New approach for representation of molecular surface

A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1805–1815, 1998     

Orthogonal addressable monolayers for integrating molecular logic

Plug and play: The mimicking of integrated circuits by using two individual monolayers (molecular chips) is shown. These monolayers can be individually addressed using identical inputs. Upon combination of their optical outputs, the input/output characteristics of a molecular encoder is obtained. Since the encoder functionality is only displayed when both chips are active, the device behaves according to a plug-and-play principle (In=input; see picture).     

Investigation of chiral recognition by molecular micelles with molecular dynamics simulations

Molecular dynamics simulations were used to characterize the binding of the chiral drugs chlorthalidone and lorazepam to the molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The project’s goal was to characterize the nature of chiral recognition in capillary electrophoresis separations that use molecular micelles as the chiral selector. The shapes and charge distributions of the chiral molecules investigated, their orientations within the molecular micelle chiral binding pockets, and the formation of stereoselective intermolecular hydrogen bonds with the molecular micelle were all found to play key roles in determining where and how lorazepam and chlorthalidone enantiomers interacted with the molecular micelle.     

Porphyrin-based switchable molecular turnstiles

The design, synthesis and structural characterisation, in solution, of two new molecular turnstiles based on Sn-porphyrin derivatives are described. The system is composed of a stator (5-(4-pyridyl)-10,15,20-triphenylporphyrin), a hinge (Sn(IV)) and a rotor (handle equipped with 2,6-pyridinedicarboxamide as a tridentate coordinating site or its Pd(II) complex). The presence of interaction sites, both on the stator and the rotor, offers the possibility of switching between an open state (free rotation of the handle around the porphyrin) and a closed state (blockage of the rotation) by either establishment of hydrogen bonds between the stator and the rotor or by the simultaneous binding of Pd by both coordinating groups.     

Quantum molecular dynamics

Electron or ion dynamics are treated using spin‐dependent quantum trajectories. These trajectories are inferred from the Dirac current, which contributes Schroedinger's current and additional spin‐dependent terms, all of which are of order c⁰ in the nonrelativistic regime of particle velocity, where c is the speed of light. The many‐body problem is treated precisely as in classical dynamics. Each electron or ion has its own equation of motion, which is the time‐dependent Dirac or the time‐dependent Schroedinger equation in the relativistic or nonrelativistic regime of particle velocity, respectively. As an example the theory is applied to the electronic structure of the helium atom, in which two electrons with opposite spin states are shown to correlate such that their quantum trajectories keep them on average on opposite sides of the nucleus. As the theory is time dependent, excited states are also generated. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

基于分子模拟技术煤焦分子模型构建

煤、焦是过程工业的重要原料。因此，有必要深入了解煤、焦分子结构以揭示其反应性。采用Materials Studio 7.0软件，从分子层次研究煤、焦的分子结构。根据已报道的文献，构建煤、焦的初始结构；基于分子力学原理对这些结构进行优化，使得模型物性与煤、焦物性相符；基于退火模拟算法对模型进行优化，从而使得模型密度、元素分析数据与真实值吻合；基于能量最小化原理，对煤、焦模型再次优化，从而获得其稳定、真实的分子构型。由计算结果发现，模型的估算密度、元素组成与已报道一致，说明构建的模型是有效、合理的；在模型优化过程中，相对于其他能量而言，库伦能和范德华能起着重要的作用。因此可以推断在煤、焦热加工过程中，弱键占据主要地位。另外，本文采用分子模拟技术构建煤、焦模型的方法对于构建其他复杂大分子结构有着重要的借鉴作用。     

Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory

Based on the molecular face (MF) theory, the molecular face surface area (MFSA) and molecular face volume (MFV) are defined. For a variety of organic molecules and several inorganic molecules, the MFSA and MFV have been studied and calculated in terms of an algorithm of our own via the Matlab package. The MFV shows a very good linear relationship with the experimentally measured critical molar volume. It is also found that the MFSA and MFV have significant linear correlations with those of the commonly used hard‐sphere model and the electron density isosurface. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Quantum mechanical/molecular mechanical self-consistent Madelung potential method for treatment of polar molecular crystals

The self-consistent Madelung potential (SCMP) approach for calculating molecular wave functions for a subunit embedded in a symmetrical environment constituted by the copies of the subunit is implemented with semiempirical NDDO model Hamiltonians and supplemented with empirically parameterized dispersion–repulsion interaction potentials. This model yields sublimation enthalpies in good agreement with available experimental data for a series of molecular crystals, including imidazol, benzimidazole, urea, urethane, dicyaneamide, formamide, uracil, cytosine, maleic anhydride, succinic anhydride, and 1,3,5-triamino-2,4,6-trinitro-benzene. The SCMP-NDDO method, which avoids difficulties concerning the parametrization of charges in the molecular mechanics force fields, is proposed mainly for the treatment of molecular crystals with large unit cells. It might be particularly useful where important charge reorganization is expected under the effect of the crystal field. Charge distributions, obtained by the SCMP and the simple dielectric cavity self-consistent reaction field models, are compared and analyzed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 38–50, 1998     

An introduction to molecular spintronics

We review the progress and future possibilities in the emerging area of molecular spintronics. We first provide an overview of the different transport regimes in which electronic nanodevices can operate, then briefly overview the important characteristics of molecular magnetic materials that can be useful for application in spintronics and we eventually present several schemes to include such systems into spintronic nanodevices. We hightlight the importance of a chemical approach to the area, and in the last section we showcase some approaches to the creation of hybrids made of carbon nanostructures and molecular magnets, which are gaining increasing attention.     

轮烷研究－从超分子组装到分子器件

轮烷是一类由两端带有大的基团的线性分子和有机环化合物组成的互相锁连的分子化合物。主要综述了近年来这类超分子化合物的合成方法进展、在合成中的应用及其作为分子器件方面的研究进展。     

双光子吸收材料的分子设计研究

介绍了双光子吸收材料分子设计原理.为了设计有大的双光子吸收响应的材料,对多种分子进行了系统的理论研究.用量子化学密度泛函理论和AM1方法进行分子几何构型优化.在优化结构的基础上,用ZINDO和自编程序求得分子的单、双光子吸收性质.设计了一些未知化合物,以期为合成新的具有大的双光子吸收截面的材料提供理论根据.以双层二聚二甲苯邻甲酸衍生物、铂乙炔化物、卟啉衍生物、C60、C70、八极矩分子为例,报道了我们在这方面的研究结果.     

Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations

Different integrator time steps in NVT and NVE simulations of protein and nucleic acid systems are tested with the GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple SWitching) methods. The simulation stability and energy conservation is investigated in relation to the agreement with the Poisson theory. It is found that very close agreement between generalized Born methods and the Poisson theory based on the commonly used sharp molecular surface definition results in energy drift and simulation artifacts in molecular dynamics simulation protocols with standard 2-fs time steps. New parameters are proposed for the GBMV method, which maintains very good agreement with the Poisson theory while providing energy conservation and stable simulations at time steps of 1 to 1.5 fs.     

Parking and restarting a molecular shuttle in situ

Herein we report an easy-to-synthesize [2]rotaxane, which incorporates two ionic monopyridinium stations and one 2,2'-bipyridine station as the shaft of the dumbbell-shaped component and a bis-p-xylyl[26]crown-6 (BPX26C6) unit as the macrocyclic component. In this molecular shuttle, the BPX26C6 unit can be docked selectively on either the central 2,2'-bipyridine station or one of the two terminal pyridinium stations, and subsequently, returned to its shuttling molecular motion through the in situ addition of simple reagents (acid/base or metal ion/metal-ion-complexing ligand pairs).     

The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials

The Dynamo module library has been developed for the simulation of molecular systems using hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials. Dynamo is not a program package but is a library of Fortran 90 modules that can be employed by those interested in writing their own programs for performing molecular simulations. The library supports a range of different types of molecular calculation including geometry optimizations, reaction‐path determinations and molecular dynamics and Monte Carlo simulations. This article outlines the general structure and capabilities of the library and describes in detail Dynamo's semiempirical QM/MM hybrid potential. Results are presented to indicate three particular aspects of this implementation—the handling of long‐range nonbonding interactions, the nature of the boundary between the quantum mechanical and molecular mechanical atoms and how to perform path‐integral hybrid‐potential molecular dynamics simulations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1088–1100, 2000     

功能分子体系的设计与构建

功能分子在外界刺激(酸、碱、光等)的诱导下能发生分子构型、构象变化,并引起相应的物理化学性质变化,或能实现特定的功能,例如具有方向性的电子、能量转移,对分子/离子的识别能力的调控,以及光/电开关功能.功能分子的设计是分子材料科学研究的基础.作者将就我们在分子机器,化学传感器等功能分子的设计合成与性质研究领域取得的进展作一总结,并对未来的发展进行了描述.     

Examination of stabilty of molecular agglomerates in molecular crystals

We report an examination algorithm of stability of molecular aggregates based on the estimation of rigidity of intermolecular contacts in a crystal structure. The algorithm includes the intermolecular interaction energy calculation (in the atom-atom potential approximation) of a pair of molecules selected in the crystal structure. Further, the energy is minimized using a least-squares technique by varying the position and orientation of one of the molecules. The contact rigidity is quantitatively assessed by the minimized rms difference between the positions of the atoms in the original and optimized structures (Zorkii’s criterion). Every rigid contact revealed in the structure determines finite or infinite stable agglomerates. The paper presents the results of testing the computer program based on this algorithm with a number of real crystal structures previously determined by single crystal X-ray diffraction, and also the examples of the most common stable molecular agglomerates found with the aid of the program.