PM3 Level Research Articles

Thermodynamic Analysis of Benzene Alkylation with Ethylene

Thermodynamic and kinetic regularities of benzene alkylation with ethylene in the presence of aluminium chloride with the methods of quantum chemistry were defined. The method used in this study is Semi-empirical method based on Neglecting of Diatomic Overlap approximation at PM3 level. All obtained data will be used for the mathematical model development of the considered process possessing high predictive potential.

Synthesis, characterization, biological studies, and molecular modeling of mixed ligand bivalent metal complexes of Schiff bases based on $N$-aminopyrimidine-2-one/2-thione

New mixed Schiff bases, Cu(II), Co(II), Ni(II), and Mn(II) complexes, were synthesized derived from 5-chloro-2-hydroxyacethophenone and 1-amino-5-benzoyl-4-phenyl-1H-pyrimidine-2-one/thione. These complexes were characterized by elemental analysis, magnetic measurements, molar conductivity, IR, electronic, NMR, and mass spectral studies. All the complexes showed nonelectrolytic behavior. Moreover, the newly synthesized mixed ligand complexes were evaluated for their in vitro antimicrobial efficiency against bacteria and yeast. The compound named Co(L$_{1}$L) had good antifungal activity against Candida species, but no profound antibacterial effect against bacterial strains. In addition, the ground state geometries of the complexes were optimized using a semi-empirical method at PM6 level, which is a suitable and effective basis set for organometallic and large structures to obtain information about their 3D geometries and electronic structures.

Spectral, Electrochemical and Molecular Orbital Studies on a New Solvatochromic Binuclear Mixed Ligand Copper(II) Complexes

A new series of solvatochromic binuclear mixed ligand complexes with the general formula: Cu2(DMCHD)(Am)2X3 (where, DMCHD: 5.5-Dimethyl cyclohexanate 1,3-dione, Am=N,N,N’-trimethylethylenediamine (Me3en), N,N,N’,N’- tetramethylethylenediamine (Me4en), or N,N,N’,N’,N’’-penta-methyldiethylenetriamine (Me5dien) and X=ClO4- or Clhave been synthesized and characterized by the analytical, spectral methods, magnetic and molar conductance as well as electrochemical measurements. The formation constant values for HDMCHD ligand with various metal ions are much lower than expected for similar β-diketones revealing a monobasic unidentate nature of this ligand. The d-d absorption bands of the prepared complexes in weak donor solvents suggest square-planar, distorted octahedral and/ or distorted trigonal bipyramid geometries for the perchlorate and chloride of diamine in addition to triamine complexes, respectively. However, an octahedral structure was identified for the complexes in strong donor solvents. Perchlorate of diamine complexes show a remarkable color change from violet to green as the Lewis basicity of the donor solvent or anions increases, whereas chloride complex is mainly affected by the Lewis acidity of the acceptor solvent. Specific and non-specific interactions of solvent molecules with the complexes have been investigated using the unified solvation model. Band’s oscillator strength of the d-d transition has been calculated and discussed. Cyclic voltammetric measurements on the prepared complexes in different solvents showed a quasi-reversible or irreversible and mainly diffusion controlled reduction process. Such behavior has been explained according to the EECE mechanism. A linear correlation has been found between the Cu(II) reduction potential and the spectral data. Structural parameters of the free ligands and their Cu(II)- complexes have been calculated on the basis of semiemperical PM3 level and correlated with the experimental data.

Reactivity and molecular modeling of new solvatochromic mixed-ligand copper(II) chelates of 2-acetylbutyrolactone and dinitrogen bases

A new series of solvatochromic mononuclear mixed ligand chelates with the general formula: Cu(AcBL)(L)X; where AcBL=2-acetylbutyrolactonate, L=N,N,N′,N′-tetramethylethylenediamine (Me4en), N,N,N′,N′-tetramethylpropylene diamine (Me4pn), 1,10-phenanthroline (Phen) or 2,2′-bipyridyl (Bipy) and X=ClO4−, NO3− or Br− have been synthesized and characterized by the analytical and spectral methods, as well as magnetic and molar conductance measurements. The d–d absorption bands of Me4en-chelates as Nujol mulls or weak donor solvents solutions revealed square-planar, distorted octahedral and/or distorted trigonal bipyramid geometries for the perchlorate, nitrate and bromide chelates, respectively. However, an octahedral structure is identified for chelates in strong donor solvents. Perchlorate chelates show a remarkable color change from violet to green as the Lewis basicity of the donor solvent increases, whereas bromide chelates are mainly affected by the Lewis acidity of solvent. Specific and non-specific interactions of solvent molecules with the chelates were investigated on the basis of unified solvation model. Structural parameters of the free ligands and their Cu(II)-chelates have been calculated on the basis of semiempirical PM3 level and correlated with the experimental data.

Spectroscopic, thermal, antimicrobial and molecular modeling studies of mononuclear pentafunctional Schiff base metal chelates derived from 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)-dione

A new pentafunctional N3O2 Schiff base, H2L ligand, and its metal chelates with Cu(II), Ni(II), Co(II), VO(IV), Zn(II), Cd(II), Ce(III), Cr(III), Fe(III) and UO2(VI) have been synthesized and characterized by elemental analysis, spectral, molar conductance, magnetic and thermal gravimetric studies. The results showed that the complexes have octahedral geometry except UO2 complex which has pentagonal bipyramidal arrangement. The TGA analyses suggest high stability for most complexes followed by thermal decomposition in different steps. The kinetic and thermodynamic parameters for decomposition steps of metal complexes thermograms have been calculated. Molecular orbital calculations were performed for the ligand and its metal complexes by means of hyperchem 7.52 program on the bases of semiempirical PM3 level and the results were correlated with the experimental data. The antimicrobial activity of the synthesized compounds were tested in vitro against some Gram-positive and Gram-negative bacteria; yeast and fungus strains and the results were discussed in terms of extended Lewis acid–base interactions.

Two-Photon Absorption Spectra Predicted by Semiempirical Methods

The molecular markers with large two-photon absorption cross-sections are highly sought for many applications, from photodynamic therapy to optical information processing. One may envision computational design of the chromophores combining desirable oneand two-photon absorption (1PA and 2PA) optical features with other properties important for the specific applications (solubility, toxicity etc.). Semiempirical methods are fast and seem to be well suited for the high throughput computational screening, which may be a part of such rational design strategy. Here we apply several semiempirical methods for prediction of 2PA spectra for substituted olygophenylvinylenes of donor-acceptor type. The predictions are compared to the experiment and previously reported results of the density functional theory (DFT) methods. We find ZINDO/S spectroscopic parameterization combined with single configuration interaction (CIS) method to perform far superior to the general purpose PM6 parameterization combined with various CI schemes. The poor performance in the prediction of 2PA cross-sections at PM6 level is traced to inaccurate excitation energies and incorrect transition dipoles between the 1PA and 2PA states. The state-to-state transition dipoles predicted by the ZINDO/S method are much better, as 2PA cross-sections reach the accuracy comparable to TD-DFT predictions after empirical corrections to the excitation energies. We conclude that semiempirical parameterizations can be used only for qualitative analysis of the 2PA properties. The excitation energies are in need of empirical correction, such as QSPR a linear regression for specific class of molecules. The ZINDO/S parameterization combined with multi-reference CI schemes (such as MR-CIS) could yield a good description of the intensities of 1PA and 2PA excitations, provided the right selection in reference configurations, order of excitation and active space. It can not be considered a black-box method, which makes it unsuitable choice for the high throughput screening technique.

Stereoselective Synthesis of cis,cis‐Configured Vicinal Triamines

AbstractThe first stereoselective synthesis of a cis,cis‐configured vicinal triamine was achieved, starting from N‐cyclohexenylpyrrolidone (10). The reaction sequence consists of the stereoselective construction of the trans‐configured 1,3‐diamide 14, trans‐to‐cis isomerization via enols or enamines, and subsequent highly stereoselective reduction of the intermediate imine 17D to the amine 18A. The postulated reaction pathway explains the observed stereoconvergence and is supported by calculation of the heats of formation of its intermediates at the PM3 level. LiAlH4 reduction of 18A yielded the tetracyclic aminal 19, which was converted into the pyrrolidinylquinoxaline 7, which showed low to moderate affinity towards κ and σ1 receptors.

Spectroscopic and biological studies of new binuclear metal complexes of a tridentate ONS hydrazone ligand derived from 4-amino-6-methyl-3-thioxo-3,4-dihydro-1,2,4-triazin-5(2H)-one and 4,6-diacetylresorcinol

The binuclear hydrazone, H2L, ligand derived from 4-amino-6-methyl-3-thioxo-3,4-dihydro-1,2,4-triazin-5(2H)-one and 4,6-diacetylresorcinol, in the molar ratio 2:1, and its copper(II), nickel(II), cobalt(II), zinc(II), cadmium(II), cerium(III), iron(III), oxovanadium(IV) and dioxouranium(VI) complexes have been synthesized. Structures of the ligand and its metal complexes were characterized by elemental analyses, spectral (infrared, electronic, mass, 1H NMR and ESR) data, magnetic susceptibility, molar conductivity measurements and thermal gravimetric analysis (TGA). The ligand acts as dibasic with two ONS tridentate sites. The bonding sites are the azomethine nitrogen, phenolate oxygen and sulfur atoms. The metal complexes exhibit different geometrical arrangements such as square planer, tetrahedral and octahedral. The Coats–Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. The ligand and its metal complexes showed antimicrobial activity towards Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), Gram-negative bacteria (Salmonella typhimurium and Escherichia coli), yeast (Candida albicans) and fungus (Aspergillus fumigatus). Structural parameters of the ligand and its metal complexes were theoretically computed on the basis of semiempirical PM3 level, and the results were correlated with their experimental data.

Spectroscopic study on encapsulation of two structurally similar donor–acceptor dyes in model cyclodextrin nanocavity

Encapsulation of two structurally similar donor–acceptor dyes in β-cyclodextrin (β-CD) nanocavity has been studied by steady state and time resolved fluorescence spectroscopic procedures. In the dye, (E)-2-((E)-3-(methyl(phenyl)amino)allylidene)-2,3-dihydro-1H-inden-1-one, the rotation about C–N bond is possible, while such a rotation is strategically restricted in the dye (E)-2-((1-methyl-3a,7a-dihydro-1H-indol-3-yl)methylene)-2,3-dihydro-1H-inden-1-one. Results indicate that both the dyes form complexes with β-CD but the stoichiometry and the nature of encapsulation are different. The dye in which the C–N bond rotation is permissible forms a 1:1 complex, with the acceptor centre (carbonyl group), rather than the donor centre (N atom) being encapsulated. The dye where the above mentioned rotation is restricted forms a 1:1 complex at a lower concentration of β-CD, encapsulating the donor centre (indole N). However, at a higher concentration of β-CD, 1:2 complex is formed involving both the acceptor and donor centres. Semi-empirical calculations at the PM3 level provide support to experimental findings. It is evidenced that the molecular structure of the guest is extremely important for encapsulation.

Structural, molecular orbital and optical characterizations of binuclear mixed ligand copper (II) complex of phthalate with N,N,N′,N′-tetramethylethylenediamine and its applications

A new binuclear mixed ligand complex, [Cu2(Phth)(Me4en)2(H2O)2(NO3)2]·H2O (where, Phth=phthalate, and (Me4en)=N,N,N′,N′tetramethylethylenediamine) was synthesized and characterized using analytical, spectral, magnetic, molar conductance, thermal gravimetric analysis (TGA), X-ray diffraction (XRD) and transmission electron microscope (TEM) measurements. The XRD data of Cu(II)-complex was analyzed on the basis of Williamson–Hall (W–H) and compared with TEM results. The results indicate that the complex is well crystalline and correspond to hexagonal crystal structure. Analysis of the absorption coefficient near the absorption edge reveals that the optical band gaps are indirect allowed transition with values of 1.17 and 1.78eV. The d–d absorption bands of the complex (dissolved in various solvents) exhibit a color changes (solvatochromic). Specific and non-specific interactions of solvent molecules with the complex were investigated using Multiple Linear Regression Analysis (MLRA). Transient photocurrent characteristics of Cu(II)-complex/n-Si heterojunctions indicate that photocurrent under illumination increase with increasing of light intensity and explained by continuous distribution of traps. Structural parameters of the free ligands and their Cu(II) – complex were calculated on the basis of semi-empirical PM3 level and compared with the experimental data. The present copper (II) complex was screened for its antimicrobial activity against some Gram-positive and Gram-negative bacteria and fungus strain.

Spectral characterization, molecular modeling and antimicrobial studies on hydrazone metal complexes of 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)dione and S-methyl dithiocarbazate

Metal complexes of copper(II), nickel(II), cobalt(II), oxovanadium(IV), chromium(III) and cadmium(II) with a new bridged ONS dibasic tridentate hydrazone (H2L) derived from 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)-dione with S-methyl dithiocarbazate have been synthesized and characterized by elemental analysis, molar conductance, magnetic susceptibility measurements, spectral (infrared, electronic, mass, 1H NMR and ESR) studies as well as thermal gravimetric analysis (TGA). The synthesized complexes have dimeric structures with the general formula [ML(NO3)m(H2O)x]2·nH2O·zMeOH, L=dianion of the hydrazone, m=0–1, x=0–2, n=0–4 and z=0–1. The metal complexes exhibited square planar, tetrahedral and octahedral geometrical arrangements, the molar conductivity data indicates that all complexes are neutral. The Coats–Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition stages of some complexes. Structural parameters of the ligand and its metal complexes have been theoretically computed on the basis of semiempirical PM3 level and the results were correlated with their experimental data. Antibacterial activities of the free ligand and its metal complexes were screened against various organisms.

Staudinger ligation towards cyclodextrin dimers in aqueous/organic media. Synthesis, conformations and guest-encapsulation ability.

β-Cyclodextrin (β-CD) dimers have been prepared using the bioorthogonal Staudinger ligation for the first time. In addition to a known linker, methyl 2-(diphenylphosphanyl)terephthalate, a doubly active linker was specifically developed that enabled connection of two β-CD units in a single step and in aqueous/organic media, under mild conditions and with good yields. A three-carbon spacer between the β-CD torus and the azido group was required for facile dimer formation. The products, as studied by NMR spectroscopy, were found to adopt closed conformations by intramolecular self-inclusion. On the other hand, association via intermolecular binding was also observed in aqueous solution, confirmed by DOSY NMR experiments. Despite self-inclusion, the β-CD cavities were capable of guest encapsulation, as shown by titration experiments: the binding constant with 1-adamantylamine was similar to that of natural β-CD. Theoretical calculations for isolated molecules (PM3 level of theory) and in the presence of solvent [water, PM3(COSMO)] as well as DFT calculations suggested that the compounds prefer to adopt conformations which bring the phenyl groups either inside the β-CD cavity (inclusion) or over its narrow side (vicinal). Thus, Staudinger ligation could be the method of choice for linking CDs exhibiting (i) ease of preparation in aqueous media, in short steps, under mild conditions and in good yields, (ii) satisfactory aqueous solubility and independent binding capacity of the cavities.

Fast method for quantum chemical calculations of large molecules with the approximation of the DFT Hamiltonian

The fundamentally new method NESE is proposed for quantum chemical calculations of large molecules, which employs the approximation of the Hamiltonian of the commonly used DFT method and is as fast as the AM1 and PM3 semi-empirical methods or the DFTB method. The parameters for the new method were chosen by the least-squares method based on the comparison of its matrix elements with the reference DFT/PBE Hamiltonian. The initial non-iterative version NESE-0 was computer-implemented and approved on many thousands of various molecules containing H, C, N, and O atoms. The NESE-0 method moderately outperforms the DFTB approach and is an order of magnitude better than the AM1, PM3, and PM6 levels in reproducing the one-electron energies calculated in terms of the DFT/PBE.

Structural Characterization of Heavy Metal Toxicity in a Human DNA Repair Glycosylase

The DNA base excision repair pathway consists of several enzymes, some of which require metal cations for catalysis. Human Uracil DNA Glycosylase (hUNG), a DNA glycosylase responsible for the initial detection and removal of carcinogenic lesions from DNA, is a non-metal requiring enzyme. Using biochemical assays we showed that cadmium II (Cd), a known human carcinogen, inhibits hUNG activity in the micromolar range. To provide mechanistic insights for metal enzyme interactions, we employed computational approaches based on MD and QM calculations. Initially, our 1 μs explicit solvent Molecular Dynamics simulations using the AMBER force field showed Cd entering the hUNG pocket, interacting with the catalytic D64 residue. Subsequent simulation at the PM3 level showed that Cd additionally interacts with H67 and the peptide oxygen of P65 in the presence of a chloride ion. This position effectively replaces the catalytic water essential for hUNG activity. Further quantum mechanical refinement using M06L/QZVP ONIOM of Gaussian 09 on structures obtained from the PM3 simulations produced two distinct geometries of Cd in coordination 5. Both hUNG-Cd complexes are in agreement with metal sites found in a recent database of protein-metal complexes (MetalPDB). This work for the first time demonstrates a possible binding interaction between hUNG and toxic metal. In concert with our biochemical data we propose that metal inhibition of hUNG is due to replacement of the catalytic water, where a stable metal complex forms and prevents catalysis. The inhibition of hUNG by Cd will enhance the mutagenic and carcinogenic potentials of a variety of parental genotoxic compounds.

Computational Studies of 1,3-Dipolar [3 + 2]-Cycloaddition Reactions of Fullerene-C60 with Nitrones

Solubility of fullerene-C60 improves with functionalization. 1,3-dipolar [3+2]-cycloaddition reactions of fullerene-C60 with substituted nitrones, a versatile method for fullerene functionalization, were investigated at the MO6/6-31G*//PM3 level of theory to elucidate the effect of electron-releasing (-CH3, -CH2CH3, -CH2CH2CH3, C6H5CH2) substituents and electronwithdrawing substituents (-F, -Cl, -Br, -NC, and -NO2) on the energetics of the reaction; the regio- and stereo-selectivity of the mono- and bis-addition of nitrones; and global reactivity descriptors of the molecular systems to rationalize and predict their chemical reactivity and site selectivity. The results show that electron-withdrawing groups on the nitrones increase the activation barrier of the reaction whereas electron-donating groups decrease the activation barriers. However, electron-withdrawing groups on the nitrones result in more stable products compared to the electron-donating groups. It was found that the reactions with electron-donating substituents on the nitrone are normal electron demand reactions, with C60 as the dipolarophile and the substituted nitrones as the dipoles while the reactions with electron-withdrawing substituents on the nitrones are inverse electron demand reactions. The chemical hardness values show greater positive values for adducts with electron-withdrawing substituents on the nitrone and smaller negative values for adducts with electron-donating substituents on the nitrone, confirming the trend that larger activation barriers accompany reactions with electron-withdrawing substituents on the nitrone while electron-donating substituents lower activation barriers. The activation barriers of the second nitrone addition (bisadduct formation) were found to be lower than the barriers for the first nitrone addition (monoadduct formation). Stereo-chemically, syn-bisaddition was found to be thermodynamically and kinetically stable favoured over anti-bisaddition. Electron donating and electron-withdrawing substituents have a marked effect on the energetics of the reaction.

Structural, molecular orbital and optical characterizations of solvatochromic mixed ligand copper(II) complex of 5,5-Dimethyl cyclohexanate 1,3-dione and N,N,N′,N′N″-pentamethyldiethylenetriamine

In this work, a new solvatochromic mononuclear mixed ligand complex with the formula, Cu(DMCHD)(Me5dien)NO3 (where, DMCHD=5,5-Dimethyl cyclohexanate 1,3-dione and (Me5dien)=N,N,N′,N′N″-pentamethyldiethylenetriamine was synthesized and characterized by analytical, spectral, magnetic, molar conductance, thermal gravimetric analysis (TGA), X-ray diffraction (XRD) and transmission electron microscope (TEM) measurements. The formation constant-value for copper (II)-DMCHD was found to be much lower than the expected for similar β-diketones, revealing monobasic unidentate nature of this ligand. The d–d absorption bands of the prepared complex exhibit a color changes in various solvent (solvatochromic). Specific and non-specific interactions of solvent molecules with the complex were investigated using Multi Parametric Linear Regression Analysis (MLRA). Structural parameters of the free ligands and their Cu (II) – complex were calculated on the basis of semi-empirical PM3 level and compared with the experimental data. The crystallite size and morphology of Cu(DMCHD)(Me5dien)NO3 were examined using XRD analysis and TEM, revealing that the complex is well crystalline and correspond to the monoclinic crystal structure. The lattice strain and mean crystallite size were estimated by Williamson–Hall (W–H) plot using X-ray diffraction data. The main important absorption parameters such as extinction molar coefficient, oscillator strength and electric dipole strength of the principal optical transitions in the UV–Vis region were calculated. The analysis of absorption coefficient near the fundamental absorption edge reveals that the optical band gaps are direct allowed transitions with values of 2.78eV and 3.59eV. The present copper (II) complex was screened for its antimicrobial activity against Staphylococcus Aureus and Bacillus Subtilis as Gram-positive bacteria, Escherichia Coli and Salmonella Typhimurium as Gram-negative bacteria and Candida Albicans as fungus strain.

Synthesis, spectral characterization, molecular modeling and antimicrobial activity of new potentially N2O2 Schiff base complexes

Metal complexes of a new potentially tetradentate symmetrical Schiff base ligand (H2L) with Cu(II), Ni(II), Co(II), VO(IV), Zn(II), Cd(II), Ce(III), Fe(III) and UO2(VI) metal ions have been synthesized and characterized based on their elemental analyses, spectral (IR, UV–Vis, 1H NMR and mass spectra), magnetic and molar conductance studies as well as thermal gravimetric analysis (TGA). The synthesized complexes have the general formula [MHxL(H2O)yXn]: x=0–1, y=0–4 and n=0–1; where: L=dianion of 6-hydroxy-5-[N-(2-{[(1E)-1-(6-hydroxy-2,4-dioxo-3,4-dihydro-2H-1,3-thiazin-5-yl)ethylidene]amino}ethyl) ethanimidoyl]-2H-1,3-thiazine-2,4(3H)-dione and X=nitrate or sulphate anion. The ligand behaves as diabasic tetradentate N2O2 sites, except in cases of Co(II), VO(IV) and UO2(VI) metal ions, it behaves as monobasic tetradentate Schiff base ligand. The metal complexes exhibited square planar, square-pyramidal and octahedral geometrical arrangements except for Ce(III) and UO2(VI) complexes, they are octa-coordinated. The Coats-Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition stages of some complexes. Structural parameters of the ligand and its metal complexes have been theoretically computed on the basis of semiemperical PM3 level, and the results were correlated with their experimental data. The antimicrobial activities of the ligand and its metal complexes were tested against some Gram-positive and Gram-negative bacteria; and fungus strain and the results were discussed.

Variability of phenological stages of Dactylis glomerata in dependence on meteorological conditions in the Czech Republic

pressure (SLP) and 500 hPa geopotential height pattern over Europe on days with high concentration of ragweed pollen in Poznan in years 1996-2010. Methods: Ambrosia pollen data was collected by Hirst-type volumetric spore trap. Pollen grains were counted under the optical microscope (magni cation: 400x) and expressed as P m-3. Daily pollen concentrations were clustered in three intervals: low ( 30 Pm3) levels. For days attributed to these groups, synoptic charts were created on the basis of see level pressure (SLP) records from NCEP/NCAR reanalysis [2]. In addition, maps of 500 hPa geopotential heights were constructed. e method of interpolation was kriging. Results: Overall, 206, 23 and 17 days with low, medium and high concentration of ragweed pollen (respectively) were recorded in Poznan in years 1996-2010. Synoptic charts showed (Fig. 1) that during days with high pollen count of Ambrosia in Poznan the high pressure center was located in the area of northern Belorussia. e lowest pressure center was located over Iceland and the Atlantic Ocean in the south of the Iceland. As the geostrophic wind is parallel to the isobars and approximately determines the air mass transfer, it can be concluded that presented pressure pattern causes the air motion exactly from the Pannonian Plain to Poland, with south-east direction. Conclusions: e mechanism of long-range transport of Ambrosia pollen from Balkans to Poland highlighted by Sikoparija et al. [1] seems to be valid in all days with high concentrations of Ambrosia pollen in Poznan, 1996-2010. Averaged synoptic charts con rm that the air mass transport occurs from southeast to northwest with the strong high pressure center over Belorussia. When that pressure pattern is observed in weather forecast during August or September there is a possibility to record Ambrosia pollen in Poznan.

The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties

A new Web application called The Molecule Calculator (MolCalc) is described. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats of formation and other thermodynamic properties, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies. These properties are computed using the GAMESS program at either the RHF/STO-3G (orbitals and orbital energies) or PM3 level of theory (all other properties) in a matter of seconds or minutes depending on the size of the molecule. The results, though approximate, can help students develop a chemical intuition about how molecular structure affects molecular properties, without performing the underlying calculations by hand, a nearly impossible task for all but the simplest chemical systems.

Conformational studies of diosgenyl 2-amino-2-deoxy-β-d-glucopyranosides at the PM3 and DFT levels of theory

Geometry optimizations at the PM3 level were performed for diosgenyl 2-amino-2-deoxy-β-d-glucopyranoside and its N-protonated form. Next, B3LYP/6-311++G∗∗ level geometry optimizations were carried out, albeit on a simpler model. The relative Gibbs free energies and geometry parameters are presented for the optimized structures. Conformational analysis concerning the clockwise (cw) and counterclockwise (ccw) arrangements of the OH groups as well as the three orientations of the NH2 and CH2OH groups was performed. Furthermore, a full scan of all the possible locations of the diosgenyl moiety in relation to the sugar ring in the target compounds was done. The PM3 optimization results indicate that diosgenyl 2-amino-2-deoxy-β-d-glucopyranoside exists as a mixture of many rotamers. Of these, ccw conformers as well as the −ac orientation of the aglycone (ca −100° for torsion angle ϕ) are preferred. In the case of the N-protonated glucoside one rotamer is dominant in the mixture (population>60%). Only the cw arrangement is stable in the protonated form, because of steric and electronic repulsion between the charged ammonium group and the hydrogen atom of the neighbouring 3-OH group. The gauche-trans (gt) orientation of the CH2OH group is favourable to both neutral and protonated forms of diosgenyl glucosides at the PM3 level. DFT studies also predict conformational mixtures for both neutral and protonated forms of simplified diosgenyl 2-amino-2-deoxy-β-d-glucopyranosides. These investigations showed unequivocally the preference for the ccw arrangement over cw, and that values of angle ϕ concur with the exo-anomeric effect. The B3LYP functional predicts the greater stability of the gt and tg orientations for the neutral and protonated analogues respectively. According to both PM3 and B3LYP calculations, torsion angle ψ has only a minor influence on the conformational energy. The importance of the geometry parameters affecting the stability of these conformers appears to be as follows: angle ϕ≈NH2/ccw/cw>gg/gt/tg>angle ψ.