The spectral-structural relationship of a series of oxyluciferin derivatives.

The absorption and emission spectra of a series of oxyluciferin derivatives with different substituents, as well as 6'-amino oxyluciferins in different enol and keto forms, with or without an active-site model of luciferase, were systematically investigated using density functional theory. The effects of substituents, microenvironment, and the luciferase on the structures, absorption spectra, and fluorescent emission were all taken into account. It was found that a wide range of emission colors can be obtained from various oxyluciferin derivatives with the inclusion of active site residues modeling the luciferase active site. Enol and keto forms are responsible for the emissions observed in experiments. It was suggested that the active site of luciferase must be included in the calculation in order to determine the form of the emitters.

Theoretical investigation on the origin of yellow-green firefly bioluminescence by time-dependent density functional theory.

The question whether the emitter of yellow-green firefly bioluminescence is the enol or keto-constrained form of oxyluciferin (OxyLH(2)) still has no definitive answer from experiment or theory. In this study, Arg220, His247, adenosine monophosphate (AMP), Water324, Phe249, Gly343, and Ser349, which make the dominant contributions to color tuning of the fluorescence, are selected to simulate the luciferase (Luc) environment and thus elucidate the origin of firefly bioluminescence. Their respective and compositive effects on OxyLH(2) are considered and the electronic absorption and emission spectra are investigated with B3LYP, B3PW91, and PBE1KCIS methods. Comparing the respective effects in the gas and aqueous phases revealed that the emission transition is prohibited in the gas phase but allowed in the aqueous phase. For the compositive effects, the optimized geometry shows that OxyLH(2) exists in the keto(-1) form when Arg220, His247, AMP, Water324, Phe249, Gly343, and Ser349 are all included in the model. Furthermore, the emission maximum wavelength of keto(-1)+Arg+His+AMP+H(2)O+Phe+Gly+Ser is close to the experimental value (560 nm). We conclude that the keto(-1) form of OxyLH(2) is a possible emitter which can produce yellow-green bioluminescence because of the compositive effects of Arg220, His247, AMP, Water324, Phe249, Gly343, and Ser349 in the luciferase environment. Moreover, AMP may be involved in enolization of the keto(-1) form of OxyLH(2). Water324 is indispensable with respect to the environmental factors around luciferin (LH(2)).

SERS of beta-thioglucose adsorbed on nanostructured silver electrodes.

Highly ordered microporous films of silver-containing regular arrays of spherical pores of differing diameters were prepared by electrochemical deposition into the interstitial spaces of a template formed by nanosphere lithography. These nanostructured electrodes in conjunction with a Raman microprobe spectrometer were used to obtain surface-enhanced Raman spectra (SERS) of beta-thioglucose (beta-TG) under potential control. The SERS results were compared with SERS of beta-TG on an electrochemically roughened silver electrode surface. The bands in the experimental spectra were assigned to particular vibrations with the help of ab initio predictions of the spectra. The results of this study show that beta-TG self-assembled at a silver electrode forms a hydrophilic film that may be used in biomimetic research to enhance interactions between the electrode and the hydrophilic portion of a model membrane, and to prevent interactions of proteins inserted into this membrane with the metal surface. However, in contact with the aqueous electrolyte an anomerization reaction takes place and the beta-TG film is a mixture of the alpha- and beta-anomers of thioglucose. A partial oxidation of the self-assembled molecules was also observed. In addition, the orientation of the adsorbed molecules changes as a function of the applied potential.

A time-dependent density functional theory investigation on the origin of red chemiluminescence.

Is the resonance-based anionic keto form of oxyluciferin the chemical origin of multicolor bioluminescence? Can it modulate green into red luminescence? There is as yet no definitive answer from experiment or theory. The resonance-based anionic keto forms of oxyluciferin have been proposed as a cause of multicolor bioluminescence in the firefly. We model the possible structures by adding sodium or ammonium cations and investigating the ground- and excited-state geometries as well as the electronic absorption and emission spectra. A role for the resonance structures is obvious in the gas phase. The absorption and emission spectra of the two structures are quite different--one in the blue and another in the red. The differences in the spectra of the models are small in aqueous solution, with all the absorption and emission spectra in the yellow-green region. The resonance-based anionic keto form of oxyluciferin may be one origin of the red-shifted luminescence but is not the exclusive explanation for the variation from green (approximately 530 nm) to red (approximately 635 nm). We study the geometries, absorption, and emission spectra of the possible protonated compounds of keto(-1) in the excited states. A new emitter keto(-1)'-H is considered.

Predictions of the fluorine NMR chemical shifts of perfluorinated carboxylic acids, CnF(2n+1)COOH (n = 6-8).

Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C(6)-C(27)) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3 degrees in C(6)F(13)COOH to 17.0 degrees in C(27)F(55)COOH. This study predicts (19)F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C(6)F(13)COOH, C(7)F(15)COOH, and C(8)F(17)COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the (19)F chemical shifts revealed the differences among the CF(3), CF(2), and CF groups. In general, the absolute values for the chemical shifts for the CF(3) group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF(2) between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF(3) groups, the more hindered the CF(3), the greater the decrease in the (19)F chemical shifts. The predicted (19)F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO(3)H or -SO(3)NH(2)CH(2)CH(3).

In situ PM-IRRAS studies of an archaea analogue thiolipid assembled on a au(111) electrode surface.

Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) has been applied to determine the conformation, orientation, and hydration of a monolayer of 2,3-di-O-phytanyl-sn-glycerol-1-tetraethylene glycol-dl-alpha-lipoic acid ester (DPTL) self-assembled at a gold electrode surface. This Archaea analogue thiolipid has been recently employed to build tethered lipid bilayers. By synthesizing DPT(d16)L, a DPTL molecule with a deuterium substituted tetraethylene glycol spacer, it was possible to differentiate the C-H stretch vibrations of the phytanyl chains from the tetraethylene glycol spacer and acquire the characteristic IR spectra for the chains, spacer, and lipoic acid headgroup separately. Our results show that the structure of the monolayer displays remarkable stability in a broad range of electrode potentials and that the phytanyl chains remain in a liquid crystalline state. The tetraethylene glycol chains are coiled, and the IR spectrum for this region shows that it is in the disordered state. The most significant result of this study is the information that in contrast to expectations the spacer region is poorly hydrated. Our results have implications for the design of a tethered lipid membrane based on this thiolipid.

Color-tuning mechanism in firefly luminescence: theoretical studies on fluorescence of oxyluciferin in aqueous solution using time dependent density functional theory.

The first singlet excited state geometries of various isomers and tautomers of firefly oxyluciferin (OxyLH2), as well as their fluorescence spectra in aqueous solution, were studied using time dependent density functional theory (TDDFT). With changing pH in aqueous solution, three fluorescence peaks, blue (450 nm), yellow-green(560 nm), and red (620 nm) correspond to neutral keto and enolic forms, the monoanionic enolic form,and the monocationic keto form respectively. A counterion, Na+, was predicted to cause a blue shift in the fluorescence of anionic OxyLH2. The contributions of a charge transfer (CT) state upon electronic excitation of the planar and twisted structures were predicted. CT was large for the twisted structures but small for the planar ones. The differences between pK and pK* of various oxyluciferin species were predicted using a Forster cycle. A new possible light emitter, namely, the monocation keto form (keto+1), was considered.

Concerted and stepwise reaction mechanisms for the addition of ozone to acetylene: a computational study.

The mechanism of the reaction between acetylene and ozone to form a primary ozonide (POZ) in the gas phase has been studied theoretically. The concerted pathway, HCCH + O3 --> POZ, proceeds via a biradicaloid transition state TS0. The stepwise pathway is a three-step reaction, HCCH + O3 --> M1 --> M2 --> POZ, involving two biradical TSs and two biradical intermediates M1 and M2. The segment of the global potential energy surface (PES) for the concerted pathway is characterized as a R-PES, which is obtained from the restricted (R) density functional theory and Hartree-Fock-based methods. The RDFT and RHF solutions of TS0 and O3 are unstable toward spin-symmetry breaking. The wave function instability for TS0 and O3 results in a discontinuity between the R-PES and the region of the global PES encompassing the biradical TSs and the intermediates of the stepwise pathway, which are characterized with unrestricted (U) methods. The global PES is characterized separately as an U(R)-PES using a combination of the R and U methods. Several different values of barriers for the concerted pathway and the energy of concert (Ec) can be estimated due to complications arising from the discontinuity between the R- and the U(R)-PES and the existence of two different RDFT and UDFT O3 equilibrium geometries. RCCSD(T)//RDFT predicts a barrier of 8.2 kcal/mol. U(R)CCSD(T)/U(R)DFT predicts a barrier of 13.8 kcal/mol for the concerted and 15.3 kcal/mol for the stepwise pathway. Comparison between the R-PES barrier to the concerted pathway and the U(R)-PES barrier to the stepwise pathway suggests the former to be the only significant mechanism. Consideration of the energy difference between TS1, the TS for the first step of the stepwise mechanism, and TS0 within the global PES leads to a significantly smaller Ec. Geometry optimization with CASSCF and energy point calculations with MRMP2 are employed to characterize TS0 and TS1. MRMP2//CASSCF predicts the energy level of TS1 to be higher than that of TS0 by 2 kcal/mol. Analysis of experimental and computational data based on the low estimate of Ec shows that the possibility of the stepwise pathway being a secondary channel at elevated temperatures cannot be ruled out.

Predictions of the geometries and fluorescence emission energies of oxyluciferins.

The complete active space self-consistent field (CASSCF) method and multiconfigurational second-order perturbation theory (CASPT2) have been used to study the structures and spectra of oxyluciferins (OxyLH2). The ground and lowest-lying singlet excited states geometries have been optimized using CASSCF. CASPT2 has been used to predict relaxed emission energies. The focus is on the lowest-lying singlet excited states of the anionic keto and enol forms of OxyLH2(-1) at the optimized excited-state geometries. The planar keto and enol forms of OxyLH2(-1) are minima on both the S0 and the S1 potential energy surfaces. The twisted keto and enol forms of OxyLH2(-1) are transition states on the S0 and S1 potential energy surfaces. The S1 --> S0 fluorescence emission energies are in the range of 54.2-58.4 kcal/mol for the anionic planar keto forms of OxyLH2, and in the range of 55.7-63.2 kcal/mol for the anionic enol forms of OxyLH2. S0 and S1 potential energy surfaces and thus are not implicated in the emission spectra in the gas phase.

Remote substituent effects in ruthenium-catalyzed [2+2] cycloadditions: an experimental and theoretical study.

The effects of a remote substituent on the regioselectivity of ruthenium-catalyzed [2+2] cycloadditions of 2-substituted norbornenes with alkynes have been investigated experimentally and theoretically using density functional theory. Most of the cycloadditions occurred smoothly at room temperature, giving the exo cycloadducts in excellent yields. Regioselectivities of 1.2:1 to 15:1 were observed with various substituents on the C-2 position of the norbornenes. Exo-C-2-substituents usually showed greater remote substituent effects on the regioselectivities of the cycloadditions than the corresponding endo-C-2-substituents. The regioselectivity of the cycloadditions with C-2 substituents containing an exocyclic double bond (sp2 hybridized carbon at C-2) are much higher than the cycloadditions with the exo and endo 2-substituted norbornenes. Theoretical studies predicted the same trends as experiment and matched the experimental product ratios well. The nature of the regioselectivity in this reaction is discussed. Different strengths of the pi(C5-C6)-->pi(C2-Y) or pi(C5-C6)-->sigma(C2-Y) orbital interactions in 2-substituted norbornenes result in different degrees of C5-C6 double bond polarization. Stronger C5-C6 polarization will increase the difference in the activation energies between the major and minor pathways and thus lead to greater regioselectivities.

Predictions of the electronic absorption and emission spectra of luciferin and oxyluciferins including solvation effects.

The ground and excited state properties of luciferin (LH(2)) and oxyluciferin (OxyLH(2)), the bioluminescent chemical in the firefly, have been characterized using the configuration interaction singles (CIS) and time dependent density functional (TDDFT) methods. The effects of solvation on the electronic absorption and emission spectra of luciferin and oxyluciferin are predicted with a self-consistent isodensity polarized continuum model of the solvent using both the configuration interaction singles model and time dependent density functional theory. The S(0)-->S(1) vertical excitation energies in the gas phase and in water are obtained with both methods. Optimizations of the excited state geometries permit the first predictions of the fluorescence spectra for these biologically important molecules. Shifts in both the absorption and emission spectra on proceeding from the gas phase to aqueous solution also are predicted.

Electrochemical and PM-IRRAS studies of the effect of the static electric field on the structure of the DMPC bilayer supported at a Au(111) electrode surface.

Differential capacity, charge density measurements, and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) were employed to study the fusion of small unilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) on a Au(111) electrode surface. The differential capacity and charge density data showed that the vesicles fuse onto the gold surface at charge densities between -10 microC/cm(2) < sigma(M) < 10 microC/cm(2) to form a bilayer. When sigma(M) < -10 microC/cm(2), the film is detached from the surface but it remains in close proximity to the surface. PM-IRRAS experiments provided IR spectra for the bilayer in the adsorbed and the desorbed state. Ab initio normal coordinate calculations were performed to assist interpretation of the IR spectra. The IR bands were analyzed quantitatively, and this analysis provided information concerning the conformation and orientation of the acyl chains and the polar head region of the DMPC molecule. The orientation of the chains, hydration, and conformation of the headgroup of the DMPC molecule strongly depend on the electrode potential.

Ruthenium-catalyzed [2 + 2] cycloadditions between 7-substituted norbornadienes and alkynes: an experimental and theoretical study.

The ruthenium-catalyzed [2 + 2] cycloadditions of 7-substituted norbornadienes with an alkyne have been investigated. The cycloadditions were found to be highly regio- and stereoselective, giving only the anti-exo cycloadducts as the single regio- and stereoisomers in good yields. The results on the relative rate of different 7-substituted norbornadienes in the Ru-catalyzed [2 + 2] cycloadditions with an alkyne indicated that the reactivity of the alkene component decreases dramatically as the alkene becomes more electron deficient. Ab initio computational studies on the ruthenium-catalyzed [2 + 2] cycloadditions provided important information about the geometries and the arrangements of the four different groups on the Ru in the initial Ru-alkene-alkyne pi-complex, 14, and in the metallacyclopentene 15. Based on our computational studies, we also found that the first carbon-carbon bond formed in the [2 + 2] cycloaddition is between the C(5) of the alkene and the C(b) (the acetylenic carbon attached to the ester group) of the alkyne 8. Our computational studies on the potential energy profiles of the cycloadditions showed that the activation energy relative to the reactants for the oxidative addition step is in the range of 9.3-9.8 kcal/mol. The activation energy relative to the metallacyclopentene for the reductive elimination step is much higher than for the oxidative addition step (in the range of 25.9-27.6 kcal/mol).

The role of nonbonded sulfur-oxygen interaction in the dissociative electron transfer to nitro-substituted arenesulfenyl chlorides.

The electrochemical reduction of p-nitrophenyl sulfenyl chloride, o-nitrophenyl sulfenyl chloride as well as bis(4-nitrophenyl) disulfide and bis(2-dinitrophenyl) disulfide was investigated in acetonitrile at an inert electrode. Reduction standard potentials as well standard heterogeneous electron-transfer rate constants have been determined using convolution analysis. An unexpected big difference in the thermodynamics and kinetics of the initial electron-transfer process as well as a striking change in the reductive cleavage mechanism of the S-Cl bond as a function of the nitro group position on the aryl ring of the aryl sulfenyl chloride is observed. A computational study at the B3LYP level shows that this difference in behavior is due to the through-space nonbonded S...O interaction in the o-nitrophenyl sulfenyl chloride.

Lowest singlet and triplet potential energy surfaces of S2N2.

Forty four stationary points have been located on the lowest singlet and triplet potential energy surfaces of S(2)N(2). Ten minima and ten saddle points on the lowest singlet surface and eleven minima and thirteen saddle points on the lowest triplet surface were found. All saddle points were connected to minima or lower-order saddle points by following the intrinsic reaction coordinate. Renner-Teller effects in the linear isomers were studied by examining their bending curves. The S(2)N(2) polymerization mechanism was investigated by first locating the transition state corresponding to ring opening and then considering all species connected to it that are close in energy. The commonly accepted mechanism is problematic due to the number of species that would lead to dissociation to SN + SN. Other possible isomers that are consistent with the experimental evidence but do not connect to SN radicals in the dissociation limit were examined. A mechanism of polymerization to (SN)(x)() is proposed that involves excitation of the square planar singlet molecule to the triplet surface. The triplet species then undergoes a puckering, and polymerization occurs in a direction approximately perpendicular to the S(2)N(2) plane. Consideration of the predicted vibrational frequencies suggests the structure of the second isomer of S(2)N(2). This isomer has a trans-NSSN structure with a long SS bond. The energetics of trans-NSSN are consistent with the observed temperature effects in the dimerization of SN. Analysis of the bending curves of linear NSSN and NSNS indicates that trans-NSSN is the only isomer which has a small yet significant barrier to that dimerization.

Theoretical study of the amazing firefly bioluminescence: the formation and structures of the light emitters.

Reaction mechanisms for the formation of the keto-form of oxyluciferin (OxyLH(2)) from the luciferin of fireflies via a dioxetanone intermediate are predicted using the B3LYP/6-31G theoretical method. The ring opening of a model dioxetanone and the decarboxylation proceed in one step via a singlet diradical transition structure with an activation barrier of 18.1 and an exothermicity of 90.8 kcal/mol. The S(0) --> S(1) vertical excitation energies predicted with time dependent density functional theory, TDDFT B3LYP/6-31+G, for the anionic and neutral forms of OxyLH(2) are in the range of 60 to 80 kcal/mol. These energetic results support the generally accepted theory of chemically initiated electron exchange luminescence (CIEEL). The chemical origin of the multicolor bioluminescence from OxyLH(2) is examined theoretically using the TDDFT B3LYP/6-31+G, ZINDO//B3LYP/6-31+G, and CIS/6-31G methods. A change in color of the light emission upon rotation of the two rings in the S(1) excited state of OxyLH(2) is unlikely because both possible emitters, the planar keto- and enol-forms, are minima on the S(1) potential energy surface. The participation of the enol-forms of OxyLH(2) in bioluminescence is plausible but not required to explain the multicolor emission. According to predictions at the TDDFT B3LYP level, the color of the bioluminescence depends on the polarization of the OxyLH(2) in the microenvironment of the enzyme-OxyLH(2) complex.

Regioselective silylation of sugars through palladium nanoparticle-catalyzed silane alcoholysis.

Palladium(0)-catalyzed silane alcoholysis was applied to sugars for the first time using tert-butyldimethylsilane (TBDMS-H) and Ph(3)SiH as the silanes. The catalyst is a colloidal solution of Pd(0) generated in situ from PdX(2) (X = Cl(-), OAc(-)) and TBDMS-H in N,N-dimethylacetamide. The colloid has been characterized by dynamic light scattering and transmission electron microscopy and consists of catalytically highly active nanoparticles of approximately 2 nm diameter. The silane alcoholysis reaction is an effective method for the regioselective silylation of methyl and phenyl glycosides and generates hydrogen gas as the only side product. For many of the sugar substrates investigated, the distribution of regioisomers obtained is complementary to that of the traditional R(3)SiCl/base (base = pyridine, imidazole) methodology and gives convenient access to the 3,6- rather than the 2,6-silylated pyranosides, obtained as the main product by the silyl chloride method. The method also allows a selective axial silylation of levoglucosan and 1,3,5-O-methylidene-myo-inositol. In an attempt to rationalize the observed regioselectivities, ab initio predictions (HF/3-21G) have been made on the relative energies of some of the silylated products. They suggest that the observed regioselectivities do not reflect a kinetic vs thermodynamic product distribution but are induced by the silylation agent employed. Models for the possible origin of the observed regioselectivity in both silylation methods (silane- and silyl chloride-based) are discussed.