Non-symmetrically substituted phenoxazinones from laccase-mediated oxidative cross-coupling of aminophenols: an experimental and theoretical insight

Oxidative cross-coupling reactions of substituted o-aminophenols were catalyzed by a commercial laccase to produce non-symmetrically substituted phenoxazinones for the first time. Identification by (1)H-, (13)C- and (31)P-NMR, and by HPLC-PDA and HPLC-MS/MS of exclusively two kinds of substituted phenoxazinones out of four potential heterocyclic frameworks was confirmed by a DFT study. The redox-properties of the substrates, their relative rates of conversion and the rigid docking of selected substrates led to a revisited mechanistic pathway for phenoxazinones biosynthesis. Our suggestions concern both the first formal two-electron oxidation by laccase and the first intermolecular 1,4-conjugated addition which secures the observed regioselectivity.     

Efficient preparation of 2,4-diaminopyrimidine nucleosides: total synthesis of lysidine and agmatidine

An efficient route for the synthesis of 2,4-diaminopyrimidine ribosides from cytidine is described consisting of six steps with overall yields >50% and only one chromatographic step. The key amine addition step utilizes LiCl and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) to ensure clean conversion to a single tautomeric product. This route has been used to prepare the modified tRNA nucleosides lysidine and agmatidine in quantities suitable for structural characterization.     

New insight into experimental and theoretical mechanistic study on a green synthesis of functionalized 4H-chromenes using magnetic nanoparticle catalyst

A green synthesis of functionalized 4H-chromenes using one-pot, three-component reaction of salicylaldehyde ( 1 ), active methylene ( 2 ), and carbon-based nucleophile ( 3 ) using Fe₃O₄@CONa nanoparticles in water has been performed at 60°C. The Fe₃O₄@CONa nanoparticle as an efficient, green, and magnetically reusable heterogeneous catalyst was applied in these reactions up to the nine runs. Green catalyst and solvent, short reaction time, high product yields, as well as simple work-up procedure were found as some advantages of this methodology. The density functional theory calculations were applied to all-inclusive perception of the one-pot, three-component reaction mechanism. The most reactions progressed through the following route: (a) nucleophilic addition of 2 to 1 ; (b) ring closing, dehydration; (c) nucleophilic substitution of 3 (2-naphtol, 4-hydroxycumarin) to intermediate. Sometimes mechanism mutated to: (a) nucleophilic addition of 3 (indole, 2-methylindole) to 1 , and dehydration; (b) nucleophilic addition of 2 to intermediate; and (c) ring closing, and dehydration. The frontier molecular orbitals, NBO analyses, molecular electrostatic potential of reactants, and intermediates confirmed the proposal mechanisms. Theoretical study could be so helpful to pick out suitable reactants of the reaction.     

Pyrimidine N-oxides. Preparation of 6-chloro-2,4-diaminopyrimidine 3-N-oxide and its reactions

The peroxyacid oxidation of 6-chloro-2,4-diaminopyrimidine ( 1 ) led to two products, 6-chloro-2,4-diaminopyrimidine 3-N-oxide ( 2 ) and 2,4-diamino-5,6-dichloropyrimidine 3-N-oxide ( 3 ). The assignment of structure of both of these compounds was made on the basis of ir, uv, nmr, and mass spectral data. A discussion of the pathways involved in the formation of 3 is presented.     

Analysis of a cycloheptenone derivative: an experimental and theoretical approach

A detailed analysis with total assignment of (1)H and (13)C NMR spectral data for a cycloheptenone derivative, a key intermediate for the synthesis of perhydroazulene terpenoids, is related. These assignments are based on 1D (1)H and (13)C NMR and on 2D NMR techniques including gCOSY, gHSQC, gHMBC, J-resolved and NOEDIF experiments. The unequivocal assignments were supported by theoretical chemical shifts and scalar coupling constant calculations at GIAO B3LYP/cc-pVDZ level from optimized structures at the same level of theory.     

Towards an insight on the photoluminescence of disordered CaWO4 from a joint experimental and theoretical analysis

A joint experimental and theoretical study has been carried out to rationalize for the first time the photoluminescence (PL) properties of disordered CaWO₄ (CWO) thin films. From the experimental side, thin films of CWO have been synthesized following a soft chemical processing, their structure has been confirmed by X-ray diffraction data and corresponding PL properties have been measured using the 488 nm line of an argon ion laser. Although we observe PL at room temperature for the crystalline thin films, the structurally disordered samples present much more intense emission. From the theoretical side, first principles quantum mechanical calculations, based on density functional theory at B3LYP level, have been employed to study the electronic structure of a crystalline (CWO-c) and asymmetric (CWO-a) periodic model. Electronic properties are analyzed in the light of the experimental results and their relevance in relation to the PL behavior of CWO is discussed. The symmetry breaking process on going from CWO-c to CWO-a creates localized electronic levels above the valence band and a negative charge transfer process takes place from threefold, WO₃, to fourfold, WO₄, tungsten coordinations. The correlation of both effects seems to be responsible for the PL of amorphous CWO.     

Silylium-arene adducts: an experimental and theoretical study

The solvent-coordinated [Me(3)Si·arene][B(C(6)F(5))(4)] salts (arene = benzene, toluene, ethylbenzene, n-propylbenzene, isopropylbenzene, o-xylene, m-xylene, p-xylene, 1,2,3-trimethylbenzene, 1,2,4-trimethylbenzene, 1,3,5-trimethylbenzene) are prepared and fully characterized. As an interesting decomposition product the formation of bissilylated fluoronium ion [Me(3)Si-F-SiMe(3)](+) was observed and even cocrystallized with [Me(3)Si·arene][B(C(6)F(5))(4)] (arene = benzene and toluene). Investigation of the degradation of [Me(3)Si·arene][B(C(6)F(5))(4)] reveals the formation of fluoronium salt [Me(3)Si-F-SiMe(3)][B(C(6)F(5))(4)], B(C(6)F(5))(3), and a reactive "C(6)F(4)" species which could be trapped with CS(2). Upon addition of CS(2), the formation of a formal S-heterocyclic carbene adduct, C(6)F(4)CS(2)-B(C(6)F(5))(3), was observed. The structure and bonding of substituted [Me(3)Si·arene][B(C(6)F(5))(4)] with arene = R(n)C(6)H(6-n) (R = H, Me, Et, Pr, and Bu; n = 0-6) is discussed on the basis of experimental and theoretical data. X-ray data of [Me(3)Si·arene][B(C(6)F(5))(4)] salts reveal nonplanar arene species with significant cation···anion interactions. As shown by different theoretical approaches (charge transfer, partial charges, trimethylsilyl affinity values) stabilizing inductive effects occur; however, the magnitude of such effects differs depending on the degree of substitution and the substitution pattern.     

Selective recognition of fluoride and acetate by a newly designed ruthenium framework: experimental and theoretical investigations

An effective anion sensor, [Ru(II)(bpy)(2)(H(2)L(-))](+) (1(+)), based on a redox and photoactive {Ru(II)(bpy)(2)} moiety and a new ligand (H(3)L = 5-(1H-benzo[d]imidazol-2-yl)-1H-imidazole-4-carboxylic acid), has been developed for selective recognition of fluoride (F(-)) and acetate (OAc(-)) ions. Crystal structures of the free ligand, H(3)L and [1](ClO(4)) reveal the existence of strong intramolecular and intermolecular hydrogen bonding interactions. The structure of [1](ClO(4)) shows that the benzimidazole N-H of H(2)L(-) is hydrogen bonded with the pendant carboxylate oxygen while the imidazole N-H remains free for possible hydrogen bonding interaction with the anions. The potential anion sensing features of 1(+) have been studied by different experimental and theoretical (DFT) investigations using a wide variety of anions, such as F(-), Cl(-), Br(-), I(-), HSO(4)(-), H(2)PO(4)(-), OAc(-) and SCN(-). Cyclic voltammetry and differential pulse voltammetry established that 1(+) is an excellent electrochemical sensor for the selective recognition of F(-) and OAc(-) anions. 1(+) is also found to be a selective colorimetric sensor for F(-) or OAc(-) anions where the MLCT band of the receptor at 498 nm is red shifted to 538 nm in the presence of one equivalent of F(-) or OAc(-) with a distinct change in colour from reddish-orange to pink. The binding constant between 1(+) and F(-) or OAc(-) has been determined to be logK = 7.61 or 7.88, respectively, based on spectrophotometric titration in CH(3)CN. The quenching of the emission band of 1(+) at 716 nm (λ(ex) = 440 nm, Φ = 0.01 at 298 K in CH(3)CN) in the presence of one equivalent of F(-) or OAc(-), as well as two distinct lifetimes of the quenched and unquenched forms of the receptor 1(+), makes it also a suitable fluorescence-based sensor. All the above experiments, in combination with (1)H NMR, suggest the formation of a 1:1 adduct between the receptor (1(+)) and the anion (F(-) or OAc(-)). The formation of 1:1 adduct {[1(+)·F(-)] or [1(+)·OAc(-)]} has been further evidenced by in situ ESI-MS(+) in CH(3)CN. Though the receptor, 1(+), is comprised of two N-H protons associated with the coordinated H(2)L(-) ligand, only the free imidazole N-H proton participates in the hydrogen bonding interactions with the incoming anions, while the intramolecularly hydrogen bonded benzimidazole N-H proton remains intact as evidenced by the crystal structure of the final product (1). The hydrogen bond mediated anion sensing mechanism, over the direct deprotonation pathway, in 1(+) has been further justified by a DFT study and subsequent NBO analysis.     

Water-assisted alkaline hydrolysis of monobactams: a theoretical study

A theoretical study of the water-assisted alkaline hydrolysis of 2-azetidinone, 3-formylamino-2-azetidinone and 3-formylamino-2-azetidine-1-sulfonate ion is carried out at the B3LYP/6-31+G* level. The effect of bulk solvent is taken into account using the PCM solvation model while specific solvent effects are represented by the inclusion of an ancillary water molecule along the reaction profile. The calculated free energy barriers in solution are in reasonable agreement with experimental values. The observed substituent effects due to the presence of the 3-formylamino and the SO(3) groups attached to the beta-lactam ring are crucial factors determining the hydrolysis of monobactam antibiotics.     

Formation of trichlorinated dibenzo-p-dioxins from 2,4-dichlorophenol and 2,4,5-trichlorophenolate: a theoretical study.

The reaction of the 2,4,5-trichlorophenolate anion with 2,4-dichlorophenol to afford trichlorinated dibenzo-p-dioxins (T3CDDs) is investigated at the B3LYP/6-31+G(d) and B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d)+ZPVE(B3LYP/6-31+G(d)) levels of theory. The first stage of the process corresponds to the formation of a predioxin, which can evolve through four different routes. Two of them lead directly to the products 2,3,7-T3CDD and 1,3,8-T3CDD, and the other two afford different predioxin-type intermediates, which in turn can evolve through all or some of the four routes to give new predioxins or T3CDD. Consequently, the theoretical results obtained show plainly the complex chemistry implied in the formation of dioxins from chlorophenols via anionic mechanisms by disclosing all the critical structures through which the system evolves, thus allowing assessment of the viability of the different mechanistic routes and the accessible products. The statistical thermodynamics treatment at 1 atm and 298.15, 600, 900, and 1200 K indicates that at higher temperatures, the Gibbs energy barrier for the formation of the initial predioxin is clearly the rate-determining step for the whole process, but at lower temperatures the Gibbs energy barrier for this step is similar to those for its evolution into 2,3,7-T3CDD. This result is in contrast with previous proposals that the closure of the central ring is the rate-limiting step. Finally, according to our results the rate constant for the formation of polychlorinated dibenzo-p-dioxins increases with the temperature, in agreement with the experimental observation that the conversion of trichlorophenols increases when going from 600 to 900 K in the gas phase in the absence of catalysts, and with DFT molecular dynamics results.     

New insight into selective catalytic reduction of nitrogen oxides by ammonia over H-form zeolites: a theoretical study

Density functional theory calculations were carried out to investigate the reaction mechanism of selective catalytic reduction of nitrogen oxides by ammonia in the presence of oxygen at the Br?nsted acid sites of H-form zeolites. The Br?nsted acid site of H-form zeolites was modeled by an aluminosilicate cluster containing five tetrahedral (Al, Si) atoms. A low-activation-energy pathway for the catalytic reduction of NO was proposed. It consists of two successive stages: first NH(2)NO is formed in gas phase, and then is decomposed into N(2) and H(2)O over H-form zeolites. In the first stage, the formation of NH(2)NO may occur via two routes: (1) NO is directly oxidized by O(2) to NO(2), and then NO(2) combines with NO to form N(2)O(3), which reacts with NH(3) to produce NH(2)NO; (2) when NO(2) exceeds NO in the content, NO(2) associates with itself to form N(2)O(4), and then N(2)O(4) reacts with NH(3) to produce NH(2)NO. The second stage was suggested to proceed with low activation energy via a series of synergic proton transfer steps catalyzed by H-form zeolites. The rate-determining step for the whole reduction of NO(x) is identified as the oxidation of NO to NO(2) with an activation barrier of 15.6 kcal mol(-1). This mechanism was found to account for many known experimental facts related to selective catalytic reduction of nitrogen oxides by ammonia over H-form zeolites.     

New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide

Molecular-level structural information on amyloid aggregates is of great importance for the understanding of protein-misfolding-related deseases. Nevertheless, this kind of information is experimentally difficult to obtain. In this work, we used molecular dynamics (MD) simulations combined with a mixed quantum mechanics/molecular mechanics theoretical methodology, the perturbed matrix method (PMM), in order to study the amide I' IR spectrum of fibrils formed by a short peptide, the H1 peptide, derived from residues 109 through 122 of the Syrian hamster prion protein. The PMM/MD approach allows isolation of the amide I' signal arising from any desired peptide group of the polypeptide chain and quantification of the effect of the excitonic coupling on the frequency position. The calculated single-residue signals were found to be in good agreement with the experimental site-specific spectra obtained by means of isotope-labeled IR spectroscopy, providing a means for their interpretation at the molecular level. In particular, our results confirm the experimental hypothesis that residues ala117 are aligned in all strands and that the alignment gives rise to a red shift of the corresponding site-specific amide I' mode due to strong excitonic coupling among the ala117 peptide groups. In addition, our data show that a red shift of the amide I' band due to strong excitonic coupling can also occur for amino acids adjacent in sequence to the aligned ones. Thus, a red shift of the signal of a given isotope-labeled amino acid does not necessarily imply that the peptide groups under consideration are aligned in the β-sheet.     

Molecular photochromic systems: a theoretical and experimental investigation on zinc(II) dithizonate

Zinc(II)‐dithizone based molecular systems [Zn(HDz)₂] are intriguing candidates for the development of optical devices thanks to their interesting photochromic and nonlinear optical properties. In the present work, the behavior of Zn(HDz)₂ in different solvents was investigated by a combined theoretical and experimental approach. In particular, solutions of both dithizone (H₂Dz) and Zn(HDz)₂ were analyzed by optical absorption spectroscopy and nuclear magnetic resonance (NMR) techniques, with particular attention to structure–properties relationships. Density functional and time‐dependent density functional calculations were performed on the stable and the activated forms of the complex, obtaining information on the energetics of their interconversion, as well as on the nature of their electronic excitations. Copyright © 2007 John Wiley & Sons, Ltd.     

Amine exchange in formamidines: an experimental and theoretical study

N-H-containing formamidines combine a reasonably strong association to carboxylic acids to form complexes of well-defined geometries with a simultaneous proton-induced electrophilicity enhancement that allows for the exchange of their amine portion. The N=C(H)-NH fragment, therefore, undergoes "imine-like" exchange with N-containing nucleophiles. Because of the prototropic equilibrium, the N=C(H)-NH fragment may behave as a "bisimine" centred on the same carbon, in which both N-containing fragments can be exchanged. Considering the proton-induced sensitisation of both C-N units and the well-defined formamidine-carboxylic acid complex geometry, it should be possible to use carboxylic acids as templates for the synthesis of defined architectures by dynamic amine exchange within formamidines. This study highlights three exchange regimes based on the nature of the incoming amine (aliphatic amines, aromatic amines and alkoxyamines), as well as exchange rules based on the amine leaving groups. Following this analysis, a proof of concept for carboxylic acid templated macrocycle formation through dynamic exchange is provided.     

Solvent effects on the thioamide rotational barrier: an experimental and theoretical study.

The solvent effect on the C-N rotational barriers of N,N-dimethylthioformamide (DMTF) and N,N-dimethylthioacetamide (DMTA) has been investigated using ab initio theory and NMR spectroscopy. Selective inversion recovery NMR experiments were used to measure rotational barriers in a series of solvents. These data are compared to ab initio results at the G2(MP2) theoretical level. The latter are corrected for large amplitude vibrational motions to give differences in free energy. The calculated gas phase barriers are in very good agreement with the experimental values. Solvation effects were calculated using reaction field theory. This approach has been found to give barriers that are in good agreement with experiment for many aprotic, nonaromatic solvents that do not engage in specific interactions with the solute molecules. The calculated solution-phase barriers for the thioamides using the above solvents are also in good agreement with the observed barriers. The solvent effect on the thioamide rotational barrier is larger than that for the amides because the thioamides have a larger ground-state dipole moment, and there is a larger change in dipole moment with increasing solvent polarity. The transition-state dipole moments for the amides and thioamides are relatively similar. The origin of the C-N rotational barrier and its relation to the concept of amide "resonance" is examined.     

Vacuum ultraviolet absorbance of alkanes: an experimental and theoretical investigation

The electronic absorption spectra of alkanes are known to be broad and lack discrete band structures. Previous studies have suggested their HOMO-LUMO energy gaps could be used to understand the absorbance edges of these spectra. With the advent of a new benchtop vacuum ultraviolet (VUV) spectroscopic absorption detector, it is now possible to collect VUV absorption spectra (from 120 to 240 nm) for an extended range of structures under an inert gas phase environment more conveniently. The previously reported hypothesis was revisited and its limits were explored using a combination of new extended experimental VUV spectral data and theoretical quantum mechanics calculations. It was pointed out from this study that the first strong excitations of alkanes are not always the HOMO-LUMO transition. As a result, the HOMO-LUMO energy gap of alkanes should not be used directly as a universal and reliable parameter to understand their experimental absorbance edges. VUV spectral data for a larger variety of alkanes structures were reported and the relation between these structures and spectra was discussed.

     

Structural assignment of Diels-Alder adducts: an experimental and theoretical approach

A detailed NMR analysis with total assignment of (1)H and (13)C NMR data for the endo and the exo adducts, obtained by Diels-Alder reaction between 2-cyclohexenone and cyclopentadiene, is described. The unequivocal assignment of the endo and exo structures was performed by (1)H and (13)C NMR. These assignments were supported by theoretical chemical shift calculations at GIAO/HF level using 6-311 + g(2d, p) from optimized structures at the B3LYP/6-31g(d) level.     

Cationic prevesicle and vesicle nanoaggregates: an experimental and theoretical study

The formation of spontaneous mixed prevesicles and vesicles consisting of a cationic double-chain surfactant, didecyldimethylammonium bromide (di-C(10)DMAB), and a cationic single-chain alkyltrimethylammonium bromide with 10 and/or 14 carbon atoms (decyltrimethylammonium bromide, C(10)TAB, and/or tetradecyltrimethylammonium bromide, C(14)TAB) has been investigated by means of a series of (i) highly precise experimental techniques, such as conductometry, transmission electronic microscopies (TEM and cryo-TEM), laser Doppler electrophoresis (LDE), and steady-state fluorescence spectroscopy and (ii) theoretical models, such as the DLVO theory and two of its main further modifications, Inoues's and Sogami's models. Two new potentials, based on the combination of DLVO or Inoue potentials with that of Sogami, have been proposed and checked. This theoretical analysis has been carried out not only for the aggregates studied in this work but also for other di-C(m)DMAB + C(n)TAB (m = 10, 12 and n = 10, 12, 14) systems previously reported by us. In respect to the experimental study, special emphasis has been devoted to the prevesicle domain. We have confirmed the existence of two critical aggregation concentrations in the very diluted concentration domain, where the conductivity plot shows a zigzag pattern: the so-called mixed critical aggregate concentration, CAC* and the mixed critical vesicle concentration, CVC*. Contrarily, only CVC* is detected. The pre-CAC* nanoaggregates, with a variety of sizes and shapes, do not show a clear aggregation pattern, but even at such low concentrations a small number of nanoaggregates with a clear and ordered aggregation pattern has been visualized. In the postvesicle domain, the aggregates (vesicles) are unilamellar and spherical with a medium polidispersity and a net averaged surface density charge of around 14 x 10(-3) (pure vesicles) and 24 x 10(-3) C m(-2) (mixed vesicles). The hydrophobicities of the lipidic bilayer and the surface of the vesicles resemble those of media with dielectric constants of around 30 and 75, respectively. Finally, theoretical predictions confirm the stability of the pure and mixed vesicles studied in this work and in other works previously reported.     

Selectivity under microwave irradiation. Benzylation of 2-pyridone: an experimental and theoretical study

The reaction of 2-pyridone with benzyl bromide in the absence of base and under solvent-free conditions has been studied experimentally and by computational methods. This reaction was one of the first reported examples in which modification of selectivity under microwave irradiation was observed. C- and/or N-alkylations were obtained depending on the benzyl halide and the heating system. N-Alkylation through mechanism A (S_N2 mechanism) is kinetically favoured while C-alkylation through an S_N1-type mechanism is thermodynamically favoured and is observed under microwave irradiation. Two S_N1-type mechanisms (mechanisms B and C) have been calculated, mechanism C being a kind of S_Ni. The influence of the pyridone/benzyl bromide ratio was studied. A second molecule of pyridone stabilizes the transition state and assists the leaving of the bromide ion. The occurrence of C-alkylation under microwave irradiation is explained by the predominance of the thermodynamic control in these conditions. Under microwave irradiation N-alkylation through an S_N1-type mechanism (mechanism C) can also occur. The dependence of the outcome of N-alkylation on the benzyl bromide ratio has been explained by a shift in the mechanism from S_N2 to S_N1 under microwave irradiation. Computational calculations have shown to be a useful tool for determination of the origin of the selectivity under microwave irradiation.     

New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid

We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.