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.     

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.     

Hydrogen-bond structures in poly(2-hydroxyethyl methacrylate): Infrared spectroscopy and quantum chemical calculations with model compounds

Hydrogen-bond structures in poly(2-hydroxyethyl methacrylate) (PHEMA) were investigated by infrared (IR) spectroscopy and quantum chemical calculations (QCC). A monomer of 2-hydroxyethyl methacrylate (HEMA) and model compounds of methyl acetate (MA) and methanol (MeOH) were also used. Evidences for OHOC and OHOH types of hydrogen-bonds were observed in an IR spectrum of a PHEMA solid. It was estimated from the present study that 47.3% of OH groups on the PHEMA side chain terminal are engaged in the OHOC type of hydrogen-bond, while the rest contributes to the OHOH type of hydrogen-bond.     

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.     

Blue-shifting intramolecular CH O(S) contacts in sterically strained systems

A group of model systems which may form chelate-type structures with intramolecular CH  Y (Y = O, S) contact is investigated computationally. The existence of several conformers permits to identify a reference molecule without the CH  Y intramolecular contact and to establish the blue-shifting character of this interaction. The CH stretching frequency in chelate forms is found to increase with respect to its value in the reference system. A parallel decrease of the CH bond distance is also established. The blue-shifting character of the intramolecular CH  Y contact is interpreted in terms of the sterically enforced repulsion between the hydrogen atom in CH and the electron donor Y. This interpretation is supported by the negative (repulsive) estimates of the energy contribution due to CH  Y contacts.     

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).     

The catalytic effects of various third molecules on reaction channels of weakly bound complex CO2HF systems in the vapor phase

In this investigation, reaction channels of weakly bound complexes CO₂HF, CO₂HFH₂O, CO₂HFNH₃, CO₂HFCH₃OH, CO₂HFNH₂CH₃, CO₂HFNH(CH₃)₂ and CO₂HFN(CH₃)₃ systems were studied at the B3LYP/6-311++G(3df,2pd) level. The conformers of syn-fluoroformic acid or syn-fluoroformic acid plus a third molecule (H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃) were found to be more stable than the conformers of the related anti-fluoroformic acid or anti-fluoroformic acid plus a third molecule (H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃). However, the weakly bound complexes were found to be more stable than either the related syn- and anti- type fluoroformic acid or the acid plus third molecule (H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃) conformers. They decomposed into CO₂+HF, CO₂+H₃OF, CO₂+NH₄F, CO₂+(CH₃)OH₂F, CO₂+NH₃(CH₃)F, CO₂+NH₂(CH₃)₂F, or CO₂+NH(CH₃)₃F combined molecular systems. The weakly bound complexes have seven reaction channels, each of which includes weakly bound complexes and their related systems. Moreover, each reaction channel includes two transition state structures. The transition state between the weakly bound complex and anti-fluoroformic acid type structure (T₁₃) is significantly higher than that of internal rotation (T₂₃) between the syn- and anti-FCO₂H (or FCO₂HH₂O, FCO₂HNH₃, FCO₂HCH₃OH, FCO₂HNH₂CH₃, FCO₂HNH(CH₃)₂, or FCO₂HN(CH₃)₃) structures. However, adding the third molecule H₂O, NH₃, CH₃OH, NH₂CH₃, NH(CH₃)₂ or N(CH₃)₃ can significantly reduce the activation energy of T₁₃. The catalytic strengths of the third molecules are predicted to follow the order H₂O<NH₃<CH₃OH<.NH₂CH₃<NH(CH₃)₂<N(CH₃)₃.     

DFT study on second-order nonlinear optical properties of the derivatives of 7-vertex cobalt–carborane metallocenyl

Density functional theory (DFT) B3LYP method was employed to calculate electron properties and the second-order nonlinear optical (NLO) responses of the derivatives which were formed by (C₅H₅)Co(C₂B₄H₆) and CHCHC₆H₄NO₂, CHCHC₆H₄NH₂. The results show: when H atom of (C₅H₅)Co(C₂B₄H₆) is substituted by CHCHC₆H₄NO₂, the β_tot values of isomers are all slightly smaller than that of ferrocene (Fc) derivative (FcCHCHC₆H₄NO₂). However, when H atom of (C₅H₅)Co(C₂B₄H₆) is substituted by CHCHC₆H₄NH₂, the β_tot values of isomers are close to that of ferrocene (Fc) derivative (FcCHCHC₆H₄NH₂). It indicates that (C₅H₅)Co(C₂B₄H₆) can be either a donator or an acceptor.     

Influence of hydration on the protomeric tautomerism in selenium analogue of methimazole: A computational chemistry study

Hydrogen bond assisted proton transfer reactions were investigated in 3-methyl-1H-imidazole-2(3H)-selone (MSeI) and 1H-imidazole-2(3H)-selone (SeI) at B3LYP/6-311++G(2d,2p) level of theory. The B3LYP results predict that the direct proton transfer process in MSeI and SeI is more difficult than the water-assisted one. The results also show that the selone complexes are more stable than corresponding selenol ones. Interaction energies for a single NHSe hydrogen bond in dimers MSeI and SeI are −31.3 and −32.7 kJ/mol, respectively. ZPE-corrected binding energies in the self-association complexes of the MSeI and SeI are greater than the water-associated complexes. The small negative value of H(r) obtained by AIM analysis at B3LYP/6-311++G(2d,2p) level reveals some contribution of sharing interaction (partially covalent) to the SeHN bond in dimers of the MSeI and SeI. AIM data also reveal the partially covalent nature of SeH6 interaction and electrostatic nature of OH5 interaction in water-associated complexes. Results of charge analysis show that the selenium analogue of the methimazole is more nucleophilic than the methimazole. Our results confirm that the selenium analogue of methimazole can exist as a zwitterionic form.     

Vibrational satellite of Na(3d ← 3s) dipole-forbidden transition in Na/CF4 mixture

Excitation spectra of Na fluorescence in mixtures with CF₄ display a new band shifted by the energy of one-vibrational quantum of the IR active ν₃-mode of CF₄ (1281 cm⁻¹) from Na 3d states. This band is attributed to a Na(3s)CF₄(ν₃ = 0) → Na(3d)CF₄(ν₃ = 1) transition and its intensity is explained by coupling with Na(4p)CF₄(v₃ = 0) resonance state which lies  180 cm⁻¹ below in energy. An analogous satellite of the Na 6p state combined with the same vibration and lying close to the Na 7p state is reported and discussed.     

Nucleophilic destruction of organophosphate toxins: A computational investigation

Computed reaction enthalpies, free energies, and activation barriers in vacuo are presented for the nucleophilic detoxification of the organophosphorus compounds (H)(HO)P(O)F, (H)(H₃CO)P(O)F and (H₃C)(CH(CH₃)₂O)P(O)F via the reaction R₁OH + (R₂)(R₃O)P(O)F → (R₂)(R₃O)P(O)(OR₁) + HF for a wide variety of R₁OH nucleophiles. Density functional theory at the B3LYP/6-311++G(d,p) computational level was employed for all the calculations. A multi-step Wright-type reaction mechanism [J. B. Wright, W.E. White, J. Mol. Struct. (THEOCHEM) 454 (1998) 259], which proceeds via a proton transfer from the nucleophile to the fluorine atom through the phosphinyl oxygen atom, was consistently found to have a lower activation barrier in the gas-phase than for the corresponding mechanism that operates via a proton transfer from the nucleophile directly to the fluorine atom. Of the nucleophilic agents investigated, peroxybenzoic acid and o-iodosobenzoic acid had the lowest classical activation barrier for the Wright-type mechanism.     

Reaction of diacetylmonoxime with morpholine N-thiohydrazide in the absence and in presence of a metal ion: Facile synthesis of a thiadiazole derivative with non-bonded SS interaction

The condensation of diacetylmonoxime (damnx) with morpholine N-thiohydrazide (mth) in 1:1 molar ratio in ethanol (16 h) afforded a nitrogen–sulfur zwitterionic heterocyclic compound, N-(3,4-dimethyl-1,2,5-thiadiazole-2-ium-2-yl)morpholine-4-carbothioate (dtmc). However, the same reaction in presence of [Zn(OAc)₂]·2H₂O in ethanol under gentle reflux on (3 h) yielded the zinc complex, [Zn(Hdammthiol)(OAc)(H₂O)]·H₂O, where H₂dammthiol (H₂L²) is the thiol form of tridentate NNS donor thiohydrazone ligand, diacetylmonoxime morpholine N-thiohydrazone (Hdammth). Both the nitrogen–sulfur heterocyclic compound and the zinc complex have been characterized by elemental analyses, spectroscopy (IR, UV–Vis, ¹H NMR and ¹³C NMR) and single crystal X-ray crystallography. It is noteworthy that the heterocyclic compound shows SS interaction with distance 2.738 Å in its planar conformation. The heterocyclic compound forms two dimensional supramolecular sheets through C–HO and ππ interactions while the zinc complex, with distorted square pyramidal geometry, forms 1D supramolecular chain. A mechanism has been proposed for the formation of nitrogen–sulfur heterocyclic compound.     

Magnetic field effect on chemical compositions of spherical Fe/Co fine particles synthesized from a gaseous mixture of iron pentacarbonyl and cobalt tricarbonyl nitrosyl

Under UV light irradiation on a gaseous mixture of Fe(CO)₅ and Co(CO)₃NO, both the crystalline deposits with sizes of 5 and 18 μm and the spherical particles with a mean diameter of 0.3 μm were produced. From FT-IR spectra and SEM–EDS analysis, it was suggested that the chemical structure of the crystalline deposits was the one of Fe₂(CO)₉ being modified by involving Fe(CO)Co bond. By decreasing a partial pressure of Fe(CO)₅ to 0.5 Torr in the gaseous mixture, only the spherical aerosol particles could be produced. Chemical composition of the particles was rich in Co species. From the disappearance of bridging CO band in the FT-IR spectra of the particles and the appearance of CO bands coordinated to a metal atom, Fe atom in Fe(CO)₄ was suggested to be coordinated by the O atom in bridging CO bond in Co(CO)Co structure and/or in α-diketone structure which was formed from two CO groups in dicobalt species. Chemical compositions of the crystalline deposits and the spherical particles were influenced differently by the application of a magnetic field. Atomic ratio of Fe to Co atom decreased in the crystalline deposits whereas it increased in the spherical particles with increasing magnetic field up to 5 T. Linearly aggregated particles (i.e., particle wires) as long as 30 μm were produced on the front side of a glass plate placed at the bottom of the irradiation cell.     

Structural role of hydrogen bond networks in amino acid–acid systems. (I) The network with highly polarizable OHO hydrogen bonds in sarcosine–methanesulfonic acid (2:1) crystal

The sarcosine–methanesulfonic acid (2:1) crystal was selected for examination of two problems: relations between different components of the amino acid–acid hydrogen bond network and a role of very strong and highly polarizable OHO hydrogen bond in the main structural units of the crystal: sarcosinium–sarcosine dimers (complexes). Our observations are based on phase transitions of the crystal monitored by DSC, X-ray diffraction and temperature evolutions of selected bands of IR spectra. Our experimental and DFT results provide information on the potential energy profile of the OHO proton and its evolution with temperature. The OO distance of the primary hydrogen bond remains almost unchanged and its proton is strongly delocalized and sensitive on neighbour NHO hydrogen bond. We propose a possible mechanism of the phase transitions and coupling between νCO vibrations of the carboxyl group and moving of the proton in neighbour OHO hydrogen bridge.     

Ba2In2O4(OH)2: Proton sites, disorder and vibrational properties

The structure of Ba₂In₂O₄(OH)₂ is analysed by the explicit full optimization of a large number of possible proton arrangements using periodic density functional theory. It is shown that the experimental assignments in which protons appear to be located at high symmetry positions with unphysical bond lengths do not correspond to minima on the potential energy hypersurface. The apparent sites are averages of a number of possible proton locations involving a set of possible local structural environments in which the internuclear separations are more realistic. Such problems with structural refinements are common where profile refinement programs place the atoms at the average position due to dynamic and/or static disorder. Thus while the calculations support a previous neutron diffraction analysis of the structure in that the average structure contains two different proton sites, they also reveal substantial information about the local environments of the protons. In all optimizations, the protons moved from the average positions suggested in the neutron diffraction study with calculated O–H and OHO distances consistent with those observed in other oxides. The energies of different proton distributions vary significantly so the protons are not randomly distributed. We also present an analysis of the vibrational properties of the O–H bonds. Since the strength of the hydrogen bonds is closely related to the local structural environments of the protons, a range of vibrational frequencies is obtained providing a prediction of the vibrational spectra. In O–HO linkages, O–H stretching modes soften with increasing HO hydrogen bond strength, while the in-plane and out-of-plane bending or libration modes stiffen. Together, our results show how modern theoretical methods can provide a clearer understanding of the structure and dynamics of a complex inorganic material.     

The syntheses and structures of mono- and di-bromovinylidenes

Reactions of metal acetylide complexes M(CCAr)(PP)Cp′ (M = Fe, Ru; Ar = C₆H₅, C₆H₄Me-4; PP = (PPh₃)₂, dppe; Cp′ = Cp, Cp*; not all combinations), or the analogous vinylidene, with cyanogen bromide yield monobromovinylidene complexes [M{CC(Br)Ar}(PP)Cp′]⁺, isolated as PF₆⁻ salts. The trimethylsilyl-capped acetylides M(CCSiMe₃)(PP)Cp′ react with cyanogen bromide to give [M(CCBr₂)(PP)Cp′]⁺, the first examples of metal complexes containing a terminal dihalovinylidene ligand, which can be isolated as the BF₄⁻ salts. Molecular structures of representative mono- and di-bromovinylidene complexes are reported, together with those of Ru(CCSiMe₃)(PPh₃)₂Cp and Ru(CCSiMe₃)(dppe)Cp*.     

Structural and vibrational studies of molecular conductors using quantum mechanical methods: 1,3-Dithiole-2-thione, 1,3-dithiole-2-one, 1,3-dioxole-2-one and 1,3-dioxole-2-thione

Computations were carried out by employing the RHF and density functional theory (DFT) methods to investigate the geometries, atomic charges, harmonic vibrational frequencies for the 1,3-dithiole-2-thione (DTT), 1,3-dithiole-2-one (DTO), 1,3-dioxole-2-thione (DOT) and 1,3-dioxole-2-one (DOO) molecules and their radical cations. The geometrical parameters and atomic charges on various atomic sites of the DTT and DOT molecules and their radical cations suggest extended conjugation in these systems. Contrary to this, for the DOO⁺ and DTO⁺ ions there is no evidence in favour of such conjugation, however, the neutral molecules exhibit some conjugation. Harmonic forced field and vibrational mode calculations provided convincing theoretical evidence for the reassignment of some fundamental vibrational modes for all the four molecules. In going from the neutral species to the charged ions for all the four cases the CC stretching frequency is found to decrease drastically. The CS stretching frequency reduces drastically for the DTT and DOT molecules as compared to their radical cations whereas the CO stretching frequency is found to increase in going from the neutral molecule to its radical cation for the DOO and DTO molecules. The ring stretching mode with a₁ symmetry and CC and CO/S stretching modes in these molecules appear to help in conversion of neutral molecule into respective radical cation and neighbouring radical cation into respective neutral molecule. Thus, there appears the feasibility of stretching vibrational mode coupling with electron transfer.     

Vibrational spectroscopy of 4-hydroxybenzhydrazide and its O,N-deuterated isotopologue accompanied by X-ray structure refinement

The vibrations of crystalline 4-hydroxybenzhydrazide were investigated by IR and Raman spectroscopy. Spectral changes resulting from O,N-deuteration together with DFT calculations were employed for band assignment presented in terms of potential energy distribution. The characteristic absorptions of the hydrazide group were located at 1623 (CO stretching), 1588 (NH₂ bending) and 1532 cm⁻¹ (NH bending). The greatest contributions of the NN and CN stretching vibrations were found in the 1208 and 1109 cm⁻¹ modes, respectively. The predominant contribution of the CO stretching vibration was observed for the 1282 cm⁻¹ absorption. The computations at the B3LYP level with 6-311++G(d,p) basis set were based on structural parameters taken from refined single crystal X-ray investigations. The details of hydrogen bonding and crystal packing are also presented.     

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.     

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.