Wiktor Zierkiewicz

Electronic structures, vibrational spectra, and revised assignment of aniline and its radical cation: Theoretical study

Comprehensive studies of the molecular and electronic structures, vibrational frequencies, and infrared and Raman intensities of the aniline radical cation, C6H5NH2+ have been performed by using the unrestricted density functional (UB3LYP) and second-order Moller–Plesset (UMP2) methods with the extended 6-311++G(df,pd) basis set. For comparison, analogous calculations were carried out for the closed-shell neutral aniline. The studies provided detailed insight into the bonding changes that take place in aniline upon ionization. The natural bond orbital (NBO) analysis has revealed that the pπ-radical conjugative interactions are of prime importance in stabilizing the planar, quinoid-type structure of the aniline radical cation. It is shown that the natural charges calculated for aniline are consistent with the chemical properties of this molecule (an ortho- and para-directing power of the NH2 group in electrophilic substitutions), whereas Mulliken charges are not reliable. The theoretical vibrational freque...

Study of the Nature of Improper Blue‐Shifting Hydrogen Bonding and Standard Hydrogen Bonding in the X3CH⋅⋅⋅OH2 and XH⋅⋅⋅OH2 Complexes (X=F, Cl, Br, I): A Correlated Ab Initio Study

Weak hydrogen bonding was studied in the XH...OH2 and X3CH...OH2 complexes (X = F, Cl, Br, I) using the correlated MP2 ab initio method with relativistic Stuttgart/Dresden pseudopotentials and basis set (SDD). The accuracy of the method was tested for selected nonrelativistic complexes by performing MP2 calculations with all-electron basis sets (6-311G** and TZVPP). The characteristics of bonding in the hydrogen halide complexes correspond to the standard H-bonding (an elongation of the X-H bond and red shift of its stretch frequency), whereas those in the X3CH...OH2 complexes (X = F, Cl) are typical of improper blue-shifting H-bonding (a contraction of the CH bond and blue shift of the respective stretch frequency). A natural bond orbital analysis revealed some important differences between both classes of complexes: a) the electron density transfer (EDT) in the former complexes is considerably larger than that in the latter complexes: b) the EDT in the former complexes is almost completely directed to the sigma*-antibonding orbital of the XH bond, which causes a weakening of this bond, its elongation, and a concomitant decrease of the XH stretch frequency. In the latter complexes, only a small portion of the EDT goes to the sigma*-antibonding orbital of the CH bond of the proton donor and a larger part is transferred to the remote (nonparticipating) part of the proton donor. As a consequence, the structural reorganization of the proton donor occurred, leading to the contraction of the C-H bond. The fact that a small red shift of the C-H stretch frequency was found in bromoform-water and iodoform-water complexes was explained by the competition of both the above-mentioned mechanisms with dominating passage of electron density to the sigma*-antibonding orbital of the C-H bond. For an explanation of all the geometric features of both types of complexes, it is however necessary to consider both charge transfer and electrostatic effects. The electrostatic effects fail sometimes to interpret the geometry changes in the proton donor.

The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine.

The amino group in adenine plays a key role in formation of hydrogen bonds in nucleic acids and in other molecular systems. Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. Ab initio MP2 and density functional B3LYP methods with various basis sets have been used to calculate the optimized structure and the infrared spectrum of adenine (the N9-H tautomer). Calculations at the MP2 level with larger basis sets tend to decrease the degree of pyramidalization of the C-NH2 group, whereas the B3LYP method consistently yields the planar or nearly planar structure of adenine. MP2 complete basis set (CBS) limit method with the aug-cc-pVTZ --> aug-cc-pVQZ (aTZ --> aQZ) extrapolation scheme has predicted very small planarization barrier of adenine, 0.015 kcal/mol, which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III, J. Chem. Phys. 2006, 124, 044303. Similar results were obtained in calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be concluded that the amino group in adenine, in the gas phase, is very flexible with a small degree of nonplanarity. Extremely low planarization barrier implies that adenine requires very little energy to conform the structure of the amino group to formation of the complementary hydrogen bonds with other molecules. This fact is very important for base pairing in nucleic acids or other polymers containing adenine residues. The anharmonic frequencies of adenine have been calculated at the B3LYP/6-311++G(df,pd) level of theory. The theoretical results show excellent agreement with the available experimental data. The revised assignment of the infrared spectrum of adenine in Ar matrix has been made. The predicted anharmonic frequency of the NH2 inversion, 181 cm(-1), is supported by the experimental data. It is demonstrated that the vibrational frequencies and potential energy distribution (PED) obtained from the B3LYP calculations are more reliable than those obtained at the MP2 level.

Theoretical investigation of the conformation, acidity, basicity and hydrogen bonding ability of halogenated ethers

MP2/6-311++G(d,p) calculations have been carried out to investigate the conformation, protonation and the hydrogen bonding interactions with water of several halogenated ethers (CH(3)OCH(2)Cl, CH(2)ClOCH(2)Cl, CH(3)OCHCl(2), CHFClOCHF(2)). The optimized geometries, ν(CH) harmonic vibrational frequencies and the SAPT decomposition of the interaction energies are studied. The interaction with one water molecule gives several stable structures characterized by O(w)H(w)...O and CH...O(w) hydrogen bonds or by O...Cl halogen bonding. The MP2/CBS calculated binding energies of different complexes between the halogenated ethers and water vary between 1.7 and 7.7 kcal mol(-1). The energies of these structures are discussed as a function of the proton affinity of the ethers and the deprotonation enthalpy of the CH bonds. The contraction of the CH bonds and blue shifts of the corresponding stretching vibrations in the O-protonated ethers and their O...H(w)O(w) complexes are compared. A natural bond orbital analysis has revealed that substitution of the H atoms by one or several halogen atoms has a great influence on the hyperconjugative effects from the two non-equivalent O lone pairs to relevant antibonding orbitals, and the subsequent geometry of the hydrogen bonded complexes.

Unusual Noncovalent Interaction Between the Chelated Cu(II) Ion and the π Bond in the Vitamin B13 Complex, cis-Diammine(orotato)copper(II): Theoretical and Vibrational Spectroscopy Studies

The crystal structure of the Cu(II) complex with Vitamin B(13) (orotic acid), cis-[Cu(oro)(NH(3))(2)] has revealed the presence of unusual, noncovalent pi-type interaction between the chelated Cu(II) ion and the C horizontal lineC bond of the uracilate ring [Michalska et al. Polyhedron 2007, 26, 4303]. In this work, the origin and strength of this interaction is thoroughly investigated. Comprehensive studies of the molecular structures and vibrational spectra of the title complex have been performed by using the unrestricted density functional theory methods, B3LYP, and the newly developed M05-2X functional. Calculations at the UMP2 level were also carried out for comparison. A variety of basis sets have been employed in the DFT calculations, including aug-cc-pVTZ, D95V(d,p), SDD, and LanL2DZ. The (63)Cu/(65)Cu isotope substitution technique was applied to identify the copper-ligand vibrations in the infrared spectra. The clear-cut assignment of all the bands in the FT-IR and Raman spectra of the title complex has been made on the basis of the calculated potential energy distribution, PED. It is shown that an extremely intense band at 1210 cm(-1) in the Raman spectrum of cis-[Cu(oro)(NH(3))(2)] is diagnostic for the N-1 deprotonation of the uracilate ring and coordination to the copper(II) ion. The B3LYP functional performs better than M05-2X in predicting vibrational frequencies of this complex in the solid state. Intermolecular interactions in crystal were modeled by the supramolecular system consisting of cis-[Cu(oro)(NH(3))(2)], ethylene (above), and formaldehyde (below the copper coordination plane). The stable structure of this system has been predicted only by the M05-2X and MP2 methods, which include dispersion energy, whereas the B3LYP calculations failed in geometry optimization. The distance between the Cu atom and the C horizontal lineC bond, predicted by the M05-2X method (3.00 A) is similar to the van der Waals contacts between the stacking bases in DNA. The calculated interaction energy between the chelated Cu(II) complex and ethylene amounts to -7.33 kcal mol(-1), which is similar to that determined for stacked uracil dimer. It is concluded that the London dispersion energy plays a significant role in the noncovalent interaction between the chelated Cu(II) ion and the uracilate ring in the crystal of cis-[Cu(oro)(NH(3))(2)]. Many copper enzymes in their active sites contain the chelated Cu(II) ion and the aromatic groups (Phe, Tyr and Trp) as the potential binding sites; therefore, the noncovalent copper(II)-pi interaction can be very important for the structure and functioning of these enzymes.

Theoretical investigation of the halogen bonded complexes between carbonyl bases and molecular chlorine

The halogen bonded complexes between six carbonyl bases and molecular chlorine are investigated theoretically. The interaction energies calculated at the CCSD(T)/aug‐cc‐pVTZ level range between −1.61 and −3.50 kcal mol−1. These energies are related to the ionization potential, proton affinity, and also to the most negative values (Vs,min) on the electrostatic potential surface of the carbonyl bases. A symmetry adapted perturbation theory decomposition of the energies has been performed. The interaction results in an elongation of the ClCl bond and a contraction of the CF and CH bonds accompanied by a blue shift of the ν(CH) vibrations. The properties of the Cl2 molecules are discussed as a function of the σ*(ClCl) occupation, the hybridization, and the occupation of the Rydberg orbitals of the two chlorine atoms. Our calculations predict a large enhancement of the infrared and Raman intensities of the ν(ClCl) vibration on going from isolated to complexed Cl2.

Blue Shifts and Unusual Intensity Changes in the Infrared Spectra of the Enflurane···Acetone Complexes: Spectroscopic and Theoretical Studies

Blue-shifting C-H···O hydrogen-bonded complexes between enflurane (CHFCl-CF(2)-O-CHF(2)) and deuterated acetone have been identified in CCl(4) solution by FT-IR spectroscopy. For the two ν(C-H) stretching vibrations of enflurane the observed blue shifts are +17 and +11 cm(-1). The corresponding two infrared ν(C-H) bands show the opposite changes of their intensity, one is decreasing, and the other is significantly increasing, upon formation of the hydrogen bonding. The structures, binding energies, and theoretical infrared spectra of the enflurane-acetone complexes were calculated by MP2 and B3LYP methods using the 6-311++G(d,p) basis set. The interaction energies were evaluated by the complete basis set limit (CBS) calculations at the HF, MP2, and CCSD(T) levels of theory. Although the MP2 method slightly overestimates the blue shifts, the MP2 predicted frequency difference and the relative IR intensities of two ν(C-H) stretching bands for the enflurane-acetone complexes show good agreement with experiment. Unfortunately, the B3LYP method predicts incorrect IR intensities of these hydrogen-bonded systems. The NBO analysis was performed to unravel the origin of the unusual intensity changes of two ν(C-H) stretching bands, in enflurane complexes.

Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study

The self-organized adenine ribbon is studied theoretically. The experimental evidence for the formation of such a ribbon has been found in the crystal structure of the supramolecular system [Dobrzyńska and Jerzykiewicz, J. Am. Chem. Soc., 2004, 126, 11118], and the striking structural feature is the fact that both the Watson-Crick and Hoogsteen faces of adenine are involved in the hydrogen bonding within the ribbon. The structure and physical properties of the monomer and five clusters of adenine (Ade)(n) (where n = 2, 3, 4, 5, 6) with AA2(2) configuration have been studied by means of the B3LYP, RI-TPSS, RI-TPSS-D (augmented with the dispersion term) and RI-MP2 methods using the 6-311+G(d,p), cc-pVTZ and TZVP basis sets. It is shown that among the investigated adenine clusters only the dimer has the planar structure. The evaluation of the three-body contribution to the total binding energy of adenine trimer has been performed at different levels of theory. All the methods consistently indicate that this term is positive and small (less than 0.5 kcal mol(-1)) which corresponds to a weak anti-cooperative effect, in adenine trimer. The differences between the total electronic energies obtained at the RI-TPSS/TZVP-D and RI-TPSS/TZVP levels of theory have shown that the London dispersion forces stabilize the adenine cluster containing 12 or more molecules by about -8 kcal mol(-1) per molecule. The results from the DFT symmetry adapted perturbation theory analysis have revealed that the contribution of dispersion to the binding energy of the adenine ribbon is about 25%.

Atypical calcium coordination number: Physicochemical study, cytotoxicity, DFT calculations and in silico pharmacokinetic characteristics of calcium caffeates.

Two complexes of calcium ions containing monodeprotonated caffeate ligands were synthesized and physicochemically (IR, FIR, NMR, thermal analysis) and theoretically (DFT and pharmacokinetical parameters) characterized. [Ca(C(9)H(7)O(4))(2)].2H(2)O 1a and [Ca(C(9)H(7)O(4))(2)].2H(2)O KNO(3)1b are compounds with unusual four coordinate calcium ion containing the ligand coordinated to the metal ion through two carboxylic groups arranged with tetrahedrally-like mode (CaO(4)). Two water molecules are outside the first coordination sphere bound non-equivalently to the ligand through a net of hydrogen bonding. The compounds were found to be cytotoxically inactive. Finally, in silico parameters predict the potential application of the compound as a supplement and/or drug.

On the nature of unusual intensity changes in the infrared spectra of the enflurane⋯acetone complexes

Recently, the blue-shifting hydrogen bonded complexes between enflurane and acetone have been investigated [W. Zierkiewicz, B. Czarnik-Matusewicz and D. Michalska, J. Phys. Chem. A, 2011, 115, 11362]. It has been shown that enflurane is a particularly interesting system due to its ability to form the blue-shifting C-H···O hydrogen bonded complexes accompanied by both a decrease and an increase of IR intensity of the corresponding ν(C-H) bands. In the current paper the origin of different intensity changes of the two C-H stretching vibrations in these complexes is elucidated based on solid quantitative grounds. The derivatives of the components of the dipole moment along the C-H stretching normal modes in the enflurane monomer and their changes upon complexation are discussed. Moreover, ten different exchange-correlation functionals were tested with regard to their performance in the prediction of IR intensity changes of the ν(C-H) stretching vibrations, in the title complexes.