Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations

We present a simple and practical method to include ligand electronic polarization in molecular dynamics (MD) simulation of biomolecular systems. The method involves periodically spawning quantum mechanical (QM) electrostatic potential (ESP) calculations on an extra set of computer processors using molecular coordinate snapshots from a running parallel MD simulation. The QM ESPs are evaluated for the small-molecule ligand in the presence of the electric field induced by the protein, solvent, and ion charges within the MD snapshot. Partial charges on ligand atom centers are fit through the multi-conformer restrained electrostatic potential (RESP) fit method on several successive ESPs. The RESP method was selected since it produces charges consistent with the AMBER/GAFF force-field used in the simulations. The updated charges are introduced back into the running simulation when the next snapshot is saved. The result is a simulation whose ligand partial charges continuously respond in real-time to the short-term mean electrostatic field of the evolving environment without incurring additional wall-clock time. We show that (1) by incorporating the cost of polarization back into the potential energy of the MD simulation, the algorithm conserves energy when run in the microcanonical ensemble and (2) the mean solvation free energies for 15 neutral amino acid side chains calculated with the quantum polarized fluctuating charge method and thermodynamic integration agree better with experiment relative to the Amber fixed charge force-field.     

The opsin shift and mechanism of spectral tuning in rhodopsin

Molecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of -980 cm(-1) was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)-binding site of the opsin. The conformational change from a 6-s-cis-all-trans configuration in solution to the 6-s-cis-11-cis conformer contributes additional -200 cm(-1), and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm(-1) was obtained, in reasonable accord with experiment (2730 cm(-1)). Dynamics simulations revealed that the 6-s-cis bond can occupy two main conformations for the β-ionone ring, resulting in a weighted average dihedral angle of about -50°, which may be compared with the experimental estimate of -28° from solid-state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB.     

Time-resolved red luminescence from europium-catalyzed single walled carbon nanotubes

The photo-physical properties of Eu-SWCNTs indicate that intrinsic excitonic properties of SWCNTs sensitize the lanthanoid element europium (Eu) to emit time-resolved red luminescence.     

A Triptycene‐Based Approach to Solubilising Carbon Nanotubes and C60

We describe herein the synthesis of a triptycene‐based surfactant designed with the ability to solubilise single‐walled carbon nanotubes (SWNTs) and C₆₀ in water through non‐covalent interactions. Furthermore, an amphiphilic naphthalene‐based surfactant with the same ability to solubilise SWNTs and C₆₀ has also been prepared. The compounds synthesised were designed with either two ionic or non‐ionic tails to ensure a large number of supramolecular interactions with the solvent, thereby promoting strong solubilisation. The surfactants produced stable suspensions in which the SWNTs are dispersed and the surfactant/SWNT complexes formed are stable for more than one year. UV/Vis/NIR absorption spectroscopy, TEM and AFM were employed to probe the solubilisation properties of the dispersion of surfactants and SWNTs in water.     

A robust doubly interpenetrated metal-organic framework constructed from a novel aromatic tricarboxylate for highly selective separation of small hydrocarbons

A microporous metal-organic framework, for the first time, has been developed for highly selective separation of industrially important C(1), C(2) and C(3) hydrocarbons at room temperature.     

Induced Fit of C2H2 in a Flexible MOF Through Cooperative Action of Open Metal Sites

Porous materials that can undergo pore‐structure adjustment to better accommodate specific molecules are ideal for separation and purification. Here, we report a stable microporous metal‐organic framework, JNU‐1, featuring one‐dimensional diamond‐shaped channels with a high density of open metal sites arranged on the surface for the cooperative binding of acetylene. Together with its framework flexibility and appropriate pore geometry, JNU‐1 exhibits an induced‐fit behavior for acetylene. The specific binding sites and continuous framework adaptation upon increased acetylene pressure are validated by molecular modeling and in situ X‐ray diffraction study. This unique induced‐fit behavior endows JNU‐1 with an unprecedented increase in the acetylene binding affinity (adsorption enthalpy: up to 47.6 kJ mol^?1 at ca. 2.0 mmol g^?1 loading).     

Dynamic response of composite plates with cut-outs,part I: Simply-supported plates

The effect of square cut-outs on the natural frequencies of square, simply-supported composite plates is investigated. The forced and free dynamic response of plates with cut-outs is formulated. Laminations are assumed to be symmetric about the mid-plane and the plates are considered analytically as homogeneous anisotropic plates. In the method of solution it is assumed that the effect of the cut-out is equivalent to an external loading on the plate. For free vibration, the method leads to an infinite system of frequency equations. Depending upon the accuracy required, a suitable size of the system of frequency equations is selected. Results are given for square, simply-supported composite plates with centrally located square cut-outs for different modulus ratios. A comparison of results obtained from this method for isotropic plates with cut-outs with available literature is made and excellent agreement is obtained.     

Bimodal Functionality in a Porous Covalent Triazine Framework by Rational Integration of an Electron‐Rich and ‐Deficient Pore Surface

A porous covalent triazine framework (CTF) consisting of both an electron‐deficient central triazine core and electron‐rich aromatic building blocks is reported. Taking advantage of the dual nature of the pore surface, bimodal functionality has been achieved. The electron deficiency in the central core has been utilized to address one of the pertinent problems in chemical industries, namely separation of benzene from its cyclic saturated congener, that is, cyclohexane. Also, by virtue of the electron‐rich aromatic rings with Lewis basic sites, aqueous‐phase chemical sensing of a nitroaromatic compound of highly explosive nature (2,4,6‐trinitrophenol; TNP) has been achieved. The present compound supersedes the performance of previously reported COFs in both the aspects. Notably, this reports the first example of pore‐surface engineering leading to bimodal functionality in CTFs.     

Tuning Pore Polarization to Boost Ethane/Ethylene Separation Performance in Hydrogen-Bonded Organic Frameworks

Hydrogen-bonded organic frameworks (HOFs) show great potential in energy-saving C₂H₆/C₂H₄ separation, but there are few examples of one-step acquisition of C₂H₄ from C₂H₆/C₂H₄ because it is still difficult to achieve the reverse-order adsorption of C₂H₆ and C₂H₄. In this work, we boost the C₂H₆/C₂H₄ separation performance in two graphene-sheet-like HOFs by tuning pore polarization. Upon heating, an in situ solid phase transformation can be observed from HOF-NBDA(DMA) (DMA=dimethylamine cation) to HOF-NBDA , accompanied with transformation of the electronegative skeleton into neutral one. As a result, the pore surface of HOF-NBDA has become nonpolar, which is beneficial to selectively adsorbing C₂H₆. The difference in the capacities for C₂H₆ and C₂H₄ is 23.4 cm³ g⁻¹ for HOF-NBDA , and the C₂H₆/C₂H₄ uptake ratio is 136 %, which are much higher than those for HOF-NBDA(DMA) (5.0 cm³ g⁻¹ and 108 % respectively). Practical breakthrough experiments demonstrate HOF-NBDA could produce polymer-grade C₂H₄ from C₂H₆/C₂H₄ (1/99, v/v) mixture with a high productivity of 29.2 L kg⁻¹ at 298 K, which is about five times as high as HOF-NBDA(DMA) (5.4 L kg⁻¹). In addition, in situ breakthrough experiments and theoretical calculations indicate the pore surface of HOF-NBDA is beneficial to preferentially capture C₂H₆ and thus boosts selective separation of C₂H₆/C₂H₄.     

Structure, self-assembly, and dual role of a beta-defensin-like peptide from the Chinese soft-shelled turtle eggshell matrix

Biomineral matrix formation and molecular recognition are two important processes associated with eggshell biomineralization. To understand these two processes, a major intracrystalline peptide, pelovaterin, was isolated from turtle (Pelodiscus sinensis) eggshell and its tertiary and quaternary structures were established. The global fold of pelovaterin is similar to that of human beta-defensins but has a large hydrophobic core and a short hydrophilic N-terminal segment, which is not preserved in defensins. Pelovaterin exhibits strong antimicrobial activity against two pathogenic gram-negative bacteria, Pseudomonas aeruginosa and Proteus vulgaris, and stabilizes a thin film of metastable vaterite. We show that pelovaterin self-aggregates in the form of micellar nanospheres and the aggregation in solution is entropy-driven. It is suggested that the micellar aggregation of pelovaterin is responsible for the induction and stabilization of the metastable phase by altering the interfacial energy. The results demonstrate the adaptability of an extracellular matrix protein to perform multiple tasks: polymorph discrimination and protection of the contents of the egg against bacterial invasion.