Nature of weak inter- and intramolecular interactions in crystals. 1. The F...O and F...H contacts in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole

The topological analysis of the electron density distribution in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole revealed that the F...H and F...O intermolecular contacts correspond to attractive interactions. The energies of these interactions were estimated from the experimental data and it was shown that these contacts are similar to the C—H...O contacts. Analysis of the deformation electron density revealed that the F...O contacts correspond to transfer of the lone electron pair of a fluorine atom to the antibonding -orbital of the C=O bond.     

Quantitative evaluation of weak nonbonded Se...F interactions and their remarkable nature as orbital interactions

To evaluate weak intramolecular nonbonded Se...F interactions recently characterized for a series of o-selenobenzyl fluoride derivatives (Iwaoka et al., Chem. Lett. 1998, 969-970), the temperature dependence of the nuclear spin coupling between Se and F (J(Se...F)) was investigated for 2-(fluoromethyl)phenylselenenyl cyanate (1a) and bis[2-(fluoromethyl)phenyl] diselenide (1e) in CD2Cl2 and CD3CN. A significant increase in the magnitude of J(Se...F) was observed for both 1a and 1e upon lowering temperature, whereas the values of J(Se...F) for the corresponding trifluoromethyl compounds slightly reduced or remained unchanged at low temperatures. Application of the rapid equilibrium model between two possible conformers revealed that conformer A with an intramolecular Se...F interaction is more stable in enthalpy (DeltaH) by 1.23 kcal/mol for 1a (in CD2Cl2) and by 0.85 and 0.83 kcal/mol for 1e (in CD2Cl2 and CD3CN, respectively) than conformer B, which does not have close Se...F contact. The negligible solvent effects for 1e suggested marginal electrostatic nature of the Se...F interactions. Instead, importance of the n(F) -->sigma*(Se-X) orbital interaction was suggested by quantum chemical (QC) calculations and the natural bond orbital (NBO) analysis.     

Supramolecular chemistry of halogens: complementary features of inorganic (M-X) and organic (C-X') halogens applied to M-X...X'-C halogen bond formation

Electronic differences between inorganic (M-X) and organic (C-X) halogens in conjunction with the anisotropic charge distribution associated with terminal halogens have been exploited in supramolecular synthesis based upon intermolecular M-X...X'-C halogen bonds. The synthesis and crystal structures of a family of compounds trans-[MCl(2)(NC(5)H(4)X-3)(2)] (M = Pd(II), Pt(II); X = F, Cl, Br, I; NC(5)H(4)X-3 = 3-halopyridine) are reported. With the exception of the fluoropyridine compounds, network structures propagated by M-Cl...X-C halogen bonds are adopted and involve all M-Cl and all C-X groups. M-Cl...X-C interactions show Cl...X separations shorter than van der Waals values, shorter distances being observed for heavier halogens (X). Geometries with near linear Cl...X-C angles (155-172 degrees ) and markedly bent M-Cl...X angles (92-137 degrees ) are consistently observed. DFT calculations on the model dimers {trans-[MCl(2)(NH(3))(NC(5)H(4)X-3)]}(2) show association through M-Cl...X-C (X not equal F) interactions with geometries similar to experimental values. DFT calculations of the electrostatic potential distributions for the compounds trans-[PdCl(2)(NC(5)H(4)X-3)(2)] (X = F, Cl, Br, I) demonstrate the effectiveness of the strategy to activate C-X groups toward halogen bond formation by enhancing their electrophilicity, and explain the absence of M-Cl...F-C interactions. The M-Cl...X-C halogen bonds described here can be viewed unambiguously as nucleophile-electrophile interactions that involve an attractive electrostatic contribution. This contrasts with some types of halogen-halogen interactions previously described and suggests that M-Cl...X-C halogen bonds could provide a valuable new synthon for supramolecular chemists.     

Supramolecular synthons based on N-H...N and C-H...O hydrogen bonds. Crystal engineering of a helical structure with 5,5-diethylbarbituric acid

5,5-Diethylbarbituric acid is a convenient molecular precursor for a newly identified N-H...N/C-H...O synthon, which is robust enough for the design of a helix architecture.     

Fluorinated tetrathiafulvalenes with preserved electron-donor properties and segregated fluorous bilayer structures based on F...F nonbonded interactions

The synthesis of the fluorinated 4,5-(2,2'-difluoropropylenedithio)-1,3-dithiol-2-one heterocycle with DAST allows for the preparation of several symmetrical and unsymmetrical di- and tetrafluoro-substituted tetrathiafulvalenes with accessible oxidation potentials (0.6 < E1(1/2) < 0.85 V vs SCE) despite the presence of the electron-withdrawing CF2 groups. The flexibility of the fluorinated seven-membered ring identified from room-temperature NMR data has been thoroughly investigated by temperature-variable 1H and 19F NMR experiments, allowing for the identification of two independent folding processes, whose coalescence temperatures (Tc) and activation energies (deltaGdouble dagger) were determined (Tc = -15 degrees C, deltaGdouble dagger = 50.2 kJ mol(-1) and Tc = 47 degrees C, deltaGdouble dagger = 51.1 kJ mo(-1)). The analysis of the X-ray crystal structures of three of those fluorinated TTF demonstrates the efficiency of the nonbonded fluorine exclusion interactions for the stabilization of layered structures with fluorous bilayers, together with S...S van der Waals interactions and C-H...F hydrogen bonds.     

CH...O and CH...F links form the cage structure of dioxane-trifluoromethane

The molecular beam Fourier transform microwave spectrum of 1,4-dioxane-trifluoromethane has been assigned and measured. The two subunits form a cage stabilized by one C-H...O and two C-H...F weak hydrogen bonds. The C-H...O link involves the axial lone pair of one of the two equivalent ring oxygens, while the two C-H...F bridges connect trifluoromethane to the two axial hydrogens in positions 3 and 5. The dissociation energy has been estimated from the D(J) centrifugal distortion parameter to be approximately 6.8 kJ/mol.     

Crystal engineering of urea alpha-network via I...O2N synthon and design of SHG active crystal N-4-iodophenyl-N'-4'-nitrophenylurea

Crystalline nitrodiphenyl ureas adopt the N-H...O tape alpha-network only when stabilization accrues from the I...O(2)N or C[triple bond]C-H...O(2)N synthon, otherwise the ureanitro motif is preferred; soft, weak interactions can direct polar self-assembly in strong N-HO hydrogen-bonded crystals.     

Organic chlorine as a hydrogen-bridge acceptor: evidence for the existence of intramolecular O--H...Cl--C interactions in some gem-alkynols

The acceptor capabilities of "organic" halogen, CX (X=F, Cl, Br, I), with respect to hydrogen bonding are controversial, and unactivated organic chlorine is generally deemed to be a poor acceptor. Hydrogen bridges of the type O--H...Cl--C are uncommon and occur mainly in an intramolecular situation when the donor group is sterically hindered, so that the formation of intermolecular interactions is difficult. In this paper, intramolecular O--H...Cl--C interactions in a series of chloro-substituted gem-alkynols are studied. We describe various features of this interaction using crystallographic, spectroscopic and computational methods. The O--H...Cl--C interaction occurs in five of the six compounds under consideration here (CDDA, 14DDDA, 15DDDA, 18DDDA, 15MKA). Solution (1)H NMR spectroscopy shows that the interaction is intramolecular and that it is a true hydrogen bond. DFT calculations give a stabilisation energy around 4.0 kcal mol(-1). In the crystal structures of the compounds studied, the intramolecular O--H...Cl--C interactions fit into the overall scheme of cooperative interactions. These structures may be derived from that of the unsubstituted compound DDA by means of synthon exchange and the O--H...Cl--C interaction fares surprisingly well in the presence of competing stronger acceptors. The crystal structures show an unusual degree of modularity for compounds that generally form interactions that are weak and variable. It is noteworthy that the so-called "weak" acceptor, organic chlorine, is able to sustain a good intramolecular hydrogen bridge that is of an attractive and stabilizing nature and which is of potential importance in crystal engineering and supramolecular chemistry.     

Gold liquid crystals displaying luminescence in the mesophase and short F...F interactions in the solid state

Rodlike gold(I) complexes, [Au(C6F4OCmH2m+1)(C(triple bond)NC6H4C6H4OCnH2n+1)] (m=2, n=4, 10; m=6, n=10; m=10, n=6, 10), display interesting features. They are liquid crystals and show photoluminescence in the mesophase, as well as in the solid state and in solution. The single-crystal, X-ray diffraction structure of [Au(C6F4OC2H5)(C(triple bond)NC6H4C6H4OC4H9)] confirms its rodlike structure, with a linear coordination around the gold atom, and reveals the absence of any Au...Au interactions (such interactions are often present in luminescent gold complexes). Well-defined, intermolecular Fortho...Fmeta interactions, with remarkably short intermolecular FF distances (2.66 A), are observed; these interactions seem to be responsible for the crystal packing, which consists of an antiparallel arrangement of molecules. Experiments under different conditions support the explanation that the photoluminescence has an intramolecular origin.     

Relationship between the bond lengths in N-H...N,O-H...O,F-H...F,and Cl-H...Cl hydrogen bridges

The applicability of the equation $ e^{ - ((r_1 - r_0 )/b)^{5/3} } + e^{ - ((r_2 - r_0 )/b)^{5/3} } = 1 $ e^{ - ((r_1 - r_0 )/b)^{5/3} } + e^{ - ((r_2 - r_0 )/b)^{5/3} } = 1 has been studied. The equation defines the relationship between the experimental values of the covalent (r ₁) and hydrogen (r ₂) bond lengths in O-H...O bridges for describing the relation between the experimental interatomic distances in N-H...N bridges and the parameters of X-H...X fragments (X = O, N, F, Cl) calculated by the density functional method (B3LYP/6-31++G(d,p)) for neutral, positive, and negative molecular complexes. Here r ₀ is the mean value of the X-H bond length in free molecules; r _sym is the X...H distance in the symmetrical bridge; and b is the coefficient defined by the equation b = (r _sym − r ₀)/(ln2)^3/5. This equation allows us to adequately describe the relationships between bond lengths in nearly linear hydrogen bridges formed by oxygen, nitrogen, fluorine, and chlorine atoms. It is thus universal and can be used in studies of a wide range of substances.     

Crystal packing of 8,9,10,12-tetrafluoro-<Emphasis Type="Italic">o</Emphasis>-carborane: H...F versus H...H contacts

Detailed study of the crystal packing of 8,9,10,12-tetrafluoro-o-carborane by the topological analysis of the electron density distribution function was performed and the competing between the F...H and H...H interactions in the crystal was investigated.     

Steric effect on construction of extended architectures of Ni(II) complexes directed by intermolecular C-H...F and C-H...O interactions

Five new Ni(II) complexes with pyridine carboxamide ligands have been synthesized and the crystal structures of three of the complexes were determined. Strong distortion effects of 6-methyl substitution were observed in the complexes with 6-methyl-substituted pyridyl bpb ligands. The C-H...F and C-H...O hydrogen bond interactions build extended architectures in the crystals studied. This result suggests that the steric effect of 6-methyl substitution plays an important role in the distortion of the structure, and the 6-methyl substitution can facilitate hydrogen bond interactions between methyl hydrogen atoms and O(carbonyl) or F atoms. Twelve Ni(II) complexes, including seven complexes reported previously, show reversible redox behavior, implying that the reduced Ni(I) state of each complex is stable in the time scale of CV measurement. The steric effect of R₁ substituent and the electronic effects of X₁ and X₂ groups were found to be the main factors contributing to the shift of the redox potential of the Ni(II) complexes     

Inefficiency of specific intramolecular C-H...X interactions (X=F,Cl, Br) in N-vinylazoles as indicated by1H and13C NMR spectroscopy

¹H and¹³C NMR spectroscopy indicates the low efficiency of specific intramolecular C-H...Hal (Hal=F, Cl, Br) interactions in comparison with analogous C-H...Y (Y=N, O, S) interactions despite their formal similarity. This is seen in the absence of anomalous downfield PMR shifts of the hydrogen atom and increase in the corresponding direct¹³C-¹H coupling.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 6, pp. 1442–1446, June, 1991.     

The sign and magnitude of 2hJ(F,F) and 1hJ(F,H) in FH...FH. A CLOPPA analysis of their distance dependence

The sign change of the intermolecular (2h)J(F,F) coupling in the (HF)2 dimer as a function of the F-F distance is discussed by means of the CLOPPA method. It is found that it is due to the competition of positive and negative contributions involving the interaction of the sigma lone pair of the acceptor nucleus with vacant molecular orbitals localized in the F-H...F moiety and with other molecular orbitals localized in the donor molecule. The origin of the sign of each contribution is fully determined by analyzing the response of the electronic system to the magnetic perturbation at the acceptor F nucleus. (2h)J(F,F) coupling in the FH...F-, which is positive for all F-F distances, is also analyzed in order to look for the differences with the former case.     

Zwitterionic pi-radical involving EDT-TTF-imidazole and F4TCNQ: redox properties and self-assembled structure by hydrogen-bonds and multiple S...S interactions

The reaction between an imidazole-functionalized EDT-TTF and F(4)TCNQ produced a zwitterionic pi-radical, which formed a self-assembled structure by the cooperation of hydrogen-bonds and multiple S...S interactions and exhibited three-step oxidation processes and a high electrical conductivity as a single-component organic molecule.     

Theoretical investigation of the weakly dihydrogen bonded complexes FArCCH...HBeX (X = H, F, Cl, Br)

An ab initio computational study of the properties of four linear dihydrogen-bonded complexes formed between the first compound with an Ar-C chemical bond (FArCCH) and HBeX (X = H, F, Cl, and Br) molecules was undertaken at the MP2/6-311++G(2d,2p) level of theory. The calculated complexation energy at MP2 and G2(MP2) levels decreases in the order HBeH...HCCArF > BrBeH...HCCArF > ClBeH...HCCArF > FBeH...HCCArF. The intermolecular stretching frequency, and shifts within the monomers, are compared with the energetic strength of complexation.     

C-H...N and C-H...S hydrogen bonds--influence of hybridization on their strength

Simple complexes connected through C-H...S and C-H...N interactions are investigated: CH4...NH3, C2H4...NH3, C2H2...NH3, CH4...SH2, C2H4...SH2, and C2H2...SH2. Ab initio and DFT calculations are performed (SCF, MP2, B3LYP) using different basis sets up to the MP2/aug-cc-pVQZ//MP2/aug-cc-pVDZ level of approximation. The Bader theory is applied since MP2/6-311++G(d,p) wave functions are used to find and to characterize bond critical points in terms of electron densities and their Laplacians. The influence of hybridization on the properties of C-H...S and C-H...N systems is also studied showing that the strength of such interactions increases in the following order: C(sp3)-H...Y, C(sp2)-H...Y, C(sp)-H...Y, where Y = S, N--it is in line with the previous findings on C-H...O hydrogen bonds. The results also show that CH4...SH2 and C2H4...SH2 complexes should be rather classified as van der Waals interactions and not as hydrogen bonds. The frequency associated with the C-H stretch of C(sp3)-H...S is blue-shifted.     

C-H...F hydrogen bonding: the origin of the self-assemblies of bis(2,2'-difluoro-1,3,2-dioxaborine)

The effect of the molecular structure on the self-assembly of specially designed two-core 1,3,2-dioxaborines has been studied with various techniques. It was found that the molecules spontaneously adsorbed on HOPG surfaces and self-organized into well-ordered two-dimensional (2D) monolayers. The structural details of the 2D assemblies were investigated by scanning tunneling microscopy (STM). From X-ray analysis of the corresponding three-dimensional (3D) crystal and from theoretical calculation, we were able to reveal the driving force behind the specific self-assembly. The C-H...F hydrogen bonding between the ortho carbon of the phenyl ring and the fluorine of the BF2 group plays an important role in the formation of the adlayers. The different electron affinities and geometries of the molecules affect the intermolecular interactions which further lead to different properties in the bulk materials.     

Theoretical study of binding interactions and vibrational Raman spectra of water in hydrogen-bonded anionic complexes: (H2O)n- (n = 2 and 3), H2O...X- (X = F, Cl, Br, and I), and H2O...M- (M = Cu, Ag, and Au)

Binding interactions and Raman spectra of water in hydrogen-bonded anionic complexes have been studied by using the hybrid density functional theory method (B3LYP) and ab initio (MP2) method. In order to explore the influence of hydrogen bond interactions and the anionic effect on the Raman intensities of water, model complexes, such as the negatively charged water clusters ((H2O)n-, n = 2 and 3), the water...halide anions (H2O...X-, X = F, Cl, Br, and I), and the water-metal atom anionic complexes (H2O...M-, M = Cu, Ag, and Au), have been employed in the present calculations. These model complexes contained different types of hydrogen bonds, such as O-H...X-, O-H...M-, O-H...O, and O-H...e-. In particular, the last one is a dipole-bound electron involved in the anionic water clusters. Our results showed that there exists a large enhancement in the off-resonance Raman intensities of both the H-O-H bending mode and the hydrogen-bonded O-H stretching mode, and the enhancement factor is more significant for the former than for the latter. The reasons for these spectral properties can be attributed to the strong polarization effect of the proton acceptors (X-, M-, O, and e-) in these hydrogen-bonded complexes. We proposed that the strong Raman signal of the H-O-H bending mode may be used as a fingerprint to address the local microstructures of water molecules in the chemical and biological systems.     

Molecular tectonics: self-complementary supramolecular Se...N synthons directing assembly of 1D silver chains into 3D porous molecular architectures

Reaction of 2,1,3-benzoselenadiazole (bsd) with AgNO3 results in the formation of a novel model example of a Se...N synthon directed molecular network of different polymorphs at different temperatures. Alpha-[Ag(bsd)2(NO3)] x 0.5bsd formed at ambient temperature, has a 3D porous molecular network constructed with monomeric [Ag(bsd)2(NO3)] motif, and has 1D channels that are encapsulated with 1D arrays of two-fold-disordered dimeric (bsd)2 guests aggregated by the self-complementary nonbonded Se...N interactions. This is the first molecular net directed by supramolecular Se...N synthons. The second polymorph, beta-[Ag(bsd)2(NO3)] x 0.5bsd, formed from an analogous reaction at 50 degrees C, contains a similar 3D molecular network constructed with tetrameric [Ag4(bsd)8(NO3)4] motif and 1D arrays of well-ordered dimeric (bsd)2 guests are encapsulated in the channels. Such ordered (bsd)2 dimers provide an excellent simplified dimeric model for MO calculations of intermolecular nonbonded Se...N interactions.