Crystals2014, 4(2), 74-103; doi:10.3390/cryst4020074 - published online 31 March 2014 Show/Hide Abstract
Abstract: The development of terahertz technology in the last few decades has made it possible to obtain a clear terahertz (THz) spectrum. THz vibrations clearly show the formation of weak bonds in crystals. The simultaneous progress in the code of first-principles calculations treating noncovalent interactions has established the position of THz spectroscopy as a powerful tool for detecting the weak bonding in crystals. In this review, we are going to introduce, briefly, the contribution of weak bonds in the construction of molecular crystals first, and then, we will review THz spectroscopy as a powerful tool for detecting the formation of weak bonds and will show the significant contribution of advanced computational codes in treating noncovalent interactions. From the second section, following the Introduction, to the seventh section, before the conclusions, we describe: (1) the crystal packing forces, the hydrogen-bonded networks and their contribution to the construction of organic crystals; (2) the THz vibrations observed in hydrogen-bonded molecules; (3) the computational methods for analyzing the THz vibrations of hydrogen-bonded molecules; (4) the dispersion correction and anharmonicity incorporated into the first-principles calculations and their effect on the peak assignment of the THz spectrum (5) the temperature dependence; and (6) the polarization dependence of the THz spectrum.
Crystals2014, 4(1), 64-73; doi:10.3390/cryst4010064 - published online 12 March 2014 Show/Hide Abstract
Abstract: Three new compounds, (GuaH)4[W10O32](H2O)4 (1), (ThbH)3(H3O)[(W10O32](H2O)7.5 (2) and (ThbH)2[W6O19](H2O)2 (3) (GuaH = guaninium, thbH = theobrominium) were synthesized in acidified acetonitrile solutions. The polyoxotungstates in all of these compounds are surrounded by an organic matrix consisting of protonated purine bases and water molecules. The distinctive structural arrangement of the aromatic organic cations around the polyoxoanions parallel to their faces is reminiscent of nanosized boxes. The results of IR spectroscopy are consistent with previously reported results for polyoxotungstates and neat organic compounds. The polyoxoanions are reduced to tungsten(IV) oxide upon heating over 400 °C in an intramolecular redox reaction.
Crystals2014, 4(1), 53-63; doi:10.3390/cryst4010053 - published online 4 March 2014 Show/Hide Abstract
Abstract: Four novel organic salts of piperazine and 2-methylpiperazine with p-toluenesulfonic acid and chloroacetic acid have been synthesized and structurally characterized. The hydrogen-bonding ring synthons that exist between the cation/anion pairs are compared and contrasted alongside database results.
Crystals2014, 4(1), 42-52; doi:10.3390/cryst4010042 - published online 4 March 2014 Show/Hide Abstract
Abstract: Polyoxomolybdate inorganic-organic hybrid crystals were synthesized with 1-decyl-3-methylimidazolium and 1-dodecyl-3-methylimidazolium as ionic-liquid surfactants. Both hybrid crystals possessed alternate stacking of surfactant layers and octamolybdate (Mo8) monolayers, while the molecular structures of Mo8 were different depending on the surfactants and solvents employed for crystallization. Each Mo8 anion was connected by two sodium cations to form infinite one-dimensional chain. The surfactant chains in these crystals were arranged in a complicatedly bent manner, which will be induced by the weak C–H···O hydrogen bonds between the Mo8 anions and ionic-liquid surfactants.
Crystals2014, 4(1), 32-41; doi:10.3390/cryst4010032 - published online 26 February 2014 Show/Hide Abstract
Abstract: Two new Cu(II) complexes of the ligand 3-carboxy-5-(2-pyridyl)-1H-pyrazole, H2L1, have been prepared and structurally characterized and found to be comprised of a similar [M2L2] dimer motif. Subtle variation in the synthetic conditions allowed isolation of two metal complexes: [Cu2L12(MeOH)2],1, a discrete dimer linked by hydrogen bonding interactions in the solid state, and poly-[Cu2L12], 2, a polymeric material where the dimer motif is linked by carboxylate bridges to give an extended two-dimensional sheet. The selective isolation of each phase by careful synthetic control highlights the subtlety and importance of the underlying synthetic conditions.
Crystals2014, 4(1), 12-31; doi:10.3390/cryst4010012 - published online 26 February 2014 Show/Hide Abstract
Abstract: Covalently-bonded atoms of Groups IV–VII tend to have anisotropic charge distributions, the electronic densities being less on the extensions of the bonds (σ-holes) than in the intervening regions. These σ-holes often give rise to positive electrostatic potentials through which the atom can interact attractively and highly directionally with negative sites (e.g., lone pairs, π electrons and anions), forming noncovalent complexes. For Group VII this is called “halogen bonding” and has been widely studied both computationally and experimentally. For Groups IV–VI, it is only since 2007 that positive σ-holes have been recognized as explaining many noncovalent interactions that have in some instances long been known experimentally. There is considerable experimental evidence for such interactions involving groups IV and VI, particularly in the form of surveys of crystal structures. However we have found less extensive evidence for Group V. Accordingly we have now conducted a survey of the Cambridge Structural Database for crystalline close contacts of trivalent nitrogen, phosphorus and arsenic with six different types of electronegative atoms in neighboring molecules. We have found numerous close contacts that fit the criteria for σ-hole interactions. Some of these are discussed in detail; in two instances, computed molecular electrostatic potentials are presented.