Investigating the influence of substituent groups in TTM based radicals for the excitation process: a theoretical study.

Tri-(2,4,6-trichlorophenyl)methyl (TTM) based radicals can be promising in providing relatively high fluorescence quantum efficiency. In this study, we have evaluated the photoluminescence properties of a series of TTM-based radicals by means of DFT and TD-DFT methods. The optimized structures of the ground states (D0) and the first excited states (D1) of all the radicals are calculated and the computed emission bands are comparable with previous experimental results. knr is determined from transition dipole moments (µ12) and the energy gaps between D0 and D1 (ΔE), both of which can be regulated by the conjugated structures from the substituent groups. knr was derived from the mode-averaging method and is consistent with the experimental results. Factors influencing kr and knr, including the potential energy differences (ΔG0), the vibrational reorganization energies (λ) and the electron coupling term (Hab), are discussed. By comparing kr and knr in solvents with different polarities (cyclohexane, toluene, and chloroform), TTM based radicals in cyclohexane exhibit the most promising fluorescence efficiencies. Besides, two substituted radicals, namely 2Br-TTM-3PCz and 2F-TTM-3PCz, have been fabricated. The results show that fluorine atoms are able to increase ΔG0 and a considerably small knr has been predicted. We expect that our calculation can benefit the design of light-emitting molecules in further experiments.

A novel T-C3N and seawater desalination.

A structurally stable stacked multilayer carbonitride is predicted with the aid of ab initio calculations. This carbonitride consists of C3N tetrahedra, and is similar to T-carbon and thus named T-C3N. Its 2-dimensional (2D) monolayer is also carefully investigated in this work. The studies on electronic properties reveal that bulk and 2D T-C3N are insulators with a 5.542 eV indirect band gap and a 5.741 eV direct band gap, respectively. However, the monolayer T-C3N exhibits an excellent uniform porosity. Its 5.50 Å pore size is perfect for water nanofiltration. The adsorption and permeation of water molecules on the monolayer T-C3N are investigated. Its promising potential application in highly efficient nanofiltration membranes for seawater desalination is discussed.

Investigating detailed mechanism of hydrogen molecules adsorbing on single-wall carbon nanotubes using fitted force field parameters containing carbon-carbon interactions.

The nonbonded and bonded force field parameters for carbon atoms in single-wall carbon nanotubes (SWNT) are fitted by means of quantum chemistry calculations with considering the periodic boundary conditions. The nonbonded parameters between carbon atoms and hydrogen atoms are fitted as well. All the fitted parameters are verified by comparing to quantum chemistry results and by calculating Young's modulus. Adsorption of Hydrogen molecules are then carried out on a bundle of self-assembled SWNTs. The adsorption isotherms are consistent to the Freundlich equation. Both hydrogen molecules adsorbed outside and inside the SWNTs are counted. According to our result, hydrogen molecules adsorbed inside the SWNTs are more stable at a relatively high temperature and are playing an important part in total amount of the adsorbed molecules. While C(10,10) have the highest adsorption capacities in most of the temperatures, hydrogen molecules inside C(5,5) are the most stable of all the four kinds of SWNTs. Thus, balancing adsorption capacities and strength of interaction can be important in choosing SWNT for gas adsorption. Besides, we deduct an equation that can describe the relation between hydrogen pressure and amount of SWNTs based on our simulation results. The hydrogen pressure may decrease by adding SWNTs in the system. The fitting method in our system is valid to SWNTs and can be tested in further studies of similar systems. © 2018 Wiley Periodicals, Inc.

Theoretical analysis of electrochromism under redox of bis(3-thienyl)/(2-thienyl)hexafluorocyclopentene: effects of charged and substituted systems.

Electrochromism with the ring-closing or ring-opening isomerization of substituted and unsubstituted bis(3-thienyl)/(2-thienyl)hexafluorocyclopentene is discussed using the DFT method. In the neutral ground state, bond making and breaking between two reactive C atoms on thienyls are thermodynamically forbidden. Under redox conditions, the gain or loss of electrons can have a significant effect on the frontier molecular orbital distribution of both open- and closed-ring isomers, particularly in reactive sites. Corresponding structural changes show a trend toward isomerization. The reaction energy barrier shows greater reduction for dication than monocation and even becomes barrierless for dianion. During the isomerization in different states, the conjugated system switches distinctively, which is attributed to the special redistribution of molecular orbitals and spin population in each state. In monocation and monoanion, for the involvement of a single electron, isomerization is inclined to proceed sequentially between right and left thienyls, whereas it becomes synchronous in dication. The direction depends on the stabilization achieved by the formation of a global conjugated system and more average spin population on the molecule. The effect of substituents on thienyls is demonstrated in the promotion of the extent of conjugation and the determination of the spin population level on the reactive C atoms. Moreover, according to their electron-donating and withdrawing abilities, they can kinetically support or suppress the electron transfer pattern in the process from isomer to transition state, which leads to the control of reaction efficiency.

Structural features and dynamic investigations of the membrane-bound cytochrome P450 17A1.

Cytochrome P450 (CYP) 17A1 is a dual-function monooxygenase with a critical role in the synthesis of many human steroid hormones. The enzyme is an important target for treatment of breast and prostate cancers that proliferate in response to estrogens and androgens. Despite the crystallographic structures available for CYP17A1, no membrane-bound structural features of this enzyme at atomic level are available. Accumulating evidence has indicated that the interactions between bounded CYPs and membrane could contribute to the recruitment of lipophilic substrates. To this end, we have investigated the effects on structural characteristics in the presence of the membrane for CYP17A1. The MD simulation results demonstrate a spontaneous insertion process of the enzyme to the lipid. Two predominant modes of CYP17A1 in the membrane are captured, characterized by the depths of insertion and orientations of the enzyme to the membrane surface. The measured heme tilt angles show good consistence with experimental data, thereby verifying the validity of the structural models. Moreover, conformational changes induced by the membrane might have impact on the accessibility of the active site to lipophilic substrates. The dynamics of internal aromatic gate formed by Trp220 and Phe224 are suggested to regulate tunnel opening motions. The knowledge of the membrane binding characteristics could guide future experimental and computational works on membrane-bound CYPs so that various investigations of CYPs in their natural, lipid environment rather than in artificially solubilized forms may be achieved.

Investigation of properties of Mg(n) clusters and their hydrogen storage mechanism: a study based on DFT and a global minimum optimization method.

The global minimum structures of Mgn clusters have been determined using the so-called "kick method". With the improved DFT method of B3PW91 functional and Grimme's dispersion correction, a series of the most stable structure of Mgn have been found and a novel Mg9 structure has been located. Subsequently, the chemisorption of hydrogen onto Mg clusters was systemically studied. Considering the average adsorption energies and the ratio of Mg and H, we developed a function that can describe the relation between average adsorption energy and number of Mg and H atoms. Our results may be helpful in the future for developing different kinds of gas chemisorption materials.

Heparin makes differences: a molecular dynamics simulation study on the human ßII-tryptase monomer.

Human ß-tryptase, an enzyme with trypsin-like activity in mast cells, is an important target for the treatment of inflammatory and allergy related diseases. Heparin has been inferred to play a vital role in the stabilization of the tryptase structure and the maintenance of its active form. Up to now, the structure-function relationship between heparin and the ßII-tryptase monomer has not been studied with atomic resolution due to the lack of a complex structure of tryptase and heparin. To this end, the exact effect of heparin bonding to the ßII-tryptase monomer structure has been investigated using molecular docking and molecular dynamics (MD) simulation. The MD simulation results combined with MM-GB/SA calculations showed that heparin stabilized the ß-tryptase structure mainly through salt bridge interaction. The averaged noncovalent interaction (aNCI) method was employed for the visualization of nonbonding interactions. A crucial loop, which is located in the core region of ßII-tryptase monomer structure, has been found. Arg188 and Asp189 from this loop act as a salt bridge intermediary between 4-mer heparin and 0GX. The observation of a salt bridge between Asp189 and P1 groups of 0GX confirms the supposed interaction between these two groups. These two residues have been proved to be responsible for the direction of the P1 group of 0GX. Our study revealed that how heparin affected the activity of the human ßII-tryptase monomer (hBTM) through salt bridge interactions. The knowledge of heparin binding characteristics and the key residue contributions in this study may enlighten further the inhibitor design of this enzyme and may also improve our understanding of inflammatory and allergy related diseases.

Mechanism of a pH-induced peptide inserting into a POPC bilayer: a molecular dynamic study.

Membrane insertion peptides have been developed in recent years and serve as cargos to deliver small molecules into cells. A class of membrane insertion peptides is the so called pH-induced peptides (pHLIPs), which are able to insert into membrane when the environment pH is acidic. Despite a number of experimental studies, the insertion process as well as the penetration mechanism is still worth study with computational methods. Thus, we performed molecular dynamics simulations in this study to elucidate the detailed penetration process and mechanism. Both protonated and unprotonated peptides are employed to interact with a POPCs bilayer. By analyzing the trajectory of the simulation, the peptide travelling across membrane is expected to take milliseconds or seconds. While the peptide penetrating through the POPC bilayer boundary is much faster (several nanoseconds). More importantly, the elaborate energies between a peptide and water molecules, the energies between a peptide and POPCs have been analyzed throughout the simulation time correspondingly. A constant decrease of interaction energies have been observed for peptide-water interaction in the protonated condition. At last, we employ the statistics of hydrogen bonds to explain the penetration mechanism tentatively. For the protonated system, the decrease of hydrogen bonds of peptide-water and the increase of hydrogen bonds of peptide- POPCs have been considered as the main driven force for the peptide insertion.

The molecular configuration of a DOPA/ST monolayer at the air-water interface: a molecular dynamics study.

In this study, surface pressure-area isotherms for N-stearoyldopamine (DOPA) and 4-stearylcatechol (ST) monolayers are obtained by means of molecular dynamics simulations and compared to experimental isotherms. The difference between DOPA and ST is an amide group, which is present in the alkyl tails of DOPA molecules. We find a large difference between the isotherms for DOPA and ST monolayers. Upon using TIP4P/2005 for water and OPLS force fields for the organic material and a relatively large system size, the simulated results are found to be consistent with experiments. With molecular dynamics simulations, the configurations of molecules in the monolayers can be directly analyzed. When the surface pressure is high, a regular molecular orientation is observed for ST molecules, whereas regular orientations are only observed in local domains for DOPA molecules. The differences between DOPA and ST monolayers are attributed to the amide groups in DOPA molecules, which are useful for both steric effects and the formation of hydrogen bonds in the DOPA monolayers. This study clearly demonstrates that hydrogen bonds, due to the presence of the amide group in DOPA, are the cause of the disorder in its Langmuir monolayers. Thus, the conclusion may be helpful in making ordered organic monolayers in the future.

Molecular dynamics simulation of a DOPA/ST monolayer on the Au(111) surface.

In order to study the influence of molecular structure on the formation of a monolayer, two molecules have been considered, namely N-stearoyldopamine (DOPA) and 4-stearyl-catechol (ST). The difference between these two molecules is the amide group in DOPA. By investigating these monolayers at different surface areas per molecule, the molecular configurations of a DOPA/ST monolayer on the Au(111) surface were obtained. We conclude that for both kinds of molecules, the π-interaction between the catechol group and the Au(111) surface is important. Compared to experimental results, the catechol groups are found either parallel or perpendicular to the Au(111) surface in MD simulation. The difference between DOPA and ST systems is that when there are fewer molecules on the Au(111) surface, in the DOPA system, the amount of catechol groups perpendicular with their hydroxyls orienting towards the surface is less than that of the ST system. Further analysis of catechol groups and amide groups indicates that various kinds of hydrogen bonds formed in the DOPA system have a profound influence on the structure and regularity of the monolayer.