DFT study of the hydrogen bond strength and IR spectra of formic,oxalic, glyoxylic and pyruvic acids in vacuum,acetone and water solution

The molecular geometries of the possible conformations of formic, oxalic, glyoxylic and pyruvic acids have been fully optimized at DFT B3LYP/6‐311++G(d,p) levels of calculation in vacuum as well as in water and acetone solution. Solutions were treated according to the SCRF PCM approach but some formic acid–water and formic acid–acetone clusters as well as adducts of oxalic acid with two or four water molecules were also taken into account for testing the importance of specific solute–solvent effects. All the most stable isomers of the title compounds are characterized by weak intramolecular hydrogen bonds, whose strengths (E_HB) cannot be correctly estimated as stability difference between the open and chelate forms since the energy of the former isomer is, in turn, stabilized by a weak hydrogen bridge due to the formic acid moiety. Following the Rotation Barrier Method (RBM), proposed some years ago, E_HB in the examined molecules (gas phase) falls in the range of 18–22 kJ/mol for oxalic acid (9.6 kJ/mol for the c‐C‐t isomer), 16.8 kJ/mol for glyoxylic acid and 19.8 kJ/mol for pyruvic acid. Most of them disappear at all, or nearly at all, both in acetone and aqueous solution, in consequence of the solvent effect. The frequencies of the OH and C?O stretching modes, calculated according to the anharmonic oscillator model, are in very good agreement with the experimental literature data, where available. Copyright © 2009 John Wiley & Sons, Ltd.     

Solvent effects on guanidinium‐anion interactions and the problem of guanidinium Y‐aromaticity

We have calculated the complexes formed by guanidine/guanidinium and HCl/Cl^?, HNO₃/NO₃^? and H₂SO₄/HSO₄^? both in the gas and aqueous Polarizable Continuum Model (PCM) phase to understand the effect that solvation has on their interaction energies. In the gas phase, the cation–anion complexes are much more stable than the rest; however, when PCM‐water is considered, this energetic difference is not as large due to the extra stabilization that the ions suffer when in aqueous solution. All the complexes were analyzed in terms of their AIM and NBO properties. In all cases, water solvation seems to “dampen” those properties observed in the gas phase. The values of Nucleus Independent Chemical Shift (NICS)(1) and NICS(2) indicate a huge influence of the proximity of the carbon atom for short distances; thus, the 3D NICS values on the van der Waal isosurfaces have been used to evaluate the possible Y‐aromaticity of the guanidinium system. The isosurface in this system is more similar to cyclohexane than to benzene as indication of poor aromaticity. Copyright © 2013 John Wiley & Sons, Ltd.     

The water‐promoted Diels–Alder reaction in quaternary ammonium salts

Prevailing classification of salts based on their effect in solubility and stability of proteins in aqueous solution predicts that tetraalkylammonium salts, guanidinium chloride (GnCl), LiClO₄ act as salting‐in (S/I) and LiCl, NaCl act as salting‐out (S/O) in aqueous conditions. In the same context the behaviour of GnCl, LiClO₄ and LiCl are contradictory in polar solvents like ethylene glycol and formamide. In these solvents, expected salt effect shows just opposite nature from their usual expectation. However, in the aqueous solution salts like tetraalkylammonium halide (R₄NX, R = alkyl group, X = Br group) behave like salting‐in salts. The physicochemical origin of the salting in effect of R₄NX type of salts has been discussed elaborately in the present work. The role of cations in terms of substitution of various alkyl groups on R₄NX has been systematically presented here on the basis of experimental kinetic and thermodynamic studies. The abnormal behaviour of R₄NX salts in aqueous solution has also been explained by the Setschenov equation (k_s) and Δμ_solvation values, which highlights their individual nature out of common properties of R₄NX. Copyright © 2015 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and DFT calculations of di‐amino acid cyclic peptides. Part I: cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly‐Gly), cyclo(L‐Ala‐L ‐Ala) and cyclo(L ‐Ala‐Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid‐state and aqueous protonated samples, as well as their corresponding N‐deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3‐LYP/cc‐pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas‐phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di‐amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C₂ and C₁ symmetries for the six‐membered rings of cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L‐Ala‐Gly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis‐peptide linkage are shown to be significantly different from those of the trans‐peptides. For example, deuterium shifts have shown that the cis‐amide I vibrations found in cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala), and cyclo(L‐Ala‐Gly) have larger N‐H contributions compared to their trans‐amide counterparts. Compared to trans‐amide II vibrations, cis‐amide II vibrations show a considerable decrease in N H character. Copyright © 2009 John Wiley & Sons, Ltd.     

Theoretical study of keto–enol tautomerism by quantum mechanical calculations (the QM/MC/FEP method)

In this study, the tautomeric equilibrium between the keto and enol forms has been studied for five typical ketones and aldehydes: i‐butanal, acetaldehyde, acetone, acetylacetone, and dimedone. The level of theory used in the gas‐phase calculation was Becke, three‐parameter, Lee–Yang–Parr/6‐311G(d,p)//Becke, three‐parameter, Lee–Yang–Parr/6‐31G(d). The free energies of solvation were included in the calculation by using the free‐energy perturbation method based on Monte Carlo simulation, that is, the quantum mechanical/Monte Carlo/free‐energy perturbation method. Three different models, incorporating no‐water, one‐water, and two‐waters, were adopted. The results showed that in the gas phase the addition of water molecules to the reaction mechanism caused the activation barriers (ΔG^?_gas) to decrease by half relative to the water‐free mechanism, but there was no effect on the relative difference in free energy, ΔG_gas. The solvation effects (ΔG_sol), based on quantum mechanical/Monte Carlo/free‐energy perturbation calculations, were added to those of the gas‐phase results of the one‐water and two‐waters models. The two‐waters model produced values that were very consistent with the experimental data for all of the tautomers. The differences in the relative Gibbs free energy (ΔG_rxn) were less than 1.0 kcal mol^–1. In summary, the inclusion of solvent molecules in gas‐phase calculations plays a very important role in producing results consistent with experimental data. Copyright © 2012 John Wiley & Sons, Ltd.     

Pulse radiolysis studies of 2‐ and 3‐hydroxybenzyl alcohols: inhibition of dehydration of ·OH‐(hydroxybenzyl alcohols) adducts by H2PO4− ions

Reactions of ·OH/O ^.? radicals and H‐atoms as well as specific oxidants such as Cl₂^.? and N₃· radicals have been studied with 2‐ and 3‐hydroxybenzyl alcohols (2‐ and 3‐HBA) at various pH using pulse radiolysis technique. At pH 6.8, ·OH radicals were found to react quite fast with both the HBAs (k = 7.8 × 10⁹ dm³ mol^?1 s^?1 with 2‐HBA and 2 × 10⁹ dm³ mol^?1 s^?1 with 3‐HBA) mainly by adduct formation and to a minor extent by H‐abstraction from ? CH₂OH groups. ·OH‐(HBA) adduct were found to undergo decay to give phenoxyl type radicals in a pH dependent way and it was also very much dependent on buffer‐ion concentrations. It was seen that ·OH‐(2‐HBA) and ·OH‐(3‐HBA) adducts react with HPO₄^2? ions (k = 2.1 × 10⁷ and 2.8 × 10⁷ dm³ mol^?1 s^?1 at pH 6.8, respectively) giving the phenoxyl type radicals of HBAs. At the same time, this reaction is very much hindered in the presence of H₂PO ions indicating the role of phosphate ion concentration in determining the reaction pathway of ·OH adduct decay to final stable product. In the acidic region adducts were found to react with H⁺ ions. At pH 1, reaction of ·OH radicals with HBAs gave exclusively phenoxyl type radicals. Proportion of the reducing radicals formed by H‐abstraction pathway in ·OH/O ^.? reactions with HBAs was determined following electron transfer to methyl viologen. H‐atom abstraction is the major pathway in O ^.? reaction with HBAs compared to ·OH radical reaction. H‐atom reaction with 2‐ and 3‐HBA gave transient species which were found to transfer electron to methyl viologen quantitatively. Copyright © 2010 John Wiley & Sons, Ltd.     

Relationship between experimental pKa values in aqueous solution and a gas phase bond length in bicyclo[2.2.2]octane and cubane carboxylic acids

Linear correlations were established between the calculated bond lengths and the pK_a or σ_I values for a series of 4‐substituted bicyclo[2.2.2]octane‐1‐carboxylic acid and 4‐cubane‐1‐carboxylic acid derivatives. The bond lengths have been calculated at a modest computational level, HF/6‐31G(d), both in the gas phase and with the continuum solvation model, polarisable continuum model (PCM). In general, the best correlations are obtained when the PCM model is taken into account, especially when neutral and charged molecules are considered together. The best models in each case show square correlation coefficients (R²) larger than 0.9 and indicate that they can be used as predictive tools. These results expand previous results that indicate the possibility of a relationship between gas phase bond length and pK_a values in aqueous solution and indicate that such relationships are more general than hitherto expected. Copyright © 2013 John Wiley & Sons, Ltd.     

Raman and ab initio study of the conformational isomerism in the 1‐ethyl‐3‐methyl‐imidazolium bis(trifluoromethanesulfonyl)imide ionic liquid

The calculated and experimental Raman spectra of the (EMI⁺)TFSI⁻ ionic liquid, where EMI⁺ is the 1‐ethyl‐3‐methylimidazolium cation and TFSI⁻ the bis(trifluoromethanesulfonyl)imide anion, have been investigated for a better understanding of the EMI⁺ and TFSI⁻ conformational isomerism as a function of temperature. Characteristic Raman lines of the planar (p) and non‐planar (np) EMI⁺ conformers are identified using the reference (EMI⁺)Br⁻ salt. The anion conformer of C₂ symmetry is confirmed to be more stable than the cis (C₁) one by 4.5 ± 0.2 kJ mol⁻¹. At room temperature, the population of trans (C₂) anions and np cations is 75 ± 2% and 87 ± 4%, respectively. Fast cooling quenches a metastable glassy phase composed of mainly C₂ anion conformers and p cation conformers, whereas slow cooling gives a crystalline phase composed of C₁ anion conformers and of np cation conformers. Copyright © 2006 John Wiley & Sons, Ltd.     

Alkane oxidation by the system ‘tert‐butyl hydroperoxide–[Mn2L2O3][PF6]2 (L = 1,4,7‐trimethyl‐1,4,7‐triazacyclononane)–carboxylic acid’

The kinetics of cyclohexane (CyH) oxygenation with tert‐butyl hydroperoxide (TBHP) in acetonitrile at 50 °C catalysed by a dinuclear manganese(IV) complex 1 containing 1,4,7‐trimethyl‐1,4,7‐triazacyclononane and co‐catalysed by oxalic acid have been studied. It has been shown that an active form of the catalyst (mixed‐valent dimeric species ‘Mn^IIIMn^IV’) is generated only in the interaction between complex 1 and TBHP and oxalic acid in the presence of water. The formation of this active form is assumed to be due to the hydrolysis of the Mn? O? Mn bonds in starting compound 1 and reduction of one Mn^IV to Mn^III. A species which induces the CyH oxidation is radical tert‐BuO ^. generated by the decomposition of a monoperoxo derivative of the active form. The constants of the equilibrium formation and the decomposition of the intermediate adduct between TBHP and 1 have been measured: K = 7.4 mol^?1 dm³ and k = 8.4 × 10^?2 s^?1, respectively, at [H₂O] = 1.5 mol dm^?3 and [oxalic acid] = 10^?2 mol dm^?3. The constant ratio for reactions of the monomolecular decomposition of tert‐butoxy radical (tert‐BuO ^. → CH₃COCH₃ + CH) and its interaction with the CyH (tert‐BuO ^. + CyH → tert‐BuOH + Cy ^. ) was calculated: 0.26 mol dm^?3. One of the reasons why oxalic acid accelerates the oxidation is due to the formation of an adduct between oxalic acid and 1 (K ≈ 10³ mol^?1 dm³). Copyright © 2007 John Wiley & Sons, Ltd.     

Proton and Carbon‐13 NMR Studies of the Phencyclone Adducts of Medium Alkyl Chain‐Length N‐n‐Alkylmaleimides. Hindered Rotations and Magnetic Anisotropic Effects. Ab initio Calculations for Optimized Structures

Abstract

The Diels–Alder adducts, 3a–e, of phencyclone, 1, have been prepared from a series of N‐n‐alkylmaleimides, 2, with medium chain‐length n‐alkyl groups. The maleimides were obtained by cyclodehydration of the N‐n‐alkylmaleamic acids, 4, formed from reaction of maleic anhydride with the corresponding n‐alkylamines. The five adducts prepared included derivatives from n‐heptyl, 3a; n‐octyl, 3b; n‐nonyl, 3c; n‐decyl, 3d; and n‐dodecyl, 3e. The NMR spectra of the adducts were studied in CDCl₃ at ambient temperatures at 300 MHz for proton and 75 MHz for carbon‐13, with full proton assignments achieved by high‐resolution COSY45 spectra for the aryl and the alkyl regions. Slow exchange limit (SEL) spectra were observed for both ¹H and ¹³C spectra showing slow rotation on the NMR timescales of the unsubstituted bridgehead phenyl groups. Endo Diels–Alder adduct stereochemistry was supported by striking magnetic anisotropic shielding effects in the ¹H spectra of the alkyl groups, with the NCH₂ CH ₂ signal of each adduct appearing upfield of tetramethylsilane (TMS) at ca. ?0.32 ppm. Proton NMR spectra for precursor maleamic acids and maleimides are reported, with some solvent effects found (CDCl₃ vs. d ₆‐acetone) for the carbon‐bound HC?CH protons of 4. Ab initio molecular modeling calculations at the Hartree‐Fock level using the 6‐31G* basis set have been performed for two key conformers of the phencyclone adduct of N‐n‐octylmaleimide, as a representative structure for these hindered adducts, to estimate geometric parameters for the adduct. A syn conformer, with the alkyl chain directed into the adduct cavity, was found to be ca. 0.23 kcal/mol lower energy than an anti conformer (in which the alkyl chain was directed away from the phenanthrenoid moiety).     

Extended X‐ray absorption fine structure and multiple‐scattering simulation of nickel dithiolene complexes Ni[S2C2(CF3)2]2n (n = −2, −1, 0) and an olefin adduct Ni[S2C2(CF3)2]2(1‐hexene)

A series of Ni dithiolene complexes Ni[S₂C₂(CF₃)]₂ⁿ (n = ?2, ?1, 0) ( 1 , 2 , 3 ) and a 1‐hexene adduct Ni[S₂C₂(CF₃)₂]₂(C₆H₁₂) ( 4 ) have been examined by Ni K‐edge X‐ray absorption near‐edge structure (XANES) and extended X‐ray absorption fine‐structure (EXAFS) spectroscopies. Ni XANES for 1 – 3 reveals clear pre‐edge features and approximately +0.7 eV shift in the Ni K‐edge position for `one‐electron' oxidation. EXAFS simulation shows that the Ni—S bond distances for 1 , 2 and 3 (2.11–2.16 Å) are within the typical values for square planar complexes and decrease by ～0.022 Å for each `one‐electron' oxidation. The changes in Ni K‐edge energy positions and Ni—S distances are consistent with the `non‐innocent' character of the dithiolene ligand. The Ni—C interactions at ～3.0 Å are analyzed and the multiple‐scattering parameters are also determined, leading to a better simulation for the overall EXAFS spectra. The 1‐hexene adduct 4 presents no pre‐edge feature, and its Ni K‐edge position shifts by ?0.8 eV in comparison with its starting dithiolene complex 3 . Consistently, EXAFS also showed that the Ni—S distances in 4 elongate by ～0.046 Å in comparison with 3 . The evidence confirms that the neutral complex is `reduced' upon addition of olefin, presumably by olefin donating the π‐electron density to the LUMO of 3 as suggested by UV/visible spectroscopy in the literature.     

Nature of the transient species formed in the pulse radiolysis of 4‐hydroxybenzyl alcohol in aqueous solutions: observation of equilibrium in the reaction of OH‐adducts with HPO ions

Reactions of ^. OH/O ^.? radicals, H‐atoms as well as specific oxidants such as N and Cl radicals with 4‐hydroxybenzyl alcohol (4‐HBA) in aqueous solutions have been investigated at various pH values using the pulse radiolysis technique. At pH 6.8, ^. OH radicals were found to react with 4‐HBA (k = 6 × 10⁹ dm³ mol^?1 s^?1) mainly by contributing to the phenyl moiety and to a minor extent by H‐abstraction from the ? CH₂OH group. ^. OH radical adduct species of 4‐HBA, i.e., ^. OH‐(4‐HBA) formed in the addition reaction were found to undergo dehydration to give phenoxyl radicals of 4‐HBA. Decay rate of the adduct species was found to vary with pH. At pH 6.8, decay was very much dependent on phosphate buffer ion concentrations. Formation rate of phenoxyl radicals was found to increase with phosphate buffer ion concentration and reached a plateau value of 1.6 × 10⁵ s^?1 at a concentration of 0.04 mol dm^?3 of each buffering ion. It was also seen that ^. OH‐(4‐HBA) adduct species react with HPO ions with a rate constant of 3.7 × 10⁷ dm³ mol^?1 s^?1 and there was no such reaction with H₂PO ions. However, the rate of reaction of ^. OH‐(4‐HBA) adduct species with HPO ions decreased on adding KH₂PO₄ to the solution containing a fixed concentration of Na₂HPO₄ which indicated an equilibrium in the H⁺ removal from ^. OH‐(4‐HBA) adduct species in the presence of phosphate ions. In the acidic region, the ^. OH‐(4‐HBA) adduct species were found to react with H⁺ ions with a rate constant of 2.5 × 10⁷ dm³ mol^?1 s^?1. At pH 1, in the reaction of ^. OH radicals with 4‐HBA (k = 8.8 × 10⁹ dm³ mol^?1 s^?1), the spectrum of the transient species formed was similar to that of phenoxyl radicals formed in the reaction of Cl radicals with 4‐HBA at pH 1 (k = 2.3 × 10⁸ dm³ mol^?1 s^?1) showing that ^. OH radicals quantitatively bring about one electron oxidation of 4‐HBA. Reaction of ^. OH/O ^.? radicals with 4‐HBA by H‐abstraction mechanism at neutral and alkaline pH values gave reducing radicals and the proportion of the same was determined by following the extent of electron transfer to methyl viologen. H‐atom abstraction is the major pathway in the reaction of O ^.? radicals with 4‐HBA compared to the reaction of ^. OH radicals with 4‐HBA. At pH 1, transient species formed in the reactions of H‐atoms with 4‐HBA (k = 2.1 × 10⁹ dm³ mol^?1 s^?1) were found to transfer electrons to methyl viologen quantitatively. Copyright © 2009 John Wiley & Sons, Ltd.     

Monitoring synchrotron X‐ray‐induced radiolysis effects on metal (Fe,W) ions in high‐temperature aqueous fluids

Radiolysis‐induced effects on aqueous tungsten ions are observed to form a precipitate within seconds upon exposure to a synchrotron X‐ray micro‐beam in a WO₃ + H₂O system at 873 K and 200 MPa. In situ Fe K‐edge energy‐dispersive X‐ray absorption spectroscopy (ED‐XAS) measurements were made on Fe(II)Cl₂ aqueous solutions to 773 K in order to study the kinetics of high‐temperature reactions of Fe²⁺ and Fe³⁺ ions with transient radiolysis species. The radiolytic reactions in a fluid sample within a hydrothermal diamond anvil cell result in oxidation of the Fe²⁺ ion at 573 K and reduction of Fe³⁺ at temperatures between 673 and 773 K and of the Fe²⁺ ion at 773 K. The edge‐energy drift evident in the ED‐XAS data directly reflects the kinetics of reactions resulting in oxidation and/or reduction of the Fe²⁺ and Fe³⁺ ions in the aqueous solutions at high temperatures. The oxidation and reduction trends are found to be highly consistent, making reliable determinations of reaction kinetics possible.     

Vibrational spectroscopy and crystal structure analysis of two polymorphs of the di‐amino acid peptide cyclo(L‐Glu‐L‐Glu)

Cyclo(L ‐Glu‐L ‐Glu) has been crystallised in two different polymorphic forms. Both polymorphs are monoclinic, but form 1 is in space group P2₁ and form 2 is in space group C2. Raman scattering and FT‐IR spectroscopic studies have been conducted for the N,O‐protonated and deuterated derivatives. Raman spectra of orientated single crystals, solid‐state and aqueous solution samples have also been recorded. The different hydrogen‐bonding patterns for the two polymorphs have the greatest effect on vibrational modes with N H and CO stretching character. DFT (B3‐LYP/cc‐pVDZ) calculations of the isolated cyclo(L ‐Glu‐L ‐Glu) molecule predict that the minimum energy structure, assuming C₂ symmetry, has a boat conformation for the diketopiperazine ring with the two L ‐Glu side chains being folded above the ring. The calculated geometry is in good agreement with the X‐ray crystallographic structures for both polymorphs. Normal coordinate analysis has facilitated the band assignments for the experimental vibrational spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Experimental and theoretical study on 3,5‐(oxo/thioxo) derivatives of 2,7‐dimethyl‐1,2,4‐triazepines–iodine molecular complexes

Intermolecular charge‐transfer (CT) spectra of 3‐thioxo‐5‐oxo‐, 5‐thioxo‐3‐oxo‐, and 3,5‐dithioxo‐ derivatives of 2,7‐dimethyl‐[1,2,4]‐triazepine 1:1 molecular complexes with molecular iodine were studied in the UV‐visible region. Equilibrium constants and free energy changes of the formed complexes were determined in solution. Ab initio calculations at HF/LANL2DZ* and MP2/LANL2DZ* were carried out to establish the nature of the complexation site, to determine the complex structures, and to examine the basicity of these compounds toward molecular iodine. The 3,5‐dithioxo‐2,7‐dimethyl‐[1,2,4]‐triazepine is the most basic one toward molecular iodine. In all cases, the complexation takes place at the heteroatom attached to position 3 of the triazepine. Hence, although in general, thiocarbonyls are stronger bases than carbonyls in the gas phase, 5‐thioxo‐2,7‐dimethyl‐[1,2,4]‐triazepin‐3‐one behaves as an oxygen base towards I₂. Experimental free energies in solution and gas‐phase computational values are linearly correlated. Copyright © 2009 John Wiley & Sons, Ltd.     

Tris‐amidoximate uranyl complexes via η2 binding mode coordinated in aqueous solution shown by X‐ray absorption spectroscopy and density functional theory methods

The present study sheds some light on the long‐standing debate concerning the coordination properties between uranyl ions and the amidoxime ligand, which is a key ingredient for achieving efficient extraction of uranium. Using X‐ray absorption fine structure combined with theoretical simulation methods, the binding mode and bonding nature of a uranyl–amidoxime complex in aqueous solution were determined for the first time. The results show that in a highly concentrated amidoxime solution the preferred binding mode between UO₂²⁺ and the amidoxime ligand is η² coordination with tris‐amidoximate species. In such a uranyl–amidoximate complex with η² binding motif, strong covalent interaction and orbital hybridization between U 5f/6d and (N, O) 2p should be responsible for the excellent binding ability of the amidoximate ligand to uranyl. The study was performed directly in aqueous solution to avoid the possible binding mode differences caused by crystallization of a single‐crystal sample. This work also is an example of the simultaneous study of local structure and electronic structure in solution systems using combined diagnostic tools.     

IR/Raman spectroscopy and DFT calculations of cyclic di‐amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L‐Ser‐L‐Ser)

B3‐LYP/cc‐pVDZ calculations of the gas‐phase structure and vibrational spectra of the isolated molecule cyclo(L ‐Ser‐L ‐Ser), a cyclic di‐amino acid peptide (CDAP), were carried out by assuming C₂ symmetry. It is predicted that the minimum‐energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L ‐seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol⁻¹) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X‐ray crystallographic structure of cyclo(L ‐Ser‐L ‐Ser), shows that the DKP ring displays a near‐planar conformation, with both the two L ‐seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier‐transform infrared (FT‐IR) spectra of solid state and aqueous solution samples of cyclo(L ‐Ser‐L ‐Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid‐state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm⁻¹, IR: 1666 and 1680 cm⁻¹), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ∼30 cm⁻¹, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm⁻¹. The occurrence of this cis amide II mode at a wavenumber above 1500 cm⁻¹ concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C^α atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd.     

Isomerization and rearrangement of (E)‐ and (Z)‐phenylhydrazones of 3‐benzoyl‐5‐phenyl‐1,2,4‐oxadiazole: evidence for a ‘new’ type of acid‐catalysis by copper(II) salts in mononuclear rearrangement of heterocycles

A kinetic investigation in methanol of the title reaction has evidenced the occurrence of two processes: the 1‐ E 1‐ Z isomerization and the rearrangement of the (Z)‐isomer into the relevant 4‐benzoylamino‐2,5‐diphenyl‐1,2,3‐triazole ( 1‐ Z → T ). The latter reaction is in line with the ability of the (Z)‐phenylhydrazones of 3‐benzoyl‐1,2,4‐oxadiazoles to undergo the so called mononuclear rearrangement of heterocycles (MRH). The occurrence of both the examined reactions is dependent on a Lewis‐acid‐catalysis. The obtained results have shown the possibility of a ‘new’ type of acid‐catalysis (bifunctional catalysis by Lewis salts) in the MRH. This catalysis operates through a completely different mechanism with respect to the one recently observed, and deeply investigated, in the presence of protic acids for the (Z)‐phenylhydrazone of 5‐amino‐3‐benzoyl‐1,2,4‐oxadiazole, in both dioxane/water and toluene, for which the catalytic process was dependent on the protonation of N(4) ring‐nitrogen of the 1,2,4‐oxadiazole. As a matter of fact, the copper salts seem able to interact with the >C?N? NH? C₆H₅ moiety, yielding adducts which, in some cases, are prone to both isomerize and rearrange. Therefore, a similar behaviour in some manner parallel to that already observed in benzene in the presence of aliphatic amines (base‐catalysis) has been evidenced. Copyright © 2008 John Wiley & Sons, Ltd.     

Mechanism for enhancing dispersion of Co3O4 nanoparticles in Co/SiO2 Fischer–Tropsch synthesis catalyst by adding glycol to impregnating solution: a quick‐XAFS study

In situ Co K‐edge quick‐EXAFS (QEXAFS) coupled with temperature‐programmed oxidation as well as ex situ XAFS was applied to investigating the mechanism for enhancing the dispersion of Co₃O₄ nanoparticles in a calcined Co/SiO₂ Fischer–Tropsch synthesis catalyst prepared by adding triethylene glycol (TEG) to a Co(NO₃)₂.6H₂O impregnating solution. Ex situ Co K‐edge XAFS indicated that, regardless of whether the catalysts were prepared with or without using TEG, the hexaaqua Co (II) complex was formed in impregnated samples which then underwent the dehydration process to some extent during the subsequent drying step at 393 K. In situ QEXAFS and ex situ EXAFS results also indicated that small oxide clusters were formed in the TEG‐modified catalyst calcined at ～400–470 K which interacted with polymer species derived from TEG. Since the Fischer–Tropsch synthesis activity of the TEG‐modified catalyst increased with an increase in the calcination temperature in a similar temperature range [Koizumi et al. (2011), Appl. Catal. A, 395 , 138–145], it was suggested that such an interaction enables the clusters to be distributed over the support surface uniformly, resulting in enhancing their dispersion. After combustion of polymer species, Co₃O₄‐like species were formed, and agglomeration of the Co₃O₄‐like species at high calcination temperatures was suppressed by the addition of TEG to the impregnating solution. It was speculated that the addition of TEG induced the formation of some surface silicate which worked as an anchoring site for Co₃O₄ and Co⁰ nanoparticles during calcination and H₂ reduction, respectively.     

Conformational analysis of N‐phenyl‐ and N‐trifyl‐4,4‐dimethyl‐4‐silathiane 1‐sulfimides

N‐Substituted 4,4‐dimethyl‐4‐silathiane 1‐sulfimides [R = Ph ( 1 ), CF₃ ( 2 )] were studied experimentally by variable temperature dynamic NMR spectroscopy. Low temperature ¹³C NMR spectra of the two compounds revealed the frozen ring inversion process and approximately equal content of the axial and equatorial conformers. Calculations of the 4‐silathiane derivatives 1 , 2 and the model compound [R = Me ( 3 )] as well as their carbon analogs, the similarly N‐substituted thiane 1‐sulfimides [R = Ph ( 4 ), CF₃ ( 5 ), Me ( 6 )] at the DFT/B3LYP/6–311G(d,p) level in the gas phase and in chloroform solution using the PCM model at the same level of theory showed a strong dependence of the relative stability of the conformer on the solvent. The electronegative trifluoromethyl group increases the relative stability of the axial conformer. Copyright © 2010 John Wiley & Sons, Ltd.