Search results for "laskennallinen kemia"
showing 10 items of 40 documents
Crystal Structures and Density Functional Theory Calculations of o-and p-Nitroaniline Derivatives: Combined Effect of Hydrogen Bonding and aromatic i…
2013
The interplay of strong and weak hydrogen bonds, dipole–dipole interactions, and aromatic interactions of o- and p-nitroaniline derivatives was studied by combining crystal structure analysis and density functional theory (DFT) calculations. Crystal structures of four 2-nitroaniline derivatives, 2-((2-nitrophenyl)amino)ethyl methanesulfonate (1A), 2-((2-nitrophenyl)amino)ethyl 4-methylbenzenesulfonate (2A), N,N′-((1,3-phenylenebis(oxy))bis(ethane-2,1-diyl))bis(2-nitroaniline) (3A), and N-(2-chloroethyl)-2-nitroaniline (4A), and crystal structures of three 4-nitroaniline derivatives, 2-((4-nitrophenyl)amino)ethyl methanesulfonate (1B), 2-((4-nitrophenyl)amino)ethyl 4-methylbenzenesulfonate (…
Machine Learning for Predicting Chemical Potentials of Multifunctional Organic Compounds in Atmospherically Relevant Solutions
2022
We have trained the Extreme Minimum Learning Machine (EMLM) machine learning model to predict chemical potentials of individual conformers of multifunctional organic compounds containing carbon, hydrogen, and oxygen. The model is able to predict chemical potentials of molecules that are in the size range of the training data with a root-mean-square error (RMSE) of 0.5 kcal/mol. There is also a linear correlation between calculated and predicted chemical potentials of molecules that are larger than those included in the training set. Finding the lowest chemical potential conformers is useful in condensed phase thermodynamic property calculations, in order to reduce the number of computationa…
Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
2019
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…
Computational studies of biomolecular screening and interactions
2015
Vibrational Spectrum of HXeSH revisited : Combined computational and experimental study
2020
Vibrational spectrum of HXeSH embedded in low-temperature matrix is experimentally studied. To support the spectrum interpretation, anharmonic vibrational analysis is performed using different models and basis sets and the data is compared with previous experimental and theoretical analyses. Computations of overtones and combination modes allowed for new band assignments. The HXeSH molecule exhibits high anharmonicity similarly as other molecules from the noble-gas hydride family. Comparison of the employed computational methods shows once again that the modelling of the noble-gas compounds faces theoretical challenges to yield quantitatively reliable results. peerReviewed
Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers
2022
Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with …
Benson group additivity values of phosphines and phosphine oxides: Fast and accurate computational thermochemistry of organophosphorus species
2018
Composite quantum chemical methods W1X-1 and CBS-QB3 are used to calculate the gas phase standard enthalpy of formation, entropy, and heat capacity of 38 phosphines and phosphine oxides for which reliable experimental thermochemical information is limited or simply nonexistent. For alkyl phosphines and phosphine oxides, the W1X-1, and CBS-QB3 results are mutually consistent and in excellent agreement with available G3X values and empirical data. In the case of aryl-substituted species, different computational methods show more variation, with G3X enthalpies being furthest from experimental values. The calculated thermochemical data are subsequently used to determine Benson group additivity …
Benson group additivity values of phosphines and phosphine oxides : Fast and accurate computational thermochemistry of organophosphorus species
2019
Composite quantum chemical methods W1X-1 and CBS-QB3 are used to calculate the gas phase standard enthalpy of formation, entropy and heat capacity of 38 phosphines and phosphine oxides for which reliable experimental thermochemical information is limited or simply nonexistent. For alkyl phosphines and phosphine oxides, the W1X-1 and CBS-QB3 results are mutually consistent and in excellent agreement with available G3X values and empirical data. In the case of aryl-substituted species, different computational methods show more variation, with G3X enthalpies being furthest from experimental values. The calculated thermochemical data are subsequently used to determine Benson group additivity co…
Frozen or dynamic? : An atomistic simulation perspective on the timescales of electrochemical reactions
2023
Electrochemical systems span a wide range of timescales, and several recent works have put forth the idea that the reaction environment should remain frozen and out of equilibrium during electrochemical electron or proton transfer reactions. Furthermore, simplified treatments of the electrochemical interface model the solvent and ions as frozen molecules. However, the claims and practices of a frozen environment strongly clash with most theoretical and simulation approaches developed to study electrochemical reaction rates. It has also been suggested that the electrode potential should not be fixed when simulating reaction rates due to conductivity limitations, which indicates constant pote…