The semantic smart laboratory: a system for supporting the chemical eScientist

One goal of eScience is to enable the end-to-end publication of experiments and results. In the Combechem project we have developed an innovative human-centred system which captures the process of a chemistry experiment from plan to execution. The system comprises an electronic lab book replacement, which has been successfully trialled in a synthetic organic chemistry laboratory, and a flexible back-end storage system. Working closely with the users, we found that a light touch and a high degree of flexibility was required in the user interface. In this paper, we concentrate on the representation and storage of human-scale experiment metadata, introducing an ontology to describe the record of an experiment, and a storage system for the data from our lab book software. Just as the interfaces need to be flexible to cope with whatever a chemist wishes to record, so the back end solutions need to be similarly flexible to store any metadata that may be created. The storage system is based on Semantic Web technologies, such as RDF, and Web Services. It gives a much higher degree of flexibility to the type of metadata it can store, compared to the use of rigid relational databases.     

Chemical markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators

Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information.     

A web service infrastructure for thermochemical data

W3C standardized Web Services are becoming an increasingly popular middleware technology used to facilitate the open exchange of chemical data. While several projects in existence use Web Services to wrap existing commercial and open-source tools that mine chemical structure data, no Web Service infrastructure has yet been developed to compute thermochemical properties of substances. This work presents an infrastructure of Web Services for thermochemical data retrieval. Several examples are presented to demonstrate how our Web Services can be called from Java, through JavaScript using an AJAX methodology, and within commonly used commercial applications such as Microsoft Excel and MATLAB for use in computational work. We illustrate how a JANAF table, widely used by chemists and engineers, can be quickly reproduced through our Web Service infrastructure.     

Internet推动的化学信息学重要进展*

Internet的普及为专业人员获取数据信息、利用计算工具提供了统一的平台,由此为化学信息学的发展带来了新的空间,推动了化学信息学以网络为基础,以化学相关的数据、信息及计算资源共享为目标的快速发展。本文将从不同侧面回顾近10年来化学信息学的重要进展, 包括：(1) 网络化学信息检索：索引对象从化学浅层网向化学深层网发展;检索工具从Web化学信息资源导航向化学专业搜索引擎(包括文本信息和化合物标识信息)、及化学深层网检索引擎 (化合物物性数据提取)发展;索引粒度从Web站点向页面、乃至页面中的特定内容发展,一般页面特定内容的数据提取(即非结构化数据提取)是未来发展的方向。(2)可共享的化学数据库：从可免费访问和使用的化学数据库向数据库内容通过集成多来源数据(包括数据库拥有者主动收集、多来源数据主动提交达到共享的方式,repository)实现数据库内容免费下载和共享,以及不同数据库之间的相关内容实现无缝连接的方向发展(如NIH建成的药物小分子共享数据库PubChem)。(3) 开源(open source)化学软件工具包：从化学结构基本处理模块如CDK、JOELib向集成开发环境如化学信息学与生物信息学集成环境Bioclipse发展。(4) 与化合物及其数据共享相关的推荐标准：包括用于共享数据交换的化学标记语言CML、IUPAC推荐的学术论文相关热力学实验数据提交标准ThermoML及化合物结构唯一描述码InChI。(5) 计算化学资源共享及基于网格的应用：从可执行程序的下载向在线计算、基于网格的应用发展。(6) eChemistry和虚拟研究环境：网络也成为化学相关日常的科学活动中不可缺少的平台。构建以网络为平台、支持开展科研活动的数字化基础设施和服务的eChemstry探索开始出现,根据需要自主集成多来源数据和计算资源,形成不同层次的支持协同工作的虚拟研究环境是未来数据和计算资源共享方式的发展方向。     

Web service infrastructure for chemoinformatics

The vast increase of pertinent information available to drug discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future.     

A Gaussian-3X prediction on the enthalpies of formation of chlorinated phenols and dibenzo-p-dioxins

The standard gas-phase enthalpies of formation of chlorinated benzenes, phenols and dibenzo-p-dioxins have been predicted using G3X and/or G3XMP2 model chemistries coupled with isodesmic reactions and compared to the previous theoretical and experimental values. A set of values for chlorinated benzenes are first suggested based on experimental measurements and the closed agreed G3X calculations with different isodesmic reactions. The results on polychlorinated dibenzo-p-dioxins (PCDDs) show a large difference between G3XMP2 and previous experimental measurements and predictions using group additivity methods, semiempirical quantum chemistry, and DFT calculations, especially for highly chlorinated species. Using the well-balanced isodesmic reactions (IR3 and IR5), the discrepancies between G3XMP2 and DFT predictions on PCDDs can be reduced to within 16 kJ/mol. The relative stability of PCDD isomers can be rationalized by the positional interactions, and the overestimation by DFT with less balanced isodesmic reactions is due to the overestimation of the ortho-Cl-Cl repulsive interactions when comparing with G3XMP2. Our calculations suggest further experimental measurements, especially on highly chlorinated phenols and PCDDs.     

Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2 – a free in‐house NMR database with integrated LIMS for academic service laboratories

nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a ‘QuickCheck’ function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. Copyright © 2015 John Wiley & Sons, Ltd.     

Probing the molecular orbitals and charge redistribution in organometallic (PP)Pd(XX) complexes. A Pd K-edge XANES study

Pd K-edge X-ray absorption near-edge spectroscopy (XANES) is used to probe the unoccupied molecular orbitals in bidentate diphosphine Pd complexes. Complexes containing a series of bidentate diphosphine ligands (PP) are examined to study the effect of the ligand bite angle on the charge redistribution in these complexes. Different coordinating moieties (XX) have been used to induce a range of Pd oxidation states. A full interpretation of the Pd K-edge XANES data is presented. The negative second derivative of these XANES data provides direct information on the energy and electronic distribution of the different unoccupied molecular orbitals probed. The charge redistributions within the complexes, as reflected in the effective Pd oxidation state, are indicated by both the intensity of the first edge feature, the "Pd d peak", and the energy of the second edge feature, the "Pd p peak", which can be easily observed in the negative second derivative of the XANES data. Additionally, the changing covalent interaction between the Pd and coordinated moieties via the Pd p orbitals is reflected directly in the energy splitting of the "Pd p" peak. Thus, investigation of these (PP)Pd(XX) complexes, some used as catalysts in organic synthesis, with XANES spectroscopy provides new essential information on their electronic properties. Further, the XANES analysis techniques described in this paper can be applied to investigate the unoccupied molecular orbitals and charge redistributions within a wide range of samples.     

A new dimension in thermal analysis

Summary An enormous development has taken place within the last five years in synchronous teaching over the Internet, i.e. both the teacher and the students are simultaneously in direct communication with each other as in a normal class-room or auditorium. With this concept it is possible to communicate orally, to exchange Power Point Presentations, documents, programmes and live web-camera pictures. It is even possible to use an electronic black board on which both the teacher and the students can work simultaneously. The great advantage with this type of teaching is that it is not restricted to a single class-room/auditorium with limited access, but in a virtual room accessible to everybody in principle all over the world, and which certainly open up new possibilities in teaching. The purpose of this paper is to present and to discuss the concept of virtual class-room teaching, how the system operates in practice, its advantages and, finally, how its inherent limitations can be overcome.     

Topology, connectivity, and electronic structure of C and B cages and the corresponding nanotubes

After a brief discussion of the structural trends which appear with an increasing number of atoms in B cages, a one-to one correspondence between the connectivity of B cages and C cage structures will be proposed. The electronic level spectra of both systems from Hartree-Fock calculations is given and discussed. The relation of curvature introduced into an originally planar graphitic fragment to pentagonal "defects" such as are present in buckminsterfullerene is also briefly treated. A study of the structure and electronic properties of B nanotubes will then be introduced. We start by presenting a solution of the free-electron network approach for a "model boron" planar lattice with local coordination number 6. In particular the dispersion relation E(k) for the pi-electron bands, together with the corresponding electronic Density Of States (DOS), will be exhibited. This is then used within the zone-folding scheme to obtain information about the electronic DOS of different nanotubes obtained by folding this model boron sheet. To obtain the self-consistent potential in which the valence electrons move in a nanotube, "the March model" in its original form was invoked, and the results are reported for a carbon nanotube. Finally, heterostructures, such as BN cages and fluorinated buckminsterfullerene, will be briefly treated, the new feature here being electronegativity difference.     

Acid-base and metal-ion-binding properties of xanthosine 5'-monophosphate (XMP) in aqueous solution: complex stabilities, isomeric equilibria, and extent of macrochelation

The four acidity constants of threefold protonated xanthosine 5'-monophosphate, H3(XMP)+, reveal that at the physiological pH of 7.5 (XMP-H)(3-) strongly dominates (and not XMP(2-) as given in textbooks); this is in contrast to the related inosine (IMP(2-)) and guanosine 5'-monophosphate (GMP(2-)) and it means that XMP should better be named as xanthosinate 5'-monophosphate. In addition, evidence is provided for a tautomeric (XMP-HN1)(3-)/(XMP-HN3)(3-) equilibrium. The stability constants of the M(H;XMP)+ species were estimated and those of the M(XMP) and M(XMP-H)- complexes (M2+=Mg2+, Ca2+, Sr2+, Ba2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+) measured potentiometrically in aqueous solution. The primary M2+ binding site in M(XMP) is (mostly) N7 of the monodeprotonated xanthine residue, the proton being at the phosphate group. The corresponding macrochelates involving P(O)2(OH)- (most likely outer-sphere) are formed to approximately 65% for nearly all M2+. In M(XMP-H)- the primary M2+ binding site is (mostly) the phosphate group; here the formation degree of the N7 macrochelates varies widely from close to zero for the alkaline earth ions, to approximately 50% for Mn2+, and approximately 90% or more for Co2+, Ni2+, Cu2+, Zn2+, and Cd2+. Because for (XMP-H)(3-) the micro stability constants quantifying the M2+ affinity of the xanthosinate and PO3(2-) residues are known, one may apply a recently developed quantification method for the chelate effect to the corresponding macrochelates; this chelate effect is close to zero for the alkaline earth ions and it amounts to about one log unit for Co2+, Ni2+, Cu2+. This method also allows calculation of the formation degrees of the monodentatally coordinated isomers; this information is of relevance for biological systems because it demonstrates how metal ions can switch from one site to another through macrochelate formation. These insights are meaningful for metal-ion-dependent reactions of XMP in metabolic pathways; previous mechanistic proposals based on XMP(2-) need revision.     

垃圾衍生燃料等温快速热解和燃烧反应特性

利用热天平和管式炉对RDF(Refuse Derived Fuel)等温快速热解和燃烧反应特性进行了研究。实验发现，在等温快速升温的条件下，RDF热解和燃烧的反应速率都非常快，从受热开始到反应结束需60 s～80 s;从开始失重到完成反应为20 s。RDF热解和燃烧热重反应曲线非常类似，都只有一个反应失重区;RDF组成对其燃烧和热解反应性有重要影响，含有橡胶的RDF的热解和燃烧反应速率较小。在650 ℃～800 ℃RDF快速热解产物中气、液产物的产率可达80%～90%，而固体产物的产率只有10%～20%，热解气体的热值为20kJ/m3，RDF较适合进行热解处理。     

RADIAL DISTRIBUTION FUNCTION OF cis-1,4-POLYBUTADIENE BY ELECTRON DIFFRACTION

The interatomic distance function of rareearth catalyzed cis-1,4-polybutadiene was studied by" radial distribution function (RDF) derived from electron diffraction. Two intramolecular peaks and three interrnolecular peaks have been found on the RDF. The appearance of such a number of intermolecular maxima on the RDF can be explained by the local parallel packing of long molecular chains of the amorphous polymers.     

Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM

We describe the development of a structured method of representing chemistry on the World-Wide Web using an object-oriented approach to information objects. We show how a document object model (DOM) for chemistry can be constructed using as its basis Chemical Markup Language (CML). Application of the CMLDOM to the development of chemical tools is described.     

Mass spectrometry and Web 2.0

The term Web 2.0 is a convenient shorthand for a new era in the Internet in which users themselves are both generating and modifying existing web content. Several types of tools can be used. With social bookmarking, users assign a keyword to a web resource and the collection of the keyword 'tags' from multiple users form the classification of these resources. Blogs are a form of diary or news report published on the web in reverse chronological order and are a popular form of information sharing. A wiki is a website that can be edited using a web browser and can be used for collaborative creation of information on the site. This article is a tutorial that describes how these new ways of creating, modifying, and sharing information on the Web are being used for on-line mass spectrometry resources.     

Design of high‐performance chlorine type dyes for dye‐sensitized solar cells

Intrinsic defect of electronic structure for the chlorine‐type porphyrin 1, which was synthesized for use in dye‐sensitized solar cell (DSSC), is found by theoretical calculation including density functional method (DFT), time‐dependent DFT, and C+/C? function. It is believed that the limited cell performance obtained by using dye 1 as the sensitizer is due to the existence of this electronic defect. To avoid this defect, a series of novel molecules with electron deficient π bridge were designed. The subsequent theoretical calculation indicated that the electron deficient π bridge in the newly designed molecule is quite effective in offsetting the electronic defect observed for dye 1. The parameters for the designed molecules closely associated with open‐circuit voltage and short‐circuit current density including dipole moment of dye vertical to the surface of semiconductor and light‐harvesting efficiency were then evaluated. By comparing these parameters of designed dyes with those of dye 1, we can predict that the DSSC based on dye 4 (2, 6‐cyan benzoic acid as anchoring group) should possess enhanced performance, which would be a valuable theoretical guidance for the practical work. © 2013 Wiley Periodicals, Inc.     

Prepeak in the structural factor. Inhomogeneous packings of Lennard-Jones atoms

This work reports on the effects of structural inhomogeneities within the models of spherical atomic packings on the radial distribution function (RDF) and the structural factor (SF). Models of inhomogeneous packings were constructed by removing some atoms from homogeneous packing according to a predetermined template. Thus various additional voids, leading to specific structural correlations of atoms on a middle scale (several atomic sizes), are introduced in the model. A dense noncrystalline packing of 27,000 Lennard-Jones atoms serves as the initial system. Three various templates were used, and models containing different fractions of additional voids were constructed with each of these templates. It is demonstrated that RDF is only slightly sensitive to such inhomogeneities; in contrast, the SF has additional peaks at small q, these peaks being notable even after removal of a small fraction of atoms. Some models yield a single narrow prepeak, which is akin to that observed in diffraction experiment for some glasses.