Specific crystal structure of poly(3-hydroxybutyrate) thin films studied by infrared reflection–absorption spectroscopy

Infrared reflection–absorption (IR-RAS) and transmission spectra were measured for poly(3-hydroxybutyrate) (PHB) thin films to explore its specific crystal structure in the surface region. As IR-RAS is sensitive to the vibration mode of perpendicular orientation of the surface, differences between IR-RAS and transmission spectra indicate an orientation of the lamella structure in the surface of PHB thin films. The relative intensity of the crystalline CO stretching band in the IR-RAS spectrum is significantly weaker than that in the transmission spectrum. It may be concluded that the transient dipole moment of the CO stretching mode of the crystalline state is not oriented perpendicular but nearly parallel to the substrate surface. On the other hand, the relative intensity of the band at 3009 cm⁻¹ due to the C–H stretching mode of the C–HOC hydrogen bonding is similar between the IR-RAS and transmission spectra, suggesting that the C–H bond is oriented neither perpendicular nor parallel to the substrate surface but in an intermediate direction. Since the CO group of the C–HOC hydrogen bonding is oriented nearly parallel to the surface and its C–H group is in the intermediate direction, it is very likely that the C–HOC hydrogen bonding has a somewhat bent structure. These results are in good agreement with our previous conclusion that the C–HOC hydrogen bonding of PHB exists along the a-axis (not the b-axis) between the CH₃ group of one helix and the CO group of another helix.     

Investigations of molecular interactions in propionic acid–N,N-dimethyl formamide binary system—FTIR study

FTIR spectra of propionic acid (PA), N,N-dimethyl formamide (DMF) and its binary mixtures with varying molefractions of the PA were recorded in the region 500–3500 cm⁻¹, to investigate the formation of hydrogen bonded complexes in a mixed system. The observed features in ν(CO), δ(OC–N) and ν_as(CN) of DMF, ν(CO) and ν(CO) of PA have been explained in terms of the hydrogen bonding interactions between DMF and PA and dipole–dipole interaction. The intrinsic bandwidth for the vibrational modes ν_as(CN) and ν(CO) has been elucidated using Bondarev and Mardaeva model.     

H NMR Dynamic study of thermal Z/E isomerization of 5-substituted 2-alkylidene-4-oxothiazolidine derivatives: Barriers to rotation about CC bond

The rotational barriers between the configurational isomers of two structurally related push–pull 4-oxothiazolidines, differing in the number of exocyclic CC bonds, have been determined by dynamic ¹H NMR spectroscopy. The equilibrium mixture of (5-ethoxycarbonylmethyl-4-oxothiazolidin-2-ylidene)-1-phenylethanone (1a) in CDCl₃ at room temperature to 333 K consists of the E- and Z-isomers which are separated by an energy barrier ΔG^# 98.5 kJ/mol (at 298 K). The variable-temperature ¹H NMR data for the isomerization of ethyl (5-ethoxycarbonylmethylidene-4-oxothiazolidin-2-ylidene)ethanoate (2b) in DMSO-d₆, possessing the two exocyclic CC bonds at the C(2)- and C(5)-positions, indicate that the rotational barrier ΔG^# separating the (2E,5Z)-2b and (2Z,5Z)-2b isomers is 100.2 kJ/mol (at 298 K). In a polar solvent-dependent equilibrium the major (2Z,5Z)-form (>90%) is stabilized by the intermolecular resonance-assisted hydrogen bonding and strong 1,5-type S · · · O interactions within the SCCCO entity. The ¹³C NMR Δδ_C(2)C(2′) values, ranging from 58 to 69 ppm in 1a–d and 49-58 ppm in 2a–d, correlate with the degree of the push-pull character of the exocyclic C(2)C(2′) bond, which increases with the electron withdrawing ability of the substituents at the vinylic C(2′) position in the following order: COPh COEt > CONHPh > CONHCH₂CH₂Ph. The decrease of the Δδ_C(2)C(2′) values in 2a–d has been discussed for the first time in terms of an estimation of the electron donor capacity of the S fragment on the polarization of the CC bonds.     

Conformational influences of the polymorphic forms on the CO and C–H stretching modes of five saturated monoacid triglycerides studied by Raman spectroscopy at various temperatures

A study of the vibrational behavior of five saturated monoacid triacylglycerides is performed by Raman spectroscopy at various temperatures in two separate spectral ranges: 1780–1700 and 3100–2650 cm⁻¹. The samples are studied in polycrystalline phase at room temperature, in isotropic liquid phase, and in polycrystalline phase after cooling from the isotropic liquid phase. The CO stretching mode of these triglycerides changes significantly according to the temperature: we observe three components, or an unresolved doublet, or a resolved doublet. The I(2845)/I(2880) ratios (in the C–H stretching spectral region) of the different saturated monoacid triglycerides vary also according to the temperature. The study of these two indicators (the CO stretching mode and the I(2845)/I(2880) ratio) has permitted us to determine the polymorphic forms of the studied triglycerides.     

Fourier transform infrared study of mercury interaction with carboxyl groups in humic acids

An interaction between humic acid, an organic part of soil and mercury was studied by Fourier transform infrared spectroscopy (FTIR) and by ICP-AES analysis under given pH and concentration conditions. First the spectroscopic model was validated on the interaction of simple molecules representing the structural components of humic acid such as benzoic acid, catechol and salicylic acid with mercury. The interaction of carboxylic parts of humic acid with mercury is very interesting and easily characterised by infrared spectroscopy, an ideal mean for molecular study. Under the salt form (commercial humic acid Fluka TM: FHA), humic acid reacts with mercury in a different way from its acid form (FHA purified noted PFHA) and the Leonardite (LHA). Because of the straightforward exchange between Na⁺, Ca²⁺ and Hg²⁺, fixation of the latter is much more important with the salt form (FHA). However, this reaction is reduced under the acid form (PFHA, LHA) because the exchange with protons is difficult. The effect of this exchange was studied by FTIR showing the intensity decrease of ν_CO (COOH), the carboxylic functional group band of the acid, and the shifting of ν_as (COO⁻), the carboxylate functional group band under given pH and mercury conditions. For the FHA salt form, the characteristic band ν_CO (COOH) represented by a shoulder did not evolute, whereas the corresponding band to ν_as (COO⁻) strongly shifted (40 cm⁻¹) for a maximum Hg²⁺ concentration (1 g l⁻¹). On the other hand, for the acid form (PFHA, LHA), the intense band of ν_CO (COOH) disappeared proportionally to the increase of Hg²⁺concentration and the ν_as (COO⁻) band moved for about 20 cm⁻¹. The same results were reached with pH variations. Our results were confirmed by ICP-AES mercury analysis. This study shows that humic acids react differently according to their chemical and structural state.     

A bonding study of cyclopentene (c-C5H8) adsorption on Ni(1 1 1) surface

The adsorption of cyclopentene (c-C₅H₈) on Ni(1 1 1) was studied using DFT and semiempirical calculations. Preferred site and geometry calculations were carried out considering a Ni(1 1 1) surface and a unit cell of 64-atoms. The tetrahedral threefold hollow position was identified as the most favorable site, with a surface-molecule minimum distance of 1.83 Å. A bending structure is adopted when the molecule is adsorbed where the carbon atoms of the double bond are closer to the surface forming an angle of 160° among non-equivalents carbon atoms. The metal surface was represented by a two-dimensional slab with an overlayer of c-C₅H₈/Ni of 1/9 ratio. We also computed the density of states (DOS) and the crystal orbital overlap populations (COOP) corresponding to CC, CNi, CH, and NiNi bonds. We found that both NiNi bonds interacting with the ring, and the CC bond are weakened after adsorption, this last bond is linked significantly to the surface. The hydrogen atoms belonging to the saturated carbon atoms also participate in the adsorbate–surface bonding. The main interactions include the 4s, 3p_z and 5d_z² bands of nickel and 2p_z bands of the carbon atoms of the double bond.     

Interligand interactions involved in the molecular recognition between copper(II) complexes and adenine or related purines

The available crystal structure information in the CSD database on ternary species prepared by the reaction of diverse copper(II) complexes (CuL) and purine, adenine and guanine or related purine derivatives is considered in order to deepen the intra-molecular interligand interactions affecting the molecular recognition patterns of the ‘metal complex + purine nucleobase’ and closely related systems. The degree of protonation and the possibilities of different tautomeric forms in the purine-like moieties are taken into account. The main conclusion is a general trend to form a CuN(purine-like) coordination bond which can be reinforced by an intra-molecular interligand H-bonding interaction. NH(purines)A (O or Cl acceptor) or NH(amino ligand L)O6(oxo-purines) are commonly observed. In addition, selected examples revealed that the presence of a variety of non-coordinating groups in L or in the purine-like nucleobases can significantly influence the structurally observed molecular recognition pattern. Moreover, examples are known where binuclear cores of the types Cu^II₂(μ₂-N3,N9-adeninate)₄(aqua)₂ or Cu^I₂(μ₂-N3,N9-adeninate)₂(aqua)₂ recognise CuL chelates by means of the expectable pattern (CuN7 coordination bond + N6HO(L) interaction).     

Charge transfer interactions and nonlinear optical properties of push–pull chromophore benzaldehyde phenylhydrazone: A vibrational approach

FT Raman and IR spectra of the crystallized nonlinear optic (NLO) molecule, benzaldehyde phenylhydrazone (BPH) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of BPH have been investigated with the help of B3LYP density functional theory (DFT) method. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). From the optimized geometry, the decrease in C–N bond length indicates the electron delocalization over the region of the molecule. The vibrational analysis confirm the charge transfer interaction between the phenyl rings through CN–N skeleton.     

Transformations of allylamine and N-allylacetamide on triosmium cluster complexes with hemilabile ligands

The cluster complexes (μ-H)Os₃(μ-OCR)(СО)₁₀ (R = Me (1); R = Ph (2)) catalyze the allylic rearrangement of N-allylacetamide at room temperature. Microwave irradiation greatly (by more than several thousand-fold) accelerates the reaction between the solution of 2 and allylacetamide. The interaction of cluster 2 with allylamine both at room and elevated temperatures results in cleavage of the C–N bond and coordination of the allylic fragment to one of the osmium atoms with the formation of Os₃(CO)₉(μ,η²-OC-Ph)(η³-C₃H₅) (4) cluster.     

Molecular structure and conformation of diethylmethylamine determined by gas electron diffraction and vibrational spectroscopy combined with theoretical calculations

We have investigated the molecular structure and conformation of diethylmethylamine, C(4)H₃C(2)H₂N(1)[CH₃]C(3)H₂C(5)H₃, by gas electron diffraction and vibrational spectroscopy with the aid of theoretical calculations. Diffraction data are consistent with a conformational mixture of 35(14)% tt + 27(14)% g⁺t + 20(17)% g⁻t + 18(23)% g⁺g⁺ where the numbers in parentheses denote three times the standard errors (3σ). Normal-coordinate analysis based on B3LYP/6-311+G^** calculations supports the existence of the four conformers. The dihedral angle ₁(C4C2N1C3) (= −₂(C5C3N1C2)) of the tt conformer was 170(4)° whereas the ₁ and ₂ values of the other conformers were fixed at the B3LYP/6-311++G(2df,p) values: 72.4° and −163.3° for the g⁺t, −66.0° and −158.2° for the g⁻t, and 60.3° and 63.5° for the g⁺g⁺. Average values of the structural parameters (r_g/Å and _α/°) with 3σ are: r(N–C) = 1.462(2), r(C–C) = 1.523(3), r(C–H) = 1.113(2), CNC = 111.6(5), NCC = 114.5(5), NCH/CCH_Me = 110.6(5).     

The effect of the solvents on the specific intramolecular C-H...N interactions studied by1H NMR spectroscopy

The analysis of the effect of the solvents on the proton chemical shifts in¹H NMR spectra of 2-vinyloxypyridine indicates that the C—H...N interaction of weak intramolecular hydrogen bond type hinders the formation of intermolecular hydrogen C—H...X and C-H... bonds. The protonating solvents reduce the intramolecular C—H...N interaction due to association with the N atom of the pyridine cycle.Translated fromIzvestiya Akademii Nauk. Seriya Khimieheskaya, No. S, pp. 1202–1204, May, 1996.     

Weak hydrogen-, halogen- and stacking ππ bonding in crystalline 5-chloro-1-indanone. An analysis by using X-ray diffraction, vibrational spectroscopy and theoretical methods

Intermolecular forces of C–HO, C–Hπ, COCl and ππ types are present in the stable triclinic crystal structure of 5-chloro-1-indanone. They are analysed from a geometrical point of view supported in some extent by the analysis of the vibrational spectrum of the titled compound. Moreover, the molecular structure of the isolated species is calculated by using ab initio as well as density functional theory (DFT) methods together an assortment of basis sets. In order to obtain some information about the influence of intermolecular forces on the molecular structure, the calculated geometries of a free molecule were compared with the experimental solid phase geometry determined by X-ray crystallography.An analysis and assignment of the vibrational spectrum of the 5-chloro-1-indanone is accomplished by using IR and Raman experimental data along with Pulay et al.’s scaled quantum mechanical force field (SQM) methodology starting from the theoretical B3LYP/6-31G(d) and BLYP/6-31G(d) force fields under C_s symmetry.     

C–HPt(II) interaction-controlled self-assembly and photophysics of chiral bis(pyrrol-2-ylmethyleneamino)cyclohexane platinum(II) complexes

Reaction of (R,R)-(−)- and (S,S)-(+)-1,2-bis(pyrrol-2-ylmethyleneamino)cyclohexane with K₂PtCl₄ afforded chiral, neutral platinum(II) Schiff base complexes of (R,R)-PtL and (S,S)-PtL with high yields. The rare C–HPt(II) intermolecular interaction was found to show considerable strength and directionality for controlling M and P helical supramolecular architectures of (R,R)-PtL and (S,S)-PtL, respectively, in crystal lattices. More importantly, the open square-planar geometry of platinum(II) complexes allows axial C–HPt(II) interaction, resulting in the ³(ππ^*) excited state with some mixing of the Pt(II) metal character observed both in concentrated solutions and in the solid state at room temperature.     

Strontium Sorption on Hematite at Elevated Temperatures

Acid–base reactions and surface complexation of Sr(II) at the hematite/water interface have been studied by means of potentiometric titrations at three different temperatures: 25, 50, and 75°C. Equilibrium measurements were performed in 0.1 M NaCl. In the evaluation of equilibrium models for the acid–base reactions and complexation reactions in the three-component system H⁺ ---(FeOH)---Sr²⁺, the constant capacitance model was applied. During the titrations with Sr, aliquots of the suspension were sampled at in several points. The aqueous concentrations of Sr were analyzed by atomic absorption spectrometry. Treatment of data included tests for formation of both inner-sphere and outer-sphere complexes of different stoichiometric composition. The proposed equilibrium model consists of the following surface complexes of inner sphere type: FeOHSr²⁺ and FeOSrOH. Besides the stability constants for the surface complexes, the thermodynamic parameters ΔH and ΔS were evaluated. The combined effect of a decrease in pH_pzc with increasing temperature and positive enthalpies of surface complex formation favors adsorption of Sr at elevated temperatures.     

A DFT study on the mechanism of the gas phase reaction of ground-state Y (4d5s,D) with 2-butyne

The reaction of ground-state Y with 2-butyne has been investigated in detail using B3LYP method. Four pathways for elimination of H₂ were identified. Two isomers, Y(HCCC)CH₃ and Y(H₂CCCCH₂) were assigned to the observed product, YC₄H₄. The calculated PESs suggest that the concerted H₂-elimination leading to Y(H₂CCCCH₂) + H₂ product is the most favorable pathway. For the elimination of CH₃, combining the results of this work with our previous study on Y + propyne reaction, a general mechanism for the reactions of Y with 2-alkynes bearing RCCCH₃ structure was established: Y + RCCCH₃ → π-complex → TS(H-migration) → HY(CH₂CC)R → TS (CC insertion) → (CH₂)HYCCR → TS(H-migration) → H₃CYCCR → CH₃ + YC₂R. Such mechanism was found to be always energetically more favorable than the direct sp–sp³ CC bond insertion mechanism. Further, such mechanism can also be applied to the elimination of CH₄ and it can be described as: Y + CH₃CCCH₃ → π-complex → TS (H-migration) → HY(H₂CCC)CH₃ → TS(CC insertion) → (H₂CCC)HYCH₃ → TS(H-migration) → CH₄ + YC₃H₂.     

Unimolecular chemistry of metastable dimethyl isophthalate radical cations

The MS/MS spectrum of the metastable molecular ions of dimethyl isophthalate 1 differs from that of the isomeric dimethyl terephthalate 2 by the observation of, inter alia, a quite intense loss of C,H₂,O ascribed to formaldehyde. Results obtained using a combination of mass spectrometry techniques suggest that this process could consist of an isomerization reaction of the molecular ion into an ion–neutral complex (INC) linking a benzoyl radical and neutral formaldehyde to a proton [ArCOHOCH₂]⁺. Within the complex, a proton transfer catalyzed by formaldehyde occurs resulting in the production of an ionized cyclohexadienylidene methanone (ketene) structure.     

Effects of dipole interaction and solvation on the CO stretching band of N,N-dimethylacetamide in nonpolar solutions: Infrared, isotropic and anisotropic Raman measurements

The concentration dependence of the CO stretching (ν_CO) band of N,N-dimethylacetamide (NdMA) in cyclohexane, n-hexane, and CCl₄ has been investigated by infrared (IR) and polarized Raman spectroscopy. For the neat liquid of NdMA, the noncoincidence of the aniso- and isotropic Raman wavenumbers is evident. In the 0.47 M cyclohexane solution of NdMA, the noncoincidence effect almost disappears and the ν_CO envelopes in both the Raman and IR spectra are asymmetric to the low-wavenumber side. When the concentration of NdMA decreases from 0.33 to 0.023 M, the peak of these bands slightly shifts to a higher wavenumber and the band shape becomes symmetric. The shape of the ν_CO envelope does not show any significant change below 0.023 M. These results suggest that the asymmetric shape of the ν_CO band observed for the 0.33 M cyclohexane solution is associated with the intermolecular interaction among NdMA molecules, which vanishes at around 0.02 M. Spectral changes for the CCl₄ solution of NdMA show a similar tendency. However, the shape and peak wavenumber of the ν_CO band observed in a highly diluted CCl₄ solution (≤0.023 M) indicate that the solvation effect of CCl₄ is more complicated than those of cyclohexane and n-hexane. The analyses of the ν_CO band, which is sensitive to the intermolecular interaction between solutes and between solute and solvent for NdMA dissolved in nonpolar solvents, would serve to clarify the electronic property of the molecule in a solution.     

Investigations on the local angular distortions and the spin-Hamiltonian parameters for Ni in sulfides

The local angular distortions and the spin-Hamiltonian parameters (the g factors and the hyperfine parameters) for Ni⁺ in ABS₂ (ACu, Ag; BAl, Ga) ternary sulfides are theoretically investigated from the perturbation formulas of these parameters for 3d⁹ ions in a tetragonally distorted tetrahedron. In view of the strong covalency of such systems, the ligand orbital and spin–orbit coupling contributions are taken into account using the cluster approach. The local impurity-ligand bond angles in the Ni⁺ centers are found to be about 1.4–4.5° smaller than those of the host monovalent A sites in the pure crystals, due to size mismatching substitution. As a result, the ligand tetrahedra exhibit slight elongation in CuBS₂:Ni⁺ and slight compression in AgGaS₂:Ni⁺. The calculated spin-Hamiltonian parameters, optical transitions and the relative intensity ratios show reasonable agreement with the experimental data.     

DFT study on the intermolecular interactions between Aun (n = 2–4) and thymine

Density functional B3LYP method with 6-31++G** basis set is applied to optimize the geometries of the luteolin, water and luteolin–(H₂O)_n complexes. The vibrational frequencies are also studied at the same level to analyze these complexes. We obtained four steady luteolin–H₂O, nine steady luteolin–(H₂O)₂ and ten steady luteolin–(H₂O)₃, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) are used to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are within −13.7 to −82.5 kJ/mol. The strong hydrogen bonding mainly contribute to the interaction energies, Natural bond orbital analysis is performed to reveal the origin of the interaction. All calculations also indicate that there are strong hydrogen bonding interactions in luteolin–(H₂O)_n complexes. The OH stretching modes of complexes are red-shifted relative to those of the monomer.     

Heterobimetallic aluminium and zinc complex with N-arylanilido-imine ligand: Synthesis, structure and catalytic property for ring-opening polymerization of ε-caprolactone

Treatment of a N-arylanilido-imine ligand [ortho-C₆H₄(NHAr)CHN]₂CH₂CH₂ (Ar = 2,6-Me₂C₆H₃) (LH₂) with one equiv. of AlMe₃ affords a monometallic complex [C₆H₄(NHAr)–CHN)]CH₂CH₂(C₆H₄(NAr)CHNAlMe₂) (1). The monometallic complex 1 reacts with one equiv. of ZnEt₂ to give a heterobimetallic complex [C₆H₄(NAr)–CHNZnEt]CH₂CH₂[C₆H₄(NAr)–CHNAlMe₂] (2). Both complexes were characterized by ¹H and ¹³C NMR spectroscopy and elemental analyses, and the molecular structures of 1 and 2 were determined by X-ray diffraction analysis. The complexes 1 and 2 both are efficient catalysts for ring-opening polymerization of ε-caprolactone in the presence of benzyl alcohol yielding polymers with narrow polydispersity values and complex 2 initiates the polymerization in a controllable manner.