Krzysztof Mierzwicki

Investigations of the Very Short Hydrogen Bond in the Crystal of Nitromalonamide via Car–Parrinello and Path Integral Molecular Dynamics

In this paper are presented the results of theoretical studies of the structure in proton motion in a very short O···O and two weak N-H···O intramolecular hydrogen bonds in the nitromalonamide crystal. The dynamics of proton motion in hydrogen bonds were investigated in the NVT ensemble at 298 K using the Car-Parrinello and the path integral molecular dynamics. A very large delocalization of proton in the slightly asymmetrical single well of free energy potential of O-H···O intramolecular hydrogen bond was noted especially in the path integral simulation where quantum effects are taken into account. This hydrogen bond is very strong with the estimated energy of hydrogen bond ca. -27 kcal/mol. The nature of intra- and intermolecular interactions was studied by means of quantum theory of atoms in molecules. The infrared spectra were calculated and compared with available experimental data. CPMD vibrational results appear to be in good agreement with the experimental ones.

Molecular modeling study of leflunomide and its active metabolite analogues.

Leflunomide is known as a compound with various sorts of biological activity, which found a practical application in medicine. Search of current literature revealed an active metabolite of Leflunomide together with its eight analogues synthesized as protein tyrosine kinase inhibitors with potential anticancer activity. Accurate description of the molecular structure of these compounds is valuable. The detailed geometrical parameters description was performed using DFT theory. The conformational analysis and intramolecular proton transfer were considered. Using the most stable conformation the detailed electronic structure description was obtained by analysis of electron density and electrostatic potential distribution in the first step. Next, the topological analysis of the electron density by AIM method and electron localization function (ELF) theories supplemented this study. The AIM and ELF theories were applied to study the topology of the molecules, atomic charges distribution, and details of bonding. The theoretical investigations were performed in the gas phase and by using SCRF/PCM solvent reaction field. In this study the molecular modeling results for Leflunomide and the analogues of its active metabolite are presented.

Clustering of sulfamic acid: ESI MS and theoretical study

Sulfamic acid has wide application in industry and has been suggested to act as an effective nucleation agent for the formation of aerosols and cloud particles. From the point of view of the role that sulfamic acid may play in aerosol formation, the study of its homoaggregation is important. Gas phase clustering study was performed for sulfamic acid H3N·SO3, (ASA), from water and methanol-water solutions, by help of a TOF-Q spectrometer equipped with electrospray ionization source, in the negative-ion mode. The structure and stability of the (H3N·SO3)n and [(H3N·SO3)n-H](-) (n = 1-6) were studied using DFT/B3LYP/aug-cc-pVDZ method. The ESI MS study evidenced that both singly and doubly charged clusters are formed when the acids are electrosprayed from water solutions; they may be described as [(H3N·SO3)n-zH](z-) where z = 1 or 2. The largest identified clusters are built of 20 monomers. The theoretical studies showed that formation of higher order (ASA)n aggregates in the gas phase is energetically profitable. In contrast with the gas phase, aqueous solution does not favor the formation of (ASA)n aggregates. The study led to the conclusion that the ASA clusters are formed in the gas phase under the experimental conditions of the mass spectrometer. A hypothetical mechanism concerning the formation of the doubly negatively charged anionic aggregates is discussed. The obtained data suggest that small (NH3·SO3)n aggregates may also contribute to formation of aerosols in heavily polluted atmospheres with relatively large NH3 concentration.

Nonadditivity of interaction in Li(NH3)n and Li(NH3)n+ (n=1–4) clusters

Abstract Two- and three-body interactions are calculated by means of the B3LYP and MP4 methods to assess the nonadditivity of interactions in Li(NH 3 ) n and Li(NH 3 ) n + ( n =1–4) clusters. It is found that the three-body contributions to the total interaction energy are more important for Li(NH 3 ) n clusters than for Li(NH 3 ) n + ones. For lithium ion–ammonia complexes correlation effects do not contribute significantly to the interaction energy. On the other hand, for the lithium atom–ammonia complexes the electron correlation seems to be rather important. The density functional approach is reliable to estimate the total interaction energies and nonadditive effects, especially for larger systems ( n ⩾4).

Matrix‐Isolated Hydrogen‐Bonded and Van der Waals Complexes of Hydrogen Peroxide with OCS and CS2

Matrix isolation spectroscopy has been combined with ab initio calculations to characterize the 1:1 complexes of H2O2 with OCS and CS2. The infrared spectra of the argon and nitrogen matrices doped with H2O2 and OCS or CS2 have been measured and analyzed. The geometries of the complexes were optimized at the MP2/6-311++G(3df,3pd) level of theory. Four structures were found for the OCS-H2O2 complex and five for the CS2-H2O2 one; every pair of the corresponding structures showed close correspondence. For every optimized structure the interaction energy was partitioned according to the SAPT Scheme and the topological distribution of the charge density (AIM theory) was performed. The SAPT analysis and AIM results indicate that only one complex among the nine optimized ones is stabilized by the hydrogen bonding, namely the OCS-H2O2 one with the OH group of H2O2 bonded to an oxygen atom of OCS. The other structures are stabilized by van der Waals interaction. The spectra analysis evidences that at least two types of the complexes are trapped in the argon matrices including the most stable ones: hydrogen bonded structure in the case of the OCS-H2O2 complex and the structure stabilized by the S···H and C···O interactions in the case of the CS2-H2O2 complex. The solid nitrogen environment triggers the formation of the structures of C2v symmetry with a sulfur atom of OCS or CS2 directed toward the center of O-O bond of H2O2, stabilized by S···O interactions.

Nature of chemical bonds in MCCH (M=Li, Na, K) based on the topological analysis of electron localisation function (ELF) and electron density

Abstract Topological analysis of the electron localisation function (ELF) and the theory of atoms in molecules are applied to analyse the nature of bonds in MCCH (M=Li, Na, K) molecules. The substitution of hydrogen by alkali metal leads to a transfer of about one electron from M to C 1 C 2 H and all alkali metal acetylides may be described by the M + [C 1 C 2 H] − formula. This means that the bonding between carbon and metal is mainly of ionic nature. One can explain the observed difference in properties of organosodium compounds by rather high electronegativity of sodium according to the Allred–Rochow scale.

OH-Induced Oxidative Cleavage of Dimethyl Disulfide in the Presence of NO

We report the results of the theoretical study of (•)OH-induced oxidative cleavage of dimethyl disulfide (DMDS) and the experimental study of the CH3SSCH3 + (•)OH reaction in the presence of (•)NO. Infrared low temperature argon matrix studies combined with ab initio calculations allowed us to identify cis-CH3SONO, which evidences the formation of the CH3SO(•) and CH3SH molecules in the course of the CH3SSCH3 + (•)OH reaction. Ab initio/quantum chemical topology calculations revealed details of the oxidative cleavage of dimethyl disulfide, which is a complex multistep process involving an alteration of S-O and S-S covalent bonds as well as a hydrogen atom transfer. The ability of delocalization of the unpaired electron density by sulfur atoms and a formation of a hydrogen bond by CH3SO(•) and CH3SH are the factors which seem to explain antiradical properties of DMDS.

Effects of xenon insertion into hydrogen bromide. Comparison of the electronic structure of the HBr···CO2 and HXeBr···CO2 complexes using quantum chemical topology methods: electron localization function, atoms in molecules and symmetry adapted perturbation theory.

Quantum chemistry methods have been applied to study the influence of the Xe atom inserted into the hydrogen-bromine bond (HBr → HXeBr), particularly on the nature of atomic interactions in the HBr···CO2 and HXeBr···CO2 complexes. Detailed analysis of the nature of chemical bonds has been carried out using topological analysis of the electron localization function, while topological analysis of electron density was used to gain insight into the nature of weak nonbonding interactions. Symmetry-adapted perturbation theory within the orbital approach was applied for greater understanding of the physical contributions to the total interaction energy.

Crystal structure and bonding properties of Li2I(OH)

Abstract Quantum-mechanical calculations have been performed to investigate the crystal structure and the nature of chemical bonding in Li 2 I(OH). All simulations have been carried out using the density functional approach. The structural parameters have been optimized and their good agreement with the experimental data has been demonstrated. Computed topological properties of the electron density at the bond critical points and also the AIM charges reveal the dominant role of closed-shell interaction in this compound. The nature of the bonding in Li 2 I(OH) was also discussed on the basis of an analysis of the electron localization function (ELF).