Geometrical and electronic structure of LaI3 molecule from the gas electron diffraction data and quantum chemical calculations

The saturated vapor over LaI₃ has been studied using the electron diffraction method with mass-spectral monitoring. It was determined that at a temperature 1142(10) K, along with monomer molecules, dimers are present in the vapor in the quantity of 0.7 mol.%. Effective configuration parameters of LaI₃ molecule were obtained: r _g(La-I) 2.961(6) Å, ∠_g(I-La-I) 116.5(9)°, l(La-I) 0.106(1) Å and l(I…I) 0.412(7) Å. A small deviation of the valence angle ∠_g(I-L-I) from 120° can be totally caused by a contraction effect of the distance r _g(I…I) of LaI₃ molecule with planar equilibrium configuration. The electronic structure of LaI₃ molecule was examined by the B3LYP/SDD method. In terms of the NBO-analysis, the participation of lanthanum 4f-AO in bonding orbitals La-I is noted. It is shown that the NBO-analysis describes the bond La-I in LaI₃ molecule as predominantly ionic one with a noticeable covalence component. The energy of the heterolytic bond breakage E(La-I)_het = 1216 kJ/mole was calculated.     

Molecular structure of p-diisocyanobenzene from gas-phase electron diffraction and theoretical calculations and effects of intermolecular interactions in the crystal on the benzene ring geometry

In this study, the molecular structure of p-diisocyanobenzene has been determined by gas-phase electron diffraction and quantum chemical calculations. The electron diffraction intensities from a previous study by Colapietro et al. (J Mol Struct 125:19–32, 1984) have been reanalyzed using geometrical constraints and initial values of vibrational amplitudes from computations. The equilibrium structure of the molecule has D _2h symmetry, whereas the average geometry in the gaseous phase is best described by a non-planar model of C _2v symmetry. The lowering of symmetry is due to large-amplitude motion of the substituents out of the plane of the benzene ring. The non-planar model has an internal ring angle at the ipso position, ∠_aC2–C1–C6 = 120.6 ± 0.2°, about 1° smaller than that from the previous study, but consistent with the quantum chemical calculations. The mean length of the ring C–C bonds and the length of the triple bond are accurately determined as 〈r _g(C–C)〉 = 1.398 ± 0.003 Å and r _g(N≡C) = 1.177 ± 0.002 Å, respectively. Comparison with the gaseous isoelectronic molecules p-diethynylbenzene and p-dicyanobenzene shows that the differences in the mean lengths of the ring C–C bonds and in the lengths of the triple bonds determined by electron diffraction are equal or closely similar to the corresponding differences from quantum chemical calculations. The present experimental value of the ipso angle in free p-diisocyanobenzene is slightly, but significantly smaller than that obtained by X-ray crystallography. The difference is confirmed by computational modeling of the crystal structure and appears to be due to –N≡C···H–C intermolecular interactions in the crystal.     

Efforts toward developing direct probes of protein dynamics

We report the first IR characterization of a single C-D bond within a protein, methyl-d1 Met80 of horse heart cytochrome c. A comparison was made to methyl-d1/d3 methionine as well as methyl-d3 Met80. We found that for methyl-d1 and the asymmetric stretches of methyl-d3, line widths/line shapes are dominated by inhomogeneous broadening, whereas the symmetric stretch of methyl-d3 has a significant homogeneous component. Vibrational energy relaxation calculations found that a significantly stronger Fermi resonance exists for the symmetric stretch than for the asymmetric stretches, thereby suggesting that a difference in intramolecular vibrational relaxation (IVR) causes the observed line width/line shape difference between the symmetric and asymmetric stretches.     

Crystal structure of three solvated Alpinumisoflavones

Single crystals of alpinumisoflavone, C₂₀H₁₆O₅, {systematic name: 5-hydroxy-7-(4 hydroxyphenyl)-2, 2-dimethyl-2H, 6H-benzo [1, 2-b: 5, 4-b′]-dipyran-6-one}, solvated with water, methanol, and ethanol, have been obtained. The incorporation of the solvent molecules into the crystal structure creates a new short inter-molecular O–H···O and C–H···O contacts between the alpinumisoflavone moiety and its solvate molecule. The temperatures at which the solvated molecules lose their solvent molecules are 53, 54, and 65 °C for water, methanol, and ethanol, respectively. The observed temperatures at which the solvates efflorescence are reflective of the progressive increase in mass of the solvates from water to ethanol in the series. The benzopyrone moiety shows the usual planar conformation with the pyran ring deformed into a half-chair conformer as seen previously in the other analogous compounds with puckering parameters [Å], 0.2656(8), 0.3703(8), and 0.3957(9), respectively, for the water, ethanol, and methanol solvates. These are higher than the non-solvated alpinumisoflavone compound previously studied. The size of a substituent group proximal to the keto group has a more pronounced effect on the degree of puckering than substitution on the terminal phenyl ring. The attached phenyl ring shows consistent out-of-plane twist from the mean plane of the benzopyrone system as observed previously for this class of compounds. The observed dihedral angles are 30.26(3), 37.75(3), and 34.00(3)°, respectively, for the water, methanol, and ethanol solvates.     

Rearrangement of Langmuir-Blodgett stearic acid films and band assignments in deuterated stearic acid monolayers

Band assignments in the C-D stretching region of straight chain hydrocarbon species are derived from the spectra of stearic acid monolayers on gold. The fatty acid molecules reorient with respect to the metal surface as the films age. Correlating the changes in the IR spectra of both the undeuterated and deuterated acids allows one to identify the vibrational modes of the latter based on the accepted assignments of the former. The CD₂ asymmetric and symmetric stretches are observed at 2194 and 2086 cm^–1, respectively. Bands at 2212 and 2221 cm^–1 are attributed to asymmetric in-plane and out-of-plane CD₃ stretches. Assignments of several other features in this region are given while one band remains unassigned.     

Synthesis,spectral, and thermal properties,and crystal structure of cobalt (III) complex derived from Imazameth

A novel metal–organic coordination compound [Co(Imazameth)₃]·0.5DMF·4H₂O (where Imazameth = (±)-2-(4,5-dihydro-4-methyl-4-(1-methylethyl)-5-oxo-1H- imidazol-2-yl)-5-methyl-3-pyridinecarboxylic acid; DMF = N,N-dimethylformamide) has been prepared and characterized by spectral method (IR), elemental analysis, thermal gravimetric analysis (TGA), fluorescence properties, and single crystal X-ray diffraction techniques. It crystallizes in the trigonal system, space group R-3 and the asymmetric unit contains four water molecules. The four lattice water molecules and their symmetric equivalent form a slight distorted cubical water cluster through hydrogen bonds. The O···O bonds of the water cluster are in the range of (2.80(7)–2.99(2) Å), and O···O···O angles are in the range of (82.54°–101.38°). In the cubical water clusters, the six O(5) atoms of each cube are connected to six O(1) atoms of the six molecules (O(1)···O(5) = 2.77(1) Å) by hydrogen bonding, respectively. The Co atom is six-coordinated by six N atoms in distorted octahedron coordination geometry. Intramolecular N–H···O and intermolecular O–H···O hydrogen bonds result in the formation of a supermolecular crystal, in which they seem to be effective in the stabilization of the structure. The complex displays strong fluorescence property and good thermal stability.     

Thermal behaviour of <Emphasis Type="Italic">sym</Emphasis>-octahydroacridines and their corresponding N(10)-oxides

We present and discuss results on the thermal behaviour of 1,2,3,4,5,6,7,8-octahydroacridine (OHA), together with six 9-substituted congeners, i.e. R = –Br, –OCH₃, –NH₂, –NO₂, –OH, and furyl (–C₄H₃O), and their corresponding N(10)-oxides, under nitrogen atmosphere and with alumina as reference, at a heating rate of 5 °C min^?1 from room temperature to 300 °C. Chromatography has been carried out on aluminium sheets, with aluminium oxide 60 F254 neutral (Merck). Melting effects are observed for almost all compounds in their corresponding curves, precisely determined by using a Boetius apparatus. Homolysis of the carbon-substituent bond occurs in most cases, a phenomenon which is consistent with the values of the bond dissociation energy. For all compounds, except for hydroxyl congeners, thermal decomposition started with an endothermic peak. Octahydroacridines readily decompose into volatile products, an effect which correlates with their low melting points, while little amounts of residue remain in place of the aromatic amines compared to the N(10)-oxides. The presence of N–O bonds greatly influences the thermal stability of the compound, in the sense of increasing it compared with the parent amine. Quantitative studies of the decomposition products reveal that the melting points, the 9-position substituent, and N–O bond all play an important role upon the thermal behaviour. Mechanistic/kinetic pathways are also proposed as such results are important in further designing laser processing protocols, i.e. matrix-assisted pulsed laser evaporation (MAPLE) or laser-induced forward transfer (LIFT), for thin film deposition and/or device printing.     

Conformation and hydrogen bonding for the bicyclic compound 3‐thiabicyclo[3.2.0]heptane‐6,7‐dicarboxylic acid 3,3‐dioxide

The initial goal of this work was to verify the geometry of the product of a photochemical reaction, viz. the title compound, C₈H₁₀O₆S, (II). Our crystallographic study firmly establishes the cis–anti–cis nature of the substituents on the cyclobutane ring. The geometry is also designated as exo, where exo signifies that the five‐membered ring is on the opposite side of the central cyclobutane ring from the carboxylic acid substituents. The structure determination reveals two molecules, A and B, in the asymmetric unit that display substantially different conformations of the bicyclic core: the cyclobutane ring puckering angles are 22 and 3°, and the sulfolane ring conformations are twist (S‐exo) and envelope (S‐endo). Intrigued by this variation, we then compared the conformations of other molecules in the Cambridge Structural Database that have sulfolane rings fused to cyclobutane rings. In this class of compound, there are five examples of saturated cyclobutane rings, with ring puckering angles ranging from 3 to 35°. The sulfolane rings were more similar: four of the six molecules exhibit envelope conformations with S‐endo, as in molecule B of (II). Despite the conformational differences, the hydrogen‐bonding scheme for both molecules is similar: carboxyl –OH groups form hydrogen bonds with carboxyl and sulfone O atoms. Alternating A and B molecules joined by hydrogen bonds between sulfone O atoms and carboxyl –OH groups form parallel chains that extend in the ac plane. Other hydrogen bonds between the carboxyl groups link the chains along the b axis.     

Competition between chalcogen bond and halogen bond interactions in YOX<Subscript>4</Subscript>:NH<Subscript>3</Subscript> (Y = S,Se; X = F,Cl, Br) complexes: An ab initio investigation

Using ab initio calculations, the geometries, interaction energies and bonding properties of chalcogen bond and halogen bond interactions between YOX₄ (Y = S, Se; X = F, Cl, Br) and NH₃ molecules are studied. These binary complexes are formed through the interaction of a positive electrostatic potential region (σ-hole) on the YOX₄ with the negative region in the NH₃. The ab initio calculations are carried out at the MP2/aug-cc-pVTZ level, through analysis of molecular electrostatic potentials, quantum theory of atoms in molecules and natural bond orbital methods. Our results indicate that even though the chalcogen and halogen bonds are mainly dominated by electrostatic effects, but the polarization and dispersion effects also make important contributions to the total interaction energy of these complexes. The examination of interaction energies suggests that the chalcogen bond is always favored over the halogen bond for all of the binary YOX₄:NH₃ complexes.     

Theoretical investigation of a high density cage compound 1,3,5,7,9,11-hexanitrotetradecahydro-1H-1,3,4,5,7,7b,9,11,12a,12b1,12b2,13-dodecaaza-4,8,12-(epimethanetriyl)cyclohepta[l]cyclopenta[def] phenanthrene

The B3LYP/6-31G** method was used to investigate IR and Raman spectra, heat of formation, and thermodynamic properties of a new designed polynitro cage compound 1,3,5,7,9,11-hexanitrotetradecahydro-1H-1,3,4,5,7,7b,9,11,12a,12b¹,12b²,13-dodecaaza-4,8,12-(epimethanetriyl)cyclohepta[l]cyclopenta[def]phenanthrene. The detonation and pressure were evaluated using the Kamlet–Jacobs equations based on the theoretical density and HOFs. The bond dissociation energies and bond orders for the weakest bonds were analyzed to investigate the thermal stability of the title compound. The results show that N₈–NO₂ bond is predicted to be the trigger bond during pyrolysis. There exists an essentially linear relationship between the WBIs of N–NO₂ bonds and the charges – $ Q_{{{\text{NO}}_{ 2} }} $ on the nitro groups. The crystal structure obtained by molecular mechanics belongs to the P2₁ space group, with lattice parameters Z = 2, a = 11.4658 Å, b = 15.2442 Å, c = 10.2451 Å, ρ = 2.07 g cm^?3. The designed compound has high thermal stability and good detonation properties and is a promising high-energy density compound.     

Structure and energetic properties of 1,5-dinitrobiuret

The two-dimensional potential energy scan shows that the pseudo-trans conformer of 1,5-dinitrobiuret (DNB) is the most stable form of isolated molecule, while the pseudo-cis conformer is about 7.5 kJ/mol higher in energy. Thus, the structure of gaseous DNB is different from that in crystal state, where the molecules have pseudo-cis conformation. The value of enthalpy of formation of gaseous DNB (?257 ± 5 kJ/mol) is calculated from isodesmic reactions using G4 energies. Combining this value with empirically estimated enthalpy of sublimation, the enthalpy of formation of crystal DNB is predicted to be ?415 ± 15 kJ/mol. The bond dissociation enthalpies are calculated for all bonds. The energy of the weakest N–NO₂ bonds is equal to 190–200 kJ/mol. Similar calculations were carried out for biuret. The gaseous biuret exists predominantly in the pseudo-trans form. The calculated enthalpy of formation of gaseous biuret agrees well with the experimental one. The correlation of calculated bond energies with corresponding bond distances and electron density is discussed for biuret and DNB.     

Theoretical investigation of carboranylpyrrole structures and the thermal resistance and conducting properties of carboranylpyrrole polymers

The carboranylpyrrole polymers are functional materials with superior thermal resistance and conducting performances. The carboranylpyrrole structures and Laplacian bond order (LBO) of carborane moiety, as well as the thermal resistance and conducting properties of carboranylpyrrole dimers or polymers, were investigated theoretically. The ¹¹B NMR chemical shifts of 3-(2-methyl-o-carboranyl)alkyl-1H-pyrrole monomers (CP-1 to CP-5) were calculated and analyzed. The average LBO values of some characteristic chemical bonds in the carborane cages of CP-1 to CP-5 molecules were calculated. It is found that the average LBO values of carborane moieties change slightly with the increase in alkyl chain length. The temperature resulting in about 15–20 % weight loss for CP-1, CP-3, CP-4 and CP-5 polymers is predicted to be more than 700 °C. Apart from the C–C bonds in carborane moieties of 3-(2-R-o-carboranyl)propyl-1H-pyrrole (R = CH₂OH, CH₂OCH₃, CN, COCl, Ph) substituents, the LBO values of other bonds in these cages change slightly relative to that in the molecule of 3-(2-methyl-o-carboranyl)propyl-1H-pyrrole (CP-3). The C–C bond LBO values in the carborane cages of these substituents with electron-donating groups (R = CH₂OH, CH₂OCH₃) are bigger than that in CP-3, while those values in those substituents with electron-withdrawing groups (R = CN, COCl, Ph) are smaller than that in CP-3. The polymerization activity calculated for CP-1 to CP-5 monomers increases with the increase in alkyl chain length. The calculated orbital energy gap (?E _LUMO?HOMO) of CP-1 to CP-5 dimers decreases with the increase in alkyl chain length, and accordingly, the electronic conductivity has the potential to increase. In addition, the calculated band gaps of CP-1 to CP-5 dimers cell models also decrease with the increase in alkyl chain length.     

A computational study on the nature of the halogen bond between sulfides and dihalogen molecules

The characteristics and nature of the halogen bonding in a series of B···XY (B = H₂S, H₂CS, (CH₂)₂S; XY = ClF, Cl₂, BrF, BrCl, Br₂) complexes were analyzed by means of the quantum theory of “atoms in molecules” (QTAIM) and “natural bond orbital” (NBO) methodology at the second-order Møller-Plesset (MP2) level. Electrostatic potential, bond length, interaction energy, topological properties of the electron density, the dipole moment, and the charge transfer were investigated systematically. For the same electron donor, the interaction energies follows the B···BrF > B···ClF > B···BrCl > B···Br₂ > B···Cl₂ > B···ClBr order. For the same electron acceptor, the interaction energies increase in the sequence of H₂S, H₂CS, and (CH₂)₂S. Topological analyses show these halogen bonding interactions belong to weak interactions with an electrostatic nature. It was found that the strength of the halogen-bonding interaction correlates well with the electrostatic potential associated with halogen atom and the amount of charge transfer from sulfides to dihalogen molecules, indicating that electrostatic interaction plays an important role in these halogen bonds. Charge transfer is also an important factor in the halogen bonds involved with dihalogen molecules.     

Vibrational analysis of sodium α-, β- and γ-hydroxybutyrates. Inter- and intramolecular hydrogen bonds

The infrared and Raman spectra of sodium α-, β- and γ-hydroxybutyrates and their deuterated analogues are examined in the 4000-100 cm⁻¹ range and an assignment of the fundamental vibrations is given. Based on the localization of the asymmetric stretching vibrations ν_asOH and the out-of-plane vibration γOH, inter- and/or intramolecularly hydrogen-bonded forms are proposed: the low frequencies of ν_asOH (<3200 cm⁻¹) and high frequencies of γOH (≈800 cm⁻¹) argue in favour of the existence of intramolecular hydrogen bonding. Sodium α-hydroxybutyrate exhibits as a chelate ring with an intramolecular hydrogen bond between hydroxyl and carboxyl groups, whereas sodium, β-hydroxybutyrate has the two association forms with inter- and intramolecular hydrogen bonds. Sodium γ-hydroxybutyrate exists as a hydrogen-bonded polymer, with an intermolecular hydrogen bond between the hydroxyl groups and between the hydroxyl and carbonyl groups. At a crystallization temperature above 50°C, only the α- salt showed a structural change indicating the existence of intra- and intermolecular hydrogen bonds. This result is confirmed by differential scanning analysis.     

Structural and electronic effects involving pyridine rings in 4-methylpyridine Cu4OX6L4 complexes. II. Correlations based on molecular structure of the Cu4OCl6(4-Mepy)4 complex

Correlations involving bond lengths and bond angles in the molecular structure of the Cu₄OCl₆(4-Mepy)₄ complex (4-Mepy = 4-methylpyridine) with four symmetrically independent molecules present in the unit cell showed that the donor-acceptor behavior involving the π-back donation into the pyridine rings of the 4-Mepy ligands is most effectively stimulated by a suitable orientation of the pyridine rings in the trigonal bipyramidal geometry. The pyridine ring planes are almost in parallel orientation with one of the three Cu-Cl bonds. The bond lengths of these Cu-Cl bonds are in a significant linear correlation with the Cu-N bond lengths and the bonds lengths of the pyridine rings. The pyridine rings orientation is affected by distortion of the trigonal bipyramidal geometry to tetragonal pyramidal coordination, by out-of plane pyridine rings deviation and in-plane pyridine rings tilting, by puckering of the pyridine rings and by the effects of the methyl groups. The pyridine rings in at least seven of the sixteen trigonal bipyramidal coordinations exhibit an orientation supporting the π-back bonding between the Cu(II) atoms and the pyridine rings.     

Hybridization in some macrocyclic polyacetylenes

The hybridization in several cyclic polyacetylene compounds has been calculated by the maximum overlap method, assuming planar and non-planar geometries of the molecules. In the planar configuration the hybrids describing the molecular skeleton deviate from the corresponding bond directions. We have a few “bent” bonds, but in contrast to the situation in small rings, here the deviation angles are negative, i.e., the hybrids point toward the inside of the ring. Non-planar structures in which acetylene groups are kept in a plane and CCH₂ or CH₂ groups are displaced out of the plane show less deviation from the bond directions of bent bonds. Furthermore, the deviation angles decrease with an increase in the out-of-plane displacement of methylene groups. Finally, when the angle of bending of the molecules approaches 50°, the deviation vanishes, predicting a puckered conformation for the molecules. Correlation between CC stretching vibration frequencies and the corresponding CC bond overlap is discussed.     

Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution

The conformational behavior of the title compounds has been investigated by Hartree-Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed gamma turn (gammal), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4-0.5 kcal/mol for helical structures and about 2 kcal/mol for gammal structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for gammal structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation.     

Infrared spectroscopy of Cr+(H2O) and Cr2+(H2O): the role of charge in cation hydration

Singly and doubly charged chromium-water ion-molecule complexes are produced by laser vaporization in a pulsed-nozzle cluster source. These species are detected and mass-selected in a specially designed time-of-flight mass spectrometer. Vibrational spectroscopy is measured for these complexes in the O-H stretching region using infrared photodissociation spectroscopy and the method of rare gas atom predissociation. Infrared excitation is not able to break the ion-water bonds in these systems, but it leads to elimination of argon, providing an efficient mechanism for detecting the spectrum. The O-H stretches for both singly and doubly charged complexes are shifted to frequencies lower than those for the free water molecule, and the intensity of the symmetric stretch band is strongly enhanced relative to the asymmetric stretch. Partially resolved rotational structure for both complexes shows that the H-O-H bond angle is greater than it is in the free water molecule. These polarization-induced effects are enhanced in the doubly charged ion relative to its singly charged analog.