The multieffects of DMF and DBU on the [5 + 1] benzannulation of nitroethane and α‐alkenoyl ketene‐(S,S)‐acetals: Hydrogen bonding and electrostatic interactions

A density functional theory (DFT) study was performed to elucidate the mechanism for the [5 + 1] benzannulation of nitroethane and α‐alkenoyl ketene‐(S,S)‐acetals. The calculation results are consistent with experimental findings, showing that the reaction proceeds via deprotonation of nitroethane, nucleophilic addition, intramolecular cyclization, elimination of HNO₂, and the keto‐enol tautomerization sequence. It was disclosed that N,N‐dimethylformamide (DMF) and 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) act as not only solvent and nonnucleophilic base, respectively, but also catalysts in the reaction by stabilizing the transition states (TSs) and intermediates via intermolecular hydrogen bonds and electrostatic interactions. Besides, the effective orbital interaction of the reaction site in TS also contributes to the intramolecular cyclization step. The new mechanistic insights obtained by DFT calculations highlight that the hydrogen bonds and electrostatic interactions are key factors for the [5 + 1] benzannulation of nitroethane and α‐alkenoyl ketene‐(S,S)‐acetals. © 2015 Wiley Periodicals, Inc.     

Studies of rearrangement reactions of protonated and lithium cationized 2-pyrimidinyloxy-N-arylbenzylamine derivatives by MALDI-FT-ICR mass spectrometry

The rearrangement reactions of protonated and lithium-cationized 2-pyrimidinyloxy-N-arylbenzylamine derivatives were studied by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and infrared multiphoton dissociation mass spectrometry (IRMPD). Our results show that three kinds of rearrangement reactions occur in IRMPD processes. First, nearly all protonated 2-pyrimidinyloxy-N-arylbenzylamine derivatives undergo Pathway A to form the K ion series. It is proposed that this rearrangement (migration of a substituted benzyl group) proceeds by way of a gas-phase intramolecular S(N)2 reaction. Second, a gas phase intramolecular S(N)Ar type rearrangement mechanism is proposed to explain the formation of the F ion series from protonated and lithium-cationized 5 (or 6). This skeletal rearrangement reaction competes with the S(N)2 reaction of the Pathway A, which produces the K ion series, in IRMPD of protonated 5 and 6. Third, the formation pathway of the W ion series is explained by a gas phase Cope type rearrangement mechanism.     

Stabilization of sulfide radical cations through complexation with the peptide bond: mechanisms relevant to oxidation of proteins containing multiple methionine residues

The recent study on the *OH-induced oxidation of calmodulin, a regulatory "calcium sensor" protein containing nine methionine (Met) residues, has supported the first experimental evidence in a protein for the formation of S therefore N three-electron bonded radical complexes involving the sulfur atom of a methionine residue and the amide groups in adjacent peptide bonds. To characterize reactions of oxidized methionine residues in proteins containing multiple methionine residues in more detail, in the current study, a small model cyclic dipeptide, c-(L-Met-L-Met), was oxidized by *OH radicals generated via pulse radiolysis and the ensuing reactive intermediates were monitored by time-resolved UV-vis spectroscopic and conductometric techniques. The picture that emerges from this investigation shows there is an efficient formation of the Met (S therefore N) radicals, in spite of the close proximity of two sulfur atoms, located in the side chains of methionine residues, and in spite of the close proximity of sulfur atoms and oxygen atoms, located in the peptide bonds. Moreover, it is shown, for the first time, that the formation of Met(S therefore N) radicals can proceed directly, via H+-transfer, with the involvement of hydrogen from the peptide bond to an intermediary hydroxysulfuranyl radical. Ultimately, the Met(S therefore N) radicals decayed via two different pH-dependent reaction pathways, (i) conversion into sulfur-sulfur, intramolecular, three-electron-bonded radical cations and (ii) a proposed hydrolytic cleavage of the protonated form of the intramolecular, three-electron-bonded radicals [Met(S therefore N)/Met(S therefore NH)+] followed by electron transfer and decarboxylation. Surprisingly, also alpha-(alkylthio)alkyl radicals enter the latter mechanism in a pH-dependent manner. Density functional theory computations were performed on the model c-(L-Met-Gly) and its radicals in order to obtain optimizations and energies to aid in the interpretation of the experiments on c-(L-Met-L-Met).     

A density functional theory-time-dependent density functional theory investigation of photo-induced hydrogen bond and proton transfer for 2-(3,5-dichloro-2,6-dihydroxy-phenyl)-benzoxazole-6-carboxylicacid

Given the paramount importance of excited-state relaxation in the photochemical process, excited-state hydrogen bonding interactions and excited-state intramolecular proton transfer (ESIPT) are always hot topics. In this work, we theoretically explore the excited-state dynamical behaviors for a novel 2-(3,5-dichloro-2,6-dihydroxy-phenyl)-benzoxazole-6-carboxylicacid (DDPBC) system. As two intramolecular hydrogen bonds (O1 H2⋯N3 and O4 H5⋯O6) exist in the DDPBC structure, we first check if the double proton transfer form cannot be formed in the S1 state. Then, we explore the changes of geometrical parameters involved in hydrogen bonds, based on which we confirm that the dual intramolecular hydrogen bonds are strengthened on photo-excitation. The O1 H2⋯N3 hydrogen bond particularly plays a more important role in excited state. When it comes to the photo-induced excitation, we find charge transfer and electronic density redistribution around O1 H2 and N3 atom moieties. We verify the ESIPT tendency arising from the O1 H2⋯N3 hydrogen bond. In the analysis of the potential energy curves, along with O1 H2⋯N3 and O4 H5⋯O6, we demonstrate that the ESIPT reaction should occur along with O1 H2⋯N3 rather than O4 H5⋯O6. This work not only clarifies the specific ESIPT mechanism for DDPBC system but also paves the way for further novel applications based on DDPBC structure in the future.     

Synthesis,Structure and Properties of C(X)NHP(Y) Fragment Containing Compounds

Abstract

N-(thio)carbonyl(thio)amidophosphate, their open-chain and crown-containing analogues with a C (X) NHP (Y) fragments are associated with intermolecular hydrogen bonds as C=X…H-N and P=Y…H-N or intramolecular hydrogen bonds of N-H…O(macrocycle). These compounds easily enter into alkylation reaction, are added according to C=N bonds of activated imines, take part in O → S and S → O exchanging reactions.     

Synthesis of benzo-fused heterocycles by intramolecular α-arylation of ketone enolate anions

A two-step synthesis of six-, seven-, eight-, and nine-member benzo-fused heterocycles in good to excellent yields is reported. The synthetic strategy involves the generation of a new intramolecular α-aryl ketone bond by the photostimulated S(RN)1 reaction of ketone enolate anions linked to a pendant haloarene as the key step. On the other hand, an intramolecular C(Ar)-C(Ar) coupling led to the formation of five- and six-member benzo-fused heterocycles (9H-carbazole and phenanthridine) when an aromatic amide anion is competitively formed.     

Dimerization of the keto tautomer of acetohydroxamic acid-infrared matrix isolation and theoretical study

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO...HON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO...HN hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular NH...O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies (DeltaE(ZPE)(CP)I, II=-7.02, -6.34 kcal mol-1) being less stable than calculated structures III and IV (DeltaE(ZPE)(CP)III, IV=-9.50, -8.87 kcal mol-1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO...HON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA)2 dimers in the studied matrixes indicates that the formation of (AHA)2 is kinetically and not thermodynamically controlled.     

Methyl transfer in glycine N-methyltransferase. A theoretical study

Density functional theory calculations using the hybrid functional B3LYP have been performed to study the methyl transfer step in glycine N-methyltransferase (GNMT). This enzyme catalyzes the S-adenosyl-L-methionine (SAM)-dependent methylation of glycine to form sarcosine. The starting point for the calculations is the recent X-ray crystal structure of GNMT complexed with SAM and acetate. Several quantum chemical models with different sizes, employing up to 98 atoms, were used. The calculations demonstrate that the suggested mechanism, where the methyl group is transferred in a single S(N)2 step, is thermodynamically plausible. By adding or eliminating various groups at the active site, it was furthermore demonstrated that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to the carboxylate group raise the barrier.     

Rhodium-catalyzed multicomponent synthesis of chiral oxazolopiperidines

A multicomponent reaction that employs an unsaturated carboxylic acid, a 1,2 or 1,3 amino alcohol and gaseous CO and H₂ has been discovered. Thus, hydrocarbonylation of the carboxylic acid double bond generates a linear aldehyde, that is, immediately transformed into an oxazolidine. Further microwave assisted intramolecular lactamization delivers oxazolopiperidines with the generation of six new bonds in a one-pot single step. Bicylic, tricyclic, tetracyclic, and spirocyclic oxazolopiperidines can be prepared in good yields and acceptable stereoselection. The reaction did not occur under conventional heating even at higher temperature and pressure and for longer time, showing that microwave heating is indispensable to the process.     

Intramolecular hydrogen bond in substituted 3-hydroxypyridines

To explain the character of the intramolecular hydrogen bond in substituted 3-hydroxypyridines, the chemical shifts in the NMR spectra of the hydroxyl group and the IR spectra were studied. It was established that the stability of the intramolecular hydrogen bond of the O-HNR₂ type in substituted 3-hydroxypyridines increases when compared with the corresponding phenols, while an opposite pattern is observed for bonds of the O-H0₂ N type. An approximate evaluation of the energy of the intramolecular hydrogen bond in substituted 3-hydroxypyridines was achieved. When reacting with bases of the same strength, 3-hydroxypyridine forms more stable complexes than phenol.     

Calculation of vibrational spectra of linear tetrapyrroles. 3. Hydrogen-bonded hexamethylpyrromethene dimers

The structure and vibrational spectra of hexamethylpyrromethene (HMPM) have been investigated by X-ray crystallography, IR and Raman spectroscopies, and density functional theory calculations. HMPM crystallizes in the form of dimers, which are held together by bifurcated N-H(...N)(2) hydrogen bonds, involving one intramolecular and one intermolecular N-H...N interaction. The monomers are essentially planar, and the mean planes of the monomers lie approximately perpendicular to one another, so that the four N atoms in the dimer form a distorted tetrahedron. The structure of the HMPM dimer is well-reproduced by B3LYP/6-31G calculations. A comparison of the calculated geometry of the dimer with that of the monomer reveals only small changes in the N-H...N entity and the methine bridge angles upon dimerization. These are a result of weakening of the intramolecular N-H...N hydrogen bond and the formation of a more linear N-H...N intermolecular hydrogen bond. Using an empirical relation between the shift of the N-H stretching frequency of pyrrole and the enthalpy of adduct formation with bases [Nozari, M. S.; Drago, R. S. J. Am. Chem. Soc. 1970, 92, 7086-7090], estimates of the strength of the intra- and intermolecular hydrogen bonds are obtained. IR and Raman spectroscopies of HMPM and its isotopomers deuterated at the pyrrolic nitrogen atom and at the methine bridge reveal that the molecule is monomeric in nonpolar organic solvents but dimeric in a solid Ar matrix and in KBr pellets. The matrix IR spectra show a splitting of vibrational modes for the dimer, particularly those involving the N-H coordinates. Due to intrinsic deficiencies of the B3LYP/6-31G approximation, a satisfactory reproduction of these modes of the monomeric and dimeric HMPM requires specific adjustments of the NH scaling factors for the calculated force constants and, in the case of the NH out-of-plane modes of HMPM dimers, also of intra- and intermolecular coupling constants. This parametrization does not significantly affect the other calculated modes, which in general reveal a very good agreement with the experimental data.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

Reactivity of functionalized N,S-ketene acetal: regioselective construction of tetrahydrobenzo[b]pyran and chromeno[2,3-b]quinoline derivatives

Regioselective synthesis of functionalized tetrahydrobenzo[b]pyrans has been developed by multicomponent reactions (MCRs) and tandem [3 + 3] annulations of β-benzoylthioacetanilides or β-(2-haloaroyl)thioacetanilides as valuable sources with aromatic aldehydes and 5,5-dimethyl-1,3-cyclohexanedione catalyzed by triethylamine. This MCR followed by a postcondensation cyclization via an intramolecular S(N)Ar in the presence of K(2)CO(3) led to an unprecedented novel chromeno[2,3-b]quinoline framework containing an important chromene moiety in good yields. The reactions were very mild, convenient, and o-selective to form new fused tetracyclic target molecules.     

Structure and intramolecular hydrogen bonds in Bis(trifluoromethylsulfonylamino)methane and N-[(trifluoromethylsulfonyl)aminomethyl]acetamide

Bis(trifluoromethylsulfonylamino)methane in an inert medium exists as an equilibrium mixture of monomeric forms with various types of intramolecular hydrogen bonds, whose population depends on the polarity of the medium. The energetically most favorable form is a symmetrical form containing two N-H...O=S bonds. Less stable are the isomer with two N-H...F-C bonds and the unsymmetrical isomer with two different hydrogen bonds. N-[(Trifluoromethylsulfonyl)aminomethyl]acetamide contains one intramolecular intramolecular N-H...O=C hydrogen bond and preserves ability for self-association.     

Alkylation of nitroaromatics with tetraalkylborate ion via electrochemical oxidation

Aromatic nucleophilic substitution reaction (S(N)Ar) is one of the most thoroughly studied reactions. Alkylation of nitroaromatics with Grignard reagents via chemical oxidation of the sigma(H)-complexes is the most general method to introduce an alkyl group into a nitroaromatic compound. This approach has considerable drawbacks, especially when more than one nitro group are present in the aromatic ring. In this article, we present an electrochemical approach, which offers a new very selective methodology for obtaining alkyl polynitroaromatic compounds. Different strategies based on the use of tetralkylborate anion as nucleophiles are used so as to increase efficiency and to reduce the drawbacks associated with this reaction. A wide list of dinitro- and trinitro-aromatic compounds are studied, the range of yields obtained being from fair (40%) to excellent (85%). The key to improvement in the process is the use of electrochemical techniques for the oxidation of the mixture sigma(H)-complexes/tetrabutylborate ion. The electroactive character of the nucleophile, which can be oxidized to an alkyl radical, means that the S(N)Ar of the hydrogen polar mechanism is not the only mechanism operating during the electroxidation process, since the hydrogen radical S(N)Ar mechanism is running at the same time. Electrochemical mechanistic studies allow the participation of each mechanism in the global product yield obtained to be quantified.     

Intramolecular aromatic nucleophilic substitution of the benzimidazole-activated nitro group

A wide range of 2-(2-nitrophenyl)-1H-benzimidazoles undergo high-yielding intramolecular S(N)Ar of nitrite with N-pendant alkoxides under mild conditions (DMF, rt). When this operationally simple process is carried out at elevated temperatures in the presence of excess NaH, the initially formed S(N)Ar products are converted to the corresponding N-vinyl-substituted 2-(2-hydroxyphenyl)-1H-benzimidazoles via base-catalyzed isomerization. [reaction: see text]     

Shape of 4S- and 4R-hydroxyproline in gas phase

The alpha-amino acids 4(S)-hydroxyproline and 4(R)-hydroxyproline have been studied under isolation conditions in gas phase using laser-ablation molecular-beam Fourier transform microwave spectroscopy. Two conformers of each molecule have been detected in the jet-cooled rotational spectrum. The most stable conformer in both molecules exhibits an intramolecular N...H-O hydrogen bond (configuration 1) between the hydrogen atom of the carboxylic group and the nitrogen atom. The second conformer is characterized by an intramolecular N-H...O=C hydrogen bond (configuration 2). The conformers of 4(R)-hydroxyproline adopt a C(gamma)-exo puckering, while those of 4(S)-hydroxyproline present a C(gamma)-endo ring conformation. These ring conformations, which show the same propensity observed in collagen-like peptides, are stabilized by additional intramolecular hydrogen bonds involving the 4-hydroxyl group, with the exception of the most stable form of 4(S)-hydroxyproline for which a n-pi interaction between the oxygen atom of the 4-hydroxyl group and the carboxyl group carbon seems to be established. A gauche effect could be also contributing to stabilize the observed conformers.     

Spectral tuning by switching C-H[...]O hydrogen bonds: rotation-induced spectral shifts of 7-hydroxyquinoline HCOOH isomers

Spectral tuning effects on visible chromophores by hydrogen bonds are central to the chemistry of vision and of photosynthesis. A model for large spectral tuning effects by hydrogen bond switching is provided by the 7-hydroxyquinoline x HCOOH complex, which forms two isomers, CTN1 and CTN2, both with an HCOOH[...]N hydrogen bond but with different (quinoline)C-H[...]O=C hydrogen bonds. A 180 degrees rotation of the HCOOH moiety around the O-H[...]N hydrogen bond exchanges the C-H[...]O hydrogen bonds, rotates the dipole moment of HCOOH, and leads to an approximately 850 cm(-1) shift of the electronic spectrum. Mass-selected S1<--S0 resonant two-photon ionization, UV-UV holeburning, S1-->S0 fluorescence spectra, and photoionization efficiency curves of the two 7-hydroxyquinoline x HCOOH isomers were measured in supersonic expansions. Comparison to ab initio calculations allow us to determine the H-bond connectivity and structure of the two isomers and to assign their inter- and intramolecular vibrations. The Franck-Condon factors of the intermolecular shear vibration chi in the S1<--S0 spectra indicate that the weak C-H[...]O hydrogen bond contracts markedly in the CTN1 isomer but expands in the CTN2 isomer. These changes of H-bond lengths agree with the spectral shifts. In contrast, the strong O-H[...]N hydrogen bond undergoes little change upon S1[...]S0 excitation.     

Acid-mediated four-component tandem cyclization: Access to multifused 1,3-benzoxazine frameworks

An acid-mediated multicomponent reaction has been developed for the direct synthesis of multifused 1,3-benzoxazine derivatives from simple and readily available arylglyoxal monohydrates and 2-aminobenzyl alcohols under mild conditions. This novel protocol is proposed to proceed through intramolecular poly-heterocyclizations, thus leading to the formation of three new rings and six new chemical bonds, including four CN and two CO bonds.     

N,N′‐Diethyl‐4‐nitrobenzene‐1,3‐diamine, 2,6‐bis(ethylamino)‐3‐nitrobenzonitrile and bis(4‐ethylamino‐3‐nitrophenyl) sulfone

N,N′‐Diethyl‐4‐nitrobenzene‐1,3‐diamine, C₁₀H₁₅N₃O₂, (I), crystallizes with two independent molecules in the asymmetric unit, both of which are nearly planar. The molecules differ in the conformation of the ethylamine group trans to the nitro group. Both molecules contain intramolecular N—H...O hydrogen bonds between the adjacent amine and nitro groups and are linked into one‐dimensional chains by intermolecular N—H...O hydrogen bonds. The chains are organized in layers parallel to (101) with separations of ca 3.4 Å between adjacent sheets. The packing is quite different from what was observed in isomeric 1,3‐bis(ethylamino)‐2‐nitrobenzene. 2,6‐Bis(ethylamino)‐3‐nitrobenzonitrile, C₁₁H₁₄N₄O₂, (II), differs from (I) only in the presence of the nitrile functionality between the two ethylamine groups. Compound (II) crystallizes with one unique molecule in the asymmetric unit. In contrast with (I), one of the ethylamine groups, which is disordered over two sites with occupancies of 0.75 and 0.25, is positioned so that the methyl group is directed out of the plane of the ring by approximately 85°. This ethylamine group forms an intramolecular N—H...O hydrogen bond with the adjacent nitro group. The packing in (II) is very different from that in (I). Molecules of (II) are linked by both intermolecular amine–nitro N—H...O and amine–nitrile N—H...N hydrogen bonds into a two‐dimensional network in the (10) plane. Alternating molecules are approximately orthogonal to one another, indicating that π–π interactions are not a significant factor in the packing. Bis(4‐ethylamino‐3‐nitrophenyl) sulfone, C₁₆H₁₈N₄O₆S, (III), contains the same ortho nitro/ethylamine pairing as in (I), with the position para to the nitro group occupied by the sulfone instead of a second ethylamine group. Each 4‐ethylamino‐3‐nitrobenzene moiety is nearly planar and contains the typical intramolecular N—H...O hydrogen bond. Due to the tetrahedral geometry about the S atom, the molecules of (III) adopt an overall V shape. There are no intermolecular amine–nitro hydrogen bonds. Rather, each amine H atom has a long (H...O ca 2.8 Å) interaction with one of the sulfone O atoms. Molecules of (III) are thus linked by amine–sulfone N—H...O hydrogen bonds into zigzag double chains running along [001]. Taken together, these structures demonstrate that small changes in the functionalization of ethylamine–nitroarenes cause significant differences in the intermolecular interactions and packing.