Properties of molecules and clusters from the first principles calculations

Abstrakt: 

The computational resources required in this applications should partly cover computational time needed to reach scientific goals planned in two research projects APVV-15-0105 and VEGA 1/0279/16. The topic of these projects include: non-covalent interactions, NMR properties of moelcules, confined systems, chemical reactivity, metallic clusters etc.

Odbor: 
quantum chemistry
Vedecká časť: 

A common idea of this project is providing benchmark wavefunction data (mostly CCSD(T)) that would support DFT predictions of energetics and properties of gradually complex systems. Noncovalent interactions will be analysed, contributions many-body terms to the non additivity will be evaluated. As a prototype, beryllium clusters will be studied, binding energies per atom of Be_n up to the solid state will be of interest. The focus will be on interactions of biologically relevant amino acid residue clusters extracted from protein structures in the Protein Data Bank, their geometry and stability. Another class of molecules considered are metal–ligand
complexes, including heavy metals. The main goal is to understand the bonding mechanism in context of their size, from small complexes to nanoclusters. Relativistic effects provide one of instruments for this analysis as well as for the analysis of iodine containing species relevant to coolant system of the nuclear reactor and in I2 complexes with antithyroid drugs. Many-body dispersion interactions will be treated using DFT in connection with layered materials and molecular crystals, their structure, elastic and thermal properties and adsorption. The alteration of properties of solute molecules in solvents, is another consequence of intermolecular interactions. This will be considered in relativistic calculations of NMR shielding constants.
We combine wavefunction and DFT methods having in mind controlled accuracy. Large systems are treated using DFT, but selection of functionals is supported by extensive benchmarks on model systems. This will be achieved by further extension of efficiency of the wavefunction methods towards treating model systems closer to large molecules of interest.

An artificial confinement potential is used to model effects of chemical environment of viarious systems. It is widely used for modeling physical phenomena such as in-crystal polarizabilities, electronic structure of quantum dots, high-pressure effects on atoms and molecules and the systems included into nanosized cavities etc.. In our project we will focus on particular problems namely: ab initio calculations of cationic in-crystal polarizabilities, cavity embedded molecules and NMR and hyperfine propeties of semiconductor quantum dots.

list of relevant publications of the applicants team:

Absolute shielding scales for Al, Ga, and In and revised nuclear magnetic dipole moments of Al-27, Ga-69, Ga-71, In-113, and In-115 nuclei

By: Antusek, A.; Holka, F.

JOURNAL OF CHEMICAL PHYSICS  Volume: 143   Issue: 7     Article Number: 074301   Published: AUG 21 2015

 

Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE

By: Sladek, Vladimir; Holka, Filip; Tvaroska, Igor

PHYSICAL CHEMISTRY CHEMICAL PHYSICS  Volume: 17   Issue: 28   Pages: 18501-18513   Published: 2015

CCSD(T) calculations of confined systems: In-crystal polarizabilities of F-, Cl-, O-2 (-), and S-2 (-)

By: Holka, F.; Urban, M.; Neogrady, P.; et al.

JOURNAL OF CHEMICAL PHYSICS  Volume: 141   Issue: 21     Article Number: 214303   Published: DEC 7 2014

 

Theoretical Study of Plutonium(IV) Complexes Formed within the PUREX Process: A Proposal of a Plutonium Surrogate in Fire Conditions

By: Sulka, Martin; Cantrel, Laurent; Vallet, Valerie

JOURNAL OF PHYSICAL CHEMISTRY A  Volume: 118   Issue: 43   Pages: 10073-10080   Published: OCT 30 2014

 

Ab initio study of NMR shielding of alkali earth metal ions in water complexes and magnetic moments of alkali earth metal nuclei

By: Antusek, Andrej; Rodziewicz, Pawel; Kedziera, Dariusz; et al.

CHEMICAL PHYSICS LETTERS  Volume: 588   Pages: 57-62   Published: NOV 19 2013

 

A Theoretical Study of the X-Abstraction Reactions (X = H, Br, or I) from CH2IBr by OH Radicals: Implications for Atmospheric Chemistry

By: Sulka, Martin; Sulkova, Katarina; Louis, Florent; et al.

ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS  Volume: 227   Issue: 9-11   Pages: 1337-1359   Published: NOV 2013

Socioekonomický a technologický dopad: 

This is a fundamental research project with no short term technological applicability. The main output of the project is expected in the form of publications in high impact quantum chemistry journals.

Technická časť: 

We will use standard quantum chemistry and solid state electronic structure software packages:

cfour, Quantum Espresso, gaussian, Molcas, Dalton, Dirac, Molpro

These packages are known for good scaling in parallel environment. Most packages are already available in SIVVP environment.

Prepojenie s grantovými úlohami: 
APVV-15-0105 Noncovalent interactions in systems of increasing complexity VEGA 1/0279/16 Physical properties of confined systems
Spolufinancovanie: 
800.00
Výstupy: 
Absolute shielding scales for Al, Ga, and In and revised nuclear magnetic dipole moments of Al-27, Ga-69, Ga-71, In-113, and In-115 nuclei By: Antusek, A.; Holka, F. JOURNAL OF CHEMICAL PHYSICS Volume: 143 Issue: 7 Article Number: 074301 Published: AUG 21 2015
Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE By: Sladek, Vladimir; Holka, Filip; Tvaroska, Igor PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 17 Issue: 28 Pages: 18501-18513 Published: 2015
CCSD(T) calculations of confined systems: In-crystal polarizabilities of F-, Cl-, O-2 (-), and S-2 (-) By: Holka, F.; Urban, M.; Neogrady, P.; et al. JOURNAL OF CHEMICAL PHYSICS Volume: 141 Issue: 21 Article Number: 214303 Published: DEC 7 2014
Indirect NMR spin–spin coupling constants in diatomic alkali halides by: Michał Jaszuński, Andrej Antušek, Taye B. Demissie, Stanislav Komorovsky, Michal Repisky, and Kenneth Ruud THE JOURNAL OF CHEMICAL PHYSICS 145, 244308 (2016)
Ab initio calculations of NMR shielding of Sc 3+ , Y 3+ and La 3+ ions in the water solution and 45 Sc, 89 Y, 138 La and 139 La nuclear magnetic dipole moments by: Andrej Antušek, Martin Šulka Chemical Physics Letters 660 (2016) 127–131
NMR absolute shielding scale and nuclear magnetic dipole moment of 207 Pb by: Bożena Adrjan, Włodzimierz Makulski, Karol Jackowski, Taye B. Demissie, Kenneth Ruud, Andrej Antušek and Michał Jaszuński Phys. Chem. Chem. Phys., (2016), 18, 16483
Density functional theory modeling of C–Au chemical bond formation in gold implanted polyethylene by: Andrej Antušek, Martin Blaško, Miroslav Urban, Pavol Noga, Danilo Kisić, Miloš Nenadović, Davor Lončarević and Zlatko Rakočević Phys. Chem. Chem. Phys., (2017), 19, 28897
Nuclear magnetic dipole moment of 209Bi from NMR experiments, by: Andrej Antušek, Michal Repisky, Michał Jaszuński, Karol Jackowski, Włodzimierz Makulski, and Maria Misiak, Phys. Rev. A 98, 052509, (2018)
NMR absolute shielding scales and nuclear magnetic dipole moments of transition metal nuclei by: Andrej Antušek and Michal Repisky Phys. Chem. Chem. Phys., (2020) ,22, 7065-7076
Magnetic Moments of Short-Lived Nuclei with Part-per-Million Accuracy: Toward Novel Applications of β-Detected NMR in Physics, Chemistry, and Biology by: R. D. Harding et al. Phys. Rev. X, (2020) 10, 041061