Understanding solvent effects on hyperfine coupling constants of cyclohexadienyl radicals

Quantum chemical calculations have been carried out to understand better solvent effects on the isotropic muon and proton hyperfine coupling constants in the C₆H₆Mu^• radical. Both polarizable continuum solvent models and explicit inclusion of water molecules into supermolecular complexes were used. Changes in the hyperfine couplings of in-plane hydrogen atoms are very small and difficult to discuss, partly due to relatively large experimental error bars. In contrast, the out-of-plane proton and muon hyperfine couplings exhibit more pronounced changes. These are partly due to structural changes of the radical and partly due to direct electronic polarization effects. Polarizable continuum solvent models agree well with experimental changes for benzene but overshoot the enhancement of the hyperfine couplings for water. Explicit inclusion of water molecules reduces this overestimated spin density increase and thereby tends to bring theory and experiment into closer agreement. The enhancement of the spin density on the out-of-plane hydrogen or muon atoms by the solvent environment is mainly due to an increased polarization of the singly occupied MO towards this side. Electronic Supplementary Material: Supplementary material is available in the online version of this article at dx.doi.org/10.1007/s00214-005-0680-x     

Hybrid density functional theory with a specific reaction parameter: hydrogen abstraction reaction of trifluoromethane by the hydroxyl radical

Potential energy surfaces are developed and tested for the OH + CHF₃ → H₂O + CF₃ reaction. The objective is to obtain surfaces that give calculated rate constants comparable to the experimental ones. The potential energy surfaces are constructed using hybrid and hybrid meta density functional theory methods (mPW1PW91, B1B95, and mPW1B95) with specific reaction parameters in conjunction with the 6–31+ G(d,p) basis set. The rate constants are calculated over the temperature range 200–1,500 K using variational transition state theory with multidimensional tunneling contributions. The hybrid density functional theory methods with specific-reaction-parameter Hartree-Fock exchange contributions (32.8–34.8% for mPW1PW91, 34.2–36.0% for B1B95, and 37.8–39.7% for mPW1B95, respectively) provide accurate rate constants over an extended temperature range. The classical barrier height for the hydrogen abstraction reaction is determined to be 6.5–6.9 kcal/mol on these potential energy surfaces, and the best estimate value is 6.77 kcal/mol. Electronic Supplementary Material  Supplementary material is available for this article at and is accessible for authorized users.     

Excited states of conjugated hydrocarbon radicals using the molecular mechanics – valence bond (MMVB) method

By using a parameterised Heisenberg Hamiltonian coupled to a molecular mechanics force field, excited-state geometries were optimised for three conjugated hydrocarbon radicals: cyclopentadienyl, phenalenyl (perinaphthenyl), and triphenylmethyl. The results are compared with ab initio calculations, and with recent spectroscopic measurements. Electronic Supplementary Material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0461-3     

Karplus-type relationships between scalar coupling constants: 3JHH molecular versus 4hJHH supramolecular coupling constants

The ³J_HH coupling constants in six H–X–Y–H systems (ethane, methylamine, methanol, hydrazine, hydroxylamine and hydrogen peroxide) and ^4hJ_HH coupling constants in four H–...XH...Y–H, namely [H₃NHNH₃]⁺ (two arrangements), HOHNH₃ and HOHOH₂ have been calculated theoretically as a function of the torsion angle . For covalent situations, the corresponding Karplus equations have been fitted to calculated ³J_HH=acos2 +bcos +c. The a, b and c terms have been analyzed as a function of the electronegativities of X and Y. In the case of ammonium/ammonia complexes (proton shared and not), water/ammonia, and water dimer the values are low (maximum 0.5 Hz) but follow closely a Karplus relationship. Supplementary material is available in the online version of this article at Electronic Supplementary Material Supplementary material is available in the online version of this article at     

New computational evidence for the catalytic mechanism of carbonic anhydrase

Some aspects of the catalytic mechanism of HCA have been investigated. Either a zinc-bound water or a zinc-bound hydroxide has been considered as a nucleophile attacking CO ₂. No reaction path exists in the former case, while a transition state for the nucleophilic attack has been located in the latter (barrier of 7.6 kcal mol⁻¹). This activation energy is determined by the breaking of the hydrogen-bond network that shields the zinc-bound hydroxide when the CO ₂ molecule approaches the reaction center. No ambiguity exists about the mechanism for the internal rearrangement of the zinc–bicarbonate complex. The rotation pathway (Lindskog mechanism) proposed by many authors is too energy demanding since it causes the breaking of the hydrogen-bond network around the bicarbonate. The only possible rearrangement mechanism is a proton transfer (Lipscomb) that occurs in two steps (each step corresponding to a double proton transfer) and involves the Thr199 residue as a proton shuttle. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Fernando Bernardi Memorial Issue.     

Counter-ion effect in the nucleophilic substitution reactions at silicon: a G2M(+) level theoretical investigation

Three identity nucleophilic substitution reactions at tetracoordinated silicon atom with inversion and retention pathways: Nu + SiH₃Cl → Nu + SiH₃Cl[Nu = (1)Cl⁻, (2) LiCl, and (3) (LiCl)₂], are investigated using the G2M(+) theory. Our results show that changing the nucleophile can shift the mechanism (favorable pathway), stepwise from a single-well PES for reaction 1, via a double-well PES for reaction 2, to a triple-well PES for reaction 3, indicating the importance of steric and electronic effects on the S_N2@Si. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The metrological infrastructure for gas analysis

This presentation to the Metrology in Chemistry symposium held in October 2004 in Beijing, describes the metrological infrastructure for gas analysis. The inputs from National Metrology Institutes, industry, standardisation and accreditation bodies, and organisers of proficiency testing schemes are briefly described. Electronic Supplementary Material Supplementary material is available for this article at Presented at the International Symposium on Metrology in Chemistry, 2004 Beijing, China.     

Synthesis,crystal structure and magnetic properties of a new 3D coordination polymer constructed by Co(II) with pyridine-3,4-dicarboxylate and 4,4’-bipyridine

A metal-organic framework, [Co₂(pydc)₂(bpy)₂] _n · 2nH₂O (1) (H₂pydc = pyridine-3,4-dicarboxylic acid, bpy = 4,4′-bipyridine), was synthesized under hydrothermal conditions. X-ray diffraction experiments reveal that (1) exhibits a chiral 3D metal-organic framework, which represents the rare example of 3D chiral coordination polymers containing two kinds of organic ligands. Temperature-dependent magnetic susceptibility for (1) was also studied. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Theoretical study on structures and stability of triplet SiC<Subscript>3</Subscript>O isomers

Various levels of calculations are carried out~for exploring the potential energy surface (PES) of triplet SiC₃O, a molecule of potential interest in interstellar chemistry. A total of 38 isomers are located on the PES including chain-like, cyclic and cage-like structures, which are connected by 87 interconversion transition states at the DFT/B3LYP/6-311G(d) level. The structures of the most relevant isomers and transition states are further optimized at the QCISD/6-311G(d) level followed by CCSD(T)/6-311+G(2df) single-point energy calculations. At the QCISD level, the lowest lying isomer is a linear SiCCCO 1 (0.0 kcal/mol) with the ³ ∑ electronic state, which possesses great kinetic stability of 59.5 kcal/mol and predominant resonant structure . In addition, the bent isomers CSiCCO 2 (68.3 kcal/mol) and OSiCCC 5 (60.1 kcal/mol) with considerable kinetic stability are also predicted to be candidates for future experimental and astrophysical detection. The bond natures and possible formation pathways in interstellar space of the three stable isomers are discussed. The predicted structures and spectroscopic properties for the relevant isomers are expected to be informative for the identification of SiC₃O and even larger SiC _n O species in laboratory and interstellar medium. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of protonation on proton transfer processes in Watson–Crick adenine–thymine base pair

Intermolecular proton transfer processes in the Watson and Crick adenine–thymine neutral and protonated base pairs have been studied using the density functional theory (DFT) with the non-local hybrid B3LYP density functional. Protonated systems subject to study are those resulting from protonation at the main basic sites of the base pair model, namely N₇ and N₃ of adenine and O₂^′ and O₄^′ of thymine. Protonation of adenine induces a strengthening by about 4–5 kcal/mol of the base pair and does not significantly modify the double proton transfer energy profile obtained for the unprotonated system. On the other hand, protonation at the O₄^′ and O₂^′ thymine moiety causes thymine’s N₃ proton to spontaneously transfer to adenine while non-transferred minima disappear at this level of theory. The different behaviour between protonated adenine– thymine and protonated guanine–cytosine is discussed. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Fernando Bernardi Memorial Issue.     

Modeling water exchange on monomeric and dimeric Mn centers

Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [Mn^IV(H₂O)₂(OH)₄] is only 9.6 kcal mol^–1, corresponding to a rate of 6×10⁵ s^–1. It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H₂O)₂(OH)₂Mn^IV(-O)₂Mn^IV(H₂O)₂(OH)₂] is 8.6 kcal mol^–1, while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol^–1. These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic O₂ catalyst [(terpy)(H₂O)Mn^IV(-O)₂Mn^IV(O)(terpy)]³⁺ (terpy=2,2:6,2-terpyridine). The calculated reaction barrier is 14.7 kcal mol^–1.Contribution to the Björn Roos Honorary Issue     

Structure and torsional flexibility of the linkage between guanine and fluorene residues in the deoxyguanosine–aminofluorene and deoxyguanosine–acetylaminofluorene carcinogenic adducts

Potential energy surfaces for rotations around two central CN bonds in N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF–dG) and its deacetylated derivative (AF–dG) were studied using Amber 95 molecular mechanics. Both of these adducts are known to be strong mutagens and carcinogens. New Amber 95 force field parameters were derived for the linkage connecting guanine and fluorene moieties in AAF–dG and AF–dG. For this purpose, we determined ab initio MP2/cc-pVDZ//B3-LYP/6-31G* and polarized continuum model Hartree–Fock/6-31G* potential energy surfaces of smaller model systems that included the N-methylimidazole–acetylaniline and N-methylimidazole–aniline adducts. The molecular mechanics parameters were adjusted to minimize differences between the gas-phase ab initio and molecular mechanics surfaces of these model systems. The resulting parameters were transferred to AF–dG and AAF–dG. The barrier for the rotation of the fluorene residue in AF–dG was found to be less than 2 kcal/mol. Such a small barrier renders the fluorene moiety freely rotatable at room temperature. In contrast, the fluorene rotation in AAF–dG is hindered by a significantly larger barrier of 10 kcal/mol. This barrier corresponds to conformations in which the fluorene and acetyl groups lie in the same plane, and is largely due to steric repulsion. Similarly, the coplanar arrangement of guanine and the bridging amino or acetyl groups is disfavored by 5–10 kcal/mol, with AAF–dG again being the more rigid of the two molecules. Energy minima for a rotation around a bond between guanine and the bridging nitrogen are found at ±80° in AAF–dG, and at 120° and –90° for AF–dG. Overall, the fluorene–dG linkages in AF–dG and AAF–dG adducts have significantly different equilibrium structures and torsional flexibilities. These differences may be contributing factors for the observed disparity in mutagenic effects of these adducts.Electronic Supplementary Material: Supplementary material is available in the online version of this article at Acknowledgements. This work was supported by the NSF REU grant no. CHE-0243825 to Loyola University Chicago. We thank to Tom Ellenberger and Shuchismita Dutta for providing us with their results prior to publication.     

Is the CH2OH + O2 → CH2 = O + HO2 Reaction Barrierless? An Ab Initio Study on the Reaction Mechanism

The reaction mechanism of the CH₂OH + O₂ gas-phase reaction was investigated by means of ab initio calculations. MP2 and QCISD methodologies were used to obtain the stationary points on the potential energy surface. Single-point high-level QCISD(T) calculations were performed over the QCISD results in order to refine the energy of the transition states and the minima found. A new transition state concerning the initial O₂ addition to the CH₂OH radical was found, not reported so far for this reaction. Extra CCSD optimisation and single-point high-level CCSD(T) calculations upon the QCISD results confirm this TS. Additional RASSCF calculations show that its wave function has no significant multireferential character.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Intrinsic acidity and redox properties of the adenine radical cation

The intrinsic chemical properties of the gaseous adenine radical cation were examined by using dual cell Fourier transform ion cyclotron resonance mass spectrometry. The adiabatic recombination energy of the radical cation (ionization energy of neutral adenine) was found by bracketing experiments to be 8.55 ± 0.1 eV (at 298 K; earlier literature values range from 8.3 to 8.9 eV). Based on this value, the heat of formation (ΔH_f²⁹⁸) of the adenine radical cation is estimated to be 246 ± 3 kcal/mol. The acidity (ΔH_acid²⁹⁸) of the adenine radical cation was bracketed to be 221 ± 2 kcal/mol. These thermochemical values suggest that the adenine radical cation reacts with neutral guanine by electron abstraction or proton transfer, with neutral cytosine by proton transfer, and via neither pathway with neutral thymine, molecular water or a sugar moiety of DNA (modeled by tetrahydrofuran). Experimental examination of the gas-phase reactivity of the adenine radical cation revealed a slow deuterium atom abstraction from perdeuterated tetrahydrofuran. Hence, in the absence of a nearby guanine or cytosine, the adenine radical cation may be able to abstract a hydrogen atom from a sugar moiety of DNA.     

Theoretical study of water-assisted hydrolytic deamination mechanism of adenine

The water-assisted hydrolytic deamination mechanism of adenine was studied using density functional method at B3LYP/6-311G(d,p) level. Intrinsic reaction coordinate (IRC) calculations were performed on the transition states to verify whether it is the real transition states that connect the corresponding intermediates. Single-point calculations were carried out on the previous optimized geometries obtained during IRC calculations. The activation energies have also been calculated using G3MP2//B3LYP/6-311G(d,p) method. The water molecules attack the adenine and a tetrahedral intermediate forms. Then, two different intermediates have been obtained through different bond rotations. In pathway a, the second water molecule takes part in the formation of transition state and acts as a bridge to transfer hydrogen atom, while in pathway b, the second water molecule does not involve in the creation of transition state and only acts as a medium. The energy barriers are 23.40 and 37.17 kcal/mol for pathways a and b, respectively. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Micellar and associated thermodynamic properties of binary mixtures of alkyl triphenyl phosphonium bromides in ethylene glycol and water mixtures

Micellar properties of binary combinations of a family of cationic alkyl triphenyl phosphonium bromides with varying chain length (C₁₀–C₁₆) were investigated in aqueous and aqueous ethylene glycol mixtures employing conductometric technique. The results of the mixed systems were analyzed in the light of the Regular Solution Theory and the Gibbs–Duhem equation to evaluate the composition of the mixed micelle, the activity coefficients, and the interaction parameter (β). The excess free energy and the other related thermodynamic parameters of mixing were calculated and discussed in terms of the stability of the mixed micelles in the presence of an ethylene glycol additive. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Experimental and theoretical spectral properties of ethyl 2-(7-hydroxy-2-oxo-2H-chromen-4-yl)acetate doped sol-gel materials: new materials with potential optical application

Silica xerogels and monoliths, containing ethyl 2-(7-hydroxy-2-oxo-2H-chromen-4-yl)acetate (K4) or Sm^{3 +} ions and K4 are prepared by sol-gel technique. NMR investigations, UV/Vis, IR- and luminescence spectral properties of K4 in solution and in monoliths are presented. The IR-spectroscopic properties of the prepared sol-gel materials are examined by applying the reduced-difference procedure to non-polarized IR-spectra. The results show that the sol-gel medium did not interact with K4 as well as in the presence of Sm³⁺ ions the K4 form a [Sm(L)₂(H₂O)₄] × (NO₃)₃ complex in the matrix. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Redox potential of iron–sulfur clusters as a model of the Desulfovibrio vulgaris center

A theoretical study of Heisenberg exchange and double exchange effects in clusters with four and six iron ions has been performed for [Fe₄ S₃ O] ^m+, [Fe₄ S₄]^m+ (where m = 3, 2), and [Fe₆ S₆] ⁿ⁺ (where n = 5, 4) ions as models of the Desulfovibrio vulgaris iron–sulfur centers. Assuming that the redox potential mostly depends on the Heisenberg spin coupling and the resonance delocalization, we performed an analysis of the reduction process for the [Fe₄ S₃ O] ^3+/2+, [Fe₄ S₄] ^3+/2+, and [Fe₆ S₆] ^5+/4+ ions and showed that the redox potential can be calculated as a difference between average spin energies of the tetravalent and pentavalent double cubane superclusters. For the Heisenberg parameter of J₁ = 20 cm^-1, the redox potential amounts to about 0.03 V.It complies with close to zero experimental values of the redox potential.Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

The kinetics of radiation-induced hydrogen abstraction by CCl3 radicals in the liquid phase: Cyclohexene

The kinetics of hydrogen abstraction from cyclohexene by CCl₃ radicals were studied in CCl₄ solution as a function of cyclohexene concentration and temperature in the range of 26–140°C. The CCl₃ radicals were produced both by radiolysis of CCl₄ and by photolysis of CCl₃Br. The rate constant for the reaction was found to be given by the equation where θ = 2.303 RT kcal/mol. This activation energy leads to C? H bond strength for the allylic hydrogen of 85 ± 1 kcal/mol, which means a resonance stabilization energy of 11 ± 1.5 kcal/mol for the C-C₆H₁₁ radical.