Is molecular rotation really influenced by subtle changes in molecular shape?

In an attempt to seek out whether the reorientation time of a solute molecule is influenced by marginal changes to its shape, rotational relaxation of four coumarin solutes that are almost identical in size but subtly distinct in shape has been investigated in a viscous nonpolar solvent as a function of temperature. It has been observed that the reorientation times of the four coumarins differ significantly from one another. The four solutes have been treated as asymmetric ellipsoids and Stokes-Einstein-Debye hydrodynamic theory has been employed to calculate the shape factors and boundary condition parameters. The measured reorientation times when normalized by respective shape factors and boundary condition parameters can be scaled on a common curve, which is an indication that ellipsoid based hydrodynamic theory is adequate to model the reorientation times even when the differences in the shapes of the solute molecules are minimal.     

An improved molecular connectivity index

Through modification of the delta values of the molecular connectivity indexes, and connecting the quantum chemistry with topology method effectively, the molecular connectivity indexes are converted into quantum-topology indexes. The modified indexes not only keep all information obtained from the original molecular connectivity method but also have their own virtue in application, and at the same time make up some disadvantages of the quantum and molecular connectivity methods.     

Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, first principles MD or Car-Parrinello method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics/chemistry (liquid phosphorus). Dynamical, finite temperature, simulations deriving interatomic forces from state-of-the-art density functional calculations represent a substantial advance over both (i) traditional pointwise total energy and electronic band structure calculations and (ii) classical MD simulations with empirical or semi-empirical forces, and have already yielded qualitatively new insights in several fields.     

Fractal phenomena in molecular mechanics calculation

It is proposed that in molecular mechanics calculation points belonging to various stable or meta-sta-ble conformtrs are mixed up and form fractal structures in conformation space.The calculation results show the following two phenomena:(i)Two levels of structure with fractal feature were observed.Around the conformer without mirror symmetry points belonging to the conformer and its enantiomer are mixed up and form the first level of fractal structure; on the boundary of the attractive basin o{ each atlractor,points belonging to different attractors form the second level of fractal structure.(ii) The variation of molecular mechanics parameters will influence the structure and area of each attractive basin significantly The above phenomena may become the basis of a new method for solving the troublesome multi-minimum-point problem in molecular mechanics calculation.     

Lanthanide nanoparticles ignite dark molecular triplets

Molecular triplets have attracted great interest across multidisciplinary fields of the research ranging from thermally activated delayed fluorescence[1],triplet-triplet annihilation(TTA)upconversion[2],to photodynamic therapy relying on TTA between triplet photosensitizers and surrounding triplet oxygen to generate singlet oxygen species[3].     

Nanoscale segregation,molecular recognition and fluorophobic effect – from molecular design towards complex mesophase morphologies

Mesomorphic structure formation of hydrogen-bonded complexes of amino substituted 1,3,5-triazines with complementary (semiperfluoro)alkoxybenzoic acids is presented. The substitution pattern of both components was modified systematically in order to elucidate the influence of molecular parameters on the mesophase morphologies of the binary mixed systems. The phase sequence of the triazines, and of their associates with the acids, spans the range from smectic layer structures to discontinuous cubic phases composed of closed inverted micelles. Columnar phases with various two-dimensional lattice symmetries and bicontinuous cubic phases were found as intermediates. The mesophase morphologies are discussed in terms of the microsegregation of rigid polar, lipophilic and fluorinated molecular blocks in different sub-spaces along with tailoring the shape of (curved) aggregates by the space requirement of incompatible molecular fragments.     

Investigating cyclic peptides inhibiting CD2–CD58 interactions through molecular dynamics and molecular docking methods

The CD2–CD58 protein–protein interaction is known to favor the recognition of antigen presenting cells by T cells. The structural, energetics, and dynamical properties of three known cyclic CD58 ligands, named P6, P7, and RTD-c, are studied through molecular dynamics (MD) simulations and molecular docking calculations. The ligands are built so as to mimic the C and F β-strands of protein CD2, connected via turn inducers. The MD analyses focus on the location of the ligands with respect to the experimental binding site and on the direct and water-mediated hydrogen bonds (H bonds) they form with CD58. Ligand P6, with a sequence close to the experimental β-strands of CD2, presents characteristics that explain its higher experimental affinity, e.g., the lower mobility and flexibility at the CD58 surface, and the larger number and occurrence frequency of ligand-CD58 H bonds. For the two other ligands, the structural modifications lead to changes in the binding pattern with CD58 and its dynamics. In parallel, a large set of molecular docking calculations, carried out with various search spaces and docking algorithms, are compared to provide a consensus view of the preferred ligand binding modes. The analysis of the ligand side chain locations yields results that are consistent with the CD2–CD58 crystal structure and suggests various binding modes of the experimentally identified hot spot of the ligands, i.e., Tyr86. P6 is shown to form a number of contacts that are also present in the experimental CD2–CD58 structure.     

Oligo Tröger's bases--new molecular scaffolds

Oligo Tr?ger's bases are compounds containing two or more Tr?ger's base subunits (1,5-methanodiareno[b,f][1,5]diazocines) sharing one or more arene parts. Due to their interesting molecular shapes, these compounds are studied as chiral molecular tweezers, clips, cavitands, clefts, calixes, etc. This review includes all available data on oligo Tr?ger's bases, and introduces their preparation and properties to a wide audience.     

Using molecular recognition of β-cyclodextrin to determine molecular weights of low-molecular-weight explosives by MALDI-TOF mass spectrometry

This study presents a novel method for determining the molecular weights of low molecular weight (MW) energetic compounds through their complexes of beta-cyclodextrin (beta-CD) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in a mass range of 500 to 1700 Da, avoiding matrix interference. The MWs of one composite explosive composed of 2,6-DNT, TNT, and RDX, one propellant with unknown components, and 14 single-compound explosives (RDX, HMX, 3,4-DNT, 2,6-DNT, 2,5-DNT, 2,4,6-TNT, TNAZ, DNI, BTTN, NG, TO, NTO, NP, and 662) were measured. The molecular recognition and inclusion behavior of beta-CD to energetic materials (EMs) were investigated. The results show that (1) the established method is sensitive, simple, accurate, and suitable for determining the MWs of low-MW single-compound explosives and energetic components in composite explosives and propellants; and (2) beta-CD has good inclusion and modular recognition abilities to the above EMs.     

Steered molecular dynamics simulations of protein-ligand interactions

Molecular recognition and specific protein-ligandinteractions are central to many biochemical processes,such as enzyme catalysis, assembly of organelles, en-ergy transduction, signaling, diverse control functions,and replication, expression and storage of the geneticmaterial[1]. Moreover, protein-ligand interactions pro-vide the mechanism of many drug therapies and un-derstanding of such interactions is thus significant forrational drug design[1,2]. For the experimental studiesof protein-ligan…     

Theory on the molecular characteristic contour(Ⅰ)——A new approach to defining molecular characteristic contour

Based on the classical turning point of electron movement in a molecule, a model for defining the molecular characteristic boundary contour is advanced. By using an accurate ab initio MELD program and an auxiliary program, some electron parameters in a molecule, such as the potential felt by an electron, have been evaluated. According to our model and definition, the molecular characteristic contour of the equilibrium geometry configuration is drawn and a vivid intuitive picture for describing the forming or breaking of a chemical bond is displayed.     

Lead-free molecular one-dimensional perovskite for efficient X-ray detection

In recent years,great progress has been achieved for organicinorganic halide perovskites due to their excellent optoelectronic properties and stability for photovoltaics,light emitting diodes,and high-energy radiation detection[1-5].One-dimensional(1D)perovskites,as an important derivative of three-dimensional(3D)perovskites,exhibit low exciton dissociation efficiency,which can produce strong quantum confinement and form self-trapping excited state[6],In addition,the hydrophobic properties and the inhibition of ion migration from large organic cations improve the moisture and thermal stability for optoelectronic devices.     

The chemist’s concept of molecular structure

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models.

When do molecular bowls encapsulate metal cations?

Curved carbon π surfaces have chemical and physical properties suitable for exploitation for chemical microencapsulation and the self-assembly of nanoscale materials. Advances will greatly benefit from more understanding of their host-guest interactions with guests such as metal cations. Here, quantitative predictions are made for the binding of metal cations to three prototypical surfaces using density functional theory calculations: the buckybowls C(20)H(10), C(30)H(10), and C(40)H(10). The focus was on finding the most favorable binding sites, assessing whether binding is more favorable inside or outside the bowl, and exploring factors influencing the binding site preference. Classes of cations studied included small and large monocations and cations with multiple charges: Na(+), Cs(+), NH(4)(+), Ba(+), Ba(2+), and La(3+). Factors found to favor inside binding were large ion size and high ion charge, suggesting that polarization interactions as well as short-range interactions are important in determining the preferred binding sites inside and outside these buckybowls. Unlike monocations, which at best have only a weak tendency toward encapsulation, the multiply charged cations Ba(2+) and La(3+) were found to have a strong driving force toward containment inside the bowls. Coulomb potentials were found to favor cation binding on the outside surface of the bowls, but cation microsolvation through polarization interactions presents a compensating factor that can tip the balance in favor of encapsulation. Knowledge of these factors will be a valuable tool in the design of nanocontainers and the diverse architecture possible with these structural elements.     

Microwave-assisted sol–gel synthesis for molecular imprinting

Molecularly imprinted polymers have been the subject of intense research for several decades in both academic and industrial settings. In this paper, we introduce a novel microwave-assisted sol–gel method for molecular imprinting of silica microspheres. The microspheres were characterized, and their adsorption of imprint and non-imprint molecules was investigated. The dye molecules methyl orange and ethyl orange were used as templates. Good molecular imprinting was observed as evaluated by the re-adsorption of dye into the silica matrix followed by the removal of dye from the supernatant solution.     

Diketopyrrolopyrrole-derived organic small molecular dyes for tumor phototheranostics

Cancer is one of the leading causes of human death around the world. Phototherapy, including photodynamic therapy(PDT) and photothermal therapy(PTT), is an emerging light-triggered cancer treatment and shows the advantages of non-invasiveness and low side effects. The design and preparation of efficient phototherapeutic agents are of great significance for phototherapy. Diketopyrrolopyrrole(DPP) is a small molecular organic dye featuring outstanding photophysical properties, facile tuning of str...     

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.     

Chiral kagomé lattice from simple ditopic molecular bricks

Self-assembly techniques allow for the fabrication of highly organized architectures with atomic-level precision. Here, we report on molecular-level scanning tunneling microscopy observations demonstrating the supramolecular engineering of complex, regular, and long-range ordered periodic networks on a surface atomic lattice using simple linear molecular bricks. The length variation of the employed de novo synthesized linear dicarbonitrile polyphenyl molecules translates to distinct changes of the bonding motifs that lead to hierarchic order phenomena and unexpected changes of the surface tessellations. The achieved 2D organic networks range from a close-packed chevron pattern via a rhombic network to a hitherto unobserved supramolecular chiral kagomé lattice.