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.     

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.     

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 selective oxidation of ethanol to CO2 at Ptpc/Ir/Pt metallic multilayer nanostructured electrodes

In this work, Pt_pc/Ir/Pt metallic multilayer nanostructured electrodes were prepared. The composition and number of the constituent metal layers were varied and the number of Ir and Pt layers studied were: 1.5:1.5, 1.5:10, 10:1.5, 10:10 and 250:250 Ir and Pt monolayers. The ethanol electrooxidation reaction and its products was studied using electrochemical in situ FTIR technique and could be observed as a selective cleavage of the ethanol CC bond in acidic electrolyte. Neither acetaldehyde nor acetic acid IR band could be observed for ethanol electrooxidation at 1.5 V vs. RHE over Pt_pc/Ir₂₅₀/Pt₂₅₀ metallic multilayer electrodes. Also, the enhancement on CO₂ production over this electrode was more than six times the amount observed using the Pt_pc electrodes. Thus, the complete CC cleavage bond in ethanol molecule was observed, leading only CO₂ as reaction product.     

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.     

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.     

Quantum mechanical studies of the protonation and NBr bond dissociation of the biologically important N-bromosuccinimide

N-Bromosuccinimide (NBS) is a brominating and oxidizing agent that is used as a source of bromine. The proton affinities, the tautomeric forms and NBr bond dissociation of NBS have been computed using the B3LYP functional as implemented in the density functional approach. The electronic structures of all possible tautomeric forms of NBS have been thoroughly investigated. The keto form of NBS has been shown to be more stable than any other tautomeric forms. The geometries and relative energies for various stationary structures were determined. The results indicate clearly that O-site protonation is strongly favored over N-site protonation for the studied compound in case of mono- and di-protonation. The bond dissociation energies (BDEs), involving the formation of the bromine radical, cation, and anion, of the NBr bond have been investigated. The NBr BDE of the Br radical formation is lower than that of the Br anion or cation. These conclusions are in good agreement with the experimental results.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

Facile hydrosilylation of norbornadiene by silanes R3SiH and R2SiH2 with molybdenum catalysts

Photochemically activated [Mo(CO)₆] and [Mo(CO)₄(η⁴-nbd)] have been demonstrated to be very effective catalysts for hydrosilylation of norbornadiene (nbd) by tertiary (Et₃SiH, Cl₃SiH) and secondary (Et₂SiH₂ and Ph₂SiH₂) silanes to give 5-silyl-2-norbornene, which under the same reaction conditions transform in ring-opening metathesis polymerization (ROMP) to unsaturated polymers and to a double hydrosilylation product, 2,6-bis(silyl)norbornane. The yield of a particular reaction depends very strongly on the kind of silane involved. The reaction products were identified by means of chromatography (GC–MS) and ¹H and ¹³C NMR spectroscopy. In photochemical reaction of [Mo(CO)₄(η⁴-nbd)] and Ph₂SiH₂ in cyclohexane-d₁₂, η²-coordination of the SiH bond to the molybdenum atom is supported by ¹H NMR spectroscopy due to the detection of two equal-intensity doublets with ²J_HH = 5.4 Hz at δ 6.12 and −5.86 ppm.     

(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.     

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.     

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.