Drahomír Hnyk

The Dominant Role of Chalcogen Bonding in the Crystal Packing of 2D/3D Aromatics

The chalcogen bond is a nonclassical σ-hole-based noncovalent interaction with emerging applications in medicinal chemistry and material science. It is found in organic compounds, including 2D aromatics, but has so far never been observed in 3D aromatic inorganic boron hydrides. Thiaboranes, harboring a sulfur heteroatom in the icosahedral cage, are candidates for the formation of chalcogen bonds. The phenyl-substituted thiaborane, synthesized and crystalized in this study, forms sulfur⋅⋅⋅π type chalcogen bonds. Quantum chemical analysis revealed that these interactions are considerably stronger than both in their organic counterparts and in the known halogen bond. The reason is the existence of a highly positive σ-hole on the positively charged sulfur atom. This discovery expands the possibilities of applying substituted boron clusters in crystal engineering and drug design.

Interactions of Boranes and Carboranes with Aromatic Systems: CCSD(T) Complete Basis Set Calculations and DFT-SAPT Analysis of Energy Components

The noncovalent interactions of heteroboranes with aromatic systems have only recently been acknowledged as a source of stabilization in supramolecular complexes. The physical basis of these interactions has been studied in several model complexes using advanced computational methods. The highly accurate CCSD(T)/complete basis set (CBS) value of the interaction energy for the model diborane···benzene complex in a stacking geometry exhibiting a B(2)H···π hydrogen bond was calculated to be -4.0 kcal·mol(-1). The DFT-SAPT/CBS approach, which is shown to reproduce the CCSD(T)/CBS data reliably asserted that the major stabilizing component was dispersion, followed by electrostatics. Furthermore, the effect of the benzene heteroatom- and exosubstitutions was studied and found to be small. Next, when aromatic molecules were changed to cyclic aliphatic ones, van der Waals complexes stabilized by the dispersion term only were formed. As the last step, interactions of two larger icosahedral borane cages with benzene were explored. The complex of the monoanionic CB(11)H(12)(-) exhibited two minima: the first stacked above the plane of the benzene ring with a C-H···π hydrogen bond and the second planar, in which the carborane cage bound to benzene via five B-H···H-C dihydrogen bonds. The DFT-SAPT/CBS calculations revealed that both of these binding motifs were stabilized by dispersion followed by electrostatic terms, with the planar complex being 1.4 kcal·mol(-1) more stable than the stacked one. The dianionic B(12)H(12)(2-) interacted with benzene only in the planar geometry, similarly as smaller anions do. The large stabilization energy of 11.0 kcal·mol(-1) was composed of dominant attractive dispersion and slightly smaller electrostatic and induction terms. In summary, the borane/carborane···aromatic interaction is varied both in the complex geometries and in the stabilizing energy components. The detailed insight derived from high-level quantum chemical computations can help us understand such important processes as host-guest complexation or carborane···biomolecule interactions.

Chalcogen and Pnicogen Bonds in Complexes of Neutral Icosahedral and Bicapped Square-Antiprismatic Heteroboranes

A systematic quantum mechanical study of σ-hole (chalcogen, pnicogen, and halogen) bonding in neutral experimentally known closo-heteroboranes is performed. Chalcogens and pnicogens are incorporated in the borane cage, whereas halogens are considered as exo-substituents of dicarbaboranes. The chalcogen and pnicogen atoms in the heteroborane cages have partial positive charge and thus more positive σ-holes. Consequently, these heteroboranes form very strong chalcogen and pnicogen bonds. Halogen atoms in dicarbaboranes also have a highly positive σ-hole, but only in the case of C-bonded halogen atoms. In such cases, the halogen bond of heteroboranes is also strong and comparable to halogen bonds in organic compounds with several electron-withdrawing groups being close to the halogen atom involved in the halogen bond.

Phosphacarborane Chemistry: The Synthesis of the Parent Phosphadicarbaboranesnido-7,8,9-PC2B8H11 and [nido-7,8,9-PC2B8H10]−, and Their 10-Cl Derivatives − Analogs of the Cyclopentadienide Anion

The reaction of the carborane nido-5,6-C2B8H12 (1) with PCl3 in dichloromethane in the presence of a “proton sponge” [PS = 1,8-bis(dimethylamino)naphthalene], followed by hydrolysis of the reaction mixture, resulted in the isolation of the eleven-vertex nido-phosphadicarbaboranes 7,8,9-PC2B8H11 (2) and 10-Cl-7,8,9-PC2B8H10 (10-Cl-2), depending on the ratio of the reactants. Both of these compounds can be deprotonated by PS to give the nido anions [7,8,9-PC2B8H10]− (2−) and [10-Cl-7,8,9-PC2B8H9]− (10-Cl-2−). The molecular geometries of all compounds were optimized by ab initio methods at a correlated level of theory [RMP2(fc)] using the 6-31G* basis set and their correctness was assessed by a comparison of the experimental 11B NMR chemical shifts with those calculated by the GIAO-SCF/II//RMP2(fc)/6-31G* method. Moreover, the structure of 10-Cl-2− was determined by an X-ray diffraction analysis. The anionic compounds 2− and 10-Cl-2− are analogs of the Cp (Cp = η5-C5H5−) anion. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)

Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes.

Halogen bonds are a subset of noncovalent interactions with rapidly expanding applications in materials and medicinal chemistry. While halogen bonding is well known in organic compounds, it is new in the field of boron cluster chemistry. We have synthesized and crystallized carboranes containing Br atoms in two different positions, namely, bound to C- and B-vertices. The Br atoms bound to the C-vertices have been found to form halogen bonds in the crystal structures. In contrast, Br atoms bound to B-vertices formed hydrogen bonds. Quantum chemical calculations have revealed that halogen bonding in carboranes can be much stronger than in organic architectures. These findings open new possibilities for applications of carboranes, both in materials and medicinal chemistry.

Microwave spectra and structures of 1,2-(ortho)- and 1,7-(meta)-carborane, C2B10H12.

The microwave spectra of 1,2- and 1,7-dicarba-closo-dodecaborane(12), C(2)B(10)H(12) (ortho- and meta-carborane), have been recorded for the first time at room temperature in the 32-88 and 24-80 GHz spectral ranges, respectively. The spectra of the parent species (1,2-C(2)(11)B(10)H(12) and 1,7-C(2)(11)B(10)H(12)) have been assigned, together with those of four monosubstituted ((10)B) 1,2-C(2)(10)B(11)B(9)H(12) and 1,7-C(2)(10)B(11)B(9)H(12) isotopologues. The microwave spectra confirm that the structures of each of these two molecules are slightly distorted icosahedrons of C(2v) symmetry. A previous determination of the gaseous structures of these two carboranes by the gas electron-diffraction method was based on several assumptions about the B-B bond length differences. All B-B bond lengths have now been redetermined using the substitution (r(s)) method, which is independent of such restraints. Although several of the r(s) and electron-diffraction bond lengths are in good agreement, there are also differences of up to 0.026 Å. Quantum chemical calculations at the B3LYP/6-311++G(3df,3pd) level of theory have also been performed.

New route to 1-thia-closo-dodecaborane(11), closo-1-SB11H11, and its halogenation reactions. The effect of the halogen on the dipole moments and the NMR spectra and the importance of spin–orbit coupling for the 11B chemical shifts

Reaction between nido-B10H14 (1) and elemental sulfur in CHCl3 in the presence of Et3N at room temperature, followed by treatment with Et3N.BH3 at 170-190 degrees C, resulted in the isolation of closo-1-SB11H11 (2) in 50% yield. Selected electrophilic halogenation reactions of compound led to the isolation of a series of monohalogenated derivatives of general constitution 12-X-closo-1-SB11H10 (12-X-, where X = Cl, Br, and I). The structures of 12-Cl- and 12-I- were determined by an X-ray diffraction analysis and the structures of all compounds were geometry optimised at the RMP2(fc)/6-31G* level. The constitution of all compounds is consistent with the results of mass spectrometry and multinuclear (1H and 11B) spectroscopy complemented by two-dimensional [11B-11B]-COSY and 1H{11B(selective)} NMR measurements. Experimental 11B chemical shifts generally show acceptable agreement with theoretical values calculated by GIAO methods, but spin-orbit coupling must be included for nuclei bearing heavy-atom substituents such as Br or I. The dipole moments determined for the B12-X bonds show similarities to those of aliphatic C-X bonds and confirm unambiguously the B12 --> S dipole moment orientation in the SB11 cage.

Mechanism of the antipodal effect with borane cages

With the EB11H11(1) and EB9H9(2) series, CNDO/2 and extended Huckel type calculations show that with decreasing electron density on the vertex E: AIR2– > BH2– > CH– > NH > S the electron density on the antipodal skeletal atom decreases proportionally in the tangential px and py(π) atomic orbitals and increases in the radial pz orbital through both series; this explains contradictory information about the electron density on the antipodal atom, a low electron density being indicated by the 11B NMR chemical shift and a high one being deduced from chemical behaviour.

An electron diffraction, ab initio and vibrational spectroscopic study of 1,2-di-tert-butyldisilane

Abstract The molecular structure of 1,2-di-tert-butyldisilane has been accurately determined by gas-phase electron diffraction (GED) and ab initio calculations. These techniques show that the large majority of molecules at room temperature have the anti conformation with overall symmetry C2, and vibrational spectra confirm this conclusion. Infrared spectra of the gas and liquid phases, and Raman spectra of the liquid and solid phases, have been recorded for (CH3)3CSiH2SiH2C(CH3)3 and (CH3)3CSiD2SiD2C(CH3)3. The most striking feature of this structure (ra) is a relatively large deviation of the SiSiC angle from the parent tetrahedral angle 109.5° (113.7(3)°, GED; 114.4°, SCF 6-31 G ∗ as calculated for the anti form). That the SiSi bond length does not show any substantial deviation from its usual value (234.8(3) pm, GED; 236.8 pm, SCF 6-31 G ∗ computed for the anti form) is also substantiated by the value of the SiSi valence force constant (169 N m−1) given by normal coordinate analysis. The t-butyl groups are tilted so that the SiC bonds (GED ( SCF 6-31 G ∗ ): 190.1(1) (191.9) pm) do not coincide with the local C3 axes of the C(CH3)3 groups in which the CC bond length is 154.1(1) (GED); 154.0 ( SCF 6-31 G ∗ ) pm. The conformations along all the single bonds are more or less staggered.

The molecular structures of pentaborane(11), B5H11, and hexaborane(12), B6H12, in the gas phase as determined by electron diffraction and ab initio calculations

Abstract The electron-diffraction patterns of gaseous arachno -B 5 H 11 and arachno -B 6 H 12 have been reanalysed. Inclusion of ab initio (MP2/6-31G*) computed bond-length differences in the refinements afforded new optimum geometries with improved R factors ( R G = 0.053 and 0.057, respectively) compared with the structures resported previously. In contrast to the latter, the new geometries cna be employed to calculate 11 B NMR chemical shifts (DZ//GED level) which are in good agreement with the experimental NMR data.