On the computation of protein backbones by using artificial backbones of hydrogens

NMR experiments provide information from which some of the distances between pairs of hydrogen atoms of a protein molecule can be estimated. Such distances can be exploited in order to identify the three-dimensional conformation of the molecule: this problem is known in the literature as the Molecular Distance Geometry Problem (MDGP). In this paper, we show how an artificial backbone of hydrogens can be defined which allows the reformulation of the MDGP as a combinatorial problem. This is done with the aim of solving the problem by the Branch and Prune (BP) algorithm, which is able to solve it efficiently. Moreover, we show how the real backbone of a protein conformation can be computed by using the coordinates of the hydrogens found by the BP algorithm. Formal proofs of the presented results are provided, as well as computational experiences on a set of instances whose size ranges from 60 to 6000 atoms.     

Metric techniques for convex stationary ergodic Hamiltonians

We adapt the metric approach to the study of stationary ergodic Hamilton?CJacobi equations, for which a notion of admissible random (sub)solution is defined. For any level of the Hamiltonian greater than or equal to a distinguished critical value, we define an intrinsic random semidistance and prove that an asymptotic norm does exist. Taking as source region a suitable class of closed random sets, we show that the Lax formula provides admissible subsolutions. This enables us to relate the degeneracies of the critical stable norm to the existence/nonexistence of exact or approximate critical admissible solutions.     

Cyclopropanation with gold(I) carbenes by retro-Buchner reaction from cycloheptatrienes

Cationic gold(I) promotes the retro-Buchner reaction of 7-substituted 1,3,5-cycloheptatrienes, leading to gold(I) carbenes that cyclopropanate alkenes.     

Synthesis of caffeic acid molecularly imprinted polymer microspheres and high-performance liquid chromatography evaluation of their sorption properties

In the current work, a molecularly imprinted polymer (MIP) has been synthesised and used to enable the extraction of a naturally-occurring antioxidant from complex media. More specifically, we describe the first example of a caffeic acid (CA) MIP which has been synthesised in the form of well-defined polymer microspheres, and its use for the extraction of CA from fruit juice sample. The CA MIP was synthesised by precipitation polymerisation using 4-vinylpyridine as functional monomer, divinylbenzene-80 as crosslinker and acetonitrile:toluene (75/25, v/v) as porogen. The particle sizing and morphological characterisation of the polymers was carried out by means of scanning electron microscopy (narrow particle size distribution; ～5 and 1.5 μm particle diameters for the MIP and NIP [non-imprinted polymer], respectively) and nitrogen sorption porosimetry (specific surface areas of 340 and 350 m(2)g(-1), and specific pore volumes of 0.17 and 0.19 cm(3)g(-1) for the MIP and NIP, respectively). The polymers were evaluated further by batch rebinding experiments, and from the derived isotherms their binding capacity and binding strength were determined (number of binding sites (N(K))=0.6 and 0.3 mmol g(-1) for the MIP and NIP, respectively, and apparent average adsorption constant (K(N))=10.0 and 1.6L mmol(-1) for the MIP and NIP, respectively). To evaluate the molecular recognition character of the MIP it was packed into a stainless steel column (50 mm × 4.6 mm i.d.) and evaluated as an HPLC-stationary phase. The mobile phase composition, flow rate, and the elution profile were then optimised in order to improve the peak shape without negatively affecting the imprinting factor (IF). Very interesting, promising properties were revealed. The imprinting factor (IF) under the optimised conditions was 11.9. Finally, when the imprinted LC column was used for the selective recognition of CA over eight related compounds, very good selectivity was obtained. This outcome enabled the direct extraction of CA in commercial apple juice samples with recoveries in excess of 81% and, rather significantly, without any need for a clean-up step prior to the extraction.     

Molecular aspects of the interaction between plants sterols and DPPC bilayers: an experimental and theoretical approach

The effect of sterols composition in a lipid bilayer was investigated on membranes of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and mixtures with the plant sterols β-sitosterol and stigmasterol. Differential scanning calorimetry, 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescence polarization and infrared spectroscopy studies showed that both sterols changed the packing of the membrane and the hydration of the polar headgroup of the phospholipids, disordering the gel phase and, vice versa, ordering the membrane in the liquid crystalline phase. In all cases some differences among β-sitosterol and stigmasterol could be observed, being β-sitosterol slightly more efficient than stigmasterol in ordering a fluid membrane, bringing the membrane to a more packed liquid ordered phase. Molecular dynamic simulations were carried out to better characterize the distinct behavior of both sterols in a DPPC-membrane. The calculated parameters agreed quite well with the experimental results and a molecular model is proposed to explain differences in the sterols molecules and their effect on the DPPC-bilayer.     

Direct synthesis of NNN-donor enantiopure scorpionate ligands by an efficient diastereoselective nucleophilic addition to imines

New enantiopure imines (1-9) with a chiral substrate to control the stereochemistry of a newly created stereogenic center have been synthesized by reaction of the commercially available (1R)-(-)-myrtenal and different primary amines. The diastereomerically enriched lithium-scorpionate compounds [Li(κ(3)-mobpza)(THF)] (10) (mobpza = N-p-methylphenyl-(1R and 1S)-1-[(1R)-6,6-dimethylbicyclo[3.1.1]-2-hepten-2-yl]-2,2-bis(3,5-dimethylpyrazol-1-yl)ethylamide), [Li(κ(3)-mobpza)(THF)] (11) (mobpza = N-p-methoxyphenyl-(1R and 1S)-1-[(1R)-6,6-dimethylbicyclo[3.1.1]-2-hepten-2-yl]-2,2-bis(3,5-dimethylpyrazol-1-yl)ethylamide), [Li(κ(3)-fbpza)(THF)] (12) (fbpza = N-p-fluorophenyl-(1R and 1S)-1-[(1R)-6,6-dimethylbicyclo[3.1.1]-2-hepten-2-yl]-2,2-bis(3,5-dimethylpyrazol-1-yl)ethylamide), and [Li(κ(3)-clbpza)(THF)] (13) (clbpza = N-p-chlorophenyl-(1R and 1S)-1-[(1R)-6,6-dimethylbicyclo[3.1.1]-2-hepten-2-yl]-2,2-bis(3,5-dimethylpyrazol-1-yl)ethylamide) were obtained by a diastereoselective 1,2-addition of an organolithium reagent to imines in good yield and with good diastereomeric excess (ca. 80%). The complexes [LiCl(κ(2)-R,R-fbpzaH)(THF)] (14) and [LiCl(κ(2)-R,R-clbpzaH)(THF)] (15) were obtained in enantiomerically pure form by the treatment of THF solutions of 12 or 13 with NH(4)Cl. The enantiomerically pure amines (R,R-mbpzaH) (16), (R,R-mobpzaH) (17), (R,R-fbpzaH) (18), and (R,R-clbpzaH) (19) were obtained by hydrolysis of the lithium-scorpionate compounds 10-13 with H(2)O. The lithium compound 12 was reacted with [TiCl(4)(THF)(2)] or [ZrCl(4)] to give the enantiopure complexes [MCl(3)(κ(3)-R,R-fbpza)] [M = Ti (20), Zr (21)]. The amine compound 18 reacted with [MX(4)] (M = Ti, X = O(i)Pr, OEt; M = Zr; X = NMe(2)) to give the complexes [MX(3)(κ(3)-R,R-fbpza)] (22-24). The reaction of Me(3)SiCl with [Zr(NMe(2))(3)(κ(3)-R,R-fbpza)] (24) in different molar ratios led to the halide-amide-containing complexes [ZrCl(NMe(2))(2)(κ(3)-R,R-fbpza)] (25) and [ZrCl(2)(NMe(2))(κ(3)-R,R-fbpza)] (26) and the halide complex 21. The isolation of only one of the three possible diastereoisomers of complexes 25 and 26 revealed that chiral induction from the ligand to the zirconium center took place. The structures of these compounds were elucidated by (1)H and (13)C{(1)H} NMR spectroscopy, and the X-ray crystal structures of 5, 12, 14, 15, and 24 were also established.     

Damped response theory description of two-photon absorption

Damped response theory is applied to the calculation of two-photon absorption (TPA) spectra, which are determined directly, at each frequency, from a modified damped cubic response function. The TPA spectrum may therefore be evaluated for selected frequency ranges, making the damped TPA approach attractive for calculations on large molecules with a high density of states, where the calculation of TPA using standard theory is more problematic. Damped response theory can also be applied to the case of intermediate state resonances, where the standard TPA expression is divergent. Both exact damped response theory and its application within density functional theory are discussed. The latter is implemented using an atomic-orbital based density matrix formulation, which makes the approach especially suitable for studies on large systems. A test preliminary study is presented for the TPA spectrum of R-(+)-1,1'-bi(2-naphtol).     

3,5-Bis(ethynyl)pyridine and 2,6-bis(ethynyl)pyridine spanning two Fe(Cp*)(dppe) units: role of the nitrogen atom on the electronic and magnetic couplings

The role of the nitrogen atom on the electronic and magnetic couplings of the mono-oxidized and bi-oxidized pyridine-containing complex models [2,6-{Cp(dpe)Fe-C≡C-}(2)(NC(5)H(3))](n+) and [3,5-{Cp(dpe)Fe-C≡C-}(2)(NC(5)H(3))](n+) is theoretically tackled with the aid of density-functional theory (DFT) and multireference configuration interaction (MR-CI) calculations. Results are analyzed and compared to those obtained for the reference complex [1,3-{Cp*(dppe)Fe-C≡C-)}(2)(C(6)H(4))](n+). The mono-oxidized species show an interesting behavior at the borderline between spin localization and delocalization and one through-bond communication path among the two involving the central ring, is favored. Investigation of the spin state of the dicationic complexes indicates ferromagnetic coupling, which can differ in magnitude from one complex to the other. Very importantly, electronic and magnetic properties of these species strongly depend not only upon the location of the nitrogen atom in the ring versus that of the organometallic end-groups but also upon the architectural arrangement of one terminus, with respect to the other and/or vis-à-vis the central ring. To help validate the theoretical results, the related families of compounds [1,3-{Cp*(dppe)Fe-C≡C-)}(2)(C(6)H(4))](n+), [2,6-{Cp*(dppe)Fe-C≡C-}(2)(NC(5)H(3))](n+), [3,5-{Cp*(dppe)Fe-C≡C-}(2)(NC(5)H(3))](n+) (n = 0-2) were experimentally synthesized and characterized. Electrochemical, spectroscopic (infrared (IR), M?ssbauer), electronic (near-infrared (NIR)), and magnetic properties (electron paramagnetic resonance (EPR), superconducting quantum interference device (SQUID)) are discussed and interpreted in the light of the theoretical data. The set of data obtained allows for many strong conclusions to be drawn. A N atom in the long branch increases the ferromagnetic interaction between the two Fe(III) spin carriers (J > 500 cm(-1)), whereas, when placed in the short branch, it dramatically reduces the magnetic exchange in the di-oxidized species (J = 2.14(5) cm(-1)). In the mixed-valence compounds, when the N atom is positioned on the long branch, the intermediate excited state is higher in energy than the different ground-state conformers and the relaxation process provides exclusively the Fe(II)/Fe(III) localized system (H(ab) ≠ 0). Positioning the N atom on the short branch modifies the energy profile and the diabatic mediating state lies just above the reactant and product diabatic states. Consequently, the LMCT transition becomes less energetic than the MMCT transition. Here, the direct coupling does not occur (H(ab) = 0) and only the coupling through the bridge (c) and the reactant (a) and product (b) diabatic states is operating (H(ac) = H(bc) ≠ 0).     

Unprecedented luminescent heteropolynuclear aggregates with gold thiolates as building blocks

The reaction of [AuCl(P-N)], in which P-N represents a heterofunctional phosphine ligand, with pentafluorothiophenol, HSC(6)F(5), gives the thiolate gold derivatives [Au(SC(6)F(5))(P-N)] (P-N = PPh(2)py (1), PPh(2)CH(2)CH(2)py (2), or PPhpy(2) (3)). Complex [Au(SC(6)F(5))(PPh(2)py)] (1) reacts with [Au(OTf)(PPh(2)py)] in a 1:1 or 1:2 molar ratio to afford the di- or trinuclear species [Au(2)(μ-SC(6)F(5))(PPh(2)py)(2)]OTf (4) and [Au(3)(μ(3)-SC(6)F(5))(PPh(2)py)(3)](OTf)(2) (5), with the thiolate acting as a doubly or triply bridging ligand. The reactivity of the mononuclear compounds [Au(SC(6)F(5))(P-N)] toward silver or copper salts in different ratios has been investigated. Thus, the treatment of [Au(SC(6)F(5))(P-N)] with Ag(OTf) or [Cu(NCMe)(4)]PF(6) in a 1:1 molar ratio gives complexes of stoichiometry [AuAg(OTf)(μ-SC(6)F(5))(P-N)] (P-N = PPh(2)py (6), PPh(2)CH(2)CH(2)py (7), or PPhpy(2) (8)) or [AuCu(μ-SC(6)F(5))(P-N)(NCMe)]PF(6) (P-N = PPh(2)py (9), PPh(2)CH(2)CH(2)py (10), or PPhpy(2) (11)). These complexes crystallize as dimers and display different coordination modes of the silver or copper center, depending on the present functionalized phosphine ligand. The treatment of [Au(SC(6)F(5))(PPh(2)py)] with silver and copper compounds in other molar ratios has been carried out. In a 2:1 ratio, the complexes [Au(2)M(μ-SC(6)F(5))(2)(μ-PPh(2)py)(2)]X (M = Ag, X = OTf (12); M = Cu, X = PF(6) (13)) are obtained. The same reaction in a 4:3 molar ratio affords the species [Au(4)M(2)(μ-SC(6)F(5))(3)(μ-PPh(2)py)(4)]X(3) (M = Ag, X = OTf (14); M = Cu, X = PF(6) (15)). The crystal structures of some of these complexes reveal different interactions among the metallic d(10) centers. The complexes display dual emission. The band at higher energy has been attributed to intraligand (IL) transitions, and the one at lower energy has been assigned to a ligand to metal (LM) charge transfer process. The latter emission is modulated by the heterometal (silver or copper).     

Lanthanide(III)/pyrimidine-4,6-dicarboxylate/oxalate extended frameworks: a detailed study based on the lanthanide contraction and temperature effects

Detailed structural, magnetic, and luminescence studies of six different crystalline phases obtained in the lanthanide/pyrimidine-4,6-dicarboxylate/oxalate system have been afforded: {[Ln(μ-pmdc)(μ-ox)(0.5)(H(2)O)(2)]·3H(2)O}(n) (1-Ln), {[Ln(μ-pmdc)(μ-ox)(0.5)(H(2)O)(3)]·2H(2)O}(n) (2-Ln), {[Ln(μ(3)-pmdc)(μ-ox)(0.5)(H(2)O)(2)]·~2.33H(2)O}(n) (3-Ln), {[Ln(2)(μ(3)-pmdc)(μ(4)-pmdc)(μ-ox)(H(2)O)(3)]·5H(2)O}(n) (4-Ln), {[Ln(μ(3)-pmdc)(μ-ox)(0.5)(H(2)O)(2)]·H(2)O}(n) (5-Ln), and [Ln(pmdc)(1.5)(H(2)O)(2.5)] (6-Ln). The slow generation of the oxalate (ox) anion, obtained from the in situ partial hydrothermal decomposition of the pyrimidine-4,6-dicarboxylate (pmdc) ligand, allows us to obtain good shaped single crystals, while direct addition of potassium oxalate provides the same compounds but as polycrystalline samples. The crystal structures of all compounds are based on the double chelation established by the pmdc and ox ligands to provide distorted 2D honeycomb layers that, in some cases, are fused together, leading to 3D systems, by replacing some of the coordinated water molecules that complete the coordination sphere of the lanthanide by uncoordinated carboxylate oxygen atoms of the pmdc. The presence of channels occupied by crystallization water molecules is also a common feature with the exception of compounds 5-Ln. It is worth noting that compounds 3-Ln present a commensurate crystal structure related to the partial occupancy of the crystallization water molecules placed within the channels. Topological analyses have been carried out, showing a previously nonregistered topology for compounds 4-Ln, named as jcr1. The crystal structures are strongly dependent on the lanthanide ion size and the temperature employed during the hydrothermal synthesis. The lanthanide contraction favors crystal structures involving sterically less hindranced coordination environments for the final members of the lanthanide series. Additionally, reinforcement of the entropic effects at high temperatures directs the crystallization process toward less hydrated crystal structures. The magnetic data of these compounds indicate that the exchange coupling between the lanthanide atoms is almost negligible, so the magnetic behavior is dominated by the spin-orbit coupling and the ligand field perturbation. The luminescence properties that exhibit the compounds containing Nd(III), Eu(III), and Tb(III) have been also characterized.