Potential functions for hydrogen bond interactions - III. Empirical Potential Function for the Peptide N-H...O=C Hydrogen Bond

A careful comparison of the distribution in the (R, θ)-plane of all NH ... O hydrogen bonds with that for bonds between neutral NH and neutral C=O groups indicated that the latter has a larger mean R and a wider range of θ and that the distribution was also broader than for the average case. Therefore, the potential function developed earlier for an average NH ... O hydrogen bond was modified to suit the peptide case. A three-parameter expression of the form {Mathematical expression}, with △ = R - Rmin, was found to be satisfactory. By comparing the theoretically expected distribution in R and θ with observed data (although limited), the best values were found to be p1 = 25, p3 = - 2 and q1 = 1 × 10-3, with Rmin = 2·95 Å and Vmin = - 4·5 kcal/mole. The procedure for obtaining a smooth transition from Vhb to the non-bonded potential Vnb for large R and θ is described, along with a flow chart useful for programming the formulae. Calculated values of ΔH, the enthalpy of formation of the hydrogen bond, using this function are in reasonable agreement with observation. When the atoms involved in the hydrogen bond occur in a five-membered ring as in the sequence[Figure not available: see fulltext.] a different formula for the potential function is needed, which is of the form Vhb = Vmin +p1△2 +q1x2 where x = θ - 50° for θ ≥ 50°, with p1 = 15, q1 = 0·002, Rmin = 2· Å and Vmin = - 2·5 kcal/mole. © 1971 Indian Academy of Sciences.

Is a CImage C quadruple bond possible?

Ab initio computations Predict a minimum for a carbon-carbon quadruple bond in C2. While the computed C-C separation, 1.128 angstrom, fits Pauling's bond order-bond length relationship well, this result is an artifact of the restricted Hartree Fock theory.

B-H Bond Activation Using an Electrophilic Metal Complex: Insights into the Reaction Pathway

A highly electrophilic ruthenium center in the RuCl(dppe)(2)]OTf] complex brings about the activation of the B H bond in ammonia borane (H3N center dot BH3, AB) and dimethylamine borane (Me2HN center dot BH3, DMAB). At room temperature, the reaction between RuCl(dppe)(2)]OTf] and AB or DMAB results in trans-RuH(eta(2)-H-2)(dppe)(2)]OTf] trans-RuCl(eta(2)-H-2)(dppe)(2)]OTf], and trans-RuH(Cl)(dppe)(2)], as noted in the NMR spectra. Mixing the ruthenium complex and AB or DMAB at low temperature (198/193 K) followed by NMR spectral measurements as the reaction mixture was warmed up to room temperature allowed the observation of various species formed enroute to the final products that were obtained at room temperature. On the basis of the variable-temperature multinuclear NMR spectroscopic studies of these two reactions, the mechanistic insights for B-H bond activation were obtained. In both cases, the reaction proceeds via an eta(1)-B-H moiety bound to the metal center. The detailed mechanistic pathways of these two reactions as studied by NMR spectroscopy are described.

Engagement of CF3 Group in N-H center dot center dot center dot F-C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies

Unambiguous evidence for the engagement of CF3 group in N-H center dot center dot center dot F-C hydrogen bond in a low polarity solvent, the first observation of its kind, is reported. The presence of such weak molecular interactions in the solution state is convincingly established by one and two-dimensional H-1, F-19, and natural abundant N-15 NMR spectroscopic studies. The strong and direct evidence is derived by the observation of through-space couplings, such as, (1h)J(FH), (1h)J(FN), and (2h)J(FF), where the spin polarization is transmitted through hydrogen bond. In an interesting example of a molecule containing two CF3 groups getting simultaneously involved in hydrogen bond, where hydrogen bond mediated couplings are not reflected in the NMR spectrum, F-19-F-19 NOESY experiment yielded confirmatory evidence. Significant deviations in the strengths of (1)J(NH), variable temperature, and the solvent induced perturbations yielded additional support. The NMR results are corroborated by both DFT calculations and MD simulations, where the quantitative information on different ways of involvement of fluorine in two and three centered hydrogen bonds, their percentage of occurrences, and geometries have been obtained. The hydrogen bond interaction energies have also been calculated.

Regioselective Thiolation of Arenes and Heteroarenes: C-H Functionalization Strategy for C-S Bond Formation

A facile transition-metal-free oxidative cross-dehydrogenative coupling reaction involving selective formation of a C-S bond leading to the synthesis of arylthiobenzoxazoles, heteroarylthiobenzoxazoles, and arylthiobenzothiazoles has been described. This highly regioselective C-H functionalization reaction with electron-rich aromatic systems including heteroaromatics is achieved by reversing the reactivity of sulfur in the presence of a suitable oxidant and strong acid.

Design, Synthesis, and Study of Novel Platforms for Iron-N2 Chemistry and Photoinduced, Copper-mediated C-N Bond Formation

Several new ligand platforms designed to support iron dinitrogen chemistry have been developed. First, we report Fe complexes of a tris(phosphino)alkyl (CP^iPr₃) ligand featuring an axial carbon donor intended to conceptually model the interstitial carbide atom of the nitrogenase iron-molybdenum cofactor (FeMoco). It is established that in this scaffold, the iron center binds dinitrogen trans to the C_alkyl anchor in three structurally characterized oxidation states. Fe-C_alkyl lengthening is observed upon reduction, reflective of significant ionic character in the Fe-C_alkyl interaction. The anionic (CP^iPr₃)FeN₂^- species can be functionalized by a silyl electrophile to generate (CP^iPr₃)Fe-N₂SiR₃. This species also functions as a modest catalyst for the reduction of N₂ to NH₃. Next, we introduce a new binucleating ligand scaffold that supports an Fe(μ-SAr)Fe diiron subunit that coordinates dinitrogen (N₂-Fe(μ-SAr)Fe-N₂) across at least three oxidation states (Fe^IIFe^II, Fe^IIFe^I, and Fe^IFe^I). Despite the sulfur-rich coordination environment of iron in FeMoco, synthetic examples of transition metal model complexes that bind N₂ and also feature sulfur donor ligands remain scarce; these complexes thus represent an unusual series of low-valent diiron complexes featuring thiolate and dinitrogen ligands. The (N₂-Fe(μ-SAr)Fe-N₂) system undergoes reduction of the bound N₂ to produce NH₃ (~50% yield) and can efficiently catalyze the disproportionation of N₂H₄ to NH₃ and N₂. The present scaffold also supports dinitrogen binding concomitant with hydride as a co-ligand. Next, inspired by the importance of secondary-sphere interactions in many metalloenzymes, we present complexes of iron in two new ligand scaffolds ([SiP^NMe₃] and [SiP^iPr₂P^NMe]) that incorporate hydrogen-bond acceptors (tertiary amines) which engage in interactions with nitrogenous substrates bound to the iron center (NH₃ and N₂H₄). Cation binding is also facilitated in anionic Fe(0)-N₂ complexes. While Fe-N₂ complexes of a related ligand ([SiP^iPr₃]) lacking hydrogen-bond acceptors produce a substantial amount of ammonia when treated with acid and reductant, the presence of the pendant amines instead facilitates the formation of metal hydride species.

Additionally, we present the development and mechanistic study of copper-mediated and copper-catalyzed photoinduced C-N bond forming reactions. Irradiation of a copper-amido complex, ((m-tol)₃P)₂Cu(carbazolide), in the presence of aryl halides furnishes N-phenylcarbazole under mild conditions. The mechanism likely proceeds via single-electron transfer from an excited state of the copper complex to the aryl halide, generating an aryl radical. An array of experimental data are consistent with a radical intermediate, including a cyclization/stereochemical investigation and a reactivity study, providing the first substantial experimental support for the viability of a radical pathway for Ullmann C-N bond formation. The copper complex can also be used as a precatalyst for Ullmann C-N couplings. We also disclose further study of catalytic C_alkyl-N couplings using a CuI precatalyst, and discuss the likely role of [Cu(carbazolide)₂]^- and [Cu(carbazolide)₃]^- species as intermediates in these reactions.

Finally, we report a series of four-coordinate, pseudotetrahedral P₃Fe^II-X complexes supported by tris(phosphine)borate ([PhBP₃Fe^R]^-) and phosphiniminato X-type ligands (-N=PR'₃) that in combination tune the spin-crossover behavior of the system. Low-coordinate transition metal complexes such as these that undergo reversible spin-crossover remain rare, and the spin equilibria of these systems have been studied in detail by a suite of spectroscopic techniques.

An Efficient Ullmann-Type C-O Bond Formation Catalyzed by an Air-Stable Copper(I)-Bipyridyl Complex

An efficient O-arylation of phenols and aliphatic alcohols with aryl halides was developed that uses an air-stable copper(I) complex as the catalyst. This arylation reaction can be performed in good yield in the absence of Cs2CO3. A variety of functional groups are compatible with these reaction conditions with low catalyst loading levels.

General rules for predicting where a catalytic reaction should occur on metal surfaces: A density functional theory study of C-H and C-O bond breaking/making on flat, stepped, and kinked metal surfaces

To predict where a catalytic reaction should occur is a fundamental issue scientifically. Technologically, it is also important because it can facilitate the catalyst's design. However, to date, the understanding of this issue is rather limited. In this work, two types of reactions, CH4 CH3 + H and CO C + 0 on two transition metal surfaces, were chosen as model systems aiming to address in general where a catalytic reaction should occur. The dissociations of CH4 - CH3 + H and CO --> C + O and their reverse reactions on flat, stepped, and kinked Rh and Pd surfaces were studied in detail. We find the following: First, for the CH4 Ch(3) + H reaction, the dissociation barrier is reduced by similar to0.3 eV on steps and kinks as compared to that on flat surfaces. On the other hand, there is essentially no difference in barrier for the association reaction of CH3 + H on the flat surfaces and the defects. Second, for the CO C + 0 reaction, the dissociation barrier decreases dramatically (more than 0.8 eV on Rh and Pd) on steps and kinks as compared to that on flat surfaces. In contrast to the CH3 + H reaction, the C + 0 association reaction also preferentially occurs on steps and kinks. We also present a detailed analysis of the reaction barriers in which each barrier is decomposed quantitatively into a local electronic effect and a geometrical effect. Our DFT calculations show that surface defects such as steps and kinks can largely facilitate bond breaking, while whether the surface defects could promote bond formation depends on the individual reaction as well as the particular metal. The physical origin of these trends is identified and discussed. On the basis of our results, we arrive at some simple rules with respect to where a reaction should occur: (i) defects such as steps are always favored for dissociation reactions as compared to flat surfaces; and (ii) the reaction site of the association reactions is largely related to the magnitude of the bonding competition effect, which is determined by the reactant and metal valency. Reactions with high valency reactants are more likely to occur on defects (more structure-sensitive), as compared to reactions with low valency reactants. Moreover, the reactions on late transition metals are more likely to proceed on defects than those on the early transition metals.

Trends in C-O and C-N bond formations over transition metal surfaces: An insight into kinetic sensitivity in catalytic reactions

Transition metal catalyzed bond formation is a fundamental process in catalysis and is of general interest throughout chemistry. To date, however, the knowledge of association reactions is rather limited, relative to what is known about dissociative processes. For example, surprisingly little is known about how the bond-forming ability of a metal, in general, varies across the Periodic Table. In particular, the effect of reactant valency on such trends is poorly understood. Herein, the authors examine these key issues by using density functional theory calculations to study CO and CN formations over the 4d metals. The calculations reveal that the chemistries differ in a fundamental way. In the case of CO formation, the reaction enthalpies span a much greater range than those of CN formation. Moreover, CO formation is found to be kinetically sensitive to the metal; here the reaction barriers (E-a) are found to be influenced by the reaction enthalpy. CN formation, conversely, is found to be relatively kinetically insensitive to the metal, and there is no correlation found between the reaction barriers and the reaction enthalpy. Analysis has shown that at the final adsorbed state, the interaction between N and the surface is relatively greater than that of O. Furthermore, in comparison with O, relatively less bonding between the surface and N is observed to be lost during transition state formation. These greater interactions between N and the surface, which can be related to the larger valency of N, are found to be responsible for the relatively smaller enthalpy range and limited variation in E-a for CN formation. (C) 2007 American Institute of Physics.

A first principles study of methanol decomposition on Pd(111): Mechanisms for O-H bond scission and C-O bond scission

There is some dispute as to whether methanol decomposition occurs by O-H bond scission or C-O bond scission. By carrying out density functional theory calculations, we investigate both scenario of the reaction pathways of methanol decomposition on a Pd(111) surface. It is shown that the O-H bond scission pathway is much more energetically favorable than the C-O bond scission pathway. The high reaction barrier in the latter case is found to be due to the poor bonding abilities of CH3 and OH with the surface at the reaction sites. (C) 2001 American Institute of Physics.

Sequential C-H and C-Ru bond formation and cleavage during the thermally induced rearrangement of aryl ruthenium(II) complexes with [C6H3(CH2NMe2)(2)-2,6](-) as a bidentate eta(2)-C,N coordinated ligand. The crystal structures of the isomeric pairs [RuCl{eta(6)-C10H14}{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,n}] (n = 4 or 6) and [Ru(eta(5)-C5H5){(eta(2)-C,N-C6H3(CH2NMe2)(2)-2,n} (PPH3)] (n = 4 or 6)

New air-stable ruthenium(II) complexes that contain the aryldiamine ligand [C6H3(CH2-NMe2)(2)-2,6](-) (NCN) are described. These complexes are [RuCl{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,6}(eta(6)-C10H14)] (2; C10H14 = p-cymene = C6H4Me-Pr-i-4), [Ru{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,6}(eta(5)-C5H5)(PPh3)] (5), and their isomeric forms [RuCl{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,4}(eta(6)-C10H14)] (3) and [Ru{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,4}(eta(5)-C5H5)(PPh3)] (6), respectively. Complex 2 has been prepared from the reaction of [Li(NCN)](2) with [RuCl2(eta(6)-C10H14)](2), whereas complex 5 has been prepared by the treatment of [RuCl{eta(3)-N,C,N-C6H3(CH2NMe2)(2)-2,6}(PPh3)] (4) with [Na(C5H5)](n). Both 2 and 5 are formally 18-electron ruthenium(II) complexes in which the monoanionic potentially tridentate coordinating ligand NCN is eta(2)-C,N-bonded, In solution (halocarbon solvent at room temperature or in aromatic solvents at elevated temperature), the intramolecular rearrangements of 2 and 5 afford complexes 3 and 6, respectively. This is a result of a shift of the metal-C-aryl bond from position-1 to position-3 on the aromatic ring of the NCN ligand. The mechanism of the isomerization is proposed to involve a sequence of intramolecular oxidative addition and reductive elimination reactions of both aromatic and aliphatic C-H bonds. This is based on results from deuterium labeling, spectroscopic studies, and some kinetic experiments. The mechanism is proposed to contain fully reversible steps in the case of 5, but a nonreversible step involving oxidative addition of a methyl NCH2-H bond in the case of 2. The solid-state structures of complexes 2, 3, 5, and 6 have been determined by single-crystal X-ray diffraction. A new dinuclear 1,4-phenylene-bridged bisruthenium(II) complex, [1,4-{RuCl(eta(6)-C10H14)}(2){C-6(CH2NMe2)(4)-2,3,5,6-C,N,C',N'}] (9) has also been prepared from the dianionic ligand [C-6(CH2NMe2)(4)-2,3,5,6](2-) (C2N4). The C2N4 ligand is in an eta(2)-C,N-eta(2)-C',N'-bis(bidentate) bonding mode. Compound 9 does not isomerize in solution (halocarbon solvent), presumably because of the absence of an accessible C-aryl-H bond. Complex 9 could not be isolated in an analytically pure form, probably because of its high sensitivity to air and very low solubility, which precludes recrystallization.

Density Functional Theory Study on the Cleavage Mechanism of the Carbonyl Bond in Amides on Flat and Stepped Ru Surfaces: Hydrogen-Induced or Direct C-O Bond Breaking?

We have performed density functional theory (DFT) calculations to investigate the reaction mechanism of the cleavage of the carbonyl bond in amides on both flat and stepped Ru surfaces. The simplest amide molecule, N,N-dimethylacetamide (DMA), was used as the exemplar model molecule. Through the calculations, the most stable transition states (TSs) in all the pathways on both flat and stepped Ru surfaces are identified. Comparing the energy profiles of different reaction pathways, we find that a direct cleavage mechanism is always energetically favored as compared with an alternative hydrogen-induced mechanism on either the flat or stepped Ru surface. It is easier for the dissociation process to occur on the stepped surface than on the flat surface. However, as compared with the terrace, the superiority of step sites boosting the C-O bond dissociation is not as evident as that on CO dissociation.

Ruthenium mediated C–H activation of benzaldehyde thiosemicarbazones: Synthesis, structure and, spectral and electrochemical properties of the resulting complexes

Reaction of five 4R-benzaldehyde thiosemicarbazones (R = OCH3, CH3, H, Cl and NO2) with [ Ru(PPh3)(3)(-CO)(H) Cl] in refluxing methanol in the presence of a base (NEt3) affords complexes of two different types, viz. 1-R and 2-R. In the 1-R complexes the thiosemicarbazone is coordinated to ruthenium as a dianionic tridentate C,N,S-donor via C-H bond activation. Two triphenylphosphines and a carbonyl are also coordinated to ruthenium. The tricoordinated thiosemicarbazone ligand is sharing the same equatorial plane with ruthenium and the carbonyl, and the PPh3 ligands are mutually trans. In the 2-R complexes the thiosemicarbazone ligand is coordinated to ruthenium as a monoanionic bidentate N, S-donor forming a four-membered chelate ring with a bite angle of 63.91(11)degrees. Two triphenylphosphines, a carbonyl and a hydride are also coordinated to ruthenium. The coordinated thiosemicarbazone ligand, carbonyl and hydride constitute one equatorial plane with the metal at the center, where the carbonyl is trans to the coordinated nitrogen of the thiosemicarbazone and the hydride is trans to the sulfur. The two triphenylphosphines are trans. Structures of the 1-CH3 and 2-CH3 complexes have been determined by X-ray crystallography. All the complexes show intense transitions in the visible region, which are assigned, based on DFT calculations, to transitions within orbitals of the thiosemicarbazone ligand. Cyclic voltammetry on the complexes shows two oxidations of the coordinated thiosemicarbazone on the positive side of SCE and a reduction of the same ligand on the negative side.

N-H...S=C hydrogen bond in O-alkyl N-methoxycarbonyl thiocarbamates, ROC(S)N(H)C(O)O)CH(3) (R = CH(3)(-), CH(3)CH(2)-)

Pure O-methyl N-methoxycarbonyl thiocarbamate CH(3)OC(S)N(H)C(O)OCH(3) (I) and O-ethyl N-methoxycarbonyl thiocarbamate, CH(3)CH(2)OC(S)N(H)C(O)OCH(3) (II), are quantitatively prepared by the addition reaction between the CH(3)OC(O)NCS and the corresponding alcohols. The compounds are characterized by multinuclear ((1)H and (13)C) and bi-dimensional ((13)C HSQC) NMR, GC-MS and FTIR spectroscopy techniques. Structural and conformational properties are analyzed using a combined approach involving crystallographic data, vibration spectra and theoretical calculations. The low-temperature (150 K) crystal structure of II was determined by X-ray diffraction methods. The substance crystallizes in the monoclinic space group P2(1)/n with a = 4.088(1)angstrom. b = 22.346(1)angstrom, c = 8.284(1)angstrom, beta = 100.687(3)degrees and Z = 4 molecules per unit cell. The conformation adopted by the thiocarbamate group -OC(S)N(H)- is syn (C=S double bond in synperiplanar orientation with respect to the N-H single bond), while the methoxycarbonyl C=O double bond is in antiperiplanar orientation with respect to the N-H bond. The non-H atoms in II are essentially coplanar and the molecules are arranged in the crystal lattice as centro-symmetric dimeric units held by N-H center dot center dot center dot S=C hydrogen bonds Id(N center dot center dot center dot S) = 3.387(1)angstrom, <(N-H center dot center dot center dot S) = 166.4(2)degrees]. Furthermore, the effect of the it electronic resonance in the structural and vibrational properties is also discussed. (C) 2009 Elsevier Ltd. All rights reserved.