Search results for "Covalent Interaction"
showing 10 items of 83 documents
2014
The interest in RNA modification enzymes surges due to their involvement in epigenetic phenomena. Here we present a particularly informative approach to investigate the interaction of dye-labeled RNA with modification enzymes. We investigated pseudouridine (Ψ) synthase TruB interacting with an alleged suicide substrate RNA containing 5-fluorouridine (5FU). A longstanding dogma, stipulating formation of a stable covalent complex was challenged by discrepancies between the time scale of complex formation and enzymatic turnover. Instead of classic mutagenesis, we used differentially positioned fluorescent labels to modulate substrate properties in a range of enzymatic conversion between 6% and…
Magneto-structural versatility of copper(II)-3-phenylpropionate coordination polymers with N-donor coligands.
2015
A novel series of copper(II) coordination polymers [Cu2(O2CC8H9)4(pyz)]n (1), [Cu2(O2CC8H9)4(dps)]n (2), {[Cu(O2CC8H9)2(dps)(H2O)]·H2O}n (3), {[NaCu(O2CC8H9)2(bpm)(NO3)]·H2O}n (4), and [Cu4(O2CC8H9)6(OH)2(bpp)2]n (5) [O2CC8H9− = 3-phenylpropionate anion, pyz = pyrazine, dps = di(4-pyridyl)sulfide, bpm = 2,2′-bipyrimidine, and bpp = 1,3-bis(4-pyridyl)propane] have been synthesized and magneto-structurally investigated. Compounds 1 and 2 belong to a large group of copper(II) carboxylates where bis-monodentate pyz (1) and dps (2) ligands connect the paddle-wheel [CuII2(μ-O2CC8H9)4] units leading to alternating copper(II) chains. The structure of 3 consists of uniform chains of trans-[CuII(O2CC…
B-DNA Structure and Stability as Function of Nucleic Acid Composition. Dispersion-Corrected DFT Study of Dinucleoside-Monophosphate Single and Double…
2013
actions of the sugar-phosphate skeleton with water; (6) hydrophobic interactions of the DNA cylindrical core, made up by the hydrogen-bonded and stacked nitrogen bases, with the water solvent. Recently, there has been increasing effort in developing and applying quantum chemical methods able to reproduce the structure of native B-DNA and to correctly describe the energy involved in the intrastrand and interstrand noncovalent interactions between the nucleotide monomers. This topic has been approached by both wave function methods and density functional theory. [2] Water solvent and sodium counterions also play an important role in the formation and relative stabilization of the double-helic…
Mukaiyama–Michael Reactions with trans-2,5-Diarylpyrrolidine Catalysts: Enantioselectivity Arises from Attractive Noncovalent Interactions, Not from …
2013
The scope of the enantioselective Mukaiyama-Michael reactions catalyzed by trans-2,5-diphenylpyrrolidine has been expanded to include both α- and β-substituted enals. However, the rationalization of the observed enantioselectivity is far from obvious since the catalyst is not very sterically hindered. DFT calculations were carried out to rationalize the observed stereoselectivities. Transition states of the C-C bond formation between iminium intermediates and silyloxyfurans were located and their relative energies were used to estimate the stereoselectivity data. We find excellent agreement between the predicted and observed stereoselectivities. The analysis of intermolecular forces reveals…
One‐Dimensional Coordination Polymers of Mn II , Cu II , and Zn II Supported by Carboxylate‐Appended (2‐Pyridyl)alkylamine Ligands – Structure and Ma…
2009
Four new complexes [MnII(L1OO)(H2O)][ClO4]·2H2O (1), [ZnII(L1OO)][ClO4]·2H2O (2), [CuII(L3OO)][CF3SO3]·H2O (3), and [ZnII(L3OO)][ClO4] (4) (L1OO– = 3-[(2-(pyridine-2-yl)ethyl){2-(pyridine-2-yl)methyl}amino]propionate; L3OO– = 3-[(2-(pyridine-2-yl)ethyl){(dimethylamino)ethyl}amino]propionate) have been synthesized and characterized by elemental analysis, IR, and UV/Vis spectroscopy. Structural analysis revealed that 1, 3, and 4 are one-dimensional chain-like coordination polymers. In 1 distorted octahedral MnN3O3 and in 3 square-pyramidal CuN3O2 coordination is satisfied by three nitrogen atoms and an appended carboxylate oxygen atom of the ligand, and an oxygen atom belonging to the carboxy…
Bridge-Clamp Bis(tetrazine)s with [N] 8 π-Stacking Interactions and Azido- s -Aryl Tetrazines: Two Classes of Doubly Clickable Tetrazines
2020
Click chemistry at a tetrazine core is useful for bioorthogonal labeling and crosslinking. Introduced here are two new classes of doubly clickable s-aryl tetrazines synthesized by Cu-catalyzed cross-coupling. Homocoupling of o-brominated s-aryl tetrazines leads to bis(tetrazine)s structurally characterized by tetrazine cores arranged face-to-face. [N]8 π-stacking interactions are essential to the conformation. Upon inverse electron demand Diels-Alder (iEDDA) cycloaddition, the bis(tetrazine)s produce a unique staple structure. The o-azidation of s-aryl tetrazines introduces a second proximal intermolecular clickable function that leads to double click chemistry opportunities. The stepwise i…
Nonlocal van der Waals Approach Merged with Double-Hybrid Density Functionals: Toward the Accurate Treatment of Noncovalent Interactions
2015
Noncovalent interactions drive the self-assembly of weakly interacting molecular systems to form supramolecular aggregates, which play a major role in nanotechnology and biochemistry. In this work, we present a thorough assessment of the performance of different double-hybrid density functionals (PBE0-DH-NL, revPBE0-DH-NL, B2PLYP-NL, and TPSS0-DH-NL), as well as their parent hybrid and (meta)GGA functionals, in combination with the most modern version of the nonlocal (NL) van der Waals correction. It is shown that this nonlocal correction can be successfully coupled with double-hybrid density functionals thanks to the short-range attenuation parameter b, which has been optimized against ref…