Understanding glycine conformation through molecular orbitals

The four most stable C(s) conformers of glycine have been investigated using a variety of quantum-mechanical methods based on Hartree-Fock theory, density-functional theory (B3LYP and statistical average of orbital potential), and electron propagation (OVGF) treatments. Information obtained from these models were analyzed in coordinate and momentum spaces using dual space analysis to provide insight based on orbitals into the bonding mechanisms of glycine conformers, which are generated by rotation of C-O(H) (II), C-C (III), and C-N (IV) bonds from the global minimum structure (I). Wave functions generated from the B3LYP/TZVP model revealed that each rotation produced a unique set of fingerprint orbitals that correspond to a specific group of outer valence orbitals, generally of a' symmetry. Orbitals 14a', 13a', 12a', and 11a' are identified as the fingerprint orbitals for the C-O(H) (II) rotation, whereas fingerprint orbitals for the C-C (III) bond rotation are located as 16a' [highest occupied molecular orbital (HOMO)], 15a' [next highest molecular occupied molecular orbital (NHOMO)], 14a', and 12a' orbitals. Fingerprint orbitals for IV generated by the combined rotations around the C-C, C-O(H), and C-N bonds are found as 16a', 15a', 14a', 13a', and 11a', as well as in orbitals 2a" and 1a". Orbital 14a' is identified as the fingerprint orbital for all three conformational processes, as it is the only orbital in the outer valence region which is significantly affected by the conformational processes regardless rotation of which bond. Binding energies, molecular geometries, and other molecular properties such as dipole moments calculated based on the specified treatments agree well with available experimental measurements and with previous theoretical calculation.     

Kinetic and thermodynamic consequences of the substitution of SMe for OMe substituents of cryptophane hosts on the binding of neutral and cationic guests

To investigate the origin of the high selectivity of cryptophane-E (1) towards Me3NH+, Me4N+, and CHCl3, and particularly to discriminate the different contributions that stabilize the supramolecular complexes, we have synthesized the new cryptophane 2 bearing six MeS groups instead of MeO groups in 1. This led to a decrease of the negative charge density in the equatorial region of 2 without affecting notably the size of the molecular cavity. The binding properties of 1 and 2 towards the three guests were examined in solution and showed a slight decrease of the deltaGa favoring the complexes of 1, accompanied by a significant modification of the deltaHa vs. deltaSa balance. The binding of the ammonium guests to 1 and 2 was strongly entropy driven, while that of CHCl3 was purely enthalpy driven. A combination of spectroscopic and computational techniques was used to assign the main intermolecular interactions that occurred during the inclusion process. The neutral CHCl3 molecule is more stabilized in the less negatively charged CTV cap of 1. The different behavior towards the ammonium cations can be explained in term of interactions with the electronegative heteroatoms and cation-pi interactions. Moreover, this study revealed a considerable slowing down of the guest exchange kinetics with host 2, for which the association and dissociation rates are reduced by a factor 10(3) to 10(4) with respect to 1. For example, at room temperature, the Me4N+@2 complex exhibits a half-life of ca. 2 years, instead of a few hours for the corresponding complex of 1.     

Docking macromolecules with flexible segments

We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA.     

Voltammetric properties of electrodes modified by poly-[N-(9,10-anthraquinone-2-carbonyl)ethylenimine] and used in aqueous solution

Three differently loaded anthraquinone polymers have been prepared by condensation of 2-anthraquinonecarbonylchloride and poly(ethylenimine). They have been adsorbed on vitreous carbon or mercury electrodes by dipping the electrode in a solution of pyridine or methylene chloride containing 0.01–0.05% polymer. The influence of adsorption parameters and of electrochemical variables on the voltammetric behavior of the polymer-coated electrodes in aqueous buffer solutions is described. Changing the dip time in pyridine from 30 s to 5 min and changing the polymer concentration have very little effect on the apparent coverage (=1.3-1.8×10^?9 mol cm^?2) and peak shape. In contrast, an increase of the loading (the number of monomer units loaded with quinone) or the use of methylene chloride as a dip-coating solvent instead of pyridine affected the shape of the cathodic and anodic peaks which broaden and tend to separate. The peak shape is characterized by a tailing which tends to disappear at slow scan rate. The modifications of the peak shape and position when the scan rate is changed, have been shown to fit qualitatively with a proposed polylayer model in which electron (proton) transfer to the sublayer nearest the underlying conductor is slow. It has been observed that the weak acid dissociation constants for the dihydroanthraquinone and hydroanthraquinone anion are both different for the corresponding monomer in solution (pK_A=8.65 and 11.6) and the adsorbed polymer (pK_A=9 and 13).     

Bimodal system (luminophore and paramagnetic contrastophore) derived from Ln(III) complexes based on a bipyridine-containing macrocyclic ligand

The synthesis of a new 15-membered polyaza-macrocyclic ligand L3H3, which is based on a 2,2'-bipyridine moiety and a diethylenetriaminetriacetic acid core, is reported. The lanthanide chelates of this octadentate ligand were programmed for bimodal probes, luminescent agents (Sm, Eu, Tb, Dy), and magnetic resonance imaging agents (Gd3+). The neutral 1:1 complexes with these Ln3+ ions were prepared and studied in aqueous solution by luminescence and NMR techniques. The main photophysical characteristics of these complexes (i.e., the absorption and luminescence spectra, the metal-centered lifetimes, and the overall luminescence yields, Phi) were measured. In addition, the role played by nonradiative pathways (vibrational energy transfer involving coordinated water molecules, involvement of ligand-to-metal charge-transfer excited states, or metal --> ligand back transfer) is discussed. The L3.Eu and L3.Tb complexes show very bright luminescence when photoexcited from the lowest-energy absorption band of the bipyridine chromophore. The luminescence quantum yields in an air-equilibrated water solution at room temperature are 0.10 and 0.21, respectively, despite the presence of one water molecule in the first coordination sphere of the metal ion. NMR data show that L3.Gd contains also one H2O molecule in the inner sphere. The proton longitudinal relaxivity, r1, of this complex is 3.4 s(-1) mM(-1) (0.47 T, 310 K) and the rotational correlation time, tau(R), is 57 ps (310 K). These values are comparable to those of the clinically used Gd-DTPA. Interestingly, the water exchange rate between the coordination site and the bulk solvent is slow (tau(M) = 3.5 micros at 310 K). The presence of water molecules in the second sphere and in rapid exchange with the solvent is discussed. Finally, it was found by luminescence and NMR experiments that these lanthanide complexes are stable versus transmetalation by several cations (especially Ca2+ and Zn2+) at physiological pH and have no interaction with blood proteins.     

Cover Feature: OH Radical-Induced Oxidation in Nucleosides and Nucleotides Unraveled by Tandem Mass Spectrometry and Infrared Multiple Photon Dissociation Spectroscopy (ChemPhysChem 23/2023)

OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS²) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS² results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2’-deoxyadenosine (dA(O)H⁺), 2’-deoxyadenosine 5’-monophosphate (dAMP(O)H⁺), 2’-deoxycytidine (dC(O)H⁺), and 2’-deoxycytidine 5’-monophosphate (dCMP(O)H⁺) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations. We show that a carbonyl group is formed at the C8 position after oxidation of 2’-deoxyadenosine and its monophosphate derivative. For 2’-deoxycytidine and its monophosphate derivative, the oxygen atom is added to the C5 position to form a C−OH group. IRMPD spectroscopy has been employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.     

Bismuth triflate-catalyzed oxa- and thia-Pictet-Spengler reactions: access to iso- and isothio-chroman compounds

A new route to functionalized iso(thio)chromans is described. The compounds are accessible easily in a one pot-reaction by using different benzaldehydes and phenylethanethiol or phenylethanol in presence of bismuth triflate.     

A battery-supercapacitor hybrid device composed of metallic zinc,a biodegradable ionic liquid electrolyte and graphite

The integration of a battery-type electrode and of a capacitor-type electrode in a single device by proper design is an effective strategy in developing energy storage devices with high energy and power densities. Herein, we present a battery-supercapacitor hybrid device using metallic zinc as anode, a biodegradable ionic liquid (IL) as electrolyte, and graphite as cathode. The recently developed choline acetate ([Ch]OAc) biodegradable IL-based electrolyte enables reversible deposition/stripping of Zn(II). Spongy-like Zn with a high surface area is obtained, which allows fast charge/discharge at high rates. The adsorption/desorption of ions on the surface of the graphite cathode and intercalation/deintercalation of anions into/from the graphite layers occur at the graphite cathode. Raman spectra and X-ray photoelectron reveal the intercalation of IL into and the adsorption of IL on the graphite. Highly reversible adsorption/desorption of ions on the surface of the graphite electrodes in the [Ch]OAc-based electrolyte was demonstrated by a symmetric cell. The Zn/graphite hybrid device delivers an energy density of 53 Wh kg^?1 at a power density of ~ 145 W kg^?1 and 42 Wh kg^?1 at ~ 400 W kg^?1. The hybrid device also exhibits a long cycle life with ～ 86% specific capacitance retained after 1000 cycles at a current density of 0.5 A g^?1. The combination of well-available zinc, inexpensive graphite, and a biodegradable IL electrolyte in a cell could open new avenues for sustainable energy applications.

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Aminopeptidase B,a glucagon-processing enzyme: site directed mutagenesis of the Zn<Superscript>2+</Superscript>-binding motif and molecular modelling

Background  

Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the N-terminus of peptides and processes glucagon into miniglucagon. The enzyme exhibits, in vitro, a residual ability to hydrolyze leukotriene A₄ into the pro-inflammatory lipid mediator leukotriene B₄. The potential bi-functional nature of Ap-B is supported by close structural relationships with LTA₄ hydrolase (LTA₄H ; EC 3.3.2.6). A structure-function analysis is necessary for the detailed understanding of the enzymatic mechanisms of Ap-B and to design inhibitors, which could be used to determine the complete in vivo functions of the enzyme.