Theoretical studies on reaction mechanism of H2 with COS

The reaction mechanisms of H₂ with OCS have been investigated theoretically by using density function theory method. Three possible pathways leading to major products CO and H₂S, as well as two possible pathways leading to by-product CH₄ have been proposed and discussed. For these reaction pathways, the structure parameters, vibrational frequencies and energies for each stationary point have been calculated, and the corresponding reaction mechanism has been given by the potential energy surface, which is drawn according to the relative energies. The calculated results show that the corresponding major products CO and H₂S as well as by-product CH₄ are in agreement with experimental findings, which provided a new illustration and guidance for the reaction of H₂ with OCS.     

Theoretical study of the interaction between X (H,F) and graphene

This study investigates the interaction between X (X = H and F) and graphene C₅₄H₁₈ (D_6 h), and the potential energy surface of the graphene radical. The calculations on the structures and energies are further discussed thermodynamically and kinetically using the density function theory method at the B3LYP/6-31G (d) level. Our findings show that there are four distinct isomers of C₅₄H₁₈–X. C₅₄H₁₈–H² and C₅₄H₁₈–F⁴ are the most stable isomers in their own systems. In addition, the transition states, as well as reaction pathways of H transferring between different key points on representative patch, are given to explore the possible reaction mechanism. Finally, the stability of C₅₄H₁₈–X₂ is discussed through the density functional theory.     

Theoretical study of the catalytic reaction mechanism of MndD

Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho-dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a catalytic mechanism has been suggested. Models of different size were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the substrate first binds at the active site as a monoanion. Next the dioxygen is bound, forming a hydroperoxo intermediate. The O–O bond, activated in this way undergoes homolytic cleavage leading to an oxyl and then to an extra epoxide radical with subsequent opening of the aromatic ring. The lactone ring is then hydrolyzed by the Mn-bound OH group, and the final product is obtained in the last reaction steps. Alternative reaction paths were considered, and their calculated barriers were found to be higher than for the suggested mechanism. The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Theoretical study of the reaction of CH2XO (X = F, Cl, Br) radicals with the NO radical

In this paper, we focus on the multiple-channel reactions of CH₂XO (X = F, Cl, Br) radicals with the NO radical by means of direct dynamic methods. All structures of the stationary points were obtained at the MP2/6-311+G(d,p) level and vibrational frequency analysis was also performed at this level of theory. The minimum energy path (MEP) was obtained via the intrinsic reaction coordinate (IRC) theory at the MP2/6-311+G(d,p) level, and higher-level energetic information was refined by the MC-QCISD method. The rate constants for the three hydrogen abstraction reaction channels over the temperature range 200–1,500 K were calculated by the improved canonical variational transition state theory (ICVT) with a correction for small-curvature tunneling (SCT). The rate constants calculated in this manner were in good agreement with the available experimental data, and the three-parameter rate–temperature formulae for the temperature range 200–1,500 K were $ {k_{1{\text{a}} }}(T)=0.32\times {10^{-18 }}{T^{1.83 }}\exp \left( {1748.54/T} \right) $ , $ {k_{2{\text{a}} }}(T)=0.22\times {10^{-19 }}{T^{2.19 }}\exp \left( {1770.19/T} \right) $ , $ {k_{3{\text{a}} }}(T)=0.88\times {10^{-20 }}{T^{2.20 }}\exp \left( {1513.82/T} \right) $ (in units of cm³ molecule^?1?s^?1).     

Theoretical study of the discrimination between O(2) and CO by myoglobin

Combined quantum chemical and molecular mechanics geometry optimisations have been performed on myoglobin without or with O(2) or CO bound to the haem group. The results show that the distal histidine residue is protonated on the N(epsilon 2) atom and forms a hydrogen bond to the haem ligand both in the O(2) and the CO complexes. We have also re-refined the crystal structure of CO[bond]myoglobin by a combined quantum chemical and crystallographic refinement. Thereby, we probably obtain the most accurate available structure of the active site of this complex, showing a Fe[bond]C[bond]O angle of 171 degrees, and Fe[bond]C and C[bond]O bond lengths of 170-171 and 116-117 pm. The resulting structures have been used to calculate the strength of the hydrogen bond between the distal histidine residue and O(2) or CO in the protein. This amounts to 31-33 kJ/mol for O(2) and 2-3 kJ/mol for CO. The difference in hydrogen-bond strength is 21-22 kJ/mol when corrected for entropy effects. This is slightly larger than the observed discrimination between O(2) or CO by myoglobin, 17 kJ/mol. We have also estimated the strain of the active site inside the protein. It is 2-4 kJ/mol larger for the O(2) complex than for the CO complex, independent of which crystal structure the calculations are based on. Together, these results clearly show that myoglobin discriminates between O(2) and CO mainly by electrostatic interactions, rather than by steric strain.     

Theoretical study of AlH(2+)n (n=1-7) dications

The structures and stability of 1–7 dications were calculated at the ab initio MP2/aug-cc-pVTZ level of theory. The dications AlH²⁺ 1 and 2 were characterized to be unstable thermodynamically. However, these and the stable dications, 3–7 have considerable kinetic barriers for deprotonation. Each of the structures 3–7 contains one or more two-electron three-center (2e–3c) bonds. Aluminum atoms of these dications carry most of the positive charges, as indicated by NBO charge calculations.Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday     

A modelling study of a non-concerted hydrolytic cycloaddition reaction by the catalytic antibody H11

H11 is the first antibody reported to have dual activity as a non-concerted, Diels-Alderase and hydrolytic catalyst. It was previously shown to catalyse the cycloaddition of acetoxybutadiene 1a to N-alkyl maleimides 2 to afford hydroxy-substituted bicyclic adducts 3 with a 30% ee of a major isomer. To better understand this mechanism and the partial stereospecificity, a homology model of H11 was constructed and used in docking studies to evaluate potential antibody-ligand complexes. The model suggested the hydrolytic nature of H11 was due to Glu 95H acting as a catalytic base, and evaluation of the shape complementarity of the proposed antibody-ligand complexes confirmed at a semi-quantitative level the observation that the major enantiomer is produced in a 30% ee.     

Electrochemical investigations of the reaction mechanism and kinetics between NADH and redox-active (NC)2C6H3-NHOH/(NC)2C6H3-NO from 4-nitrophthalonitrile-(NC)2C6H3-NO2-modified electrode

A simple and sensitive method for the electrocatalytic detection of NADH on a carbon paste electrode modified with a redox-active (NC)(2)C(6)H(3)-NO/(NC)(2)C(6)H(3)-NHOH (NOPH/NHOHPH) electrogenerated in situ from 4-nitrophthalonitrile (4-NPHN) is presented. The electrode modified with 4-NPHN showed an efficient electrocatalytic activity towards the oxidation of NADH with activation overpotential of 0.12V vs. Ag/AgCl. The formation of an intermediate charge transfer complex is proposed for the charge transfer reaction between NADH and the 4-NPHN-resulting system. The second-order rate constant for electrocatalytic oxidation of NADH, kappa(obs), and the apparent Michaelis-Menten constant K(M), at pH 7.0 were evaluated with rotating disk electrode (RDE) experiments, giving 1.0x10(4)mol(-1)Ls(-1) and 2.7x10(-5)molL(-1), respectively. Employing the Koutecky-Levich approach indicated that the NADH oxidation reaction involves two electrons. The sensor provided a linear response range for NADH from 0.8 up to 8.5mumolL(-1) with sensitivity, detection, quantification limits and time response of 0.50muALmumol(-1), 0.25mumolL(-1), 0.82mumolL(-1) and 0.1s, respectively. The repeatability of the measurements with the same sensor and different sensors, evaluated in terms of relative standard deviation, were 4.1 and 5.0%, respectively, for n=10.     

Ab initio and DFT conformational study on N-nitrosodiethylamine, (C2H5)2N-N=O

Ab initio (MP2) and DFT (B3LYP) calculations, using the cc-pVTZ and aug-cc-pVTZ basis sets, have been performed to characterize some stationary points on the ground state potential energy surface of the title molecules. Several properties as, for instance, relative energies, the barriers for NO rotation around the NN bond, NBO charges on O and amino N atoms, as well as the dipole moments, have been calculated and analyzed in the light of the structures found. Both computational levels here employed yield three minima, in which the C₂NNO frame is ‘planar’ or ‘quasi-planar’. Important correlations between NBO charges and geometric parameters, as well as between some structural features and dipole moments are also discussed. A total of 17 structures have been found for the (C₂H₅)₂N-N=O molecule. Two ranges of values have been obtained for the dipole moment, with the largest values occurring for the structures in which the nitrogen lone pair is parallel to the NO group π system. For instance, these two ranges are from ~4.1 to 4.5 D, and from ~1.6 to 2.1 D, at the MP2/cc-pVTZ level. These ranges are consistent with a larger and a smaller contribution of a dipolar resonance structure, respectively. As the method or basis set changes the values of the dipole moments change by at most ~0.23 D.     

FACE-selective fluorogenic cycloaddition reaction between coumarin azides and sugar terminal alkynes: an experimental and computational study

Copper catalyzed azide–alkyne cycloaddition reaction (CuAAC) of non-fluorescent coumarin azides and sugar terminal alkynes afforded intense fluorescent 1,2,3-triazoles in 75–85% of yield. The photophysical properties of coumarin–sugar triazoles influenced greatly, upon introducing different substituents at 6th and 7th positions. The experimental observations were further supported by TD-DFT computational studies.     

The reaction of H(2)S with oxidized thiols: generation of persulfides and implications to H(2)S biology

Hydrogen sulfide is an endogenously generated molecule with many reported physiological functions. Although several biological targets have been proposed, the biochemical mechanisms by which it elicits activity are not established. Thus, in an effort to begin to delineate the fundamental biological chemistry of H₂S, we have examined the reaction of H₂S with oxidized thiols and thiol proteins in order to determine whether persulfide formation occurs, is stable and how this may affect protein function. We have found that persulfides are easily generated, relatively stable and can alter enzyme activity. Moreover, we have begun to develop methodology for in situ generation of persulfides to facilitate further study of this potentially important species.     

Kinetics and DFT studies on the reaction of copper(II) complexes and H2O2

Copper(II) complexes supported by bulky tridentate ligands L1^H (N,N-bis(2-quinolylmethyl)-2-phenylethylamine) and L1^Ph (N,N-bis(2-quinolylmethyl)-2,2-diphenylethylamine) have been prepared and their crystal structures as well as some physicochemical properties have been explored. Each complex exhibits a square pyramidal structure containing a coordinated solvent molecule at an equatorial position and a weakly coordinated counter anion (or water) at an axial position. The copper(II) complexes reacted readily with H₂O₂ at a low temperature to give mononuclear hydroperoxo copper(II) complexes. Kinetics and DFT studies have suggested that, in the initial stage of the reaction, deprotonated hydrogen peroxide attacks the cupric ion, presumably at the axial position, to give a hydroperoxo copper(II) complex retaining the coordinated solvent molecule (H ^R ·S). H ^R ·S then loses the solvent to give a tetragonal copper(II)-hydroperoxo complex (H ^R ), in which the –OOH group may occupy an equatorial position. The copper(II)–hydroperoxo complex H ^R exhibits a relatively high O–O bond stretching vibration at 900 cm⁻¹ compared to other previously reported examples.Electronic Supplementary Material Supplementary material is available for this article at     

Kinetics and mechanism of the reaction between 1,2-diaminopropanetetra-acetatoferrate(III) and cyanide ion

The present study examines the kinetics and mechanism of the system [FePDTA(OH)]²⁻ + 5CN⁻ ⇌ [Fe(CN)₅OH]³⁻ + PDTA⁴⁻ at pH= 11.0±0.02, I= 0.25 M and temperature = 25 ± 0.1 °C. The reaction has been studied spectrophotometrically at 395 nm (λ_max of [Fe(CN)₅OH]³⁻). The data show that the reaction has three distinguishable stages; the first stage is formation of [Fe(CN)₅OH]³⁻, the second is conversion of [Fe(CN)₅OH)]³⁻ to [Fe(CN)₆]³⁻ and last is reduction of [Fe(CN)₆]³⁻ to [Fe(CN)₆]³⁻ by the released ligand, viz., PDTA. The first reaction shows variable order dependence on cyanide concentration, one at high cyanide concentration and two at low cyanide concentration. The second reaction exhibits first order dependence on the concentration of [Fe(CN)₅OH]³⁻ as well as cyanide. The reverse reaction between [Fe(CN)₅OH]³⁻ and PDTA is first order in [Fe(CN)₅OH]³⁻ and PDTA, and inverse first order in cyanide. On the basis of forward and reverse rate studies, a five-step mechanism has been proposed for the first reaction.     

Characterization of bis(levuglandinyl) urea derivatives as products of the reaction between prostaglandin H2 and arginine

Levuglandins are gamma-keto aldehydes formed by rearrangement of prostaglandin (PG) H(2) in aqueous solution. Levuglandins are highly reactive with primary amines. We had previously characterized adducts formed after reaction of levuglandin E(2) (LGE(2)) or PGH(2) with lysine. In this study, we assessed whether reaction of PGH(2) with arginine yielded covalent adducts. Using N(alpha)-acetylarginine and both PGH(2) and synthetic LGE(2), we discovered a novel series of levuglandinyl adducts derived from reaction of two levuglandin moieties with the guanidino group of arginine. Subsequent spontaneous hydrolysis of the adducted amino acid yields bis(levuglandinyl) urea and the corresponding ornithine residue. Using liquid chromatography tandem mass spectrometry, we characterized the molecular structure of these novel adducts and demonstrated their formation after coincubation of PGH(2) with synthetic peptides and proteins. The soluble characteristic of these molecules provides a potential strategy for development of biological markers of lipid modification of proteins following cyclooxygenase activity or lipid peroxidation.     

Inhibitory and enhancing effects of NO on H(2)O(2) toxicity: dependence on the concentrations of NO and H(2)O(2)

Nitric oxide (NO) has been shown to both enhance hydrogen peroxide (H(2)O(2)) toxicity and protect cells against H(2)O(2) toxicity. In order to resolve this apparent contradiction, we here studied the effects of NO on H(2)O(2) toxicity in cultured liver endothelial cells over a wide range of NO and H(2)O(2) concentrations. NO was generated by spermine NONOate (SpNO, 0.001-1 mM), H(2)O(2) was generated continuously by glucose/glucose oxidase (GOD, 20-300 U/l), or added as a bolus (200 microM). SpNO concentrations between 0.01 and 0.1 mM provided protection against H(2)O(2)-induced cell death. SpNO concentrations >0.1 mM were injurious with low H(2)O(2) concentrations, but protective at high H(2)O(2) concentrations. Protection appeared to be mainly due to inhibition of lipid peroxidation, for which SpNO concentrations as low as 0.01 mM were sufficient. SpNO in high concentration (1 mM) consistently raised H(2)O(2) steady-state levels in line with inhibition of H(2)O(2) degradation. Thus, the overall effect of NO on H(2)O(2) toxicity can be switched within the same cellular model, with protection being predominant at low NO and high H(2)O(2) levels and enhancement being predominant with high NO and low H(2)O(2) levels.     

Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases

N6-methyladenine (m⁶A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH₃. Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m⁶A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH₃ changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m⁶A:G and trans-m⁶A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m⁶A to cis-m⁶A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m⁶A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory.

Theoretical study of structure, bonding, and electronic behavior of novel sandwich compounds M3(C6R6)2 (M = Ni, Pd, Pt; R = H, F)

The correlations between the structural and electronic properties of the monolayer clusters M(3) (where M = Ni, Pd, Pt) and the sandwich complexes M(3)(C(6)R(6))(2) (where M = Ni, Pd, Pt; R = H, F) were studied by performing quantum-chemical calculations. All of the sandwich complexes are strongly donating and backdonating metal-ligand bonding structures. The influence of the ligand as well as significant variations in the M-C, M-M, and C-C bond lengths and binding energies were examined to obtain a qualitative and quantitative picture of the intramolecular interactions in C(6)R(6)-M(3). Our theoretical investigations show that the binding energies of these sandwich complexes gradually decrease from Ni to Pt as well as from H to F, which can be explained via the frontier orbitals of the clusters M(3) and C(6)R(6).