NH Sites Research Articles

Inside Cover: Watching Water Migration around a Peptide Bond (Angew. Chem. Int. Ed. 27/2012)

The motion of a single water ligand around a peptide bond in acetanilide was probed in real time by time-resolved IR spectroscopy. In their Communication on page 6604 ff., O. Dopfer, M. Fujii et al. observe that triggered by photo-ionization, the H2O ligand is released from the CO site of the peptide linkage and trapped after a migration time of 5 ps at the NH site of the same peptide bond. The migration occurs via an intermediate in which the H2O molecule binds neither to the CO nor the NH site.

Watching Water Migration around a Peptide Bond

A long and winding road: The motion of a single water ligand around a peptide bond in acetanilide was probed in real time by time-resolved IR spectroscopy. Triggered by photoionization, the H2O ligand is released from the CO site of the peptide linkage and trapped after a migration time of 5 ps at the NH site of the same peptide bond (see picture).

An innovative method for the non-destructive identification of photodegradation products in solid state: 1H–14N NMR–NQR and DFT/QTAIM study of photodegradation of nifedipine (anti-hypertensive) to nitrosonifedipine (potential anti-oxidative)

Stability of the antihypertensive drug nifedipine (NIF) has been studied experimentally in solid state by 1H–14N NMR–NQR double resonance (NQDR) and theoretically by the Density Functional Theory (DFT). Photodegradation of NIF to its metabolite in vivo nitrosonifedipine, NO–NIF (antioxidative agent) upon long term daylight exposure was detected and the changes in the molecular structure of NIF were analysed. The photoconversion of NIF to NO–NIF in solid was found to be accompanied with the electron density redistribution at nitrogen sites (NH to N and NO2 to NO) and proved to be successfully detected with identification of photoproducts by 1H–14N NQDR and DFT methods. The increase in the e2qQ/h and η describing EFG tendency towards non-spherical symmetry was significantly greater upon the reduction of NO2 site than upon hydrogen abstraction from NH site. The level of sensitivity of detection of the photodegradation product was about 1% of the original sample. The Quantum Theory of Atoms in Molecules (QTAIM) analysis has been found useful in predicting photoreactive sites in the molecules and finding the explanation of differences in reactivity between parent NIF and its photoproduct NO–NIF. Using NIF as a model, this study demonstrates the suitability of NQDR supported by DFT for non-destructive determination of the photodegradation products in solid state.

Molecular Description of Indigo Oxidation Mechanisms Initiated by OH and OOH Radicals

In this work, we report a quantum chemistry mechanistic study of the hydroxyl (•OH) and hydroperoxyl (•OOH) radicals initiated oxidation of indigo, within the density functional theory framework. All possible hydrogen abstraction and radical addition reaction pathways have been considered. We find that the reaction between a free indigo molecule and an •OH radical occurs mainly through two competing mechanisms: H-abstraction from an NH site and •OH addition to the central C═C double bond. Although the latter is favored, both channels occur, the indigo chromophore group structure is modified, and thus the color is changed. This mechanism adequately accounts for the loss of chromophore in urban air, including indoor air such as in museums and in urban areas. Regarding the reactivity of indigo toward •OOH radicals, only •OOH-addition to the central double bond is thermodynamically feasible. The corresponding transition state free energy value is about 10 kcal/mol larger than the one for the •OH initiated oxidation. Therefore, even considering that the •OOH concentration is considerably larger than the one of •OH, this reaction is not expected to contribute significantly to indigo oxidation under atmospheric conditions.

Tautomeric transformations and reactivity of alloxan

The various tautomers and rotamers of alloxan are investigated in this work. Alloxan has a unique structure: it contains four hydrogen bond acceptor CO and two donor NH sites. This allows it to exhibit various tautomeric forms. The density functional calculations (B3LYP/6-311+G(d,p)) reported in this work indicate that the tetraketo form is the most stable, both in the gas and solution phase, followed by the two monohydroxy forms. We have also studied the mechanism of tautomerization. The charge transfer interactions indicate that the entity that migrates is a proton and not a hydrogen atom. The four-membered ring transition states for the direct processes are highly strained and lead to high activation barriers. However, the involvement of even a single water molecule reduces the barrier to a plausible level. This occurs because of the release of strain due to the formation of six-membered rings, and also due to resonance stabilization. The mechanism also changes to almost a two-step process involving first the extraction of the proton by the nucleophilic attack by water which leads to the formation of the transition state, followed by transfer of one of its own protons by water to the alloxan oxygen. Hydration of alloxan results in stabilization of the molecule, but significantly reduces its electrophilicity. The anions and cations of alloxan are also investigated, as are its spectral characteristics.

ChemInform Abstract: Acyclic Oligopyrrolic Anion Receptors

AbstractReview: 150 refs.

2-( p-Nitrophenylthioureido)-3-aminonaphtho-1,4-quinone as a water tolerant F − anion probe

Title probe favored by cooperative binding of three NH sites and entropy enhancement due to release of water molecules during complex formation with F − ion, selectively detects F − ion, both as TBAF or KF salts in competitive aqueous DMSO (1:9) solution using UV–Vis spectroscopy and visible to naked eye.

Mass-analyzed threshold ionization of deuterium substituted indazole and benzimidazole and site-specific H/D exchange reaction

We have applied the mass-analyzed threshold ionization spectroscopic technique to record the cation spectra of deuterium substituted indazole and benzimidazole. The deuterium substitution causes red shifts in the ionization energies of these aza-aromatic bicyclic molecules by only a few tens wavenumbers. Comparing these data with those of deuterated aniline and indole suggests that the H/D exchange mainly takes place on the NH or CH sites of the five-membered ring.

Polymer complexes: XLXII-interplay of coordination π–π stacking and hydrogen bonding in supramolecular assembly of [sulpha drug derivatives-N,S:N,O] complexes

A novel series of nickel(II) polymer complexes of 5-sulphadiazineazo-3-phenylamino-2-thio-4-thiazolidinone (HL 1), 5-sulphamethazine-3-phenylamino-2-thioxo-4-thiazolidinone (HL 2), 5-sulphamethoxazole-3-phenylamino-2-thioxo-4-thiazolidinone (HL 3), 5-sulphacetamide-3-phenyl-2-thioxo-4-thiazolidinone (HL 4) and 5-sulphaguanidine-3-phenylamino-2-thioxo-4-thiazolidinone (HL 5) were prepared and characterized. IR spectra show that HL n ( n = 1–5) is coordinated to the metal ion in a neutral tetradentate manner with NSNO donor sites of NH (hydrazone's), NH (3-phenylamine), carbonyl group and Ph-NH. The title [Ni 3(HL n ) 2(μ-OAc) 2(OAc) 4] n consists of three Ni(II) atoms linked by interchain π–π interaction are observed between aromatic rings of two ligands (HL n ) which are further doubly bridged two adjacent nickel atoms by acetate group. The geometrical structures of these complexes are found to be octahedral. The nature of bonding and the stereochemistry of the complexes have been deduced from elemental analyses, thermal, infrared, 1H NMR, electronic spectra, magnetic susceptibility and conductivity measurements. The richness of electronic spectral in these complexes is also supporting evidence for the trinuclearity of the Ni(II) polymer complexes.

Adsorption of acid dyes on fungal biomass: Equilibrium and kinetics characterization

Dyes adsorption on granular particles of lyophilised Cunninghamella elegans was characterized in terms of adsorption isotherm and kinetics. The study refers to dyes of an acid bath for wool: Acid Blue 62, Acid Red 266 and Acid Yellow 49. The dye concentration in model solutions – containing a single dye or the three dyes all together in order to mimic the wastewater – was increased up to about 500 mg/L. Tests showed that the maximum adsorption capacity of the biomass ranges between 300 and 600 mg dye/g DM. Mutual interferences among dyes caused the reduction of the adsorption capacity of the biomass towards the model wastewater. An experimental procedure for the assessment of biosorption kinetics was developed in order to control the effects of the interphase mass transfer on the biosorption rate. The biosorption kinetics were described by both pseudo-first order and pseudo-second order models, depending on the saturation level of the sorbent, and was characterized by a time scale of 1–10 min. The role of the molecular structures of the dyes was discussed. In particular, both kinetics and equilibrium tests confirm that the biomass is more selective towards AR266, probably for the high negative charge density of the –CF 3 functional group that can interact with –NH x active sites of the biomass.

Enhancement of activity of Ir catalysts for selective catalytic reduction of NO with CO by physical mixing with SiO 2

The selective catalytic reduction of NO x by CO (CO-SCR) over Ir–Ba/WO 3–SiO 2 was studied. Physical mixing of the Ir catalyst with SiO 2, which is inert for CO-SCR, enhanced NO x conversion, and NO x conversion increased with increasing amounts of SiO 2 in the physical mixture. HNCO was formed over the physical mixture at low oxygen concentrations. The dependence of CO-SCR activity on contact time in 0.5% O 2 suggested that HNCO was an intermediate species. In contrast, Ir catalysts that were not mixed with SiO 2 exhibited only trace amounts of HNCO formation, even at low O 2 concentrations. Temperature-programmed desorption of HNCO from non-mixed and mixed Ir catalysts, which were pretreated in H 2 followed by H 2O, revealed that the former had strong adsorption sites for NH 3 formed by hydrolysis of HNCO, whereas the latter exhibited a smaller amount of these strong adsorption sites. The Ir catalyst showed high NH 3 oxidation capacity under NH 3-SCR conditions. The observed enhancement of CO-SCR activity over the mixed Ir catalyst was suspected to result from the decrease in the number of NH 3 adsorption sites, which may have caused NH 3 to be oxidized to NO.

Spin‐coupling and hyperfine interaction of the nitrogen donors in 6H‐SiC

AbstractThe X‐, Q‐band field‐sweep electron spin echo (FS ESE) study of n‐type 6H‐SiC wafers shows besides the well known hyperfine (hf) triplet lines of14N on two quasi‐cubic (Nc1, Nc2) and hexagonal (Nh) sites additional triplet lines (Nx) of comparatively low intensity with ag‐tensor of about the average value of the Nc2and Nhspectrum at 4.2 K. The Nxtriplet has half of the hf splitting with respect to the nitrogen residing at cubic sites Nc2. Pulsed electron nuclear double resonance (ENDOR) measurements performed on the NxEPR triplet line demonstrate that there is an efficient spin‐coupling between Nhand Nxnitrogen related centers. The Nxtriplet lines were attributed to distant donor Nc–Nhpairs between nitrogen atoms residing at quasi‐cubic and hexagonal sites having a total electron spinS= 1, which were found before in n‐type 4H‐SiC. Based on Q‐band FS ESE and X‐band pulsed ENDOR measurements the values of the hf interaction for Nc1, Nc2were reassigned with respect to the assignment accepted hitherto.The super hyperfine (shf) interaction with neighboring atoms of nitrogen on the quasi‐cubic lattice sites was studied by FS ESE and pulsed ENDOR. The new shf lines due to29Si and13C atoms with large shf interaction which were not observed previously were found in nitrogen FS ESE and ENDOR spectra. One of them, with the largest shf splitting (23.12 MHz), were attributed to the29Si atoms along thec‐axis in nearest‐neighbor positions of nitrogen on the quasi‐cubic sites which unambiguously confirms that nitrogen substitute carbon lattice site in 6H‐SiC. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Modeling the H bond donor strength of OH, NH, and CH sites by local molecular parameters

A quantum chemical model is introduced to predict the H-bond donor strength of monofunctional organic compounds from their ground-state electronic properties. The model covers -OH, -NH, and -CH as H-bond donor sites and was calibrated with experimental values for the Abraham H-bond donor strength parameter A using the ab initio and density functional theory levels HF/6-31G** and B3LYP/6-31G**. Starting with the Morokuma analysis of hydrogen bonding, the electrostatic (ES), polarizability (PL), and charge transfer (CT) components were quantified employing local molecular parameters. With hydrogen net atomic charges calculated from both natural population analysis and the ES potential scheme, the ES term turned out to provide only marginal contributions to the Abraham parameter A, except for weak hydrogen bonds associated with acidic -CH sites. Accordingly, A is governed by PL and CT contributions. The PL component was characterized through a new measure of the local molecular hardness at hydrogen, eta(H), which in turn was quantified through empirically defined site-specific effective donor and acceptor energies, EE(occ) and EE(vac). The latter parameter was also used to address the CT contribution to A. With an initial training set of 77 compounds, HF/6-31G** yielded a squared correlation coefficient, r(2), of 0.91. Essentially identical statistics were achieved for a separate test set of 429 compounds and for the recalibrated model when using all 506 compounds. B3LYP/6-31G** yielded slightly inferior statistics. The discussion includes subset statistics for compounds containing -OH, -NH, and active -CH sites and a nonlinear model extension with slightly improved statistics (r(2) = 0.92).

New Tetrachlorocyclodiphosph(V)azane Complexes of Co(II), Ni(II), and Cu(II): Preparation, Characterization, Solid State Electrical Conductivity, and Biological Activity Studies

Tetrachlorocyclodiphosph(V)azane of thiazole, H2L (1,3-diphenyl -2,4-bis(3-phenyl-2-iminothiazole)-2,2,4,4-tetrachlorocyclodiphos(V)azane, reacts with stoichiometric amounts of transition metal salts such as Co(II), Ni(II), and Cu(II) to afford colored complexes in a moderate to high yield. The structure of the isolated complexes was suggested based on elemental analyses, IR, molar conductance, UV-Vis, 1H and 31P NMR, mass spectra, solid reflectance, magnetic susceptibility measurements and dark electrical conductivity of solid state from room temperature up to 450 k. The data obtained obeyed the relation σ = σ ° exp (−E/2kT) over the temperature range 30–150°C. The observed conductivities of the different complexes follow the order Co < Ni < Cu. It is clear that this trend is depending on the decreasing of the ionic radii and the increasing stability of metal complexes. The calculated mobility of charge carriers is ranged from 10−5 to 10−9 cm2/V s suggesting that the conduction of the studied complexes takes place by hopping mechanism. The solid-state electrical conductivity obtained reveals that the metal complexes behave as semiconducting materials. The powder XRD studies confirm the amorphous nature of the complexes. From the elemental analyses data, 1: 2 (H2L: M) ratio is suggested and the complexes are found to have the general formula [(MX2)2(H2L)(H2O) m ]. nH2O where M = Co(II) (X = SCN, n = 2, m = 0), Ni(II) (X = Cl, n = 4, m = 4), and Cu(II) (X = Cl, n = 2, m = 0). The complexes have been investigated in solution by the spectrophotometric molar ratio and conductometric methods. IR spectra show that the ligand is coordinated to the metal ions in a bidentate manner with NN donor sites of the imine NH and thiazole N. The UV-Vis, solid reflectance, and magnetic-moment data have shown that the ligand is coordinated to the metal ions in an octahedral, tetrahedral, or square planar manner. The molar conductance data show that the complexes are nonelectrolytes. The prepared complexes showed high to moderate bactericidal activity compared with the ligand.

Trans-Bis(1H-indole-3-carbaldehyde thiosemicarbazonato-κ2N1,S)nickel(II)

The Ni atom in the centrosymmetric title compound, [Ni(C10H9N4S)2], is N,S-chelated by the deprotonated Schiff bases in a square-planar geometry. The –CH=N—N=C(S)—NH2 frament is planar. Adjacent mol­ecules are linked by hydrogen bonds between the indolyl –NH (donor) site and the double-bond =N– (acceptor) site of an adjacent mol­ecule, forming a layer motif.

Bis[1,5-bis(1H-indol-3-ylmethylene)thiocarbazonato-κ2N,S]nickel(II) dimethyl sulfoxide disolvate

The Ni atom in the crystal structure of the centrosymmetric title compound, [Ni(C19H15N6S)2]·2C2H6OS, is N,S-chelated by the deprotonated Schiff bases in a square-planar geometry. The –CH=N—N=C(S)—NH—N=CH– frament is planar. The two indolyl –NH (donor) sites inter­act with dimethyl sulfoxide mol­ecules to furnish a layer motif.

Dichloridobis(2-{1-[2-(1H-indol-3-yl)ethyliminio]ethyl}phenolate-κO)zinc(II)–2-{1-[2-(1H-indol-3-yl)ethyliminio]ethyl}phenolate (1/2)

In the mononuclear complex mol­ecule of the title compond, [ZnCl2(C18H18N2O)2]·2C18H18N2O, the Zn atom, which lies on a twofold rotation axis, is coordinated by phenolate O atoms in a tetra­hedral coordination geometry. The coordinated Schiff base uses its indole NH donor site to form a hydrogen bond to the negatively charged phenolate O atom of the uncoordinated zwitterionic Schiff base. There is an intra­molecular N—H⋯O hydrogen bond in the coordinated and uncoordinated Schiff bases. The indole NH site of the uncoordinated Schiff base does not engage in a hydrogen-bond inter­action. The CH2—CH2 group in the uncoordinated Schiff base is disordered equally over two positions.

Trends of nitrogen in air and precipitation: Model results and observations at EMEP sites in Europe, 1980–2003

We analyze trends of some nitrogen compounds using long-term measurements and results from the EMEP (co-operative programme for monitoring and evaluation of the long-range transmissions of air pollutants in Europe) chemical transport model at EMEP sites. We find statistically significant declines at the majority of sites for NH x (sum of ammonia and ammonium) in air and for nitrate and ammonium in precipitation, but only at a few sites for xNO 3 (sum of nitrate and nitric acid) in air. Model calculations and measurements give similar results. We demonstrate that the lack of trends for xNO 3 in air at least partly can be attributed to a shift in the equilibrium between nitric acid and ammonium nitrate towards particulate phase, caused by reductions in the sulfur dioxide emissions.

A study of chemical aging effects on HDD Fe–zeolite SCR catalyst

The effect of phosphorus (P) on iron (Fe)–zeolite based selective catalytic reduction (SCR) monolith catalysts was studied in the absence and the presence of sulfur, and at two different exposure temperatures (220 and 450 °C). It was found that exposure of Fe–zeolite SCR catalyst to P resulted in a loss of NOx conversion and an increase of NH 3 slip relative to a degreened baseline sample. Some of the increased slip was attributed to a loss of NH 3 storage capacity due to P blockage of adsorption sites. Additional increased slip resulted from a rise in the slip to storage ratio, likely due to a shorter effective channel length for NH 3 adsorption since most of the P blocked sites at the sample inlet. DeNOx activity was then reduced due to the decreased amount of adsorbed NH 3. P exposure using zero sulfur fuel resulted in the same amount of deactivation as aging done using low sulfur (350 ppm S) fuel, suggesting that this amount of S did not affect this formulation. An initial loss of activity proved to be due to hydrocarbon exposure, and was reversible simply by ramping the sample up in temperature during the evaluation test. Increasing the exposure temperatures also increased the loss of DeNOx performance. It is proposed that P impacts these catalysts by physically blocking adsorption sites for NH 3, primarily at the monolith channel inlet.

Branching Ratios of Aliphatic Amines + OH Gas-Phase Reactions: A Variational Transition-State Theory Study.

A theoretical study on the mechanism of the OH + aliphatic amines reactions is presented. Geometry optimization and frequencies calculations have been performed at the BHandHLYP/6-311++G(2d,2p) level of theory for all stationary points. Energy values have been improved by single-point calculations at the above geometries using CCSD(T) and the same basis set. All the possible hydrogen abstraction channels have been modeled, involving the rupture of C-H and N-H bonds. It was found that as the temperature decreases the contributions of the channels involving NH sites to the overall reaction also decrease, suggesting that for upper layers in the troposphere these channels become less important. Their percentage contributions to the overall reaction, at 298 K, were found to be about 20%, 2%, and 48% for methylamine, ethlylamine, and dimethylamine, respectively.