Temperature-dependent optical Kerr effect spectroscopy of aromatic liquids

Ultrafast optical Kerr effect (OKE) spectroscopy has been used to study the temperature-dependent dynamics of five aromatic liquids: benzene, benzene-d(6), hexafluorobenzene, mesitylene, and 1,3,5-trifluorobenzene. The intermediate response time of all of the liquids was found to scale with the collective orientational correlation time, as has been observed for other simple liquids. The spectra of hexafluorobenzene, 1,3,5-trifluorobenzene, and mesitylene are qualitatively different from those of the other liquids and exhibit different behavior with temperature. These spectra allow us to assess the influence of different molecular parameters on the shape of the OKE spectrum. On the basis of these data, we propose a model that links the differences in the OKE spectra to corresponding differences in the local ordering of the liquids.     

C. fumago chloroperoxidase is also a dehaloperoxidase: oxidative dehalogenation of halophenols

We have examined the H2O2-dependent oxidative dehalogenation of 2,4,6-trihalophenols and p-halophenols catalyzed by Caldariomyces fumago chloroperoxidase (CCPO). CCPO is significantly more robust than other peroxidases and can function under harsher reaction conditions, and so its ability to dehalogenate halophenols could lead to its use as a bioremediation catalyst for aromatic dehalogenation reactions. Optimal catalysis occurred under acidic conditions (100 mM potassium phosphate solution, pH 3.0). UV-visible absorption spectroscopy, high-performance liquid chromatography, and gas chromatography/mass spectrometry clearly identified the oxidized reaction product for CCPO-catalyzed dehalogenation of 2,4,6-trihalophenols as the corresponding 2,6-dihalo-1,4-benzoquinones. This reaction has previously been reported for two His-ligated heme-containing peroxidases (see Osborne, R. L.; Taylor, L. O.; Han, K. P.; Ely, B.; Dawson, J. H. Biochem. Biophys. Res. Commun. 2004, 324, 1194-1198), but this is the first example of a Cys-ligated heme-containing peroxidase functioning as a dehaloperoxidase. The relative catalytic efficiency (turnover number) of CCPO reported herein is comparable to that of horseradish peroxidase (Ferrari, R. P.; Laurenti, E.; Trotta, F. J. Biol. Inorg. Chem. 1965, 4, 232-237). The mechanism of dehalogenation has been probed using p-halophenols as substrates. Here the major product is a dimer with 1,4-benzoquinone as the minor product. An electron-transfer mechanism is proposed that accounts for the products formed from both the 2,4,6-trihalo- and p-halophenols. Finally, we note that this is the first case of a peroxidase known primarily for its halogenation ability being shown to also dehalogenate substrates.     

Molecular dynamics study of polarizability anisotropy relaxation in aromatic liquids and its connection with local structure

The collective polarizability anisotropy dynamics in a set of three aromatic liquids, benzene (Bz), hexafluorobenzene (HFB), and 1,3,5-trifluorobenzene (TFB), has been studied by molecular dynamics simulation. These liquids have very similar shapes, but different electrostatic interactions due to opposite polarities of C-H and C-F bonds, giving rise to different local intermolecular structures in the liquid phase. We have investigated how these structural arrangements affect polarizability anisotropy dynamics observed in optical Kerr-effect (OKE) spectroscopy. We have modeled the interaction-induced polarizability with the first-order dipole-induced dipole approximation, with the molecular polarizability distributed over the carbon sites. Local contributions to the librational OKE spectrum were computed separately for molecules participating in parallel or perpendicular relative orientations within the first coordination shell. We found that the relative locations of parallel and perpendicular librational bands of the OKE spectra are closely related to the corresponding pair energy distributions of the closest four neighbors of a given molecule, corresponding to a model of a harmonic oscillator in a cage of nearest neighbors. This model predicts higher librational frequencies for more attractive intermolecular interactions, which in all three liquids correspond to parallel local arrangements. On the diffusive orientational time scale, all three liquids exhibit slower relaxation of molecules in parallel arrangements, although the difference in relaxation rates is substantial only in TFB, which has the strongest tendency toward parallel stacking. The analysis of the collective polarizability relaxation was performed using two different approaches, the projection scheme (J. Chem. Phys. 1980, 72, 2801) and the theory developed by Steele (Mol. Phys. 1987, 61, 1031) for the second time derivatives applied to collective time correlations. Both approaches allow the decomposition of the OKE response into contributions from orientational relaxation and other dynamical processes. We find that they lead to different predictions on how the response depends on collective reorientation and processes arising from fluctuations in the interaction-induced polarizability. We discuss the reasons for these differences and the advantages and disadvantages of the two analysis schemes.     

Depolarized light scattering versus optical Kerr effect. II. Insight into the dynamic susceptibility of molecular liquids

We have previously discussed [J. Chem. Phys. 125, 114502 (2006)] that optical Kerr effect (OKE) and depolarized light scattering (DLS) data of molecular liquids reveal, each in their native domain, the same characteristic signatures of the glass transition dynamics; in particular, the intermediate power law of OKE is equivalent with the excess wing of the frequency-domain data, long since known in dielectric spectroscopy. We now extend the discussion to show that the excess wing is an equally common feature in DLS. We further discuss the time-temperature superposition property of OKE data in relation to our DLS and literature dielectric-spectroscopic results, and the merits of their mode coupling theory analyses. Spectroscopic signatures of a liquid-crystal-forming system (nematogen) are discussed in the same frame.     

Nanostructural organization and anion effects on the temperature dependence of the optical Kerr effect spectra of ionic liquids

The intermolecular spectra of three imidazolium ionic liquids were studied as a function of temperature by the use of optical heterodyne-detected Raman-induced Kerr effect spectroscopy. The ionic liquids comprise the 1,3-pentylmethylimidazolium cation ([C(5)mim]+), and the anions, bromide (Br-), hexafluorophosphate (PF(6)-), and bis(trifluoromethanesulfonyl)imide (NTf(2)-). Whereas the optical Kerr effect (OKE) spectrum of [C(5)mim][NTf(2)] is temperature-dependent, the OKE spectra of [C(5)mim]Br and [C(5)mim][PF6] are temperature-independent. These results are surprising in light of the fact that the bulk densities of these room temperature ionic liquids (RTILs) are temperature-dependent. The temperature independence of the OKE spectra and the temperature dependence of the bulk density in [C(5)mim]Br and [C(5)mim][PF(6)] suggest that there are inhomogeneities in the densities of these liquids. The existence of density inhomogeneities is consistent with recent molecular dynamics simulations that show RTILs to be nanostructurally organized with nonpolar regions arising from clustering of the alkyl chains and ionic networks arising from charge ordering of the anions and imidazolium rings of the cations. Differences in the temperature dependences of the OKE spectra are rationalized on the basis of the degree of charge ordering in the polar regions of the RTILs.     

Nanostructural organization and anion effects in the optical Kerr effect spectra of binary ionic liquid mixtures

This article reports a study of the effect of anions on the optical Kerr effect (OKE) spectra of binary ionic liquid mixtures with one mixture comprising the 3-methyl-1-pentylimidazolium ([C 5mim] (+)) cation and the anions PF 6 (-) and CF 3CO 2 (-) (TFA (-)), and another mixture comprising the [C 5mim] (+) cation and the anions Br (-) and bis(trifluomethanesulfonyl)imide (NTf 2 (-)). The spectra were obtained by the use of optical heterodyne-detected Raman-induced Kerr Effect Spectroscopy at 295 K. The OKE spectra of the mixtures are compared with the calculated mole-fraction weighted sum of the normalized OKE spectra of the neat liquids. The OKE spectra are nearly additive for [C 5mim]Br/[C 5mim][NTf 2] mixtures, but nonadditive for [C 5mim][PF 6]/[C 5mim][TFA] mixtures. In the case of the equimolar [C 5mim][PF 6]/[C 5mim][TFA] mixture, the nonadditivity is such that the experimental OKE spectrum is narrower than the calculated OKE spectrum. The additivity or nonadditivity of OKE spectra for IL mixtures can be explained by assuming ionic liquids are nanostructurally organized into nonpolar regions and ionic networks. The ionic networks in mixtures will be characterized by "random co-networks" for anions that are nearly the same in size (PF 6 (-) and TFA (-)) and by "block co-networks" for anions that differ greatly in size (Br (-) and NTf 2 (-)).     

Why does the intermolecular dynamics of liquid biphenyl so closely resemble that of liquid benzene? Molecular dynamics simulation of the optical-Kerr-effect spectra

The combination of optical-Kerr-effect (OKE) spectroscopy and molecular dynamics simulations has provided us with a newfound ability to delve into the librational dynamics of liquids, revealing, in the process, some surprising commonalities among aromatic liquids. Benzene and biphenyl, for example, have remarkably similar OKE spectra despite marked differences in their shapes, sizes, and moments of inertia--and even more chemically distinct aromatics tend to have noticeable similarities in their spectra. We explore this universality by using a molecular dynamics simulation to investigate the librational dynamics of molten biphenyl and to predict its OKE spectrum, comparing the results with our previous calculations for liquid benzene. We suggest that the impressive level of quantitative agreement between these two liquids is largely a reflection of the fact that librations in these and other aromatic liquids act as torsional oscillations with oscillator frequencies selected from the liquid's librational bands. Since these bands are centered about the librational Einstein frequencies, the quantitative similarities between the liquids are essentially reflections of the near identities of their Einstein frequencies. Why then are the Einstein frequencies themselves so insensitive to molecular details? We show that, for nearly planar molecules, mean-square torques and moments of inertia tend to scale with molecular dimensions in much the same way. We demonstrate that this near cancellation provides both a quantitative explanation of the close relationship between benzene and biphenyl and a more general perspective on the similarities seen in the ultrafast dynamics of aromatic liquids.     

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.     

Investigation of the reduced high-potential iron-sulfur protein from chromatium vinosum and relevant model compounds: a unified picture of the electronic structure of [Fe(4)S(4)](2+) systems through magnetic and optical studies

Magnetization measurements and variable temperature optical spectroscopy have been used to investigate, within the 4-300 K temperature range, the electronic structure of the reduced high-potential iron protein (HiPIP) from Chromatium vinosum and the model compounds (Cat)(2)[Fe(4)S(4)(SR)(4)], where RS(-) = 2,4,6-triisopropylphenylthiolate (1), 2,6-diphenylphenylthiolate (2), diphenylmethylthiolate (3), 2,4,6-triisopropylbenzylthiolate (4, 4'), 2,4,6-triphenylbenzylthiolate (5, 5'), 2,4,6-tri-tert-butylbenzylthiolate (6), and Cat(+) = (+)NEt(4) (1, 2, 3, 4', 5', 6), (+)PPh(4) (4, 5). The newly synthesized 2(2)(-), 3(2)(-), 5(2)(-), and 6(2)(-) complexes are, as 1(2)(-) and 4(2)(-), excellent models of the reduced HiPIPs: they exhibit the [Fe(4)S(4)](3+/2+) redox couple, because of the presence of bulky ligands which stabilize the [Fe(4)S(4)](3+) oxidized core. Moreover, the presence of SCH(2) groups in 4(2)(-), 5(2)(-), and 6(2)(-), as in the [Fe(4)S(4)] protein cores, makes them good biomimetic models of the HiPIPs. The X-ray structure of 2 is reported: it crystallizes in the orthorhombic space group Pcca with no imposed symmetry and a D(2)(d)()-distorted geometry of the [Fe(4)S(4)](2+) core. Fit of the magnetization data of the reduced HiPIP and of the 1, 2, 3, 4, 5, and 6 compounds within the exchange and double exchange theoretical framework leads to exchange coupling parameters J = 261-397 cm(-)(1). A firm determination of the double exchange parameters B or, equivalently, the transfer integrals beta = 5B could not be achieved that way. The obtained |B| values remain however high, attesting thus to the strength of the spin-dependent electronic delocalization which is responsible for lowest lying electronic states being characterized by delocalized mixed-valence pairs of maximum spin (9)/(2). Electronic properties of these systems are then accounted for by the population of a diamagnetic ground level and excited paramagnetic triplet and quintet levels, which are respectively J and 3J above the ground level. Optical studies of 1, 2, 4', 5', and 6 but also of (NEt(4))(2)[Fe(4)S(4)(SCH(2)C(6)H(5))(4)] and the isomorph (NEt(4))(2)[Fe(4)S(4)(S-t-Bu)(4)] and (NEt(4))(2)[Fe(4)Se(4)(S-t-Bu)(4)] compounds reveal two absorption bands in the near infrared region, at 705-760 nm and 1270-1430 nm, which appear to be characteristic of valence-delocalized and ferromagnetically coupled [Fe(2)X(2)](+) (X = S, Se) units. The |B| and |beta| values can be directly determined from the location at 10|B| of the low-energy band, and are respectively of 699-787 and 3497-3937 cm(-)(1). Both absorption bands are also present in the 77 K spectrum of the reduced HiPIP, at 700 and 1040 nm (Cerdonio, M.; Wang, R.-H.; Rawlings, J.; Gray, H. B. J. Am. Chem. Soc. 1974, 96, 6534-6535). The blue shift of the low-energy band is attributed to the inequivalent environments of the Fe sites in the protein, rather than to an increase of |beta| when going from the models to the HiPIP. The small differences observed in known geometries of [Fe(4)S(4)](2+) clusters, especially in the Fe-Fe distances, cannot probably lead to drastic changes in the direct Fe-Fe interactions (parameter beta) responsible for the delocalization phenomenon. These differences are however magnetostructurally significant as shown by the 261-397 cm(-)(1) range spanned by J. The cluster's geometry, hence the efficiency of the Femicro(3)-S-Fe superexchange pathways, is proposed to be controlled by the more or less tight fit of the cluster within the cavity provided by its environment.     

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.     

Catalytic asymmetric formal [4 + 1] annulation leading to optically active cis-isoxazoline N-oxides

The catalytic asymmetric synthesis of densely functionalized cis-isoxazoline N-oxides was realized with novel use of an organocatalyst, (S)-2-(azidodiphenylmethyl)pyrrolidine (4e) (Tan, B.; Zhu, D.; Zhang, L.; Chua, P. J.; Zeng, X.; Zhong, G. Chem.-Eur. J. 2010, 16, 3842; Olivares-Romero, J. L.; Juaristi, E. Tetrahedron 2008, 64, 9992), via an elegant formal [4 + 1] annulation strategy using readily available 2-nitroacrylates and α-iodoaldehydes.     

Ultrafast decay of electronically excited singlet cytosine via a pi,pi* to n(O),pi* state switch

Singlet fluorescence lifetimes of adenosine, cytidine, guanosine, and thymidine, determined by femtosecond pump-probe spectroscopy (Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2000, 122, 9348. Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001, 123, 10370), show that the excited states produced by 263 nm light in these nucleosides decay in the subpicosecond range (290-720 fs). Ultrafast radiationless decay to the ground state greatly reduces the probability of photochemical damage. In this work we present a theoretical study of isolated cytosine, the chromophore of cytidine. The experimental lifetime of 720 fs indicates that there must be an ultrafast decay channel for this species. We have documented the possible decay channels and approximate energetics, using a valence-bond derived analysis to rationalize the structural details of the paths. The mechanism favored by our calculations and the experimental data involves (1) a two-mode decay coordinate composed of initial bond length inversion followed by internal vibrational energy redistribution (IVR) to populate a carbon pyramidalization mode, (2) a state switch between the pi,pi* and nO,pi* (excitation from oxygen lone pair) excited states, and (3) decay to the ground state through a conical intersention. A second decay path through the nN,pi* state (excitation from the nitrogen lone pair), with a higher barrier, involves out-of-plane bending of the amino substituent.     

Capturing a synergistic effect of a conical push and an inward pull in fluoro derivatives of Li@B10H14 basket: toward a higher vertical ionization potential and nonlinear optical response

We present the design of fluoro derivatives of B(10)H(14) and Li@B(10)H(14) baskets. A synergistic effect of conical push and inward pull (reported independently in previous lithium nonlinear optical (NLO) complexes) has been explored in these derivatives to achieve a robustly large NLO response and a higher vertical ionization potential. Li@1,3,6,9-F(4)B(10)H(10), Li@6,9-F(2)B(10)H(12), and Li@2,4,6,9-F(4)B(10)H(10) exhibit first hyperpolarizability (β(0)) values as large as 181?624, 133?199, and 32?314 au; their vertical ionization potentials are 6.45, 6.30, and 6.78 eV, respectively. These values are significantly higher than those previously reported in Li-doped fluorocarbon chains at the same MP2/6-31+G* level of theory (Xu, H. L.; Li, Z. R.; Wu, D.; Wang, B. Q.; Li, Y.; Gu, F. L.; Aoki, Y. J. Am. Chem. Soc. 2007, 129, 2967). They also exceed those from our earlier designed Li@B(10)H(14) basket (Muhammad, S.; Xu, H. L.; Liao, Y.; Kan, Y. H.; Su , Z. M. J. Am. Chem. Soc. 2009, 131, 2967). In addition, new quantum chemical calculations of enthalpies of reaction (Δ(r)H°) at 298 K for B(10)H(14) and its lithium/fluoro derivatives highlight the changes in their thermodynamical aspects. The calculated enthalpies of lithiation reactions are -10.04, -11.29, and -13.18 kcal/mol for B(10)H(14), 6,9-F(2)B(10)H(12), and 2,4-F(2)B(10)H(12), respectively, demonstrating a higher probability of fluoro decaboranes for reaction with lithium. The obtained results not only explain the effect of position and number dependence of substituted fluoro atom(s) in B(10)H(14) and Li@B(10)H(14) but also elucidate a synergistic behavior to polarize a lithium excess electron for high NLO responses and vertical ionization potentials.     

Exploring the electron transfer pathways in photosystem I by high-time-resolution electron paramagnetic resonance: observation of the B-side radical pair P700(+)A1B(-) in whole cells of the deuterated green alga Chlamydomonas reinhardtii at cryogenic temperatures

Crystallographic models of photosystem I (PS I) highlight a symmetrical arrangement of the electron transfer cofactors which are organized in two parallel branches (A, B) relative to a pseudo-C2 symmetry axis that is perpendicular to the membrane plane. Here, we explore the electron transfer pathways of PS I in whole cells of the deuterated green alga Chlamydomonas reinhardtii using high-time-resolution electron paramagnetic resonance (EPR) at cryogenic temperatures. Particular emphasis is given to quantum oscillations detectable in the tertiary radical pairs P700(+)A1A(-) and P700(+)A1B(-) of the electron transfer chain. Results are presented first for the deuterated site-directed mutant PsaA-M684H in which electron transfer beyond the primary electron acceptor A0A on the PsaA branch of electron transfer is impaired. Analysis of the quantum oscillations, observed in a two-dimensional Q-band (34 GHz) EPR experiment, provides the geometry of the B-side radical pair. The orientation of the g tensor of P700(+) in an external reference system is adapted from a time-resolved multifrequency EPR study of deuterated and 15N-substituted cyanobacteria (Link, G.; Berthold, T.; Bechtold, M.; Weidner, J.-U.; Ohmes, E.; Tang, J.; Poluektov, O.; Utschig, L.; Schlesselman, S. L.; Thurnauer, M. C.; Kothe, G. J. Am. Chem. Soc. 2001, 123, 4211-4222). Thus, we obtain the three-dimensional structure of the B-side radical pair following photoexcitation of PS I in its native membrane. The new structure describes the position and orientation of the reduced B-side quinone A1B(-) on a nanosecond time scale after light-induced charge separation. Furthermore, we present results for deuterated wild-type cells of C. reinhardtii demonstrating that both radical pairs P700(+)A1A(-) and P700(+)A1B(-) participate in the electron transfer process according to a mole ratio of 0.71/0.29 in favor of P700(+)A1A(-). A detailed comparison reveals different orientations of A1A(-) and A1B(-) in their respective binding sites such that formation of a strong hydrogen bond from A1(-) to the protein backbone is possible only in the case of A1A(-). We suggest that this is relevant to the rates of forward electron transfer from A1A(-) or A1B(-) to the iron-sulfur center F(X), which differ by a factor of 10. Thus, the present study sheds new light on the orientation of the phylloquinone acceptors in their binding pockets in PS I and the effect this has on function.     

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.     

Theoretical isotropic hyperfine coupling constants of third-row nuclei (29Si, 31P, and 33S)

In a previous paper (Hermosilla, L.; Calle, P.; Garcia de la Vega, J. M.; Sieiro, C. J. Phys. Chem. A 2005, 109, 1114), an adequate computational protocol for the calculation of isotropic hyperfine coupling constants (hfcc's) was proposed. The main conclusion concerns the reliability of the scheme B3LYP/TZVP//B3LYP/6-31G* in the predictions of hfcc's with low computational cost. In the present study, we gain insight into the behavior of the above functional/basis set scheme on nuclei of the third row, for which few systematic studies have been carried out up to the present date. The systems studied are neutral, cationic, anionic, localized, and conjugated radicals, containing (29)Si, (31)P, and (33)S nuclei. After carrying out a regression analysis, we conclude that density functional theory (DFT) predictions on the hfcc's of the third-row nuclei are reliable for B3LYP/TZVP by using an optimized geometry with B3LYP/6-31G* combination. By comparison with other much more computationally demanding schemes, namely, B3LYP/cc-pVTZ and B3LYP/cc-pVQZ, we conclude that the B3LYP functional in conjunction with the TZVP basis set is the most useful computational protocol for the assignment of experimental hfcc's, not only for nuclei of first and second rows, but also for those of the third row.     

Enthalpy-entropy contributions to salt and osmolyte effects on molecular-scale hydrophobic hydration and interactions

Salts and additives can significantly affect the strength of water-mediated interactions in solution. We present results from molecular dynamics simulations focused on the thermodynamics of hydrophobic hydration, association, and the folding-unfolding of a hydrophobic polymer in water and in aqueous solutions of NaCl and of an osmolyte trimethylamine oxide (TMAO). It is known that addition of NaCl makes the hydration of hydrophobic solutes unfavorable and, correspondingly, strengthens their association at the pair as well as the many-body level (Ghosh, T.; Kalra, A.; Garde, S. J. Phys. Chem. B 2005, 109, 642), whereas the osmolyte TMAO has an almost negligible effect on the hydrophobic hydration and association (Athawale, M. V.; Dordick, J. S.; Garde, S. Biophys. J. 2005, 89, 858). Whether these effects are enthalpic or entropic in origin is not fully known. Here we perform temperature-dependent simulations to resolve the free energy into entropy and enthalpy contributions. We find that in TMAO solutions, there is an almost precise entropy-enthalpy compensation leading to the negligible effect of TMAO on hydrophobic phenomena. In contrast, in NaCl solutions, changes in enthalpy dominate, making the salt-induced strengthening of hydrophobic interactions enthalpic in origin. The resolution of total enthalpy into solute-solvent and solvent-solvent terms further shows that enthalpy changes originate primarily from solvent-solvent energy terms. Our results are consistent with experimental data on the hydration of small hydrophobic solutes by Ben-Naim and Yaacobi (Ben-Naim, A.; Yaacobi, M. J. Phys. Chem. 1974, 78, 170). In combination with recent work by Zangi, Hagen, and Berne (Zangi, R.; Hagen, M.; Berne, B. J. J. Am. Chem. Soc. 2007, 129, 4678) and the experimental data on surface tensions of salt solutions by Matubayasi et al. (Matubayasi, N.; Matsuo, H.; Yamamoto, K.; Yamaguchi, S.; Matuzawa, A. J. Colloid Interface Sci. 1999, 209, 398), our results highlight interesting length scale dependences of salt effects on hydrophobic phenomena. Although NaCl strengthens hydrophobic interactions at both small and large length scales, that effect is enthalpy-dominated at small length scales and entropy-dominated for large solutes and interfaces. Our results have implications for understanding of additive effects on water-mediated interactions, as well as on biocompatibility of osmolyte molecules in aqueous solutions.     

Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.     

Detection of vibrational bending mode ν8 and overtone bands of the propargyl radical, HCCCH2 X̃ 2B1

Infrared (IR) absorption spectra of matrix-isolated HCCCH(2) have been measured. Propargyl radicals were generated in a supersonic pyrolysis nozzle, using a method similar to that described in a previous study (Jochnowitz, E. B.; Zhang, X.; Nimlos, M. R.; Varner, M. E.; Stanton, J. F.; Ellison, G. B. J. Phys. Chem. A 2005, 109, 3812-3821). Besides the nine vibrational modes observed in the previous study, this investigation detected the HCCCH(2) X? (2)B(1) out-of-plane bending mode (ν(8)) at 378.0 (±1.9) cm(-1) in a cryogenic argon matrix. This is the first experimental observation of ν(8) for the propargyl radical. In addition, seven overtone and combination bands have also been detected and assigned. Ab initio coupled-cluster anharmonic force field calculations were used to guide the analysis. Furthermore, ν(12), the HCCCH(2) in-plane bending mode, has been assigned to 333 (±10) cm(-1) based on the detection of its overtone (2ν(12), 667.7 ± 1.0 cm(-1)) and a possible combination band (ν(10) + ν(12), 1339.0 ± 0.8 cm(-1)). This is the first experimental estimation of ν(12) for the propargyl radical.