The molecular structure of (PSH+)(nido-7,8-C2B9H12-) determined by neutron diffraction (PS = proton sponge, 1,8-bis(dimethylamino)naphthalene)

Accurate crystal structures and chemical properties from NoSpherA2

The relationship between the structure and the properties of a drug or material is a key concept of chemistry. Knowledge of the three-dimensional structure is considered to be of such importance that almost every report of a new chemical compound is accompanied by an X-ray crystal structure – at least since the 1970s when diffraction equipment became widely available. Crystallographic software of that time was restricted to very limited computing power, and therefore drastic simplifications had to be made. It is these simplifications that make the determination of the correct structure, especially when it comes to hydrogen atoms, virtually impossible. We have devised a robust and fast system where modern chemical structure models replace the old assumptions, leading to correct structures from the model refinement against standard in-house diffraction data using no more than widely available software and desktop computing power. We call this system NoSpherA2 (Non-Spherical Atoms in Olex2). We explain the theoretical background of this technique and demonstrate the far-reaching effects that the improved structure quality that is now routinely available can have on the interpretation of chemical problems exemplified by five selected examples.

NoSpherA2 brings quantum crystallography to routine structure determination and to the analysis of chemical properties for any class of materials.

Accessing the First nido-Carborane-Substituted Diphosphetane: A Ligand and Synthon for nido-Carboranylphosphanes

Deboronation of a carborane-substituted diphosphetane 2 in toluene yielded the first nido-carboranyldiphosphetane 1. The P-P bond in 1 can be broken via dismutation reactions with diaryl dichalcogenides yielding nido-carboranyl bis-phosphanes that were not accessible via established synthetic protocols. Additionally, transition metal complexes of 1 could be isolated including one coordination polymer. Notably, when the deboronation of 2 is carried out in ethanol, unprecedented nido-carborane-substituted secondary bis-phosphane monoxides (3, 4) are obtained. These compounds are interesting starting materials for further reactivity studies due to their P-H bonds. Experimental findings are supported by DFT calculations including the calculation of reaction mechanisms and NMR spectroscopic parameters.

A systematic examination of classical and multi-center bonding in heteroborane clusters

A systematic revision of bonding types on a broad series of heteroboranes covering closo, nido, arachno and hypho architectures with incorporated tetrel, pnictogen or chalcogen heterovertices.

Direct synthesis of dicarbollides

A substantially new synthesis of dicarbollides based on the dicarbon insertion of alkynes into the nine-vertex 4-Et₃N-arachno-B₉H₁₃ framework is reported.

Ab initio and 1H NMR study of the Zn(II) complexes of a nido- and a closo-carboranylporphyrin

An ab initio study of a promising nido-carboranylporphyrin for the boron neutron capture therapy of tumors, and of its closo precursor is reported. Base-induced deboronation of neutral ZnDCP , believed to exist as a mixture of 3 stereoisomers, produces the tetraanionic ZnDCP 4- as a complex mixture of isomers. 1 H NMR data and ab initio calculations support these findings. The position of the axial pyridine ligand in ZnDCP 4- and the orientation of the endo hydrogen atoms on the open faces of the nido-carborane cages significantly influence the total energy of the ZnDCP 4- structures. It is suggested that the "cocktail" of isomers possibly enhances the biological activity of tetra(nido-carboranyl)porphyrins, such as ZnDCP 4-.

Elongation of phenoxide C-O bonds due to formation of multifold hydrogen bonds: statistical, experimental, and theoretical studies

Statistical studies using the Cambridge Structural Database have revealed that there are several elongated phenoxide C-O bonds. They are characterized by the formation of 3-fold (or occasionally 2-fold) hydrogen bonds to the phenoxide oxygen atoms, and their mean bond length extends up to 1.320 Å, which is quite different from the theoretically predicted carbon-oxygen bond length of C(6)H(5)O(-) (1.26 Å). Elongated phenoxide C-O bonds associated with the formation of 3-fold hydrogen bonds were also observed in the X-ray structures of proton-transfer complexes (2X-O(-))(TEAH(+))s derived from 5'-X-substituted 5,5''-dimethyl-1,1':3',1''-terphenyl-2,2',2''-triols (2X-OHs, where X = NO(2), CN, COOCH(3), Cl, F, H, and CH(3)) and triethylamine (TEA). By comparing the X-ray structures, C-O bond elongation was found to be only slightly affected by an electron-withdrawing substituent at the para position (X). This along with strong bathochromic shifts of N-H(···O(-)) and O-H(···O(-)) stretching vibrations in the IR spectra indicates that the elongated C-O bonds in (2X-O(-))(TEAH(+))s essentially have single-bond character. This is further confirmed by molecular orbital calculations on a model complex, showing that the negatively charged phenoxide oxygen atom is no longer conjugated to the central benzene ring, and the NICS values of the three benzene rings are virtually identical. However, C-O bond elongation in (2X-O(-))(TEAH(+))s was considerably influenced by a change in the hydrogen-bond geometry. This also suggests that hydrogen bonds significantly affect phenoxide C-O bond elongation.

Synthesis and reactivity of 4,5-[1,2-dicarba-closo-dodecaborano(12)]-1,3-diselenacyclopentane: opening of the icosahedron to give a zwitterionic intermediate and conversion into 7,8-dicarba-nido-undecaborate(1-)

The reaction of the 1,2-diselenolato-1,2-dicarba-closo-dodecaborane(12) dianion [1,2-(1,2-C(2)B(10)H(10))Se(2)](2-) with dichloromethane (CH(2)Cl(2) or CD(2)Cl(2)) in the presence of donor solvents gave 4,5-[1,2-dicarba-closo-dodecaborano(12)]-1,3-diselenacyclopentane, the title compound, which was characterized by X-ray structural analysis and NMR spectroscopy ((1)H, (11)B, (13)C, and (77)Se). In the presence of pyridine, opening of the icosahedron took place, and a zwitterionic intermediate was isolated and fully characterized in the solid state by X-ray diffraction and in solution by multinuclear magnetic resonance techniques. Although such types of intermediates, prior to deboronation of the ortho-carborane cage, have been proposed several times, this is first example for which the structure has been confirmed unambiguously. This intermediate possesses a nido structure and contains a 7,8-dicarba-nido-undecaborate(1-) anion and a boronium cation, the latter with two pyridine rings linked to the boron atom, which has been extruded from the cage. It was shown that this process is reversible as long as the deboronation is not complete. The formation of the intermediate is accompanied by deboronation, which leads to the 7,8-dicarba-nido-undecaborate(1-) anion. The latter was prepared independently by conventional routes from the title compound, isolated as crystalline material as the tetrabutyl ammonium salt, and characterized by X-ray structural analysis and multinuclear magnetic resonance spectroscopy ((1)H, (11)B, (13)C, and (77)Se).

Bond lengths in organic and metal-organic compounds revisited: X-H bond lengths from neutron diffraction data

The number of structures in the Cambridge Structural Database (CSD) has increased by an order of magnitude since the preparation of two major compilations of standard bond lengths in mid-1985. It is now of interest to examine whether this huge increase in data availability has implications for the mean bond-length values published in the late 1980s. Those compilations reported mean X-H bond lengths derived from rather sparse information and for rather few chemical environments. During the intervening years, the number of neutron studies has also increased, although only by a factor of around 2.25, permitting a new analysis of X-H bond-length distributions for (a) organic X = C, N, O, B, and (b) a variety of terminal and homometallic bridging transition metal hydrides. New mean values are reported here and are compared with earlier results. These new overall means are also complemented by an analysis of X-H distances at lower temperatures (T < or = 140 K), which indicates the general level of librational effects in X-H systems. The study also extends the range of chemical environments for which statistically acceptable mean X-H bond lengths can be obtained, although values from individual structures are also collated to further extend the chemical range of this compilation. Updated default 'neutron-normalization' distances for use in hydrogen-bond and deformation-density studies are also proposed for C-H, N-H and O-H, and the low-temperature analysis provides specific values for certain chemical environments and hybridization states of X.

Carborane clusters in computational drug design: a comparative docking evaluation using AutoDock, FlexX, Glide, and Surflex

Compounds containing boron atoms play increasingly important roles in the therapy and diagnosis of various diseases, particularly cancer. However, computational drug design of boron-containing therapeutics and diagnostics is hampered by the fact that many software packages used for this purpose lack parameters for all or part of the various types of boron atoms. In the present paper, we describe simple and efficient strategies to overcome this problem, which are based on the replacement of boron atom types with carbon atom types. The developed methods were validated by docking closo- and nido-carboranyl antifolates into the active site of a human dihydrofolate reductase (hDHFR) using AutoDock, Glide, FlexX, and Surflex and comparing the obtained docking poses with the poses of their counterparts in the original hDHFR-carboranyl antifolate crystal structures. Under optimized conditions, AutoDock and Glide were equally good in docking of the closo-carboranyl antifolates followed by Surflex and FlexX, whereas Autodock, Glide, and Surflex proved to be comparably efficient in the docking of nido-carboranyl antifolates followed by FlexX. Differences in geometries and partial atom charges in the structures of the carboranyl antifolates resulting from different data sources and/or optimization methods did not impact the docking performances of AutoDock or Glide significantly. Binding energies predicted by all four programs were in accordance with experimental data.

Mass spectrometric evidence for collisionally induced removal of H(2) from monoanions of (10)B nido-carborane derivatives investigated by electrospray ionization quadrupole linear ion trap and Fourier transform ion cyclotron resonance mass spectrometry

Some newly synthesized (10)B nido-carborane derivatives, i.e., 7,8-dicarba-nido-undecaborane monoanions ([7-Me-8-R-C(2)B(9)H(10)](-)K(+), R = H, butyl, hexyl, octyl and decyl), have been fully characterised and examined by electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry with liquid chromatographic separation (LC/ESI-FTICR-MS). These boron-containing compounds exhibit abundant molecular ions ([M](-)) at m/z 140.22631 [C(3) (10)B(9)H(14)](-), m/z 196.28883 [C(7) (10)B(9)H(22)](-), m/z 224.32032 [C(9) (10)B(9)H(26)](-), m/z 252.35133 [C(11) (10)B(9)H(30)](-) and m/z 280.38354 [C(13) (10)B(9)H(34)](-) at the normal tube lens voltage setting of -90 V, which was an instrumental parameter value selected in the tuning operation. Additional [M-nH(2)](-) (n = 1-4) ions were observed in the mass spectra when higher tube lens voltages were applied, i.e., -140 V. High-resolution FTICR-MS data revealed the accurate masses of fragment ions, bearing either an even or an odd number of electrons. Collision-induced dissociation of the [M-nH(2)](-) ions (n = 0-4) in the quadrupole linear ion trap (LTQ) analyzer confirmed the loss of hydrogen molecules from the molecular ions. It is suggested that the loss of H(2) molecules from the alkyl chain is a consequence of the stabilization effect of the nido-carborane charged polyhedral skeleton.

Gas-phase electron diffraction studies of the icosahedral carbaboranes, ortho-, meta- and para-C2B10H12

The molecular structures of the three closo-carbaboranes, ortho-, meta- and para-C2B10H12, were experimentally determined using gas-phase electron diffraction (GED). All unique bond distances for ortho and meta carbaboranes were determined experimentally for the first time. For ortho-carbaborane (RG= 0.046), a model with C2v symmetry refined to give bond distances of 1.624(8) A for C-C, 1.093(8)A for C-H and 1.192(3)-1.196(3) A for B-H. For meta-carbaborane (RG= 0.040) a model with C2v symmetry refined to give a CC distance of 2.575(9) A. For para-carbaborane (RG= 0.062) a model with D5d symmetry refined to give a C-B bond distance of 1.698(3) A, B2-B3 of 1.785(1), B2-B7 of 1.774(4) and CC of 3.029(5)A. These GED structures are compared with geometries from other experimental diffraction methods (neutron, X-ray) and ab initio calculations.

Gas-Phase Electron Diffraction Studies on Two 11-Vertex Dicarbaboranes, closo-2,3-C2B9H11 and nido-2,9-C2B9H13

The molecular structures of two carbaboranes, closo-2,3-C(2)B(9)H(11) and nido-2,9-C(2)B(9)H(13), were determined experimentally for the first time using gas-phase electron diffraction (GED). For closo-2,3-C(2)B(9)H(11), a model with C(2)(v)() symmetry was refined to give C-B bond distances ranging 158.3-167.0 pm and B-B distances ranging 177.4-200.0 pm. The structure of nido-2,9-C(2)B(9)H(13) was refined using a model with C(s)() symmetry to give C-B bond lengths ranging 160.3-171.9 pm and B-B lengths ranging 173.0-196.1 pm. Ab initio computations (up to MP2/6-311+G) were also carried out on these and the related nido-7,8-C(2)B(9)H(13), which was not sufficiently stable to allow determination of its molecular structure by GED.

Exo-π-bonding to an ortho-carborane hypercarbon atom: systematic icosahedral cage distortions reflected in the structures of the fluoro-, hydroxy- and amino-carboranes, 1-X-2-Ph-1,2-C2B10H10 (X = F, OH or NH2) and related anions

The structures of derivatives of phenyl-ortho-carborane bearing on the second cage hypercarbon atom a pi-donor substituent (F, OH, O-, NH2, NH- and CH2-) were investigated by NMR, X-ray crystallography and computational studies. The molecular structures of these compounds, notably their cage C1-C2 distances and the orientations of their pi-donor substituents (OH, NH2, NH- and CH2-) show remarkable and systematic variations with the degree of exo pi-bonding, which varies as expected with the pi-donor characteristics of the substituent.