Type II beta-turn conformation of pivaloyl-L-prolyl-a-aminoiso-butyryl-N-methylamide: Theoretical, spectroscopic and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamihdaes been shown to possess one intramolecular hydrogen bond in (CD&SO solution, by 'H-nmr methods, suggesting the existence of p-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II P-turn conformations are about 2 kcal mol-' more stable than Type 111 structures. A crystallographic study has established the Type I1 /%turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 8, b = 11.421 A, c = 12.966 A, /3 = 97.55", and 2 = 2. The structure has been refined to a final R value of 0.061. The Type I1 p-turn conformation is stabilized by an intramolecular 4 - 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are @pro= -57.8", $pro = 139.3', @Aib = 61.4', and $Ajb = 25.1'. The Type 11 /%turn conformation for Pro-Aib in this peptide is compared with the Type I11 structures observed for the same segment in larger peptides.

Scattering and Refraction as Contrast Mechanisms in X-Ray Imaging

Differentiation of various types of soft tissues is of high importance in medical imaging, because changes in soft tissue structure are often associated with pathologies, such as cancer. However, the densities of different soft tissues may be very similar, making it difficult to distinguish them in absorption images. This is especially true when the consideration of patient dose limits the available signal-to-noise ratio. Refraction is more sensitive than absorption to changes in the density, and small angle x-ray scattering on the other hand contains information about the macromolecular structure of the tissues. Both of these can be used as potential sources of contrast when soft tissues are imaged, but little is known about the visibility of the signals in realistic imaging situations. In this work the visibility of small-angle scattering and refraction in the context of medical imaging has been studied using computational methods. The work focuses on the study of analyzer based imaging, where the information about the sample is recorded in the rocking curve of the analyzer crystal. Computational phantoms based on simple geometrical shapes with differing material properties are used. The objects have realistic dimensions and attenuation properties that could be encountered in real imaging situations. The scattering properties mimic various features of measured small-angle scattering curves. Ray-tracing methods are used to calculate the refraction and attenuation of the beam, and a scattering halo is accumulated, including the effect of multiple scattering. The changes in the shape of the rocking curve are analyzed with different methods, including diffraction enhanced imaging (DEI), extended DEI (E-DEI) and multiple image radiography (MIR). A wide angle DEI, called W-DEI, is introduced and its performance is compared with that of the established methods. The results indicate that the differences in scattered intensities from healthy and malignant breast tissues are distinguishable to some extent with reasonable dose. Especially the fraction of total scattering has large enough differences that it can serve as a useful source of contrast. The peaks related to the macromolecular structure come to angles that are rather large, and have intensities that are only a small fraction of the total scattered intensity. It is found that such peaks seem to have only limited usefulness in medical imaging. It is also found that W-DEI performs rather well when most of the intensity remains in the direct beam, indicating that dark field imaging methods may produce the best results when scattering is weak. Altogether, it is found that the analysis of scattered intensity is a viable option even in medical imaging where the patient dose is the limiting factor.

Patient exposure monitoring and radiation qualities in two-dimensional digital x-ray imaging

The methods for estimating patient exposure in x-ray imaging are based on the measurement of radiation incident on the patient. In digital imaging, the useful dose range of the detector is large and excessive doses may remain undetected. Therefore, real-time monitoring of radiation exposure is important. According to international recommendations, the measurement uncertainty should be lower than 7% (confidence level 95%). The kerma-area product (KAP) is a measurement quantity used for monitoring patient exposure to radiation. A field KAP meter is typically attached to an x-ray device, and it is important to recognize the effect of this measurement geometry on the response of the meter. In a tandem calibration method, introduced in this study, a field KAP meter is used in its clinical position and calibration is performed with a reference KAP meter. This method provides a practical way to calibrate field KAP meters. However, the reference KAP meters require comprehensive calibration. In the calibration laboratory it is recommended to use standard radiation qualities. These qualities do not entirely correspond to the large range of clinical radiation qualities. In this work, the energy dependence of the response of different KAP meter types was examined. According to our findings, the recommended accuracy in KAP measurements is difficult to achieve with conventional KAP meters because of their strong energy dependence. The energy dependence of the response of a novel large KAP meter was found out to be much lower than with a conventional KAP meter. The accuracy of the tandem method can be improved by using this meter type as a reference meter. A KAP meter cannot be used to determine the radiation exposure of patients in mammography, in which part of the radiation beam is always aimed directly at the detector without attenuation produced by the tissue. This work assessed whether pixel values from this detector area could be used to monitor the radiation beam incident on the patient. The results were congruent with the tube output calculation, which is the method generally used for this purpose. The recommended accuracy can be achieved with the studied method. New optimization of radiation qualities and dose level is needed when other detector types are introduced. In this work, the optimal selections were examined with one direct digital detector type. For this device, the use of radiation qualities with higher energies was recommended and appropriate image quality was achieved by increasing the low dose level of the system.

X-ray and neutron scattering studies on some nanoscale structures in molecular biology

Scattering of X-rays and neutrons has been applied to the study of nanostructures with interesting biological functions. The systems studied were the protein calmodulin and its complexes, bacterial virus bacteriophage phi6, and the photosynthetic antenna complex from green sulfur bacteria, chlorosome. Information gathered using various structure determination methods has been combined to the low resolution information obtained from solution scattering. Conformational changes in calmodulin-ligand complex were studied by combining the directional information obtained from residual dipole couplings in nuclear magnetic resonance to the size information obtained from small-angle X-ray scattering from solution. The locations of non-structural protein components in a model of bacteriophage phi6, based mainly on electron microscopy, were determined by neutron scattering, deuterium labeling and contrast variation. New data are presented on the structure of the photosynthetic antenna complex of green sulfur bacteria and filamentous anoxygenic phototrophs, also known as the chlorosome. The X-ray scattering and electron cryomicroscopy results from this system are interpreted in the context of a new structural model detailed in the third paper of this dissertation. The model is found to be consistent with the results obtained from various chlorosome containing bacteria. The effect of carotenoid synthesis on the chlorosome structure and self-assembly are studied by carotenoid extraction, biosynthesis inhibition and genetic manipulation of the enzymes involved in carotenoid biosynthesis. Carotenoid composition and content are found to have a marked effect on the structural parameters and morphology of chlorosomes.

Characterisation of properties of coniferous wood tracheids by x-ray diffraction, laser scattering and microscopy

In recent years there has been growing interest in selecting suitable wood raw material to increase end product quality and to increase the efficiency of industrial processes. Genetic background and growing conditions are known to affect properties of growing trees, but only a few parameters reflecting wood quality, such as volume and density can be measured on an industrial scale. Therefore research on cellular level structures of trees grown in different conditions is needed to increase understanding of the growth process of trees leading to desired wood properties. In this work the cellular and cell wall structures of wood were studied. Parameters, such as the mean microfibril angle (MFA), the spiral grain angles, the fibre length, the tracheid cell wall thickness and the cross-sectional shape of the tracheid, were determined as a function of distance from the pith towards the bark and mutual dependencies of these parameters were discussed. Samples from fast-grown trees, which belong to a same clone, grown in fertile soil and also from fertilised trees were measured. It was found that in fast-grown trees the mean MFA decreased more gradually from the pith to the bark than in reference stems. In fast-grown samples cells were shorter, more thin-walled and their cross-sections were rounder than in slower-grown reference trees. Increased growth rate was found to cause an increase in spiral grain variation both within and between annual rings. Furthermore, methods for determination of the mean MFA using x-ray diffraction were evaluated. Several experimental arrangements including the synchrotron radiation based microdiffraction were compared. For evaluation of the data analysis procedures a general form for diffraction conditions in terms of angles describing the fibre orientation and the shape of the cell was derived. The effects of these parameters on the obtained microfibril angles were discussed. The use of symmetrical transmission geometry and tangentially cut samples gave the most reliable MFA values.

A study of the nanostructure of the cell wall of the tracheids of conifer xylem by x-ray scattering

The purpose of this study was to develop practical and reliable x-ray scattering methods to study the nanostructure of the wood cell wall and to use these methods to systematically study the nanostructure of Norway spruce and Scots pine grown in Finland and Sweden. Methods to determine the microfibril angle (MFA) distribution, the crystallinity of wood, and the average size of cellulose crystallites using wide-angle x-ray scattering were developed and these parameters were determined as a function of the number of the year ring. The mean MFA in Norway spruce decreases rapidly as a function of the number of the year ring and after the 7th year ring it varies between 6° and 10°. The mean MFA of Scots pine behaves the same way as the mean MFA of Norway spruce. The thickness of cellulose crystallites for Norway spruce and Scots pine appears to be constant as a function of the number of the year ring. The obtained mean values are 32 Å for Norway spruce and 31 Å for Scots pine. The length of the cellulose crystallites was also quite constant as a function of the year ring. The mean length of the crystallites for Norway spruce was 364 Å, while the standard deviation was 27 Å. The mass fraction of crystalline cellulose in wood is the crystallinity of wood and the intrinsic crystallinity of cellulose is the crystallinity of cellulose. The crystallinity of wood increases from the 2nd year ring to the 10th year ring from the pith and is constant after the 10th year ring. The crystallinity of cellulose obtained using nuclear magnetic resonance spectroscopy was 52% for both species. The crystallinity of wood and the crystallinity of cellulose behave the same way in Norway spruce and Scots pine. The methods were also applied to studies on thermally modified Scots pine wood grown in Finland. Wood is modified thermally by heating and steaming in order to improve its properties such as biological resistance and dimensional stability. Modification temperatures varied from 100 °C to 240 °C. The thermal modification increases the crystallinity of wood and the thickness of cellulose crystallites but does not influence the MFA distribution. When the modification temperature was 230 °C and time 4 h, the thickness of the cellulose crystallites increased from 31 Å to 34 Å.

Characterization of non-imaging semiconductor X-ray solar monitors

The first observations of solar X-rays date back to late 1940 s. In order to observe solar X-rays the instruments have to be lifted above the Earth s atmosphere, since all high energy radiation from the space is almost totally attenuated by it. This is a good thing for all living creatures, but bad for X-ray astronomers. Detectors observing X-ray emission from space must be placed on-board satellites, which makes this particular discipline of astronomy technologically and operationally demanding, as well as very expensive. In this thesis, I have focused on detectors dedicated to observing solar X-rays in the energy range 1-20 keV. The purpose of these detectors was to measure solar X-rays simultaneously with another X-ray spectrometer measuring fluorescence X-ray emission from the Moon surface. The X-ray fluorescence emission is induced by the primary solar X-rays. If the elemental abundances on the Moon were to be determined with fluorescence analysis methods, the shape and intensity of the simultaneous solar X-ray spectrum must be known. The aim of this thesis is to describe the characterization and operation of our X-ray instruments on-board two Moon missions, SMART-1 and Chandrayaan-1. Also the independent solar science performance of these two almost similar X-ray spectrometers is described. These detectors have the following two features in common. Firstly, the primary detection element is made of a single crystal silicon diode. Secondly, the field of view is circular and very large. The data obtained from these detectors are spectra with a 16 second time resolution. Before launching an instrument into space, its performance must be characterized by ground calibrations. The basic operation of these detectors and their ground calibrations are described in detail. Two C-flares are analyzed as examples for introducing the spectral fitting process. The first flare analysis shows the fit of a single spectrum of the C1-flare obtained during the peak phase. The other analysis example shows how to derive the time evolution of fluxes, emission measures (EM) and temperatures through the whole single C4 flare with the time resolution of 16 s. The preparatory data analysis procedures are also introduced in detail. These are required in spectral fittings of the data. A new solar monitor design equipped with a concentrator optics and a moderate size of field of view is also introduced.

Interaction of metal ions with 6-oxopurine nucleotides. Part 2. X-Ray structures of ternary nickel(II) complexes with 2'-deoxyguanosine 5'-monophosphate or guanosine 5'-monophosphate

The ternary metal nucleotide complexes [Ni(en)1.3(H2O)1.4(H2O)2][Ni(5?-dGMP)2(en)0.7-(H2O)0.6(H2O)2]·7H2O (1) and [Ni(en)2(H2O)2][Ni(5?-GMP)2(H2O)4]·6H2O (2)(en = ethylenediamine, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate, 5?-GMP = guanosine 5?-monophosphate) have been prepared and their structures analyzed by X-ray diffraction methods. Both compounds crystallise in the space group C2221 with a= 8.810(1), b= 25.090(4), c= 21.084(1)Å, and Z= 4 for (1) and a= 8.730(1), b= 25.691(4), c= 21.313(5)Å, and Z= 4 for (2). The structures were deduced from the analogous CoIII complexes and refined by full-matrix least-squares methods to final R values of 0.087 and 0.131 for 1 211 and 954 reflections for (1) and (2) respectively. An interesting feature of the deoxyribonucleotide complex (1) is that en is not totally labilized from the metal centre on nucleotide co-ordination, as observed in corresponding ribonucleotide complexes. Apart from extensive intra- and inter-molecular hydrogen bonding, the structures are stabilized by significant intracomplex base�base and base�sugar interactions. The nucleotides in both complexes have an anti base, C(2?)-endo sugar pucker, and gauche�gauche conformation about the C(4?)�C(5?) bond.

X-ray studies on crystalline complexes involving amino acids and peptides. XV. Crystal structures of L-lysine D-glutamate and L-lysine D-aspartate monohydrate and the effect of chirality on molecular aggregation

L-Lysine D-glutamate crystallizes in the monoclinic space group P2(1) with a = 4.902, b = 30.719, c = 9.679 A, beta = 90 degrees and Z = 4. The crystals of L-lysine D-aspartate monohydrate belong to the orthorhombic space group P2(1)2(1)2(1) with a = 5.458, b = 7.152, c = 36.022 A and Z = 4. The structures were solved by the direct methods and refined to R values of 0.125 and 0.040 respectively for 1412 and 1503 observed reflections. The glutamate complex is highly pseudosymmetric. The lysine molecules in it assume a conformation with the side chain staggered between the alpha-amino and the alpha-carboxylate groups. The interactions of the side chain amino groups of lysine in the two complexes are such that they form infinite sequences containing alternating amino and carboxylate groups. The molecular aggregation in the glutamate complex is very similar to that observed in L-arginine D-aspartate and L-arginine D-glutamate trihydrate, with the formation of double layers consisting of both types of molecules. In contrast to the situation in the other three LD complexes, the unlike molecules in L-lysine D-aspartate monohydrate aggregate into alternating layers as in the case of most LL complexes. The arrangement of molecules in the lysine layer is nearly the same as in L-lysine L-aspartate, with head-to-tail sequences as the central feature. The arrangement of aspartate ions in the layers containing them is, however, somewhat unusual. Thus the comparison between the LL and the LD complexes analyzed so far indicates that the reversal of chirality of one of the components in a complex leads to profound changes in molecular aggregation, but these changes could be of more than one type.

New computational approaches for inelastic x-ray scattering

Inelastic x-ray scattering spectroscopy is a versatile experimental technique for probing the electronic structure of materials. It provides a wealth of information on the sample's atomic-scale structure, but extracting this information from the experimental data can be challenging because there is no direct relation between the structure and the measured spectrum. Theoretical calculations can bridge this gap by explaining the structural origins of the spectral features. Reliable methods for modeling inelastic x-ray scattering require accurate electronic structure calculations. This work presents the development and implementation of new schemes for modeling the inelastic scattering of x-rays from non-periodic systems. The methods are based on density functional theory and are applicable for a wide variety of molecular materials. Applications are presented in this work for amorphous silicon monoxide and several gas phase systems. Valuable new information on their structure and properties could be extracted with the combination of experimental and computational methods.

X-ray studies on crystalline complexes involving amino acids and peptides XIX. Effects of change in chirality in the complexes of succinic acid with dl- and l-arginine

Crystals of dl-arginine hemisuccinate dihydrate (I)(monoclinic; P21/c; a = 5.292, b = 16.296, c = 15.203 Å; α= 92.89°; Z = 4) and l-arginine hemisuccinate hemisuccinic acid monohydrate (II) (triclinic; P1; a = 5.099; b = 10.222, c = 14.626 Å; α= 77.31, β= 89.46, γ= 78.42°; Z = 2) were grown under identical conditions from aqueous solutions of the components in molar proportions. The structures were solved by direct methods and refined to R = 0.068 for 2585 observed reflections in the case of (I) and R = 0.036 for 2154 observed reflections in the case of (11). Two of the three crystallographically independent arginine molecules in the complexes have conformations different from those observed so far in the crystal structures containing arginine. The succinic acid molecules and the succinate ions in the structures are centrosymmetric and planar. The crystal structure of (II) is highly pseudosymmetric. Arginine-succinate interactions in both the complexes involve specific guanidyl-carboxylate interactions. The basic elements of aggregation in both the structures are ribbons made up of alternating arginine dimers and succinate ions. However, the ribbons pack in different ways in the two structures. (II) presents an interesting case in which two ionisation states of the same molecule coexist in a crystal. The two complexes provide a good example of the effect of change in chirality on stoichiometry, conformation, aggregation, and ionisation state in the solid state.

Structure of 2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9-hexadecafluorodecyl 1,10-ditosylate by X-ray crystallography and F-19-NMR spectroscopy

2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9-hexadecafluorodecyl 1,10-ditosylate and its precursors were synthesized and characterized by H-1- and F-19-NMR spectroscopic methods and X-ray crystallography. These compounds are building blocks for the syntheses of the surfactants containing polyperfluoromethylene spacer. The molecule has extended all-trans conformation with molecular symmetry (1) over bar (C-i). There is a reasonably strong C-H ... O interaction in the crystal and there are two F ... F intermolecular contact distances less than the sum of van der Waals radii. (C) 1999 Elsevier Science B.V. All rights reserved.

Synthesis, spectroscopic properties and biological evaluation of transition metal complexes of salicylhydrazone of anthranilhydrazide: X-ray crystal structure of copper complex

The transition metal complexes of salicylhydrazone of anthranilhydrazide (H2L) were synthesised. The structures of metal complexes were characterized by various spectroscopic [IR, NMR, UV-Vis, EPR], thermal and other physicochemical methods. The single-crystal X-ray diffraction study of [Cu(HL)Cl]center dot H2O reveal its orthorhombic system with space group P2(1)2(1)2 and Z=4. The copper center has a distorted square planar geometry with ONO and Cl as the donor atoms. The ligand and its metal chelates have been screened for their antimicrobial and anti-tubercular activities using serial dilution method. Metal complexes in general have exhibited better antibacterial and antifungal activity than the free ligand and in few cases better than the standard used. Among the bacterial strains used, the complexes are highly potent against Gram-positive strains compared to Gram-negative. Anti-tubercular activity exhibited by the Co(II) complex is comparable with the standard used. (C) 2011 Elsevier B. V. All rights reserved.

Probing complex heterostructures using hard X-ray photoelectron spectroscopy (HAXPES)

X-ray Photoelectron Spectroscopy (XPS) plays a central role in the investigation of electronic properties as well as compositional analysis of almost every conceivable material. However, a very short inelastic mean free path (IMFP) and the limited photon flux in standard laboratory conditions render this technique very much surface sensitive. Thus, the electronic structure buried below several layers of a heterogeneous sample is not accessible with usual photoemission techniques. An obvious way to overcome this limitation is to use a considerably higher energy photon source, as this increases the IMFP of the photo-ejected electron, thereby making the technique more depth and bulk sensitive. Due to this obvious advantage, Hard X-ray Photo Electron Spectroscopy (HAXPES) is rapidly becoming an extremely powerful tool for chemical, elemental, compositional and electronic characterization of bulk systems, more so with reference to systems characterized by the presence of buried interfaces and other types of chemical heterogeneity. The relevance of such an investigative tool becomes evident when we specifically note the ever-increasing importance of heterostructures and interfaces in the context of a wide range of device applications, spanning electronic, magnetic, optical and energy applications. The interest in this nondestructive, element specific HAXPES technique has grown rapidly in the past few years; we discuss critically its extensive use in the study of depth resolved electronic properties of nanocrystals, multilayer superlattices and buried interfaces, revealing their internal structures. We specifically present a comparative discussion, with examples, on two most commonly used methods to determine internal structures of heterostructured systems using XPS. (C) 2015 Elsevier B.V. All rights reserved.

Macropores generated during shrinkage in two paddy soils using X-ray micro-computed tomography

Soil shrinkage curve represents a decrease of total porosity or an increase of bulk density with water loss. However, our knowledge of the dynamics of pores and their geometry during soil shrinkage is scarce, partially due to lack of reliable methods for determining soil pores in relation to change in soil water. This study aimed to investigate the dynamics of macropores (>30 mu m) of paddy soils during shrinkage. Two, paddy soils, which were sampled from one paddy field cultivated for 20 years (YPF) and the other one for over 100 years (OPF), represented difference in crack geometry in the field. Macropore parameters (volume, connectivity, and orientation of pores) and soil shrinkage parameters were determined on the same undisturbed soil cores by X-ray microtomography and shrinkage curve, respectively. Macroporosity was on average four times larger in the YPF than in the OPF whereas the shrinkage capacity was lower in the YPF as compared to the OPF (0.09 vs. 0.15 COLE). Soil shrinkage increased the volume of pores by 3.7% in the YPF and by 1.6% in the OPF as well as their connectivity. The formation of macropores occurred mostly in the proportional shrinkage phase. As a result, the slope of the proportional shrinkage phase was smaller in the YPF (0.65) than in the OPF (0.89). New macropores were cracks and extended pre-existing pores in the range of 225-1215 pm size without any preferential orientation. This work provides image evidences that in paddy soils with high shrinkage capacity more macropores are generated in the soil presenting a smaller proportional shrinkage slope. (C) 2015 Elsevier B.V. All rights reserved.