Ab initio study on deactivation pathways of excited 9H-guanine

The complete active space with second-order perturbation theory/complete active space self-consistent-field method was used to explore the nonradiative decay mechanism for excited 9H-guanine. On the 1pipi* (1L(a)) surface we determined a conical intersection (CI), labeled (S0pipi*)(CI), between the 1pipi* (1L(a)) excited state and the ground state, and a minimum, labeled (pipi*)min. For the 1pipi* (1L(a)) state, its probable deactivation path is to undergo a spontaneous relaxation to (pipi*)min first and then decay to the ground state through (S0pipi*)(CI), during which a small activation energy is required. On the 1n(N)pi* surface a CI between the 1n(N)pi* and 1pipi* (1L(a)) states was located, which suggests that the 1n(N)pi* excited state could transform to the 1pipi* (1L(a)) excited state first and then follow the deactivation path of the 1pipi* (1L(a)) state. This CI was also possibly involved in the nonradiative decay path of the second lowest 1pipi* (1L(b)) state. On the 1n(O)pi* surface a minimum was determined. The deactivation of the 1n(O)pi* state to the ground state was estimated to be energetically unfavorable. On the 1pisigma* surface, the dissociation of the N-H bond of the six-membered ring is difficult to occur due to a significant barrier.     

Conformational polymorphism of solid tetramesityldisilene Mes2Si=SiMes2 (Raman,UV-vis,IR and fluorescence study)

Conformational polymorphism of solid tetramesityldisilene (1) has been studied by the methods of optical spectroscopy. The three known modifications of 1: orange unsolvated 1a and two 1:1 solvates with toluene (1b) and THF (1c) have been found to transform under specific conditions to a new, most thermodynamically stable polymorph, yellow unsolvated powder 1d. The latter has been characterized by the Raman, IR, UV-vis and fluorescence data. All forms of 1 exhibit Raman spectra differing in details, which reflect their different crystal and molecular structures. Unsolvated 1a and 1d differ significantly in electronic absorption and fluorescence emission. The yellow form 1d can be converted to the orange form 1a upon illumination with laser light in the region 514-457 nm. Similarity of the Raman and UV-vis spectra of 1d to those of the solutions of 1 provides some evidence for a quasi-trans conformation of 1d.     

Nickel oxidation states of F(430) cofactor in methyl-coenzyme M reductase

Magnetic circular dichroism (MCD) spectroscopy and variable-temperature variable-field MCD are used in combination with density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations to characterize the so-called ox1-silent, red1, and ox1 forms of the Ni-containing cofactor F430 in methyl-coenzyme M reductase (MCR). Previous studies concluded that the ox1 state, which is the precursor of the key reactive red1 state of MCR, is a Ni(I) species that derives from one-electron reduction of the Ni(II)-containing ox1-silent state. However, our absorption and MCD data provide compelling evidence that ox1 is actually a Ni(II) species. In support of this proposal, our DFT and TD-DFT calculations indicate that addition of an electron to the ox1-silent state leads to formation of a hydrocorphin anion radical rather than a Ni(I) center. These results and biochemical evidence suggest that ox1 is more oxidized than red1, which prompted us to test a new model for ox1 in which the ox1-silent species is oxidized by one electron to form a thiyl radical derived from coenzyme M that couples antiferromagnetically to the Ni(II) ion. This alternative ox1 model, formally corresponding to a Ni(III)/thiolate resonance form but with predicted S = 1/2 EPR parameters reminiscent of a Ni(I) (3dx2-y2)1 species, rationalizes the requirement for reduction of ox1 to yield the red1 species and the seemingly incongruent EPR and electronic spectra of the ox1 state.     

Crystal engineering of photochromic diarylethene single crystals

Photochromic performance of diarylethene single crystals was controlled by crystal engineering using non-covalent aromatic-aromatic interactions as the directional intermolecular force. A diarylethene derivative with two pentafluorophenyl groups, 1,2-bis(2-methyl-5-pentafluorophenyl-3-thienyl)perfluorocyclopentene (1a), formed stoichiometric co-crystals with benzene (Bz) and naphthalene (Np) by aryl-perfluoroaryl interactions. Face-to-face pi-stacking interactions between the pentafluorophenyl groups of 1a and the aromatic molecules are responsible for 2:1 and 1:1 stoichiometric compositions in 1a/Bz and 1a/Np co-crystals, respectively. The diarylethene underwent thermally stable and photoreversible photochromic reactions in a homo-crystal of 1a and co-crystals 1a/Bz and 1a/Np. The absorption spectra of the photogenerated closed-ring isomers varied depending on the conformation of the diarylethene molecules packed in the crystals. The diarylethene 1a also formed 1:1 stoichiometric co-crystals with different kinds of diarylethenes, 1,2-bis(2-ethyl-5-phenyl-3-thienyl)perfluorocyclopentene (2a) and 1,2-bis[2-methyl-5-(1-naphthyl)-3-thienyl]perfluorocyclopentene (3a). Both co-crystals 1a/2a and 1a/3a showed photochromism. Although 1a, 2a, and 3a underwent efficient photocyclization reactions in their homo-crystals, highly selective photocyclization reactions of 2a or 3a were observed in the co-crystals. The selective reactions were confirmed by HPLC and X-ray crystallography. Excited energy transfers from 1a to 2a and from 1a to 3a are considered to occur and cause the selective reactions.     

Local diffusion in paramagnetic solutions by NMR relaxometry at one frequency

The relative diffusion coefficient D of a paramagnetic species and a diamagnetic probe molecule bearing nuclear spins is obtained from their measured relaxation times T1 and T2 (or T1rho). This is achieved by introducing the longitudinal relaxivity, r1, a linear expression of 1/T1, and the mixed relaxivity, rmix, a linear expression of 1/T1 and 1/T2 (or 1/T1rho). Under weak assumptions, D is proportional to (rmix - r1) to the power -2/3 and to rmix to the power -1, with easy-to-determine proportionality factors. The method is noninvasive and easy to use on standard NMR spectrometers and imagers. It is validated through the study of various solutions of a Gd(III)-based contrast agent for magnetic resonance imaging.     

Theoretical study of the main fragmentation pathways for protonated glycylglycine

Quantum chemical and RRKM calculations were carried out on protonated glycylglycine in order to determine the atomic details of the main fragmentation pathways leading to formation of a1 and y1 ions. Two possible mechanisms were considered. The first path results in elimination of aziridinone as a neutral counterpart of the y1 ion formed. Our calculations show that this pathway has a relatively high threshold energy (48.6 kcal/mol) and the corresponding unimolecular rate constants are quite small even at large internal energy. An alternative pathway (a1-y1) proposed in the present paper seems, however, to be favored against the above 'aziridinone' one from the points of view of both energetics and kinetics. The 'a1-y1' pathway leads to simultaneous formation of a1 and y1 ions, the ratio of which depends on the energy distribution of the fragmenting species for a particular dipeptide. However, even if y1 ions are formed via the 'a1-y1' pathway, the corresponding neutrals eliminated do not have a strained cyclic aziridinone structure. Instead, in a two-step process, CO and NHCH2 are formed leading to neutral products energetically more favored than aziridinone. The available experimental data reevaluated in the present paper lend support to the 'a1-y1' pathway.     

Kinetics of surface modification induced by submonolayer electrochemical oxygen adsorption on Pt(1 1 1)

Electrochemical oxygen adsorption/desorption below monolayer level leads to a disordering of platinum single-crystal surfaces vicinal to the (1 1 1) plane. The kinetics can be described by means of a consecutive reaction from (1 1 1)-terrace sites to (1 1 0)-defect sites, in which (1 0 0)-defects act as intermediates. The first oxidation of the electrode reflects independent contributions from terrace and step sites, the latter being structure sensitive. Oxygen adsorption charges amount to a mean value of one electron per step site.     

Synthesis and characterization of an anomeric sulfur analogue of CMP-sialic acid

alpha-2,3-Sialyltransferase catalyzes the transfer of sialic acid from CMP-sialic acid (1) to a lactose acceptor. An analogue of 1 was synthesized in which the anomeric oxygen atom was replaced with a sulfur atom (1S). The key step in the synthesis of 1S was a tetrazole-promoted coupling of a cytidine-5'-phosphoramidite with a glycosyl thiol of a protected sialic acid. Compounds 1 and 1S were characterized for their activity in a sialyl transfer assay. The rate of solvolysis in aqueous buffer of analogue 1S was 50-fold slower than that of 1. Analogue 1S was found to be substrate for alpha-2,3-sialyltransferase. The K(m) of 1S was just 3-fold higher than that of 1, while the k(cat) of 1S was 2 orders of magnitude lower compared to 1.     

Multireference configuration interaction studies on higher valence and Rydberg states of OClO, ionization potentials, and electron detachment energies

MRCI results are reported for the vertical excitation energies (VEE) and oscillator strengths f of doublet states of OClO up to 11 eV, including 3b(1) → 4s, 4p, 3d, 5s, 5p, 4d, and most 1a(2), 8a(1), 5b(2) → 4s and 4p Rydberg states. The lowest Rydberg states 3b(1) → 4s and 3b(1) → 4p(x) have mixed valence-Rydberg character. The observed spectral bands were reassigned to include valence states which have generally higher oscillator strengths. The well-known valence state 1(2)A(2) has a VEE of 3.63 eV, and a relatively high f of 0.042. Overall, the calculated oscillator strengths are in good agreement with measured values. The lowest quartet state, 1(4)B(2), lies at 6.95 eV. Quartet Rydberg states start with 1a(2) → 4s at 9.28 eV. According to calculated vertical ionization potentials (VIP) of OClO, the second VIP at 12.59 eV is reassigned from 1(3)B(1) to 1(3)B(2) (ionization from 1a(2), rather than 8a(1)), and the third VIP at 12.63 eV from 1(1)B(1) to 1(3)B(1) (ionization from 8a(1)). Vertical electron detachment energies of OClO(-) have been calculated up to 8.9 eV. There is good agreement with experimental values.     

1H-NMR Study on Inclusion Modes of 2-Chloronaphthalene and α-Cyclodextrin in D2

Abstract

With a 1:1 and a 2:1 host-guest stoichiometry, α-cyclodextrin (α-CD) forms inclusion complexes with 2-chloronaphthalene. From simulations concerning observed chemical-shift differences (Δδ_obs) of proton signals of 2-chloronaphthalene, intrinsic Δδ values are estimated for all the guest protons in the 1:1 and 2:1 inclusion complexes. The intrinsic Δδ values indicate that α-CD first binds to a part of a naphthalene ring bearing a C1 atom to form the 1:1 inclusion complex. In the 1:1 and 2:1 inclusion complexes, the symmetry axes of α-CD are tilted approximately 30° relative to a naphthalene longitudinal axis. In the 2:1 inclusion complex, the association through hydrogen bonding most likely occurs between two α-CD molecules whose symmetry axes are laterally shifted.     

Luminescence mechanochromism in cyclometallated Ir(III) complexes containing picolylamine

The synthesis, crystal structure and luminescence properties of three cyclometalated Ir(III) complexes of general formula [(ppy)(2)Ir(pam)]X, where X = Cl(-) (1), PF(6)(-) (2), ClO(4)(-)(3), and pam = 2-picolylamine, are described. While 2 and 3 crystallize in a unique form, two pseudo-polymorphs, a solvated (1a) and a non-solvated (1b) species, have been observed for compound 1. 1a crystallizes in the monoclinic centrosymmetric space group P2(1)/c. On the contrary, 1b, 2 and 3 crystallize in the non-centrosymmetric space group P2(1)2(1)2(1) (1b) and Pca2(1) (2 and 3), respectively. All the crystalline supramolecular materials have been fully photophysically characterized. While 1 shows a bright blue-green emission in both solution and solvated crystalline state 1a, crystals of 1b, 2 and 3 show a significantly red shifted emission with respect to solution. Unexpectedly, and differently from 1a, mechanical stimuli-responsive colour and luminescence changes have been observed for 1b, 2 and 3. Upon mechanical grinding the colour of the crystalline solids changes from orange to yellow while the emission energy is partially (2 and 3) or completely (1b) converted from orange to green. The grinding-triggered colour and luminescence changes have been attributed to a crystal-to-amorphous phase conversion for all crystalline solids.     

Calculations find that tunneling plays a major role in the reductive elimination of methane from hydridomethylbis(trimethylphosphine)platinum: how to confirm this computational prediction experimentally

DFT calculations, including the effects of small curvature tunneling, have been performed on the reductive elimination of methane from hydridomethylbis(trimethylphosphine)platinum (1d). The calculations find that at 250 K tunneling results in an increase in the rate constant for reductive elimination by a factor of 4, a lowering of Ea by 1.7 kcal/mol, and a decrease in A by a factor of nearly 10. Tunneling is also calculated to increase the primary H/D kinetic isotope effect (KIE) from k(1d)/k(1f) = 2.26 to k(1d)/k(1f) = 4.12 and to result in a large secondary KIE of k(1d)/k(1e) = 1.35. In addition, tunneling is predicted to result in a violation of the rule of the geometric mean, so that the secondary KIE for reductive elimination of methane-d1 from 1f is calculated to be k(1f)/k(1g) = 1.06, which is much smaller than the secondary KIE of k(1d)/k(1e) = 1.35 for reductive elimination of methane from 1d. Comparison of the measured values of k(1d)/k(1e) and k(1f)/k(1g) is therefore proposed as an experimental test of the prediction that tunneling plays an important role in the reductive elimination of methane from 1d.     

Benchmarking the accuracy of coverage-dependent models: adsorption and desorption of benzene on Pt (1 1 1) and Pt3Sn (1 1 1) from first principles

Bimetallic catalysts have demonstrated properties favorable for upgrading biofuel through catalytic hydrodeoxygenation. However, the design and optimization of such bimetallic catalysts requires the ability to construct accurate, predictive models of these systems. To generate a model that predicts the kinetic behavior of benzene adsorbed on Pt (1 1 1) and a Pt₃Sn (1 1 1) surface alloy (Pt₃Sn (1 1 1)), the adsorption of benzene was studied for a wide range of benzene coverages on both surfaces using density functional theory (DFT) calculations. The adsorption energy of benzene was found to correlate linearly with benzene coverage on Pt (1 1 1) and Pt₃Sn (1 1 1); both surfaces exhibited net repulsive lateral interactions. Through an analysis of the d-band properties of the metal surface, it was determined that the coverage dependence is a consequence of the electronic interactions between benzene and the surface. The linear coverage dependence of the adsorption energy allowed us to quantify the influence of the lateral interactions on the heat of adsorption and temperature programmed desorption (TPD) spectra using a mean-field model. A comparison of our simulated TPD to experiment showed that this mean-field model adequately reproduces the desorption behavior of benzene on Pt (1 1 1) and Pt₃Sn (1 1 1). In particular, the TPD correctly exhibits a broadening desorption peak as the initial coverage of benzene increases on Pt (1 1 1) and a low temperature desorption peak on Pt₃Sn (1 1 1). However, due to the sensitivity of the TPD peak temperature to the desorption energy, precise alignment of experimental and theoretical TPD spectra demands an accurate calculation of the adsorption energy. Therefore, an analysis of the effect of the exchange-correlation functional on TPD modeling is presented. Through this work, we show the necessity of incorporating lateral interactions into theoretical models in order to correctly predict experimental behavior.     

Specific binding of GM1-binding peptides to high-density GM1 in lipid membranes

The ganglioside Galbeta1-3GalNAcbeta1-4(Neu5Acalpha2-3)Galbeta1-4Glcbeta1-1'Cer (GM1) is an important receptor. We have previously identified GM1-binding peptides based on affinity selection from a random peptide library. In the present study, we determined the amino acids essential for binding GM1 and investigated the specific interaction with GM1 in the lipid membrane. Arginines and aromatic amino acids in the consensus sequence (W/F)RxL(xP/Px)xFxx(Rx/xR)xP contributed to the ability of the peptides to bind GM1. The peptide p3, VWRLLAPPFSNRLLP, having the consensus sequence, showed high affinity for GM1 with a dissociation constant of 1.2 microM. Furthermore, the density-dependent binding of p3 was investigated using mixed monolayers of GM1 and Glcbeta1-1'Cer (GlcCer). p3 binds preferentially to high-density GM1, and its interaction with GM1 was found to be cooperative based on a Hill plot. These results indicated that a lateral assembly of GM1 molecules was required for the recognition of carbohydrates by p3. The GM1-binding peptide played a role as a unique anti-GM1 probe differing from the cholera toxin B subunit or antibodies.     

A fluorescent sensor for 2,3-bisphosphoglycerate using a europium tetra-N-oxide bis-bipyridine complex for both binding and signaling purposes

Host 1 was designed and synthesized as a fluorescent sensor for 2,3-bisphosphoglycerate (BPG, 3). The design features a tris-functionalized triethylbenzene core to preorganize binding groups. The three cationic moieties, a tetra-N-oxide bipyridine-europium complex and two ammonium groups, were included to complement the three anionic functionalities on the guest. Beyond acting as a binding site, the europium complex was used to signal binding of the guest through modification of the charge transfer emission. A 1:1 complex with BPG was determined in 50 % methanol/acetonitrile with a K(a) of 6.7 x 10(5) mol(-1) by monitoring the reduction of the fluorescence signal upon guest addition. In the titration of related glycolytic intermediates lacking a second phosphate (4-6) into host 1, 2:1 host to guest binding was observed. Similarly, control compound 2, which lacks the ammonium groups, binds BPG and 4-6 in a 2:1 fashion. Also, phenylphosphate 7 binds to host 1 in a 1:1 stoichiometry with a K(a) over three times less than 3.     

Sub-Doppler rotationally resolved spectroscopy of lower vibronic bands of benzene with Zeeman effects

Sub-Doppler high-resolution excitation spectra and the Zeeman effects of the 6(0)(1), 1(0)(1)6(0)(1), and 1(0)(2)6(0)(1) bands of the S1(1)B2u<--S(0)(1)A1g transition of benzene were measured by crossing laser beam perpendicular to a collimated molecular beam. 1593 rotational lines of the 1(0) (1)6(0) (1) band and 928 lines of the 1(0)(2)6(0)(1) band were assigned, and the molecular constants of the excited states were determined. Energy shifts were observed for the S1(1)B2u(v1=1,v6=1,J,Kl=-11) levels, and those were identified as originating from a perpendicular Coriolis interaction. Many energy shifts were observed for the S1(1)B2u(v1=2,v6=1,J,Kl) levels. The Zeeman splitting of a given J level was observed to increase with K and reach the maximum at K=J, which demonstrates that the magnetic moment lies perpendicular to the molecular plane. The Zeeman splittings of the K=J levels were observed to increase linearly with J. From the analysis, the magnetic moment is shown to be originating mostly from mixing of the S1(1)B2u and S2(1)B1u states by the J-L coupling (electronic Coriolis interaction). The number of perturbations was observed to increase as the excess energy increases, and all the perturbing levels were found to be a singlet state from the Zeeman spectra.     

Fluorescence enhancement of trans-4-aminostilbene by N-phenyl substitutions: the "amino conjugation effect"

The synthesis, structure, and photochemical behavior of the trans isomers of 4-(N-phenylamino)stilbene (1c), 4-(N-methyl-N-phenylamino)stilbene (1d), 4-(N,N-diphenylamino)stilbene (1e), and 4-(N-(2,6-dimethylphenyl)amino)stilbene (1f) are reported and compared to that of 4-aminostilbene (1a) and 4-N,N-dimethylaminostilbene (1b). Results for the corresponding 3-styrylpyridine (2) and 2-styrylnaphthalene analogues (3) are also included. The introduction of N-phenyl substituents to 4-aminostilbenes leads to a more planar ground-state geometry about the nitrogen atom, a red shift of the absorption and fluorescence spectra, and a less distorted structure with a larger charge-transfer character for the fluorescent excited state. Consequently, the N-phenyl derivatives 1c-e have low photoisomerization quantum yields and high fluorescence quantum yields at room temperature, in contrast to the behavior of 1a, 1b, and most unconstrained monosubstituted trans-stilbenes. The isomerization of 1c and 1d is a singlet-state process, whereas it is a triplet-state process for 1e, presumably due to a relatively higher singlet-state torsional barrier. The excited-state behavior of 1f resembles 1a and 1b instead of 1c-e as a consequence of the less planar amine geometry and weaker orbital interactions between the N-phenyl and the aminostilbene groups. Such an N-phenyl substituent effect is also found for 2 and 3 and thus appears to be general for stilbenoid systems. The nature of this effect can be described as an "amino conjugation effect".     

Screening of threading bis-intercalators binding to duplex DNA by electrospray ionization tandem mass spectrometry

The DNA binding of novel threading bis-intercalators V1, trans-D1, and cis-C1, which contain two naphthalene diimide (NDI) intercalation units connected by a scaffold, was evaluated using electrospray ionization mass spectrometry (ESI-MS) and DNAse footprinting techniques. ESI-MS experiments confirmed that V1, the ligand containing the -Gly3-Lys- peptide scaffold, binds to a DNA duplex containing the 5'-GGTACC-3' specific binding site identified in previous NMR-based studies. The ligand formed complexes with a ligand/DNA binding stoichiometry of 1:1, even when there was excess ligand in solution. Trans-D1 and cis-C1 are new ligands containing a rigid spiro-tricyclic scaffold in the trans- and cis- orientations, respectively. Preliminary DNAse footprinting experiments identified possible specific binding sites of 5'-CAGTGA-5' for trans-D1 and 5'-GGTACC-3' for cis-C1. ESI-MS experiments revealed that both ligands bound to DNA duplexes containing the respective specific binding sequences, with cis-C1 exhibiting the most extensive binding based on a higher fraction of bound DNA value. Cis-C1 formed complexes with a dominant 1:1 binding stoichiometry, whereas trans-D1 was able to form 2:1 complexes at ligand/DNA molar ratios >or=1 which is suggestive of nonspecific binding. Collisional activated dissociation (CAD) experiments indicate that DNA complexes containing V1, trans-D1, and cis-C1 have a unique fragmentation pathway, which was also observed for complexes containing the commercially available bis-intercalator echinomycin, as a result of similar binding interactions, marked by intercalation in addition to hydrogen bonding by the scaffold with the DNA major or minor groove.     

Tetrakis- and tris(1-Methyluracil) complexes of Pt(II): formation and properties of a carbon-bonded nucleobase species as well as of heternonuclear derivatives

The reaction of K2PtCl4 with an excess of 1-methyluracilate (1-MeU) in water at 60 degrees C leads to the formation of two major products, K2[Pt(1-MeU-N3)4].10H2O (1) and trans-K[Pt(1-MeU-N3)2(1-MeU-C5)(H2O)].3H2O (2). Addition of CuCl2 to an aqueous solution of 2 yields the mixed-metal complex trans-[PtCl(1-MeU-N3,O4)2(1-MeU-C5,O4)Cu(H2O)].H2O (4). Single-crystal X-ray analysis was carried out for 1 and 4. In both compounds, the heterometals (K+ in 1 and Cu2+ in 4) are bonded to exocyclic oxygens atoms of the 1-MeU ligands, giving rise to intermetallic distances of 3.386(2) and 3.528(2) A in 1 and 2.458(1) A in 4. The shortness of the Pt-Cu separation in 4 is consistent with a dative bond between PtII and CuII. The aqua ligand in 2 is readily substituted by a series of other ligands (e.g., 1-MeC, 9-MeGH, and CN-), as demonstrated by 1H NMR spectroscopy, with 3J(195Pt-1H(6)) coupling constants being sensitive indicators. Acid-base equilibria of 1 and 2 have been studied in detail and reveal some unexpected features: 1 has a relatively high basicity, with protonation starting below pH 5, and first and second pKa values being ca. 3.4 and 0.4, respectively. These pKa values are markedly higher than those of related neutral 2:1 or cationic 1:1 complexes and are attributed to both charge effects (-2 charge of 1) and a favorable stabilization of oxygen-protonated species by the arrangement of four exocyclic oxygen groups of 1-MeU ligands at either sides of the platinum coordination planes. Whereas in 2, H+ affinities of the three uracil ligands are in the normal range, there is a surprisingly low acidity of N(3)H of the C5-bonded uracil with a pKa of approximately 12.2, which compares with 9.75 for free 1-methyluracil. This implies that the C5-bonded PtII does not induce the typical acidifying effect of a PtII metal entity when bonded to a ring nitrogen atom of a neutral nucleobase. Rather, the effect is qualitatively similar to that of a metal ion bonded to N3 of an anionic 1-MeU ligand, which likewise increases its overall basicity as compared to neutral 1-MeUH.