Origin of the nonplanarity of tetrafluoro cyclobutadiene, C4F4

Density functional theory as well as M?ller-Plesset investigations has been carried out on tetrafluoro cyclobutadiene, C4F4, to explore the origin of its nonplanarity. Although Petersson et al. (Petersson, E. J.; Fanuele, J. C.; Nimlos, M. R.; Lemal, D. M.; Ellison, G. B.; Radziszewski, J. G. J. Am. Chem. Soc. 1997, 119, 11122-11123) had earlier predicted a nonplanar geometry of this compound on the basis of spectral and bond orbital analysis, the explanation of the same from a more fundamental point of view is still missing. In the present study, we provide a heuristic explanation for the origin of nonplanarity of C4F4. The two major driving forces behind this nonplanar geometry are the unusual aromaticity of this cyclic homoatomic 4pi electron system and the second-order Jahn-Teller effect (SOJTE). These driving forces can well be explained by various energy and density parameters and also by nucleus-independent chemical shift (NICS) values. Aromaticity of a cyclic homoatomic 4pi electron system is quite remarkable. The enhancement of pi- delocalization as evidenced from molecular orbital analysis may be attributed to s-ppi mixing in nonplanar C4F4.     

Copper chemistry of beta-diketiminate ligands: monomer/dimer equilibria and a new class of bis(mu-oxo)dicopper compounds

A series of Cu(I) and Cu(II) complexes of a variety of beta-diketiminate ligands (L(-)) with a range of substitution patterns were prepared and characterized by spectroscopic, electrochemical, and, in several cases, X-ray crystallographic methods. Specifically, complexes of the general formula [LCuCl](2) were structurally characterized and their magnetic properties assessed through EPR spectroscopy of solutions and, in one instance, by variable-temperature SQUID magnetization measurements on a powder sample. UV-vis spectra indicated reversible dissociation to 3-coordinate monomers LCuCl in solution at temperatures above -55 degrees C. The Cu(I) complexes LCu(MeCN) exhibited reversible Cu(I)/Cu(II) redox couples with E(1/2) values between +300 and +520 mV versus NHE (cyclic voltammetry, MeCN solutions). These complexes were highly reactive with O(2), yielding intermediates that were identified as rare examples of neutral bis(mu-oxo)dicopper complexes on the basis of their EPR silence, diagnostic UV-vis absorption data, and O-isotope-sensitive resonance Raman spectroscopic features. The structural features of the compounds [LCuCl](2) and LCu(MeCN) as well as the proclivity to form bis(mu-oxo)dicopper products upon oxygenation of the Cu(I) complexes are compared to data previously reported for complexes of more sterically hindered beta-diketiminate ligands (Aboelella, N. W.; Lewis, E. A.; Reynolds, A. M.; Brennessel, W. W.; Cramer, C. J.; Tolman, W. B. J. Am. Chem. Soc. 2002, 124, 10600. Spencer, D. J. E.; Aboelella, N. W.; Reynolds, A. M.; Holland, P. L.; Tolman, W. B. J. Am. Chem. Soc. 2002, 124, 2108. Holland, P. L.; Tolman, W. B. J. Am. Chem. Soc. 1999, 121, 7270). The observed structural and reactivity differences are rationalized by considering the steric influences of both the substituents on the flanking aromatic rings and those present on the beta-diketiminate backbone.     

Product distribution of peroxynitrite decay as a function of pH, temperature, and concentration.

The decay of peroxynitrite [O=NOO(-), oxoperoxonitrate(1-)] was examined as a function of concentration (0.050-2.5 mM), temperature (5-45 degrees C), and pH (2.2-10.0). Below 5 degrees C and pH 7, little amounts of the decomposition products nitrite and dioxygen are formed, even when the peroxynitrite concentration is high (2.5 mM). Instead, approximately > or =90% isomerizes to nitrate. At higher pH, decomposition increases at the expense of isomerization, up to nearly 80% at pH 10.0 at 5 degrees C and 90% at 45 degrees C. Much less nitrite and dioxygen per peroxynitrite are formed when the peroxynitrite concentration is lower; at 50 microM and pH 10.2, < or =40% decomposes. In contrast to two other reports (Pfeiffer, S.; Gorren, A. C. F.; Schmidt, K.; Werner, E. R.; Hansert, B.; Bohle, D. S.; Mayer, B. J. Biol. Chem. 1997, 272, 3465-3470, and Coddington, J. W.; Hurst, J. K.; Lymar, S. V. J. Am. Chem. Soc. 1999, 121, 2438-2443), we find that the extent of decomposition is dependent on the peroxynitrite concentration.     

Determinants of cyanuric acid and melamine assembly in water

While the recognition of cyanuric acid (CA) by melamine (M) and their derivatives has been known to occur in both water and organic solvents for some time, analysis of CA/M assembly in water has not been reported (Ranganathan, A.; Pedireddi, V. R.; Rao, C. N. R. J. Am. Chem. Soc.1999, 121, 1752-1753; Mathias, J. P.; Simanek, E. E.; Seto, C. T.; Whitesides, G. M. Macromol. Symp.1994, 77, 157-166; Zerkowski, J. A.; MacDonald, J. C.; Seto, C. T.; Wierda, D. A.; Whitesides, G. M. J. Am. Chem. Soc.1994, 116, 2382-2391; Mathias, J. P.; Seto, C. T.; Whitesides, G. M. Polym. Prepr.1993, 34, 92-93; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1993, 115, 905-916; Zerkowski, J. A.; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1992, 114, 5473-5475; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1990, 112, 6409-6411; Wang, Y.; Wei, B.; Wang, Q. J. Chem. Cryst.1990, 20, 79-84; ten Cate, M. G. J.; Huskens, J.; Crego-Calama, M.; Reinhoudt, D. N. Chem.-Eur. J.2004, 10, 3632-3639). We have examined assembly of CA/M, as well as assembly of soluble trivalent CA and M derivatives (TCA/TM), in aqueous solvent, using a combination of solution phase NMR, isothermal titration and differential scanning calorimetry (ITC/DSC), cryo-transmission electron microscopy (cryo-TEM), and synthetic chemistry. While the parent heterocycles coprecipitate in water, the trivalent system displays more controlled and cooperative assembly that occurs at lower concentrations than the parent and yields a stable nanoparticle suspension. The assembly of both parent and trivalent systems is rigorously 1:1 and proceeds as an exothermic, proton-transfer coupled process in neutral pH water. Though CA and M are considered canonical hydrogen-bonding motifs in organic solvents, we find that their assembly in water is driven in large part by enthalpically favorable surface-area burial, similar to what is observed with nucleic acid recognition. There are currently few synthetic systems capable of robust molecular recognition in water that do not rely on native recognition motifs, possibly due to an incomplete understanding of recognition processes in water. This study establishes a detailed conceptual framework for considering CA/M heterocycle recognition in water which enables the future design of molecular recognition systems that function in water.     

Interprotein electron transfer in a confined space: uncoupling protein dynamics from electron transfer by sol-gel encapsulation

In this paper, we describe the first observations of photoinitiated interprotein electron transfer (ET) within sol-gels. We have encapsulated three protein-protein complexes, specifically selected because they represent a full range of affinities, are sensitive to different types of dynamic processes, and thus are expected to respond differently to sol-gel encapsulation. The three systems are (i) the [Zn, Fe(3+)L] mixed-metal hemoglobin hybrids, where the alpha(1)-Zn and beta(2)-Fe subunits correspond to a "predocked" protein-protein complex with a crystallographically defined interface (Natan, M. J.; Baxter, W. W.; Kuila, D.; Gingrich, D. J.; Martin, G. S.; Hoffman, B. M. Adv. Chem. Ser. 1991, 228 (Electron-Transfer Inorg., Org., Biol. Syst.), 201-213), (ii) the Zn-cytochrome c peroxidase complex with cytochrome c, [ZnCcP, Fe(3+)Cc], having an intermediate affinity between its partners (Nocek, J. M.; Zhou, J. S.; De Forest, S.; Priyadarshy, S.; Beratan, D. N.; Onuchic, J. N.; Hoffman, B. M. Chem. Rev. 1996, 96, 2459-2489), and (iii) the [Zn-deuteromyoglobin, ferricytochrome b(5)] complex, [ZnDMb, Fe(3+)b(5)], which is loosely bound and highly dynamic (Liang, Z.-X.; Nocek, J.; Huang, K.; Hayes, R. T.; Kurnikov, I. V.; Beratan, D. N.; Hoffman, B. M. J. Am. Chem. Soc. 2002, 124, 6849-6859. Intersubunit ET within the hybrid does not involve second-order processes or subunit rearrangements, and thus is influenced only by perturbations of high-frequency motions coupled to ET. For the latter two complexes, sol-gel encapsulation eliminates second-order processes: protein partners encapsulated as a complex must stay together throughout a photoinitiated ET cycle, while proteins encapsulated alone cannot acquire a partner. It further modulates intracomplex motions of the two partners.     

Optimizing the performance of the multiconfiguration molecular mechanics method

Multiconfiguration molecular mechanics (MCMM) is a general algorithm for constructing potential energy surfaces for reactive systems (Kim, Y.; Corchado, J. C.; Villà, J.; Xing, J.; Truhlar, D. G. J. Chem. Phys. 2000, 112, 2718). This paper illustrates how the performance of the MCMM method can be improved by adopting improved molecular mechanics parameters. We carry out calculations of reaction rate constants using variational transition state theory with optimized multidimensional tunneling on the MCMM PESs for three hydrogen transfer reactions, and we compare the results to direct dynamics. We find that the MCMM method with as little as one electronic structure Hessian can describe the dynamically important regions of the ground-electronic state PES, including the corner-cutting-tunneling region of the reaction swath, with practical accuracy.     

Theoretical study of the electronic and optical properties of photochromic dithienylethene derivatives connected to small gold clusters

In the course of developing electronic devices on a molecular scale, dithienylethenes photochromic molecules constitute promising candidates for optoelectronic applications such as memories and switches. There is thus a great interest to understand and control the switching behavior of photochromic compounds deposited on metallic surfaces or nanoparticles. Within the framework of the density functional theory, we studied the effect of small gold clusters (Au3 and Au9) on the electronic structure and absorption spectrum of a model dithienylethene molecule. The molecular orbital interactions between the photochromic molecule and the gold cluster made it possible to rationalize some experimental findings (Dulic, D.; van der Molen, S. J.; Kudernac, T.; Jonkman, H. T.; de Jong, J. J. D.; Bowden, T. N.; van Esch, J.; Feringa, B. L.; van Wees, B. J. Phys. Rev. Lett. 2003, 91, 207402). For the closed-ring isomer, grafting a photochromic molecule on a small gold cluster does not change the characteristics of the electronic transition involved in the ring-opening reaction. On the opposite, the absorption spectrum of the photochromic open-ring isomer is strongly modified by the inclusion of the metallic cluster. In agreement with experimental results, our study thus showed that the cycloreversion reaction which involves the closed-ring isomer should be still possible, whereas the ring-closure reaction which involves the open-ring isomer should be inhibited. Connecting a dithienylethene molecule to a small gold cluster hence provides a qualitative comprehension of the photochromic activities of dithienylethenes connected to a gold surface.     

Validation studies of the site-directed docking program LibDock

The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G. L.; Andrews, W. C.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Walls, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. J. Med. Chem. 2006, 49, 5912-5931). Docking experiments were performed to assess both the accuracy in reproducing the binding mode of the ligand and the retrieval of active compounds in a virtual screening protocol using both the DJD (Diller, D. J.; Merz, K. M., Jr. Proteins 2001, 43, 113-124) and LigScore2 (Krammer, A. K.; Kirchoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. J. Mol. Graphics Modell. 2005, 23, 395-407) scoring functions. This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 A for the crystallographic poses when the LigScore2 scoring function was used. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms.     

Rate constants and H atom branching ratios of the gas-phase reactions of methylidyne CH(X2Pi) radical with a series of alkanes

The reactions of the CH radical with several alkanes were studied, at room temperature, in a low-pressure fast-flow reactor. CH(X2Pi, v = 0) radicals were obtained from the reaction of CHBr(3) with potassium atoms. The overall rate constants at 300 K are (0.76 +/- 0.20) x 10(-10) [Fleurat-Lessard, P.; Rayez, J. C.; Bergeat, A.; Loison, J. C. Chem. Phys. 2002, 279, 87],1 (1.60 +/- 0.60) x 10(-10)[Galland, N.; Caralp, F.; Hannachi, Y.; Bergeat, A.; Loison, J.-C. J. Phys. Chem. A 2003, 107, 5419],2 (2.20 +/- 0.80) x 10(-10), (2.80 +/- 0.80) x 10(-10), (3.20 +/- 0.80) x 10(-10), (3.30 +/- 0.60) x 10(-10), and (3.60 +/- 0.80) x 10(-10) cm3 molecule(-1) s(-1), (errors refer to +/-2sigma) for methane, ethane, propane, n-butane, n-pentane, neo-pentane, and n-hexane respectively. The experimental overall rate constants correspond to those obtained using a simple classical capture theory. Absolute atomic hydrogen production was determined by V.U.V. resonance fluorescence, with H production from the CH + CH4 reaction being used as a reference. Observed H branching ratios were for CH4, 1.00[Fleurat-Lessard, P.; Rayez, J. C.; Bergeat, A.; Loison, J. C. Chem. Phys. 2002, 279, 87];1 C(2)H(6), 0.22 +/- 0.08 [Galland, N.; Caralp, F.; Hannachi, Y.; Bergeat, A.; Loison, J.-C. J. Phys. Chem. A 2003, 107, 5419];2 C(3)H(8), 0.19 +/- 0.07; C(4)H(10) (n-butane), 0.14 +/- 0.06; C(5)H(12) (n-pentane), 0.52 +/- 0.08; C(5)H(12) (neo-pentane), 0.51 +/- 0.08; C(5)H(12) (iso-pentane), 0.12 +/- 0.06; C(6)H(14) (n-hexane), 0.06 +/- 0.04.     

Infrared spectroscopy and theoretical studies on gas-phase protonated leu-enkephalin and its fragments: direct experimental evidence for the mobile proton

The gas-phase structures of the protonated pentapeptide Leu-enkephalin and its main collision-induced dissociation (CID) product ions, b4 and a4, are investigated by means of infrared multiple-photon dissociation (IR-MPD) spectroscopy and detailed molecular mechanics and density functional theory (DFT) calculations. Our combined experimental and theoretical approach allows accurate structural probing of the site of protonation and the rearrangement reactions that have taken place in CID. It is shown that the singly protonated Leu-enkephalin precursor is protonated on the N-terminus. The b4 fragment ion forms two types of structures: linear isomers with a C-terminal oxazolone ring, as well as cyclic peptide structures. For the former structure, two sites of proton attachment are observed, on the N-terminus and on the oxazolone ring nitrogen, as shown in a previous communication (Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2005, 127, 17154-17155). Upon leaving the ions for longer radiative cooling delays in the ion cyclotron resonance (ICR) cell prior to IR spectroscopic investigation, one observes a gradual decrease in the relative population of oxazolone-protonated b4 and a corresponding increase in N-terminal-protonated b4. This experimentally demonstrates that the mobile proton is transferred between two sites in a gas-phase peptide ion and allows one to rationalize how the proton moves around the molecule in the dissociation process. The a4 fragment, which is predominantly formed via b4, is also confirmed to adopt two types of structures: linear imine-type structures, and cyclic structures; the former isomers are exclusively protonated on the N-terminus in sharp contrast to b4, where a mixture of protonation sites was found. The presence of cyclic b4 and a4 fragment ions is the first direct experimental proof that fully cyclic structures are formed in CID. These results suggest that their presence is significant, thus lending strong support to the recently discovered peptide fragmentation pathways (Harrison, A. G.; Young, A. B.; Bleiholder, B.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2006, 128, 10364-10365) that result in scrambling of the amino acid sequence upon CID.     

Ethylene spacer-linked bis-acetamidopyridine for dicarboxylic acid recognition and polymeric new wave-like anti-perpendicular arrangement of a host–guest in the solid state

In this paper, 1,2-bis(2-acetamido-6-pyridyl)ethane, receptor 1, having an ethylene spacer is reported to recognise dicarboxylic acids. The binding study in the solution phase is carried out using ¹H NMR (1:1) and UV–vis experiments and in the solid phase by single-crystal X-ray analysis. In ¹H NMR, the downfield shifts of specific amide protons of receptor 1 in 1:1 complexes of receptor and guest diacids, and in the UV–vis experiment, the appearance of an isosbestic point as well as significant binding constants are observed, which thus unambiguously support the complexation of receptor 1 with dicarboxylic acids in solution. Receptor 2, simple 2-acetamido-6-methylpyridine, has lower binding constants than receptor 1 due to cooperative binding of two pyridine amide groups with two acid groups of diacids. In the solid phase, the ditopic receptor 1 shows a grid-like polymeric hydrogen-bonded network that changes to a polymeric wave-like 1:1 anti-perpendicular network instead of the syn–syn polymeric 1:1 (Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett. 2005 (a) Goswami, S., Ghosh, K. and Dasgupta, S. 2000. J. Org. Chem., 65: 1907–1914. (b) Goswami, S.; Ghosh, K.; Mukherjee, R. Tetrahedron2001, 57, 4987–4993. (c) Goswami, S.; Ghosh, K.; Halder, M. Tetrahedron Lett.1999, 40, 1735–1738. (d) Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett.2005, 46, 7187–7191. (e) Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem.2006, 18, 571–574. (f) Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm.2008, 10, 507–517. (g) Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron2008,64, 6426–6433. (h) Goswami, S.; Dey, S.; Jana, S. Tetrahedron2008, 64, 6358–6363 [Google Scholar], 46, 7187–7191), anti–anti polymeric 1:1 (Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem. 2006 (a) Goswami, S., Ghosh, K. and Dasgupta, S. 2000. J. Org. Chem., 65: 1907–1914. (b) Goswami, S.; Ghosh, K.; Mukherjee, R. Tetrahedron2001, 57, 4987–4993. (c) Goswami, S.; Ghosh, K.; Halder, M. Tetrahedron Lett.1999, 40, 1735–1738. (d) Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett.2005, 46, 7187–7191. (e) Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem.2006, 18, 571–574. (f) Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm.2008, 10, 507–517. (g) Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron2008,64, 6426–6433. (h) Goswami, S.; Dey, S.; Jana, S. Tetrahedron2008, 64, 6358–6363 [Google Scholar], 18, 571–574; Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm. 2008, 10, 507–517; Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron 2008, 64, 6426–6433), syn–syn 2:2 (Karle, I.L.; Ranganathan, D.; Haridas, V. J. Am. Chem. Soc. 1997 (a) Garcia-Tellado, F., Goswami, S., Chang, S.K., Geib, S.J. and Hamilton, A.D. 1990. J. Am. Chem. Soc., 112: 7393–7394. (b) Geib, S.J.; Vicent, C.; Fan, E.; Hamilton, A.D. Angew. Chem. Int. Ed. Engl.1993, 32, 119–121. (c) Garcia-Tellado, F.; Geib, S.J.; Goswami, S.; Hamilton, A.D. J. Am. Chem. Soc.1991, 113, 9265–9269. (d) Karle, I.L.; Ranganathan, D.; Haridas, V. J. Am. Chem. Soc.1997, 119, 2777–2783. (e) Moore, G.; Papamicaël, C.; Levacher, V.; Bourguignon, J.; Dupas, G. Tetrahedron2004, 60, 4197–4204. (f) Korendovych, I.V.; Cho, M.; Makhlynets, O.V.; Butler, P.L.; Staples, R.J.; Rybak-Akimova, E.V. J. Org. Chem.2008, 73, 4771–4782. (g) Ghosh, K.; Masanta, G.; Fröhlich, R.; Petsalakis, I.D.; Theodorakopoulos, G. J. Phys. Chem. B2009, 113, 7800–7809 [Google Scholar], 119, 2777–2783) or top–bottom-bound 1:1 (Garcia-Tellado, F.; Goswami, S.; Chang, S.K.; Geib, S.J.; Hamilton, A.D. J. Am. Chem. Soc. 1990 (a) Goswami, S., Ghosh, K. and Dasgupta, S. 2000. J. Org. Chem., 65: 1907–1914. (b) Goswami, S.; Ghosh, K.; Mukherjee, R. Tetrahedron2001, 57, 4987–4993. (c) Goswami, S.; Ghosh, K.; Halder, M. Tetrahedron Lett.1999, 40, 1735–1738. (d) Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett.2005, 46, 7187–7191. (e) Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem.2006, 18, 571–574. (f) Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm.2008, 10, 507–517. (g) Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron2008,64, 6426–6433. (h) Goswami, S.; Dey, S.; Jana, S. Tetrahedron2008, 64, 6358–6363 [Google Scholar], 112, 7393–7394) co-crystals.

     

Electron magnetic resonance and density functional theory study of room temperature X-irradiated β-D-fructose single crystals

Stable free radical formation in fructose single crystals X-irradiated at room temperature was investigated using Q-band electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three main crystallographic planes allowed an unambiguous determination of 12 proton HFC tensors. From the EIE studies, these hyperfine interactions were assigned to six different radical species, labeled F1-F6. Two of the radicals (F1 and F2) were studied previously by Vanhaelewyn et al. [Vanhaelewyn, G. C. A. M.; Pauwels, E.; Callens, F. J.; Waroquier, M.; Sagstuen, E.; Matthys, P. J. Phys. Chem. A 2006, 110, 2147.] and Tarpan et al. [Tarpan, M. A.; Vrielinck, H.; De Cooman, H.; Callens, F. J. J. Phys. Chem. A 2009, 113, 7994.]. The other four radicals are reported here for the first time and periodic density functional theory (DFT) calculations were used to aid their structural identification. For the radical F3 a C3 carbon centered radical with a carbonyl group at the C4 position is proposed. The close similarity in HFC tensors suggests that F4 and F5 originate from the same type of radical stabilized in two slightly different conformations. For these radicals a C2 carbon centered radical model with a carbonyl group situated at the C3 position is proposed. A rather exotic C2 centered radical model is proposed for F6.     

The reaction OH + C2H4: an example of rotational channel switching

The low-temperature data for the reaction between OH and C(2)H(4) is treated canonically as either a two-well or one-well problem using the "Multiwell" suite of codes, in which a "well" refers to a minimum in the potential energy surface. The former is analogous to the two transition state model of Greenwald et al. [Greenwald, E. E.; North, S. W.; Georgievskii, Y.; Klippenstein, S. J. J. Phys. Chem. A2005, 109, 6031], while the latter reflects the dominance of the so-called "inner transition state". External rotations are treated adiabatically, causing changes in the magnitude of effective barriers as a function of temperature. Extant data are well-described with either model using only the average energy transferred in a downward direction, upon collision, ΔE(d)(T), as a fitting parameter. The best value for the parameters describing the rate coefficient as a function of temperature (200 < T/K < 400) (Data at lower temperature is too sparse to yield a recommendation.) and pressure in the form used in the NASA/JPL format [Sander, S. P.; Abbatt, J.; Barker, J. R.; Burkholder, J. B.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Moortgat, G. K et al., Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 17, Jet Propulsion Laboratory, 2011] are k(0) = 1.0 × 10(-28)(T/300)(-3.5) cm(6) molecule(-2) s(-1) and k(∞) to 8.0 × 10(-12)(T/300)(-2.3) cm(3) molecule(-1) s(-1).     

The ionic work function and its role in estimating absolute electrode potentials

The experimental determination of the ionic work function is briefly described. Data for the proton, alkali metal ions, and halide ions in water, originally published by Randles (Randles, J. E. B. Trans Faraday Soc. 1956, 52, 1573) are recalculated on the basis of up-to-date thermodynamic tables. These calculations are extended to data for the same ions in four nonaqueous solvents, namely, methanol, ethanol, acetonitrile, and dimethyl sulfoxide. The ionic work function data are compared with estimates of the absolute Gibbs energy of solvation obtained by an extrathermodynamic route for the same ions. The work function data for the proton are used to estimate the absolute potential of the standard hydrogen electrode in each solvent. The results obtained here are compared with those published earlier by Trasatti (Trasatti, S. Electrochim. Acta 1987, 32, 843) and more recently by Kelly et al. (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2006, 110, 16066. Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2007, 111, 408). A comparison of the ionic work function with the absolute Gibbs solvation energy permits an estimation of the surface potential of the solvent. The results show that the surface potential of water is small and positive whereas the surface potential of the nonaqueous solvents considered is negative. The sign of the surface potential is consistent with the known structure of each solvent.     

The high-valent iron-oxo species of polyoxometalate, if it can be made, will be a highly potent catalyst for C-H hydroxylation and double-bond epoxidation

This study uses density functional theory (DFT) calculations to explore the reactivity of the putative high-valent iron-oxo reagent of the iron-substituted polyoxometalate (POM-FeO4-), derived from the Keggin species, PW12O40(3-). It is shown that POM-FeO4- is in principle capable of C-H hydroxylation and C=C epoxidation and that it should be a powerful oxidant, even more so than the Compound I species of cytochrome P450. The calculations indicate that in a solvent, the barriers, and especially those for epoxidation, become sufficiently small that one may expect an extremely fast reaction. An experimental investigation (by R.N. and A.M.K.) shows, however, that the formation of POM-FeO4- using the oxygen donor, F5PhI-O, leads to a persistent adduct, POM-FeO-I-PhF5(4-), which does not decompose to POM-FeO4- + F5Ph-I at the working temperature and exhibits sluggish reactivity, in accord with previous experimental results (Hill, C. L.; Brown, R. B., Jr. J. Am. Chem. Soc. 1986, 108, 536 and Mansuy, D.; Bartoli, J.-F.; Battioni, P.; Lyon, D. K.; Finke, R. G. J. Am. Chem. Soc. 1991, 113, 7222). Subsequent calculations indeed reveal that the gas-phase binding energy of F5PhI to POM-FeO4- is high (ca. 20 kcal/mol) compared to the corresponding binding energy of propene (ca. 2-3 kcal/mol). As such, the POM-FeO-I-PhF5(4-) complex is expected to be persistent toward the displacement of F5PhI by a substrate like propene, leading thereby to sluggish oxidative reactivity. According to theory, overcoming this technical difficulty may turn out to be very rewarding. The question is, can POM-FeO4- be made?     

Unraveling the aflatoxin-FAPY conundrum: structural basis for differential replicative processing of isomeric forms of the formamidopyrimidine-type DNA adduct of aflatoxin B1

Aflatoxin B1 (AFB) epoxide forms an unstable N7 guanine adduct in DNA. The adduct undergoes base-catalyzed ring opening to give a highly persistent formamidopyrimidine (FAPY) adduct which exists as a mixture of forms. Acid hydrolysis of the FAPY adduct gives the FAPY base which exists in two separable but interconvertible forms that have been assigned by various workers as functional, positional, or conformational isomers. Recently, this structural question became important when one of the two major FAPY species in DNA was found to be potently mutagenic and the other a block to replication [Smela, M. E.; Hamm, M. L.; Henderson, P. T.; Harris, C. M.; Harris, T. M.; Essigmann, J. M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6655-6660]. NMR studies carried out on the AFB-FAPY bases and deoxynucleoside 3',5'-dibutyrates now establish that the separable FAPY bases and nucleosides are diastereomeric N5 formyl derivatives involving axial asymmetry around the congested pyrimidine C5-N5 bond. Anomerization of the protected beta-deoxyriboside was not observed, but in the absence of acyl protection, both anomerization and furanosyl --> pyranosyl ring expansion occurred. In oligodeoxynucleotides, two equilibrating FAPY species, separable by HPLC, are assigned as anomers. The form normally present in duplex DNA is the mutagenic species. It has previously been assigned as the beta anomer by NMR (Mao, H.; Deng, Z. W.; Wang, F.; Harris, T. M.; Stone, M. P. Biochemistry 1998, 37, 4374-4387). In single-stranded environments the dominant species is the beta anomer; it is a block to replication.     

Explicitly correlated coupled cluster calculations for the benzenium ion (C6H7(+)) and its complexes with Ne and Ar

Explicitly correlated coupled cluster theory at the CCSD(T)-F12x (x = a, b) level (Adler, T. B.; Knizia, G.; Werner, H.-J. J. Chem. Phys. 2007, 127, 221106) has been employed in a study of the benzenium ion (C6H7(+)) and its complexes with a neon or an argon atom. The ground-state rotational constants of C6H7(+) are predicted to be A0 = 5445 MHz, B0 = 5313 MHz, and C0 = 2731 MHz. Anharmonic vibrational wavenumbers of this cation were obtained by combination of harmonic CCSD(T*)-F12a values with anharmonic contributions calculated by double-hybrid density functional theory at the B2PLYP-D level. For the complexes of C6H7(+) with Ne or Ar, the lowest energy minimum is of π-bonded structure. The corresponding dissociation energies D0 are estimated to be 160 and 550 cm(-1), respectively. There is no indication of H-bonds to the aromatic or aliphatic hydrogen atoms. Instead, three nonequivalent local energy minima were found for nuclear configurations where the rare-gas atom lies in the ring-plane and approximatly points to the center of one of the six CC bonds.     

DFT investigation of structural, electronic, and catalytic properties of diiron complexes related to the [2Fe](H) subcluster of Fe-only hydrogenases

Hydrogenases catalyze the reversible oxidation of dihydrogen to protons and electrons. The structures of two Fe-only hydrogenases have been recently reported [Peters, J. W.; Lanzilotta, W. N.; Lemon, B. J.; Seefeldt, L. C. Science 1998, 282, 1853-1858. Nicolet, Y.; Piras, C.; Legrand, P.; Hatchikian, E. C.; Fontecilla-Camps, J. C. Structure 1999, 7, 13-23], showing that the likely site of dihydrogen activation is the so-called [2Fe](H) cluster, where each Fe ion is coordinated by CO and CN(-) ligands and the two metals are bridged by a chelating S-X(3)-S ligand. Moreover, the presence of a water molecule coordinated to the distal Fe2 center suggested that the Fe2 atom could be a suitable site for binding and activation of H(2). In this contribution, we report a density functional theory investigation of the structural and electronic properties of complexes derived from the [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) species, which is related to the [2Fe](H) cluster observed in Fe-only hydrogenases. Our results show that the structure of the [2Fe](H) cluster observed in the enzyme does not correspond to a stable form of the isolated cluster, in the absence of the protein. As a consequence, the reactivity of [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) derivatives in solution may be expected to be quite different from that of the active site of Fe-only hydrogenases. In fact, the most favorable path for H(2) activation involves the two metal atoms and one of the bridging S atoms and is associated with a very low activation energy (5.3 kcal mol(-1)). The relevance of these observations for the catalytic properties of Fe-only hydrogenases is discussed in light of available experimental and theoretical data.     

Excluded volume effect for large and small solutes in water

The cavitation effect, i.e., the process of the creation of a void of excluded volume in bulk solvent (a cavity), is considered. The cavitation free energy is treated in terms of the information theory (IT) approach [Hummer, G.; Garde, S.; Garcia, A. E.; Paulaitis, M. E.; Pratt, L. R. J. Phys. Chem. B 1998, 102, 10469]. The binomial cell model suggested earlier is applied as the IT default distribution p(m) for the number m of solute (water) particles occupying a cavity of given size and shape. In the present work, this model is extended to cover the entire range of cavity size between small ordinary molecular solutes and bulky biomolecular structures. The resulting distribution consists of two binomial peaks responsible for producing the free energy contributions, which are proportional respectively to the volume and to the surface area of a cavity. The surface peak dominates in the large cavity limit, when the two peaks are well separated. The volume effects become decisive in the opposite limit of small cavities, when the two peaks reduce to a single-peak distribution as considered in our earlier work. With a proper interpolation procedure connecting these two regimes, the MC simulation results for model spherical solutes with radii increasing up to R = 10 A [Huang, D. H.; Geissler, P. L.; Chandler, D. J. Phys. Chem. B 2001, 105, 6704] are well reproduced. The large cavity limit conforms to macroscopic properties of bulk water solvent, such as surface tension, isothermal compressibility and Tolman length. The computations are extended to include nonspherical solutes (hydrocarbons C1-C6).