Search results for "kyy"
showing 10 items of 296 documents
Non-syndromic Mitral Valve Dysplasia Mutation Changes the Force Resilience and Interaction of Human Filamin A
2018
International audience; Filamin A (FLNa), expressed in endocardial endothelia during fetal valve morphogenesis, is key in cardiac development. Missense mutations in FLNa cause non-syndromic mitral valve dysplasia (FLNA-MVD). Here, we aimed to reveal the currently unknown underlying molecular mechanism behind FLNA-MVD caused by the FLNa P637Q mutation. The solved crystal structure of the FLNa3-5 P637Q revealed that this mutation causes only minor structural changes close to mutation site. These changes were observed to significantly affect FLNa's ability to transmit cellular force and to interact with its binding partner. The performed steered molecular dynamics simulations showed that signi…
Solution- and gas-phase study of binding of ammonium and bisammonium hydrocarbons to oxacalix[4]arene carboxylate
2023
Oxacalixarenes represent a distinctive class of macrocyclic compounds, which are closely related to the parent calixarene family, offering binding motifs characteristic of calixarenes and crown ethers. Nevertheless, they still lack extensive characterization in terms of molecular recognition properties and the subsequent practical applicability. We present here the results of binding studies of an oxacalix[4]arene carboxylate macrocycle toward a variety of organic ammonium cationic species. Our results show that the substituents attached to the guest ammonium compound largely influence the binding strengths of the host. Furthermore, we show that the characteristic binding pattern changes up…
UV laser induced photolysis of glycolic acid isolated in argon matrices
2021
The photochemistry of matrix-isolated glycolic acid, induced by UV light, was studied by FTIR spectroscopy and B3LYPD3/6-311++G(3df,3pd) calculations. Several decomposition pathways were found to take place upon 212 nm and 226 nm wavelengths irradiation. A number of complexes formed between photoproducts were identified, among them those of formaldehyde with water, carbon monoxide and carbon dioxide as well as the H2O-CO complexes. The structure and spectroscopic assignment of the photoproducts were made comparing the experimental results with the theoretical predictions and available literature data. The observed formation of different complexes indicates various pathways for their formati…
Encapsulation of xenon by bridged resorcinarene cages with high 129Xe NMR chemical shift and efficient exchange dynamics
2023
Functionalized cages encapsulating xenon atoms enable highly sensitive, background-free molecular imaging through a technique known as HyperCEST 129Xe MRI. Here, we introduce a class of potential biosensor cage structures based on two resorcinarene macrocycles bridged either by aliphatic carbon chains or piperazines. First-principles-based modeling predicts a high chemical shift (about 345 ppm) outside the typical experimental observation window for 129Xe encapsulated by the aliphatically bridged cage and two 129Xe resonances for the piperazine-bridged cages corresponding to single and double loading. Based on the computational predictions as well as 129Xe chemical exchange saturation trans…
Ab initio molecular dynamics study of overtone excitations in formic acid and its water complex
2018
In this article, we present results from ab initio molecular dynamics simulation of overtone excitation in formic acid monomer and its water complex in the gas phase. For the monomer, a conformation change is observed employing both OH and CH vibrational excitations, which supports experimental findings. In the formic acid–water complex, interconversion also takes place, but it proceeds via hydrogen exchange rather than via intramolecular reaction. Simulations raise a question on effect of quantum and matrix effects to the results. Also, a brief test of different computation methods was done on the system. peerReviewed
Effect of a Rigid Sulfonamide Bond on Molecular Folding: A Case Study
2015
A disulfonamide compound with bulky aromatic side chains was prepared, and its properties as a potential building block for foldamers were evaluated. Two different solvate crystal forms of the compound were identified and compared to the structures of an analogous oligoamide and related disulfonamides. The disulfonamide is unfolded in one of the solvates, whereas in the other one, a loosely folded conformer stabilized by an intramolecular hydrogen bond is found. Density functional calculations indicated that the loosely folded conformer is slightly more stable than its unfolded isomer. The calculations also identified a third, more tightly folded and more extensively hydrogen bonded, confor…
Scalable Constant pH Molecular Dynamics in GROMACS
2022
Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to…
Intra- vs Intermolecular Aurophilic Contacts in Dinuclear Gold(I) Compounds: Impact on the Population of the Triplet Excited State.
2022
Two series of dinuclear gold(I) complexes that contain two Au–chromophore units (chromophore = dibenzofurane or dimethylfluorene) connected through a diphosphane bridge that differs in the flexibility and length (diphosphane = dppb for 1,4-bis(diphenylphosphino)butane, DPEphos for bis[(2-diphenylphosphino)phenyl]ether, xanthphos for 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene, and BiPheP for 2,2′-bis(diphenylphosphino)-1,1′-biphenyl) have been synthesized and structurally characterized. Their photophysical properties have been carefully investigated, paying attention to the role of the presence, or absence, of aurophilic contacts and their nature (intra- or intermolecular character). Th…
Binding of ion pairs and neutral guests by aryl-extended meso‑p-hydroxyphenyl calix[4]pyrrole : The interplay between three binding sites
2023
An aryl-extended calix[4]pyrrole with four meso‑p-hydroxyphenyl substituents was investigated as a host for chloride, acetate, and benzoate anions. Crystal structures of pyridinium and imidazolium chloride complexes were obtained in which chloride ions are hydrogen bonded exo-cavity to the upper rim hydroxyl groups, and the aromatic cations are bound to the shallow cavity of the host. Furthermore, the calix[4]pyrrole formed a hydrogen bonded dimeric capsule templated by inclusion of adiponitrile guest in the endo-cavity binding site. NMR titrations revealed the preference of the OH groups of the host to bind anionic guests in solution. Benzoate anion had the highest binding constant (4 700 …