Solid state characterization of an antioxidant alkaloid boldine using vibrational spectroscopy and quantum chemical calculations

Boldo (Peumus boldus Mol.), a Chilean tree traditionally employed in folk medicine and recognized as a herbal remedy in a number of pharmacopoeias, mainly for the treatment of liver ailment, has recently been the subject of increasing attention. Boldine, in particular, the major and most characteristic alkaloid constituent of this plant species, now emerges as its most interesting active principle from the pharmacological viewpoint.In the present work the structural and spectral characteristics of boldine have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and infrared spectra of boldine molecule.     

Structure and vibrational modes of AgI-doped AsSe glasses: Raman scattering and ab initio calculations

We report an investigation of the structure and vibrational modes of (AgI)_x (AsSe)_100−x, bulk glasses using Raman spectroscopy and first principles calculations. The short- and medium-range structural order of the glasses was elucidated by analyzing the reduced Raman spectra, recorded at off-resonance conditions. Three distinct local environments were revealed for the AsSe glass including stoichiometric-like and As-rich network sub-structures, and cage-like molecules (As₄Se_n, n=3, 4) decoupled from the network. To facilitate the interpretation of the Raman spectra ab initio calculations are employed to study the geometric and vibrational properties of As₄Se_n molecular units that are parts of the glass structure. The incorporation of AgI causes appreciable structural changes into the glass structure. AgI is responsible for the population reduction of molecular units and for the degradation of the As-rich network-like sub-structure via the introduction of As-I terminal bonds. Ab initio calculations of mixed chalcohalide pyramids AsSe_mI_3−m provided useful information augmenting the interpretation of the Raman spectra.     

Conformational study of lanthanide(III) complexes of N-(2-salicylaldiminatobenzyl)-1-aza-18-crown-6 by using X-ray and ab initio methods

A structural study of lanthanide complexes with the deprotonated form of the monobracchial lariat ether N-2-salicylaldiminatobenzyl-aza-18-crown-6 (L⁴) (Ln = La(III)–Tb(III)) is presented. Attempts to isolate complexes of the heaviest members of the lanthanide series were unsuccessful. The X-ray crystal structures of [Pr(L⁴)(H₂O)](ClO₄)₂ · H₂O · C₃H₈O and [Sm(L⁴)(H₂O)](ClO₄)₂ · C₃H₈O show the metal ion being bound to the eight donor atoms of the ligand backbone. Coordination number nine is completed by the oxygen atom of an inner-sphere water molecule. Two different conformations of the crown moiety (labelled as A and B) are observed in the solid state structure of the Pr(III) complex, while for the Sm(III) complex only conformation A is observed. The complexes were also characterized by means of theoretical calculations performed in vacuo at the HF level, by using the 3-21G^∗ basis set for the ligand atoms and a 46 + 4fⁿ effective core potential for lanthanides. The optimized geometries of the Pr(III) and Sm(III) complexes show an excellent agreement with the experimental structures obtained from X-ray diffraction studies. The calculated relative energies of the A and B conformations for the different [Ln(L⁴)(H₂O)]²⁺ complexes (Ln = La, Pr, Sm, Ho or Lu) indicate a progressive stabilization of the A conformation with respect to the B one upon decreasing the ionic radius of the Ln(III) ion. For the [Ln(L⁴)(H₂O)]²⁺ systems, most of the calculated bond distances between the metal ion and the coordinated donor atoms decrease along the lanthanide series, as usually observed for Ln(III) complexes. However, our ab initio calculations provide geometries in which the Ln–O(5) bond distance [O(5) is an oxygen atom of the crown moiety] increases across the lanthanide series from Sm(III) to Lu(III).     

Ab initio calculation of the band structure of some boron polymers

Ab initio calculations using a STO-3G basis set have been performed on the polymer systems (HBX) _n where X = Be, BH, CH₂, NH, and O. Energy band diagrams and accompanying density-of-states plots have been obtained. The highest filled orbital of (HBNH) _n and (HBO) _n occurs at the X-point and possesses character while the - framework orbital at the X- point is the highest filled level for (HBBe) _n , (HBBH) _n , and (HBCH₂) _n . The conduction band for all five species has symmetry and the band gap of the (HBX) _n species increases in the order X = Be < BH < NH < O < CH₂. An estimate of the energy of polymerisation of the (HBX) _n systems suggests that HBNH is particularly stabilised by polymerisation. The electron distribution in (HBBe) _n shows a - electron drift towards boron, while in the other four systems the net electron transfer is directed away from boron. There is significant electron back-donation to boron in (HBO) _n and (HBNH) _n .     

Structural, electronic properties and inter-atomic bonding in layered chalcogenide oxides LaMChO (where M = Cu, Ag, and Ch = S, Se) from FLAPW-GGA calculations

Using the first principles FLAPW-GGA method, comparative study of structural, electronic properties and of chemical bonding in four 1111-like chalcogenide oxides LaMChO (LaCuSO, LaCuSeO, LaAgSO, and LaAgSeO) with ZrCuSiAs-type structure was performed. Our studies showed that: (i) replacements of d metal atoms (Cu ↔ Ag) and chalcogen atoms (S ↔ Se) lead to anisotropic deformations of the crystal structure; this effect is related to strong anisotropy of inter-atomic bonds; (ii) all of the examined chalcogenide oxides are semiconducting; the band gap decreases both at S → Se and Cu → Ag substitutions; and (iii) the bonding in LaMChO phases can be classified as a high-anisotropic mixture of ionic and covalent contributions, where mixed covalent-ionic bonds take place inside [La₂O₂] and [M₂Ch₂] blocks, whereas between the adjacent [La₂O₂]/[M₂Ch₂] blocks, ionic bonds emerge owing to [La₂O₂] → [M₂Ch₂] charge transfer. Since the near-Fermi bands of LaMChO phases originate mainly from electronic states of [M₂Ch₂] blocks, we speculate that chemical substitutions inside these blocks can result in striking differences in electronic properties of these systems; therefore, this approach can be promising for significant enlargement of the functional properties of these materials.     

The influence of the ligand structure on activation of hafnocene polymerization catalysts: A theoretical study

The influence of ligand structure of hafnocenes on activation of the polymerization catalysts has been studied by quantum chemical methods. Altogether 54 hafnocenes were included in the analysis, supplemented by four zirconocenes for comparison. The trends in structural and electronic parameters relevant in the catalyst activation step were studied for the dichloride, dimethyl and cationic monomethyl forms of the catalysts. The effects of ligand modifications were analyzed as functions of the metal, ancillary cyclopentadienyl-based ligand, ligand substituent and the ligand bridge, making comparisons to experimental data. Generally, large aromatic ligands together with electron donating ligand substituents stabilize the catalytically active species, thus facilitating the catalyst activation process. The obtained trends are expected to aid in the development of new high-performance polymerization catalysts.     

Theoretical investigations of the elastic,electronic, optical and thermodynamics properties of SrSi

The crystal structural, electronic, optical and thermodynamic properties of SrSi are investigated by using the first-principles plane-wave pseudopotential density function theory within the generalized gradient approximation (GGA). We have calculated the ground states properties and they are in good agreement with the available experimental data and other theoretical results. We have obtained the electronic structure and density of states, and the results showed that both of Immm and Cmcm phases are metal material. The elastic properties such as elastic constants, shear modulus, Young's modulus and Poisson's ratio are obtained for the first time. Furthermore, the optical properties are reported for radiation up to 30 eV. Finally, the thermodynamic properties of Cmcm phase such as free energy, entropy, enthalpy, heat capacity and Debye temperature are given for reference.     

Structural and physical properties of the new intermetallic compound Yb3Pd2Sn2

The crystal structure of the ternary intermetallic compound Yb₃Pd₂Sn₂ has been determined ab initio from powder X-ray diffraction data. The compound crystallizes as a new structure type in the orthorhombic space group Pbcm and lattice constants a=0.58262(3), b=1.68393(8), c=1.38735(7) nm. Yb₃Pd₂Sn₂ is composed of a complex _∞[Pd₂Sn₂]^δ− polyanionic network in which the Yb ions are embedded. A comparison between this structure and those of Eu₃Pd₂Sn₂ and Ca₃Pd₂Sn₂, other novel polar intermetallic compounds, was made. DC susceptibility and ¹⁷⁰Yb Mössbauer spectroscopic measurements indicate a close-to divalent Yb behavior. Moreover, a hybridization between 4f and conduction electrons is suggested by electronic structure calculations and heat capacity measurements.     

Nature of the chemical bond and prediction of radiation tolerance in pyrochlore and defect fluorite compounds

The radiation tolerance of synthetic pyrochlore and defect fluorite compounds has been studied using ion irradiation. We show that the results can be quantified in terms of the critical temperature for amorphization, structural parameters, classical Pauling electronegativity difference, and disorder energies. Our results demonstrate that radiation tolerance is correlated with a change in the structure from pyrochlore to defect fluorite, a smaller unit cell dimension, and lower cation-anion disorder energy. Radiation tolerance is promoted by an increase in the Pauling cation-anion electronegativity difference or, in other words, an increase in the ionicity of the chemical bonds. A further analysis of the data indicates that, of the two possible cation sites in ideal pyrochlore, the smaller B-site cation appears to play the major role in bonding. This result is supported by ab initio calculations of the structure and bonding, showing a correlation between the Mulliken overlap populations of the B-site cation and the critical temperature.     

New type dithiolene complex based on 4,5-(1,4-dioxane-2,3-diyldithio)-1,3-dithiol ligand: Synthesis,experimental and theoretical investigation

A new Nickel complex with an extended multisulfur dithiolene ligand Ni(edodddt)₂ (edodddt = 2,3,4α,8α-tetrahydro-dithiine [2,3-b] [1,4] dioxo-6,7-dithiolene) has been synthesized and characterized by electrochemical measurements, IR, UV–Vis and NMR spectroscopy. Its crystal structure was resolved by X-ray diffraction on a single crystal. DFT calculations were made in order to compare the results with the experimental findings and gain an insight of the properties of this new dithiolene complex.     

A fluoroaryl substituent with spectator function: Reactivity and structures of cyclic and acyclic HF4C6-substituted phosphanes

The reactivity of a series of phosphanes with a fluoroaryl group (HF₄C₆-) carrying a spectator function in para position has been explored with respect to the formation of low coordinated and phosphorus rich phosphanes. An asymmetric diphosphene has been indentified as an intermediate in the synthesis of a linear 1,3-dihydrophosphane, while the symmetric diphosphene undergoes 2 + 2 cycloaddition under formation of the corresponding cyclotetraphosphetane for which a crystal structure could be obtained. Attempts to synthesize HF₄C₆-substituted iminophosphanes generally failed, which is attributed to the electronic nature of the corresponding precursors as suggested by quantum chemical calculations.     

P-C bond formation via P-H addition of a fluoroaryl phosphinic acid to ketones

The synthesis, structure and reactivity of the fluoroaryl phosphinic acid HF₄C₆-P(O)HOH is reported and compared to a sterically comparable yet non-fluorinated analog with similar size. The fluoroaryl phosphinic acid undergoes reversible P-H addition to the carbonyl functionality of ketones under formation of a P-C bond which is retained in the resulting α-hydroxy phosphinic acid. The latter shows an extended 2D hydrogen bonded network in the solid state.     

Theoretical calculation of the low-lying sextet electronic states of CrF molecule

The potential energy curves have been investigated for the 12 lowest sextet electronic states in the ^2s+1Λ^(±)${}^{2s+1}{\mathrm{\Lambda }}^{(\pm )}$ representation below 53,000 cm⁻¹ of the molecule CrF via CASSCF and MRCI (single and double excitation with Davidson correction) calculations. Seven electronic states have been studied theoretically for the first time. The harmonic frequency ω_e, the internuclear distance R_e, the rotational constant B_e, the electronic energy with respect to the ground state T_e, and the permanent dipole moment μ have been calculated. By using the canonical functions approach, the eigenvalues E_v, the rotational constant B_v and the abscissas of the turning points R_min and R_max have been calculated for the considered electronic states up to the vibrational level v = 39. The comparison of these values to the theoretical and experimental results available in the literature shows a good agreement.     

Conformational study of a strained tolanophane by dynamic 1H NMR spectroscopy and computational methods

The existence of a short C–H ⋯ π (alkyl–alkyne) interaction in the structure of a strained and relatively rigid tolanophane is expected to hinder the rotation about the C–C sp³ single bond. Variable-temperature NMR experiments (performed in three solvents, CDCl₃, THF-d₈, and acetone-d₆) and ab initio density functional calculations were carried out to investigate its dynamic nature. An energy barrier of 48.6 kJ/mol is determined at coalescence (210 K) with acetone-d₆ which is in good agreement with calculation result (54 kJ/mol). Correspondence: Hossein Reza Darabi, Chemistry and Chemical Engineering Research Center of Iran, Pajoohesh Blvd., km 17, Karaj Hwy, 14968-13151 Tehran, Iran.     

A Theoretical and Experimental Study of the Interaction of C6F6 with Electron Donors

The NMR effects produced on the nitrogen absolute shieldings in a series of electron donors when they interact with hexafluorobenzene, C₆F₆, have been theoretically studied. The complexes have been optimized at the B3LYP/6-311++G** level and the NMR shieldings have been calculated using the GIAO method. The results obtained have allowed devising an experiment (C₆F₆···NCCH₃ complex) that is compatible with the theoretical calculations.     

Theoretical study on singlet oxygen adsorption onto surface of graphene-like aromatic hydrocarbon molecules

Recently, graphene sheet is one of interesting systems to realize novel electronic properties. Especially, interaction between graphene and adsorbed oxygen molecule is very important to control electronic condition. In this paper, we employed some aromatic hydrocarbons as simple systems of graphene sheet and ab initio MO calculations were carried out to investigate inter-molecular interaction. It is found that not triplet but singlet O₂ molecule have potential of chemisorption onto graphene surface. From the calculated potential energy surface (PES) for distance between benzene and O₂ molecules, meta-stable structure is found at about 1.5 Å with potential barrier. In the optimized structure of its meta-stable state, structural strain can be relaxed through bending of planer benzene ring. Its energy is estimated at 70.10 kcal/mol for benzene. We also estimated the strain effects for naphthalene and pyrene molecules as larger case of graphene and they were 80.85 and 72.45 kcal/mol, respectively.     

Ab initio study on structure and phase transition of A- and B-type rare-earth sesquioxides Ln2O3 (Ln=La-Lu, Y, and Sc) based on density function theory

Ab initio energetic calculations based on the density functional theory (DFT) and projector augmented wave (PAW) pseudo-potentials method were performanced to determine the crystal structural parameters and phase transition data of the polymorphic rare-earth sesquioxides Ln₂O₃ (where Ln=La-Lu, Y, and Sc) with A-type (hexagonal) and B-type (monoclinic) configurations at ground state. The calculated results agree well with the limited experimental data and the critically assessed results. A set of systematic and self-consistent crystal structural parameters, energies and pressures of the phase transition were established for the whole series of the A- and B-type rare-earth sesquioxides Ln₂O₃. With the increase of the atomic number, the ionic radii of rare-earth elements Ln and the volumes of the sesquioxides Ln₂O₃ reflect the so-called “lanthanide contraction”. With the increase of the Ln³⁺-cation radius, the bulk modulus of Ln₂O₃ decreases and the polymorphic structures show a degenerative tendency.     

Thermodynamic properties of caffeine: Reconciliation of available experimental data

Molar enthalpies of sublimation of two crystal forms of caffeine were obtained from the temperature dependence of the vapour pressure measured by the transpiration method. A large number of primary experimental results on the temperature dependences of vapour pressure and phase transitions have been collected from the literature and have been treated in a uniform manner in order to derive sublimation enthalpies of caffeine at T = 298.15 K. This collection together with the new experimental results reported here has helped to resolve contradictions in the available sublimation enthalpies data and to recommend a consistent and reliable set of sublimation and formation enthalpies for both crystal forms under study. Ab initio calculations of the gaseous molar enthalpy of formation of caffeine have been performed using the G3MP2 method and the results are in excellent agreement with the selected experimental data.     

Crystal structure and ab initio calculations of a cyano-carbamimidic acid ethyl ester

The structure of one tautomer (amine form) of cyano-carbamimidic acid ethyl ester or (amino-ethoxy-methylidene)aminoformonitrile (CAS: 13947-84-7) was determined by single crystal X-ray diffraction. Ab initio quantum chemical calculations at the B3LYP, MP2 and G3 levels were performed to investigate the stability and the formation of the different tautomers and conformers. The calculations indicate that the amine form is the more stable tautomer, showing a high degree of electron conjugation. The most stable amine conformer located by the calculations corresponds to the crystallized structure. On the contrary, in the less stable imine form, the conjugation is separated by a N2–C2 single bond.     

Theoretical studies on quinones I. The structure of p-benzoquinone and two of its excited triplet states

Ab initio calculations on the ground and two excited triplet states (³B_1g and ³B_1u) of p-benzoquinone are described. The geometries of the three states were fully optimised at the SCF level using the 3-21G basis set. For the excited states, both D_2h and C_2v geometries were investigated. Comparison was made between UHF and ROHF levels of theory.