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.     

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.     

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.     

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.     

Dihydrogen, dihydride and in between: NMR and structural properties of iron group complexes

Tabulating the structures and characteristic NMR properties of 17 iron complexes, 98 ruthenium complexes and 70 osmium complexes that contain dihydrogen or compressed dihydride ligands reveals a variety of trends. The HH bond lengths increase from similar Fe(II) to Ru(II) to Os(II) complexes. Iron(II) displays a narrow range of HH distances for stable complexes. Electronegative atoms Cl and O, when attached on the metal trans to the dihydrogen ligand, result in elongation of the HH bond relative to more electropositive atoms H, C, P and N. The family of cyclopentadienyl ligands also causes this elongating effect. The dihydrogen ligands with short HH distances and weak interactions with the metal, especially on iron and ruthenium are in the fast spinning regime. One exception is the biporphyrin complex of ruthenium with the side-on bridging H₂ ligand which has an HH distance of 118 pm but is in the fast spinning regime. There are some ruthenium complexes with HH distances greater than 110 pm that are in the slow motion regime and several complexes of osmium with HH distances greater than 130 pm that are in this regime. The large J_HH due to quantum mechanical exchange coupling are observable for some of these osmium complexes with HH distances in the range of 140–160 pm. The dihydrogen ligands in many complexes appear to have librational motions or other motions that place them in the intermediate motion regime. New equations to correlate J_HD with HH distances for ruthenium dihydrogen complexes and for osmium dihydrogen complexes are introduced here.     

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.     

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.     

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.     

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.     

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.     

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).     

Comparative study on interaction between copper (II) and chitin/chitosan by density functional calculation

The DMol³ calculations, based on density functional theory (DFT), have been employed to investigate the interactions between Cu²⁺ and chitin/chitosan residues. The possible initial conformations were optimized at the generalized gradient approximation (GGA) level, with spin unrestricted approach, symmetric unrestriction, doublet multiplicity and BLYP/DND methods. For all initial complexes considered, the Cu²⁺ was completed with H₂O and/or OH⁻ groups to neutralize the initial complexes with hexacoordination geometries. The tendency of ligands to coordinate with Cu²⁺ is NH₂ > C₃OH > H₂O > NHCOCH₃, suggesting that amine groups (NH₂) on chitosan prefer to bind Cu²⁺ and acetamide groups (NHCOCH₃) on chitin lose their coordination with Cu²⁺ in aqueous solution. The geometries of bridge and pendant models have been comparatively analyzed. The results show that bridge model is more favorable than pendant model. In terms of the optimized geometries, the initial hexacoordination structures of Cu²⁺ designed seem more reasonable than initial tetracoordination ones designed.     

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.     

Assessing the MALDI-TOF MS sample preparation procedure to analyze the influence of thermo-oxidative ageing and thermo-mechanical degradation on poly (Lactide)

Multiple processing by means of successive injection cycles was used to simulate the thermo-mechanical degradation effects on the oligomeric distribution of PLA under mechanical recycling. Likewise, an accelerated thermal ageing over PLA glass transition was performed in order to simulate its service life. MALDI-TOF MS was used for the analysis and the sample preparation procedure was assessed by means of a statistical Design of Experiments (DoE). The quality effects in use for the analysis were signal-to-noise ratio and Resolution. Different matrixes, analyte/matrix proportions and the use of NaTFA as cationization agent were considered. A deep inspection of the statistical results provided a better understanding of the influence of the different factors, individually or in combination, to the signal. The application of DoE for the improvement of the MALDI measurement of PLA stated that the best combination of factors (levels) was the following: matrix (s-DHB), proportion analyte/matrix (1/5 V/V), and no use of cationization agent. Degradation primarily affected the initially predominant cyclic [LA_C]_n and linear H[LA_L]_nOH species, where LA stands for a PLA repeating unit. Intramolecular and intermolecular transesterifications as well as hydrolytic and homolytic reactions took place during the formation and disappearance of oligomeric species. In both degradation mechanisms induced by thermal ageing and thermo-mechanical degradation, the formation of H[LA_L]_nOCH₃ by intermolecular transesterifications was highlighted.     

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.     

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.     

A theoretical study on NH bond dissociation enthalpies of oxo, thio and seleno carbamates and their N-protonated and N-deprotonated species

The effect of N-protonation and N-deprotonation on structure, NH bond dissociation enthalpies (BDEs) and stabilities of radicals formed on H-abstraction from nitrogen atom of carbamates and their thio- and seleno-analogs have been investigated. For those molecules where experimental results are available for comparison, the ROB3LYP/6-311++G(d,p)//B3LYP/6-31+G* theoretical level is in agreement within the estimated experimental uncertainty. The NH BDE of carbamates H₂NC(=X)YCH₃ [X = O; Y = O, S, Se] are higher but lower when X = S, Se and Y = O, S, Se in comparison to NH BDE of NH₃. DFT calculations indicate that the NH bond dissociation enthalpies are decreased by protonation and deprotonation at nitrogen atom; but the effect of deprotonation is rather smaller than the protonation. The variations are analyzed in terms of stabilities of molecules, their protonated and deprotonated species along with their respective radicals. The electron delocalization from nitrogen, X and Y atoms, electrostatic interactions, conjugative interactions and spin delocalization are the important factors affecting the stability. The spin delocalization and shift of radical center to chalcogen X (X = S, Se) are the main determinants for radical stability.     

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.