Assessing frequency-dependent site polarisabilities in linear response polarisable embedding

ABSTRACT

In this paper, we discuss the impact of using a frequency-dependent embedding potential in quantum chemical embedding calculations of response properties. We show that the introduction of a frequency-dependent embedding potential leads to further model complications upon solving the central equations defining specific molecular properties. On the other hand, we also show from a numerical point of view that the consequences of using such a frequency-dependent embedding potential is almost negligible. Thus, for the kind of systems and processes studied in this paper the general recommendation is to use frequency-independent embedding potentials since this leads to less complicated model issues. However, larger effects are expected if the absorption bands of the environment are closer to that of the region treated using quantum mechanics.     

Mapping prehistoric ghosts in the synchrotron

The detailed chemical analysis of fossils has the potential to reveal great insight to the composition, preservation and biochemistry of ancient life. Such analyses would ideally identify, quantify, and spatially resolve the chemical composition of preserved bone and soft tissue structures, but also the embedding matrix. Mapping the chemistry of a fossil in situ can place constraints on mass transfer between the enclosing matrix and the preserved organism(s), and therefore aid in distinguishing taphonomic processes from original chemical zonation remnant within the fossils themselves. Conventional analytical methods, such as scanning electron microscopy (SEM) and pyrolysis–gas chromatography/mass spectrometry (Py-GC/MS) have serious limitations in this case, primarily, an inability to provide large (i.e., decimeter) scale chemical maps. Additionally, vacuum chamber size and the need for destructive sampling preclude analysis of large and precious fossil specimens. However, the recent development of Synchrotron Rapid Scanning X-ray Fluorescence (SRS-XRF) at the Stanford Synchrotron Radiation Lightsource (SSRL) allows the non-destructive chemical analysis and imaging of major, minor, and trace element concentrations of large paleontological and archeological specimens in rapid scanning times. Here we present elemental maps of a fossil reptile produced using the new SRS-XRF method. Our results unequivocally show that preserved biological structures are not simply impressions or carbonized remains, but possess a remnant of the original organismal biochemistry. We show that SRS-XRF is a powerful new tool for the study of paleontological and archaeological samples.     

Effects of soft X‐ray radiation damage on paraffin‐embedded rat tissues supported on ultralene: a chemical perspective

Radiation damage is an important aspect to be considered when analysing biological samples with X‐ray techniques as it can induce chemical and structural changes in the specimens. This work aims to provide new insights into the soft X‐ray induced radiation damage of the complete sample, including not only the biological tissue itself but also the substrate and embedding medium, and the tissue fixation procedure. Sample preparation and handling involves an unavoidable interaction with the sample matrix and could play an important role in the radiation‐damage mechanism. To understand the influence of sample preparation and handling on radiation damage, the effects of soft X‐ray exposure at different doses on ultralene, paraffin and on paraffin‐embedded rat tissues were studied using Fourier‐transform infrared (FTIR) microspectroscopy and X‐ray microscopy. Tissues were preserved with three different commonly used fixatives: formalin, glutaraldehyde and Karnovsky. FTIR results showed that ultralene and paraffin undergo a dose‐dependent degradation of their vibrational profiles, consistent with radiation‐induced oxidative damage. In addition, formalin fixative has been shown to improve the preservation of the secondary structure of proteins in tissues compared with both glutaraldehyde and Karnovsky fixation. However, conclusive considerations cannot be drawn on the optimal fixation protocol because of the interference introduced by both substrate and embedding medium in the spectral regions specific to tissue lipids, nucleic acids and carbohydrates. Notably, despite the detected alterations affecting the chemical architecture of the sample as a whole, composed of tissue, substrate and embedding medium, the structural morphology of the tissues at the micrometre scale is essentially preserved even at the highest exposure dose.     

Analytical Instrumental Techniques to Study Archaeological Wood Degradation

Abstract

Historically, a very large variety of everyday artifacts were made of wood, which makes them representative of their historical period or social context and valuable for archaeologists and historians. In order to preserve degraded wood and to develop and apply suitable conservation treatments, chemical and physical characterization of archaeological wood is needed. This review provides the reader with a survey on state-of-the-art of instrumental analytical tools available to understand the morphology and the chemical composition of archaeological wood. The focus is on microscopic and spectroscopic techniques such as scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), Raman, nuclear magnetic resonance (NMR) and analytical techniques based on pyrolysis, such as direct exposure–mass spectrometry (DE-MS), pyrolysis–mass spectrometry (Py-MS), pyrolysis–gas chromtography–mass spectrometry (Py-GC/MS), with emphasis on their respective potentialities and limitations. The advantages of techniques based on synchrotron radiation are also discussed. In addition, the applicability of each examined technique is illustrated and discussed through specific examples from the literature.     

Studies on ion-beam modifications of ADP and KDP crystal surfaces

Experimental investigations on He⁺ ion (150 keV) beam modifications of the (100) surfaces of ADP and KDP single crystals, relative to asgrown surfaces have been made, to assess the nature and extent of radiation damage. Studies on the surface micromorphology, defect substructure, defect concentration, surface conductivity and microhardness have been made. Studies on chemical etching in both ion irradiated and asgrown surfaces revealed drastic changes in etchpit morphology and defect concentration. Measurement of surface electrical conductivity, employing four-point probe method, showed enhancement in conductivity at all the temperatures of observation which is attributed to enhanced proton migration. Measurement of microhardness and studies on planar plastic anisotropy in asgrown surfaces relative to ion bombarded surfaces have been made employing Knoop indenter and the results are interpreted in terms of the nature of bonding, bond strength and radiation damage on ion bombardment. Plastic anisotropy in these surfaces is found to be in conformity with the (100) plane on which the indentations were made.     

Surface Modification of Poly (ether ether ketone) with a Medlite C6 (ND-YAG Q-Switched) Skin Treatment Laser

Poly ether ether ketone (PEEK), a synthetic polymer, is expected to be useful as a biomaterial due to its appropriate mechanical, chemical, and biocompatibility properties. However, this polymer is biologically inert, requiring surface modification to improve its adhesion to bone cells for use as a bone substrate. Surface properties, such as roughness and hydrophilicity, are important factors in the adhesion of biomaterials to the surrounding tissue; therefore, in this study, laser treatment was performed for surface modification. The aim of the research described here was to investigate the effect of two laser parameters, fluency and wavelength, on the surface roughness and hydrophilicity to determine the optimum parameters for improving surface adhesion. The surface topography and average roughness (R_a) were investigated by atomic force microscopy (AFM). Surface morphology was also observed with an optical microscope, and the hydrophilicity of the surfaces was investigated with static contact angle tests. The results obtained showed that the samples treated at the wavelength of 532?nm with fluency of 8?J/cm², compared to fluencies of 4 and 12?J/cm², showed improved surface properties. However, in terms of radiation wavelength, the wavelength of 1064?nm at these three fluencies showed the most promising results for enhancing the surface properties of PEEK for bone implant applications.     

Effects of evolving surface morphology on yield during focused ion beam milling of carbon

We investigate evolving surface morphology during focused ion beam bombardment of C and determine its effects on sputter yield over a large range of ion dose (10¹⁷-10¹⁹ ions/cm²) and incidence angles (Θ = 0-80°). Carbon bombarded by 20 keV Ga⁺ either retains a smooth sputtered surface or develops one of two rough surface morphologies (sinusoidal ripples or steps/terraces) depending on the angle of ion incidence. For conditions that lead to smooth sputter-eroded surfaces there is no change in yield with ion dose after erosion of the solid commences. However, for all conditions that lead to surface roughening we observe coarsening of morphology with increased ion dose and a concomitant decrease in yield. A decrease in yield occurs as surface ripples increase wavelength and, for large Θ, as step/terrace morphologies evolve. The yield also decreases with dose as rippled surfaces transition to have steps and terraces at Θ = 75°. Similar trends of decreasing yield are found for H₂O-assisted focused ion beam milling. The effects of changing surface morphology on yield are explained by the varying incidence angles exposed to the high-energy beam.     

Spectroscopy of Molecular Ions

Abstract

Traditionally, molecular ions have been studied by mass spectrometers or ion-counting techniques. The great sensitivity and versatility of these techniques are clearly attested to by the vast amount of mass spectrometric literature. However, it is equally true that mass spectroscopy has its limitations; basically, it provides one only with a charge-to-mass ratio for an ion. Obviously, all quantum state information is lost, particularly the vibrational and rotational, and usually even the electronic distributions of the ions. Similarly, no structural information such as bond lengths and angles is obtained. Indeed, in some cases the information obtained is so slight that one cannot even write a structural formula for the ion or distinguish between different chemical isomers.     

Wetting modifications of uhmwpe surfaces induced by ion implantation

Ultra-high-molecular-weight-polyethylene (UHMWPE) surfaces are characterized in terms of roughness and wetting. Changes in the surface morphology of the polymer were induced macroscopically by mechanical friction and microscopically by ion implantation. The ion irradiation was obtained by using 300?keV Xe⁺ beams with doses ranging between 10¹⁴ and 10¹⁵?ions/cm².

Roughness and wetting measurements were performed in order to investigate the UHMWPE surface properties before and after the surface treatments. The wetting angle of the polymeric surface increases with the decrease of the roughness and with the increase of the absorbed dose. Results are discussed from the point of view of the biological reactions that could degrade the UHMWPE biocompatible surfaces employed in different mobile prostheses.     

Fiber-optic acoustic sensor for nondestructive evaluation

An experimental study was conducted to investigate the applicability of fiber-optic acoustic sensors to detect internal flaws in polymeric materials. A polarimetric fiber-optic sensor embedded in a plexiglass model received the acoustic signals generated by an ultrasonic transducer. It is shown that proper control of the polarization and phase of the optical beam is required to obtain meaningful results from the amplitude of the fiber-optic sensor signal. The sensor has shown promising results in determining acoustical properties of plexiglass and locating internal defects. The attractive feature of this sensing scheme is that the optical fibers are not modified prior to embedding. Therefore, they preserve their mechanical properties which makes the embedding process much easier.     

Laser Raman Investigation of Solid State Reactions

Abstract

Traditionally, molecular ions have been studied by mass spectrometers or ion-counting techniques. The great sensitivity and versatility of these techniques are clearly attested to by the vast amount of mass spectrometric literature. However, it is equally true that mass spectroscopy has its limitations; basically, it provides one only with a charge-to-mass ratio for an ion. Obviously, all quantum state information is lost, particularly the vibrational and rotational, and usually even the electronic distributions of the ions. Similarly, no structural information such as bond lengths and angles is obtained. Indeed, in some cases the information obtained is so slight that one cannot even write a structural formula for the ion or distinguish between different chemical isomers.     

固体核磁共振技术在骨基生物材料研究中的应用

骨是人体的结构组织之一,又是重要的造血器官,它在支持和保护体内器官、贮存钙和磷、参与人体代谢和为肌肉提供附着等方面具有重要的作用,因此了解骨的微观结构对预防和治疗骨疾病有重要意义.由于骨形态多样化,无机和有机成分共存,而且骨样品对物理和化学处理十分敏感,因此对其研究存在许多实验困难.与其他表征技术相比,固体核磁共振（NMR）检测对骨样品不需要任何处理,不会破坏其自身结构,可以实现原位检测.另外,骨头中的许多元素（¹H、¹³C、³¹P、¹⁹F、⁴³Ca、²⁹Si、²⁵Mg和⁸⁷Sr）都是NMR可观察核,因此高分辨固体NMR技术是研究骨基生物材料的强有力工具.该文综述了近年来固体NMR技术在骨基生物材料研究中的应用进展.     

Focused ion beam milling and ultramicrotomy of mineralised ivory dentine for analytical transmission electron microscopy

The use of focused ion beam (FIB) milling for preparation of sections of mineralised ivory dentine for transmission electron microscopy (TEM) is investigated. Ivory dentine is essentially composed of fibrillar type-I collagen and apatite crystals. The aim of this project is to gain a clearer understanding of the relationship between the organic and inorganic components of ivory dentine using analytical TEM, in order to utilise these analytical techniques in the context of common skeletal diseases such as osteoporosis and arthritis. TEM sections were prepared in both single and dual beam FIB instruments, using two standard lift-out techniques, in situ and ex situ. The FIB sections were systematically compared with sections prepared by ultramicrotomy, the traditional preparation route in biological systems, in terms of structural and chemical differences. A clear advantage of FIB milling over ultramicrotomy is that dehydration, embedding and section flotation can be eliminated, so that partial mineral loss due to dissolution is avoided. The characteristic banding of collagen fibrils was clearly seen in FIB milled sections without the need for any chemical staining, as is commonly employed in ultramicrotomy. The FIB milling technique was able to produce high-quality TEM sections of ivory dentine, which are suitable for further investigation using electron energy-loss spectroscopy (EELS) and energy-filtering TEM (EFTEM) to probe the collagen/apatite interface.     

Molecular SIMS – A journey from single crystal to biological surface studies

The development of Static or Molecular secondary ion mass spectrometry (SIMS) is reviewed with particular reference to the journey made by the Manchester group and its collaborators. The earliest studies focussed on the application of static SIMS to single crystal surface studies. These studies successfully demonstrated that static SIMS delivered information on the delicate adsorbate state that mirrored that obtained by other surface science techniques. Subsequent application of the technique to studying the state and reactivity of bimetallic surfaces stimulated by collaboration with the Ertl group, demonstrated that static SIMS could be applied to the investigation of quite complex surface chemistry. This success stimulated the application of the technique to surface chemistry studies of much more complex systems such as polymers, ice mimics of polar stratospheric clouds, aerosols, culminating in biological systems. The need to enhance ion yields of the larger biological molecules led to the development and introduction of polyatomic primary ion beams, most notably based on C₆₀ buckminsterfullerene. This type of ion beam has transformed molecular analysis by SIMS. Not only have the yields of larger molecular ions been greatly increased, the bombardment induced damage that necessitated the static limit has been dramatically reduced such that for many materials the static limit requirement can be abandoned. A completely new analytical regime has opened up so that molecular depth profiling and 3D chemical imaging is possible. To fully realise the new capabilities for biological analysis a new generation of ToF-SIMS instrument is being developed that overcomes the compromises of pulsed beam instruments and that enables high mass resolution, high spatial resolution and high duty cycle to be attained simultaneously.     

Phase diagrams of polar surface reconstructions of zinc oxide

Due to the formation of surface dipoles the truncated-bulk like {0 0 0 1} surfaces of zinc oxide (ZnO) are electrostatically unstable. These dipoles can neither be compensated by the formation of surface dimers nor by a relaxation of near surface layers. Hence, the driving force for the reconstruction of ZnO must be a deviation of the surface stoichiometry. To study this stabilization effect, we have performed density functional theory calculations on (2×2) and (3×3) periodic non-stoichiometric reconstructions of the ZnO polar surfaces. Among the 24 possible (2×2) periodic structures that preserve bulk symmetry, a class of ad-atom reconstructions shows the lowest energy of formation. To facilitate comparability with experimental conditions we calculate the Gibbs free energy of each reconstruction as a function of temperature and chemical conditions. However, the established calculation method is ambiguous in case of non-stoichiometric surfaces and must be extended by taking into account the temperature dependence of the ZnO enthalpy of formation. From the resulting data phase diagrams of the stable reconstructions of ZnO polar surfaces are constructed which are discussed in terms of epitaxial growth.     

Scattering from axisymmetric obstacles embedded in axisymmetric dielectrics: The method of moments solution

The electromagnetic scattering from axisymmetric conducting or nonconducting (dielectric) obstacles, embedded in an axisymmetric dielectric body is treated. A surface integral equation formulation, consisting of coupled Fredholm equations of the first kind for the electric and magnetic fields, is solved by the method of moments. The outer surfaces of the internal obstacles and the embedding dielectrics can be nonconcentric, depart significantly from a spherical shape, but must be rotationally symmetric about a common axis. The embedding dielectric can be multilayered. Computer implementable expressions are given for the scattering cross sections for any desired polarization and for both backscatter (monostatic) and bistatic illumination. Comparisons are made with the extended boundary condition method for homogeneous dielectric bodies and the Mie theory extended for dielectrically clad conducting spheres. The generality of the present formulation is demonstrated for several other cladded scatterer configurations. This research was conducted under the McDonnell Douglas Independent Research and Development Program.     

Exact vibration-rotation kinetic energy operators in two sets of valence coordinates for centrally connected penta-atomic molecules

The exact vibration-rotation quantum mechanical kinetic energy operator (KEO) for centrally-connected penta-atomic molecules such as methane and its isotopomers is derived for two sets of internal valence coordinates: the polyspherical coordinates and the bond-angle valence coordinates. The vibrational KEO including the pseudo-potential term is discussed for two forms of the modified Jacobian. For the rotational and vibration-rotation coupling KEO, results for two schemes of embedding the body-fixed coordinate system are presented: the bond embedding and the bisector embedding. Full expressions for the bisector embedding are too complicated to give in detail, but the working connection between the two embedding schemes is given. The future applications, including the perturbative and variational calculation of the vibrations and/or rotations for centrally connected penta-atomic molecules using the vibration-rotation KEO expressions derived in this work, are discussed.     

Embedding atom-jellium model for metal surface

To describe metal surfaces efficiently and accurately, an embedding atom-jellium model is proposed. Within density functional theory, we consider a multiscale scheme that combines jellium and atomistic approaches. We use the former to model layers deep inside a metal surface to reduce the computational cost and the later to maintain the accuracy required for chemical bonding. Work functions of Al(111) and Cu(111) surfaces are studied using this model with comparisons to all-atom and pure jellium models. The much closer results of the embedding atom-jellium model to the all-atom results than to the pure jellium results show a good prospect for our approach in large-scale density functional calculations.     

Versatile vacuum chamber for in situ surface X‐ray scattering studies

A compact portable vacuum‐compatible chamber designed for surface X‐ray scattering measurements on beamline ID01 of the European Synchrotron Radiation Facility, Grenoble, is described. The chamber is versatile and can be used for in situ investigation of various systems, such as surfaces, nanostructures, thin films etc., using a variety of X‐ray‐based techniques such as reflectivity, grazing‐incidence small‐angle scattering and diffraction. It has been conceived for the study of morphology and structure of semiconductor surfaces during ion beam erosion, but it is also used for the study of surface oxidation or thin film growth under ultra‐high‐vacuum conditions. Coherent X‐ray beam experiments are also possible. The chamber is described in detail, and examples of its use are given.