EPR, 1H and 2H NMR, and reactivity studies of the iron-oxygen intermediates in bioinspired catalyst systems

Complexes [(BPMEN)Fe(II)(CH(3)CN)(2)](ClO(4))(2) (1, BPMEN = N,N'-dimethyl-N,N'-bis(2-pyridylmethyl)-1,2-diaminoethane) and [(TPA)Fe(II)(CH(3)CN)(2)](ClO(4))(2) (2, TPA = tris(2-pyridylmethyl)amine) are among the best nonheme iron-based catalysts for bioinspired oxidation of hydrocarbons. Using EPR and (1)H and (2)H NMR spectroscopy, the iron-oxygen intermediates formed in the catalyst systems 1,2/H(2)O(2); 1,2/H(2)O(2)/CH(3)COOH; 1,2/CH(3)CO(3)H; 1,2/m-CPBA; 1,2/PhIO; 1,2/(t)BuOOH; and 1,2/(t)BuOOH/CH(3)COOH have been studied (m-CPBA is m-chloroperbenzoic acid). The following intermediates have been observed: [(L)Fe(III)(OOR)(S)](2+), [(L)Fe(IV)═O(S)](2+) (L = BPMEN or TPA, R = H or (t)Bu, S = CH(3)CN or H(2)O), and the iron-oxygen species 1c (L = BPMEN) and 2c (L = TPA). It has been shown that 1c and 2c directly react with cyclohexene to yield cyclohexene oxide, whereas [(L)Fe(IV)═O(S)](2+) react with cyclohexene to yield mainly products of allylic oxidation. [(L)Fe(III)(OOR)(S)](2+) are inert in this reaction. The analysis of EPR and reactivity data shows that only those catalyst systems which display EPR spectra of 1c and 2c are able to selectively epoxidize cyclohexene, thus bearing strong evidence in favor of the key role of 1c and 2c in selective epoxidation. 1c and 2c were tentatively assigned to the oxoiron(V) intermediates.     

N(4S)+CH3X(X=Cl、Br)反应机理的理论研究

The reaction of N(4S)+CH3X(X=Cl、Br) was studied by the ab initio method. The geometries of the reactants, transition states and products were optimized at the MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single-point calculations for all the stationary points were carried out at the MP2/6-311++G(3df,2p) and the QCISD(T)/6-311+G(d,p) levels using the MP2/6-311+G(d,p) optimized geometries. The energies of all the stationary points were calculated by the G2MP2 method. The results of this theoretical study indicate that the reaction has three reaction channels: H abstraction reaction channel a, Cl or Br abstraction reaction channel b and substitution reaction channel c. For the N(4S)+CH3Cl reaction, reaction channel a is the main reaction channel. Reaction channels b and c may have a slight contribution in the reaction. For the N(4S)+CH3Br reaction, reaction channel a is the main reaction channel. Reaction channels b and c may have some contribution in the reaction.     

Communication: theoretical exploration of Au(+)+H2, D2, and HD reactive collisions

A quasi-classical study of the endoergic Au(+)((1)S) + H(2)(X(1)Σ(g)(+)) → AuH(+) ((2)Σ(+)) + H((2)S) reaction, and isotopic variants, is performed to compare with recent experimental results [F. Li, C. S. Hinton, M. Citir, F. Liu, and P. B. Armentrout, J. Chem. Phys. 134, 024310 (2011)]. For this purpose, a new global potential energy surface has been developed based on multi-reference configuration interaction ab initio calculations. The quasi-classical trajectory results show a very good agreement with the experiments, showing the same trends for the different isotopic variants of the hydrogen molecule. It is also found that the total dissociation into three fragments, Au(+)+H+H, is the dominant reaction channel for energies above the H(2) dissociation energy. This results from a well in the entrance channel of the potential energy surface, which enhances the probability of H-Au-H insertion.     

The reaction of tricarbon with acetylene: an ab initio/RRKM study of the potential energy surface and product branching ratios

Ab initio calculations of the potential energy surface for the C3(1Sigmag+)+C2H2(1Sigmag+) reaction have been performed at the RCCSD(T)/cc-pVQZ//B3LYP/6-311G(d,p) + ZPE[B3LYP/6-311G(d,p)] level with extrapolation to the complete basis set limit for key intermediates and products. These calculations have been followed by statistical calculations of reaction rate constants and product branching ratios. The results show the reaction to begin with the formation of the 3-(didehydrovinylidene)cyclopropene intermediate i1 or five-member ring isomer i7 with the entrance barriers of 7.6 and 13.8 kcal/mol, respectively. i1 rearranges to the other C5H2 isomers, including ethynylpropadienylidene i2, singlet pentadiynylidene i3, pentatetraenylidene i4, ethynylcyclopropenylidene i5, and four- and five-member ring structures i6, i7, and i8 by ring-closure and ring-opening processes and hydrogen migrations. i2, i3, and i4 lose a hydrogen atom to produce the most stable linear isomer of C5H with the overall reaction endothermicity of approximately 24 kcal/mol. H elimination from i5 leads to the formation of the cyclic C5H isomer, HC2C3, +H, 27 kcal/ mol above C3+C2H2. 1,1-H2 loss from i4 results in the linear pentacarbon C5+H2 products endothermic by 4 kcal/mol. The H elimination pathways occur without exit barriers, whereas the H2 loss from i4 proceeds via a tight transition state 26.4 kcal/mol above the reactants. The characteristic energy threshold for the reaction under single collision conditions is predicted be in the range of approximately 24 kcal/mol. Product branching ratios obtained by solving kinetic equations with individual rate constants calculated using RRKM and VTST theories for collision energies between 25 and 35 kcal/mol show that l-C5H+H are the dominant reaction products, whereas HC2C3+H and l-C5+H2 are minor products with branching ratios not exceeding 2.5% and 0.7%, respectively. The ethynylcyclopropenylidene isomer i5 is calculated to be the most stable C5H2 species, more favorable than triplet pentadiynylidene i3t by approximately 2 kcal/mol.     

A comparative study on the nature and strength of O–O, S–S, and Se–Se bond

A computational study on dichalcogenide molecules (R₂X₂; X = O, S, Se; R = H, CH₃, NH₂) has been carried out employing B3LYP and MP2 levels using 6-31+G*, 6-311+G*, 6-311++G**, and PVDZ basis sets. The relative energies have been evaluated at G2MP2 also. The rotational barriers and bond dissociation energies indicate that S–S bond is stronger than Se–Se and O–O bond. NBO analysis at MP2/6-31+G* suggest the presence of partial π character between X–X bond that decreases in the order S–S > Se–Se > O–O. Fuki functions for nucleophilic and electrophilic attack fail to distinguish the reactivity of S and Se. The proton affinities of the O₂H₂, S₂H₂, Se₂H₂ decrease in the order Se > S > O.     

C(3P)与H2S反应的反应机理

The mechanisms of the C(3P)+H 2S→HCS+H and C(3P)+H 2S → HSC+H reactions have been studied at the UMP2/6-31G(d,p),UMP2/6-311G(d,p),and G2 levels, and six transition states and three intermediates have been located along the reaction paths. The predicted path for the C(3P)+H2S→HCS+H reaction is: C(3P)+H2S→IM1→TS1→IM2→TS4→HCS+H, in line with the reaction process suggested by Lee et al. [1] in which only the intermediates were given. Our energetic results indicate that the C(3P)+H2S→HCS+H reaction is more favorable than the C(3P)+H 2S→HSC+H reaction, in agreement with experiment.     

Quantum chemical and theoretical kinetics study of the O(3P) + C2H2 reaction: a multistate process

The potential energy surfaces of the two lowest-lying triplet electronic surfaces 3A' and 3A' for the O(3P) + C2H2 reaction were theoretically reinvestigated, using various quantum chemical methods including CCSD(T), QCISD, CBS-QCI/APNO, CBS-QB3, G2M(CC,MP2), DFT-B3LYP and CASSCF. An efficient reaction pathway on the electronically excited 3A' surface resulting in H(2S) + HCCO(A2A') was newly identified and is predicted to play an important role at higher temperatures. The primary product distribution for the multistate multiwell reaction was then determined by RRKM statistical rate theory and weak-collision master equation analysis using the exact stochastic simulation method. Allowing for nonstatistical behavior of the internal rotation mode of the initial 3A' adducts, our computed primary-product distributions agree well with the available experimental results, i.e., ca. 80% H(2S) + HCCO(X2A' + A2A') and 20% CH2(X3B1) + CO(X1sigma+) independent of temperature and pressure over the wide 300-2000 K and 0-10 atm ranges. The thermal rate coefficient k(O + C2H2) at 200-2000 K was computed using multistate transition state theory: k(T) = 6.14 x 10(-15)T (1.28) exp(-1244 K/T) cm3 molecule(-1) s(-1); this expression, obtained after reducing the CBS-QCI/APNO ab initio entrance barriers by 0.5 kcal/mol, quasi-perfectly matches the experimental k(T) data over the entire 200-2000 K range, spanning 3 orders of magnitude.     

Spectral analysis of Mn2+, Co2+ and Ni2+: B2O3-ZnO-PbO glasses

This paper reports on the spectral properties of Mn2+, Co2+ and Ni2+ ions doped B2O3-ZnO-PbO glasses. XRD, FT-IR spectra and DSC profiles of these glasses have also been carried out, and the FT-IR profiles have shown the presence of both BO3 and BO4 units. It is interesting to notice that the FT-IR peak positions are slightly shifted towards higher energy with an increase in transition metal ion concentration change. From the measured DSC thermograms, glass transition (T(g)), crystallization (T(c)) and temperature of melting (T(m)) have been evaluated. From the UV absorption spectra of Mn2+, Co2+ and Ni2+ ions doped glasses, both direct and indirect optical band gaps have been calculated. The visible absorption spectra of Mn2+:glasses have shown a broad absorption band at 520 nm (6A1g(S) --> 4T1g(G)); with Co2+ ions one absorption band at 605 nm (4A2(4F) --> 4T1(4P)) and another at 1450 nm (4A2(4F) --> 4T1(4F)); and for Ni2+:glasses three absorption bands at 420 nm (3A2g(F) --> 3T1g(P)), 805 nm (3A2g(F) --> 1Eg(D)) and 880 nm (3A2g(F) --> 3T1g(F)) have been observed. For Mn2+:glasses, upon excitation with 262 nm, a green emission (539 nm) with a slight blue shift; and with 392 nm, a green emission (534 nm) with a slight red shift with Mn2+ ions concentration change (0.2-0.5 mol%) has been observed. This green emission has been assigned to (4T1(G) --> 6A1(S)) d-d transition of Mn2+ ions that are in tetrahedral co-ordination. For 0.5 mol% Co2+ ions doped glass, upon excitation with 580 nm, a red emission (625 nm) has been observed which originates from 2E(2G) --> 4A2(4F) transition of Co2+ ions in tetrahedral co-ordination. For Ni2+ ions doped glasses upon excitation with 420 nm, a green (577 nm) and red (670 nm) emissions are observed and are assigned to (1T2g(D) --> 3A2g(F)) and (1T2g(D) --> 3T2g(F)) d-d transitions of Ni2+ ions in octahedral co-ordination.     

Amorphous/crystalline (A/C) thermodynamic "rules of thumb": estimating standard thermodynamic data for amorphous materials using standard data for their crystalline counterparts

Standard thermochemical data (in the form of Δ(f)H° and Δ(f)G°) are available for crystalline (c) materials but rarely for their corresponding amorphous (a) counterparts. This paper establishes correlations between the sets of data for the two material forms (where known), which can then be used as a guideline for estimation of missing data. Accordingly, Δ(f)H°(a)/kJ mol(-1) ≈ 0.993Δ(f)H°(c)/kJ mol(-1) + 12.52 (R(2) = 0.9999; n = 50) and Δ(f)G°/kJ mol(-1) ≈ 0.988Δ(f)H°(c)/kJ mol(-1) + 0.70 (R(2) = 0.9999; n = 10). Much more tentatively, we propose that S°(298)(c)/J K(-1) mol(-1) ≈ 1.084S°(298)(c)/J K(-1) mol(-1) + 6.54 (R(2) = 0.9873; n = 11). An amorphous hydrate enthalpic version of the Difference Rule is also proposed (and tested) in the form [Δ(f)H°(M(p)X(q)·nH(2)O,a) - Δ(f)H°(M(p)X(q),a)]/kJ mol(-1) ≈ Θ(Hf)n ≈ -302.0n, where M(p)X(q)·nH(2)O represents an amorphous hydrate and M(p)X(q) the corresponding amorphous anhydrous parent salt.     

Role of singlet diradicals in reactions of 2-carbenabicyclo[3.2.1]octa-3,6-diene

The generation of 2-carbenabicyclo[3.2.1]octa-3,6-diene (1) results in the formation of C(8)H(8) hydrocarbons endo-6-ethynylbicyclo[3.1.0]hex-2-ene (4), semibullvalene (5), and 5-ethynyl-1,3-cyclohexadiene (6), and C(8)H(10) hydrocarbons bicyclo[3.2.1]octa-2,6-diene (7), tricyclo[3.2.1.0(4,6)]oct-2-ene (8), and tetracyclo[3.3.0.0(2,8)0(4,6)]octane (9). Focus is placed on three mechanistic pathways for the formation of the C(8)H(10) hydrocarbon fraction: (a) abstraction of hydrogen by triplet carbene 1T to produce an equilibrating set of monoradicals, (b) interconversion of triplet carbene 1T into tricyclic triplet diradical 19T and tetracyclic triplet diradical 20T, and (c) interconversion of singlet 1S with analogous singlet diradical 19S and 20S. Ab initio calculations at the (U)B3LYP/6-311+G(3df,2p)//(U)B3LYP/6-31G(d,p) and broken spin symmetry UBS B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d,p) levels rule out choices (a) and (b) and are consistent with the singlet diradical process.     

Spin trapping by 5-carbamoyl-5-methyl-1-pyrroline N-oxide (AMPO): theoretical and experimental studies

The nitrone 5-carbamoyl-5-methyl-1-pyrroline N-oxide (AMPO) was synthesized and characterized. Spin trapping of various radicals by AMPO was demonstrated for the first time by electron paramagnetic resonance (EPR) spectroscopy. The resulting spin adducts for each of these radicals gave unique spectral profiles. The hyperfine splitting constants for the superoxide adduct are as follows: isomer I (80%), a(nitronyl)(-)(N) = 13.0 G and a(beta)(-)(H) = 10.8 G; isomer II (20%), a(nitronyl)(-)(N) = 13.1 G, a(beta)(-)(H) = 12.5 G, and a(gamma)(-)(H) = 1.75 G. The half-life of the AMPO-O(2)H was about 8 min, similar to that observed for EMPO but significantly shorter than that of the DEPMPO-O(2)H with t(1/2) approximately 16 min. However, the spectral profile of AMPO-O(2)H at high S/N ratio is distinguishable from the spectrum of the (*)OH adduct. Theoretical analyses using density functional theory calculations at the B3LYP/6-31+G//B3LYP/6-31G level were performed on AMPO and its corresponding superoxide adduct. Calculations predicted the presence of intramolecular H-bonding in both AMPO and its superoxide adduct. The H-bonding interaction was further confirmed by an X-ray structure of AMPO, and of the novel and analogous amido nitrone 2-amino-5-carbamoyl-5-methyl-1-pyrroline N-oxide (NH(2)-AMPO). The thermodynamic quantities for superoxide radical trapping by various nitrones have been found to predict favorable formation of certain isomers. The measured partition coefficient in an n-octanol/buffer system of AMPO was similar to those of DMPO and DEPMPO. This study demonstrates the suitability of the AMPO nitrone for use as a spin trap to study radical production in aqueous systems.     

The crystal structure of 1-(4-chlorophenyl)-3-(4-methylbenzoyl)thiourea

1-(4-Chlorophenyl)-3-(4-methylbenzoyl)thiourea was synthesized and characterized by IR,¹H and ¹³C NMR, mass spectroscopy and the elemental analysis. The crystal structure was confirmed from single crystal X-ray diffraction data. It crystallizes in the monoclinic space group P2₁/c with unit cell dimensions a=12.038(3), b=6.330(6), c=18.912(5) Å and β=100.32(3)°. There is a strong intramolecular hydrogen bond of the type N?H...O, with distance N1...O1=2.659(3) Å. The structure is composed of dimers related by inversion centers. The dimers are formed by intermolecular interactions of the type N?H...S with N...S separation of 3.440(2) Å. The mass fragmentation pattern has also been discussed.     

Structural investigation of asymmetrical dimer radical cation system (H2O-H2S)+: proton-transferred or hemi-bonded?

Ab initio molecular orbital and hybrid density functional methods have been employed to characterize the structure and bonding of (H2O-H2S)+, an asymmetrical dimer radical cation system. A comparison has been made between the two-center three-electron (2c-3e) hemi-bonded system and the proton-transferred hydrogen-bonded systems of (H2O-H2S)+. Geometry optimization of these systems was carried out using unrestricted Hartree Fock (HF), density functional theory with different functionals, and second-order M?ller-Plesset perturbation (MP2) methods with 6-311++G(d,p) basis set. Hessian calculations have been done at the same level to check the nature of the equilibrium geometry. Energy data were further improved by calculating basis set superposition error for the structures optimized through MP2/6-311++G(d,p) calculations. The calculated results show that the dimer radical cation structure with H2O as proton acceptor is more stable than those structures in which H2O acts as a proton donor or the 2c-3e hemi-bonded (H2O thereforeSH2)+ system. This stability trend has been further confirmed by more accurate G3, G3B3, and CCSD(T) methods. On the basis of the present calculated results, the structure of H4OS+ can best be described as a hydrogen-bonded complex of H3O+ and SH with H2O as a proton acceptor. It is in contrast to the structure of neutral (H2O...H2S) dimer where H2O acts as a proton donor. The present work has been able to resolve the ambiguity in the nature of bonding between H2O and H2S in (H2O-H2S)+ asymmetrical dimer radical cation.     

Ligation independent cloning (LIC) as a rapid route to families of recombinant biocatalysts from sequenced prokaryotic genomes

A technique is presented for the high throughput generation of families of recombinant biocatalysts sourced from prokaryotic genomes, providing rapid access to the naturally evolved diversity of enzyme specificity for biocatalyst discovery. The method exploits a novel ligation independent cloning strategy, based on the locally engineered vector pET-YSBLIC and has been used for the rapid generation of a suite of expression plasmids containing genes encoding a family of six Baeyer-Villiger monooxygenases (BVMOs) from Mycobacterium tuberculosis H37Rv (MTb). The six resultant recombinant strains of E. coli B834 (DE3) expressing the genes were assayed for oxygenating activity in respect of the target reaction; the resolution of bicyclo[3.2.0]hept-2-en-6-one. The analysis of biotransformations catalysed by growing cells of E. coli was complicated by the production of indole in the reaction mixtures, possibly resulting from the in vivo activity of E. coli tryptophanase. Four of the recombinant strains expressing different BVMOs catalysed the oxidation of one or more of four screening substrates, well above controls that had been transformed with the re-ligated parent vector. One of the recombinant strains, E. coli B834 (DE3) pDB5, expressing the Rv3049c gene from MTb, was found to effectively resolve the target substrate, yielding a 19% yield of (1R, 5S)-(+)-bicyclo[3.2.0]hept-2-en-6-one with >95% enantiomeric excess in a 4 L fermentation reaction.     

Theoretical study on the mechanism of the (3)CH(2) + NO(2) reaction

The complex doublet potential energy surface of the CH(2)NO(2) system is investigated at the B3LYP/6-31G(d,p) and QCISD(T)/6-311G(d,p) (single-point) levels to explore the possible reaction mechanism of the triplet CH(2) radical with NO(2). Forty minimum isomers and 92 transition states are located. For the most relevant reaction pathways, the high-level QCISD(T)/6-311 + G(2df,2p) calculations are performed at the B3LYP/6-31G(d,p) geometries to accurately determine the energetics. It is found that the top attack of the (3)CH(2) radical at the N-atom of NO(2) first forms the branched open-chain H(2)CNO(2) a with no barrier followed by ring closure to give the three-membered ring isomer cC(H(2))ON-O b that will almost barrierlessly dissociate to product P(1) H(2)CO + NO. The lesser followed competitive channel is the 1,3-H-shift of a to isomer HCN(O)OH c, which will take subsequent cis-trans conversion and dissociation to P(2) OH + HCNO. The direct O-extrusion of a to product P(3) (3)O + H(2)CNO is even much less feasible. Because the intermediates and transition states involved in the above three channels are all lower than the reactants in energy, the title reaction is expected to be rapid, as is consistent with the measured large rate constant at room temperature. Formation of the other very low-lying dissociation products such as NH(2) + CO(2), OH + HNCO and H(2)O + NCO seems unlikely due to kinetic hindrance. Moreover, the (3)CH(2) attack at the end-O of NO(2) is a barrier-consumed process, and thus may only be of significance at very high temperatures. The reaction of the singlet CH(2) with NO(2) is also briefly discussed. Our calculated results may assist in future laboratory identification of the products of the title reaction.     

Microsolvation of hydrogen sulfide: exploration of H2S.(H2O)n and SH-.H3O+.(H2O)n-1 (n = 5-7) cluster structures on ab initio potential energy surfaces by the scaled hypersphere search method

The scaled hypersphere search method was applied to ab initio potential energy surfaces of the H2S.(H2O)n/SH-.H3O+.(H2O)n-1 system with n = 5-7. Local minima databases including 121, 326, and 553 structures for n = 5-7, respectively, were obtained based on calculations at the MP2/6-311++G(3df,2p)//B3LYP/6-31+G** level. In these small cluster sizes, the SH-.H3O+.(H2O)n-1 type is still unstable relative to the H2S.(H2O)n type, and the global minima for H2S.(H2O)n are very similar to those of pure water clusters of (H2O)n+1. Thermodynamic simulations based on the present databases showed a structure transition from the well-mixed (H2O)n+1-like global minimum at low temperatures to unmixed complexes between H2S and (H2O)n at high temperatures.     

Low-energy paths for the unimolecular decomposition of CH3OH: a G2M/statistical theory study

The potential energy surface (PES) of the CH3OH system has been characterized by ab initio molecular orbital theory calculations at the G2M level of theory. The mechanisms for the decomposition of CH3OH and the related bimolecular reactions, CH3 + OH and 1CH2 + H2O, have been elucidated. The rate constants for these processes have been calculated using variational RRKM theory and compared with available experimental data. The total decomposition rate constants of CH3OH at the high- and low-pressure limits can be represented by k infinity = 1.56 x 10(16) exp(-44,310/T) s-1 and kAr0 = 1.60 x 10(36) T-12.2 exp(-48,140/T) cm3 molecule-1 s-1, respectively, covering the temperature range 1000-3000 K, in reasonable agreement with the experimental values. Our results indicate that the product branching ratios are strongly pressure dependent, with the production of CH3 + OH and 1CH2 + H2O dominant under high (P > 10(3) Torr) and low (P < 1 atm) pressures, respectively. For the bimolecular reaction of CH3 and OH, the total rate constant and the yields of 1CH2 + H2O and H2 + HCOH at lower pressures (P < 5 Torr) could be reasonably accounted for by the theory. For the reaction of 1CH2 with H2O, both the yield of CH3 + OH and the total rate constant could also be satisfactorily predicted theoretically. The production of 3CH2 + H2O by the singlet to triplet surface crossing, predicted to occur at 4.3 kcal mol-1 above the H2C...OH2 van der Waals complex (which lies 82.7 kcal mol-1 above CH3OH), was neglected in our calculations.     

Theoretical study on the unimolecular decomposition of thiophenol

The potential energy surface for the unimolecular decomposition of thiophenol (C(6)H(5)SH) is mapped out at two theoretical levels; BB1K/GTlarge and QCISD(T)/6-311+G(2d,p)//MP2/6-31G(d,p). Calculated reaction rate constants at the high pressure limit indicate that the major initial channel is the formation of C(6)H(6)S at all temperatures. Above 1000 K, the contribution from direct fission of the S-H bond becomes important. Other decomposition channels, including expulsion of H(2) and H(2)S are of negligible importance. The formation of C(6)H(6)S is predicted to be strong-pressure dependent above 900 K. Further decomposition of C(6)H(6)S produces CS and C(5)H(6). Overall, despite the significant difference in bond dissociation, i.e., 8-9 kcal/mol between the S-H bond in thiophenol and the O-H bond in phenol, H migration at the ortho position in the two molecules represents the most accessible initial channel.     

The NICS (Nucleus-Independent Chemical Shift) as a probe of the relative stability of β-chalcogenovinylaldehydes stabilized through intramolecular chalcogen–chalcogen interactions

Density functional calculations, at the B3LYP/6-311+G(3df,2p) level, have been carried out for the complete series of β-chalcogenovinylaldehydes, CH(X)–CHCH–YH (X, Y=O, S, Se, Te), to estimate the strength of H–XY or XY–H intramolecular chalcogen–chalcogen interactions, through the use of appropriate homodesmotic reactions. For the same set of compounds the value of the nucleus-independent chemical shift (NICS), on points 1 Å above the corresponding ring critical point, has been obtained at the B3LYP/6-311+G(3df,2p) level. For non-stabilizing chalcogen–chalcogen interactions the NICS value is positive, while the opposite is found when the interaction is stabilizing. In general, there is a good linear correlation between both magnitudes and therefore, we can conclude that NICS value is a reliable probe of the strength of intramolecular chalcogen–chalcogen interactions in this set of compounds.     

Guanosine distribution and oxidation resistance in eight eukaryotic genomes

Reactive oxygen species that attack DNA are continuously generated in living cells. Both the guanosine (G) mole fraction and its distribution should affect the stability of genomes and their parts to oxidation. At a lesser G content, genomes should be more oxidation resistant or "ennobled". Oxidant scavenging by G's in nonessential parts of introns and intergenic domains should decrease G oxidation in the essential exons. To determine whether genomes are indeed ennobled and whether oxidant-scavenging domains exist in genomes, the relative rates of guanosine oxidation in average exons, introns, and intergenic domains were estimated. Comparison among genomes indicated that average exons are ennobled in the genomes of Caenorhabditis (worm), Arabidopsis (plant), Saccharomyces (yeast), Schizosaccharomyces (yeast), and Plasmodium (malaria parasite), and that average introns and intergenic domains are ennobled in these genomes and in the genome of Drosophila (fly). The exon oxidation rates estimated for these genomes were less than the rate for the hypothetical "standard" genome, with a 0.25 mole fraction of uniformly distributed G. For Plasmodium the rate was half of that estimated for the standard genome. Average exons were not ennobled in the human or fly genomes; their G distributions were comparable to that in the standard genome. Instead, their exons were situated between introns and intergenic domains that could protect them by oxidant scavenging, the G's of their introns and intergenic domains outnumbering those of their exons 50-fold in humans and 4-fold in flies. The G distribution in the Encephalitozoon (parasite) genome was not protective relative to that of the standard genome.