Pawel Rodziewicz

Structural flexibility of 4,4′-methylene diphenyl diisocyanate (4,4′-MDI): evidence from first principles calculations

A reactant used globally in the production of polyurethane is the molecule 4,4′-methylene diphenyl diisocyanate (4,4′-MDI). The structural flexibility of 4,4′-MDI is one of the most important molecular properties influencing the polymerization process and this property was therefore modeled using density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (MD) simulations. Global and local minima structures were found and confirmed by vibrational analysis. The energy barriers related to rotation of the aromatic rings were estimated by DFT calculations. The stability of global and local minima was verified by Car-Parrinello (MD) runs at finite temperature. The presence of weak C–H⋯π hydrogen bonds was confirmed by atoms in molecules analysis and found to be responsible for the low energy barriers.

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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.

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 C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation.

Triple helical collagen-like peptide interactions with selected polyphenolic compounds.

Because collagen is the most abundant component of connective tissue, it is an excellent biomaterial in numerous medical applications. However, the utility of collagen is limited by its low mechanical strength in aqueous solutions and its susceptibility to proteolytic degradation in vivo. To improve the physical properties of collagen and to enhance its chemical resistance, it is necessary to stabilize its structure through chemical or physical modifications. In this study, we analyzed the interactions of a model molecule, a synthetic triple helical collagen-like peptide, with polyphenols such as curcumin, rutin, quercetin, naringin, and hypericin. Interactions between the peptide and polyphenolic compounds were analyzed using various techniques. The layer-by-layer assembly processes of a gold surface using the peptide and polyphenols was performed via surface plasmon resonance (SPR), atomic force microscopy (AFM), and ellipsometry. SPR screening of polyphenols was conducted in real time to select compounds that bind to the collagen-like peptide and could thus be applied to the stabilization of collagen. Selected polyphenols, especially naringin and hypericin, demonstrated notable binding to the peptide. To determine the nature of these interactions, experiments were supplemented with crystallographic studies and molecular docking of plant metabolites and collagen-like peptides.

Structural flexibility of the sulfur mustard molecule at finite temperature from Car-Parrinello molecular dynamics simulations.

Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum.

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

The asymmetric unit of the title compound, [Ru(C15H11N3)2](ClO4)2·0.5H2O, contains one ruthenium–terpiridine complex cation, two perchlorate anions and one half-molecule of water. Face-to-face and face-to-edge π-stacking interactions between terpyridine units [centroid–centroid distances = 3.793 (2) and 3.801 (2)  Å] stabilize the crystal lattice The partially occupied water molecule interacts 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.

Structural stability of diclofenac vs. inhibition activity from ab initio molecular dynamics simulations. Comparative study with ibuprofen and ketoprofen

Diclofenac is the world known nonsteroidal anti-inflammatory drug (NSAID) predicted before its syntesis on the basis of the model COX enzyme. Due to its specific structural properties the drug possesses high reactivity and outstanding tolerability. Among the key features defining the diclofenac structure is intramolecular N-H ⋯O hydrogen bond confirmed during the X-ray analysis. In the present research we use static DFT calculations, the Quantum Theory of Atoms in Molecules and non-covalent interactions (NCI) index to confirm the additional intramolecular interactions, which influence the drug molecular structure. We focus on the structural stability of diclofenac as the result of the hydrogen bonds breaking/formation at finite temperature utilizing ab initio molecular dynamics simulations. The lifetime of different intramolecular hydrogen bonds is estimated. We perform also the comparative analysis of the structural stability of ibuprofen and ketoprofen molecules in the gas phase at 300 K with respect to diclofenac in terms of the NSAID inhibition activity. Due to the detailed description of diclofenac intramolecular interactions, possible drug modifications for its enhanced water solubility can be suggested.

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.

Tris(1,10-phenanthroline-κ2N,N′)ruthenium(II) bis­(perchlorate)

The asymmetric unit of the title compound, [Ru(C12H8N2)3](ClO4)2, contains one octahedrally coordinated RuII 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).