Molecular dynamics interpretation of structural changes in quartz

 Constant temperature and constant pressure molecular dynamics (MD) simulations were applied to quartz to calculate the structural details which are indeterminable in usual X-ray structure studies. The dynamics of the structural changes was analyzed by means of time-dependent atomic displacement parameters. The Si-O bonds expand with increasing temperatures through the α- and β-phases, and atoms vibrate around the α₁- (or α₂-) sites at lower temperatures in the α-phase, and over the energy barriers between the α₁- and the α₂-sites at higher temperatures in the α- and the β-phases. The ratios of time lengths spent by atoms in the α₁- and α₂-sites determine the apparent atomic positions as obtained in usual structure studies of α-quartz. More frequent transfer of atoms over the α₁- and the α₂-sites contributes positively to the thermal expansions, whereas larger amplitudes of vibrations, which carry atoms more distantly and more frequently from the β-sites, contribute negatively. The well-known steep thermal expansion in the α-phase is attributed to the additive contribution from the expansions of the Si-O bond lengths, the widening of Si-O-Si angles, and the increase of the atomic transfer-frequency between the α₁- and the α₂-sites. The nearly zero or negative expansion in the β-phase is caused by balancing the negative to the positive effects. The MD crystal transforms to the β-phase via a transitional state, where the α- and β-structures appear alternately with time, or coexist. The slight and continuous expansions observed right after the steep rise(s) of the volume or cell dimensions up to the nearly horizontal curve(s) are attributed to the continuous changes within the transitional state. Received: 17 July 2000 / Accepted: 13 January 2001     

On the diffusivity of trace gases under stratospheric conditions

Transport of trace gases within the gas phase to a cloud or a sulphate aerosol droplet proceeds by molecular diffusion at the gas-liquid interface. An accurate determination of the molecular diffusion coefficient has a direct bearing on estimates of trace gas uptake and scavenging. A literature search revealed that this parameter is often chosen rather arbitrarily and the choice of a particular value is constrained by the availability of experimental data which are usually available at one atmospheric pressure under laboratory conditions. Since the process of trace gas transport to droplets occur at heights much above the ground level, it is important to determine an accurate value of the diffusion coefficient at varying levels in the atmosphere. This was achieved theoretically by estimating diffusivities for some important trace gases under stratospheric conditions by a Lennard-Jones method. Molecular diffusivity of 22 trace gases (including ClONO₂, HNO₃, SO₂ and H₂O₂ which may lead to heterogeneous reactions on various surfaces) have been estimated which can be used by modellers for improved scavenging estimates.     

SHORT COMMUNICATION EFFECT OF STANDARDIZATION ON FRAGMENT-BASED MEASURES OF STRUCTURAL SIMILARITY

Substructural fragment occurrence data are widely used as the basis for measures of inter-molecularstructural similarity.This paper investigates the effect of standardization on the effectiveness of suchmeasures using eight data sets for which both structural and biological activity data are available.Eightdifferent standardization methods are studied and it is shown that there is no significant difference in theeffectivenesses of the various methods;accordingly,any of them can be used for the calculation ofintermolecular structural similarity.     

岩浆玻璃相和工业硅酸盐玻璃相的结构和应用研究

采用电子探针、拉曼探针、x衍射和高温高压试验等手段对火山岩和超基性岩岩浆包裹体、珍珠岩、黑曜岩、绝热SiO_2纤维、锆铝硅耐火材料和人工合成硅酸盐中玻璃相的成分、分子网络结构、断键程度,径向分布函数、Si-O键长和Si-O-Si键角等进行了系统研究并获得下列结论: 1)无论是地质体玻璃相还是工业硅酸盐玻璃相,其分子网络结构都是由单体[SiO_4]、二聚体[Si_2O_7]、环与链[SiO_3]、层[Si_2O_5]、架[Al Si_3O_8]和纯架状[SiO_2]6种网络单元所组成。 2)建立了在1μm~2范围内测量玻璃相网络类型和断键程度的拉曼微探针法。对国际上有争议的非晶玻相网络结构理论提出了新的模式和研究方法。 3)对含铬超基性岩岩浆包裹体的研究发现,强结晶化和半结晶化的岩浆玻璃包裹体是钠长石质玻璃相,以层状和架状网络为主,对应于铬尖晶石结晶的早期,而弱结晶化的岩浆玻璃包裹体是绿泥石质玻璃相,以层状和链状网络为主,架状网络为次,形成于铬尖晶石结晶的晚期。显而易见,对玻璃相分子网络结构的研究有助于重溯天然岩浆结晶和演化的物理化学历史,对研究矿藏的生成条件和提高工业硅酸盐材料的性能具有重要的意义。     

The nature and fate of natural resins in the geosphere--VIII. NMR and Py-GC-MS characterization of soluble labdanoid polymers, isolated from Holocene class I resins

Soluble polylabdanoids isolated by sequential solvent extraction have been characterized by liquid-state ¹³C- and ¹H NMR and ¹³C-¹H HMQC (heteronuclear correlation) NMR spectroscopy in addition to solid-state NMR and Py-GC-MS techniques. Two Holocene resins originating from Santander, Colombia and Mombasa, Kenya were analyzed. Soluble polymers were isolated by extraction with a 1:1 (v/v) methylene chloride-methanol mixture following sequential extractions with methylene chloride and methanol. The molecular weight of polymer extracts was shown by GPC analyses to exceed that of non-polymeric occluded terpenoids. Py-GC-MS, solid-state ¹³C CP/MAS and ¹³C cross-polarization/depolarization NMR spectroscopy results indicated that chemical compositions of soluble polymers isolated from immature resins are highly representative of the structure of corresponding insoluble polymers, i.e. polylabdatrienes. These data provide evidence for cross-linking or cyclization of side-chain olefinic carbons during or shortly after polymerization. Generally, the characterization of soluble resin polymers by liquid-state NMR spectroscopy has proven to be an excellent means for investigating the maturation mechanism of polylabdanoid resinites, and has potential for furthering the application of Class I resinites as geothermal indicators.     

Modelling the formation of fission tracks in apatite minerals using molecular dynamics simulations

We introduce a simple method to simulate the “ion explosion spike” mechanism of fission track formation within the framework of classical molecular dynamics. The method is applied to six apatite compositions and the resulting tracks are compared with each other as well as with the damage produced by another mechanism—the “Displacement spike”. In contrast to experimentally observed tracks, the radii of simulated tracks are not dependent on their direction in the crystal. Since the simulations model accurately the elastic response of apatites, this suggests that the experimentally observed difference in track radii for tracks along different crystal directions is not entirely caused by anisotropy in the elasticity of apatite. We suggest that anisotropy in the interactions between the electric fields of fission fragments and the crystal ions is a major factor in the final radii of fission tracks. In fluorapatite, the simulations also reveal the formation of small clusters of fluorite-like material in the core of the fission track, a phenomenon which has yet to be confirmed experimentally.

Plastic deformation of orthoenstatite and the ortho- to high-pressure clinoenstatite transition: a metadynamics simulation study

Atomic-scale mechanisms of plastic deformation in orthoenstatite, MgSiO₃ are studied by computer simulation methods. The combined use of metadynamics and molecular dynamics allows a direct observation of the structural changes during the creation of stacking faults in the (100) plane. A sequence of slip deformations in two different (100) planes at P = 15 GPa and T = 1,000 K reveals a probable transformation mechanism for the ortho- to high-pressure clinopyroxene transition. Each of the observed slips consists of at least four partial deformations crossing high-energy intermediate structures. In agreement with experimental studies, both (100)[010] and (100)[001] slip systems are activated in the deformation process. The observation of a dominant (100)[001] single slip system in pyroxenes may be related to the fact that high-energy intermediate dislocations with (100)[010] component are not stable on geological or experimental timescales.     

Formation and photodestruction of pahs

Photodissociation processes of PAHs are studied in the interstellar medium (ISM) and in the envelopes of carbon-rich C-stars.     

Micro-FTIR spectroscopy of liptinite macerals in coal

Reflectance FTIR microspectroscopy has been used to investigate the chemical structure of the liptinite macerals, alginite, bituminite, sporinite, cutinite and resinite in bituminous coals of Carboniferous to Tertiary age. In comparison with the spectra of vitrinite in the same coals, the micro-FTIR spectra of liptinite macerals are characterized by stronger aliphatic CH_x absorptions at 3000–2800 and 1460–1450 cm⁻¹, less intense aromatic C=C ring stretching vibration and aromatic CH out of plane deformation at 1610–1560 and 900–700 cm⁻¹ respectively and various intense acid C=O group absorptions at 1740–1700 cm⁻¹. The peaks at 1000–900 cm⁻¹ due to aliphatic CH₂ wagging vibrations in olefins and at 730–720 cm⁻¹ due to CH₂ rocking vibration in long chain aliphatic substances ([CH₂]_n, n≥4), are characteristic of liptinite macerals. Collectively the micro-FTIR spectral characteristics indicate that liptinite is composed of greater numbers of long chain aliphatics, fewer aromatics and a broader range of oxygen-containing groups than other macerals. Marked differences exist in micro-FTIR spectra within the liptinite maceral group. Alginite has the strongest aliphatic and least aromatic absorptions followed by bituminite, resinite, cutinite and sporinite. The aliphatic components in alginite are the longest chained and least branched whereas those in sporinite are the shortest chained and most branched. Bituminite, resinite and cutinite are intermediate. Notable differences in micro-FTIR spectra of individual liptinite macerals, such as intensities and peak locations of aromatic C=C in alginite, C=O groups in bituminite and resinite and substituted aromatic CH and C–O–C groups in cutinite and sporinite, also exist, which are attributed to differences in depositional environments or biotaxonomy.     

Microbial and chemical characterization of a groundwater flow system in an intermontane basin of southern New Mexico,USA

Groundwater of the southern Jornada del Muerto Basin, an intermontane basin structure associated with the Rio Grande rift located in south-central New Mexico, USA, was analyzed chemically and microbially. A microbial phospholipid fatty acids (PLFA) analysis revealed a sparse microbial population consisting of relatively simple microorganisms with no major population changes along the flow system. A nucleic acid (DNA) analysis of the groundwater resulted in the identification of ten eubacterial and one archeal species. Chemical analyses revealed that sulfate along with calcium, magnesium, iron, and manganese is removed by about an order of magnitude in concentration from the recharge area to the discharge area. The removal of iron, manganese, magnesium, and to some extent calcium can be explained by oxidation reactions and the precipitation of dolomite. Sulfate and additional calcium are most likely removed by the precipitation of gypsum. Thiobacillus spp. are oxidizing metal sulfides that occur as subsurface sulfide mineral deposits to sulfuric acid, which subsequently reacts with calcium carbonate and water to precipitate gypsum. The presence of these sulfide deposits exposed to oxygenated water in the deep groundwater flow system significantly alters its chemical and bacteriological composition. Electronic Publication