Experimental and computational studies of sulfided NiMo supported on pillared clay: catalyst activation and guaiacol adsorption sites

We report on intermediate (oxysulfides) and sulfided structures of NiMo supported on aluminium pillared clay (Al-PILC) during the catalyst activation process and the prefered guaiacol adsorption sites on the sulfided catalyst. In situ X-ray absorption fine structure (XAFS) together with density functional theory (DFT) calculations confirm the existence of ill-defined suboxides (MoO_x, NiO_x) and the well-known subsulfides (Mo₂S₉, Ni₃S₂) at the first stage which, at a later stage in the process, transform into MoS₂ with two edges, oxygen-decorated Mo and Ni with zero sulfur coverage. The freshly sulfided NiMoS₂ catalyst under sulfiding agents is mainly terminated by Mo-edge surface with 50% sulfur coverage (Mo-S50) with a disordered Ni-edge surface that can be assigned as NiMoS (1̄010). When exposed to an inert atmosphere such as He gas, the Mo and Ni edges evolved partially into new structures of Mo and Ni edges with zero sulfur coverage, labelled as Mo-Bare and Ni-Bare. Guaiacol is often used as a model compound for lignin and a series of calculations of guaiacol on the structural edges of a sulfided NiMoS₂ catalyst show relatively good agreement between the observed and calculated inelastic neutron scattering (INS) spectra for Mo-S50, Ni-Bare, and NiMoS (1̄010) where guaiacol weakly chemisorbed via oxygen atom of OH group. The results also confirm that guaiacol is physisorbed on the basal plane of NiMoS₂ in a horizontal (flat-lying) configuration via van der Waals interaction at a separation of about 3.25 Å.

Vibrational spectroscopy to study ancient Roman funerary practices at the "Hypogeum of the Garlands" (Italy)

The “Hypogeum of the Garlands” is a sepulchral site, recently found in Grottaferrata (Lazio, Italy), dating back to the first-second century AD. Two sarcophagi were discovered inside, hosting the human remains of Aebutia Quarta, a rich Roman woman, and her son Carvilius Gemellus. While the body of Carvilius is exceptionally well-preserved, following its embalming and perfect sealing of the sarcophagus, in the case of Aebutia only the bones were preserved because of the sarcophagus’s seal breaking down, although she was covered with perfectly preserved flower garlands. Embalming of the body was a rare ritual in the Imperial Roman times when corpses were more often cremated. The remains of Aebutia showed possible traces of heating. Burned bones from a third individual were discovered on the chamber’s floor and preliminary anthropological survey showed that this individual was a male of 40–50 years old. Here, a combination of spectroscopic techniques, including non-destructive inelastic neutron scattering and Raman spectroscopy, and minimally destructive Fourier transform infrared spectroscopy, were applied to the analysis of these bone samples to give information about ancient Roman funerary practices. The temperature and burning conditions were thus determined, showing that Aebutia Quarta was exposed to mild temperatures (200 °C) only in the upper part of the body, while the third individual was likely cremated as its bones were exposed to temperatures up to 900 °C in quasi-anaerobic conditions.

The impact of moderate heating on human bones: an infrared and neutron spectroscopy study

This study aims to analyse human bones exposed to low/medium temperatures (200-650°C) under experimentally controlled conditions, both oxidizing and reducing, using complementary optical and neutron vibrational spectroscopy techniques. Clear differences were observed between the aerobically and anaerobically heated bones. The organic constituents disappeared at lower temperatures for the former (ca 300°C), while they lingered for higher temperatures in anaerobic environments (ca 450-550°C). Unsaturated non-graphitizing carbon species (chars) were detected mainly for anaerobically heated samples, and cyanamide formation occurred only at 650°C in reducing settings. Overall, the main changes were observed from 300 to 400°C in anaerobic conditions and from 450 to 500°C in aerobic environments. The present results enabled the identification of specific spectroscopic biomarkers of the effect of moderate temperatures (less than or equal to 650°C) on human bone, thus contributing to a better characterization of forensic and archaeological skeletal remains subject to heating under distinct environmental settings. In particular, these data may provide information regarding cannibalism or ancient bone boiling and defleshing rituals.

Profiling of human burned bones: oxidising versus reducing conditions

Complementary optical and neutron-based vibrational spectroscopy techniques (Infrared, Raman and inelastic neutron scattering) were applied to the study of human bones (femur and humerus) burned simultaneously under either aerobic or anaerobic conditions, in a wide range of temperatures (400 to 1000 °C). This is the first INS study of human skeletal remains heated in an oxygen-deprived atmosphere. Clear differences were observed between both types of samples, namely the absence of hydroxyapatite's OH vibrational bands in bone burned anaerobically (in unsealed containers), coupled to the presence of cyanamide (NCNH2) and portlandite (Ca(OH)2) in these reductive conditions. These results are expected to allow a better understanding of the heat effect on bone´s constituents in distinct environmental settings, thus contributing for an accurate characterisation of both forensic and archaeological human skeletal remains found in distinct scenarios regarding oxygen availability.

First analysis of ancient burned human skeletal remains probed by neutron and optical vibrational spectroscopy

Burned skeletal remains are abundant in archaeological and paleontological sites, the result of fire or of ancient funerary practices. In the burning process, the bone matrix suffers structural and dimensional changes that interfere with the reliability of available osteometric methods. Recent studies showed that these macroscopic changes are accompanied by microscopic variations are reflected in vibrational spectra. An innovative integrated approach to the study of archaeological combusted skeletal remains is reported here, where the application of complementary vibrational spectroscopic techniques-INS (inelastic neutron scattering), FTIR (Fourier transform infrared), and micro-Raman-enables access to the complete vibrational profile and constitutes the first application of neutron spectroscopy to ancient bones. Comparison with data from modern human bones that were subjected to controlled burning allowed identification of specific heating conditions. This pioneering study provides archaeologists and anthropologists with relevant information on past civilizations, including regarding funerary, burial, and cooking practices and environmental settings.

Human bone probed by neutron diffraction: the burning process

The first neutron diffraction study of human burned bone – for understanding heat-induced changes, relevant for archaeology, biomaterials and forensic science.

Heat-induced Bone Diagenesis Probed by Vibrational Spectroscopy

Complementary vibrational spectroscopic techniques - infrared, Raman and inelastic neutron scattering (INS) - were applied to the study of human bone burned under controlled conditions (400 to 1000 °C). This is an innovative way of tackling bone diagenesis upon burning, aiming at a quantitative evaluation of heat-induced dimensional changes allowing a reliable estimation of pre-burning skeletal dimensions. INS results allowed the concomitant observation of the hydroxyl libration (OHlibration), hydroxyl stretching (ν(OH)) and (OHlibration + ν(OH)) combination modes, leading to an unambiguous assignment of these INS features to bioapatite and confirming hydroxylation of bone's inorganic matrix. The OHlib, ν(OH) and ν4(PO43-) bands were identified as spectral biomarkers, which displayed clear quantitative relationships with temperature revealing heat-induced changes in bone's H-bonding pattern during the burning process. These results will enable the routine use of FTIR-ATR (Fourier Transform Infrared-Attenuated Total Reflectance) for the analysis of burned skeletal remains, which will be of the utmost significance in forensic, bioanthropological and archaeological contexts.

Novel platinum-based anticancer drug: a complete vibrational study

The introduction of cisplatin to oncology, in the 1970s, marked the onset of the search for novel and improved metal-based anticancer drugs. Polynuclear PtII and PdII complexes with linear alkylamines as bridging ligands are a class of potential antineoplastic agents that have shown promising cytotoxicity against low-prognosis human cancers, such as metastatic breast adenocarcinoma and osteosarcoma. The present study reports an analysis of [μ-N,N′-bis(3-aminopropyl)butane-1,4-diamine-κ4 N,N′:N′′,N′′′]bis[dichloridoplatinum(II)], [Pt2Cl4(C10H26N4)], denoted Pt2Spm (Spm is spermine), by vibrational spectroscopy coupled to theoretical calculations. Within the latter, the Density Functional Theory (DFT – mPW1PW/6-31G*) and Effective Core Potential (ECP – LANL2DZ) approaches were used, in order to ensure the most accurate representation of the molecule and achieve a maximum agreement with the experimental data. The solid-state geometry of Pt2Spm corresponds to Ci symmetry, displaying 132 vibrational modes. A complete assignment of the experimental vibrational profile of the system was attained through the combined application of complementary Raman, FT–IR and Inelastic Neutron Scattering (INS) techniques. INS allowed an unequivocal identification of the CH2 and NH2 rocking modes, not clearly detected by the optical techniques, while Raman measurements led to a clear discrimination of the Pt—N stretching frequencies from the two distinct Pt—N moieties within the chelate. The metal-to-metal distances calculated for the molecule under study were found to allow the establishment of effective inter- and intrastrand crosslinks with DNA. These results will hopefully help to clarify the mode of action of the compound, at the molecular level, contributing to the development of improved cisplatin-like chemotherapeutic drugs having a higher efficacy and specificity coupled to lower acquired resistance and deleterious side effects.

Biomaterials from human bone – probing organic fraction removal by chemical and enzymatic methods

Two different deproteination and defatting processes of human bone were investigated, by combined infrared and neutron techniques: a previously reported hydrazine extraction and a newly developed multi-enzymatic treatment. Complementary Fourier transform infrared total attenuated reflectance and inelastic neutron scattering spectroscopies were applied, allowing access to all vibrational modes of the samples. The effectiveness of the different experimental protocols for removing the organic constituents of bone (lipids and protein) was probed, as well as their effect on bone's structural and crystallinity features. The results thus gathered are expected to have an impact on bioanthropological, archaeological and medical sciences, namely regarding the development of novel biocompatible materials for orthopaedic xenografts.

The effectiveness of two defatting & deproteination processes of human bone were assessed by combined infrared and inelastic neutron scattering spectroscopies.

The effects of MTG catalysis on methanol mobility in ZSM-5

QENS shows that methanol is immobile in a fresh ZSM-5 catalyst and one used for methanol conversion at 623 K, but undergoes isotropic rotation within the mesopores generated in a catalyst used for methanol conversion at 673 K.

Inelastic neutron scattering study of reline: shedding light on the hydrogen bonding network of deep eutectic solvents

Goldilocks conditions of hydrogen bond strength on the basis of deep eutectic behavior.

Correction: Evidence for a surface gold hydride on a nanostructured gold catalyst

Correction for 'Evidence for a surface gold hydride on a nanostructured gold catalyst' by I. P. Silverwood et al., Chem. Commun., 2016, 52, 533-536.

Osteometrics in burned human skeletal remains by neutron and optical vibrational spectroscopy

Vibrational spectroscopic techniques are applied to the osteometric study of burned human skeletal remains.

Evidence for a surface gold hydride on a nanostructured gold catalyst

Inelastic neutron scattering and isotopic infrared spectroscopy shows formation of surface Au–H, an important intermediate in catalytic mechanisms.

(C4H12N2)[CoCl4]: tetrahedrally coordinated Co2+without the orbital degeneracy

We report on the synthesis, crystal structure and magnetic properties of a previously unreported Co2+S = {3\over 2} compound, (C4H12N2)[CoCl4], based upon a tetrahedral crystalline environment. The S = {3\over 2} magnetic ground state of Co2+, measured with magnetization, implies an absence of spin-orbit coupling and orbital degeneracy. This contrasts with compounds based upon an octahedral and even known tetrahedral Co2+[Cottonet al.(1961).J. Am. Chem. Soc.83, 4690] systems where a sizable spin-orbit coupling is measured. The compound is characterized with single-crystal X-ray diffraction, magnetic susceptibility, IR and UV–vis spectroscopy. Magnetic susceptibility measurements find no magnetic ordering above 2 K. The results are also compared with the previously known monoclinic hydrated analogue.

Determination of the magnetic contribution to the heat capacity of cobalt oxide nanoparticles and the thermodynamic properties of the hydration layers

We present low temperature (11 K) inelastic neutron scattering (INS) data on four hydrated nanoparticle systems: 10 nm CoO·0.10H(2)O (1), 16 nm Co(3)O(4)·0.40H(2)O (2), 25 nm Co(3)O(4)·0.30H(2)O (3) and 40 nm Co(3)O(4)·0.026H(2)O (4). The vibrational densities of states were obtained for all samples and from these the isochoric heat capacity and vibrational energy for the hydration layers confined to the surfaces of these nanoparticle systems have been elucidated. The results show that water on the surface of CoO nanoparticles is more tightly bound than water confined to the surface of Co(3)O(4), and this is reflected in the reduced heat capacity and vibrational entropy for water on CoO relative to water on Co(3)O(4) nanoparticles. This supports the trend, seen previously, for water to be more tightly bound in materials with higher surface energies. The INS spectra for the antiferromagnetic Co(3)O(4) particles (2-4) also show sharp and intense magnetic excitation peaks at 5 meV, and from this the magnetic contribution to the heat capacity of Co(3)O(4) nanoparticles has been calculated; this represents the first example of use of INS data for determining the magnetic contribution to the heat capacity of any magnetic nanoparticle system.

Phonon driven proton transfer in crystals with short strong hydrogen bonds

Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dynamics of these systems as functions of temperature. The mechanism determined in a previous work on urea phosphoric acid of low frequency vibrations stabilizing average crystal structures, in which the potential energy well of the hydrogen bond has its minimum shifted towards the center of the bond, is found to be valid here. The new feature of the N-H...O hydrogen bonds studied in this work is that the proton is transferred from the donor atom to the acceptor atom. Molecular dynamics simulations show that in an intermediate temperature regime, in which the proton is not completely transferred, the proton is bistable, jumping from one side of the hydrogen bond to the other. In the case of 3,5-pyridine dicarboxylic acid, which has been studied in most detail, specific phonons are identified, which influence the potential energy surface of the proton in the short, strong hydrogen bond.

Neutron spectroscopic study of hydrogen bonding dynamics in L-serine

Inelastic incoherent neutron scattering (IINS) spectra were obtained at 10 K for normal and deuterated L-serine. The geometry of L-serine molecule was optimized for the zwitterion form using ab initio HF, MP2 and DFT (B3LYP) levels with 6-31G* and 6-311 + +G4** basis sets. The theoretical frequencies of normal and d4-L-serine were compared with IINS spectra. Normal coordinate analysis and band assignments based on ab initio calculations and experimental data were presented. IINS frequencies due to the out-of-plane gamma(N-H...O) hydrogen bond motions were observed and identified.

Neutron scattering, infra red, Raman spectroscopy and ab initio study of L-threonine

Inelastic incoherent neutron scattering spectra (IINS) were obtained for normal and deuterated L-threonine. Raman and infrared spectra were also recorded. Geometries were optimized for the zwitterion form using ab initio Hartree-Fock (HF) levels with 6-31G*, 6-311G*, 6-311G** and 6-311 + + G** basis sets. Force fields and normal modes were calculated and used as basis for an assignment of the spectral features.

The vibrational spectrum of methyltrioxorhenium(VII)

The inelastic neutron scattering and high-resolution FT-Raman spectra of methyltrioxorhenium are reported. Literature assignments of the modes below 1600 cm(-1) are largely confirmed with the exceptions of the methyl torsion and the ReO3 bending modes. The methyl torsion is observed for the first time at 200 cm(-1), while the band at 230 cm(-1) assigned previously to the torsion is shown to be a component of the factor group splitting of the solid. In the FT-Raman spectrum, the bands that derive from the E modes in the isolated molecule are split by the Cs site symmetry of the crystal. This allows an unambiguous assignment of these modes to be made. On this basis, the assignment of the ReO3 bending modes is reversed with the asymmetric mode at 325 cm(-1) and the symmetric mode at 276 cm(-1).

The Vibrational Inelastic Neutron Scattering Spectrum of Dodecahedrane: Experiment and DFT Simulation

Vibrational frequencies that are forbidden in Raman and IR absorption can be observed by inelastic neutron scattering. In the case of the I(h)-symmetrical molecule dodecahedrane (shown schematically), the resulting spectrum agrees with a DFT calculation.

Distinct domains of adenovirus E1A interact with specific cellular factors to differentially modulate human immunodeficiency virus transcription

Transcription of human immunodeficiency virus (HIV) type 1 and other viruses is regulated by the transcription factor NF-kappaB, which interacts with the multifunctional cellular protein p300. p300, originally identified by its ability to bind adenovirus early region 1A (E1A), has also been shown to regulate HIV transcription through its interaction with NF-kappaB. The 13S form of E1A activates HIV gene expression, while the 12S form represses its transcription. In this report, we have investigated whether these divergent effects of E1A are dependent upon common or distinct cellular cofactors, including p300, pRb, and the TATA box-binding protein (TBP). Unlike activation in the absence of E1A, cooperative stimulation of HIV gene expression by 13S E1A and RelA was independent of the ability of E1A to bind p300 but was critically dependent on the E1A CR3 region which associates with TBP. In contrast, inhibition of basal HIV gene expression by the 12S form of E1A was dependent on p300 but not pRb or TBP. Interestingly, mutation of the CR2 region of 12S E1A responsible for pRb binding abolished the repression of HIV transcription stimulated by tumor necrosis factor alpha, suggesting that repression of cytokine-activated transcription involves cofactors different from those used in unstimulated cells. Repression and activation of HIV transcription by different forms of E1A are mediated by distinct sets of cellular cofactors. These findings suggest that E1A has evolved to interact by alternative mechanisms with a transcriptional coactivator and its associated cofactors to differentially modulate cellular and viral gene expression.

A cooperative interaction of human T-cell leukemia virus type 1 Tax with the p21 cyclin-dependent kinase inhibitor activates the human immunodeficiency virus type 1 enhancer

Interactions between the Tax transactivator of human T-cell leukemia virus type 1 (HTLV-1) and a cell cycle regulatory protein have been examined. We report cooperative stimulation of human immunodeficiency virus type 1 gene expression by Tax and a regulator of cell cycle progression, the p21 cyclin-dependent kinase inhibitor (CKI). This cooperativity results from the effect of p21 on transcriptional coactivation by Tax-induced NF-kappaB. This effect was abrogated by a mutation in Tax which specifically eliminated NF-kappaB induction, was inhibitable by IkappaB-alpha, and was markedly reduced in human immunodeficiency virus reporter plasmids with mutant kappaB sites. These studies demonstrate that transcriptional activation by Tax is influenced by cell cycle regulatory proteins.

Vibrational neutron spectroscopy of collagen and model polypeptides

A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views of the proton-dominated modes of a protein over a wide energy range from the low frequency phonon region to the rich spectrum of localized high frequency modes. Several bands show a level of fine structure approaching that of optical data. The principal features of the spectra are assigned. A difference spectrum is obtained for protein associated water, which displays an acoustic peak similar to pure ice and a librational band shifted to lower frequency by the influence of the protein. Hydrogen-weighted densities of states are extracted for collagen and the model polypeptides, and compared with published calculations. Proton mean-square displacements are calculated from Debye-Waller factors measured in parallel quasi-elastic neutron-scattering experiments. Combined with the collagen density of states function, these yield an effective mass of 14.5 a.m.u. for the low frequency harmonic oscillators, indicating that the extended atom approximation, which simplifies analyses of low frequency protein dynamics, is appropriate.