含脂肪链聚苯并咪唑的合成及其气体透过性能

对含脂肪链聚苯并咪唑的聚合反应进行了比较系统的研究，在此基础上，合成了一系列含脂肪链聚苯并咪唑．以甲酸为溶剂，在减压下，制备了聚合物的均质膜．对聚合物的气体选择透过性能进行了研究，并从化学结构与气体透过性能关系的角度进行了讨论，发现同一聚合物对不同气体的透过系数符合一般玻璃态聚合物的规津；增加柔性链段中亚甲基数目，可提高聚合物的气体透过系数，降低分离系数；刚性链段中引入柔性基因，可增大气体透过系数；温度升高，聚合物的气体透过系数提高，分离系数一般下降．     

Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors

Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force—the binding free energy between a flexible ligand and a rigid receptor—for a small organic ligand and a biological macromolecule. Multiple BPMFs can be used to rigorously compute binding affinities between flexible partners. AlGDock uses replica exchange between thermodynamic states at different temperatures and receptor–ligand interaction strengths. Receptor–ligand interaction energies are represented by interpolating precomputed grids. Thermodynamic states are adaptively initialized and adjusted on-the-fly to maintain adequate replica exchange rates. In demonstrative calculations, when the bound ligand is treated as fully solvated, AlGDock estimates BPMFs with a precision within 4 kT in 65% and within 8 kT for 91% of systems. It correctly identifies the native binding pose in 83% of simulations. Performance is sometimes limited by subtle differences in the important configuration space of sampled and targeted thermodynamic states. © 2019 Wiley Periodicals, Inc.     

Chemical Vapor Deposition Synthesis of Large-Area Graphene Films

Graphene films were synthesized with the method of chemical vapor deposition using gaseous methane as the source of carbon and copper foil as the substrate for the deposition. The following conditions were found optimal to grow large-area high quality graphene films: preliminary annealing of the foil in the argon/hydrogen mixture at 970–990 °С for 30–40 min; simultaneous supply of the argon/hydrogen mixture (100 cm³/min) and methane (10 cm³/min) for 5–10 minutes, and subsequent cooling in an inert atmosphere. As a result, 1–10 layered graphene films were obtained to fully coat the copper foil over the area up to 50 cm². Several methods have been developed to transfer graphene to dielectric substrates such as silicon oxide and flexible polymer films. The obtained graphene films were used to create a flexible transparent conductive touch panel and a highly sensitive resistive humidity sensor exhibiting fast response-recovery time.     

Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations.

A comparison of different treatments of bond-stretching interactions in molecular dynamics simulation is presented. Relative free energies from simulations using rigid bonds maintained with the SHAKE algorithm, using partially rigid bonds maintained with a recently introduced flexible constraints algorithm, and using fully flexible bonds are compared in a multi-configurational thermodynamic integration calculation of changing liquid water into liquid methanol. The formula for the free energy change due to a changing flexible constraint in a flexible constraint simulation is derived. To allow for a more direct comparison between these three methods, three different pairs of models for water and methanol were used: a flexible model (simulated without constraints and with flexible constraints), a rigid model (simulated with standard hard constraints), and an alternative flexible model (simulated with flexible constraints and standard hard constraints) in which the ideal or constrained bond lengths correspond to the average bond lengths obtained from a short simulation of the unconstrained flexible model. The particular treatment of the bonds induces differences of up to 2 % in the liquid densities, whereas (excess) free energy differences of up to 5.7 (4.3) kJ mol(-1) are observed. These values are smaller than the differences observed between the three different pairs of methanol/water models: up to 5 % in density and up to 8.5 kJ mol(-1) in (excess) free energy.     

Ab initio calculation of some low-lying electronic excited states of methane

The energies of some low-lying electronic excited states of methane are calculated by using wave functions built up in terms of plane waves modulated by multicenter Gaussian factors. The wave functions of the various states are evaluated by a two steps iterative process. In the first step, each excited orbital is determined while keeping all other rigid; in the second, rearrangement effects are introduced. Final results are in good agreement with experimental data and allow to enhance an assignement hypothesis for the first electronic transitions.     

主链含硅的芳族聚酰胺的合成及其气体选择透过性能

采用界面缩合聚合方法，合成了一系列主链含硅的芳族聚酰胺，从化学结构与气体透过性能关系的角度研究了此类聚合物均质膜的气体透过性能，结果表明，此类聚合物膜对Ｈ２、Ｏ２、Ｎ２、ＣＯ２、ＣＨ４的气体透过系数大小顺序符合一般玻璃态聚合物规律；在刚性强的高分子链段中引进柔性基因，可提高聚合物的气体透过系数；高分子主链有较强内旋转能力的聚合物，气体透过系数大；高分子主链的化学结构相同，苯环上带有侧甲基的聚合物有高的气体透过系数；硅原子上带有侧苯基的聚合物，其气体扩散系数大于而溶解系数小于硅原子上携有侧甲基的聚合物．结论为，在刚性高分子主链中引入柔性基团和提高刚性链间隙是增大气体透过含硅聚酰胺膜速率的有利因素．     

Curvature-coupled hydration of Semicrystalline Polymer Amphiphiles yields flexible Worm Micelles but favors rigid Vesicles: polycaprolactone-based block copolymers

Crystallization processes are in general sensitive to detailed conditions, but our present understanding of underlying mechanisms is insufficient. A crystallizable chain within a diblock copolymer assembly is expected to couple curvature to crystallization and thereby impact rigidity as well as preferred morphology, but the effects on dispersed phases have remained unclear. The hydrophobic polymer polycaprolactone (PCL) is semi-crystalline in bulk (T(m) = 60°C) and is shown here to generate flexible worm micelles or rigid vesicles in water from several dozen polyethyleneoxide-based diblocks (PEO-PCL). Despite the fact that `worms' have a mean curvature between that of vesicles and spherical micelles, `worms' are seen only within a narrow, process-dependent wedge of morphological phase space that is deep within the vesicle phase. Fluorescence imaging shows worms are predominantly in one of two states - either entirely flexible with dynamic thermal undulations or fully rigid; only a few worms appear rigid at room temperature (T < T(m)), indicating suppression of crystallization by both curvature and PCL hydration. Worm rigidification, which depends on molecular weight, is also prevented by copolymerization of caprolactone with just 10% racemic lactide that otherwise has little impact on bulk crystallinity. In contrast to worms, vesicles of PEO-PCL are always rigid and typically leaky. Defects between crystallite domains induce dislocation-roughening with focal leakiness although select PEO-PCL - which classical surfactant arguments would predict make worms - yield vesicles that retain encapsulant and appear smooth, suggesting a gel or glassy state. Hydration in dispersion thus tends to selectively soften high curvature microphases.     

A comparison of field-based similarity searching methods: CatShape, FBSS, and ROCS

Three field-based similarity methods are compared in retrospective virtual screening experiments. The methods are the CatShape module of CATALYST, ROCS, and an in-house program developed at the University of Sheffield called FBSS. The programs are used in both rigid and flexible searches carried out in the MDL Drug Data Report. UNITY 2D fingerprints are also used to provide a comparison with a more traditional approach to similarity searching, and similarity based on simple whole-molecule properties is used to provide a baseline for the more sophisticated searches. Overall, UNITY 2D fingerprints and ROCS with the chemical force field option gave comparable performance and were superior to the shape-only 3D methods. When the flexible methods were compared with the rigid methods, it was generally found that the flexible methods gave slightly better results than their respective rigid methods; however, the increased performance did not justify the additional computational cost required.     

INTRAMOLECULAR FLUORESCENCE QUENCHING IN COVALENT ACRYLAMIDE-INDOLE ADDUCTS

Abstract— Indole derivatives have been prepared which have a covalently linked quencher, acrylamide. One of these adducts, N-acrylyltryptamine, has a flexible linkage and the other, N-acrylyl-1,2,3,4-tetrahydropyridoindole, has a rigid bridge between indole and the quencher. The intensity decays of these adducts were obtained using multi-frequency phase and modulation fluorometry. The fluorescence of these adducts appears to be dynamically quenched; dominant lifetimes of 64 ps and 31 ps are found for the flexible and rigid adducts. This indicates that very rapid intramolecular quenching occurs, even when the quencher and fluorophore cannot collide. Quenching in the rigid molecule probably involves electron transfer through two sigma bonds. Anisotropy decay data were also collected and rotational correlation times of 62 ps and 163 ps are reported for the flexibile and rigid adducts, respectively.     

Effect of flexibility on surface tension and coexisting densities of water

Molecular dynamics simulations of pure water at the liquid-vapor interface are performed using direct simulation of interfaces in a liquid slab geometry. The effect of intramolecular flexibility on coexisting densities and surface tension is analyzed. The dipole moment profile across the liquid-vapor interface shows different values for the liquid and vapor phases. The flexible model is a polarizable model. This effect is minor for liquid densities and is large for surface tension. The liquid densities increase from 2% at 300 K to 9% at 550 K when the force field is changed from a fully rigid simple point charge extended (SPCE) model to that of a fully flexible model with the same intermolecular interaction parameters. The increases in surface tension at both temperatures are around 11% and 36%, respectively. The calculated properties of the flexible models are closer to the experimental data than those of the rigid SPCE. The effect of the maximum number of reciprocal vectors (h(z) (max)) and the surface area on the calculated properties at 300 K is also analyzed. The coexiting densities are not sensitive to those variables. The surface tension fluctuates with h(z) (max) with an amplitude larger than 10 mN m(-1). The effect of using small interfacial areas is slightly larger than the error in the simulations.     

Statistical evaporation of rotating clusters. III. Molecular clusters

Unimolecular evaporation of weakly bound clusters made of rigid molecules is considered from the points of view of statistical theories and molecular dynamics simulations. We explicitly work out expressions for the kinetic energy released and product angular momentum distributions within the sphere+sphere and sphere+linear rigid body assumptions of phase space theory (PST). Various approximations are investigated, including the shape of the interaction potential between the two fragments and the anharmonicity of the vibrational density of states. The comparison between phase space theory and simulation for nitrogen and methane clusters shows a quantitative agreement, thereby suggesting that PST is accurate in predicting statistical observables in a wide range of systems under various physical conditions.     

Full protein flexibility is essential for proper hot-spot mapping

A traditional technique for structure-based drug design (SBDD) is mapping of protein surfaces with probe molecules to identify "hot spots" where key functional groups can best complement the receptor. Common methods, such as minimization of probes or calculation of grids, use a fixed protein structure in the gas phase, ignoring both protein flexibility and proper competition between the probes and water. As a result, the potential surface is quite rugged, and many spurious local minima are identified. In this work, we compared rigid and fully flexible proteins in mixed-solvent molecular dynamics, which allows for flexibility and full solvent effects. We were surprised to find that the large number of local minima are still found when a protein's conformational sampling is restricted; the dynamic averaging of probes and competition with water do not smooth the potential surface as one might expect. Only when a protein is allowed to be fully flexible in the simulation are the proper minima located and the spurious ones eliminated. Our results indicate that inclusion of full protein flexibility is critical to accurate hot-spot mapping for SBDD.     

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.     

A first principles simulation of rigid water

We present the results of Car-Parrinello (CP) simulations of water at ambient conditions and under pressure, using a rigid molecule approximation. Throughout our calculations, water molecules were maintained at a fixed intramolecular geometry corresponding to the average structure obtained in fully unconstrained simulations. This allows us to use larger time steps than those adopted in ordinary CP simulations of water, and thus to access longer time scales. In the absence of chemical reactions or dissociation effects, these calculations open the way to ab initio simulations of aqueous solutions that require time scales substantially longer than presently feasible (e.g., simulations of hydrophobic solvation). Our results show that structural properties and diffusion coefficients obtained with a rigid model are in better agreement with experiment than those determined with fully flexible simulations. Possible reasons responsible for this improved agreement are discussed.     

The influence of bond rigidity and cluster diffusion on the self-diffusion of hard spheres with square well interaction

Hard spheres interacting through a square well potential were simulated by using two different methods: Brownian cluster dynamics (BCD) and event driven Brownian dynamics (EDBD). The structure of the equilibrium states obtained by both methods was compared and found to be almost identical. Self-diffusion coefficients (D) were determined as a function of the interaction strength. The same values were found by using BCD or EDBD. Contrary to EDBD, BCD allows one to study the effect of bond rigidity and hydrodynamic interaction within the clusters. When the bonds are flexible, the effect of attraction on D is relatively weak compared to systems with rigid bonds. D increases first with increasing attraction strength, and then decreases for stronger interaction. Introducing intracluster hydrodynamic interaction weakly increases D for a given interaction strength. Introducing bond rigidity causes a strong decrease in D which no longer shows a maximum as function of the attraction strength.     

Nematogenic block copolymers of rigid and flexible aromatic units. I. Synthesis and characterization

Three types of wholly aromatic block copolymers were synthesized using the phosphorylation reactions of Yamazaki and Higashi. Each copolymer contained blocks of rigid and flexible units. The first copolymer, PBA/PABH-T, contains blocks of poly(p-benzamide) and the polyterephthalamide of p-aminobenzhydrazide. The second copolymer, PBA/MPD-I, contains blocks of poly(p-benzamide) and poly(p-phenylene isophthalamide), whereas the third, PPD T/MPD-I, contains blocks of poly(p-phenylene terephthalamide) and poly(m-phenylene isophthalamide). Three synthetic routes were used for the preparation of the block copolymers. In the two-step polycondensation (A), monomers of the flexible block are added to the rigid prepolymer. The multistep method (B) differs in that the rigid prepolymer is carboxy-terminated prior to addition of the monomers of the flexible block. Carboxy-terminated prepolymer of the rigid block is reacted with amine-terminated prepolymer of the flexible block in the two-pot condensation (C). The presence of a considerable amount of the flexible homopolymer is indicated by viscosity, extraction, and NMR studies, particularly when methods A and C were used. The flexible homopolymer can be extracted by using a nonsolvent for the rigid blocks. Extraction of the rigid homopolymer (which may also be presumed to be produced) entails a more elaborate procedure. In principle, one can use these methods to obtain pure block copolymer for study of mixtures with the rigid and flexible homopolymers. Phase studies of some of these systems will be reported in a following paper.     

Influence of steric symmetry and electronic dissymmetry on the enantioselectivity in palladium-catalyzed allylic substitutions

Chiral P,N-ligands with pseudo-C2 and pseudo-Cs symmetry based on chiral pyrrolidine and phospholane rings or on dinaphthatodihydroazepino and dinaphthatodihydrophosphepino moieties were prepared and assessed in the palladium-catalyzed allylic substitutions of allylic acetates. Higher selectivity was achieved with pseudo-C2-symmetric ligands based on the binaphthyl skeleton than with the analogous C2-symmetric P,P- and N,N-analogues. Pseudo-C2-type ligands had properties superior to those of pseudo-meso-type ligands when 1,3-diphenyl-2-propenyl acetate was used as a substrate, whereas the reverse situation was found for 3-cyclohexenyl acetate. Chirally flexible ligands, prepared by substitution of one of the rigid binaphthyl skeletons for a flexible biphenyl system, were found to induce chirality to the same extent as a 1:1 mixture of the rigid ligands.     

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

Synthesis and photophysics of silicon phthalocyanine-perylenebisimide triads connected through rigid and flexible bridges

Three new bisperylenebisimide-silicon phthalocyanine triads [(PBI)(2)-SiPcs 1, 2, and 3] connected with either rigid or flexible bridges were synthesized and characterized. A new synthetic approach to connect SiPc and PBI moieties through click chemistry produced triad 3 with an 80% yield. In (PBI)(2)-SiPc 1, PBI and SiPc are orthogonal and were connected with a rigid connector; triads 2 and 3 bear flexible aliphatic bridges, resulting in a tilted (2) or nearly parallel arrangement (3) of PBI and SiPc. Photoinduced intramolecular processes in these (PBI)(2)-SiPcs were studied and the results are compared with those of the reference compounds SiPc-ref and PBI-ref. The occurrence of electron-transfer processes between the SiPc and PBI units was confirmed by time-resolved emission and transient absorption techniques. Charge-separated (CS) states with lifetimes of 0.91, 1.3 and 2.0 ns for triads 1, 2, and 3, respectively, were detected using femtosecond laser flash photolysis. Upon the addition of Mg(ClO(4))(2), an increase in the lifetime of the CS states to 59, 110 and 200 μs was observed for triads (PBI)(2)-SiPcs 1, 2, and 3, respectively. The energy of the CS state (SiPc(·+)-PDI(·-)/Mg(2+)) is lower than the energy of both silicon phthalocyanine ((3)SiPc*-PDI) and perylenebisimide (SiPc-(3)PDI*) triplet excited states, which decelerates the metal ion-decoupled electron-transfer process for charge recombination to the ground state, thus increasing the lifetime of the CS state. The photophysics of the three triads demonstrate the importance of the rigidity of the spacer and the orientation between donor and acceptor units.     

Synthesis and Structures of Dinuclear Aluminum Complexes Based on Bis(β-diketiminate) Ligands

A series of ten dinuclear aluminum alkyl complexes based on rigid, semirigid, and flexible bis(β-diketiminate) ligands (NacNac) has been obtained from the reaction of trimethylaluminum and the corresponding bis(β-diketimine)s. All compounds were fully characterized using NMR and IR spectroscopy and elemental analysis. The molecular structures of five compounds have been investigated by means of single-crystal X-ray diffraction analysis.