Relative stabilities of cholestadienes calculated by molecular mechanics and semi-empirical methods: application to the acid-catalyzed rearrangement reactions of cholesta-3,5-diene     

Patrick Y. Schüpfer  Fazil O. Gülaar 《Organic Geochemistry》2000,31(12)

The study of geochemical transformations undergone by ‘biological markers’ after their incorporation into sediments is an important field of organic geochemistry. Combined with laboratory simulation experiments, molecular mechanics calculations have been shown to be very useful to establish the reaction pathways, and to predict intermediate components and stable reaction end products, especially in the case of the acid-catalyzed isomerization reactions of steroid and terpenoid hydrocarbons. Many commercially available softwares are able to optimize (minimize) the geometries of molecules and compute some of their thermodynamical data with either molecular mechanics (MM) or semi-empirical methods of quantum chemistry. In order to verify the reliability of these methods, we have computed the relative thermodynamic stabilities of a large number of steradiene isomers with MM3 (Tripos Inc.), MM+ (HYPERCHEM^TM) and MM2 (Chem3D, CambridgeSoft Corp.) empirical force fields, and with AM1 and PM3 (HYPERCHEM^TM) semi-empirical methods. The calculation results of thermodynamic stabilities of steradiene isomers are used to explain the compounds produced by the rearrangement of cholesta-3,5-diene when treated with p-toluenesulfonic acid in acetic acid at 70°C. The end products, namely the spirosteradienes 7–8, obtained by this treatment are the most stable steradiene isomers according to all computational methods. The relative thermodynamic stabilities of cholestadienes are also consistent with the mechanism postulated for the spirosteradiene formation proceeding through a pathway including cholestadienes 2–6 as intermediates.  相似文献   

第四纪气候突变研究的新工具--长链不饱和酮及其碳同位素     

孟宪伟  杜德文  韩贻兵  HAN Yibing 《海洋科学进展》2000,18(1)

长链不饱和酮是一种广泛存在于第四纪海洋沉积物中的生物标志物。其不饱和指数UK37能够在较短的时间尺度上 ( 1～ 1 0 0 0 a)定量刻划海水表层温度的灵敏变化 ,因而成为恢复古海水表层温度变化、识别气候突变事件的有效参数。长链不饱和酮分子的碳同位素与海水中的溶解 CO2 浓度之间具有确定的关系 ,因而可以用其定量恢复第四纪海水溶解 CO2 浓度和大气 CO2 分压。长链不饱和酮及其碳同位素已成为研究第四纪气候突变事件及驱动机制的新工具。  相似文献   

Combined Effects of Molecular Size and Electroendosmotic Flow on the Capillary Electrophoretic Behaviour of Humic Substances     

M. De Nobili  G. Bragato  A. Mori 《洁净——土壤、空气、水》1998,26(3):186-190

The electroendosmotic flow (EOF), generated by the migration of solvated ions near the charged capillary surface, is an important factor in determining the capillary electrophoretic behaviour of humic substances (HS). We investigated the electrophoretic mobilities of HS fractions of reduced molecular-weight polydispersity extracted from peat and from a spodosol either in the presence or after suppression of the EOF. When the EOF was not suppressed, HS migrated to the cathode in spite of their negative charge. Fractionation of HS according to molecular size was achieved in polyacrylamide-coated capillaries filled with 0.05 M tris-phosphate buffer. In uncoated capillaries filled with the same buffer, all fractions had very close mobilities. Addition of polyethylene glycol MW 4000 at concentrations above its entanglement threshold caused the migration times of larger molecules to increase more than those of smaller molecules. The separation was a linear function of molecular size up to 75000 g mol^–1 for peat HS and to 50000 g mol^–1 for HS extracted from the spodosol.  相似文献   

DNA barcode,taxonomic and ecological notes for the identification of the invasive amphipod Monocorophium acherusicum (Costa, 1851)     

Mariano J. Albano  Carlos Rumbold  Ignacio L. Chiesa  Guadalupe Vazquez  Eduardo D. Spivak  Sandra M. Obenat 《新西兰海洋与淡水研究杂志》2019,53(1):15-32

We report the occurrence of the invasive amphipod Monocorophium acherusicum in Mar del Plata port, Argentina, using morphological and molecular analysis and estimated mean abundance to detect monthly variations of this population. We compared M. acherusicum morphology with that of M. insidiosum and Crassicorophium bonelli, the two most similar locally occurring species, to establish the diagnostic characteristics for the correct identification of them; moreover, we provide some taxonomic notes about others corophiids regionally distributed. M. acherusicum were collected in a subtidal biofouling community and its mean abundance was maximum in summer. In the molecular analysis, the maximum-likelihood tree showed that specimens from Mar del Plata were clustered with M. acherusicum specimens from GenBank and Boldsystems. We support and confirm the species identity in Mar del Plata port using DNA barcoding and with taxonomic methods.  相似文献   

藤壶亚目物种的系统发育学研究进展          下载免费PDF全文

刘瀚仁  汤雁滨  刘清河  廖一波  寿鹿  曾江宁  陈全震 《海洋开发与管理》2021,38(11):97-103

藤壶亚目是目前为止海洋生物群落中种类最丰富和最重要的类群之一,也是海洋污损生物的重要组成部分,主要分布于岩石潮间带栖息地、深海热液口,有的物种会附着在红树林植物、动物和人工构筑物上。文章综述了藤壶亚目的起源以及分类系统的建立和发展,认为藤壶亚目在下白垩纪从有柄目分化而来,其中篱藤壶科(小藤壶总科)是最早分化出的一支,而后逐渐分化为星板藤壶总科、厚藤壶总科、鲸藤壶总科、笠藤壶总科、小藤壶总科和藤壶总科6支;总结了国内藤壶亚目的研究进展;比较了藤壶亚目系统发育学的研究方法;展望了未来的研究方向,即结合形态学方法与分子系统学方法研究藤壶亚目物种的系统发育关系,为今后研究藤壶亚目物种的分类及防治等工作提供借鉴和帮助。  相似文献   

基于28S rRNA 基因片段的翼形亚纲(Bivalvia:Pteriomorphia) 系统发育的初步研究     

薛东秀  王海艳  张涛  张素萍  徐凤山 《海洋与湖沼》2012,43(2):348-356

采用从GenBank下载的翼形亚纲11个总科80个种类的28S部分序列,对翼形亚纲11个总科贝类进行系统发育关系研究。在获得的1252个序列位点中,去除插入缺失位点,变异位点共359个,其中简约位点300个。翼形亚纲各总科内各种间的遗传距离为0.01—0.14,明显小于各总科间的遗传距离(除蚶总科与拟锉蛤总科,双肌蛤总科与襞蛤总科以及两总科与贻贝总科外)。贝叶斯树和最大似然树均支持翼形亚纲为单系群,并将11个总科分为3个聚类簇:聚类簇Ⅰ为珍珠贝总科(Pterioidea)、牡蛎总科(Ostreoidea)和江珧总科(Pinnoidea),聚类簇Ⅱ为贻贝总科(Mytiloidea)、蚶总科(Arcoidea)和拟锉蛤总科(Limopsoidea),聚类簇Ⅲ为襞蛤总科(Plicatuloidea)、不等蛤总科(Anomioidea)、双肌蛤总科(Dimyoidea)、扇贝总科(Pectinoidea)和锉蛤总科(Limoidea)。根据本研究的结果,并结合其他学者提出的分类系统,构建了包括4目11总科的翼形亚纲分类系统。  相似文献   

渤海湾盆地东营凹陷古近纪Paleodictyon遗迹化石的发现及其意义   总被引：2，自引：0，他引：2  

袁文芳  陈世悦  曾昌民  胡斌 《地质科学》2007,42(4):779-786

在东营凹陷古近纪沙河街组四段浊流沉积中,发现遗迹化石Paleodictyon的两个遗迹种,即Paleodictyon regulare和Paleodictyon majus;对其围岩地球化学特征的研究则发现有指示海侵发生的甲藻甾烷分子化石发育,据此推测研究区古近纪的沉积与海水相关。  相似文献   

Molecular dynamics study of structural changes in berlinite     

K. Kihara  M. Matsui 《Physics and Chemistry of Minerals》1999,26(7):601-614

Fractional coordinates and anisotropic temperature factors of atoms in berlinite, AlPO₄ with the quartz topology, were successfully simulated in a molecular dynamics simulation (MDS) at high temperatures. Time-dependent and time-averaged atomic order parameters were analyzed in detail with the aid of spectral densities calculated from trajectory data. These parameters show characteristic behavior of the order-disorder regime for a structure change, where atoms spend most of the time oscillating around the ₁-sites (or ₂-sites) in the low temperature α-phase, but oscillate over both sites in the higher temperature α-phase and the β-phase. In the spectral density functions calculated for atom order parameters, a nearly zero-frequency excitation, which is accompanied by the emergence of large-scale ₁ and ₂ clusters, appears at the Γ point of the Brillouin zone below the transition point T _o, and increases in intensity up to T _o. A low-lying optic branch along Γ-M, which is strongly temperature dependent in the small q-region, is another characteristic of the spectral density functions for the β phase. The spectrum at Γ continuously reduces its frequency from 0.6 THz at temperatures far above T _o to nearly 0 THz at temperatures approaching T _o from above. The dynamical behavior in β berlinite rapidly but continuously changes from that in less oscillatory clusters in the vicinity of T _o to that in the typical β phase at temperatures departing from T _o. Received: 10 August 1998 / Revised, accepted: 18 February 1999  相似文献   

Wave sloshing in corrugated bottom tanks with two-dimensional flow     

Abdi Kükner  Mehmet A. Baykal 《Ocean Engineering》1999,26(8):93

The boundary integral element method based on Green's formula is applied to the analysis of transient flow problem in corrugated bottom tanks. The problem is formulated as a two-dimensional linear, initial boundary value problem in terms of a velocity potential. The Laplace equation and the boundary conditions, except the dynamic boundary condition on the free surface, are transformed into an integral equation by the application of Green's formula. Finite Difference discretization is applied timewise. Initially a triangular wave on the free surface is assumed to be formed. The height of the triangular corrugated bottom is varied between 1/10 and 1/5 of the tank depth. The form of the free surface and the equipotential lines for the flow in the tank are presented at different time steps. An accuracy analysis is performed and distortion in time is considered. Proper coefficients for solutions are derived and presented. The results show that utilization of triangular corrugated bottoms may help to regulate the flow in tanks.  相似文献   

南海赤潮有毒甲藻链状-塔马亚历山大藻的分子鉴定   总被引：7，自引：0，他引：7  

陈月琴  屈良鹄  曾陇梅  齐雨藻  郑磊 《海洋学报》1999,21(3):107-112

以核糖体rDNAITS为分子指标,采用RFLP及序列分析方法对南海海域Alexandriumcatenella和Alexandriumtamarense进行分析和鉴定,并通过与日本海域不同海区A.tenella和A．tamarense的比较,得出A．catenella或A．tamarense的不同地理株的种内个体间ITS区序列非常相似,而种间序列则有显著差异,表明了ITS区用于不同海区A．catenella和A．tamarense种间鉴定是一个较稳定的指标．可看出,ITS区的研究从一个新的角度为海洋微藻种的界定提供了很好的依据．  相似文献