Molecular Hirshfeld Surface Research Articles

Towards the chemical control of molecular packing: syntheses and crystal structures of threetrans-[NiL4(NCS)2] complexes

Three nickel(II) isothiocyanato complexes of the formula trans-[NiL4(NCS)2] (L = ethylisonicotinate, methylisonicotinate and 4-benzoylpyridine) have been prepared: [Ni(ethylisonicotinate)4(NCS)2] (I), [Ni(methylisonicotinate)4(NCS)2] (II) and [Ni(4-benzoylpyridine)4(NCS)2] (III). All three complexes are monomeric and have a distorted octahedral geometry around Ni(II). Despite their apparent molecular similarity, the crystal density of (III) (1.454 g cm(-3)) is significantly higher than that of (I) and (II) (both 1.408 g cm(-3)), suggesting that the molecular packing is most efficient in (III). A study of the molecular Hirshfeld surfaces, together with density functional theory (DFT) calculations, provide insights into the origin of the molecular packing features, and it is suggested that the greater crystal density of (III) results from smaller intermolecular electrostatic repulsions.

Two new complexes with 6-methylnicotinic acid ligand: Synthesis, crystal structure and Hirshfeld surfaces

Two new complexes derived from 6-methylnicotinic acid: 1(Mn(C7H6NO2)2(H2O)2) and 2 ([Ni(C7H7NO2)2Cl2(H2O)2]·4H2O) have been synthesized and characterized. In complex 1, the MnII ion exhibits a distorted octahedral geometry and featured with 1D chain, while the NiII ion in complex 2 exhibits a regular octahedral geometry and featured with intricate 3D motif. We further compared the molecular Hirshfeld surface and fingerprint plot analysis of ligand 6-methylnicotinic acid in complexes 1 and 2 with the individual 6-methylnicotinic acid, for the purpose of investigating the influence of different metals on the intermolecular interaction around 6-methylnicotinic acid. Which revealed that the closest contacts of these two complexes were dominated by H⋯H, H⋯O, N⋯H, C–H⋯π and π⋯π (C–C) interactions, and the complexation with transition metals lead to the increase of C–H⋯π interactions while the decrease of H–H, N–H, and π⋯π interactions.

A thermally labile copper (II) complex with hetero N- and O-donor ligands: Crystal structure, Hirshfeld surfaces, thermal and luminescent properties

A new complex ([Cu(L1)2(H2O]2]⋅2H2O, 1) derived from a hetero N- and O-donor ligand 5-methyl-imidazole-3-carboxylic acid (L1H) has been synthesized and characterized. Comparisons between [Cu(L1)2(H2O]2]⋅2H2O, [Co(L2)(H2O]2⋅H2O (2), and [Cu(L2)2H2O]⋅H2O (L2H=5-methyl-isoxazole-3-carboxylic acid) revealed that the coordinated water molecules play a key role in the construction of crystal structures: two coordinated water molecules in the axial positions lead to single-deck 1D chain and 3D motif while one coordinated water molecule resulted to double-deck 1D chain and 2D stacking motif. Molecular Hirshfeld surfaces revealed that complexes 1 and 2 were supported mainly by H–H, C–H⋯π, and O–H⋯O intermolecular interactions. The room temperature solid state luminescent properties of complexes 1 and 2 were all shown as two distinct bands, which attribute to ligand–metal charge transfer and metal purterbed ligand centered emission.

Synthesis, crystal structure, Hirshfeld surfaces, and spectral properties of Cu(II) and Co(II) complexes with 3-phenoxymethyl-4-phenyl-5-(2-pyridyl)-1,2,4-triazole

A new asymmetrical substituted triazole, 3-phenoxymethyl-4-phenyl-5-(2-pyridyl)-1,2,4-triazole (L) and its complexes, cis-[Cu2 L 2Cl4]·2CH3CN (1) and trans-[CoL 2Cl2]·2H2O·2CH3CN (2), have been synthesized and characterized by IR, single-crystal X-ray diffraction, thermogravimetric analyses and Hirshfeld surfaces. In the structure, two L are mainly stabilized by an intermolecular C–H⋯N hydrogen bond. In 1 (or 2), each L involves a doubly-bidentate (or chelating bidentate) coordination mode through one pyridine and two nitrogens (or one) of triazole, respectively. Complex 1 has a distorted trigonal bipyramidal [CuN3Cl2] core with two cis Cl− while 2 shows a distorted octahedron [CoN4Cl2] with two trans Cl−. We also prepared molecular Hirshfeld surface and fingerprint plot for L, 1 and 2, which revealed the influence of different metals on coordinate of L.

Synthesis and Crystal Structures of Four New Dihydropyridine Derivatives

Four new Hantzsch 1,4-dihydropyridine derivatives, dimethyl 4-(4-hydroxy-3-methoxyphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, (I), dimethyl 4-(4-bromophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, (II), dimethyl 4-(3-bromo-4-methoxyphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, (III), and dimethyl 2-(2,5-dimethoxyphenyl)-4,6-dimethyl-1,2-dihydropyridine-3,5-dicarboxylate, (IV), have been synthesized and examined by X-ray crystallography, B3LYP/6-31 G (d) molecular orbital calculations and Hirshfeld surface and fingerprint plots. (I), C18H20NO6, is monoclinic with space group P21/n and cell constants a = 9.60810(10) A, b = 7.41900(10) A, c = 24.1821(3) A, = 94.1970(10)°, V = 1719.14(4) A3, and Z = 4. (II), C17H15BrN2O6, is orthorhombic with space group P212121 and cell constants a = 11.8865(5) A, b = 13.1157(4) A, c = 21.9515(9) A, V = 3422.2(2) A3, and Z = 8. (III), C18H20BrNO5, is orthorhombic with space group Pbca and cell constants a = 8.55470(10) A, b = 15.5248(2) A, 27.0657(5) A, V = 3594.60(9) A3, and Z = 8. (IV), C19H23NO6, is orthorhombic with space group Pbca and cell constants a = 11.6798(3) A, b = 13.6319(3) A, 23.0976(5) A, V = 3677.55(15) A3, and Z = 8. The first three have the same 2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate skeleton with different substituted phenyl ligands attached to the 4-site of the dihydropyridine ring. The fourth derivative (IV) consists of a related 4,6-dimethyl-1,2-dihydropyridine-3,5-dicarboxylate skeleton with 2,5-dimethoxyphenyl and methyl ligands attached to the 2 and 4 sites of the 1,2-dihydropyridine ring. The dihedral angle between the mean planes of the dihydropyridine and benzene rings is 89.6(2)° (I), 86.0(6)° or 87.2(9)° (II), 87.7(6)° (III), and 87.3(8)° (IV), respectively. O–H··· (I), N–H···O (II), N–H···O (IV) hydrogen bonds and weak N–H···O, C–H···O (I), C–H···O (II), N–H···O (III), C–H···O (IV) intermolecular hydrogen bond interactions help stabilize crystal packing in each of their unit cells. A comparison of the angles between mean planes of the benzene rings in the crystals and with the DFT theoretical calculation as well as inclusion of weak intermolecular hydrogen bond interactions has been included for each molecule. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing 3D molecular surface contours and 2D fingerprint plots have also been used to examine molecular shapes. Molecular orbital diagrams provide visual representations of the top level molecular orbital surfaces in each compound. Synthesis, crystal structures, density functional theory (DFT), Hirshfeld and molecular orbital surface calculations of four new dihydropyridine derivitives.

Supramolecular assembly of the potassium piperidine-4-carbodithioate dehydrate by using X-ray diffraction and DFT calculations

This work presents the synthesis, crystallization and characterization of the potassium piperidine-4-carbodithioate dehydrate (KPip), which is a dithiocarbamate-salt formed by short contacts between atoms of sulfur, potassium and oxygen. The conformational analysis was determined using X-ray diffraction (XRD) and Density Functional Theory calculations (DFT). The DFT calculations were performed to obtain the molecular electrostatic potential map and the Mullikan charges. The molecular electrostatic potential maps performed predicted two regions with different Mullikan distribution. These weak intermolecular interactions formed not linked layers spaced around 3.5Å and smaller than the sum of their van der Waals radii with supramolecular 2D chains conformation, which allows the plans sliding. The molecular Hirshfeld surface analysis shown that most of the interactions correspond to hydrogen bonds. From this fingerprints study it was possible to show that more important than the alkali metals interactions are the sulfur interactions, which is markedly hydrophilic in these cases.

Complexation of different metals with a novel N-donor bridging receptor and Hirshfeld surfaces analysis

A novel N-donor bridging receptor R: 4,4′-methanediylbis(2-ethyl-5-methyl-1H-imidazole) has been synthesized from 2-ethyl-4-methyl-1H-imidazole and formaldehyde in the presence of potassium hydroxide. This receptor then formed complexes with different transition metals ([Co(NO3)2, CoCl2, Ni(NO3)2 and CuCl2]) in different solvent systems and obtained five different complexes. Wherein, the complex formation of R with Co(NO3)2 resulted in two different structures in methanol and acetonitrile, respectively. A thorough structural investigation of the present receptor and the resulted five complexes show that the NH group of the receptor, the organic anions and solvent molecules play a key role in the construction of the five intriguing architectures. We also prepared molecular Hirshfeld surface and fingerprint plot for R as well as the five complexes, which revealed the influences of different metals to the coordinate behavior of R in terms of intermolecular interactions.

Novel tools for visualizing and exploring intermolecular interactions in molecular crystals

A new way of exploring packing modes and intermolecular interactions in molecular crystals is described, using Hirshfeld surfaces to partition crystal space. These molecular Hirshfeld surfaces, so named because they derive from Hirshfeld's stockholder partitioning, divide the crystal into regions where the electron distribution of a sum of spherical atoms for the molecule (the promolecule) dominates the corresponding sum over the crystal (the procrystal). These surfaces reflect intermolecular interactions in a novel visual manner, offering a previously unseen picture of molecular shape in a crystalline environment. Surface features characteristic of different types of intermolecular interactions can be identified, and such features can be revealed by colour coding distances from the surface to the nearest atom exterior or interior to the surface, or by functions of the principal surface curvatures. These simple devices provide a striking and immediate picture of the types of interactions present, and even reflect their relative strengths from molecule to molecule. A complementary two-dimensional mapping is also presented, which summarizes quantitatively the types of intermolecular contacts experienced by molecules in the bulk and presents this information in a convenient colour plot. This paper describes the use of these tools in the compilation of a pictorial glossary of intermolecular interactions, using identifiable patterns of interaction between small molecules to rationalize the often complex mix of interactions displayed by large molecules.

Fingerprinting intermolecular interactions in molecular crystals

We have recently described a remarkable new way of exploring packing modes and intermolecular interactions in molecular crystals using a novel partitioning of crystal space. These molecular Hirshfeld surfaces reflect intermolecular interactions in a novel visual manner, offering a hitherto unseen picture of molecular shape in a crystalline environment. The surfaces encode information about all intermolecular interactions simultaneously, but sophisticated interactive graphics are required in order to extract the information most efficiently. To overcome this we have devised a two-dimensional mapping which summarizes quantitatively the nature and type of intermolecular interaction experienced by a molecule in the bulk, and presents it in a convenient graphical format. The mapping takes advantage of the triangulation of the Hirshfeld surfaces, and plots the fraction of points on the surface as a function of the closest distances from the point to nuclei inside and outside the surface. In this manner all interaction types (for example, hydrogen bonding, close and distant van der Waals contacts, C–H⋯π interactions, π–π stacking) are readily identifiable, and it becomes a straightforward matter to classify molecular crystals by the nature of interactions, and to rapidly identify similarities and differences which can become obscured when examining crystal packing diagrams. These plots are a novel visual representation of all the intermolecular interactions simultaneously, and are unique for a given crystal structure and polymorph. Applications to a wide variety of molecular crystals and intermolecular interactions are presented, including polymorphic systems, as well as crystals where Z′ > 1.