Mariana Kozlowska
Molecular Modeling Group
Scientific research


New indenylidene-type metathesis catalysts bearing unsymmetrical N-heterocyclic ligands with mesityl and nitrobenzyl substituents

New indenylidene-type second generation catalysts bearing modified unsymmetrically substituted N-heterocyclic carbene ligands were synthesized. The complexes contain an N-mesityl and N′-nitrobenzyl substituted NHC ligand. The precursors of free carbenes—imidazolinium salts—were obtained in an easy and environment-friendly way (under aqueous or neat conditions). The new catalysts were prepared by reaction of in situ generated carbenes with a 1st generation indenylidene catalyst, containing pyridine ligands instead of cyclohexylphosphine. The complexes were tested in RCM, CM, and ene-yne metathesis model reactions in commercial-grade solvents in air. Their activities were compared with that of commercially available indenylidene catalyst. The structures of complexes and their stability were investigated using static DFT calculations with mixed basis set.

Intramolecular hydrogen bonds in low molecular weight polyethylene glycol

We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H···O and blue-shifting C-H···O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car–Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H···O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak CH···O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation.

Impact of vacancy defects in single-walled carbon nanotube on the structural properties of covalently attached aromatic diisocyanates

Ab initio molecular dynamics simulations (AIMD) are used to investigate the influence of the vacancy- and divacancy (5-8-5) defects on the surface of single-walled carbon nanotube (SWCNT)(10,0) on the structural properties of covalently attached aromatic diisocyanate molecules, namely 4,4′-methylene diphenyl diisocyanate (MDI) and toluene-2,4-diisocyanate (TDI). The structural rearrangements and flexibility of MDI and TDI attached to the defective SWCNTs are analysed and compared with the defect-free SWCNT(10,0). The results obtained indicate more than 4 times higher reactivity of vacancy defective SWCNT(10,0) comparing with the defect-free system. Due to weak C–H⋯O and C–H⋯π hydrogen bonds, formed during the covalent functionalisation, the flexibility of the attached diisocyanates is suppressed. Detailed analysis of the time evolution of the structural parameters during AIMD simulations suggests cyclically repeated mechanism of the structural rearrangements of aromatic diisocyanates on the surface of SWCNTs(10,0).

Structural, vibrational and electronic properties of defective single-walled carbon nanotubes functionalised with carboxyl groups: theoretical studies

Covalent sidewall functionalisation of defective zigzag single-walled carbon nanotubes [SWCNTs(10,0)] with COOH groups is investigated by using DFT. Four types of point defects are considered: vacancy (V), divacancy [V2(5-8-5), V2(555-777)], adatom (AA) and Stone–Wales (SW). The energetic, structural, electronic and vibrational properties of these systems are analysed. Decreasing reactivity is observed in the following order: AA>V>V2(555-777)>V2(5-8-5)>SW. These studies also demonstrate that the position in which a carboxyl group is attached to a defective SWCNT is of primary importance. Saturation of two-coordinate carbon atoms in systems with the vacancy V-7 and with the adatom AA-1(2) is 3.5–4 times more energetically favourable than saturation of three-coordinate carbon atoms for all studied systems. Vibrational analysis for these two systems shows significant redshifts of the ν(C[DOUBLE BOND]O) stretching vibration of 96 and 123 cm−1 compared to that for carboxylated pristine systems. Detailed electronic-structure analysis of the most stable carboxylated systems is also presented.

A computational study of intramolecular hydrogen bonds breaking/formation: impact on the structural flexibility of the ranitidine molecule

Ranitidine is a histamine H2-receptor antagonist that reduces gastric acid secretion. We studied the flexibility of the ranitidine molecule with the special focus on the network of diverse intramolecular hydrogen bonds: N-H ⋯O, N-H ⋯N, C-H ⋯O, C-H ⋯N and N-H ⋯S. We performed static density functional theory calculations of global and local minima and analyzed their stability at finite temperature in the Car–Parrinello molecular dynamics simulations. We observed intramolecular H-bonds breaking/formation crucial for the structural rearrangements leading to the folding process. The lifetimes of the closed structures of ranitidine were also estimated. The existence of hydrogen bonds and their strength were confirmed on the basis of topological parameters in the bond critical points utilizing Quantum Theory of Atoms in Molecules.

Covalent functionalization of single-walled carbon nanotubes through attachment of aromatic diisocyanate molecules from first principles

 We performed first-principle calculations of the covalent functionalization of metallic (6,0) and semiconducting (10,0) single-walled carbon nanotubes (SWCNTs) with aromatic diisocyanate molecules, namely, 4,4′-methylene diphenyl diisocyanate (MDI) and toluene-2,4-diisocyanate (TDI). The corresponding binding energies of the attached molecules were scrutinized. We analyzed the changes in the electronic band structure of SWCNTs caused by the amide bond formation after the functionalization process. Furthermore, the MDI–MDI and TDI–TDI mutual interactions on the nanotube surface were investigated.

Noncovalent functionalization of single-walled carbon nanotubes by aromatic diisocyanate molecules: A computational study

We investigate the noncovalent functionalization of metallic single-walled carbon nanotubes (SWCNT) (6,0) by 4,4‧-methylene diphenyl diisocyanate (MDI) and toluene-2,4-diisocyanate (TDI) molecules using the density functional theory (DFT) method with van der Waals dispersion correction. The obtained local minima show the dependence between the molecular arrangement of the adsorbates on SWCNT surface and their binding energies. We analyze the interplay between the π-π stacking interactions and isocyanate functional groups. For the analysis of the changes in the electronic structure we calculate the density of states (DOS) and charge density plots.

Tris (1, 10-phenanthroline-2N, N') ruthenium (II) bis (perchlorate)

The asymmetric unit of the title compound, [Ru(C12H8N2)3](ClO4)2, contains one octahedrally coordinated Ru(II) cation of the ruthenium-phenanthroline complex and three differently occupied perchlorate anions: two, denoted A and B, are located on the twofold axis while another, denoted C, is positioned in the proximity of the twofold screw axis. Perchlorate anions B and C are severely disordered. The occupancies of the two major conformers of anion B refined to 0.302 (6) and 0.198 (6). Perchlorate ion C was modeled in two alternate conformations which refined to occupancies of 0.552 (10) and 0.448 (10).

Bis(2,2':6',2''-terpyridine)-ruthenium(II) bis-(perchlorate) hemihydrate.

The asymmetric unit of the title compound, [Ru(C(15)H(11)N(3))(2)](ClO(4))(2)·0.5H(2)O, contains one ruthenium-terpiridine complex cation, two perchlorate anions and one half-mol-ecule of water. Face-to-face and face-to-edge π-stacking inter-actions between terpyridine units [centroid-centroid distances = 3.793 (2) and 3.801 (2) Å] stabilize the crystal lattice The partially occupied water mol-ecule inter-acts with two perchlorate ions via O-H⋯O hydrogen bonds. In the crystal lattice, the complex cations, perchlorate ion-water pairs and the second perchlorate anions are arranged into columns along b direction.



Mariana Kozlowska

PhD student at the University of Bialystok

In my research I use molecular modeling and quantum chemical-based methods for theoretical description of adsorption of different chemicals on carbon allotropes. Lately, our Group investigates covalent and noncovalent functionalization of single-walled carbon nanotubes by different molecules: diisocyanates, tetrahydrofuran, nucleic acids etc.

finished publications
happy students
drunk coffee
good ideas
Computer programs

The list of helpful programs

business zone

Homo Science w TOK FM

Homo Science is a radio broadcast about news in the science, which can be listened every Saturday at 21 o'clock in TOK FM

Crazy Nauka

The largest popular science blog in Poland

Here is a place for your logo

Do you want to collaborate with us?

Here is a place for your logo

Do you want to collaborate with us?

Marcin Stolarski Labolatory

BikeMic is a microphone placed between music player and the headphones.

Here is a place for your logo

Do you want to collaborate with us?

Here is a place for your logo

Do you want to collaborate with us?

You can use our pictures for your academic purposes, but consult this possibility with the owner of the page.

Blog posts:

The website was financed under the project  „Scholarships for PhD students of Podlaskie Voivodeship” . The project is co-financed in 85% by European Social Fund, in 7,5% by Polish Government and in 7,5% by Podlaskie Voivodeship.

Telephone number
+48 602 320 053
+48 857 457 815
Institute of Chemistry, University of Bialystok
Hurtowa Str. 1 (room 129), 15-399 Bialystok, Poland
Institute of Chemistry - University Campus
Ciolkowskiego Str. 1K (room 2010, 2012), Bialystok, Poland
See map Back to top