Integrating open‐source software applications to build molecular dynamics systems

Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc.     

Sensor biocompatibility: final frontier in bioanalytical measurement

Chemical and biosensors operate as direct sample contact systems; as such, the response of the biomatrix to their presence is as important as their response to the targeted analyte. There needs to be greater research emphasis on the response of biofluids to sensors because of the impact on sensor performance. Mainly, this is the result of deposited biolayers through the adsorption of colloids and proteins, followed by a more complex surface-active system: whole cells. Sensor surface engineering and controlled sample presentation through fluidics are likely to be able to mitigate some of these effects. Overall there needs to be a convergence with rapidly evolving research strategies in biomaterials if sensors are to make the full transition from the laboratory to the real world.     

Does a molecule have structure?

The classical model of the molecule assumes that it has a definite shape and structure like a mechanical object in the world of possible experience. This study deals with this assumption so as to shed some light on the foundations of the model. Arguments based on Kant’s theory of transcendental idealism suggest that neither shape nor structure are attributes of the molecule, but are rather contributions of the subject. This claim has great relevance to the questions of (1) whether or not a quantum treatment of the molecule can derive structure without recourse to any approximation, and (2) the possible existence of emergence and downward causation. The answer to the first question is in the negative, and to the second is that agnosticism is the only possible attitude to have toward this problem. We are creatures who can only imagine what is going on by observing phenomena. All that is accessible to us is the modal structure of the model. The causal structure of the real system is not. From the same point of view and taking the concept of the affordance into account, the adequacy of the concept of molecular structure will be argued. The point is to specify what objects the concept can legitimately be applied to. Also briefly discussed in relation to shape and structure is the idea that molecular chirality might be a probe to reveal the nature of space.     

A Supramolecular Counter Circuit Based on Cyanine Dye Assembly

Molecular computation, a rapidly developing multidisciplinary research field, has attracted increasing attention. A series of combinational logic circuits at the molecular level have been constructed, however, the development of sequential logic circuits is still in its infancy due to the lack of ideal design tools. Taking advantage of unique assembly behaviors of cyanine dyes, we constructed a two-bit molecular counter circuit that can implement fundamental sequential logic functions, including number cumulating and descending. Further introducing a guanine-rich DNA strand as the cycle index, the counter can be reused several times and eventually be scaled up to count up to 16 numbers. The supramolecular circuit shows high programmability, flexibility, and reversibility, and it is prospected that the strategy would be applied in designing other advanced molecular circuits.     

From the discovery of sodiumoxyorganoalkoxysilanes to the organosilicon dendrimers and back

Upon being discovered 20 years ago, sodiumoxyorganoalkoxysilanes became the key to the world of organoelement dendrimers. Even considering the great variety of objects that had appeared in this area during the last 20 years, the organosilicon dendrimers are still one of the most actual objects in this class. Above all, this is fair concerning the carbosilane systems. The high reactivity of the functional groups, the well controlled chemistry of their transformations, and the inertness of the molecular skeleton are the reason for making these systems highly actual in two main regards: as model objects for the deep research of the dendrimers' properties and as polyfunctional matrixes for numerous derivatives. In this review, we were mainly focusing on the importance of the former part. In the conclusion, we showed the motivation for further development of this area both in regard of synthesis of new carbosilane systems and further development of siloxane dendrimers. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4935–4948, 2008     

Photodestruction of Diatomic Molecular Ions: Laboratory and Astrophysical Application

In this work, the processes of photodissociation of some diatomic molecular ions are investigated. The partial photodissociation cross-sections for the individual rovibrational states of the diatomic molecular ions, which involves alkali metals, as well as corresponding data on molecular species and molecular state characterizations, are calculated. Also, the average cross-section and the corresponding spectral absorption rate coefficients for those small molecules are presented in tabulated form as a function of wavelengths and temperatures. The presented results can be of interest for laboratory plasmas as well as for the research of chemistry of different stellar objects with various astrophysical plasmas.     

The mean angular distance among objects and its relationships with Kohonen artificial neural networks

This job refers to classification of multidimensional objects and Kohonen artificial neural networks. A new concept is introduced, called the mean angular distance among objects (MADO). Its value can be calculated as the cosine of the mean centered vectors between objects. It can be expressed in matrix form for any number of objects. The MADO allows us to interpret the final organization of the objects in a Kohonen map. Simulated examples demonstrate the relationship between MADO and Kohonen maps and show a way to take advantage of the information present in both of them. Finally, a real analytical chemistry case is analyzed as an application on a big data set of an air quality monitoring campaign. It is possible to discover in it a subgroup of objects with different characteristics than those of the general trend. This subgroup is linked to the existence of an unidentified SO(2) source that, a priori, has not been taken into account.     

Supramolecular Antibiotic Switches: A Potential Strategy for Combating Drug Resistance

Bacterial infectious disease is a serious public health concern throughout the world. Pathogen drug resistance, arising from both rational use and abuse/misuse of germicides, complicates the situation. Aside from developing novel antibiotics and antimicrobial agents, molecular approaches have become another significant method to overcome the problem of pathogen drug resistance. Established supramolecular systems, the antibiotic properties of which can be switched “on” and “off” through host–guest interactions, show great potential in combating issues regarding antibiotic resistance in the long term, as indicated by several recent studies. In this Concept, recently developed strategies for antibacterial regulation are summarized and further directions for research into antibiotic switches are proposed.     

Minimum spanning tree: ordering edges to identify clustering structure

Ordering edges to identify clustering structure (OETICS), the clustering algorithm presented here, is based on the minimum spanning tree connecting the objects. The edges of the tree are ordered, beginning from the longest edge, to form groups of objects separated by large edges. The plot of ordered edges is the main result of the algorithm. In some aspects OETICS is similar to OPTICS, a known clustering technique that orders the objects with reference to the local density, but the solution is unique, because it does not select the value of some parameters, as the generating distance in OPTICS.OETICS is applied to many simulated and real data sets, with very different number of objects and variables, and the results are compared with those obtained by OPTICS.     

Impact of Higher‐Order Structuralization on the Adsorptive Properties of Metal–Organic Frameworks

The structural processing of metal–organic frameworks (MOFs) over multiple length scales is critical for their successful use as adsorbents in a variety of emerging applications. Although significant advances in molecular‐scale design have provided strategies to boost the adsorptive capacities of MOFs, relatively little attention has been directed toward understanding the influence of higher‐order structuralization on the material performance. Herein, we present the main strategies that are currently available for the structural processing of MOFs and discuss the influence these processes can impart on the adsorptive properties of the materials. In all, this intriguing area of research is expected to provide significant opportunities to enhance the properties of MOFs further, which will ultimately aid in their optimization in the context of specific real‐world applications.     

柔性复合热电材料及器件的研究进展

热电材料能够将热能与电能直接相互转化,在废热回收及绿色制冷领域中具有巨大的应用潜力。相比无机块体热电材料,柔性热电材料具有可弯折、体积小、质量轻等优点,还适用于制备可穿戴电子设备。近10年来,基于导电高分子、碳材料和无机纳米材料等的柔性复合热电材料及器件逐渐成为炙手可热的研究领域,受到了业内广泛的关注。本文综述了近年来基于不同材料体系的柔性热电材料及器件的研究进展、存在的亟待解决的问题和未来的发展方向。大量研究结果表明,材料的热电性能可以通过化学合成和分子设计战略、形貌控制及掺杂技术等进行有效的调控。研发满足实际应用需要的先进柔性热电材料仍然极具挑战性。     

Sorting biomolecules with microdevices

Micro- and nanofabrication techniques have provided an unprecedented opportunity to create a designed world in which separation and fractionation technologies which normally occur on the macroscopic scale can be optimized by designing structures which utilize the basic physics of the process, or new processes can be realized by building structures which normally do not exist without external design. Since microfabrication is exceedingly sophisticated in its development, it is possible to design and construct highly creative microdevices which allow one to probe specific aspects of biological objects. We give examples of uses of micro- and nanofabrication which, as opposed to simply shrinking the size of the vessels or tubes used in macroscopic lab environments, utilize our understanding of the physics of the process to take advantage of fabrication technologies.     

多肽分子自组装

源于自然界中广泛存在的蛋白质自组装现象,近年来多肽的自组装逐渐成为材料学和生物医学等领域的研究热点.通过合理调控多肽的分子结构以及改变外界的环境,多肽分子可以利用氢键、疏水性作用、π-π堆积作用等非共价键力自发或触发地自组装形成形态与结构特异的组装体.由于多肽自身具有良好的生物相容性和可控的降解性能,利用多肽自组装技术构建的各种功能性材料在药物控制释放、组织工程支架材料以及生物矿化等领域内有着巨大的应用前景.本文总结了近年来多肽自组装研究的进展,介绍了多肽自组装技术常见的几种结构模型,概括了多肽自组装的机理,并进一步阐述多肽自组装形成的组装体形态及其在材料学和生物医学等领域里的应用.     

Exploring the no-man's land between molecular nanomagnets and magnetic nanoparticles

The comparison of the structural and magnetic properties of molecular nanomagnets (MNM) and magnetic nanoparticles (MNP) can be instructive to get a deeper understanding of the magnetic behavior on the intermediate scale between molecular and bulk objects. In this respect iron oxo based clusters are particularly interesting, since they provide an increasing number of molecular systems with sizes close to that of iron oxide MNP. In this Minireview we report a survey of literature data aimed at improving our understanding of the emergence of MNP properties from MNM ones.     

Silver-ion reversed-phase comprehensive two-dimensional liquid chromatography combined with mass spectrometric detection in lipidic food analysis

The triacylglycerol (TAG) profiles present in real world lipidic samples are usually quite complex and, as such, monodimensional high-performance liquid chromatographic (HPLC) techniques are inadequate when challenged with such matrices. In this respect, the complementary use of silver-ion (Ag) and non-aqueous (NA) reversed-phase (RP) HPLC can be exploited if thorough TAG separations are required. The present investigation reports the employment of a newly developed comprehensive LC (LC x LC) system, based on the different separation mechanisms of the aforementioned techniques, and applied to a rice oil sample. The approach was successful in the separation of a high number of solutes, otherwise unachievable through monodimensional LC. Furthermore, the use of atmospheric pressure chemical ionization mass spectrometry (APCI-MS), as detection system, provided a third analytical dimension boosting the identification power of the comprehensive chromatographic method.     

Molecular electronics—the future of bioelectronics

In the last decade, molecular electronics, as an active frontier of interdisciplinary research areas, has become one of the most rapidly developing fields, and attracted worldwide interests. The fundamental element of molecular electronics is a molecular device or a supramolecular device, which is an organized molecular system constructed mainly by organic molecules or biomolecules that have some specific functions in signal detection, process, storage, and transmission through chemical or physical interactions at molecular or supramolecular levels. A molecular device (MD) can involve chemical information processes, and be relatively easy to realize a large number of links between the molecules. The links can be controlled by the external signals. These are the expected features of molecular computing and directly involve chemical and biological processes. MD may overcome some limitations of the solid-state chips, and can be directly applied to chemical and biological processes. Molecular electronics is a part of bioelectronics. It will play an important and revolutionary role in the next century. This paper intends to review the research activities of molecular electronics in China, particularly in LMBE.     

Chemical Concepts from Density Functional TheorySCI北大核心CSCD

Chemical concepts such as structure,bonding,reactivity,etc.have been widely used in the literature and text books to appreciate molecular properties and chemical transformations.Even though modern theoretical and computational chemistry is well established from the perspective of accuracy and complexity,how to quantify these concepts is a still unresolved task.Conceptual density functional theory and its related recent developments provide unique opportunities to tackle this problem.In this Special Issue,27 contributions from top investigators over the world are collected to highlight the state-of-art research on this topic,which not only showcases the status of where we are now but also unveils a number to possible future directions to be pursued.     

Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics

An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom-based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state-of-the-art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.