Papers by Artur Ratkiewicz
Water
Studies on kinetics of galaxolide (HHCB) degradation under influence of UV, simulated sunlight an... more Studies on kinetics of galaxolide (HHCB) degradation under influence of UV, simulated sunlight and some advanced oxidation processes (H2O2, UV/H2O2, and Vis/H2O2) were conducted. Galaxolide appeared to be a photolabile compound. The first-order kinetics model was assumed for all studied processes. It was observed that basic pH favored HHCB degradation. The influence of natural matrices (river water and artificial sweat) on direct photolysis of HHCB was examined. It was stated that the process of the photodegradation proceeded slower at the presence of each matrix. HHCB lactone was identified using the GC-MS technique. The recorded chromatograms showed that apart from the lactone, other degradation products were formed that we could not identify. In order to deeper understand the HHCB degradation process, DFT calculations were performed. The results pointed out that OH radicals play a key role in HHCB decomposition, which mainly proceeds via H abstractions as well as OH additions. It...
International Journal of Molecular Sciences
Eighteen previously undescribed trimethoprim (TMP) analogs containing amide bonds (1–18) were syn... more Eighteen previously undescribed trimethoprim (TMP) analogs containing amide bonds (1–18) were synthesized and compared with TMP, methotrexate (MTX), and netropsin (NT). These compounds were designed as potential minor groove binding agents (MGBAs) and inhibitors of human dihydrofolate reductase (hDHFR). The all-new derivatives were obtained via solid phase synthesis using 4-nitrophenyl Wang resin. Data from the ethidium displacement test confirmed their DNA-binding capacity. Compounds 13–14 (49.89% and 43.85%) and 17–18 (41.68% and 42.99%) showed a higher binding affinity to pBR322 plasmid than NT. The possibility of binding in a minor groove as well as determination of association constants were performed using calf thymus DNA, T4 coliphage DNA, poly (dA-dT)2, and poly (dG-dC)2. With the exception of compounds 9 (IC50 = 56.05 µM) and 11 (IC50 = 55.32 µM), all of the compounds showed better inhibitory properties against hDHFR than standard, which confirms that the addition of the am...
Kinetics of the hydrogen abstraction alkane + O2 → alkyl + HO2 reaction class: an application of the reaction class transition state theory
Structural Chemistry
In this work, the kinetics of reaction class of hydrogen abstraction from saturated hydrocarbons ... more In this work, the kinetics of reaction class of hydrogen abstraction from saturated hydrocarbons by O2 molecules has been studied. The high-pressure reaction rate constants were determined using reaction class transition state theory/structure-activity relationship (RC-TST/SAR) methodology, augmented by linear energy relationship (LER) and/or barrier height grouping (BHG) approximations for evaluation of the reaction barrier heights. The parameters needed have been derived from DFT calculations at M06-2X/aug-cc-pVTZ level for a training set of 23 reactions, involving hydrogen abstraction by O2 molecule at primary, secondary, and tertiary carbon sites. The reference reaction rate constant C2H6 + O2 → C2H5 + HO2 was obtained by extrapolation of the simplest reaction within the title family CH4 + O2 → CH3 + HO2. Kinetic parameters of the later one, calculated from canonical variational transition state theory (CVT), were taken from literature. The influence of low-frequency internal rotations has been investigated in details. The error analysis shows that the average systematic error of RC-TST/SAR-derived rate constants at low temperatures is within 25% compared to the explicit RC-TST results and diminishes at higher temperatures. This suggests that the proposed methodology can be effectively implemented in the automated mechanism generation codes to create the fuel combustion mechanisms.
Antioxidants
Vitamin E is the most active natural lipophilic antioxidant with a broad spectrum of biological a... more Vitamin E is the most active natural lipophilic antioxidant with a broad spectrum of biological activity. α-Tocopherol (α-T), the main representative of the vitamin E family, is a strong inhibitor of lipid peroxidation as a chain-breaking antioxidant. Antioxidant and antiradical properties of vitamin E result from the presence of a phenolic hydroxyl group at the C-6 position. Due to stereoelectronic effects in the dihydropyranyl ring, the dissociation enthalpy for phenolic O–H bond (BDEOH) is reduced. The high chain-breaking reactivity of α-T is mainly attributed to orbital overlapping of the 2p-type lone pair on the oxygen atom (O1) in para position to the phenolic group, and the aromatic π-electron system. The influence of the O1 atom on the antioxidant activity of vitamin E was estimated quantitatively. The all-rac-1-carba-α-tocopherol was synthesized for the first time. Along with model compounds, 1-carba-analog of Trolox and its methyl ester were screened for their in vitro ant...
Water
The photochemical behavior of doxazosin (DOX) in simulated environmental conditions using natural... more The photochemical behavior of doxazosin (DOX) in simulated environmental conditions using natural waters taken from local rivers as a solvent was studied. The chemical characteristics of applied waters was done and a correlation analysis was used to explain the impact of individual parameters of matrix on the rate of the DOX degradation. It was stated that DOX is a photoliable compound in an aqueous environment. Its degradation is promoted by basic medium, presence of environmentally important ions such as Cl−, NO3−, SO42− and organic matter. The kinetics of DOX reactions with OH− and SO4− radicals were examined individually. The UV/H2O2, classical Fenton and photo-Fenton processes, were applied for the generation of hydroxyl radicals while the UV/VIS:Fe2(SO4)3:Na2SO2 system was employed for production of SO4− radicals. The obtained results pointed that photo-Fenton, as well as UV/VIS:Fe2(SO4)3:Na2SO2, are very reactive in ratio to DOX, leading to its complete degradation in a short...
An X-ray and Natural Bond Orbital (NBO) structural study of α-tocopheryl and 2,2,5,7,8-pentamethylchroman-6-yl succinates
Journal of Saudi Chemical Society
Abstract α-Tocopheryl succinate (α-TOS) is a very promising anticancer agent; however, the mechan... more Abstract α-Tocopheryl succinate (α-TOS) is a very promising anticancer agent; however, the mechanism of its action and the role of the succinic moiety in biological activity still remains unclear. This paper, presents the first determination of the X-ray structure of α-TOS and 2,2,5,7,8-pentamethylchroman-6-yl succinate (PMCS). The X-ray data indicated high out of planarity deformation of the aryl ring in the chroman-6-ol system. α-TOS and PMCS differed in angle θ value (28.4° vs. 21.5°, respectively) and in their heterocyclic ring conformations: 2-endo-3-exo in PMCS, and 2-endo-3-exo and 2-exo-3-endo in α-TOS. Due to their strong intermolecular hydrogen bonds, both succinates form cyclically repeated dimeric structures in well assembled crystal supramolecular structures. A population analysis of α-tocopherol (α-TOC), 2,2,5,7,8-pentamethylchroman-6-ol (PMC) and their acyl derivatives was performed at B3LYP/6-31G(d,p)/CPCM level of theory using a natural bond orbital (NBO) analysis within the Gaussian 09 program package. For all compounds, relaxed scans were performed along torsion angle γ, and for low-energy conformers the Fukui functions were calculated: electron donor (ƒ−(r)), electron acceptor (ƒ+(r)), free radical (ƒo(r)) and dual descriptor (ƒ2(r)). In general, the differences observed between α-TOC and its acyl derivative structures result from the non-bonding lone pair of the phenolic oxygen and its interaction with aromatic system π electrons.
Kinetics of the Hydrogen Abstraction PAH + ∙OH → PAH Radical + H2O Reaction Class: An Application of the Reaction Class Transition State The-ory (RC-TST) and Structure-Activity Relationship (SAR)
The Journal of Physical Chemistry A
A reaction class transition state theory (RC-TST) augmented with structure-activity relationship ... more A reaction class transition state theory (RC-TST) augmented with structure-activity relationship (SAR) methodology is applied to predict high-pressure limit thermal rate constants for hydrogen abstraction by •OH radical from polycyclic aromatic hydrocarbons (PAHs) reaction class in the temperature range of 300-3000 K. The rate constants for the reference reaction of C6H6 + •OH → C6H5 + H2O is calculated by the canonical variational transition state theory (CVT) with small curvature tunneling (SCT). Only the reaction energy is needed to predict RC-TST rates for other processes within the family, the parameters needed were obtained from M06-2X/cc-pVTZ data for a training set of 34 reactions. The systematic error of the resulting RC-TST rates is smaller than 50% in comparison with explicit rate calculations, which facilitates application of the proposed methodology to the automated reaction mechanism generators (ARMGs) schemes.
On-the-fly kinetics of hydrogen abstraction from polycyclic aromatic hydrocarbons by methyl/ethyl radicals
Physical chemistry chemical physics : PCCP, Jan 19, 2018
This work provides a rigorous procedure, within the framework of the Reaction Class Transition St... more This work provides a rigorous procedure, within the framework of the Reaction Class Transition State Theory (RC-TST) and the Structure-Activity Relationship (SAR), for predicting reliable thermal rate constants on-the-fly for hydrogen abstraction reactions by methyl/ethyl radicals from Polycyclic Aromatic Hydrocarbons (PAHs) in a temperature range of 300-3000 K. All necessary RC-TST parameters were derived from ab initio calculations for a representative set of 36 reactions on which different error analyses and comparisons with available literature data were carried out. In addition to the good agreement between the RC-TST rate constants and the literature data, the detailed error analyses show that RC-TST/SAR, utilizing either the Linear Energy Relationship (LER) where only the reaction energy is needed or Barrier Height Grouping (BHG) where no additional data is needed, can predict the thermal rate constants for any reaction in the title reaction class with an average systematic e...
A study on the reaction of 16-dehydropregnenolone acetate with 2-aminobenzimidazole
Steroids, 2017
The condensation of 16-dehydropregnenolone acetate with 2-aminobenzimidazole was studied. The pol... more The condensation of 16-dehydropregnenolone acetate with 2-aminobenzimidazole was studied. The polycyclic aromatic product was formed as a single regioisomer in a cascade reaction comprising addition, cyclization, autoxidation, and aromatization, in addition to the rearranged D-homo product. The reaction mechanism based on DFT calculations is proposed.
Journal of Chemistry
The exo,anti/exo,syn-diastereoselectivity of water promoted direct aldol reactions of tropinone a... more The exo,anti/exo,syn-diastereoselectivity of water promoted direct aldol reactions of tropinone and granatanone (pseudopelletierine) is strongly dependent on the amount of water added and aromatic aldehyde used. DFT methods were applied to calculate the free energies of tropinone and granatanone enols, transition states, and isomeric aldol products. A theoretical model was verified by comparison of results from several DFT methods and functionals with experiments. The 6-31g(d)/CPCM method proved most suited to the problem, although all methods tested predicted similar trends. Explicit inclusion of a water molecule bonded to the amino ketones resulted in increased stability of the enol forms. The dependence of the anti/syn-diastereoselectivity on the amount of water used may be rationalized on the basis of change in the polarity of the reaction medium. The predicted stabilities of competing products agreed with experimental results supporting the notion of thermodynamic control. The ...
Physical Review C, 2016
The neutron-deficient nucleus 107 Sn has been studied using the one-neutron knockout reaction. By... more The neutron-deficient nucleus 107 Sn has been studied using the one-neutron knockout reaction. By measuring the decay γ rays and momentum distributions of reaction residues, the spins of the ground, 5/2 + , and first excited, 7/2 + , states of 107 Sn have been assigned by comparisons to eikonalmodel reaction calculations. Limits on the inclusive and exclusive cross sections have been measured and transitions due to neutron removals from below the N=50 closed shell have been observed. New excited states up to 5.5 MeV in 107 Sn have been identified.
Performance of First-Principles based Reaction Class Transition State Theory
The journal of physical chemistry. B, Jan 11, 2016
Performance of the Reaction Class Transition State Theory (RC-TST) for prediction of rates consta... more Performance of the Reaction Class Transition State Theory (RC-TST) for prediction of rates constants of elementary reactions is examined using data from its previously applications to a number of different reaction classes. The RC-TST theory is taking advantage of the common structure denominator of all reactions in a given family combining with structure activity relationships to provide a rigorous theoretical framework to obtain rate expression of any reaction within reaction class in a simple and cost-effective manner. This opens the possibility for integrating this methodology with Automated Mechanism Generator for 'on-the-fly' generating accurate kinetic models of complex reacting systems.
Supplementary information for Direct ab-initio Dynamics Calculations of Thermal Rate Constants for the CH4 + O2 = CH3 + HO2 reaction
Determination of the N-invertomer stereochemistry in N-substituted nortropanones and norgranatanones using computational and NMR methods
Comptes Rendus Chimie, 2015
Abstract Several N -substituted nortropane and norgranatane derivatives were synthesised from tro... more Abstract Several N -substituted nortropane and norgranatane derivatives were synthesised from tropinone and granatanone. The equilibrium distributions of the axial and equatorial N- invertomers of the free amine forms of the prepared products in methanol and their protonated forms (hydrochlorides) in water were studied by low-temperature and room-temperature NMR spectroscopy. Theoretical distributions in the gas phase, methanol and water solvents were calculated using DFT methods and compared with inverse gated 13 C NMR experiments. DFT calculations provided results in reasonable agreement with experimental data. Equatorial invertomers dominated in N-tert -butyl- and N- benzylnortropinone, and the equatorial/axial ratio for N- ethyl- and N- phenethylnortropinone was close to 1. The axial invertomers dominated in all of the granatanone derivatives and the N- isopropyl- and N- phenylnortropane. Our experiments indicated that nitrogen protonation shifted the invertomer equilibrium towards equatorial forms. DFT calculations reproduced this effect for tropanes.
Isomerisation and configurational assignment of 2-alkyltropane and 2-alkylgranatane derived hydrazones
Tetrahedron, 2015
ABSTRACT
Non-adiabatic effects in the reactions of strongly polar ions with molecules
Journal of the Chemical Society, Faraday Transactions, 1996
A theoretical study has been carried out on the effect of the inclusion of the C/r6 term, where C... more A theoretical study has been carried out on the effect of the inclusion of the C/r6 term, where C is a constant and r is the distance between the ion and the centre of mass of the molecule, into the interaction potential that describes the capture of an ion by a polar molecule. Recently, a rotationally adiabatic capture theory was used to show that the contribution from such terms alters the rate constants for the reactions of strongly polar ArH3+ with H2O and NH3 by as much as ca. 20%. It is found in this work that non-adiabatic effects resulting from the coupling of the rotational motion of a dipole with the orbital motion of the system are also of importance. The magnitude of such effects depends on the molecular parameters of the system.
Chemical graph theory approach for automated mechanism generation
Application of graph theory for automated mechanism generation
Zastosowanie metody RC-TST w kinetyce rodników alkilowych
Methods and Techniques in Computational Chemistry: METECC-94, Medium Size Systems, Vol
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Papers by Artur Ratkiewicz