IR Shifts Research Articles

Trans-dioxo Manganese(V) Porphyrins

The relatively stable oxoMn(V) porphyrins generated by oxidation of Mn(III) porphyrins in alkaline solutions using peroxides are unambiguously identified as trans-dioxo species. Raman spectra revealed symmetric OMnVO stretching frequencies between 741 and 744 cm-1 for five porphyrin complexes while the IR of dioxo-MnV-tetrapentafluoroporphyrin [MnV(O2)(TPFPP)]- displayed an antisymmetric stretch at 805 cm-1. Both half-labeled and fully labeled 18O−MnV porphyrin complexes were prepared, and the Raman and IR shifts correspond well with a linear, three-body OMnO oscillator model. Terminal, monooxo formulations such as HO−MnVO or five-coordinate MnVO are excluded by the data. The 1H NMR spectrum of [MnV(O2)(TMP)]-, which shows a single, sharp resonance for the two ortho methyl groups, is also consistent with octahedral coordination of D4h symmetry. The force constant F for the MnO double bond was calculated to be 454 N/m with a stretch−stretch force constant k = 67.2 N/m. Comparison with other Mn−O force constants revealed a very good agreement with Badger's rule spanning five Mn oxidation states. These dioxo-MnV porphyrins were shown to not exchange the oxo oxygens with bulk water solvent. Dioxo MnV porphyrins, which are anionic species [Por-MnV(O)2]-, are unreactive toward olefins in the presence of excess base but efficiently epoxidize cyclooctene upon protonation at −70 °C. These compounds are the only trans-dioxomanganese complexes of any type to be characterized as such, thus extending the known π-bonding arrangements for first-row transition metals.

Single-cell-based sensors and synchrotron FTIR spectroscopy: A hybrid system towards bacterial detection

Microarrays of single macrophage cell-based sensors were developed and demonstrated for potential real-time bacterium detection by synchrotron FTIR microscopy. The cells were patterned on gold electrodes of silicon oxide substrates by a surface engineering technique, in which the gold electrodes were immobilized with fibronectin to mediate cell adhesion and the silicon oxide background was passivated with polyethylene glycol (PEG) to resist protein adsorption and cell adhesion. Cell morphology and IR spectra of single, double, and triple cells on gold electrodes exposed to lipopolysaccharide (LPS) of different concentrations were compared to reveal the detection capability of this cell-based sensing platform. The single-cell-based system was found to generate the most significant and consistent IR spectrum shifts upon exposure to LPS, thus providing the highest detection sensitivity. Changes in cell morphology and IR shifts upon cell exposure to LPS were found to be dependent on the LPS concentration and exposure time, which established a method for the identification of LPS concentration and infected cell population. Possibility of using this single-cell system with conventional IR spectroscopy as well as its limitation was investigated by comparing IR spectra of single-cell arrays with gold electrode surface areas of 25, 100, and 400 μm 2 using both synchrotron and conventional FTIR spectromicroscopes. This cell-based platform may potentially provide real-time, label-free, and rapid bacterial detection, and allow for high-throughput statistical analyses, and portability.

Density functional theory study on lactides: Geometries, IR, NMR and electronic spectra

Density functional theory (DFT) has been used to determine the equilibrium geometries, IR, total energies and NMR chemical shifts of various kinds of lactides. According to the calculations, besides l-lactide and d-lactide, three kinds of meso-lactides have been obtained: meso-i-lactide, meso-α-lactide and meso-β-lactide. The latter two are enantiomers. It indicates that meso-i-lactide with a symmetrical center is a transition state connecting meso-α-lactide and meso-β-lactide, with activation energy only about 6.77 kJ/mol. It is assumed that meso-lactide prepared by previous experiments may be a racemate of meso-α-lactide and meso-β-lactide. The energy of l(or d)-lactide is predicted to be about 4.83 kJ/mol lower than meso-α(or β)-lactide. Time-dependent DFT calculations show that the strongest absorption peaks of l(or d)-lactide and meso-α(or β)-lactide are at about 155 and 158 nm, respectively.

Study of the spectroscopic characteristics of methyl (ligand) cobaloximes and their antibacterial activity

Spectroscopic characterization (IR, NMR and electronic spectra) of methyl (ligand) cobaloxime was done, where ligand = pyrazole, dimethyl pyrazole, alanine and alanine methyl ester. The frequency changes in the IR spectra and shifts in the NMR were explained on the basis of basicity of the ligand, steric hindrance, HSAB principle and dπ-pπ back-bonding from metal to ligand. Alanine and alanine methyl ester form more stable complexes than pyrazole and dimethyl pyrazole. Based on their IR and 1H NMR spectra it is inferred that pyrazole and dimethylpyrazole bind to Co (III) via N-2 ring nitrogen, i.e. monodentate coordination.

Influence of copper ions on the precipitation of goethite and hematite in highly alkaline media

The effects of Cu-dopant on the precipitation of α-FeOOH and α-Fe 2O 3 particles in highly alkaline media were investigated using 57Fe Mössbauer and Fourier transform infrared (FT-IR) spectroscopies and thermal field emission scanning electron microscopy (FE SEM). Only α-(Fe, Cu)OOH solid solutions were obtained between r = 0.0099 and 0.0291, where r = [Cu]/([Cu] + [Fe]). A mixture of α-(Fe, Cu)OOH and α-(Fe, Cu) 2O 3 solid solutions was obtained between r = 0.0385 and 0.0566, whereas only an α-(Fe, Cu) 2O 3 solid solution was obtained between r = 0.0698 and 0.1666. Cu-substitutions in α-(Fe, Cu)OOH and α-(Fe, Cu) 2O 3 decreased the hyperfine magnetic field 〈 B hf〉 values. With increased Cu-substitution in an α-FeOOH type structure the IR shifts were observed. With an increased r value of initial solution a gradual elongation of α-(Fe, Cu)OOH particles along the crystallographic c-axis was observed. At r = 0.0476, some α-(Fe, Cu)OOH particles were ∼700 nm long, and correspondingly the width and thickness of these particles decreased markedly. With a further increase in r the length of α-(Fe, Cu)OOH particles decreased. α-(Fe, Cu) 2O 3 particles showed varying sizes in dependence on the precipitation conditions, whereas their geometrical shapes matched those typical of α-Fe 2O 3.

Determination of the catalytically active oxidation Lewis acid sites in Sn-beta zeolites, and their optimisation by the combination of theoretical and experimental studies

Two types of Lewis acid sites are shown to exist in Sn-beta zeolite: partially hydrolysed framework tin centers ( Si O ) 3Sn OH (sites A) and fully framework coordinated tin atoms Sn( Si O ) 4 (sites B). ONIOM and DFT calculations for adsorbed acetonitrile, which is a probe molecule for Lewis acid sites, show that acetonitrile coordinates more strongly to partially hydrolysed framework Sn (sites A) in Sn-beta zeolite than to nonhydrolysed framework Sn (sites B). The corresponding IR bands associated with the ν(C N) stretching vibration were also calculated. Adsorption–desorption experiments of deuterated acetonitrile on Sn-beta give two IR bands at 2316 and 2308 cm −1 with IR shifts of 43 and 51 cm −1 with respect to gas-phase acetonitrile. These values are in excellent agreement with theoretical calculations, making it possible then to associate the Lewis sites related to 2316 and 2308 cm −1 with partially hydrolysed and nonhydrolysed framework Sn sites, respectively. Catalytic results confirm that partially hydrolysed Sn (sites A) is much more active than fully framework-integrated Sn (sites B) for Baeyer–Villiger oxidation of cyclic ketones. Finally, the ratio between these two types of sites could be influenced by postsynthesis treatments.

Dibenzodioxin Adsorption on Inorganic Materials

Dibenzodioxin adsorption/desorption on solid surfaces is an important issue associated with the formation, adsorption, and emission of dioxins. Dibenzodioxin adsorption/desorption behaviors on inorganic materials (amorphous/mesoporous silica, metal oxides, and zeolites) were investigated using in situ FT-IR spectroscopy and thermogravimetric (TG) analysis. Desorption temperatures of adsorbed dibenzodioxin are very different for different kinds of inorganic materials: approximately 200 degrees C for amorphous/mesoporous silica, approximately 230 degrees C for metal oxides, and approximately 450 degrees C for NaY and mordenite zeolites. The adsorption of dibenzodioxin can be grouped into three categories according to the red shifts of the IR band at 1496 cm(-1) of the aromatic ring for the adsorbed dibenzodioxin: a shift of 6 cm(-1) for amorphous/mesoporous silica, a shift of 10 cm(-1) for metal oxides, and a shift of 14 cm(-1) for NaY and mordenite, suggesting that the IR shifts are proposed to associated with the strength of the interaction between adsorbed dibenzodioxin and the inorganic materials. It is proposed that the dibenzodioxin adsorption is mainly via the following three interactions: hydrogen bonding with the surface hydroxyl groups on amorphous/mesoporous silica, complexation with Lewis acid sites on metal oxides, and confinement effect of pores of mordenite and NaY with pore size close to the molecular size of dibenzodioxin.

Structures and properties of octaethylporphinato(phenolate)iron(III) complexes with NH⋯O hydrogen bonds: modulation of Fe–O bond character by the hydrogen bond

Iron(III) porphinate complexes of phenolate that have NH⋯O hydrogen bonds on the coordinating oxygen, [Fe III(OEP){O-2,6-(RCONH) 2C 6H 3}] (R = CF 3 ( 1), CH 3 ( 3)) and [Fe III(OEP)(O-2-RCONHC 6H 4)] (R = CF 3 ( 2), CH 3 ( 4)) (OEP = 2,3,7,8,12,13,17,18-octaethyl-21 H, 23 H-porphinato), were synthesized and characterized as models of heme catalase. The presence of NH⋯O hydrogen bonds was established by their crystal structures and IR shifts of the amide NH band. The crystal structure of 1 shows an extremely elongated Fe–O bond, 1.926(3) Å, compared to 1.887(2) Å in 2 or 1.848(4) Å in [Fe III(OEP)(OPh)]. The NH⋯O hydrogen bond decreases an electron donation from oxygen to iron, resulting in a long Fe–O bond and a positive redox potential.

Hydrogen bonding in diols and binary diol-water systems investigated using DFT methods. II. Calculated infrared OH-stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding.

Although the two hydroxyl groups in 1,2-diols interact as evidenced by NMR and IR spectroscopic shifts, electron density topological analysis has shown a bond critical point (BCP) and atomic bond path to be absent (Klein, R. A.; J Comp Chem 2002, 23, 585-599; J Am Chem Soc 2002, 124, 13931-13937), indicating that no intramolecular hydrogen bond is formed. Here, we demonstrate that small NMR or IR shifts are neither necessarily diagnostic nor sufficient as indicators of hydrogen bond formation; moreover, modified van der Waals atomic radii are needed for estimating maximum nuclear interaction distances and nuclear interpenetration.

DFT study on cooperativity in the interactions of hydrazoic acid clusters

AbstractDensity functional theory at the B3LYP level with the 6‐311G** basis set is performed to calculate the systems consisting of up to four hydrazoic acid molecules. The dimers are found to exhibit cyclic and chain structures with N … H contacts at ca. 2.1–2.7 Å. However, there are only cyclic structures with N … H contacts at ca. 2.0–2.3 Å and 2.0–2.1 Å in the trimer and tetramer, respectively. Hydrogen bond distances in the trimer and tetramer are shorter than those in the cyclic dimer as a result of the stronger interaction between molecules. The contribution of cooperative effect to the interaction energy is significant. After the correction of the basis set superposition error and zero‐point energy, the binding energies are −10.69, −29.34, and −54.26 kJ·mol−1 for the most stable dimer, trimer, and tetramer, respectively. The calculated IR shifts for NH stretching mode increase with the size of the cluster growths, reaching more than 200 cm−1 in the tetramer. For the most stable clusters, the transition from the monomer to dimer, dimer to trimer, and trimer to tetramer involve changes of −14.40, −25.68, and −31.88 kJ·mol−1 for the enthalpies at 298.15 K and 1atm, respectively. We also perform Mulliken populations analysis and find the Mulliken populations on intermolecular N … H increasing in the sequence of the dimer, trimer, and tetramer. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 279–286, 2003

Reduction and Oxidation of the Arachno Clusters Fe2(CO)6(μ-S)2PtL2: Characterization of Distinct One- and Two-Electron Transfer Sites in Heteropolynuclear Compounds

The reduction and oxidation properties of the arachno-heteropolynuclear metal clusters Fe2(CO)6(μ3-S)2PtL2, where L2 = bipyridine (1), phenanthroline (2), diphenylphosphinoethane (3), diphenylphosphinoferrocene (4), or cyclooctadiene (5), have been examined by electrochemistry, IR spectroscopy, and ESR spectroscopy. An electron-transfer series involving up to five electrons is observed. The common characteristics are a fully reversible one-electron oxidation process to a monocation (in the range 0.13−0.38 V vs ferrocene) and a chemically reversible but electrochemically quasi-reversible two-electron reduction process (range −1.9 to −2.4 V). Complexes 1 and 2 also display a fully reversible one-electron reduction at a potential less negative (ca. −1.8 V) than the subsequent two-electron reduction. The LUMOs of 1 and 2 are predicted by EHMO calculations to be primarily π*-diimine based. Spectral data from the monoanions 1- and 2- are consistent with this orbital assignment: very small shifts of the metal−carbonyl IR frequencies (ca. −13 cm-1) from those of the neutral complexes are observed, and the 195Pt hyperfine splitting in ESR spectra is very small compared to that expected for a metal-localized radical. The two-electron reductions forming, e.g., 13- or 32-, appear to involve the Fe2S2 moiety and most likely are concomitant with breaking and making of an Fe−Fe bond. Carbonyl IR energies are lowered in excess of 100 cm-1 in the two-electron reduction. The oxidation processes appear to be localized on the Fe2(CO)6S2 fragment, with IR shifts of 46−76 cm-1 for 1+−5+ and small 195Pt hyperfine splittings. X-ray crystal structures are reported for 2 and 5.

Energetics of the Gas Phase Hydrates of trans-Formanilide: A Microscopic Approach to the Hydration Sites of the Peptide Bond

The energy of binding a water molecule to two H-bonded sites of trans-N-phenyl formamide (formanilide), an amide molecule that mimics the planar −NH−CO− peptide bond, has been measured in the gas-phase and calculated by an ab initio study. For the first time, the D0 dissociation energy of two 1:1 complexes, simultaneously observed in a supersonic expansion, is measured experimentally. They are found to be very similar. At the CO site, the water molecule acts as a proton donor and the H-bond has a energy of 5.40 ± 0.28 kcal/mol. At the NH site, the water acts as an acceptor and the binding energy is 5.65 ± 0.30 kcal/mol. Comparison of IR shifts with binding energies shows that they do not always correlate when the donor groups are different.

Investigations of Time-Dependent Delocalization and the Correlation of Carbonyl IR Shifts with ΔE1/2Values for Hydrocarbon-Linked Class II and Class III Mixed-Valent Complexes

A series of fulvalenediyl-bridged dimanganese complexes has been studied by electrochemistry and by IR, optical, and ESR spectroscopic methods. The redox site is based on the Mn(I) moiety (C5H4R)Mn(CO)2PPh3 and variations thereof. Six dinuclear complexes are each oxidized in two one-electron steps with E1/2 separations (ΔE1/2) of between 80 and 450 mV. Each of the monocations exhibits trapped valence by IR spectroscopy. Analysis of the carbonyl stretching frequencies of the mixed-valent systems allows calculation of a charge distribution parameter, Δρ, that estimates the relative charges at the two redox sites and which correlates linearly with the ΔE1/2 values. This correlation extends to mixed-valent Cr(I)Cr(0) systems linked by a biphenyl bridge. The doubly linked system [(Fulv){Mn(CO)2}2(μ-dppm)]-, 1+, displays trapped valence in its IR spectra, but delocalized valence in its ESR spectra, implying a time-dependent delocalization process.

Solvent effects on infrared, 13C and 31P NMR spectra of trimethyl phosphate : Part 1. Single solvent systems

Infrared and multinuclear magnetic resonance spectroscopy (NMR) studies of trimethyl phosphate in 24 different solvents were undertaken to investigate the solute–solvent interactions and to correlate solvent properties such as acceptor number and dielectric constant with the infrared band shift and the 13C and 31P NMR chemical shifts. Furthermore the cross-correlation between the infrared and NMR shifts in different solvents was studied. The results demonstrate that in general there is a correlation between IR and NMR shifts: the infrared, 13C and 31P shifts can be predicted for most solvents used in this study, if one of them is known.

The first basicity scale of fluoro-, chloro-, bromo- and iodo-alkanes: some cross-comparisons with simple alkyl derivatives of other elements

Formation constants (Kf) are determined for the 1∶1 hydrogen-bonded complexes between 4-fluorophenol and 42 halogenoalkanes, in CCl4 at 298 K, by FTIR spectrometry. A base parameter, pKHB = log Kf, has been defined which measures, for the first time, the relative hydrogen-bond acceptor strength of the halogens. Comparison with the basicity of group 15 and 16 elements shows that halogens are very weak bases, in the order: N O > P > S > Se > F > Cl ≈ Br ≈ I. Attempts at correlations of pKHBvs. electronegativity or vs. hardness lead to general scatter diagrams which may be partially resolved into separate trends within a given group of the periodic table. The pKHB scale of halogenoalkanes extends from +0.26 for 1-fluoroadamantane to –0.70 for 1,1,1-trichloroethane (statistically corrected to –1.15 per chlorine atom). The main substituent effects explaining these pKHB variations are for a given halogen: (i) field-inductive effects (polyhalogenoalkanes), (ii) resonance effects (cyclopropyl bromide), and (iii) polarizability effects (alkyl halides). The steric effects of bulky alkyl substituents do not appear to be significant since the basicity increases with the lengthening and branching of the alkyl groups (from methyl to 1-adamantyl). For a given halogen, pKHB increases linearly with the infrared shift, Δν(OH), produced by hydrogen bonding. However, as the group 17 is descended, IR shifts do not parallel pKHB. An increasing sensitivity of IR shifts to polarizability is suggested when going from group 15 to group 17.

Charge transfer and electron-vibron coupling in dense solid hydrogen

Abstract We examine the role of charge transfer (CT) interactions in dense molecular hydrogen in relation to recently observed spectroscopic properties at megabar pressures. Specifically, we consider virtual H 2 + H 2 − states in which an electron is transferred to a neighbor. The Mulliken CT integral t admixes H 2 + H 2 − fluctuations of overlapping molecules. The amplitude of the charge fluctuations is the ionicity γ, which is found in H 2 dimers and lattices with nonoverlapping valence and conduction bands for t small compared to the CT excitation energy ω CT . Vibronic coupling within a dimer is found using a Herzberg-Teller expansion and gives explicit expressions for vibron shifts in Raman and IR spectra and for IR oscillator strength due to electron-vibron coupling. We estimate linear electron-vibron coupling constants and other parameters required to interpret the vibrational data at and above the 150-GPa transition of dense hydrogen within a CT model. We discuss important structural implications of equal IR and Raman shifts at the transition and relate anisotropic CT processes to the orientational state of the dense molecular solid.

Delocalization Contributions to Polyacetylene Force Fields

Abstract The force fields of trans and cis-polyacetylene(PA) are obtained in internal coordinates by combining linear-response analysis of the Raman and ir shifts due to π-electrons, molecular force-field methods, and the Huckel susceptibility of k ≠ 0 phonons. We find transferable electron-phonon coupling constants, exponential transfer integrals t(R), and coupling to CCC bends through the Coulomb potential V(R). The electronic response of cis-PA is 56% of the trans susceptibility, indicative of reduced delocalization and an energy gap in the Ag manifold due to third-neighbor V(R) terms.

Pariser–Parr–Pople force field for π-electrons: Raman and infrared shifts of trans-polyacetylene

The transfer integrals t(R) and Coulomb potential V(R) of π-electron Hamiltonians He define linear electron–phonon (e–ph) coupling constants t′(R) and V′(R) for the equilibrium structure. We generalize linear response (LR) theory for Raman and ir shifts due to π-electron delocalization in Hamiltonians with arbitrary t(R) and spin independent V(R). π-electron contributions ΔFij to the force field of trans-polyacetylene (PA) are obtained in the symmetry coordinates Si, with i=1–5, for k=0 phonons. We compare ΔFij for Hückel chains with alternating transfer integrals t(1±δ) and for Pariser–Parr–Pople (PPP) models with hydrocarbon parameters derived from π–π* spectra to a phenomenological ΔFij for trans-PA and its isotopes. An exponential rather than linear t(R) is found. The molecular PPP potential V(R) accounts quantitatively for π-electron coupling to CCC bends and for the length dependence of the Raman shifts of finite polyenes. The dominant but not exclusive π-electron coupling remains the dimerization coordinate singled out in previous treatments, with substantially larger t′(R) than V′(R) contributions in the PPP force field. We comment on extensions of LR theory to PA models with interacting π-electrons and several electronic susceptibilities.

Boron oxides: Ab initio studies with natural bond orbital analysis

We employ ab initio theory and natural bond orbital (NBO) analysis to describe the structure, energetics, vibrational properties, and bonding in small boron oxides, BmOn, supplementing recent studies on isovalent aluminum oxide clusters, Al2On, in order to extend the overview of bonding tendencies in group IIIA metal oxides. The comparison of analogous boron and aluminum species reveals many surprising differences, such as the V-shaped (M=B) vs linear (M=Al) geometry of M2O3, the altered tendency toward cyclic structures (higher for M2O2 with M=Al, for M3O3 with M=B), and the diminished role of electron correlation in the boron congeners. Correlation effects are examined by a recently introduced selective, localized multiconfigurational approach. Differences in bonding patterns are traced to basic hybridization and electronegativity shifts (reduced ionic character of B–O vs Al–O bond). Detailed comparisons with recent experimental BmOn data (including isotopomer ir shifts) provide additional support for theoretical assignments in corresponding aluminum species, where significant disagreements between theory and experiment persist.

The role of nonbond and charge flux in hydrogen bond interactions. The effect on structural changes and spectral shifts in water dimer

An analysis of Hessian matrix elements in molecular systems is presented. It is shown that elements that couple nonbonded atoms lead to an exact pairwise decomposition of intermolecular potential energy surfaces. The analysis further shows that potential energy surfaces of dimers in general contain terms that couple inter and intramolecular coordinates. Such terms arise from the ‘‘flux’’ of the internal charge distribution as the monomers distort in response to each other. These fluxes may be represented analytically by allowing atomic parameters such as point charges and van der Waals parameters to be coordinate dependent. Three hydrogen bonded dimers are studied in some detail with special focus on the short-range nonbond repulsions. It is shown that the pairwise hydrogen bond interactions in water–water, water–formaldehyde, and water–formamide are very similar, and that the nonbond flux is effective mainly along the O–H bond of the donor water molecule. The flux and the functional form of the nonbonded interaction in the water dimer are parametrized. Intramolecular structural changes and IR shifts and splittings in this system are shown to be strongly dependent on charge and nonbond flux terms. It is suggested that such flux terms provide a general mechanism for controlling structural and spectral changes in dimers.