Gas Phase Conformations of Selenocysteine and Related Ions: A Comprehensive Theoretical Study

Extensive ab initio molecular calculations have been first performed to thoroughly characterize the gas-phase potential energy surfaces (PES) of the 21th amino acid selenocysteine and related ions (neutral, protonated and deprotonated). A wide range of trial structures generated by considering the combinations of all internal single-bond rotamers was surveyed at the BHandHLYP/6-31G­(d) level, and then refined at the BHandHLYP/6-311++G­(d,p) level. A total of 76, 23, 38, and 3 unique stable conformers respectively for neutral, protonated, deprotonated, and doubly deprotonated selenocysteine is identified, and neutral zwitterionic forms are found to be as local minima on the gas-phase PES. The properties of the low energy conformers, such as relative energies, dipole moments, rotational constants, and intramolecular hydrogen bonds, were determined and analyzed. The thermochemical properties of proton affinity (PA), gas-phase basicity (GB), proton dissociation energy (PDE), gas-phase acidity (GA), and the vertical ionization energies (VIEs) were computed by the theoretical approaches of BHandHLYP, B3LYP, MP2, and CCSD­(T). Moreover, the conformational equilibrium effect (CEE) on thermochemical properties was analyzed. The statistical simulation predicts that the CEE generally yields a physical correction on about a 1 <i>k</i>_B<i>T</i> scale in GA/GB calculations for multi-conformer systems

Ultrabright Pdots with a Large Absorbance Cross Section and High Quantum Yield

Semiconducting polymer dots (Pdots) are increasingly used in biomedical applications due to their extreme single-particle brightness, which results from their large absorption cross section (σ). However, the quantum yield (Φ) of Pdots is typically below 40% due to aggregation-induced self-quenching. One approach to reducing self-quenching is to use FRET between the donor (D) and acceptor (A) groups within a Pdot; however, Φ values of FRET-based Pdots remain low. Here, we demonstrate an approach to achieve ultrabright FRET-based Pdots with simultaneously high σ and Φ. The importance of self-quenching was revealed in a non-FRET Pdot: adding 30 mol % of a nonabsorbing polyphenyl to a poly­(9,9-dioctylfluorene) (PFO) Pdot increased Φ from 13.4 to 71.2%, yielding an ultrabright blue-emitting Pdot. We optimized the brightness of FRET-based Pdots by exploring different D/A combinations and ratios with PFO and poly­[(9,9-dioctylfluorenyl-2,7-diyl)-co-(1,4-phenylene)] (PFP) as donor polymers and poly­[(9,9-dioctyl-2,7-divinylenefluorenylene)-alt-co-(1,4-phenylene)] (PFPV) and poly­[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(1,4-benzo-{2,1′,3}-thiadiazole)] (PFBT) as acceptor polymers, with a fixed concentration of poly­(styrene-co-maleic anhydride) as surfactant polymer. Ultrabright blue-emitting Pdots possessing high Φ (73.1%) and σ (σR = σabs/σall, 97.5%) were achieved using PFP/PFPV Pdots at a low acceptor content (A/[D + A], 2.5 mol %). PFP/PFPV Pdots were 1.8 times as bright as PFO/PFPV Pdots due to greater coverage of acceptor absorbance by donor emissiona factor often overlooked in D/A pair selection. Ultrabright green-emitting PFO Pdots (Φ = 76.0%, σR = 92.5%) were obtained by selecting an acceptor (PFBT) with greater spectral overlap with PFO. Ultrabright red-emitting Pdots (Φ = 64.2%, σR = 91.0%) were achieved by blending PFO, PFBT, and PFTBT to create a cascade FRET Pdot at a D:A1:A2 molar ratio of 61:5:1. These blue, green, and red Pdots are among the brightest Pdots reported. This approach of using a small, optimized amount of FRET acceptor polymer with a large donor–acceptor spectral overlap can be generalized to produce ultrabright Pdots with emissions that span the visible spectrum

Time needed to compress by TRCMGene.

Time needed to compress by TRCMGene.</p

Compressed file structure.

The general structure is shown on the left. The detailed description of every compressed sequence is shown on the right. Refer to the text for details.</p

Factors that influence the performance of TRCMGene.

Factors that influence the performance of TRCMGene.</p

Compression capabilities of TRCMGene compared to method by ORCM.

Compression factor with respect to the uncompressed file size calculated as original file sizes divided by the compressed file sizes (greater is better).</p

Performance of TRCMGene compared with that of two other compression methods.

Performance of TRCMGene compared with that of two other compression methods.</p

Reading capabilities of TRCMGene.

Reading time ratio was defined as the ratio between the time of reading uncompressed file and the time of reading compressed file (greater is better).</p

Low Energy Conformations and Gas-Phase Acidity and Basicity of Pyrrolysine

The gas-phase conformational potential energy surfaces (PES) of the last, 22nd amino acid pyrrolysine and related derivatives (neutral, deprotonated, and protonated) were extensively searched for the first time. By considering all possible combinations of the single-bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach, a large set of unique low-energy conformers was identified for each pyrrolysine species, and essential properties such as vibrational frequencies, dipole moments, rotational constants, and intramolecular hydrogen bonding configurations were presented and characterized. The conformational electronic energies and thermochemical properties of proton affinity/dissociation energy (PA/PDE) and gas-phase acidity/basicity (GA/GB) were determined by the density functional BHandHLYP, B3LYP, and M062X, and Møller–Plesset MP2 methods. The MP2 and DFT methods are found to predict disparate PES for neutral and protonated conformations and sufficiently different thermochemical data. The measurements of dipole moments and characteristic IR modes at low temperature as well as GA/GB are demonstrated to be feasible approaches to verify the theoretical predictions

Thermal transport properties of single-layer black phosphorus from extensive molecular dynamics simulations

We compute the anisotropic in-plane thermal conductivity of suspended single-layer black phosphorus (SLBP) using three molecular dynamics (MD) based methods, including the equilibrium MD method, the nonequilibrium MD (NEMD) method, and the homogeneous NEMD (HNEMD) method. Two existing parameterizations of the Stillinger–Weber (SW) potential for SLBP are used. Consistent results are obtained for all the three methods and conflicting results from previous MD simulations are critically assessed. Among the three methods, the HNEMD method is the most and the NEMD method the least efficient. The thermal conductivity values from our MD simulations are about an order of magnitude larger than the most recent predictions obtained using the Boltzmann transport equation approach considering long-range interactions in density functional theory calculations, suggesting that the short-range SW potential might be inadequate for describing the phonon anharmonicity in SLBP