Search results for "laskennallinen kemia"
showing 10 items of 40 documents
A method for structure prediction of metal-ligand interfaces of hybrid nanoparticles
2019
Hybrid metal nanoparticles, consisting of a nano-crystalline metal core and a protecting shell of organic ligand molecules, have applications in diverse areas such as biolabeling, catalysis, nanomedicine, and solar energy. Despite a rapidly growing database of experimentally determined atom-precise nanoparticle structures and their properties, there has been no successful, systematic way to predict the atomistic structure of the metal-ligand interface. Here, we devise and validate a general method to predict the structure of the metal-ligand interface of ligand-stabilized gold and silver nanoparticles, based on information about local chemical environments of atoms in experimental data. In …
Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo-Switchable Fluorescent Protein
2015
Reversibly switchable fluorescent proteins (RSFPs) are essential for high-resolution microscopy of biological samples, but the reason why these proteins are photochromic is still poorly understood. To address this problem, we performed molecular dynamics simulations of the fast switching Met159Thr mutant of the RSFP Dronpa. Our simulations revealed a ground state structural heterogeneity in the chromophore pocket that consists of three populations with one, two, or three hydrogen bonds to the phenolate moiety of the chromophore. By means of non-adiabatic quantum mechanics/molecular dynamics simulations, we demonstrated that the subpopulation with a single hydrogen bond is responsible for of…
Intermolecular oxidative dehydrogenative 3,3′-coupling of benzo[b]furans and benzo[b]thiophenes promoted by DDQ/H+: total synthesis of shandougenine B
2016
With an excess of a strong acid, 2,3-dichloro-5,6-dicyano-1,4-quinone (DDQ) is shown to promote metal-free intermolecular oxidative dehydrogenative (ODH) 3,3'-coupling of 2-aryl-benzo[b]furans and 2-aryl-benzo[b]thiophenes up to 92% yield as demonstrated with 9 substrates. Based on the analysis of oxidation potentials and molecular orbitals combined with EPR, NMR and UV-Vis observations, the studied reaction is initiated by a DDQ-substrate charge transfer complex and presumably proceeds via oxidation of the substrate into an electrophilic radical cation that further reacts with another molecule of a neutral substrate. The coupling reactivity can easily be predicted from the oxidation potent…
Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2
2021
The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, th…
Magnetically induced currents and aromaticity in ligand-stabilized Au and AuPt superatoms
2021
Understanding magnetically induced currents (MICs) in aromatic or metallic nanostructures is crucial for interpreting local magnetic shielding and NMR data. Direct measurements of the induced currents have been successful only in a few planar molecules but their indirect effects are seen in NMR shifts of probe nuclei. Here, we have implemented a numerically efficient method to calculate gauge-including MICs in the formalism of auxiliary density functional theory. We analyze the currents in two experimentally synthesized gold-based, hydrogen-containing ligand-stabilized nanoclusters [HAu9(PPh3)8]2+ and [PtHAu8(PPh3)8]+. Both clusters have a similar octet configuration of Au(6s)-derived deloc…
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…
Atomikerroskasvatuksen ymmärrys molekyylitasolla
2014
Tutkielmassa käydään lyhyesti läpi atomikerroskasvatuksen historia, mitä se on ja sivutaan myös sen käyttökohteita. Atomikerroskasvatus on teollisessa mittakaavassa merkittävä sovellus ja sen käyttökohteiden määrä kasvaa entisestään. Pääosin keskitytään kahden yleisimmin käytetyn yhdisteen, alumiinioksidin Al2O3 ja hafniumoksidin HfO2, kasvatukseen, niiden reaktiomekanismeihin ja siihen kuinka reaktiomekanismit on saatu selville. Kronologinen läpileikkaus alkaen ensimmäisistä tehdyistä reaktioista aina viimeisimpiin ominaisuuksien selvittämistä koskeviin ja atomitason reaktioita kuvaaviin tutkimustuloksiin antaa yleiskuvan siitä kuinka monipuolisesta teknologiasta on kysymys. Tutkielmassa k…
Computational thermochemistry: extension of Benson group additivity approach to organoboron compounds and reliable predictions of their thermochemica…
2022
High-level computational data for standard gas phase enthalpies of formation, entropies, and heat capacities are reported for 116 compounds of boron. A comparison of the results with extant experimental and computational benchmark values reveals important trends and clear outliers. Recommendations are made to revise some of the key quantities, such as the enthalpies of formation of orthoboric acid, trimethylthioborate, and triphenylborane, the last of which is found to be considerably in error. The uncertainties associated with the experimental values are found to exceed those of high-level calculations by a clear margin, prompting the redetermination of Benson group additivity contribution…
Synthesis, Characterization and Single Crystal X-ray Diffraction Analysis of Fused Triazolo/Thiadiazole Clubbed with Indole Scaffold
2023
The present synthetic strategy involves the synthesis of indolyl-triazolo-thiadiazole heterocyclic ring systems 8–13 from the condensation of 4-amino-5-(1H-indol-2-yl)-3H-1,2,4-triazole-3-thione 1 with the aromatic carboxylic acid derivatives 2–7 in presence of POCl3 for 1 h. All compounds were obtained in very good yields and have been well-characterized using spectroscopic techniques. Exclusively, good quality crystals from the target organic hybrid 8-(1H-indol-2-yl)-5-(p-tolyl)-[1,2,4]triazolo [3,4-b][1,3,4]thiadiazole 9 were obtained and found suitable for X-ray single crystal diffraction measurement, which is used to confirm and analyze the molecular and supramolecular stru…