Tetrahedral Character Research Articles

Fixed stereochemical control in the synthesis of new mono- and disubstituted 2-phenyl-6-aza-1,3-dioxa-2-borabenzocyclononenes

Five new boronates of the type 2-phenyl-6-aza-1,3-dioxa-2-borabenzocyclononenes (6a–e) were prepared from substituted 2-[(2-hydroxyethylamino)methyl]phenols (4a–e) and phenylboronic acid (5) in benzene-EtOH (4:1) mixtures. Tridentate ligands 4a–e and boronates 6a–e were characterized by 1H, 13C, 15N, and 2D-NMR (HETCOR, NOESY, and COLOC) experiments, FT-IR, mass spectra, and elemental analysis, as well as 11B NMR for the boron derivatives. Suitable monocrystals of 2-[(2-hydroxyethylamino)methyl]phenol hydrochloride (4a), cis-2-phenyl-6-aza-1,3-dioxa-2-borabenzocyclononene (6a), (2S,5R,6S)-2,5-diphenyl-6-aza-1,3-dioxa-2-borabenzocyclononene (6b), and (2S,4R,5R,6S)-2,4-diphenyl-5-methyl-6-aza-1,3-dioxa-2-borabenzocyclononene (6e) were obtained and their structures are discussed. The X-ray structures of 6a, 6b, and 6e, as well as the NMR data established that the configurations at the nitrogen and boron atoms are both "S" and the transannular fusion is cis. A semi-empirical (SAM1) study was used to calculate the energy for all possible stereoisomers, showing that the stabilization increases as the THC (tetrahedral character of the boron atom) increases and also as the N[Formula: see text]B bond distance decreases, in agreement with the experimental results and previous work related to amino acid boronates.Key words: boron compounds, X-ray structures, NMR, boronates, synthesis.

X-ray analysis and structural characterization of 2-phenyl-6-aza-1,3-dioxa-2-borabenzocyclononenones

Nine new monomeric boronates of the type 2-phenyl-6-aza-1,3-dioxa-2-borabenzocyclononen-4-ones ( 3a– 3i) were prepared from N-(2-hydroxybenzyl)-α-aminoacids 1a– 1i and phenylboronic acid 2 using 20:1 benzene–DMSO mixtures. The compounds were characterized by 1H-, 13C-, 11B-, 15N- and 2D-NMR (HETCOR, NOESY and COLOC) experiments, FT infrared, mass spectra and elemental analysis. Suitable monocrystals of cis-2-phenyl-6-aza-1,3-dioxa-2-borabenzocyclononen-4-one ( 3a), (2 S,5 S,6 R)-2-phenyl-6-aza-1,3-dioxa-5- secbutyl-2-borabenzocyclononen-4-one ( 3e) and 2,5-diphenyl-6-aza-1,3-dioxa-2-borabenzocyclononen-4-one ( 3h) were obtained and their structures are discussed. The X-ray structures, as well as the NMR data established that the configurations at the nitrogen and boron atoms are ‘ R’ and ‘ S’, respectively and the transannular fusion is cis. A semi-empirical (SAM1) study allowed calculation of the energy for all possible stereoisomers, showing that the stabilization increases as the THC (TetraHedral Character of the boron atom) increases and also as the N→B bond distance decreases, in agreement with the experimental results.

Mechanistic comparisons among base excision repair glycosylases

The mechanisms by which various DNA glycosylases initiate the base excision repair pathways are discussed. Fundamental distinctions are made between “simple glycosylases,” that do not form DNA single-strand breaks, and “glycosylases/abasic site lyases,” that do form single-strand breaks. Several groupings of BER substrate sites are defined and some interactions between these groupings and glycosylase mechanisms discussed. Two characteristics are proposed to be common among all BER glycosylases: a nucleotide flipping step that serves to expose the scissile glycosyl bond to catalysis, and a glycosylase transition state characterized by substantial tetrahedral character at the base glycosyl atom.

Intermolecular interactions and molecular geometry in molecular complexes of N,N-dimethylaniline: the 1:1 complex with 1,2,4,5-tetracyanobenzene

The partner mol­ecules of N,N-di­methyl­aniline–1,2,4,5-tetra­cyano­benzene (1/1), C8H11N·C10H2N4, are stacked alternately in infinite columns. The N atom of the N,N-di­methyl­aniline mol­ecule has a partially tetrahedral character and the distance between neighbouring mol­ecules in the stack is relatively short on the side where the lone-pair electrons of this atom are located. Molecular-packing analysis of this and three other complexes of N,N-di­methyl­aniline shows that there is a close relationship between the strength of the intermolecular interaction on this side and the tetrahedral character of the N atom.

Intermolecular interactions and molecular geometry in molecular complexes of N,N-dimethylaniline: the 1:1 complex with 1,2,4,5-tetracyanobenzene.

The partner mol­ecules of N,N-di­methyl­aniline–1,2,4,5-tetra­cyano­benzene (1/1), C8H11N·C10H2N4, are stacked alternately in infinite columns. The N atom of the N,N-di­methyl­aniline mol­ecule has a partially tetrahedral character and the distance between neighbouring mol­ecules in the stack is relatively short on the side where the lone-pair electrons of this atom are located. Molecular-packing analysis of this and three other complexes of N,N-di­methyl­aniline shows that there is a close relationship between the strength of the intermolecular interaction on this side and the tetrahedral character of the N atom.

Self-Assembly of 3-[4‘-(Diethylboryl)phenyl]pyridine and 3-[3‘-(Diethylboryl)phenyl]pyridine: Synthesis, Structural Features, and Stability in Solution

The self-assembly of 3-[4‘-(diethylboryl)phenyl]pyridine (3) and 3-[3‘-(diethylboryl)phenyl]pyridine (4) was investigated by 1H and 11B NMR spectroscopies and vapor pressure osmometry. It can be seen that in solution 3 affords an equilibrium mixture of oligomers including a cyclic trimer as a major component via intermolecular boron−nitrogen coordination bonds, which is supported by temperature-, concentration-, and solvent-dependent behaviors of 3. In contrast, 4 seems to afford a mixture of oligomers including a cyclic dimer in solution. Judging from the low coalescence temperature in variable-temperature NMR in toluene-d8 and easy scrambling with the corresponding 3-[(diethylboryl)pheny]-5-methoxypyridines at ambient temperature, it is concluded that the intermolecular boron−nitrogen coordination bonds made by 3 or 4 are weaker than those formed by 3-(diethylboryl)pyridine (1) or 2-(diethylboryl)-5-methylpyridine (2). Poor thermal stability was supported by electrospray mass spectrometry and structural analyses utilizing a semi-empirical molecular orbital calculation AM1. It is noted that in the assembly of 4 there is a tendency to maintain high tetrahedral character at the boron atom in the complex at the expense of strain energy. Thus, these features of 3 and 4 in solution are in marked contrast to those of 1 and 2.

ChemInform Abstract: The Tetrahedral Character of the Boron Atom Newly Defined. A Useful Tool to Evaluate the N→B Bond.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

X-ray crystallographic study of three (N→B)-borinates prepared from 8-hydroxyquinoline and 2-hydroxypyridine

8-Hydroxyquinoline and 2-hydroxypyridine have been reacted with diphenylborinic acid or 9-BBN; the molecular structure of the resulting heterocycles has been studied by X-ray crystallography. A structural comparison of the so formed five- and six-membered heterocycles with similar complexes obtained from aliphatic amino alcohol and α-amino acid derivatives shows significant differences for the N→B, B−O and B−C bond lengths and some of the inner cycle bond angles. Other structural parameters discussed in this respect are the sum of bond lengths at the boron atom, the sum of bond angles in the heterocycle and the tetrahedral character of the boron atom. On the basis of these parameters a qualitative comparison of heterocycle stability is possible.

The tetrahedral character of the boron atom newly defined—a useful tool to evaluate the N→B bond

The tetrahedral character at the boron atom in boron complexes with a coordinative N→B bond has been evaluated on the basis of 144 solid state and gas phase molecular structures in order to obtain additional information on the van der Waals versus covalent relationship of the boron-nitrogen bond. The tetrahedral character has been calculated by a new formula that includes all six bond angles at the boron atom. Thereby, the N→B bond length and the tetrahedral character are correlated and permit the description of the reaction path for the formation of the N→B bond.

Tetrahedral coordination by a seven-membered chelate ring

The ligand 1,2-bis(benzimidazol-2-yl)ethane ( 1a) and its N,N′-dioctyl ( 1b), N,N′-bis(3,5-dimenthoxybenzyl) ( 1c) and 5,5′-dimethyl- N,N′-diethyl ( 1d) derivatives have been prepared. With MCl 2 the ligands give complexes [MLCl 2] (M  Mn, Fe, Co, Ni, Cu, Zn) which generally appear to have tetrahedral coordination geometry. X-ray crystal structures of [Cu( 1c)]·MeCN, [Cu( 1c)Br 2] and [Mn( 1d)Cl 2]·MeCN have been determined, and show tetrahedral coordination of the metal, the copper(II) complexes showing significant distortion from ideal tetrahedral character. Comparison with other results in the literature, coupled with simple molecular mechanics calculations, suggests that the tetrahedral character may be favoured by the seven-membered chelate ring in which puckering is limited by the presence of two double bonds in the ring.

Synthesis and Study of Monomeric and Dimeric Boronates by Spectroscopic Methods and X-ray Crystallography

A series of 2-salicylideneamino ethanol derivatives with substituents in different positions have been brought to reaction with phenylboronic acid. Depending on the number and position of the substituents in the ligand, three boronate structure types have been obtained. Thereby, it could be shown that the formation of a macrocyclic dimeric boronate is preferred over the monomeric compound and a [5.4.0]heterobicyclic system with a B(4)−O−B(3) structural unit. The three structure types have been analyzed by X-ray crystallography, where a series of parameters such as N→B bond length, torsion angles, tetrahedral character at the boron atom, deviation of the boron atom from the mean plane and sum of bond angles in the heterocyclic rings have been evaluated in order to determine the factors for the preferred formation of each compound. Finally a new synthetic strategy is presented that permits the synthesis of other macrocyclic boronates in the future.

Structure of diethyl(2-pyridyl)boranes: Rigid cyclic dimers

Diethyl(2-pyridyl)boranes (2a, 2b) comprise cyclic dimers via intermolecular boronnitrogen coordination bonds. The boron atoms of diethyl[2-(5-methylpyridyl)]borane (2b) show clear pyramidalization. The high tetrahedral character of these boron atoms in 2b indicates that the dimer is far rigid compared with the tetramer composed of diethyl(3-pyridyl)borane (1a).

Characterization of (GaxIn1−x)2Se3 Raman and Infrared Spectra for 0 ≦ x ≦ 0.5

AbstractA modified random element displacement model is used to investigate the composition dependence of Raman and infrared spectra of (GaxIn1−x)2Se3. A computer program that enables the simulation of explicit metal site substitution and stressing the tetrahedral character of the structure is developed. A good agreement with experiment is obtained by using a few free numerical parameters indicating that the vibration modes depend mainly on the structure details. A vibration type assignment to the experimental results is possible for isolated peaks, though more than one vibration mode contribute to some of them. Due to the presence of many close modes and their poor optical activity the vibration type assignment is not possible in the range higher than 180 cm−1.

Hydrogen-free amorphous carbon preparation and properties

Amorphous carbon containing very little hydrogen and having a highly tetrahedral character is deposited by filtered cathodic arc. This amorphous carbon shows photoconductivity under white light illumination. It is slightly p-type in pure form but becomes n-type when doped with nitrogen. Electron diffraction shows that nitrogen levels of less than 1% do not distort the tetrahedral network, but at higher concentrations nitrogen destabilises the tetrahedral structure. Plasmon spectroscopy shows the presence of a 1 nm “defective” surface layer even in the pure material which has implications for device applications. A junction field effect transistor structure is proposed as a possible device.

Resonance Raman spectroscopy of the azurin His117Gly mutant. Interconversion of type 1 and type 2 copper sites through exogenous ligands.

The copper center of the Pseudomonas aeruginosa His117Gly azurin mutant is accessible to exogenous ligands through an aperture in its surface created by the removal of the endogenous imidazole ligand. Depending on the exogenous ligand, a surprising variety of type 1 and type 2 copper sites can be obtained that are readily distinguished by electronic, EPR, and resonance Raman (RR) spectroscopy. The RR spectrum of type 1 H117G with exogenous imidazole is nearly identical to that of wild-type azurin, indicating that the trigonal geometry and short Cu-S(Cys) bond of approximately 2.15 A have been maintained. With anionic ligands (e.g., Cl-, Br-, N3-), the RR spectra show increased intensity at 370 and 400 cm-1 and a corresponding decrease in intensity at 410 cm-1, suggesting a lengthening of the Cu-S(Cys) bond as the site achieves a more tetrahedral character. An extreme example is the hydroxide adduct of H117G which is green in color and has optical and RR spectra reminiscent of the tetrahedral type 1 site in Achromobacter cycloclastes nitrite reductase. The fact that the basic RR pattern is little changed in most of the type 1 adducts indicates that the RR spectrum is due primarily to vibrations of the Cu-cysteinate moiety and that its coplanar conformation is conserved. Type 2 H117G proteins are formed by the addition of bidentate exogenous ligands such as histidine and histamine. They have their absorption maxima blue-shifted to 400 nm and their EPR A parallel values increased to approximately 160 x 10(-4) cm-1, both of which are characteristic of tetragonal Cu sites with Cu-S(thiolate) bonds of > 2.25 A. The RR spectra of the type 2 H117G proteins are still dominated by multiple cysteinate-related vibrational modes. However, the vibrational modes with the greatest intensity and Cu-S(Cys) stretching character have shifted approximately 100 cm-1 to lower energy compared to the type 1 sites, consistent with a longer (Cys)S-Cu bond. It is proposed that the tetragonal type 2 character of the bidentate ligand complexes is due to the addition of a fourth strong ligand in the equatorial ligand plane.

ChemInform Abstract: Structure of/and Tetrahedral Character of the Boron Atom in 9‐(2‐(1‐ Ethylthiopentyl)phenyl)‐9‐borabicyclo(3.3.1)nonane

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Structure of and Tetrahedral Character of the Boron Atom in 9-[2-(1-Ethylthiopentyl)phenyl]-9-borabicyclo[3.3.1]nonane

Abstract Structure of the title compound was determined by the X-ray analysis. The sulfur atom intramolecularly coordinates to the boron atom with a distance of 2.071 Å and the relation between the butyl group at the benzylic position and the S-ethyl group is nearly anti. The observed dynamic behavior in the compound is discussed on the basis of the structure and the results of some NMR experiments. Other structural features and the tetrahedral character of the boron atom are also reported.

Structure of Intramolecular Boron–Amine Complexes and Proposal of Tetrahedral Character for Correlation between Molecular Structure and Barrier to Dissociation of the N–B Bonds

Abstract The molecular structures of a set of intramolecular boron-amine complexes, 9-[2-(dialkylaminomethyl)phenyl]-9-borabicyclo[3.3.1]nonanes (alkyl = Me and Et) and 2-[2-(dimethylaminomethyl)phenyl]-4,4-diphenyl-1,3,2-dioxaborolane, were determined by the X-ray analyses. The boron atom has a tetrahedral geometry and the five-membered ring is puckered with the nitrogen atom out of the plane in every complex. The distances of the N–B coordination bonds, which are in the range of 1.74–1.77Å, are not always correlated to the barrier to dissociation of the N–B bonds. In order to correlate the molecular structures to the strength of the N–B coordination bonds, the tetrahedral character, which is calculated from bond angles at a boron atom, is proposed. The usefulness as well as the limitation of this parameter are discussed.

Pulsed laser deposition of diamondlike hydrogenated amorphous carbon films

Diamondlike hydrogenated amorphous carbon films have been deposited for the first time by pulsed ruby laser deposition (PLD) from pyrolytic graphite in hydrogen partial pressure. A hint in the IR absorption spectrum at 2920 cm−1 provides an evidence for the incorporation of hydrogen in the film. Raman scattering (RS) measurements display a large downward shift in the position of the intense G line to 1500 cm−1, whereas the relatively weak D line is observed near 1350 cm−1 along with a strong enhancement in RS near 1210 and 800 cm−1. These features are attributed to an increased proportion of tetrahedral (sp3) character in the amorphous carbon network due to formation of hydrogen-related complexes. Additional support for this proposal is sought from the enhanced band gap of the PLD a-C:H films compared to those of unhydrogenated PLD a-C films.

β‐Secondary deuterium isotope effect and solvent isotope effects in catalysis by subtilisin BPN′

AbstractSubtilisin BPN′ catalyzes the hydrolysis in protium and deuterium oxides of p‐NO2C6H4OCOCL2NHCO2CH2C6H5(L = H, D) in the pH(D) range 5·0–8·5 (H2O) and 5·4–9·0 (D2O), according to simple Michaelis–Menten kinetics. The parameter kcat/Km exhibits pH(D) inflection points of 7·17 ± 0·05 (H2O) and 7·69 ± 0·08 (D2O), and kcat shows 6·88 ± 0·05 (H2O) and 7·50 ± 0·07 (D2O). The ‘normal’ ΔpK values of 0·5–0·6 indicate no unusual effects of D2O on enzyme properties. The solvent isotope effects (H2O/D2O) on the limiting values of the rate constants at high pH(D) are 1·13 ± 0·07 for kcat/Km and 1·29 ± 0·05 for Kcat. These small effects indicate no more than minor contributions of general acid–base catalysis for rate‐limiting events for either kcat/Km or kcat. The β‐deuterium secondary isotope effects (2H/2D) are roughly estimated by extrapolation as 0·95 ± 0·01 for kcat/Km, corresponding to substantial tetrahedral character in the transition state, and 1·03 ± 0·03 for kcat, consistent with no tetrahedral character. Models consistent with these results have as rate‐limiting events for kcat/Km nucleophilic attack by active‐site imidazole and for kcat, among other possibilities, the release of carboxylate product from the imidazolium form of the enzyme.