Search results for "laskennallinen kemia"
showing 10 items of 40 documents
Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results
2018
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
Isolated glyoxylic acid-water 1:1 complexes in low temperature argon matrices
2015
Abstract The 1:1 hydrogen bonded complexes between glyoxylic acid (GA) and water are studied in low temperature argon matrices. Four different complex structures were found in deposited matrices. The lowest energy conformer (T1) of GA was found to form complex, where the water molecule was attached to the opposite side of the intramolecular hydrogen bond in the molecule (T1B). Interestingly, this complex was estimated to be +8.0 kJ mol −1 higher in energy than the most stable structure (T1A), where the water is inserted into the internal hydrogen bond, and also found in solid argon but in smaller abundance. For the second-lowest energy conformer of GA (T2), the two lowest-energy complex str…
Computational investigations of 18-electron triatomic sulfur–nitrogen anions
2018
MRCI-SD/def2-QZVP and PBE0/def2-QZVP calculations have been employed for the analysis of geometries, stabilities, and bonding of isomers of the 18-electron anions N2S2−, NS2−, and NSO−. Isomers of the isoelectronic neutral molecules SO2, S2O, S3, and O3 are included for comparison. The sulfur-centered acyclic NSN2−, NSS−, and NSO− anions are the most stable isomers of their respective molecular compositions. However, the nitrogen-centered isomers SNS− and SNO− lie close enough in energy to their more stable counterparts to allow their occurrence. The experimental structural information, where available, is in good agreement with the optimized bond parameters. The bonding in all investigate…
Electrocatalytic rate constants from DFT simulations and theoretical models: Learning from each other
2022
Electrochemical interfaces present an extraordinarily complex reaction environment and several, often counter-acting, interactions contribute to rate constants of electrocatalytic reactions. We compile a short review on how electrode potential, solvent, electrolyte, and pH effects on electrocatalytic rates can be understood and modelled using computational and theoretical methods. We address the connections between computational models based on DFT and (semi)analytical model Hamiltonians to extract physical or chemical insights, identify some omissions in present DFT simulation approaches and analytic models, and discuss what and how simulations and models could learn from each other. peerR…
Candida antarctica Lipase A-Based Enantiorecognition of a Highly Strained 4-Dibenzocyclooctynol (DIBO) Used for PET Imaging
2020
The enantiomers of aromatic 4-dibenzocyclooctynol (DIBO), used for radiolabeling and subsequent conjugation of biomolecules to form radioligands for positron emission tomography (PET), were separated by kinetic resolution using lipase A from Candida antarctica (CAL-A). In optimized conditions, (R)-DIBO [(R)-1, ee 95%] and its acetylated (S)-ester [(S)-2, ee 96%] were isolated. In silico docking results explained the ability of CAL-A to differentiate the enantiomers of DIBO and to accommodate various acyl donors. Anhydrous MgCl2 was used for binding water from the reaction medium and, thus, for obtaining higher conversion by preventing hydrolysis of the product (S)-2 into the starting materi…
Escaping scaling relationships for water dissociation at interfacial sites of zirconia-supported Rh and Pt clusters
2019
<p>Water dissociation is an important reaction involved in many industrial processes and a good model reaction for probing the activity of catalytic sites. In this computational study, the dissociation of water at interfacial sites of globally optimized ZrO2 sup- ported Pt and Rh clusters is investigated under the framework of density functional theory. Our findings demonstrate that the perimeter sites of these small clusters can activate water, but the dissociation behavior varies considerably between sites. It is shown that the studied clusters break scaling relationships for water dissociation, suggesting these catalysts may achieve activities beyond the maximum imposed by such rel…
A Computational Study of Adsorption of CO2, SO2, and H2CO on Free-Standing and Molybdenum-Supported CaO Films
2018
Oxide films play a significant role in a wide range of fields from catalysis to solar cell materials. CaO films are promising sorbents for many environmentally harmful molecules. Here, we report a systematic investigation of adsorption of CO2, SO2, and H2CO on bulk and Mo-supported CaO(100) films using density functional theory. Significant effects on adsorption energy, charge transfer to the molecules, and degree of the C–O bond activation were demonstrated on Mo-supported CaO films by changing the film thickness, composition, and the strength and direction of an applied external electric field. These findings are relevant for interpreting results from scanning tunneling microscopy of smal…
Comment on "Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO2"
2015
Out of focus: A recent Communication published in this journal describes the synthesis of [nBu4N]HCO3. The authors performed a single-crystal X-ray study that revealed a putative species described as an incipient hydroxide ion engaging in a long, and presumably weak, interaction with CO2. Our recent exploration of the coordination chemistry of CO2 with small ions leads us to believe that such an exceptional bonding situation is unlikely. Instead, we argue that the crystal structure is that of [nBu4N]O2CCH3 and therefore not representative of the bulk powder from the synthesis. peerReviewed
Comment on “Crystallographic Snapshot of an Arrested Intermediate in the Biomimetic Activation of CO2”
2015
Out of focus: A recent Communication published in this journal describes the synthesis of [nBu4 N]HCO3 . The authors performed a single-crystal X-ray study that revealed a putative species described as an incipient hydroxide ion engaging in a long, and presumably weak, interaction with CO2 . Our recent exploration of the coordination chemistry of CO2 with small ions leads us to believe that such an exceptional bonding situation is unlikely. Instead, we argue that the crystal structure is that of [nBu4 N]O2 CCH3 and therefore not representative of the bulk powder from the synthesis.
A Computational Study of Adsorption of CO2, SO2, and H2CO on Free-Standing and Molybdenum-Supported CaO Films
2019
Oxide films play a significant role in a wide range of fields from catalysis to solar cell materials. CaO films are promising sorbents for many environmentally harmful molecules. Here, we report a systematic investigation of adsorption of CO2, SO2, and H2CO on bulk and Mo-supported CaO(100) films using density functional theory. Significant effects on adsorption energy, charge transfer to the molecules, and degree of the C−O bond activation were demonstrated on Mo-supported CaO films by changing the film thickness, composition, and the strength and direction of an applied external electric field. These findings are relevant for interpreting results from scanning tunneling microscopy of smal…