Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study

The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.     

Preparation of α-amino acids via Ni-catalyzed reductive vinylation and arylation of α-pivaloyloxy glycine

This work emphasizes easy access to α-vinyl and aryl amino acids via Ni-catalyzed cross-electrophile coupling of bench-stable N-carbonyl-protected α-pivaloyloxy glycine with vinyl/aryl halides and triflates. The protocol permits the synthesis of α-amino acids bearing hindered branched vinyl groups, which remains a challenge using the current methods. On the basis of experimental and DFT studies, simultaneous addition of glycine α-carbon (Gly) radicals to Ni(0) and Ar–Ni(ii) may occur, with the former being more favored where oxidative addition of a C(sp²) electrophile to the resultant Gly–Ni(i) intermediate gives a key Gly–Ni(iii)–Ar intermediate. The auxiliary chelation of the N-carbonyl oxygen to the Ni center appears to be crucial to stabilize the Gly–Ni(i) intermediate.

We have developed Ni-catalyzed reductive coupling of N-carbonyl protected α-pivaloyloxy glycine with Csp²-electrophiles that enabled facile preparation of α-amino acids, including those bearing hindered branched vinyl groups.     

Hydrogen by Deuterium Substitution in an Aldehyde Tunes the Regioselectivity by a Nonheme Manganese(III)–Peroxo Complex

Mononuclear nonheme Mn^III‐peroxo complexes are important intermediates in biology, and take part in oxygen activation by photosystem II. Herein, we present work on two isomeric biomimetic side‐on Mn^III‐peroxo intermediates with bispidine ligand system and reactivity patterns with aldehydes. The complexes are characterized with UV/Vis and mass spectrometric techniques and reaction rates with cyclohexane carboxaldehyde (CCA) are measured. The reaction gives an unusual regioselectivity switch from aliphatic to aldehyde hydrogen atom abstraction upon deuteration of the substrate, leading to the corresponding carboxylic acid product for the latter, while the former gives a deformylation reaction. Mechanistic details are established from kinetic isotope effect studies and density functional theory calculations. Thus, replacement of C?H by C?D raises the hydrogen atom abstraction barriers and enables a regioselectivity switch to a competitive pathway that is slightly higher in energy.     

Ion-molecule reactions catalyzed by a single gold atom

We report that Au atoms within van der Waals complexes serve as catalysts for the first time. This was observed in ionization-induced chemistry of 1,6-hexanediol–Au and 1,8-octanediol–Au complexes formed in superfluid helium nanodroplets, where the addition of Au atom(s) made C₂H₄⁺ the sole prominent product in dissociative reactions. Density functional theory (DFT) calculations showed that the Au atom significantly strengthens all of the C–C bonds and weakens the C–O bonds in the meantime, making the C–C bonds stronger than the two C–O bonds in the ionized complexes. This leads to a preferential cleavage of the C–O bonds and thus a strong catalytic effect of the Au atoms in the reactions.

Single Au atoms within van der Waals complexes are found to serve as catalysts in ionisation-induced chemistry for the first time.     

Meloxicam and Study of Their Antimicrobial Effects against Phyto- and Human Pathogens

Recently, the design of new biological metal-ligand complexes has gained a special interest all over the world. In this research, new series of mixed ligand complexes from meloxicam (H₂mel) and glycine (Gly) were synthesized. Structures of the compounds were investigated employing elemental analyses, infrared, electronic absorption, ¹H NMR, thermal analyses, effective magnetic moment and conductivity. The estimated molar conductivity of the compounds in 1 × 10⁻³ M DMF solution indicates the non-electrolyte existence of the examined complexes. Additionally, the effective magnetic moment values refer to the complexes found as octahedral molecular geometry. The data of the infrared spectra showed the chelation of H₂mel and Gly with metal ions from amide oxygen and nitrogen of the thyizol groups of H₂mel and through nitrogen of the amide group and oxygen of the carboxylic group for Gly. Thermal analyses indicated that the new complexes have good thermal stability and initially lose hydration water molecules followed by coordinated water molecules, Gly and H₂mel. The kinetic parameters were calculated graphically using Coats–Redfern and Horowitz–Metzeger methods at n = 1 and n ≠ 1. The density functional theory (DFT) calculations were performed at B3LYP levels. The optimized geometry of the ligand and its complexes were obtained based on the optimized structures. The data indicated that the complexes are soft with η value in the range 0.114 to 0.086, while η = 0.140 for free H₂mel. The new prepared complexes were investigated as antibacterial and antifungal agents against some phyto- and human pathogens and the minimum inhibitory concentration (MIC) data showed that complex (A) has the lowest MIC for Listeria and E. coli (10.8 µg/mL).     

Synthesis of regular polypeptides including L-lysine and glycine

Conclusions The synthesis of two regular polypeptides with the composition (—Gly—L-Lys—Gly)_n and (—L-Lys—L-Lys—Gly—)_n with molecular weights of 250 and 5000 has been effected.Khimiya Prirodnykh Soedinenii, Vol. 6, No. 4, pp. 459–462, 1970The bulk of this work was carried out in the Protein Chemistry Laboratory of the Institute of Organic Chemistry, AS USSR.     

Characterization of Dominant Hydrogen Bonded Complex Structures of Dielectric Polarization and Viscous Flow Processes in Glycerol–Formamide Binary Mixtures

The static permittivity and viscosity of glycerol–formamide (Gly–FA) binary mixtures were measured at eleven concentrations over the entire composition range and at temperatures T=288.15, 303.15, 318.15 and 333.15 K. The excess static permittivity and excess viscosity of the mixtures were determined using the mole-fraction additive mixture law. Results indicated that the molecular dielectric polarization in Gly–FA mixtures is governed by 1:1 complexes with a decrease in number of H-bonded parallel aligned dipolar ordering at all of the investigated temperatures. The 2Gly:FA complexes facilitate the viscous flow process and the number of these complexes decreases with increasing temperature. The apparent activation energy of viscous flow, determined from Arrhenius plots, increases with increases of the Gly concentration in the mixtures. The electric-field-induced increment of the Helmholtz free energy and the entropy of these binary mixtures were determined from the temperature dependence of the static permittivity and its derivative, respectively.     

Mutual Effect of Functional Groups and the Radical Center on the Reactivity of Nitroxyl Radicals

This review considers the correlation between the reactivity of nitroxyl radicals (piperidine, pyrroline, pyrrolidine, imidazoline, dihydroquinoline, tetrahydroquinoline, diphenyl nitroxide, etc.) and their chemical structure in terms of the rate constants of reactions between these radicals and hydrazobenzene. 4,4′-Di(tert-butyl)diphenyl nitroxyl has the highest reactivity, and the nitroxyl radical of benzoindolopyrrolidine is the least reactive (the difference is a factor of ∼10⁴). The effects of the metal atom in stable organometallic nitroxyl radicals and of the halogen atom in halogenated nitroxyl radicals on the reactivity of the nitroxyl center are considered. Data on the effect of the nitroxyl center on the reactivity of functional groups in the piperidine nitroxyl radical are generalized. Nitroxyl radicals with an activated double bond are shown by quantum chemical calculations to form cyclic transition complexes with amines, involving both the paramagnetic center and a double bond. This explains why the activated double bond in nitroxyl radicals is more reactive in nucleophilic additions of amines than the same bond in their diamagnetic analogues. The rate constants of nitroxyl reduction with hydrazobenzene and of nitroxyl oxidation with tetranitromethane are related to the σ_ESR constant derived from isotropic hyperfine coupling constants HFC_(aN), and their correlation with Hammett constants is demonstrated. The role of solvents in the reduction and oxidation of the nitroxyl radicals is considered. The influence of hydroxyl radical-polar solvent complexes and hydroxylamine-polar solvent H complexes on the course of reactions is considered for hydrogen atom transfer in systems of a sterically hindered nitroxyl radical and hydroxylamine.__________Translated from Kinetika i Kataliz, Vol. 46, No. 4, 2005, pp. 506–528.Original Russian Text Copyright © 2005 by Malievskii, Shapiro.     

Geometry, chemical bonding, and electronic spectra of Si(n) and Si(n)-glycine (n = 3-5) complexes

Structures and spectra are calculated for Si(n) and Si(n)-Gly (n = 3-5) complexes. Relative stability differences of Gly conformers are magnified by interactions with the Si(n) cluster, so that one conformer of Si(n)-Gly is stabilized. Significant charge transfer occurs from the amino group in Gly to a Si atom in the cluster. Interactions with Gly are predicted to shift the excitation energies of Si(n) significantly to the blue to 2.1-2.7 eV, although they are still lower than in a Si cluster passivated by hydrogen.     

Spectroscopic,X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides

The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase. The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH₂ single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their ¹H-NMR spectra. Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state. XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S. The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions.     

Reaction Products of β-Aminopropioamidoximes Nitrobenzenesulfochlorination: Linear and Rearranged to Spiropyrazolinium Salts with Antidiabetic Activity

Nitrobenzenesulfochlorination of β-aminopropioamidoximes leads to a set of products depending on the structure of the initial interacting substances and reaction conditions. Amidoximes, functionalized at the terminal C atom with six-membered N-heterocycles (piperidine, morpholine, thiomorpholine and phenylpiperazine), as a result of the spontaneous intramolecular heterocyclization of the intermediate reaction product of an S_N2 substitution of a hydrogen atom in the oxime group of the amidoxime fragment by a nitrobenzenesulfonyl group, produce spiropyrazolinium ortho- or para-nitrobenzenesulfonates. An exception is ortho-nitrobenzenesulfochlorination of β-(thiomorpholin-1-yl)propioamidoxime, which is regioselective at room temperature, producing two spiropyrazolinium salts (ortho-nitrobezenesulfonate and chloride), and regiospecific at the boiling point of the solvent, when only chloride is formed. The para-Nitrobezenesulfochlorination of β-(benzimidazol-1-yl)propioamidoxime, due to the reduced nucleophilicity of the aromatic β-amine nitrogen atom, is regiospecific at both temperatures, and produces the O-para-nitrobenzenesulfochlorination product. The antidiabetic screening of the new nitrobezenesulfochlorination amidoximes found promising samples with in vitro α-glucosidase activity higher than the reference drug acarbose. ¹H-NMR spectroscopy and X-ray analysis revealed the slow inversion of six-membered heterocycles, and experimentally confirmed the presence of an unfavorable stereoisomer with an axial N–N bond in the pyrazolinium heterocycle.     

Reactivity of isomeric pyridinecarboxaldehydes in catalyic hydrogenation

It has been established by a quantum-chemical method (CNDO/2) that there are two possible mechanisms occurring in the vapor phase hydrogenation of 2-, 3-, and 4-pyridinecarboxaldehydes in the presence of a copper-chromium catalyst at 180-300°C. One of these involves a donor-acceptor interaction of aldehyde with catalyst and the addition of hydrogen to the carbon atom of the carbonyl group at the first stage. The second possible mechanism is the synchronous addition of hydrogen to the carbon and oxygen of the carbonyl group of a weakly bound a aldehyde molecule with an unchanged electronic structure.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1082–1086, August, 1994.     

Gas-phase ionic syntheses of amino acids: beta versus alpha

Both theoretical and experimental studies are reported for the gas-phase reactions of protonated hydroxylamine with acetic and propanoic acids which yield protonated glycine and alanine, GlyH+ and AlaH+, respectively. The key step for these reactions is an insertion of the amino group into a C-H bond. For the formation of AlaH+, the reaction barrier for insertion into a Cbeta-H bond is ca. 5 kcal.mol-1 lower than that for the insertion into a Calpha-H bond; the product beta-AlaH+ is ca. 6 kcal mol-1 lower in energy than alpha-AlaH+. Thus, both kinetics and thermodynamics favor formation of the beta-form. The energetic preference for the beta-form is due to more efficient hydrogen bonding between the amino group and the carbonyl oxygen in the limiting transition structure and in the beta-AlaH+ product. These theoretical results are in excellent accord with selected ion flow tube measurements of the gas-phase synthesis which show striking specificity for the beta-isomer according to multi-collision-induced dissociation of the AlaH+ product ion. The results suggest that Gly and beta-Ala found in carbonaceous chondrite meteorites are products of interstellar chemistry.     

Natural Deep Eutectic Solvent (NADES) Extraction Improves Polyphenol Yield and Antioxidant Activity of Wild Thyme (Thymus serpyllum L.) Extracts

Wild thyme (Thymus serpyllum L.) herbal dust has been recognized as a potential underutilized resource for the recovery of antioxidants. The aim of this paper was to optimize natural deep eutectic solvent (NADES) extraction of polyphenols to obtain improved antioxidant activity of extracts determined by selected in vitro assays (DPPH, FRAP, and ABTS). Twenty different NADES systems were investigated in the first step of the screening of the extraction solvent and l-proline (Pro)–glycerine (Gly) based solvents provided the best results. Preliminary experiments organized by 2⁵⁻¹ fractional factorial design narrowed down the number of extraction factors from five (temperature, extraction time, NADES type, water content and L/S ratio) to three and determined their experimental domain for the final step. A face-centered central composite design with temperature (40–55–70 °C), extraction time (60–120–180 min) and L/S ratio (10–20–30 g NADES/g sample) was applied for influence analysis and process optimization. Multi-response optimization suggested a temperature of 65 °C, time of extraction of 180 min and L/S ratio of 28 g NADES/g DW as optimal extraction parameters. Experimental validation confirmed good agreement between experimental and predicted results in the extract obtained at optimal conditions and the interactions in the most suitable NADES (N16; Pro–Gly–H₂O; 1:2:1) were confirmed by the ¹H-NMR.     

A new photoproduct of 5-methylcytosine and adenine: a theoretical study

Both the cycloaddition mechanism of 5-methylcytosine with adenine and the deamination mechanism of the cycloaddition product have been studied using density functional theory method. The results suggest that the cycloaddition reaction could occur more easily through photochemical reaction pathway than through thermal reaction pathway. The obtained four-member ring structure could be easily transformed to an eight-member ring structure through bond cleavage of C₅–C₆ (the energy barrier is <2 kcal/mol). Then hydrolytic deamination reaction takes place with water assistance. The hydroxyl group of one water molecule attacks the C₄^′ atom and the hydrogen atom of another water molecule attacks N₃^′ atom to form a tetrahedral intermediate. Subsequently, the hydrogen atom of hydroxyl group transfers to N₈^′ to produce ammonia, and the amino group of the former 5-methylcytosine changes to carboxyl oxygen. Our calculations explain the phenomena that 5-methylcytosine and adenine could obtain the same photoproduct as thymine and adenine from theoretical aspects.     

Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH₂(CH₂)_nCH₂NH₂ (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH₂(CH₂)_nCH₂NH₂ (n = 0–3) interact with BeF₂. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.     

On the Reaction Mechanism of the Rhodium‐Catalyzed Arylation of Fullerene (C60) with Organoboron Compounds in the Presence of Water

Density functional theory (DFT) calculations were carried out to study the reaction mechanism of the Suzuki–Miyaura rhodium‐catalyzed hydroarylation of fullerene (C₆₀) by phenylboronic acid in the presence of water. As found experimentally, our results confirm that addition of the phenyl group and the hydrogen atom in C₆₀ occurs at the [6,6] bond. The rate‐determining step corresponds to the simultaneous transfer of a hydrogen atom from a water molecule to C₆₀ and the recovery of the active species. The use of 2‐phenyl‐1,3,2‐dioxaborinane and the 4,4,5,5‐tetramethyl‐2‐phenyl‐1,3,2,‐dioxaborolane instead of phenylboronic acid as organoborate agents does not lead to great modifications of the energy profile. The possible higher steric hindrance of 4,4,5,5‐tetramethyl‐2‐phenyl‐1,3,2,‐dioxaborolane should not inhibit its use in the hydroarylation of C₆₀. Overall, we show how organoboron species arylate C₆₀ in rhodium‐based catalysis assisted by water as a source of protons.     

A methylenic group binds guanidinoacetic acid to glycine and serine in two novel copper(II) complexes: Synthesis,X-ray structure and spectroscopic characterization

New condensed amino acids were observed in two Cu(II) complexes, both involving guanidinoacetic acid (GAA). The copper(II) complexes, 1 and 2, were synthesized and characterized by X-ray crystallography and infrared spectroscopy. Vibrational assignments were performed with the aid of density functional theory (DFT) calculations. Both complexes present an elongation of the carbon chain of the starting amino acid, GAA. One methylenic group binds GAA to the other amino acid, which can be glycine or serine. Complex 1 presents a new condensed synthetic amino acid, glycine-3-N-methylguanidino acetic acid (Gly-mGAA) that is the result/product of the reaction between GAA and glycine, with an addition of one carbon in the chain. In complex 2, a similar ligand to Gly-mGAA was observed, but in this case it is a product of the reaction between GAA and serine, that is, serine-3-N-methylguanidino acetic acid (Ser-mGAA). Gly-mGAA and Ser-mGAA coordinate to Cu(II) through two nitrogen atoms and two oxygen atoms. In addition, we attempt to propose the mechanism for formation of Ser-mGAA and Gly-mGAA in two steps. The first one involves a deamidination reaction between two GAA species, producing the intermediate N,N′-guanidinodiacetic acid. The second step involves a decarboxylation process between GAA and Ser or Gly.     

Coordination Compounds of Copper(II) Nitrate with Products of Aminotris(hydroxymethyl)methane Condensation with Salicyl- and 5-Nitrosalicylaldehydes: Synthesis and Crystal Structures

The crystal structures of copper(II) nitrate complexes with 2-(2-hydroxybenzylideneamino)-2-hydroxymethylpropane-1,3-diol (HL) and 2-hydroxymethyl-2-(2-hydroxy-5-nitrobenzylideneamino)propane-1,3-diol (HL¹) were determined. The resulting complexes were formulated as [Cu₃OL₃(H₂O₂]NO₃ · 3H₂O (I) and [Cu(H₂O)L¹]NO₃ (II). The crystals of I are monoclinic, a = 17.809(4) Å, b = 30.549(6) Å, c = 18.962(4) Å, β = 115.36(3)°, space group Cc, Z = 8, R = 0.0482. Complex I is composed of two independent three-dimensional µ₃-oxo complexes; the coordination polyhedron of the copper atoms in both compounds is an elongated tetragonal bipyramid. The coordination polyhedron of the third Cu atom is a tetragonal pyramid. The bases of the pyramids are composed of the oxygen atoms of the phenol and alcohol OH groups, the imine N atom of ligand L, and µ ₃-oxo atoms. The phenol and water O atoms serve as the apices in both the tetragonal bipyramids. The crystals of II are triclinic, a = 6.062(1) Å, b = 7.701(2) Å, c = 16.162(3) Å, α = 88.15(3)°, β = 84.94(3)°, γ = 78.13(3)°, space group P1¯, Z = 2, R = 0.0272. Complex II is composed of polymer chains formed by coordination bonds between the copper atom and two O atoms of the amino alcohol in the azomethine of the neighboring complex connected to the initial one by translation along the x axis. These chains are linked through hydrogen bonds involving the oxygen atoms of the NO₂ groups. The benzene rings of the azomethine ligands of the adjoining complexes from different chains are antiparallel to each other. The coordination polyhedron of the central atom is an elongated tetragonal bipyramid. Its equatorial plane is formed by the phenol O atom, one of the alcohol O atoms, the N atom of ligand L¹, and the O atom of the amino alcohol in the neighboring complex. The apices are the O atom of the water molecule and the O atom of the amino alcohol in the neighboring azomethine molecule. In complexes I and II, the outer-sphere nitrato group mainly serves to unite trimers and polymers in the crystal by means of hydrogen bonds.__________Translated from Koordinatsionnaya Khimiya, Vol. 31, No. 8, 2005, pp. 621–629.Original Russian Text Copyright © 2005 by Chumakov, Tsapkov, Simonov, Antosyak, Bocelli, Perrin, Starikova, Samus, Gulea.     

The Two Faces of the Guanyl Radical: Molecular Context and Behavior

The guanyl radical or neutral guanine radical G(-H)^• results from the loss of a hydrogen atom (H^•) or an electron/proton (e^–/H⁺) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC^•+ pair. The role of the two G(-H)^• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.