Materials properties from electron density distributions: Molecular magnetism and linear optical properties

The general goal of this thesis is correlating observable properties of organic and metal-organic materials with their ground-state electron density distribution. In a long-term view, we expect to develop empirical or semi-empirical approaches to predict materials properties from the electron density of their building blocks, thus allowing to rationally engineering molecular materials from their constituent subunits, such as their functional groups. In particular, we have focused on linear optical properties of naturally occurring amino acids and their organic and metal-organic derivatives, and on magnetic properties of metal-organic frameworks. For analysing the optical properties and the magnetic behaviour of the molecular or sub-molecular building blocks in materials, we mostly used the more traditional QTAIM partitioning scheme of the molecular or crystalline electron densities, however, we have also investigated a new approach, namely, X-ray Constrained Extremely Localized Molecular Orbitals (XC-ELMO), that can be used in future to extracted the electron densities of crystal subunits. With the purpose of rationally engineering linear optical materials, we have calculated atomic and functional group polarizabilities of amino acid molecules, their hydrogen-bonded aggregates and their metal-organic frameworks. This has enabled the identification of the most efficient functional groups, able to build-up larger electric susceptibilities in crystals, as well as the quantification of the role played by intermolecular interactions and coordinative bonds on modifying the polarizability of the isolated building blocks. Furthermore, we analysed the dependence of the polarizabilities on the one-electron basis set and the many-electron Hamiltonian. This is useful for selecting the most efficient level of theory to estimate susceptibilities of molecular-based materials. With the purpose of rationally design molecular magnetic materials, we have investigated the electron density distributions and the magnetism of two copper(II) pyrazine nitrate metal-organic polymers. High-resolution X-ray diffraction and DFT calculations were used to characterize the magnetic exchange pathways and to establish relationships between the electron densities and the exchange-coupling constants. Moreover, molecular orbital and spin-density analyses were employed to understand the role of different magnetic exchange mechanisms in determining the bulk magnetic behaviour of these materials. As anticipated, we have finally investigated a modified version of the X-ray constrained wavefunction technique, XC-ELMOs, that is not only a useful tool for determination and analysis of experimental electron densities, but also enables one to derive transferable molecular orbitals strictly localized on atoms, bonds or functional groups. In future, we expect to use XC-ELMOs to predict materials properties of large systems, currently challenging to calculate from first-principles, such as macromolecules or polymers. Here, we point out advantages, needs and pitfalls of the technique. This work fulfils, at least partially, the prerequisites to understand materials properties of organic and metal-organic materials from the perspective of the electron density distribution of their building blocks. Empirical or semi-empirical evaluation of optical or magnetic properties from a preconceived assembling of building blocks could be extremely important for rationally design new materials, a field where accurate but expensive first-principles calculations are generally not used. This research could impact the community in the fields of crystal engineering, supramolecular chemistry and, of course, electron density analysis.

Geochemistry of manganese nodules from a British Columbia fjord

Concretions of iron and manganese oxides and hydrous oxidesóobjects commonly called manganese nodulesóare widely distributed not only on the deep-sea floor but also in shallow marine environments1. Such concretions were not known to occur north of Cape Mendocino in the shallow water zones bordering the North-East Pacific Ocean until the summer of 1966 when they were recovered by one of us (J. W. M.) in dredge samples from Jervis Inlet, a fjord approximately 50 miles north-west of Vancouver, British Columbia.

The amount of water loss was determined by drying at 110°C

Deep-sea deposits, which resemble in nearly every respect the deep-sea oozes have been observed in many islands of the East-Indian Archipelago, notably the islands of Borneo, Rotti and Timor. Manganese nodules are found in equivalents of deeep-sea red clays on Timor and Rotti island. In this paper, those relative to red clay deposits dating from a Cretaceous ocean are analysed in detail in the vicinity of the town of Niki Niki in Western Timor.

Analysis of Mn-nodules from the Indian Ocean

This report studies the principal paramters governing the distribution of iron-manganese concretions on the sea floor of the Indian Ocean, as well as their petrography and mineralogy. The results are mainly based on the recoveries made during voyages 31, 33 and 35 of the "Vityaz"' (1959-1962) and partly during voyages 36 and 41 (1964-1966). During these voyages samples of Mn concretions and Mn crust were collected (by bottom grabs, cores, trawlings, and dredgings) at 39 stations. The following account is devoted to the problems concerning the geochemistry of these concretions.

Documentation of manganese nodules form the northwest Indian Ocean

Microscopic and electron probe examination of some manganese nodules show that they consist of segregations of manganese-iron oxides in an interstitial material almost free of manganese but rich in iron and silicates. The segregations are widely spaced in the volcanic cores of the nodules but become more abundant towards their outer crusts where they form the centres of linked polygons of interstitial materials. Most of the minor elements are concentrated in the segregations compared to the interstitial materials. It is suggested that the structures observed result partly from solution and reprecipitation of elements in the original volcanic cores of the nodules and partly from the replacement and coating of these cores by manganese-iron oxides precipitated from sea water.

Chemistry on manganese nodules from the Pacific Ocean

Three manganese nodules from the Pacific Ocean have been analysed for 35 elements by using mainly spectrophotometric and spectrographic methods. Cu, Co, Ni, Zn, and Pb were found in amounts approaching 1 %, which far exceeds their average concentrations in igneous rocks. On the other hand, elements having readily hydrolysable ions, such as Ga, Sc, Zr, Y, La and Ti, are present only in amounts comparable with their concentrations in igneous rocks. Sb, Bit Be, and Cr were not detected. The hydrochloric acid-insoluble fraction of nodules is practically free of the heavy metals that are characteristic of the acid-soluble fraction; it consists principally of clay minerals, together with lesser amounts of quartz, apatite, biotite and sodium and potassium felspars.

Geochemistry of primary and secondary mineral phases in ODP Leg 209 sediments

Primary and secondary mineral phases from Holes 1268A (11 samples), 1272A (9 samples), and 1274A (12 samples) were analyzed by electron microprobe in Bonn and Cologne (Germany). Bulk rock powders of these samples were also analyzed geochemically, including major and trace elements (Paulick et al., 2006, doi:10.1016/j.chemgeo.2006.04.011). Ocean Drilling Program (ODP) Leg 209 Holes 1268A, 1272A, and 1274A differ remarkably in alteration intensity and mineralogy, and details regarding their lithologic characteristics are presented in Bach et al. (2004, doi:10.1029/2004GC000744) and Shipboard Scientific Party (2004, doi:10.2973/odp.proc.ir.209.101.2004). Because of the least altered character of peridotite in Hole 1274A, abundant clinopyroxene, orthopyroxene, olivine, and spinel were analyzed at this site. In Hole 1272A, primary silicates are rare and analyses were restricted to some samples that contain traces of olivine and orthopyroxene. Because of the intensity of alteration, Hole 1268A is devoid of primary phases except spinel. Commonly, alteration is pseudomorphic and serpentinization of olivine and orthopyroxene can be distinguished. Accordingly, compositional variations of the alteration minerals with regard to the precursor minerals are one of the issues investigated in this data report.

Chemistry of secondary minerals from the deep sheeted dike complex of ODP Holes 137-504B and 140-504B

Dolerites sampled from the lower sheeted dikes from Hole 504B during Ocean Drilling Program Legs 137 and 140, between 1562.4 and 2000.4 mbsf, were examined to document the mineralogy, petrography, and mineral parageneses associated with secondary alteration, to constrain the thermal history and composition of hydrothermal fluids. The main methods used were mineral chemical analyses by electron microprobe, X-ray diffraction, and cathodoluminescence microscopy. Temperatures of alteration were estimated on the basis of single and/or coexisting mineral chemistry. Permeability is important in controlling the type and extent of alteration in the studied dike section. At the meter-scale, intervals of weakly altered dolerites containing fresh olivine are interpreted as having experienced restricted exposure to hydrothermal fluids. At the centimeter- or millimeter-scale, alteration patches and extensively altered halos adjacent to veins reflect the permeability related to intergranular primary porosity and cracks. Most of the sheeted dike alteration in this case resulted from non-focused, pervasive fluid-rock interaction. This study confirms and extends the previous model for hydrothermal alteration at Hole 504B: hydrothermal alteration at the ridge axis followed by seawater recharge and off-axis alteration. The major new discoveries, all related to higher temperatures of alteration, are: (1) the presence of hydrothermal plagioclase (An80-95), (2) the presence of deuteric and/or hydrothermal diopside, and (3) the general increasing proportion of amphiboles, and particularly magnesio-hornblende with depth. We propose that the dolerites at Hole 504B were altered in five stages. Stage 1 occurred at high temperatures (less than 500° to 700°C) and involved late-magmatic formation of Na- and Ti-rich diopside, the hydrothermal formation of Na, Ti-poor diopside and the hydrothermal formation of an assemblage of An-rich plagioclase + hornblende. Stage 2 occurred at lower temperatures (250°-320°C) and is characterized by the appearance of actinolite, chlorite, chlorite-smectite, and/or talc (in low permeability zones) and albite. During Stage 3, quartz and epidote precipitated from evolved hydrothermal fluids at temperatures between 310° and 320°C. Anhydrite appeared during Stage 4 and likely precipitated directly from heated seawater. Stage 5 occurred off-axis at low temperatures (250°C) with laumontite and prehnite from evolved fluids.

(Table 1, page 220), Spot chemical analyses of a section of nodule 5133.7

Microscopic and electron probe examination of some manganese nodules show that they consist of segregations of manganese-iron oxides in an interstitial material almost free of manganese but rich in iron and silicates. The segregations are widely spaced in the volcanic cores of the nodules but become more abundant towards their outer crusts where they form the centres of linked polygons of interstitial materials. Most of the minor elements are concentrated in the segregations compared to the interstitial materials. It is suggested that the structures observed result partly from solution and reprecipitation of elements in the original volcanic cores of the nodules and partly from the replacement and coating of these cores by manganese-iron oxides precipitated from sea water.

(Table 1, page 129) Chemical composition of ferromanganese coating on glacial erratics from Lydonia Canyon

Ferromanganese coatings have been found on glacial erratics in Lydonia Canyon, off the United States northeastern coast. The coatings, which are about 17 µm thick, consist of an outer manganese-rich layer which covers the top of the erratic, a middle transitional layer, and an internal iron-rich layer that encircles the entire surface of the erratic. Chemical analyses of the coatings, when compared with similar data on abyssal marine ferromanganese deposits, reveal comparable Mn/Fe ratios, higher P and Ti concentrations, and an order of magnitude less of Co, Ni, Cu, and most other metals. A comparison of the Lydonia Canyon coatings with desert varnishes reveals obvious chemical, mineralogical, and morphological differences.

Functional and expression analysis of the metal-inducible dmeRF system from Rhizobium legumionosarum bv. viciae

A gene encoding a homolog to the cation diffusion facilitator protein DmeF from Cupriavidus metallidurans has been identified in the genome of Rhizobium leguminosarum UPM791. The R. leguminosarum dmeF gene is located downstream of an open reading frame (designated dmeR) encoding a protein homologous to the nickel- and cobalt-responsive transcriptional regulator RcnR from Escherichia coli. Analysis of gene expression showed that the R. leguminosarum dmeRF genes are organized as a transcriptional unit whose expression is strongly induced by nickel and cobalt ions, likely by alleviating the repressor activity of DmeR on dmeRF transcription. An R. leguminosarum dmeRF mutant strain displayed increased sensitivity to Co(II) and Ni(II), whereas no alterations of its resistance to Cd(II), Cu(II), or Zn(II) were observed. A decrease of symbiotic performance was observed when pea plants inoculated with an R. leguminosarum dmeRF deletion mutant strain were grown in the presence of high concentrations of nickel and cobalt. The same mutant induced significantly lower activity levels of NiFe hydrogenase in microaerobic cultures. These results indicate that the R. leguminosarum DmeRF system is a metal-responsive efflux mechanism acting as a key element for metal homeostasis in R. leguminosarum under free-living and symbiotic conditions. The presence of similar dmeRF gene clusters in other Rhizobiaceae suggests that the dmeRF system is a conserved mechanism for metal tolerance in legume endosymbiotic bacteria.