CN Derivatives Research Articles

Coherence Spectroscopy Investigations of the Low-Frequency Vibrations of Heme: Effects of Protein-Specific Perturbations

Femtosecond coherence spectroscopy is used to probe the low-frequency (20-200 cm(-1)) vibrational modes of heme proteins in solution. Horseradish peroxidase (HRP), myoglobin (Mb), and Campylobacter jejuni globin (Cgb) are compared and significant differences in the coherence spectra are revealed. It is concluded that hydrogen bonding and ligand charge do not strongly affect the low-frequency coherence spectra and that protein-specific deformations of the heme group lower its symmetry and control the relative spectral intensities. Such deformations potentially provide a means for proteins to tune heme reaction coordinates, so that they can perform a broad array of specific functions. Native HRP displays complex spectral behavior above approximately 50 cm(-1) and very weak activity below approximately 50 cm(-1). Binding of the substrate analog, benzhydroxamic acid, leads to distinct changes in the coherence and Raman spectra of HRP that are consistent with the stabilization of a heme water ligand. The CN derivatives of the three proteins are studied to make comparisons under conditions of uniform heme coordination and spin-state. MbCN is dominated by a doming mode near 40 cm(-1), while HRPCN displays a strong oscillation at higher frequency (96 cm(-1)) that can be correlated with the saddling distortion observed in the X-ray structure. In contrast, CgbCN displays low-frequency coherence spectra that contain strong modes near 30 and 80 cm(-1), probably associated with a combination of heme doming and ruffling. HRPNO displays a strong doming mode near 40 cm(-1) that is activated by photolysis. The damping of the coherent motions is significantly reduced when the heme is shielded from solvent fluctuations by the protein material and reduced still further when T approximately < 50 K, as pure dephasing processes due to the protein-solvent phonon bath are frozen out.

Looking for high‐energy density compounds among hexaazaadamantane derivatives with CN, NC, and ONO2 groups

AbstractDensity functional theory (DFT) was employed to evaluate the heats of formation (HOFs) for hexaazaadamantane (HAA) derivatives with CN, NC, and ONO2 groups, respectively. This was done by designing isodesmic reactions at the B3LYP/6‐31G* level of theory, where the HAA cage skeletons were kept unbroken to produce more accurate results, and all HOFs for the required reference compounds, NH2CN, NH2NC, NH2ONO2, and (CH2NH)3, were derived from the G3 theory calculation based on the atomization energies. The calculation results show that the HOFs of HAA derivatives are mainly affected by the number and the position of substituent groups, all the obtained HOFs are positive, and the NC derivatives have the most HOFs among the three types of derivatives with the same number of substituent groups. The detonation velocity (D) and detonation pressure (P) were obtained from the empirical Kamlet–Jacobs equations. All the NC and CN derivatives of HAA have lower densities (ρ), heats of explosion (Q), D, and P. However, these properties of ONO2 derivatives are rather high and vary with the number of ONO2 groups. Considering the easiness for synthesis and relative stability, 2,4,6,8‐hexaazaadamantanenitrate is finally recommended as a potential candidate of a high‐energy density compound (HEDC). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Density functional calculations on dissociation reactions of radical anions of 5-fluorouracil derivatives

Fragmentation reactions upon electron attachment to 5-fluorouracil with CH2R substituents at N1 have been evaluated by means of density functional calculations. The present results show that electron attachment to R = F, HC=O or CN derivatives follows a stepwise pathway with radical anions as intermediates. For these compounds, the most stable species formed is the pi radical anion which bears an unpaired spin density at the C6=C5-C4=O pi-conjugated system of the uracil ring. Cleavage of the N1-CH2R or N1CH2-R bond of these intermediates proceeds through the mixing of the pi and sigma states by means of proper geometrical fluctuations along the reaction coordinate. No sigma radical anion could be characterised on any of these sigma basal potential surfaces. A noticeable decrease in the activation energy for the N1-CH2R bond dissociation was observed for R = H-C=O or CN. Therefore, such derivatives with unsaturated groups positioned vicinal to the N1-C1' bond are identified as targets for the development of novel radiation-activated antitumour drugs. On the other hand, the electron transfer to the compounds with R = Cl, Br is dissociative, i.e. it occurs without the mediation of radical anions. For compounds with R = halides or R = NO2, the fragmentation of the N1CH2-R bond is the preferred dissociation pathway.

Binding sites of nitrogenase: kinetic and theoretical studies of cyanide binding to extracted FeMo-cofactor derivatives.

The first kinetic study of a substrate (CN(-)) binding to the isolated active site (extracted FeMo-cofactor) of nitrogenase is described. The kinetics of the reactions between CN(-) and various derivatives of extracted FeMo-cofactor [FeMoco-L; where L is bound to Mo, and is NMF, Bu(t)NC, or imidazole (ImH)] have been followed using a stopped-flow, sequential-mix method in which the course of the reaction is followed indirectly, by monitoring the change in the rate of the reaction of the cofactor with PhS(-). The kinetic results, together with DFT calculations, indicate that the initial site of CN(-) binding to FeMoco-L is controlled by a combination of the electron-richness of the cluster core and lability of the Mo-L bond. Ultimately, the reactions between FeMoco-L and CN(-) involve displacement of L and binding of CN(-) to Mo. These reactions occur with a variety of rates and rate laws dependent on the nature of L. For FeMoco-NMF, the reaction with CN(-) is complete within the dead-time of the apparatus (ca. 4 ms), while with FeMoco-CNBu(t) the reaction is much slower and exhibits first order dependences on the concentrations of both FeMoco-CNBu(t) and CN(-) (k = 2.5 +/- 0.5 x 10(4) dm(3) mol(-1) s(-1)). The reaction of FeMoco-ImH with CN(-) occurs at a rate which exhibits a first order dependence on FeMoco-ImH but is independent of the concentration of CN(-) (k = 50 +/- 10 s(-1)). The results are interpreted in terms of CN(-) binding directly to the Mo site for FeMoco-NMF and FeMoco-ImH, but with FeMoco-CNBu(t) initial binding at an Fe site is followed by movement of CN(-) to Mo. Complementary DFT calculations are consistent with this interpretation, indicating that, in FeMoco-L, the Mo-L bond is stronger for L = ImH than for L = CNBu(t) and the binding of CN(-) to Mo is stronger than to any Fe atom in the cofactor.

Regioselective Radical Ring‐Opening Reaction of Bicyclo[4.2.0]octan‐2‐ones Promoted by Samarium(II) Iodide.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Regioselective radical ring-opening reaction of bicyclo[4.2.0]octan-2-ones promoted by samarium(II) iodide

Radical ring-opening reactions of bicyclo[4.2.0]octanones, its C6 alkyl derivatives, and tricyclic ketones promoted by SmI 2 gave cyclohexanones via fission of the external cyclobutane bond. The CO 2Me, CN, and phenyl derivatives led to the production of the eight-membered ring compounds through cleavage of the central cyclobutane bond. Using this regioselective reaction, the synthesis of (±)-acorenone was achieved.

A novel type of banana liquid crystals based on 1-substituted naphthalene-2,7-diol cores

The effect of lateral 1-substitution in naphthalene-2,7-diol with CH3, CN and Cl on mesomorphic properties is studied. DSC and X-ray diffraction, texture observation and dielectric measurements have been performed. For the non-substituted core the high-temperature BX phase and the B4 phase occur while in CH3 and Cl substituted compounds the B2 phases are found. In the CN derivatives, besides the crystalline-like phase N, the phase transition between the chiral B2 and racemic B2 phases is observed.

Unusual activation of 1-ethynyl-1-cyclohexanol by [RuCl(η5-C9H7)(PPh3)2]: synthesis and reactivity of the allenylidene derivative [Ru{CCC(C13H20)}(η5-C9H7)(PPh3)2][PF6

The reaction of [RuCl(η5-C9H7)(PPh3)2] with an excess of 1-ethynyl-1-cyclohexanol and NaPF6 in refluxing methanol yielded the allenylidene complex [Ru{CCC(C13H20)}(η5-C9H7)(PPh3)2][PF6] 1 via an unprecedented coupling of two molecules of the propargyl (prop-2-ynyl) alcohol derivative. Complex 1 can also be obtained by reaction of the vinylvinylidene derivative [Ru{CC(H)R}(η5-C9H7)(PPh3)2][PF6] 2 (R = 1-cyclohexenyl) with 1-ethynyl-1-cyclohexanol or 1-ethynylcyclohexene in refluxing methanol. The behaviour of 2 towards other 1-alkyn-3-ols has been studied but only the replacement of the vinylidene moiety by the propargyl alcohols, via an η1-vinylidene–η2-alkyne tautomerization process, to generate both vinylvinylidene [Ru{CC(H)R}(η5-C9H7)(PPh3)2][PF6] (R = 1-cyclopentenyl, 1-cycloheptenyl or 1-cyclooctenyl) or allenylidene [Ru(CCCR2)(η5-C9H7)(PPh3)2][PF6] (R = Ph or R2 = 2,2′-biphenyldiyl) complexes along with 1-ethynylcyclohexene was observed. A similar 1,3-enyne elimination also takes place in the reaction of 2 with phenylacetylene or acetonitrile to afford [Ru{CC(H)Ph}(η5-C9H7)(PPh3)2][PF6] and [Ru(NCMe)(η5-C9H7)(PPh3)2][PF6], respectively. On the basis of these observations a mechanism for the formation of 1 is proposed. The allenylidene complex 1 regioselectively reacts with NaR, in THF at –20 °C, to yield the neutral σ-alkynyl derivatives [Ru{CCC(C13H20)R}(η5-C9H7)(PPh3)2] (R = CN or OMe). Protonation of the R = CN derivative with HBF4·Et2O, in diethyl ether at –20 °C, afforded the cationic vinylidene complex [Ru{CC(H)C(C13H20)CN}(η5-C9H7)(PPh3)2][BF4]. In contrast, protonation with R = OMe gives back the starting allenylidene derivative 1.

Ruthenium complexes with bridging functionalized alkylidene ligands. Synthesis of [Ru 2CP 2(CO) 2(μ-CO){μ-C(X)N(Me)CH 2Ph}] (X = H, CN) and molecular structure of the CN derivative

The isocyanide complex [RU 2CP 2(CO) 3(CNCH 2Ph)], obtained by the reaction of [RU 2CP 2(CO) 4] with CNCH 2Ph in the presence of Me 3NO, has been N-alkylated, yielding the cationic μ-alkylidyne complex [Ru 2CP 2(CO) 3{μ-CN(Me)CH 2Ph}]SO 3CF 3. The compound yielded undergoes nueleophilic addition using NaBH 4 or NaBu 4CN at the μ-C alkylidyne carbon to give the novel μ-aminoalkylidene complexes [Ru 2Cp 2(CO){μ-C(X)N(Me)CH 2Ph}] (X = H, CN). The derivative with X = CN adopts the expected geometry and an idealized C s symmetry if the phenyl substituent is ignored. The relevant bond distances are as follows: RuRu, 2.711(1) Å; Ru-μ-C(carbene), 2.090(4) Å (ave.); C(carbene)-N, 1.477(5) Å; N-C(alkyl), 1.474(5) Å (ave.).

Photoinduced formation and reaction of benzalaniline radical anions: comparison with the radiation-induced reaction

Photoirradiation of benzalaniline ( 1) and its derivatives in a tetrahydrofuran (THF) solution yielded a THF adduct regioselectively. The reaction efficiency is strongly dependent on the substituent of both benzene rings, and photoexcitation of the intramolecular charge transfer (CT) band is effective for the product formation. In the case of the 4′-CN derivative, this reaction appears to proceed via the radical anion, the transient absorption of which was clearly observed upon the irradiation of a 2-methyltetrahydrofuran matrix at 77 K. Thus the CT excited state may be quenched by THF to form the radical anion of 1. The following reaction of the radical anion was also studied by γ-ray irradiation and pulse radiolysis techniques, and a regioselective protonation at a nitrogen atom of 1 − was observed.

Synthesis, electrochemistry, and kinetic investigations of low-spin ferrous bis(difluoroboryl)bis(dioximate) complexes

The synthesis of new trans-Fe(dioxBF 2 ) 2 (CH 3 CN) 2 complexes (diox=dimethylglyoximate, naphthoquinone dioximate, benzoquinone dioximate) complexes and their conversion to a variety of Fe(dioxBF 2 ) 2 TL complexes (T or L=acetonitrile, 1-methylimidazole, pyridine, tributyl phosphite, tributylphosphine, tert-butyl isocyanide, tosylmethyl ioscyanide, carbon monoxide) is described. Kinetic and equilibrium data for the CH 3 CN derivatives obtained by spectrophotometric and flash-photolysis methods in acetonitrile solution and in toluene are compared with data for other FeN 4 systems

Isolation, structure, and magnetic properties of a novel mononuclear rhodium(II) complex

Our current research interests is the coordination chemistry of solvated polynuclear metal cations, especially the recently reported rhodium(II,II) complex, (Rh{sub 2}(CH{sub 3}CH){sub 4})(F{sub 4}){sub 4}. In order to circumvent the problems associated with preparing and handling aqua species, we have developed a convenient synthesis for the CH{sub 3}CN derivative of RH{sub 2} (vide supra), a compound that allows easy access to other monomeric and polynuclear compounds of Rh(II). We now also report the synthesis of a pseudo-octahedral rhodium(II) monomer stabilized only by two bulky phosphine ligands.

Model compounds of aromatic nylons. 3. The conformation of the 4T Nylon, poly(tetramethylene terephthalamide), using X-ray diffraction, solid-state 13C nmr spectroscopy and ir spectroscopy

Three model compounds of poly(tetramethylene terephthalamide) or 4T Nylon have been synthesized and characterized using single crystal X-ray diffractometry, infrared spectroscopy, and 13CCP/MAS nmr spectroscopy. The model compounds are the para-substituted N,N′-tetramethylene dibenzamides, where the substituents are the—OMe, —tBu, —CN, and —CH3 groups. The crystal structure determinations reveal three distinct conformations for the CO—NH—(CH2)4—NH—CO sequence of atoms. The conformation is all trans for OMe, tgtttg−t for the tBu substituent, and tsttts−t for the CN substituent ([Formula: see text], [Formula: see text], and [Formula: see text]). In all three derivatives, the dihedral angle between the aromatic ring and the amide plane is around 30°. The OMe and tBu para-substituted molecules are interconnected by nearly linear hydrogen bonds of normal N … O distances. However, for the CN derivative the N … O distance is exceptionally short, 2.402(4) Å. On the basis of its infrared and solid state nmr spectra, it is proposed that N,N′-tetramethylene di-para-methyl benzamide has a crystal structure comparable to that of its unsubstituted analog. The methylenic sequence of the parent polyamide, 4T Nylon, has the tgtttg−t conformation. Furthermore, the polyamide chains form sheets within which the chains, parallel to one another, are connected through hydrogen bonds. Keywords: polyamide, crystal structure, solid-state nmr.

Hydrophobic properties of anticonvulsant phenylacetanilides. Relationship between octanol-water partition coefficient and capacity factor determined by reversed-phase liquid chromatography.

Partition coefficients (octanol-water), P. for a series of phenylacetanilides, PhCH2CONHC6H4-Xm, p (I), were determined by the shaking-flask method. The observed π values (π=log P(I)-log ρphCH2CONHPh) were analyzed in terms of substituent effects to give the relationship π=0.833πx+0.788σx+0.040, where πx=logphx-logphH. We also determined and analyzed the capacity factors for these compounds, K', which are regarded as an alternative hydrophobic parameter, by using reversed-phase high-performance liquid chromatography (RP-HPLC) in different H2O-organic solvent mixtures. It was observed that the substituent effects on the log κ' value are influenced by the organic modifier in the mobile phase. Linear relationships between log P and log κ' were generally observed but there were some outliers such as OH, CN and NO2 derivatives. The deviation of phenolic compounds from the log ρ-log κ' linearity can be explained in terms of the difference in partitioning behavior between the octanol-water system and the lipophilic stationary phase-mobile phase system.

ChemInform Abstract: STRUCTURES OF THE GAUCHE CONFORMERS OF SOME SUBSTITUTED DIMETHYL ETHERS. EFFECT OF ADJACENT ATOM LONE PAIRS ON METHYL GROUP ASYMMETRY

Abstract The complete equilibrium structures of CH 3 OCH 3 and of the gauche conformers of CH 3 0CH 2 F, HOCH,F, CH,OCH,Cl and CH,OCH,CN have been determined by ab initio gradient computation at the Hartree-Fock, double zeta-plus-polarization level. The very large asymmetries in CH bond distances previously reported from microwave substitution structures are shown to be non-existent in the equilibrium structures and are presumably artifacts. Small differences, different in direction from those reported from the experiments and nearly an order of magnitude smaller in size, do exist. They reflect three factors: (1) a lengthening of a CH bond which is trans to a lone pair on an adjacent atom, (2) a general shortening of CH bonds originating at a carbon atom bearing a highly electronegative substituent, and (3) a specific interaction in which a CX substituent shortens the nearly parallel CH bond on the other methyl group. The last interaction, not previously reported, is mediated by withdrawal of electron density from the oxygen lone pair which is trans to both groups. Other structural features derived from the microwave studies are supported by the new results. Inclusion of polarization functions in the basis set for oxygen is essential for correct determination of the COC angle and the dihedral angles. The dihedral angles of CH 3 OCH 2 F and HOCH 2 F are not correctly determined by the computation even at this level, although the computed values are improved when d functions are used for oxygen and still more by use of two sets of oxygen d functions. Polarization functions on carbon or on fluorine have no effect on the computed torsional angles. There is no problem in computing the correct dihedral angles with the CI or CN derivatives.

Structures of the gauche conformers of some substituted dimethyl ethers. Effect of adjacent atom lone pairs on methyl group asymmetry

The complete equilibrium structures of CH 3OCH 3 and of the gauche conformers of CH 3OCH 2F, HOCH 2F, CH 3OCH 2Cl and H 3OCH 2CN have been determined by ab initio gradient computation at the Hartree—Fock, double zeta-plus-polarization level. The very large asymmetries in CH bond distances previously reported from microwave substitution structures are shown to be non-existent in the equilibrium structures and are presumably artifacts. Small differences, different in direction from those reported from the experiments and nearly an order of magnitude smaller in size, do exist. They reflect three factors: (1) a lengthening of a CH bond which is trans to a lone pair on an adjacent atom, (2) a general shortening of CH bonds originating at a carbon atom bearing a highly electronegative substituent, and (3) a specific interaction in which a CX substituent shortens the nearly parallel CH bond on the other methyl group. The last interaction, not previously reported, is mediated by withdrawal of electron density from the oxygen lone pair which is trans to both groups. Other structural features derived from the microwave studies are supported by the new results. p ]Inclusion of polarization functions in the basis set for oxygen is essential for correct determination of the COC angle and the dihedral angles. The dihedral angles of CH 3OCH 2F and HOCH 2F are not correctly determined by the computation even at this level, although the computed values are improved when d functions are used for oxygen and still more by use of two sets of oxygen d functions. Polarization functions on carbon or on fluorine have no effect on the computed torsional angles. There is no problem in computing the correct dihedral angles with the Cl or CN derivatives.

Structures of the gauche conformers of somE substituted dimethyl ethers. Effect of adjacent atom lone pairs on methyl group asymmetry

The complete equilibrium structures of CH 3OCH 3 and of the gauche conformers of CH 30CH 2F, HOCH,F, CH,OCH,Cl and CH,OCH,CN have been determined by ab initio gradient computation at the Hartree-Fock, double zeta-plus-polarization level. The very large asymmetries in CH bond distances previously reported from microwave substitution structures are shown to be non-existent in the equilibrium structures and are presumably artifacts. Small differences, different in direction from those reported from the experiments and nearly an order of magnitude smaller in size, do exist. They reflect three factors: (1) a lengthening of a CH bond which is trans to a lone pair on an adjacent atom, (2) a general shortening of CH bonds originating at a carbon atom bearing a highly electronegative substituent, and (3) a specific interaction in which a CX substituent shortens the nearly parallel CH bond on the other methyl group. The last interaction, not previously reported, is mediated by withdrawal of electron density from the oxygen lone pair which is trans to both groups. Other structural features derived from the microwave studies are supported by the new results. Inclusion of polarization functions in the basis set for oxygen is essential for correct determination of the COC angle and the dihedral angles. The dihedral angles of CH 3OCH 2F and HOCH 2F are not correctly determined by the computation even at this level, although the computed values are improved when d functions are used for oxygen and still more by use of two sets of oxygen d functions. Polarization functions on carbon or on fluorine have no effect on the computed torsional angles. There is no problem in computing the correct dihedral angles with the CI or CN derivatives.

Absorption spectra of hematin complexes with polyhistidine and copoly-(histidine, glutamic acid)

The absorption spectra of heme and hematin complexes with poly- l-histidine and copoly-( l-histidine, l-glutamic acid) as well as their COand CNderivatives were observed as a function of pH. The spectral characteristics of both heme and hematin complexes formed on polyhistidine were similar to those of the reduced and the oxidized forms of cytochrome c or the complex with free histidine, respectively, indicating that these complexes carry two histidine residues. On the other hand, the spectrum of the hematin complex with the copolymer in a low histidine content at pH 6.2 was similar to the spectrum of methemoglobin or horse-radish peroxidase. The reduction of this complex gives a single visible peak, being in contrast with the typical double peaks of hemochromogen. It was concluded from these results that the complex at pH 6.2 carries one histidine residue and the remaining co-ordinate position is occupied by a water molecule or a glutamic carboxyl group. When the pH of the hematin-copolymer solution was raised to 7.2, the monohistidyl type of spectrum changed to the dihistidyl type. This spectral change was interpreted as due to the transition of the copolymer from the helical to the random structure. The spectrum of the yellow-green complex with the copolymer at alkaline pH was discussed with the results obtained with free lysine and N,N-dimethylformamide as well as those reported previously for the complexes with polylysine. The affinity of polyhistidine and the copolymer with hematin was found to be much greater than that of free histidine.

X‐ray investigation of d‐α‐Br, Cl and CN‐camphor . A direct determination of a molecular structure by comparison of isomorphous crystal structures

AbstractThe structure of the camphor molecule was determined by comparison of the X‐ray diagrams of the isomorphous α‐Br, Cl and CN derivatives. This rather general procedure, avoiding the usual difficulty of Fourier synthesis by a direct determination of the signs of the Fourier components, is described in the introduction of part I. The structure thus found has been checked in part II by comparison of calculated and observed intensities.