Search results for "dimer"
showing 10 items of 558 documents
Correction: “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer
2015
We present an accelerated ab initio path-integral molecular dynamics technique, where the interatomic forces are calculated “on-the-fly” by accurate coupled cluster electronic structure calculations. In this way not only dynamic electron correlation, but also the harmonic and anharmonic zero-point energy, as well as tunneling effects are explicitly taken into account. This method thus allows for very precise finite temperature quantum molecular dynamics simulations. The predictive power of this novel approach is illustrated on the example of the protonated water dimer, where the impact of nuclear quantum effects on its structure and the 1H magnetic shielding tensor are discussed in detail.
Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy
2019
Abstract Detailed study of Jensen’s polarization-consistent vs. Dunning’s correlation-consistent basis set families performance on the extrapolation of raw and counterpoise-corrected interaction energies of water dimer using coupled cluster with single, double, and perturbative correction for connected triple excitations (CCSD(T)) in the complete basis set (CBS) limit are reported. Both 3-parameter exponential and 2-parameter inverse-power fits vs. the cardinal number of basis set, as well as the number of basis functions were analyzed and compared with one of the most extensive CCSD(T) results reported recently. The obtained results for both Jensen- and Dunning-type basis sets underestimat…
New insights in chemical reactivity from quantum chemical topology.
2021
International audience; Based on the quantum chemical topology of the modified electron localization function ELFx, an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange‐correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first‐order variation in the coulomb intermolecular energy defined in terms of the response to changes in the numbe…
Etude structure/fonction du demi-transporteur ABCD2 dans le contexte de l'Adrénoleucodystrophie liée à l'X
2013
X-linked Adrenoleukodystrophy (X-ALD) is a rare neurodegenerative disease caused by deficiency of the peroxisomal half-transporter ABCD1, implicated in very long chain fatty acids import. Two additional half-transporters are located in the peroxisomal membrane: ABCD2 and ABCD3. Over-expression of ABCD2 is known to compensate for ABCD1 deficiency, making ABCD2 a therapeutic target for X-ALD treatment. In this context, the main objective of my thesis was to investigate the function and the structure of ABCD2, and more broadly, of peroxisomal ABC transporters.Half-transporters must at least dimerize to form a functional transporter. Alternative dimerization could modulate substrate specificity…
Structure-function analysis of peroxisomal ATP-binding cassette transporters using chimeric dimers
2014
Background: Peroxisomal ABC transporters are predicted to function as homodimers in mammals. [br/] Results: ABCD1 interacts with ABCD2. Chimeric proteins mimicking full-length dimers represent novel tools for functional study. Artificial homodimers and heterodimers are functional. [br/] Conclusion: Interchangeability between ABCD1 and ABCD2 is confirmed, but PUFA transport depends on ABCD2. [br/] Significance: For the first time, heterodimers in mammals are proven to be functional.[br/] ABCD1 and ABCD2 are two closely related ATP-binding cassette half-transporters predicted to homodimerize and form peroxisomal importers for fatty acyl-CoAs. Available evidence has shown that ABCD1 and ABCD2 …
New molecular aspects of regulation of mitochondrial activity by fenofibrate and fasting
2000
Abstract Fenofibrate and fasting are known to regulate several genes involved in lipid metabolism in a similar way. In this study measuring several mitochondrial enzyme activities, we demonstrate that, in contrast to citrate synthase and complex II, cytochrome c oxidase (COX) is a specific target of these two treatments. In mouse liver organelles, Western blot experiments indicated that mitochondrial levels of p43, a mitochondrial T3 receptor, and mitochondrial peroxisome proliferator activated receptor (mt-PPAR), previously described as a dimeric partner of p43 in the organelle, are increased by both fenofibrate and fasting. In addition, in PPARα-deficient mice, this influence was abolishe…
Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality—Strong Affinity Nucleic Acids Binders
2021
New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA–poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalatio…
Photoinduced DNA Lesions in Dormant Bacteria. The Peculiar Route Leading to Spore Photoproduct Unraveled by Multiscale Molecular Dynamics
2020
Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproduct in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproduct. This non-canonical photochemistry results from the dry state of DNA and the binding to small acid soluble proteins that drastically modify the structure and photoreactivity of …
One-step synthesis of resorcarene dimers composed of two tetra-benzoxazine units
1998
Abstract The condensation of resorcarene 1 with ethylenediamine and an excess of formaldehyde gives, under high dilution conditions, in up to 15% yield the octa-benzoxazine dimer 2 in which two molecules of 1 are connected by four bridges. The structure of 2 has been confirmed by 1 H NMR spectra and MALDI-TOF mass spectra and by hydrolysis of the oxazine rings yielding the secondary amine 3 .
Novel structural insights into F-actin-binding and novel functions of calponin homology domains.
2008
Tandem calponin homology (CH) domains are well-known actin filaments (F-actin) binding motifs. There has been a continuous debate about the details of CH domain-actin interaction, mainly because atomic level structures of F-actin are not available. A recent electron microscopy study has considerably advanced our structural understanding of CH domain:F-actin complex. On the contrary, it has recently also been shown that CH domains can bind other macromolecular systems: two CH domains from separate polypeptides Ncd80, Nuf2 can form a microtubule-binding site, as well as tandem CH domains in the EB1 dimer, while the single C-terminal CH domain of alpha-parvin has been observed to bind to a alp…