DFT study of adenine–cytosine mismatch in quaternary systems involving DNA bases

Structural Chemistry - In the present work, the adenine–cytosine mismatch is theoretically investigated in quaternary systems involving DNA bases. The calculations, in gas phase, are...     

The Étard reaction: a DFT study

The mechanism of the E?tard reaction of chromylchloride in toluene, discovered more than a century ago, has been investigated by DFT calculations (B3LYP/6-31G(d)). The formation of the experimentally observed product can be rationalized by multiple CH-abstraction reactions.     

Electronic properties of B12N12 fullerene–like nanoclusters functionalized with Schiff bases: a DFT study

Structural Chemistry - In the present study, electronic properties of B12N12 nanocage functionalized with Schiff bases are studied by means of density functional theory (DFT) calculations at...     

A DFT study on the effect of hydrogen bonding on the reaction of a μ-benzoquinone diruthenium complex with acetylene

A DFT study was carried out to investigate the reaction mechanisms of a model μ-benzoquinone diruthenium complex {CpRu(μ-H)}₂(μ-η²:η²-C₆H₄O₂), derived from the experimental compound {Cp*Ru(μ-H)}₂(μ-η²:η²-C₆H₃RO₂) (R = H or R = Me, Cp* = η⁵-C₅Me₅), with acetylene both in aprotic and protic solvents. Results of calculations show that the influence of the solvent methanol on the reaction is mainly on the step of acetylene coordination. Enhanced hydrogen bonding is the reason for acceleration of the reaction in protic solvent, which is supported by NBO charge analysis.     

Substituents effect on thermal electrocyclic reaction of dihydroazulene–vinylheptafulvene photoswitch: a DFT study to improve the photoswitch

Thermal cyclization for a series of substituted vinylheptafulvenes (VHFs) to dihydroazulenes (DHAs) was studied at PBE0 method of density functional theory in the gas phase and in the acetonitrile solvent (through PCM). Judicious control of the thermal reaction through substituent is quite necessary to design thermally robust DHA–VHF photoswitches. For most of the substituents, DHA was predicted thermodynamically stable over VHF except for amino (in gas phase and solvent) and hydroxyl (in acetonitrile), where DHA isomers were calculated thermally unstable compared to VHF. Activation barriers for thermal electrocyclic reaction in both media showed positive correlation with Taft’s σ _R values at positions 7 and 5, however, a negative correlation was observed at position 4 and 6. The latter unprecedented behavior is proposed to arise from the delocalization of negative charges on the seven membered ring. Activation barriers for amino-substituted VHFs were generally lower than expected from Taft’s σ _R. A fluoro group at the position 7 was quite effective in imparting very high activation barrier (31.73 kcal mol^?1) for the thermal cyclization in the gas phase. However, in the acetonitrile solvent, the highest activation barriers were observed for electron withdrawing CHO (28.10 kcal mol^?1) and NO₂ (28.13 kcal mol^?1) groups at positions 7.     

Asymmetric aza-Henry reaction with α-substituted nitroacetates catalyzed by a bifunctional thiourea-guanidine catalyst

The asymmetric aza-Henry reaction of α-substituted nitroacetates and N-Boc imines was achieved with a new-type thioureaguanidine bifunctional organocatalyst.The novel transformations exhibited high diastereoselectivities,and the adducts bearing adjacent quaternary and tertiary chiral centers were generally obtained in moderate to good enantioselectivities(up to 88%ee).     

EPR and DFT study of the ethylene reaction with O− radicals on the surface of nanocrystalline MgO

Research on Chemical Intermediates - Different radical forms of oxygen (O?, O 2 ? and O 3 ? ) on the surface of nanocrystalline MgO are well known. It was earlier demonstrated...     

Acylation of phenols with γ-chlorobutyroyl chloride and transformations of the reaction products

Alkylphenols afford only O-acyl derivatives on treatment with -chlorobutyroyl chloride in the presence of both Et₃N and AIC1₃ at 20–60 °C. They cyclize under the action of K₂CO₃ in DMSO into the respective cyclopropanes and undergo Fries rearrangement on heating with AICl₃ at 120 °C into C-acyl derivatives.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 1023–1025, April, 1996.     

Interfacing cytochrome c to electrodes with a DNA – carbon nanotube composite film

Multi-walled carbon nanotube (MWCNT) is successfully immobilized on the surface of platinum electrode by mixing with DNA. The DNA/MWCNT modified electrodes are characterized by electrochemical impedance spectroscopy and cyclic voltammetry. Further research indicates that cytochrome c can strongly adsorbed on the surface of the modified electrode, and forms an approximate monolayer. The immobilized MWCNT can promote the redox of horse heart cytochrome c which gives reversible redox peaks with a formal potential of 81 mV vs SCE.     

Formation of a vanillic Mannich base — theoretical study

One-pot anti-Mannich reaction of vanillin, aniline and cyclohexanone was successfully catalyzed by ionic liquid triethanolammonium chloroacetate, at room temperature. Yield of the obtained Mannich base was very good and excellent diastereoselectivity was achieved. Mechanism of the reaction was investigated using the density functional theory. The reaction started with a nucleophilic attack of aniline nitrogen at the carbonyl group of vanillin. The intermediate α-amino alcohol formed in this way was further subjected to protonation by the triethanolammonium ion yielding the imminium ion. Theoretically, the obtained imminium ion and the enol form of cyclohexanone can build the protonated Mannich base via the anti and syn pathways. The chloroacetic anion spontaneously abstracts the proton yielding the final product of the reaction anti 2-[1-(N-phenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-H). The syn pathway requires lower activation energy but the anti pathway yields a thermodynamically more stable product, which implies that the examined Mannich reaction is thermodynamically controlled.     

Formation of asymmetric N-hydroxyaryl-N′-aryl(hetaryl)diazenes in the reaction of N-aryl(hetaryl)-N′-phosphoryldiazene-N-oxides with bases

Aromatic and heterocyclic N-phenoxyphosphoryldiazene N-oxides react with bases to give asymmetric N-hydroxyaryl-N-aryl- and N-hydroxyaryl-N-hetaryldiazenes.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 609–610, March, 1993.     

1,2,4-Triazines – products of reaction of thiocarbohydrazide and its alkyl(aryl)-substituted derivatives with 1,2-dicarbonyl compounds

The reaction of a series of 1,2-dicarbonyl compounds with thiocarbohydrazide and its 1- and 1,4-alkyl-(aryl)-substituted analogs has been studied. Treatment of diacetyl with the polynucleophiles indicated gives monohydrazones and/or 5-methylene-4,5-dihydro-2H-[1,2,4]triazine-3-thiones. Reaction of phenylglyoxal and benzil with thiocarbohydrazide yields 5-hydroxy- or 5-alkoxy-4,5-dihydro-2H-[1,2,4]triazine-3-thiones depending on the nature of the solvent. The products of condensation with 1,1-dimethylthiocarbohydrazide showed a thiocarbonohydrazone – 5-hydroxy-4,5-dihydro-2H-[1,2,4]tri-azine-3-thione ring-chain type equilibrium.     

Synthesis and characterization of shell cross-linked micelles with hydroxy-functional coronas: a pragmatic alternative to dendrimers?

Shell cross-linked (SCL) micelles with hydroxy-functional coronas have been constructed in aqueous solution by exploiting the micellar self-assembly behavior of a new thermoresponsive ABC triblock copolymer. This copolymer was prepared via atom transfer radical polymerization in a convenient one-pot synthesis and comprised a thermoresponsive core-forming poly(propylene oxide) (PPO) block, a cross-linkable central poly(2-(dimethylamino)ethyl methacrylate) (DMA) block, and a hydroxy-functional outer block based on poly(glycerol monomethacrylate) (GMA). DMF GPC analysis confirmed a unimodal molecular weight distribution for the PPO-PDMA-PGMA triblock copolymer precursor, with an M(n) of 12 100 and a polydispersity of approximately 1.26. This copolymer dissolved molecularly in aqueous solution at 5 degrees C but formed micelles with hydroxy-functional coronas above a critical micelle temperature of around 12 degrees C, which corresponded closely to the cloud point of the PPO macroinitiator. Cross-linking of the DMA residues using 1,2-bis(2-iodoethoxy)ethane produced SCL micelles that remained intact at 5 degrees C, i.e., below the cloud point of the core-forming PPO block. Dynamic light scattering studies confirmed that the SCL micelle diameter could be varied depending on the temperature employed for cross-linking: smaller, more compact SCL micelles were formed at higher temperatures, as expected. Since cross-linking involved quaternization of the DMA residues, the SCL micelles acquired cationic surface charge as judged by aqueous electrophoresis studies. These cationic SCL micelles were adsorbed onto near-monodisperse anionic silica sols, which were used as a model colloidal substrate. Thermogravimetric analyses indicated a SCL micelle mass loading of 2.5-4.4%, depending on the silica sol diameter and the initial micelle concentration. Aqueous electrophoresis measurements confirmed that surface charge reversal occurred after adsorption of the SCL micelles, and scanning electron microscopy studies revealed a uniform coating of SCL micelles on the silica particles.     

Mössbauer spectroscopy of corrosion products of mild steel due to microbiologically influenced corrosion

Corrosion products of mild steel exposed to four different cultures of sulfur reducing bacteria (SRB) grown in a synthetic medium have been studied by transmission Mössbauer spectroscopy (TMS). Cultures of SRB studied are two hydrogenase positive strains,Desulfovibrio desulfuricans (DD) andDesulfovibrio vulgaris (DV) and two hydrogenase negative strainsDesulfotomaculum orientis orientis (DO) andDesulfotomaculum nigrificans (DN). The corrosion products generated on the coupons as well as in the broth were studied. In all the cases, the corrosion products removed from coupons showed the presence of green rust 2 (GR2), ferrous sulfides, γ-FeOOH and superparamagnetic (SPM) α-FeOOH in different proportions. The corrosion products from the broth showed a symmetrical central doublet, which indicates the presence of γ-FeOOH and SPM α-FeOOH along with ferrous sulfides. The corrosion products from coupons suspended in sewage water also showed the presence of GR 2 and ferrous sulfides together with oxyhydroxides. FTIR spectrum supports the presence of these phases in corrosion products. The formation of GR 2 on coupons seems to be the first step for the SRB induced corrosion. The corrosion rate has been found in the order of DO>DN>DV>DD.     

Chemical degradation of polyaniline by reaction with Fenton’s reagent — a spectroelectrochemical study

Changes in the various chemical and structural properties of polyaniline (PANI) films effected by interaction with Fenton’s reagent are monitored with electrochemical in situ spectroscopic and surface-sensitive techniques. Starting from a model of possible structural changes caused by chemical attack of species generated by Fenton’s reagent, particular attention is paid to the differences between the compact and highly porous (open) forms of PANI.     

A study of the color reaction of iron with “TTA”

Summary TTA, or 2-Thenoyltrifluoroacetone, gives with ferric ion, in various concentrations colorations ranging from blood red to light pink. The advantages of this test are that it is simple to perform, that it is applicable in different acid media of fairly high concentrations, and that it is somewhat sensitive in the presence of ions that usually interfere with such tests. The sensitivity (limit of identification) was found to be 0,5 and the limit of concentration 1 : 100000 when a benzene solution of the reagent was reacted with a slightly acid solution of ferric ion on spot paper.

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Zusammenfassung TTA (2-Thenoyltrifluoraceton) gibt mit Ferriionen je nach Konzentration der letzteren eine blutrote bis blaßrosa Färbung. Die Probe ist einfach ausführbar und wird durch die Gegenwart von Säuren bis zu ziemlich hohen Konzentrationen sowie durch die Gegenwart störender Ionen wenig beeinträchtigt. Wenn eine Lösung des Reagens in Benzol zu einer leicht angesäuerten Ferrisalzlösung zugesetzt wird, beträgt die Erfassungsgrenze 0,5 bei einer Grenzkonzentration von 1 : 100000.

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Résumé Le TTA, thénoyl-2 trifluoracétone, donne avec les ions ferriques, suivant leur concentration, une coloration rouge sang à rose pâle. L'essai est simple à effectuer et à peine troublé par la présence des acides jusqu'à des concentrations passablement élevées et par la présence des ions gênants. Quand on ajoute une solution du réactif dans le benzène à une solution peu acide de sel ferrique, on observe une limite de sensibilité de 0,5 pour une limite de dilution de 1 : 100000.

     

On study of chemoselectivity of reaction of trialkylalanes with alkenes, catalyzed with Zr π-complexes

The influence of the organoaluminium compound nature, Zr π-ligand environment, solvent type and reagent ratio on the chemoselectivity of reactions of trialkylalanes (AlMe₃, AlEt₃) with alkenes, catalyzed with L₂ZrCl₂ [L = Cp, Cp′ (Cp′-η⁵-C₅H₄CH₃), Cp^∗ (Cp^∗-η⁵-C₅(CH₃)₅), Ind (indenyl), Flu (fluorenyl)] has been studied. It is shown that in the case of AlMe₃, the hydro- and carboalumination products, and alkene dimers are formed. The catalytic reaction of AlEt₃ with the olefins yields aluminacyclopentanes altogether with the hydro- and carboalumination products, and the dimers. A probable reaction mechanism has been proposed.     

Orientation of photosynthetic reaction center in Langmuir–Blodgett film by formation of cross-linked complex with cytochrome c

Cross-linked complex between photosynthetic reaction center and horse heart cytochrome c (cyt c) was prepared for the control of molecular orientation in Langmuir–Blodgett (LB) method. The surface of cyt c is highly hydrophilic whereas that of RC is hydrophobic. A polar distribution of hydrophobicity/hydrophilicity in the complex was realized by the cross-linkage of the different protein molecules. An index was introduced to evaluate the hydrophobicity of the surface of the proteins. The orientation of RCs in an LB film was evaluated by the displacement current. The complex showed a response 1.5 times larger than that of RC.     

Direct dynamics study on the reaction of N2H4 with F atom: a hydrogen abstraction reaction?

We present a systematic direct ab initio dynamics investigation of the reaction between N2H4 and F atom, which is predicted to have three possible reaction channels. The structures and frequencies at the stationary points and the points along the minimum energy paths (MEPs) of all reaction channels were calculated at the UB3LYP/6-31+G(d,p) level of theory. Energetic information of stationary points and the points along the MEPs was further refined by means of the CCSD(T)/aug-cc-pVTZ method. The calculated results revealed that the first two primary channels (N2H4+F-->N2H3+HF) are equivalent and occur synchronously via the formation of a pre-reaction complex with Cs symmetry rather than via the direct H abstraction. The pre-reaction complex then evolves into a hydrogen-bonding intermediate through a transition state with nearly no barrier and a high exothermicity, which finally makes the intermediate further decompose into N2H3 and HF. Another reaction channel of minor role (N2H4+F-->NH2F+NH2) was also found during the calculations, which has the same Cs pre-reaction complex but forms NH2F and NH2 via another transition state with high-energy barrier and low exothermicity. The rate constants of these channels were calculated using the improved canonical variational transition state theory with the small-curvature tunneling correction (ICVT/SCT) method. The three-parameter ICVT/SCT rate constant expressions of k(ICVT/SCT) at the CCSD(T)/aug-cc-pVTZ//UB3LYP/6-31+G(d,p) level of theory within 220-3000 K were fitted as (7.64x10(-9))T (-0.87) exp(1180/T) cm3 mole-1 s-1 for N2H4+F-->N2H3+HF and 1.45x10(-12)(T/298)(2.17) exp(-1710/T) cm3 mole-1 s-1 for N2H4+F-->NH2F+NH2.