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.     

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.     

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.     

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.     

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.     

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.     

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.     

Atmospheric chemistry of CF3CFCH2: Products and mechanisms of Cl atom and OH radical initiated oxidation

The products of Cl atom and OH radical initiated oxidation of CF₃CFCH₂ were studied in 700 Torr of N₂/O₂ diluent at 296 ± 1 K. The reactions of Cl atoms and OH radicals with CF₃CFCH₂ proceed via electrophilic addition to the double bond. The reaction with chlorine atoms proceeds 56 ± 5% via addition to the central carbon. The chlorine atom initiated oxidation of CF₃CFCH₂ gives CF₃C(O)F in a molar yield which is indistinguishable from 100% and independent of [O₂], and HC(O)Cl in a molar yield which increased from 30% to 59% as [O₂] was increased from 3 to 700 Torr. The OH radical initiated oxidation of CF₃CFCH₂ gives CF₃C(O)F as major product in a yield of 91 ± 6%. The results are discussed with respect to the atmospheric chemistry and environmental impact of CF₃CFCH₂.     

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*.     

Matrix-isolation FT-IR and theoretical investigation of the competitive intramolecular hydrogen bonding in 5-methyl-3-nitro-2-hydroxyacetophenone

The paper presents the conformational, vibrational and hydrogen bond characteristics of 5-methyl-3-nitro-2-hydroxyacetophenone studied with the combined matrix-isolation FT-IR spectroscopic and theoretical (DFT/B3LYP/6-31++G^**) technique. Theoretical calculations predict three stable conformations of the studied compound. Only two of these conformations could be identified experimentally using the matrix-isolation FT-IR technique. The conformation with the intramolecular hydrogen bond OH^…ON has been found to be more stable than the conformation with the OH^…OC type of hydrogen bond by 7.28 kJ/mol. The complete assignment of the experimental spectra could be performed based on the theoretical calculations including the normal coordinate analysis and isotopic substitution.     

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.     

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.     

(E)-1,2-Difluoro-1-iodo-2-trialkylsilanes—A useful synthon for the addition of the [IFCCF] unit to activated electrophiles

Fluoride ion catalyzed reaction of (E)-IFCCFSiR₃ with activated aromatic aldehydes and ketones and activated perfluoroaromatics, such as pentafluoropyridine and perfluorotoluenes, transfers the [IFCCF] unit to the activated electrophiles to stereospecifically provide (E)-1,2-difluoro-1-iodosubstituted derivatives. Aluminum chloride catalyzed reaction of (E)-1,2-difluoro-1-iodo-2-trialkylsilanes with alkyl or aryl acyl halides gives the corresponding (E)-1,2-difluoro-1-iodoketones stereospecifically in excellent yield. The vinyl iodide product formed via this methodology could be coupled (with Pd(0)) catalysis to provide an entry to a polyfunctionalized derivative.     

Theoretical investigation on possible mechanisms on regioselective formation of (η-siloxyallyl)tungsten complexes

Selective formation of (η³-siloxyallyl)tungsten complexes by reaction of hydrido(hydrosilylene)tungsten complexes with α,β-unsaturated carbonyl compounds was reported experimentally. The mechanisms have been investigated by employing the model reaction of [Cp(CO)₂(H)WSi(H)–{C(SiH₃)₃}] (R), derived from the original experimental complex Cp′(CO)₂(H)WSi(H)–[C(SiMe₃)₃] (1a, Cp′ = Cp*; 1b, Cp′ = η⁵-C₅Me₄Et), with methyl vinyl ketone, under the aid of the density functional calculations at the b3lyp level of theory. It is theoretically predicted that the route involving migration of the hydride to silicon to afford a 16e intermediate [Cp(CO)₂W–SiH₂–{C(SiH₃)₃}] is inaccessible (route 2), supporting the proposition by experiments. Another route, via [2 + 4] cycloaddition followed by directly Si–H reductive elimination, is theoretically predicted to be accessible (route 1). In route 1, two possible paths with different attacking directions of the oxygen of methyl vinyl ketone at Si (WSi) are put forward. The attack at the Si atom from the hydride (H1) side of the plane W–Si–H1 in R is found to be preferred kinetically. The regioselectivity for formation of (η³-siloxyallyl)tungsten complexes, where only the exo-anti isomer was obtained, is discussed based on the consideration of thermodynamics and kinetics.     

Bonding trends in MCH2 systems: Simple orbital interpretation and evidence for double bonds

MCH₂ systems, where M is a metal from 4th up to 7th period, are studied at DFT level using B3LYP functional and small-core quasirelativistic pseudopotential or fully relativistic four-component methodology. We obtained structural data for 44 elements, M, and our results can be used to infer double-bond lengths for these elements. Our results also suggest that the bonding of these MCH₂ systems can be understood by a simple pictorial approach, even when spin–orbit effects are present.     

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.     

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.     

Synthesis of N,N-bis(trifluoromethyl)amino difluoromethylene trifluorovinyl ether

The first N-containing trifluorovinyl ether monomer (CF₃)₂NCF₂OCFCF₂ was synthesized. The starting perfluoroalkyl imine CF₃–NCF₂ was converted to the perfluoroalkyl amine (CF₃)₂NH by HF. The amine was converted into the carbamoyl fluoride (CF₃)₂NC(O)F via reaction with carbonyl fluoride COF₂ in the presence of NaF. The carbamoyl fluoride was subjected to catalytic fluorination with molecular F₂ in the presence of CsF to afford the hypofluorite (CF₃)₂NCF₂(OF). The hypofluorite was added to CFClCFCl to provide a saturated halocarbon ether. Dechlorination of the ether with zinc in DMSO resulted in the title monomer. The new vinyl ether monomer readily copolymerizes with TFE.     

Density Functional Theory studies on interactions of phosphoryl ligands with the Ca cation: Affinity and associated parameters

DFT (B3LYP/6-31G(d)) and semi-empirical (PM6) calculations of Ca²⁺ affinities on a set of substituted phosphoryl ligands were performed with complete geometry optimization. Two types of ligands were calculated: a set of trivalent [OP(R)] and a set of pentavalent [OP(R)₃] ones (R = H, F, Cl, Br, OH, OCH₃, CH₃, CN, NH₂ and NO₂), with R either directly bound to the phosphorus atom or to the para position of a phenyl ring. The affinity of the Ca²⁺ cation for the ligands was quantified in terms of interaction energy. Additionally, geometric and electronic parameters were correlated with the intensity of that interaction. Our results show that the electronic nature of the substituent mainly affects the interaction energy. Donor groups are associated with more negative interaction energies, while acceptor groups are associated with less negative interaction energies.     

Competition between non-classical and classical hydrogen bonded sites in [BH3CN]: Spectral, energetic, structural and electronic features

Interaction of the salt (Ph₃PNPPh₃)BH₃CN with the various OH and NH proton donors in low polar media was studied by variable temperature (200–290 K) IR spectroscopy and theoretically by DFT calculations. The formation of two types of complexes containing non-classical dihydrogen bond to the hydride hydrogen (DHB) and classical hydrogen bond (HB) to nitrogen lone pair was shown in solution. The 1:1 complexes of both types (XHH and XHN) coexist in the presence of equimolar amount of proton donor. The addition of excess XH-acid leads to the increase of the classical HB content and appearance of the 1:2 complexes, where two basic sites work simultaneously. The structure, spectral characteristics, energy and electron redistribution were studied by DFT (B3LYP) method. The comparison DHB parameters of [BH₃CN]⁻ with those of the unsubstituted analogue [BH₄]⁻ allowed analyzing the electronic effects of the CN group on the basic properties of boron hydride moiety. The electronic influence of the BH₃ group on CN⁻HX hydrogen bond was also established by comparison with the corresponding classical HB to the CN⁻ anion.