Vibrational Spectroscopic Characterization Research Articles

Vibrational Spectroscopic Characterization and DFT Study of Palladium(II) Complexes with N-Benzyliminodiacetic Acid Derivatives

The reactions of N-benzyliminodiacetic acid (BnidaH2) and its para-substituted derivatives, namely N-(p-chlorobenzyl)iminodiacetic acid (p-ClBnidaH2), N-(p-nitrobenzyl)iminodiacetic acid (p-NO2BnidaH2), and N-(p-methoxybenzyl)iminodiacetic acid (p-MeOBnidaH2) with sodium tetrachloropalladate(II) were performed in aqueous solutions. Three new complexes [Pd(p-ClBnidaH)2]·2H2O (2), [Pd(p-NO2BnidaH)2]·2H2O (3), and [Pd(p-MeOBnidaH)2] (4) were prepared and characterized by infrared spectroscopy and thermogravimetric and differential thermal analyses. The molecular geometry and infrared spectra of these three complexes, together with the previously synthesized [Pd(BnidaH)2]·2H2O (1a) and [Pd(BnidaH)2] (1b) were also modelled using density functional theory calculations at the BP86/6–311+G(d,p) level of theory with SDD pseudopotentials.

Interaction of cisplatin with 5'-dGMP: a combined IRMPD and theoretical study.

IR multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH3)2(5'-dGMP-H)](+) and cis-[PtCl(NH3)2(5'-dGMP)](+) ions (where 5'-dGMP is 2'-deoxyguanosine-5'-monophosphate), generated in the gas phase by electrospray ionization, was performed in two spectral regions, namely, 700-1900 cm(-1) and 2800-3800 cm(-1). For structural assignment, experimental IRMPD spectra were compared to IR spectra computed at the B3LYP/LACV3P/6-311G** level of theory. In agreement with computational results, the vibrational spectroscopic characterization of the cis-[Pt(NH3)2(5'-dGMP-H)](+) ion points to macrochelate species resulting from the simultaneous interaction of the metal with both the N7 atom of the guanine residue and an O atom of the phosphate group, structures that bear features in common with those characterized in solution by NMR spectroscopy. Concerning the cis-[PtCl(NH3)2(5'-dGMP)](+) ion, our study points to a monodentate complex involving exclusively the N7 position of guanine, as observed in solution. Also this species exhibits a compact form due to the formation of two hydrogen bonds involving the same ammonia ligand. For both complexes, IRMPD experiments show that a strong intramolecular hydrogen bond is established between one ammonia hydrogen and the carbonyl group of guanine. The strength of this particular interaction can be qualitatively estimated by looking at the redshift of the CO vibration with respect to an unperturbed C═O stretching mode in the fingerprint region. This point is also highlighted in the X-H (X = N, O) stretch region, by the shift of the N-H stretch frequency as a function of the number of hydrogen bonds involving the ammonia ligand.

Escherichia coli auxotroph host strains for amino acid-selective isotope labeling of recombinant proteins.

Enrichment of proteins with isotopes such as (2)H, (15)N, and (13)C is commonly carried out in magnetic resonance and vibrational spectroscopic characterization of protein structures, mechanisms, and dynamics. Although uniform isotopic labeling of proteins is straightforward, efficient labeling of proteins with only a selected set of amino acid types is often challenging. A number of approaches have been described in the literature for amino acid-selective isotope labeling of proteins, each with its own limitations. Since Escherichia coli represents the most cost-effective and widely used host for heterologous production of foreign proteins, an efficient method to express proteins selectively labeled with isotopes would be highly valuable for these studies. However, an obvious drawback is misincorporation and dilution of input isotope labels to unwanted amino acid types due to metabolic scrambling in vivo. To overcome this problem, we have generated E. coli auxotroph strains that are compatible with the widely used T7 RNA polymerase overexpression systems and that minimize metabolic scrambling. We present several examples of selective amino acid isotope labeling of simple and complex proteins with bound cofactors, as an initial guide for practical applications of these E. coli strains.

Surface enhanced resonance Raman detection of a catalytic intermediate of DyP-type peroxidase.

We report herein the vibrational spectroscopic characterisation of a catalytic intermediate formed by the reaction of H2O2 with DyP-type peroxidase immobilised on a biocompatible coated metal support. The SERR spectroscopic approach is of general applicability to other peroxidases which form relatively stable catalytic intermediates.

Vibrational Spectroscopic Characterization of the Arsenate Mineral Barahonaite: Implications for the Molecular Structure

ABSTRACT The mineral barahonaite is in all probability a member of the smolianinovite group. The mineral is an arsenate mineral formed as a secondary mineral in the oxidized zone of sulphide deposits. We have studied the barahonaite mineral using a combination of Raman and infrared spectroscopy. The mineral is characterized by a series of Raman bands at 863 cm−1 with low wavenumber shoulders at 802 and 828 cm−1. These bands are assigned to the arsenate and hydrogen arsenate stretching vibrations. The infrared spectrum shows a broad spectral profile. Two Raman bands at 506 and 529 cm−1 are assigned to the triply degenerate arsenate bending vibration (F 2, ν4), and the Raman bands at 325, 360, and 399 cm−1 are attributed to the arsenate ν2 bending vibration. Raman and infrared bands in the 2500–3800 cm−1 spectral range are assigned to water and hydroxyl stretching vibrations. The application of Raman spectroscopy to study the structure of barahonaite is better than infrared spectroscopy, probably because of the much higher spatial resolution.

Vibrational spectroscopic characterization of the phosphate mineral barbosalite [formula omitted] – Implications for the molecular structure

Natural single-crystal specimens of barbosalite from Brazil, with general formula Fe2+Fe23+(PO4)2(OH)2 were investigated by Raman and infrared spectroscopy. The mineral occurs as secondary products in granitic pegmatites. The Raman spectrum of barbosalite is characterized by bands at 1020, 1033 and 1044cm−1cm−1, assigned to ν1 symmetric stretching mode of the HOPO33- and PO43- units. Raman bands at around 1067, 1083 and 1138cm−1 are attributed to both the HOP and PO antisymmetric stretching vibrations. The set of Raman bands observed at 575, 589 and 606cm−1 are assigned to the ν4 out of plane bending modes of the PO4 and H2PO4 units. Raman bands at 439, 461, 475 and 503cm−1 are attributed to the ν2 PO4 and H2PO4 bending modes. Strong Raman bands observed at 312, 346cm−1 with shoulder bands at 361, 381 and 398cm−1 are assigned to FeO stretching vibrations. No bands which are attributable to water vibrations were found. Vibrational spectroscopy enables aspects of the molecular structure of barbosalite to be assessed.

Vibrational spectroscopic characterization of growth bands in Porites coral from South China Sea

A series of samples from different growth bands of Porites coral skeleton were studied using Raman, infrared reflectance methods. The Raman spectra proved that skeleton samples from different growth bands have the same mineral phase as aragonite, but a band at 133cm−1 for the top layer shows a transition from ∼120cm−1 for vaterite to ∼141cm−1 for aragonite. It is inferred that the vaterite should be the precursor of aragonite of coral skeleton. The positional shift in the infrared spectra of the skeleton samples from growth bands correlate significantly to their minor elements (Li, Mg, Sr, Mn, Fe and U) contents. Mg, Sr and U especially have significant negative correlations with the positions of the antisymmetric stretching band ν3 at ∼1469cm−1. And Li shows a high negative correlation with ν2 band (∼855cm−1), while Sr and Mn show similar negative correlation with ν4 band (∼712cm−1). And Mn also shows a negative correlation with ν1 band (∼1082cm−1). A significantly negative correlation is observed for U with ν1+ν4 band (∼1786cm−1). However, Fe shows positive correlation with ν1, ν2, ν3, ν4 and ν1+ν4 bands shifts, especially a significant correlation with ν1 band (∼1082cm−1). New insights into the characteristics of coral at different growth bands of skeleton are given in present work.

Vibrational spectroscopic characterization of the sulphate mineral leightonite K2Ca2Cu(SO4)4⋅2H2O – Implications for the molecular structure

The mineral leightonite, a rare sulphate mineral of formula K2Ca2Cu(SO4)4⋅2H2O, has been studied using a combination of electron probe and vibrational spectroscopy. The mineral is characterized by an intense Raman band at 991cm−1 attributed to the SO42- ν1 symmetric stretching mode. A series of Raman bands at 1047, 1120, 1137, 1163 and 1177cm−1 assigned to the SO42- ν3 antisymmetric stretching modes. The observation of multiple bands shows that the symmetry of the sulphate anion is reduced. Multiple Raman and infrared bands in the OH stretching region shows that water in the structure of leightonite is in a range of molecular environments.

Vibrational spectroscopic characterization of the phosphate mineral phosphophyllite – Zn2Fe(PO4)2·4H2O, from Hagendorf Süd, Germany and in comparison with other zinc phosphates

This research was undertaken on phosphophyllite sample from the Hagendorf Süd pegmatite, Bavaria, Germany. Chemical analysis was carried out by Scanning Electron Microscope in the EDS mode and indicates a zinc and iron phosphate with partial substitution of manganese, which partially replaced iron. The calculated chemical formula of the studied sample was determined to be: Zn2(Fe0.65, Mn0.35)∑1.00(PO4)2·4(H2O). The intense Raman peak at 995cm−1 is assigned to the ν1PO43- symmetric stretching mode and the two Raman bands at 1073 and 1135cm−1 to the ν3PO43- antisymmetric stretching modes. The ν4PO43- bending modes are observed at 505, 571, 592 and 653cm−1 and the ν2PO43- bending mode at 415cm−1. The sharp Raman band at 3567cm−1 attributed to the stretching vibration of OH units brings into question the actual formula of phosphophyllite. Vibrational spectroscopy enables an assessment of the molecular structure of phosphophyllite to be assessed.

Vibrational spectroscopic characterization of the phosphate mineral ludlamite (Fe,Mn,Mg)3(PO4)2⋅4H2O – A mineral found in lithium bearing pegmatites

The objective of this work is to analyze ludlamite (Fe,Mn,Mg)3(PO4)2⋅4H2O from Boa Vista mine, Galiléia, Brazil and to assess the molecular structure of the mineral. The phosphate mineral ludlamite has been characterized by EMP-WDS, Raman and infrared spectroscopic measurements. The mineral is shown to be a ferrous phosphate with some minor substitution of Mg and Mn.Raman bands at 917 and 950cm−1 are assigned to the symmetric stretching mode of HOPO32- and PO43- units. Raman bands at 548, 564, 599 and 634cm−1 are assigned to the ν4PO43- bending modes. Raman bands at 2605, 2730, 2896 and 3190cm−1 and infrared bands at 2623, 2838, 3136 and 3185cm−1 are attributed to water stretching vibrations. By using a Libowitzky empirical function, hydrogen bond distances are calculated from the OH stretching wavenumbers. Strong hydrogen bonds in the structure of ludlamite are observed as determined by their hydrogen bond distances. The application of infrared and Raman spectroscopy to the study of ludlamite enables the molecular structure of the pegmatite mineral ludlamite to be assessed.

A simple and highly efficient route to the synthesis of NaLnF4–Ag hybrid nanorice with excellent SERS performances

This paper reports the synthesis of a new class of NaLnF(4)-Ag (Ln = Nd, Sm, Eu, Tb, Ho) hybrid nanorice and its application as a surface-enhanced Raman scattering (SERS) substrate in chemical analyses. Rice-shaped NaLnF(4) nanoparticles as templates are prepared by a modified hydrothermal method. Then, the NaLnF(4) nanorice particles are decorated with Ag nanoparticles by magnetron sputtering method to form NaLnF(4)-Ag hybrid nanostructures. The high-density Ag nanogaps on NaLnF(4) can be obtained by the prolonging sputtering times or increasing the sputtering powers. These nanogaps can serve as Raman 'hot spots', leading to dramatic enhancement of the Raman signal. The NaLnF(4)-Ag hybrid nanorice is found to be robust and is an efficient SERS substrate for the vibrational spectroscopic characterization of molecular adsorbates; the Raman enhancement factor of Rhodamine 6G (R6G) absorbed on NaLnF(4)-Ag nanorice is estimated to be about 10(13). Since the produced NaLnF(4)-Ag hybrid nanorice particles are firmly fastened on a silicon wafer, they can serve as universal SERS substrates to detect target analytes. We also evaluate their SERS performances using 4-mercaptopyridine (Mpy), and 4-mercaptobenzoic acid (MBA) molecules, and the detection limit for Mpy and MBA is as low as 10(-12) M and 10(-10) M, respectively, which meets the requirements of the ultratrace detection of analytes. This simple and highly efficient approach to the large-scale synthesis of NaLnF(4)-Ag nanorice with high SERS activity and sensitivity makes it a perfect choice for practical SERS detection applications.

Mid-infrared vibrational spectroscopic characterization of 5,6-dihydroxyindole and eumelanin derived from it

Mid-infrared vibrational spectroscopic study has been made on 5,6-dihydroxyindole (DHI) and DHI-derived eumelanin. It has been revealed for DHI monomer that measured infrared absorption spectrum is well reproduced by that predicted from ab initio calculations. Thus, vibrational modes of DHI monomer causing dominant absorption bands have been successfully assigned. It has been also reconfirmed that DHI-derived eumelanin includes indolequinone and/or quinone methide units in addition to DHI units.

Vibrational Spectroscopic Characterization of Hematite, Maghemite, and Magnetite Thin Films Produced by Vapor Deposition

Thin films of three iron oxide polymorphs, hematite, maghemite, and magnetite, were produced on KBr substrates using a conventional electron beam deposition technique coupled with thermal annealing. This method allowed for iron oxide thin films free from chemical precursor contaminants. The films were characterized using Fourier-transform infrared spectroscopy (FTIR), Raman microspectroscopy, and ellipsometry. These spectroscopic techniques allowed for a clear assignment of the phase of the iron oxide polymorph films produced along with an examination of the degree of crystallinity possessed by the films. The films produced were uniform in phase and exhibited decreasing crystallinity as the thickness increased from 40 to 250 nm.

Vibrational and chiroptical spectroscopic characterization of γ‐turn model cyclic tetrapeptides containing two β‐Ala residues

The optical spectroscopic characterization of gamma-turns in solution is uncertain and their distinction from beta-turns is often difficult. This work reports systematic ECD and vibrational circular dichroism (VCD) spectroscopic studies on gamma-turn model cyclic tetrapeptides cyclo(Ala-beta-Ala-Pro-beta-Ala) (1), cyclo(Pro-beta-Ala-Pro-beta-Ala) (2) and cyclo(Ala-beta-Ala-Ala-beta-Ala) (3). Conformational analysis performed at the 6-31G(d)/B3LYP level of theory using an adequate PCM solvent model predicted one predominant conformer for 1-3, featuring two inverse gamma-turns. The ECD spectra in ACN of 1 and 2 are characterized by a negative n-->pi* band near 230 nm and a positive pi-->pi* band below 200 nm with a long wavelength shoulder. The ECD spectra in TFE of 1-3 show similar spectra with blue-shifted bands. The VCD spectra in ACN-d(3) of 1 and 2 show a +/-/+/- amide I sign pattern resulting from four uncoupled vibrations in the case of 1 and a sequence of two positive couplets in the case of 2. A -/+/+/- amide I VCD pattern was measured for 3 in TFE-d(2). All three peptides give a positive couplet or couplet-like feature (+/-) in the amide II region. VCD spectroscopy, in agreement with theoretical calculations revealed that low frequency amide I vibrations (at approximately 1630 cm(-1) or below) are indicative of a C(7) H-bonded inverse gamma-turns with Pro in position 2, while gamma-turns encompassing Ala absorb at higher frequency (above 1645 cm(-1)).

Colorimetric and vibrational spectroscopic characterization of weathered surfaces of wood and rigid polyvinyl chloride–wood flour composite lumber

Rigid polyvinyl chloride–wood flour composite lumber containing either pine or maple wood flour and pine and maple lumber was subjected to accelerated weathering according to the ASTM Standard G 53 protocol. Non-weathered and weathered surfaces of all specimens were analyzed using colorimetric methods, reflectance infrared Fourier transform and Raman spectroscopic techniques. In the FT-IR spectra, conjugated ketones (1,744 cm−1) of lignin as evidenced by their skeletal vibrations (1,560–1,500 cm−1) and stretching (1,440–1,500 cm−1) were reduced in weathered specimens. Cellulose was largely unaffected by weathering. C–O bending vibrations at 1,040 cm−1 from holocellulose in pine specimens and intensity bands at 1,125–1,090 and 1,360 cm−1 (C–O stretching and O–H bending from cellulose) in the maple and wood–plastic composite (WPC)-maple specimens were unaffected. A band at 1,650 cm−1 became prominent after weathering of both pine and maple WPC specimens which is due to C=C–C=C stretching vibration of weathered PVC portion of the specimen. Raman shifts at 530 and 840–900 cm−1 are attributed to C–O and C–C–O stretching in cellulose (remain unchanged). The role of extractives in weathering of pine is shown by the disappearance of Raman shifts at 392 and 434 cm−1 (C=C deformations in pine extractives) in weathered pine. One-Way ANOVA, between-group designs showed significant effect on brightness (L*), redness (a*) and yellowness (b*) for all treatments.

Agnanostructures assembled on magnetic particles for ready SERS-based detection of dissolved chemical species

In this investigation, a novel one-step fabrication of Ag-deposited Fe(2)O(3) particles and their application as surface-enhanced Raman scattering (SERS) substrates in chemical analyses are demonstrated. To deposit Ag onto them, Fe(2)O(3) particles were dispersed in a reaction mixture consisting of ethanolic AgNO(3) and butylamine, and then the reaction mixture was incubated and shaken for 40 min at 50 degrees C. The Ag-deposited Fe(2)O(3) particles are found to be efficient SERS substrates for the vibrational spectroscopic characterization of molecular adsorbates prepared in a similar way on silver surfaces; the enhancement factor of benzenethiol adsorbed on Ag-deposited Fe(2)O(3) was estimated to be about 3 x 10(6). Since the magnetic particles are readily recovered from the solution phase without centrifugation and/or filtering, the SERS-active magnetic particles are useful especially in the Raman spectroscopic analysis of dissolved organic species. We evaluate their performance as SERS substrates using benzenethiol, adenine, riboflavin, and naphthalene as model compounds; thereby, for instance, adenine could be detected down to 10 nM concentrations, and naphthalene was also able to be detected down to 200 nM by using pentachlorobenzenethiol-adsorbed Ag-deposited Fe(2)O(3) particles as the adsorbent.

Vibrational spectroscopic characterization of some environmentally important organoarsenicals — A guide for understanding the nature of their surface complexes

Organoarsenicals are found in the environment from the biomethylation of inorganic arsenic compounds and from anthropogenic sources. It is clear that organoarsenicals pose a health and an environmental risk due to their potential cycling to the most toxic forms of arsenic as a result of redox activity in soils and natural waters. The environmental fate of arsenic compounds depends to a large extent on the surface interactions with geosorbents, mainly minerals and organic matter. Hence, elucidating the nature of surface complexes is important in understanding binding mechanisms and thermodynamics. In this paper, we report the vibrational spectra of a number of organoarsenicals in the aqueous and solid phases using attenuated total internal reflectance Fourier transform infrared (ATR-FTIR), transmission FTIR, and Raman spectroscopies. Analysis of the aqueous phase spectra revealed that for completely deprotonated anions, increasing the organic substituents on the AsOx moiety results in increasing the frequency of v(AsOx), whereas the opposite trend is observed for completely protonated molecules. Analysis of solid phase spectra showed that incorporation of water molecules in the crystalline structure and extensive hydrogen bonding with neighboring molecules significantly affect As–O bond lengths and hence frequencies of v(AsOx). Results are discussed in the context of identifying geometry of organoarsenicals surface complexes in situ using the ATR-FTIR technique.Key words: ATR-FTIR, organoarsenicals; oxyanion adsorption, arsenate, in situ spectroscopy.

ChemInform Abstract: Synthesis, NMR and Vibrational Spectroscopic Characterization, and Computational Study of the cis‐IO2F32‐ Anion.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Vibrational spectroscopic characterisation of salmeterol xinafoate polymorphs and a preliminary investigation of their transformation using simultaneous in situ portable Raman spectroscopy and differential scanning calorimetry

Knowledge and control of the polymorphic phases of chemical compounds are important aspects of drug development in the pharmaceutical industry. Salmeterol xinafoate, a long acting β-adrenergic receptor agonist, exists in two polymorphic Forms, I and II. Raman and near infrared spectra were obtained of these polymorphs at selected wavelengths in the range of 488–1064 nm; significant differences in the Raman and near-infrared spectra were apparent and key spectral marker bands have been identified for the vibrational spectroscopic characterisation of the individual polymorphs which were also characterised with X ray diffractometry. The solid-state transition of salmeterol xinafoate polymorphs was studied using simultaneous in situ portable Raman spectroscopy and differential scanning calorimetry isothermally between transitions. This method assisted in the unambiguous characterisation of the two polymorphic forms by providing a simultaneous probe of both the thermal and vibrational data. The study demonstrates the value of a rapid in situ analysis of a drug polymorph which can be of potential value for at-line in-process control.

Raman spectroscopy of a sulfur dioxide visual sensor: The origin of the two colors in the solid sample

The vibrational spectroscopic characterization of a sulfur dioxide visual sensor was carried out using a Raman microscope system. It was observed the formation of two distinct complexes, that were characterized by the position and relative intensities of the bands assigned to the symmetric stretching, ν s(SO 2), of the linked SO 2 molecules. In fact, in the yellowish orange complex, that corresponds to the 1:1 stoichiometry, only one band is observed, assigned to ν s(SO 2) at ca. 1080 cm −1 and, in the deep red complex, that corresponds to the 1:2 complex, at ca. 1070 and 1090 cm −1 are observed. The variation of the relative intensities of the bands assigned to ν s(SO 2) present in the Ni(II)·SO 2 complex, in different points of the sample, shows clearly the requirement of the Raman microscope in the vibrational characterization of this kind of molecular sensor.