Molecular Tweezers: Concepts and Applications

Taken to the molecular level, the concept of “tweezers” opens a rich and fascinating field at the convergence of molecular recognition, biomimetic chemistry and nanomachines. Composed of a spacer bridging two interaction sites, the behaviour of molecular tweezers is strongly influenced by the flexibility of their spacer. Operating through an “induced‐fit” recognition mechanism, flexible molecular tweezers select the conformation(s) most appropriate for substrate binding. Their adaptability allows them to be used in a variety of binding modes and they have found applications in chirality signalling. Rigid spacers, on the contrary, display a limited number of binding states, which lead to selective and strong substrate binding following a “lock and key” model. Exquisite selectivity may be expressed with substrates as varied as C₆₀, nanotubes and natural cofactors, and applications to molecular electronics and enzyme inhibition are emerging. At the crossroad between flexible and rigid spacers, stimulus‐responsive molecular tweezers controlled by ionic, redox or light triggers belong to the realm of molecular machines, and, applied to molecular tweezing, open doors to the selective binding, transport and release of their cargo. Applications to controlled drug delivery are already appearing. The past 30 years have seen the birth of molecular tweezers; the next many years to come will surely see them blooming in exciting applications.     

Molecular Forcefield Methods for Describing Energetic Molecular Crystals: A Review

Energetic molecular crystals are widely applied for military and civilian purposes, and molecular forcefields (FF) are indispensable for treating the microscopic issues therein. This article reviews the three types of molecular FFs that are applied widely for describing energetic crystals—classic FFs, consistent FFs, and reactive FFs (ReaxFF). The basic principle of each type of FF is briefed and compared, with the application introduced, predicting polymorph, morphology, thermodynamics, vibration spectra, thermal property, mechanics, and reactivity. Finally, the advantages and disadvantages of these FFs are summarized, and some directions of future development are suggested.     

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。     

平面环辛四烯:分子结构操纵实例

环辛四烯为一不平面分子,一般相信,理论中的平面环辛四烯需要将一对不成对电子填入两个简并不成键轨道,因而引起之伪扬-泰勒效应,可使带 D_(8h)对称性之平面环辛四烯非平面化而成“船”形的结构。本文简单介绍加减电子法、带张力环稠合法、键长缩短法和金属螫合法四种可使不平面之环辛四烯成为平面方法。然而,随有机合成方法之不断进展,在将来可能出现更多改变环辛四烯不平面结构的方法。我们在此文章提出化合物98即为一个可使环辛四烯成为平面的例子。98之合成将成为有机合成化学家的一个新的挑战。     

Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition

Recognition of small molecules by proteins depends on three-dimensional molecular surface complementarity. However, the dominant techniques for analyzing the similarity of small molecules are based on two-dimensional chemical structure, with such techniques often outperforming three-dimensional techniques in side-by-side comparisons of correlation to biological activity. This paper introduces a new molecular similarity method, termed morphological similarity (MS), that addresses the apparent paradox. Two sets of molecule pairs are identified from a set of ligands whose protein-bound states are known crystallographically. Pairs that bind the same protein sites form the first set, and pairs that bind different sites form the second. MS is shown to separate the two sets significantly better than a benchmark 2D similarity technique. Further, MS agrees with crystallographic observation of bound ligand states, independent of information about bound states. MS is efficient to compute and can be practically applied to large libraries of compounds.     

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.     

A Symmetry adapted tessellation of the GEPOL surface: applications to molecular properties in solution

A procedure to partition the GEPOL molecular surface into tesserae that respects the molecular symmetry constraints is presented. Using this method it is possible to build a solvent reaction field for the Polarizable Continuum Model with the same symmetry of the nuclear potential. Several applications are reported and discussed to evaluate the performance of this new procedure. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1262–1272, 2001     

Simulating GTP:Mg and GDP:Mg with a simple force field: A structural and thermodynamic analysis

Di‐ and tri‐phosphate nucleotides are essential cofactors for many proteins, usually in an Mg²⁺‐bound form. Proteins like GTPases often detect the difference between NDP and NTP and respond by changing conformations. To study such complexes, simple, fixed charge force fields have been used, which allow long simulations and precise free energy calculations. The preference for NTP or NDP binding depends on many factors, including ligand structure and Mg²⁺ coordination and the changes they undergo upon binding. Here, we use a simple force field to examine two Mg²⁺ coordination modes for the unbound GDP and GTP: direct, or “Inner Sphere” (IS) coordination by one or more phosphate oxygens and indirect, “Outer Sphere” (OS) coordination involving one or more bridging waters. We compare GTP: and GDP:Mg binding with OS and IS coordination; combining the results with experimental data then indicates that GTP prefers the latter. We also examine different kinds of IS coordination and their sensitivity to a key force field parameter: the optimal Mg:oxygen van der Waals distance R_min. Increasing R_min improves the Mg:oxygen distances, the GTP: and GDP:Mg binding affinities, and the fraction of GTP:Mg with β + γ phosphate coordination, but does not improve or change the GTP/GDP affinity difference, which remains much larger than experiment. It has no effect on the free energy of GDP binding to a GTPase. © 2012 Wiley Periodicals, Inc.     

Molecular weight distributions of linear polymers: Detailed analysis from GPC data

The GPC method is used widely to measure molecular weights of linear polymers. High-quality GPC data contains detailed information on many aspects of the polymer's molecular weight distribution (MWD). This information can be extracted from the data using computer analysis. Equations have been derived for the two simplest MWD functions in the GPC coordinates: the Flory function (one growing polymer chain produces one polymer molecule), and for the case when two polymer radicals combine into one polymer molecule. The equations were used to analyze MWD of two classes of polymers. The first class includes polymers with narrow MWD: polyethylene, ethylene-propylene and ethylene-hexene copolymers, syndiotactic polystyrene, and radical polystyrene. The second class includes polymers with broad MWD: ethylene copolymers and polypropylene produced with heterogeneous, Ti-based catalysts. The examples demonstrate that the resolution of complex GPC curves into their constitutents serve as an important source of information about kinetics of polymerization reactions. © 1995 John Wiley & Sons, Inc.     

Fullerenes: multitask components in molecular machinery

Molecular machines are molecular-scale devices that carry out predetermined tasks derived from molecular motion. This Minireview illustrates how fullerenes can be used as multitask building blocks in molecular machinery, providing new perspectives for fullerenes. Indeed, C(60) can be applied as a photo- and electroactive stopper owing to its size, as a probe for molecular motion as a result of its well-defined physicochemical properties, and to induce motion through pi-pi interactions. Such molecular motion can be employed to modulate light-driven electron-transfer events, extending the potential applications of molecular machines to the typical fields of application of fullerenes.     

Influence of Intermolecular Vibrations on the Electronic Coupling in Organic Semiconductors: The Case of Anthracene and Perfluoropentacene

We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure.     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

The completion of the Human Genome Project, the growing effort on proteomics, and the Structural Genomics Initiative have recently intensified the attention being paid to reliable computer docking programs able to identify molecules that can affect the function of a macromolecule through molecular complexation. We report herein an automated computer docking program, EUDOC, for prediction of ligand-receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases. This program was evaluated from the standpoints of force field and sampling issues using 154 experimentally determined ligand-receptor complexes and four "real-life" applications of the EUDOC program. The results provide evidence for the reliability and accuracy of the EUDOC program. In addition, key principles underlying molecular recognition, and the effects of structural water molecules in the active site and different atomic charge models on docking results are discussed. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1750-1771, 2001     

Conjecture: imines as unidirectional photodriven molecular motors-motional and constitutional dynamic devices

Compounds containing the C==N group, such as imines and their derivatives, may undergo syn-anti isomerization by two different routes: 1) photochemically, by out-of-plane rotation around the carbon-nitrogen double bond through a "perpendicular" form, and 2) thermally, by in-plane nitrogen inversion through a "linear" transition state. When the two interconversions occur in sequence, a full, closed process is accomplished, restoring the initial state of the system along two different steps. In a chiral imine-type compound, for example, with an asymmetric center next to the C==N function, photoinduced rotation may be expected to occur in one sense in preference to the opposite one. Thus, photoisomerization followed by thermal isomerization in a chiral imine compound generates unidirectional molecular motion. Generally, imine-type compounds represent unidirectional molecular photomotors converting light energy into mechanical motion. As they are also able to undergo exchange of the carbonyl and amine partners, they present constitutional dynamics. Thus, imine-type compounds are double dynamic, motional, and constitutional devices.     

X-ray Structures of Three Penem Antibiotics: Molecular Mechanical and Dynamic Aspects

The structures of three -lactam penem antibiotics—i.e. the sodium[5R-[5,6(R*)]]-6-(1-hydroxyethyl)-7-oxo-3-[[(1-pyrrolidinylthioxomethyl)thio]methyl]-4-thia-1-azabicyclo[3.2.0] hept-2-ene-2-carboxylate (compound 1), the [5R-[3(S*),5,6(R*)]]-3-[[2-(aminocarbonyl)-1-pyrrolidinyl] methyl]-6-(1-hydroxyethyl)-7-oxo-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid (compound 2), and the [5R-[5,6(R*)]]-3-[[(2-amino-2-oxoethyl) methylamino]methyl]-6-(1-hydroxyethyl)-7-oxo-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid (compound 3)—have been determined by X-ray analyses. In the crystal lattice two conformational isomers of 1 are present, which differ from each other in the spatial arrangement of the dithiocarbamate chain. Compounds 2 and 3 are in zwitterionic form, being the hydrogen of the carboxylic acid moved to the amino nitrogen of the chain at C2. This hydrogen atom, in both molecules, forms intramolecular hydrogen bonds with an oxygen atom of the carboxylate moiety and with the oxygen atom of the amido group of the side chain. The 3D structures of 1, 2, and 3 have been compared with those of previously reported -lactam penem antibiotics. Particularly, the Woodward parameter and the Cohen distance, which are considered important in determining the antibiotic activity, have been discussed. Least-squares minimizations (RMS) of the distances between nuclei of selected pairs of atoms defining the pharmacological pattern have been performed, comparing five common antibiotics (imipenem, ritipenem, cephaloridine, amoxycillin, and benzylpenicillin) with our compounds. Finally, molecular dynamics calculations have been carried out on the three penem antibiotics at different temperatures. The conformational behavior of the hydroxyethyl chain, the carboxylate group, and the chain at C2 is discussed by considering the variation of some selected dihedral angles.