenylene (L’) is selected as a lead compound to derive 1,3‐bis(2‐(alkylamino)acetamido)phenylene (L1‐L3). A programmed self‐assembly involving L1‐L3, CS2 and NiII, CuII or ZnII ions affords access to a new series of 32‐membered binuclear macrocyclic dithiocarbamates [MII2‐μ2‐bis‐{(κ2S,S‐S2CN(R)CH2CONH)2C6H4}]{R=Cy, M=NiII 1 a, CuII 1 b, ZnII 1 c; R=iPr, M=NiII 2 a, CuII 2 b, ZnII 2 c; R=nBu, M=NiII 3 a, CuII 3 b, ZnII 3 c}. Compounds were characterized by spectroscopic (1H, 13C, DEPT 135, 1H DOSY NMR, HRMS/ESI MS, UV‐visible, Fluorescence, IR) and by the TGA. Evidently, L’ forms a fascinating 2D infinite supramolecular molecular sheet. All the compounds were screened for their in vitro cytotoxic activity against malignant tumor Hep G2 (hepatoma) cell line by the MTT assay. A majority of compounds ca L’, L1, 1 a, 1 b, 1 c, 2 a, 2 b, 2 c, L3,3 a, 3 b, 3 c display IC50 values lower than cisplatin and specificity for carcinoma Hep G2 over normal liver cell line (WRL‐68). Evidently cytotoxic potentials of L1‐L3 improved tremendously upon formation of their corresponding bimetallic dithiocarbamate complexes. The shrinking of cells can be clearly visualized by acridine orange/ethidium bromide (AO/EB) staining indicating the induction of apoptosis as part of the mechanism of action of these compounds. Further, DFT level calculations have been performed on representative compounds to reinforce the experimental results.

Crystal structure of butane-1,4-diyl bis-(furan-2-carboxyl-ate).

The asymmetric unit of the title compound, C14H14O6, a monomeric compound of poly(butyl-ene 2,5-furandi-carboxyl-ate), consists of one half-mol-ecule, the whole all-trans mol-ecule being generated by an inversion centre. In the crystal, the mol-ecules are inter-connected via C-H⋯O inter-actions, forming a mol-ecular sheet parallel to (10). The mol-ecular sheets are further linked by C-H⋯π inter-actions.

A Preview of a Construction of a Crystal Lattice Based on Intermolecular Interactions

A general procedure of crystal packing reconstruction using a certain number of intermolecular interactions is introduced and demonstrated on the crystal structure of l-histidine·HCl·H2O. Geometric restrictions based on intermolecular interactions are used for formation of a molecular pair as a basic repetitive motif of the crystal packing. The geometric restrictions were applied gradually within a supervised procedure, narrowing the scope of possible arrangement of two adjacent molecules. Subsequently, a pair of histidine molecules was used for construction of a molecular chain. The chain formed contained translation information on histidine molecules in one dimension, which coincided with one of the cell parameters. Furthermore, the periodicity in the second and third dimensions can be accomplished by chain assembly into sheets (2D), and sheets can be arranged into the final 3D structure. For this purpose, the rest of the available intermolecular interactions could be used to control the mutual assembly of molecular chains and sheets. Complete molecular packing would enable derivation of standard crystallographic parameters that can be used for verification of the structural model obtained. However, the procedure described for construction of the whole 3D structure from molecular chains was not attempted, and is only briefly outlined here. The procedure described can be employed especially when standard crystallographic parameters are not available and traditional methods based on X-ray diffraction fail.

Crystal structure determination of two pyridine derivatives: 4-[(E)-2-(4-meth-oxy-phen-yl)ethen-yl]-1-methyl-pyridin-1-ium hexa-fluoro-λ6-phosphane and 4-{(E)-2-[4-(di-methyl-amino)-phen-yl]ethen-yl}-1-phenyl-1λ5-pyridin-1-ylium hexa-fluoro-λ6-phosphane.

The title mol-ecular salts, C16H16NO+·PF6 -, (I), and C21H21N2 +·PF6 -, (II), are pyridine derivatives. In compound (I), the cation comprises a methyl N-substituted pyridine ring and a meth-oxy-substituted benzene ring connected by a C=C double bond. The F atoms of the PF6 - anion are disordered over two sets of sites with refined occupancy factors of 0.614 (7):0.386 (7). In compound (II), the cation comprises a pyridine ring attached to unsubstituted phenyl ring and a di-methyl-aniline ring, which are connected by a C=C double bond. The anion is PF6 -. In both salts, the cation adopts an E configuration with respect to the C=C bond. The pyridine ring makes a dihedral angle of 9.86 (12)° with the meth-oxy-substituted benzene ring in compound (I) and 11.2 (3)° with the di-methyl-amine-substituted benzene ring in compound (II). In compound (I), the crystal packing is stabilized by weak C-H⋯F inter-molecular inter-actions which result in R 4 3(14) ring motifs, forming mol-ecular sheets running parallel to (03). These are further stabilized by weak P-F⋯π interactions. In compound (II), the crystal packing is stabilized by C-H⋯F inter-actions, which result in R 6 6(40) ring motifs, forming mol-ecular sheets running parallel to (101) and these are further connected by π-π inter-actions.

Theoretical DFT study of R-phenyl alanine-S mandelate

Abstract The homodesmic reactions involving the donor-acceptor interactions and charge transfer mechanisms give low energy gap novel organic compounds having the high electrochemical activity and highly reactive materials. Internal charge transfer ability in amino acids give zwitterions. The amino acids also form the salt with organic acids. The donor-acceptor ability of the organic salts stabilises the structural arrangement through inter molecular hydrogen bonding. The title compound, R-phenyl alanine -S-mandelate (RPASMA) was synthesised, single crystal was grown by slow evaporation method, characterisation studies carried out , single crystal XRD analysis and MO6 Density Functional Theory (DFT) were also carried out. The crystal parameters of the title compound was compared with the theoretical DFT study and the inter molecular hydrogen bonding interactions stabilising the molecular sheet formation was also confirmed. the non-centrosymmetric structure indicating the presence of nonlinear optical activity (NLO) due to Second Harmonic Generation (SHG) property. The title compound showed twice the NLO activity of standard NLO material, Potassium Di hydrogen ortho Phosphate (KDP) and proved that the title compound can be used in device applications as a good NLO material.

Crystal structure and Hirshfeld surface analysis of methyl 1-(2,4-dichlorobenzyl)-5-methyl-1H-pyrazole-3-carboxylate

The title compound, C13H12Cl2N2O2, crystallizes with six molecules in the asymmetric unit, such that, the 1H-pyrazole rings are essentially planar. The six molecules are stabilized by intramolecular C-H···N and C-H···Cl interactions and the crystal structure is stabilized by intermolecular C-H···O hydrogen bonds, forming molecular sheets into paralel to the (-1 1 0) plane. These sheets are connected to each other by C-H···O hydrogen bonds and C-H···π interactions. In the Hirshfeld surface analysis, the H···H, Cl···H/H···Cl, C···H/H···C, O···H/H···O, N···H/H···N, Cl···Cl, Cl···O/O···Cl interactions add to 95.8% of the intermolecular contacts of the Hirshfeld surface area. The remaining contributions (2.9%) correspond to Cl···C/C···Cl, C···O/O···C, O···O and N···N interactions. Crystal Data for C13H12Cl2N2O2 (M = 299.15 g/mol): Triclinic, space group P-1 (no. 2), a = 12.0505(10) Å, b = 12.3189(11) Å, c = 29.184(3) Å, α = 88.565(4)°, β = 89.296(4)°, γ = 76.833(4)°, V = 4217.0(7) Å3, Z = 12, T = 296(2) K, μ(MoKα) = 0.460 mm-1, Dcalc = 1.414 g/cm3, 83073 reflections measured (2.8° ≤ 2Θ ≤ 47°), 12426 unique (Rint = 0.0411, Rsigma = 0.0235) which were used in all calculations. The final R1 was 0.0662 (I > 2σ(I)) and wR2 was 0.2481 (all data).

Phenol Molecular Sheets Woven by Water Cavities in Hydrophobic Slit Nanospaces.

Despite extensive research over the last several decades, the microscopic characterization of topological phases of adsorbed phenol from aqueous solutions in carbon micropores (pore size < 2.0 nm), which are believed to exhibit a solid and quasi-solid character, has not been reported. Here, we present a combined experimental and molecular level study of phenol adsorption from neutral water solutions in graphitic carbon micropores. Theoretical and experimental results show high adsorption of phenol and negligible coadsorption of water in hydrophobic graphitic micropores (super-sieving effect). Graphic processing unit-accelerated molecular dynamics simulation of phenol adsorption from water solutions in a realistic model of carbon micropores reveal the formation of two-dimensional phenol crystals with a peculiar pattern of hydrophilic-hydrophobic stripes in 0.8 nm supermicropores. In wider micropores, disordered phenol assemblies with water clusters, linear chains, and cavities of various sizes are found. The highest surface density of phenol is computed in 1.8 nm supermicropores. The percolating water cluster spanning the entire pore space is found in 2.0 nm supermicropores. Our findings open the door for the design of better materials for purification of aqueous solutions from nonelectrolyte micropollution.

DFT Optimization of Isolated Molecular Chain Sheet Models Constituting Native Cellulose Crystal Structures.

Because of high crystallinity and natural abundance, the crystal structures of the native cellulose allomorphs have been theoretically investigated to elucidate the cellulose chain packing schemes. Here, we report systematic structure optimization of cellulose chain sheet models isolated from the cellulose Iα and Iβ crystals by density functional theory (DFT). For each allomorph, the three-dimensional chain packing structure was partitioned along each of the three main crystal planes to construct either a flat chain sheet model or two stacked chain sheet models, each consisting of four cello-octamers. Various combinations of the basis set and DFT functional were investigated. The flat chain sheet models constituting the cellulose Iα (110) and Iβ (100) planes, where the cellulose chains are mainly linked by intermolecular hydrogen bonds, exhibit a right-handed twist. More uniform and symmetrical sheet twists are observed when the flat chain sheet models are optimized using a basis set with diffuse functions (6-31+G(d,p)). The intermolecular interactions are more stable when the chain sheet models are optimized with the two hybrid functionals CAM-B3LYP and M06-2X. Optimization of the two stacked chain sheet models, where van der Waals interactions predominated between adjacent chains, gave differing results; those retaining the initial structures and those losing the sheet appearance, corresponding to the cellulose Iα/Iβ (010)/(11̅0) and (100)/(110) chain sheet models, respectively. The cellulose Iβ (11̅0) chain sheet model is more stable using the M06-2X functional than using the CAM-B3LYP functional.

Universal folding pathways of polyhedron nets

Low-dimensional objects such as molecular strands, ladders, and sheets have intrinsic features that affect their propensity to fold into 3D objects. Understanding this relationship remains a challenge for de novo design of functional structures. Using molecular dynamics simulations, we investigate the refolding of the 24 possible 2D unfoldings ("nets") of the three simplest Platonic shapes and demonstrate that attributes of a net's topology-net compactness and leaves on the cutting graph-correlate with thermodynamic folding propensity. To explain these correlations we exhaustively enumerate the pathways followed by nets during folding and identify a crossover temperature [Formula: see text] below which nets fold via nonnative contacts (bonds must break before the net can fold completely) and above which nets fold via native contacts (newly formed bonds are also present in the folded structure). Folding above [Formula: see text] shows a universal balance between reduction of entropy via the elimination of internal degrees of freedom when bonds are formed and gain in potential energy via local, cooperative edge binding. Exploiting this universality, we devised a numerical method to efficiently compute all high-temperature folding pathways for any net, allowing us to predict, among the combined 86,760 nets for the remaining Platonic solids, those with highest folding propensity. Our results provide a general heuristic for the design of 2D objects to stochastically fold into target 3D geometries and suggest a mechanism by which geometry and folding propensity are related above [Formula: see text], where native bonds dominate folding.

Two Achiral Isomers of Chloronitropyridine Crystallize as Polar Materials with Different Molecular Packing Motifs Based on Similar Intermolecular Interactions

The molecular structures of two of the ten possible isomers of chloronitropyridine have been studied by spectroscopic techniques and single crystal X-ray diffraction. The structures of 2-chloro-4-nitropyridine (1) [monoclinic, Pc, a = 3.7711(14) A, b = 8.919(3) A, c = 9.324(3) A, β = 99.506(5)°] and 5-chloro-2-nitropyridine (2) [triclinic, P1, a = 3.7559(13) A, b = 6.071(2) A, c = 6.939(2) A, α = 85.703(5)°, β = 89.619(5)°, γ = 75.189(5)°] reveal that the isomers crystallize in non-centrosymmetric space groups with different molecular packing motifs based on similar intermolecular interactions. Each compound packs into molecular sheets via short chlorine–oxygen contacts and C–H⋯X (X = O, N) interactions of the nitro oxygen atoms and the pyridine nitrogen atom. The sheets further pack with an offset face-to-face π-stacking geometrical arrangement of the aromatic rings to form the three-dimensional structures. Achiral 2-chloro-4-nitropyridine (1) crystallizes as a polar material in the non-centrosymmetric and non-enantiomorphous space group Pc while the isomeric achiral compound 5-chloro-2-nitropyridine (2) forms a polar material that approximates inversion symmetry in the non-centrosymmetric enantiomorphous space group P1. The molecular structures of achiral 2-chloro-4-nitropyridine and 5-chloro-2-nitropyridine have been studied by X-ray diffraction revealing that they crystallize as polar materials. The structures have different packing motifs based on similar intermolecular interactions consisting of π-stacked molecular sheets formed by chlorine–oxygen contacts and C–H⋯X (X = O, N) interactions.

Crystal packing analysis of in situ cryocrystallized 2,2,2-trifluoroacetophenone

Crystals of the liquid compound 2,2,2-tri-fluoro-aceto-phenone (TFAP, C8H5F3O) were obtained using the state-of-art in situ cryocrystallization technique. TFAP crystallizes in the monoclinic space group C2/c, and its crystal structure is mainly stabilized by a set of C-H⋯F, C-H⋯O, F⋯F and F⋯O supra-molecular contacts. The overall mol-ecular arrangement shows the formation of mol-ecular sheets parallel to the bc plane, which are in turn stacked along the a-axis direction. The weak inter-actions have been studied thoroughly, performing both a Hirshfeld surface analysis and theoretical calculations, to obtain the inter-molecular inter-action energies. A structural comparison of this compound with the previously reported substituted analogs was also carried out, showing a qualitative difference in terms of packing behaviour.

Functionalized MoS2 nanosheet-capped periodic mesoporous organosilicas as a multifunctional platform for synergistic targeted chemo-photothermal therapy

The combination of different therapies into a single platform has attracted increasing attention as a potential synergistic tumor treatment. Herein, the fabrication of a novel folate targeted system for chemo-photothermal therapy by using thioether-bridged periodic mesoporous organosilica nanoparticles (PMOs) as a drug-loading vehicle is described. The novel targeted molecular bovine serum albumin-folic acid-modified MoS2 sheets (MoS2-PEI-BSA-FA) were successfully synthesized and characterized, and then utilized as a capping agent to block PMOs to control the drug release and to investigate their potential in near-infrared photothermal therapy. The resulting PMOs–DOX@MoS2–PEI-BSA-FA complexes had a uniform diameter (196 nm); high DOX loading capacity (185 mg/g PMOs-SH); excellent photothermal transformation ability; and good biocompatibility in physiological conditions. The PMOs–DOX@MoS2–PEI-BSA-FA exhibited pH-dependence and near infrared (NIR) laser irradiation-triggered DOX release. In vitro experimental results confirmed that the material exhibits excellent photothermal transfer ability, outstanding tumor killing efficiency and specificity to target tumor cells via an FA-receptor-mediated endocytosis process. The in vivo experiments further demonstrated that the platform for synergistic chemo-photothermal therapy could significantly inhibit tumor growth, which is superior to any monotherapy. Meanwhile, cytotoxicity assays and histological assessments show that the engineered PMOs@MoS2–PEI-BSA-FA have good biocompatibility, further inspiring potential biomedical applications. Overall, this work describes an excellent drug delivery system for chemo-photothermal synergistic targeted therapy having good drug release properties, which have great potential in cancer therapy.

(1E,4E)-1,5-Bis(2,6-dichlorophenyl)penta-1,4-dien-3-one

The asymmetric unit of the title compound, C17H10Cl4O, consists of one independent molecule and two molecules each located on twofold symmetry axes through the central C=O bond such that they each contribute half a molecule each to the asymmetric unit. The dihedral angles between the rings in the three molecules are 73.1 (3), 65.3 (3) and 75.4 (3)°. In the crystal, molecules are linked through C—H...O hydrogen bonds, generating undulated molecular sheets lying parallel to (110).

Lactone-layered double hydroxide networks: Towards self-assembled bioscaffolds

Abstract This paper describes the conversion of a layered anionic initiator (carbonate-intercalated layered double hydroxide, (LDH-carbonate)) into a self-assembled resin-embedded network during the in-situ polymerization of one or more lactone monomers using the LDH-carbonate as the sole initiator. Uniquely in this paper, no long-chain acid intercalant is present in the LDH-carbonate to act as an additional initiator species, and this is the first known report of a copolymerisation of these lactones using LDH as an initiator. The formation of a network is in marked contrast to the behavior of most in-situ polymerisations using layered species, where the latter retains its layered structure at the molecular level and is either intercalated or exfoliated to form a nanocomposite. The molecular disintegration of the LDH sheets is unusual. Nine new insoluble materials (scaffolds) are isolated from various l , d -lactide & e-caprolactone (LC) and l , d -lactide & δ-valerolactone (LV) copolymer hybrids. The latter hybrids are polymerised using the LDH-carbonate as initiator at 150 °C for 24 h without using conventional metal catalysts. Each insoluble phase is isolated from each primary hybrid product using dichloromethane (DCM) to selectively dissolve the soluble polymer phase. X-ray diffraction (XRD) is used to verify the morphology of the insoluble phases. This demonstrates that the molecular sheets of the LDH-carbonate are fully dismantled during the polymerization. Porous, network morphology is established for some of the insoluble phase structures using scanning electron microscopy (SEM). This indicates potential suitability of these self-assembled insoluble phase materials as bioscaffolds for artificial cell growth. Nuclear magnetic resonance spectrometry (NMR) was used to determine the ratio of ester to acidic carbonyls in the insoluble phase. Energy Dispersive X-ray spectroscopy (EDX) was also used to determine the ratio of magnesium to aluminium in the insoluble phases.

Structural Characterization of 2D Zirconomolybdate by Atomic Scale HAADF-STEM and XANES and Its Highly Stable Electrochemical Properties as a Li Battery Cathode.

The structural determination of nanomaterials and their application in energy storage and transfer are of great importance. Herein, a layered zirconomolybdate with a two-dimensional structure was synthesized. Atomic resolution electron microscopy was utilized for direct visualization of the structure that was further confirmed by powder X-ray diffraction and X-ray absorption near-edge structure analyses. The structure of the molecular sheet was stable at a high temperature in an oxidative atmosphere. The electrochemical performance of the material was evaluated with a Li battery composed of the calcined material as a cathode. Li ions were reversibly inserted and extracted between the layers without collapse of the structure of the material. The electrochemical properties of the material were derived from the reversible redox activity of the Mo ions and Zr ions in the material as well as the flexibility of the molecular layer of the material.

Vibrational Characterization of Two-Dimensional Graphdiyne Sheets

Graphdiyne is formed by two acetylene bonds conjugatively connecting two phenyl rings, which then extend to a sizable two-dimensional structure. In this work, a molecular size-dependent C≡C stretching vibrational transition intensity is predicted by density functional theory in graphdiyne; in particular, the strongest infrared-active transition is enhanced in intensity by a factor of as high as 2190 from phenyl-acetylenic dimer to graphdiynic 46-mer, showing ca. 300 times enhancement per acetylene bond on average, examined at the level of B3LYP/6-31G*. Such an enhancement of vibrational transition intensity is caused by intramolecular electronic delocalization that gives rise to an enlarged transition dipole moment as well as by intramolecular vibrational delocalization that gives rise to intensity borrowing in such two-dimensionally conjugated graphdiyne molecular sheets. The enhancement is found to be diminished in defected graphdiynes. The results suggest that the periodically appearing C≡C bond may be...

Strain-induced charge transfer and polarity control of a heterosheet comprising C60 and graphene

Using density functional theory combined with the effective screening medium method, the energetics and electronic structure of a C60 molecular sheet adsorbed on graphene were studied in terms of biaxial strains. The optimum spacing and interlayer interaction monotonically decreases and increases, respectively, with an increasing biaxial tensile strain. The biaxial compressive strain induces electron transfer from the graphene to C60 at a 2% lateral compression, leading to an all-carbon charge transfer complex. The heterosheet possesses an intrinsic dipole moment along the graphene-to-C60 molecular layer direction.

Surface-Induced Frustration in Solid State Polymorphic Transition of Native Cellulose Nanocrystals.

The presence of an interface generally influences crystallization of polymers from melt or from solution. Here, by contrast, we explore the effect of surface immobilization in a direct solid state polymorphic transition on individual cellulose nanocrystals (CNCs), extracted from a plant-based origin. The conversion from native cellulose I to cellulose III crystal occurred via a host-guest inclusion of ethylene diamine inside the crystal. A 60% reduction in CNC width (height) in atomic force microscopy images suggested that when immobilized on a flat modified silica surface, the stresses caused by the inclusion or the subsequent regeneration resulted in exfoliation, hypothetically, between the van der Waals bonded sheets within the crystal. Virtually no changes in dimensions were visible when the polymorphic transition was performed to nonimmobilized CNCs in bulk dispersion. With reservations and by acknowledging the obvious dissimilarities, the exfoliation of cellulose crystal sheets can be viewed as analogous to exfoliation of 2D structures like graphene from a van der Waals stacked solid. Here, the detachment is triggered by an inclusion of a guest molecule inside a host cellulose crystal and the stresses caused by the firm attachment of the CNC on a solid substrate, leading to detachment of molecular sheets or stacks of sheets.