分子陀螺的设计、合成与组装

近来,科学家设计和合成了系列分子水平的陀螺。类似于儿童的玩具陀螺仪,这种分子陀螺由一个转子、一个定子框架和连接定子和转子的轴组成。定子框架通过自身的刚性结构为中心转子的转动提供足够的内在自由度,得以对内部的转子实施保护。并使得分子陀螺成为一个理想的分子转子。当转子上有偶极距时,则可能在外来电、磁、光的刺激下进行定向转动,成为分子马达。化学家们通过X射线晶体衍射技术、动态核磁技术、理论计算化学、热力学分析等方法表征了分子陀螺的各种特征,并积极探索其潜在的应用价值。本文着重介绍分子陀螺,以及超分子陀螺仪的发展历史以及研究进展。     

Polyatomic molecular liquids under extreme compression: facts,models, and a few predictions

Early work by Siringo, Pucci and March (Phys. Rev. B, 37, 2491 (1988)) studied solid I₂ under high pressure at T = 0. Their conclusion was that insulating crystalline I₂ at low pressures eventually transformed into a molecular metal. This has subsequently been confirmed experimentally. Later studies by Weir et al. (Phys. Rev. Lett., 76, 1860 (1996)) on solid H₂ under pressure point in the same direction, though in the solid phase the metallic state has still not been achieved at low temperatures. However, in the liquid phase, an insulating metallic transition has been proposed, as in solid iodine, again on the basis of experimental high-pressure studies. Here, attention is shifted to some polyatomic molecules, such as the 10-electron series H₂O, NH₃ and CH₄. Particular attention is focused on the measured Hugoniots of the polyatomic molecular liquids.     

Bistable organic,organometallic, and coordination compounds for molecular electronics and spintronics

The review is concerned with advances in molecular elecronics and spintronics as applied to the design of hardware components for molecular computers (molecular switches; optical, redox-based, and magnetic molecular memory; and conducting molecular materials). Based on materials of a plenary lecture held at the XVIIIth Mendeleev Congress, Moscow, Russia, 2007. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 673–703, April, 2008.     

The effect of time step,thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond,graphene, and carbon nanotube

As the sophistication of reactive force fields for molecular modeling continues to increase, their use and applicability has also expanded, sometimes beyond the scope of their original development. Reax Force Field (ReaxFF), for example, was originally developed to model chemical reactions, but is a promising candidate for modeling fracture because of its ability to treat covalent bond cleavage. Performing reliable simulations of a complex process like fracture, however, requires an understanding of the effects that various modeling parameters have on the behavior of the system. This work assesses the effects of time step size, thermostat algorithm and coupling coefficient, and strain rate on the fracture behavior of three carbon‐based materials: graphene, diamond, and a carbon nanotube. It is determined that the simulated stress‐strain behavior is relatively independent of the thermostat algorithm, so long as coupling coefficients are kept above a certain threshold. Likewise, the stress‐strain response of the materials was also independent of the strain rate, if it is kept below a maximum strain rate. Finally, the mechanical properties of the materials predicted by the Chenoweth C/H/O parameterization for ReaxFF are compared with literature values. Some deficiencies in the Chenoweth C/H/O parameterization for predicting mechanical properties of carbon materials are observed. © 2015 Wiley Periodicals, Inc.     

Molecular reactors and machines: applications, potential, and limitations

Molecular reactors are miniature vessels for the assembly of reactants at the molecular level, in order to change the nature of chemical transformations. It seems probable that those that will find most immediate applications are those that change product ratios or give products which would not readily form in the absence of the reactors, and thereby afford easy access to materials that are otherwise difficult to obtain. Molecular machines consist of interrelated parts with separate functions and perform some kind of work, at the molecular level. Practical examples are likely to be relatively uncomplicated and not based on individual functions of single-molecule devices. Instead they will probably rely on extensive redundancy of the molecular components and their interactions and reactions, as well as of the machines themselves.     

Robust Atomistic Modeling of Materials,Organometallic, and Biochemical Systems

Modern chemistry seems to be unlimited in molecular size and elemental composition. Metal-organic frameworks or biological macromolecules involve complex architectures and a large variety of elements. Yet, a general and broadly applicable theoretical method to describe the structures and interactions of molecules beyond the 1000-atom size regime semi-quantitatively is not self-evident. For this purpose, a generic force field named GFN-FF is presented, which is completely newly developed to enable fast structure optimizations and molecular-dynamics simulations for basically any chemical structure consisting of elements up to radon. The freely available computer program requires only starting coordinates and elemental composition as input from which, fully automatically, all potential-energy terms are constructed. GFN-FF outperforms other force fields in terms of generality and accuracy, approaching the performance of much more elaborate quantum-mechanical methods in many cases.     

Robust Atomistic Modeling of Materials,Organometallic, and Biochemical Systems

Modern chemistry seems to be unlimited in molecular size and elemental composition. Metal‐organic frameworks or biological macromolecules involve complex architectures and a large variety of elements. Yet, a general and broadly applicable theoretical method to describe the structures and interactions of molecules beyond the 1000‐atom size regime semi‐quantitatively is not self‐evident. For this purpose, a generic force field named GFN‐FF is presented, which is completely newly developed to enable fast structure optimizations and molecular‐dynamics simulations for basically any chemical structure consisting of elements up to radon. The freely available computer program requires only starting coordinates and elemental composition as input from which, fully automatically, all potential‐energy terms are constructed. GFN‐FF outperforms other force fields in terms of generality and accuracy, approaching the performance of much more elaborate quantum‐mechanical methods in many cases.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Biomolecular modeling: Goals, problems, perspectives

Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.     

Molecular switch triggered by solvent polarity: synthesis,Acid-base behavior,alkali metal ion complexation,and crystal structure

The synthesis and characterization of the new tetraazamacrocycle L, bearing two 1,1'-bis(2-phenol) groups as side-arms, is reported. The basicity behavior and the binding properties of L toward alkali metal ions were determined by means of potentiometric measurements in ethanol/water 50:50 (v/v) solution (298.1+/-0.1 K, I=0.15 mol dm(-3)). The anionic H(-1)L(-) species can be obtained in strong alkaline solution, indicating that not all of the acidic protons of L can be removed under the experimental conditions used. This species behaves as a tetraprotic base (log K(1)=11.22, log K(2)=9.45, log K(3)=7.07, log K(4)=5.08), and binds alkali metal ions to form neutral [MH(-1)L] complexes with the following stability constants: log K(Li)=3.92, log K(Na)=3.54, log K(K)=3.29, log K(Cs)=3.53. The arrangement of the acidic protons in the H(-1)L(-) species depends on the polarity of the solvents used, and at least one proton switches from the amine moiety to the aromatic part upon decreasing the polarity of the solvent. In this way two different binding areas, modulated by the polarity of solvents, are possible in L. One area is preferred by alkali metal ions in polar solvents, the second one is preferred in solvents with low polarity. Thus, the metal ion can switch from one location to the other in the ligand, modulated by the polarity of the environment. A strong hydrogen-bonding network should preorganize the ligand for coordination, as confirmed by MD simulations. The crystal structure of the [Na(H(-1)L)].CH(3)CN complex (space group P2(1)/c, a=12.805(1), b=20.205(3), c=14.170(2) A, beta=100.77(1) degrees, V=3601.6(8) A(3), Z=4, R=0.0430, wR2=0.1181), obtained using CH(2)Cl(2)/CH(3)CN as mixed solvent, supports this last aspect and shows one of the proposed binding areas.     

Alcohols,ethers, carbohydrates,and related compounds. III. The 1,2-dimethoxyethane system

Ethylene glycol, its dimethyl ether, and some related compounds have been studied using the MM4 molecular mechanics force field. The MM4 calculated structural and energetic results have been brought into satisfactory agreement with a considerable number of experimental data and MP2/6-311++G(2d,2p) ab initio calculations. The heats of formation of these compounds are also well calculated. The MM4 ethylene glycol conformations in particular are in good agreement, both geometrically and in terms of energy, with those from the ab initio calculations. The corresponding dimethyl ether is of special interest, because it has been suggested that the trans-gauche conformation is unusually stable due to the hydrogen bonding of a hydrogen on a methyl group with the more distant oxygen. It is shown in the present work that while this conformation is more stable than might have been expected, the energy is adequately calculated by MM4 without using any hydrogen bonding between the Cbond;H bond and the oxygen. If such hydrogen bonding occurs, it amounts to no more than about 0.5 kcal/mol in energy, and is too small to detect with certainty. Additionally, energetic relationships in trans-1,2-dimethoxycyclohexane, 1,3,5,7-tetraoxadecalin, and 3-methoxytetrahydropyran have been studied, and the calculated results are compared with experimental information, which is adequately reproduced.     

Modeling of Structural,Energetic, and Dynamic Properties of Few‐Atom Silver Clusters Embedded in Polynucleotide Strands by Using Molecular Dynamics

This work concerns the study of the structural, energetic, and dynamic properties of fluorescent systems composed of silver clusters stabilized by polynucleotide strands. To do so, classical interaction potentials relative to silver, neutral and cationic, were introduced in the AMBER force field. Molecular dynamics simulations allowed analysis of the nature and force of the interactions between the various parts of the nucleic oligomers and the silver clusters. Conformational analyses were necessary to explore the flexibility of the supramolecular assemblies, specifically by radial distribution functions and Ramachandran‐type maps.     

Design,synthesis, and characterization of molecularly imprinted solid phase extraction for alpha Mangostin analysis in blood sample

Low levels of α-mangostin (AM) in biological fluids require adequate sample preparation to be analyzed. Molecularly imprinted polymers can serve as sorbents in solid phase extraction, enabling concentration and extraction of α-mangostin from complex matrices, such as biological fluids. To date, there are no molecular imprinted polymers for the analysis of α-mangostin in biological fluids. In this study, AM molecular imprinted polymer (MIP) was designed using molecular modeling, molecular dynamic simulations, and prepared by bulk polymerization and suspension polymerization methods. The geometry optimization results showed that acrylamide (AAM) monomer forms the most stable complex with AM at the pre-polymerization with the most negative Gibbs free energy (ΔG) of −6.91818 Kcal/mol. Radial distribution function (RDF) in molecular dynamics simulation of AM:AAM:ethylene glycol dimethacrylate (EGDMA) with mol ratio 1:4:20 shows the complex with the best composition through the formation of four stable hydrogen bonds. Based on the experimental results, molecularly imprinted polymers in suspension exhibit better characteristics, selectivity, and adsorption capacity than in bulk. The suspension polymerization method showed a high recovery (85.88% ± 2.5), which was higher than C18 SPE cartridge (24.19% ± 1.47). Hence, it can be concluded that the MIPs from MD simulations were accessible and could be used in practice, such as in the separation and detection of AM in blood serum.     

Computation of internal coordinates,derivatives, and gradient expressions: torsion and improper torsion

Laplacians and gradient dot products are required for the recently developed internal coordinate quantum Monte Carlo method. New formulas are presented for these quantities for torsion and improper torsion angles. The Laplacians can also be used to economize calculation of sets of second derivatives used in molecular mechanics and other methods. Formulas for torsion angle gradient dot products and Laplacians, and completely new formulas for improper torsion, are presented. In addition, calculations of cos τ and sin τ, some suitable for energy subroutines and others for force subroutines, are shown. Finally, in a related development, several sets of conditions for three atom linearity or four atom planarity involving internal coordinate derivatives are reported. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 553–561, 2000     

1,2,5-Thiadiazole 1,1-dioxides and Their Radical Anions: Structure,Properties, Reactivity,and Potential Use in the Construction of Functional Molecular Materials

This work provides a summary of the preparation, structure, reactivity, physicochemical properties, and main uses of 1,2,5-thiadiazole 1,1-dioxides in chemistry and material sciences. An overview of all currently known structures containing the 1,2,5-thiadiazole 1,1-dioxide motif (including the anions radical species) is provided according to the Cambridge Structural Database search. The analysis of the bond lengths typical for neutral and anion radical species is performed, providing a useful tool for unambiguous assessment of the valence state of the dioxothiadiazole-based compounds based solely on the structural data. Theoretical methodologies used in the literature to describe the dioxothiadiazoles are also shortly discussed, together with the typical ‘fingerprint’ of the dioxothiadiazole ring reported by means of various spectroscopic techniques (NMR, IR, UV-Vis). The second part describes the synthetic strategies leading to 1,2,5-thiadiazole 1,1-dioxides followed by the discussion of their electrochemistry and reactivity including mainly the chemical methods for the successful reduction of dioxothiadiazoles to their anion radical forms and the ability to form coordination compounds. Finally, the magnetic properties of dioxothiadiazole radical anions and the metal complexes involving dioxothiadiazoles as ligands are discussed, including simple alkali metal salts and d-block coordination compounds. The last section is a prospect of other uses of dioxothiadiazole-containing molecules reported in the literature followed by the perspectives and possible future research directions involving these compounds.     

Alcohols,ethers, carbohydrates,and related compounds. II. The anomeric effect

The anomeric effect has been studied for a variety of compounds using the MM4 force field, and also using MP2/6-311++G(2d,2p) ab initio calculations and experimental data for reference purposes. Geometries and energies, including conformational, rotational barriers, and heats of formation were examined. Overall, the agreement of MM4 with the experimental and ab initio data is good, and significantly better than the agreement obtained with the MM3 force field. The anomeric effect is represented in MM4 by various explicit terms in the force constant matrix. The bond length changes are accounted for with torsion-stretch elements. The angle changes are accounted for with torsion-bend elements. The energies are taken into account with a number of torsional terms in the usual way. A torsion-torsion interaction is also of some importance. With all of these elements included in the calculation, the MM4 results now appear to be adequately accurate. The heats of formation were examined for a total of 12 anomeric compounds, and the experimental values were fit by MM4 with an RMS error of 0.42 kcal/mol.     

Theoretical investigation of the molecular structure,vibrational spectra,and molecular docking of tramadol using density functional theory

The optimized molecular structures, harmonic vibrational wavenumbers, and the corresponding vibrational assignments of (1S,2S)-tramadol and (1R,2R)-tramadol are computationally examined using the B3LYP density functional theory method together with the standard 6–311++G(d,p) and def2-TVZP basis sets. The optimized structures show that phenolic rings of both 1R,2R and 1S,2S tramadol adopt planar geometry, which are slightly distorted due to the substitution at the meta-position; and the six-membered cyclohexane adopts a slightly distorted chair conformation. The 1S,2S enantiomer is energetically more favorable than 1R,2R with the energy differences of 1.32 and 1.03 kcal/mol obtained at B3LYP/6–311++G(d,p) and B3LYP/Def2-TVZP levels, respectively. The analysis of the binding pocket in the silico molecular docking with the m-opioid receptor shows that it originated two clusters with the 1S,2S enantiomer and one cluster with the 1R,2R enantiomer of tramadol. The results point to a more stable complex of the m-opioid receptor with the 1R,2R enantiomer of tramadol.     

Dynamic chemical devices: modulation of photophysical properties by reversible, ion-triggered, and proton-fuelled nanomechanical shape-flipping molecular motions

The terpy-derived (terpy=terpyridine) ligand 1 has an extended W shape in which the two appended photoactive pyrenyl groups are held apart. On binding of a zinc(II) ion with a terpy group, ligand 1 is converted into complex 2 whereby it adopts a U shape, thus stacking the aromatic units. This structural modification leads to a very pronounced change in photophysical properties: from a highly fluorescent free ligand to a very weakly emitting complex. The W/U structural switching can be reversibly induced by the addition of a competitive tren ligand, which binds and releases a zinc(II) ion under protonation/deprotonation cycles, thus leading to oscillations in light emission. Therefore, the present system performs periodic modulation of optical output through a nanomechanical shape-flipping motion, triggered by metal ion binding and fuelled by acid-base neutralisation energy. Overall, it represents an ion-triggered opto-mechanical supramolecular device.