Compression behavior and spectroscopic properties of insensitive explosive 1,3,5-triamino-2,4,6-trinitrobenzene from dispersion-corrected density functional theory

Using dispersion corrected density functional theory, we systematically examined the pressure effect on crystal structure, cell volume, and band gap of 1,3,5-triamino-2,4,6-trinitrobenzene（TATB） to understand its extraordinary chemical stability. Analysis of the Mulliken population and the electron density of states implied a possible charge transfer in TATB with increasing pressure. Raman and infrared spectra of TATB under hydrostatic pressure up to 30 GPa were simulated.The observed strong coupling between NH_2 groups and NO_2 groups with increasing pressure, which is considered to have a tendency of energy transfer with these vibrational modes, was analyzed. The pressure-induced frequency shift of selected vibrational modes indicated minor changes of molecular conformation mainly by the rotation of NH_2 groups. Compression behavior and spectroscopic property studies are expected to shed light on the physical and chemical properties of TATB on an atomistic scale.

Optically probing molecular shuttling motion of[2]rotaxane by a conformation-adaptive fluorophore

A bistable[2]rotaxane with a conformation-adaptive macrocycle bearing a 9,14-diphenyl-9,14-dihydrodibenzo[a,c]phenazine(DPAC)unit was synthesized,which could be utilized to optical probe the molecular shuttling motion of the functionalized rotaxane system.The UV-vis,^(1) H NMR and PL spectroscopic data clearly demonstrated that the DPAC ring was interlocked onto the thread and the fluorescence intensity of the DPAC unit in the macrocycle was effectively regulated by the location change of the macrocycle along the thread under acid/base stimulation,which was attributed to the modulation of the intramolecular photo-induced electron transfer between the DPAC unit and the methyltriazole(MTA)unit.This bistable rotaxane system containing a conformation-adaptive fluorophore unit in the macrocycle moiety opens an alternative way to design functional bistable mechanically interlocked molecules.

RAMAN STUDIES OF STRUCTURAL PHASE TRANSITION IN[n-C_(11)H_(28)NH_8]_2ZnCl_4

The perovskite type of compound [n-C_(11)H_(23)N_3]_2ZnCl_4(abr.C_(11)Zn)exhibits two solid-solid phase transitions at T_(c1)=298.7 K and T_(c2)=360.1 K.A temperature dependence study of Raman spectra of C_(11)Zn provides the evidence of occurence of the structural phase transition related to the dynamics of the alkylammonium ions.The room temperature phase is ordered and contains the all-trans alkyl chains.The intermediate temperature phase presents a partial conformational disorder and liquidlike state of all conformational disorder occurs at high-temperature phase.

Quantum States in Templated Biological Processes

Living matter is characterized by its variegated potential energy landscape possessing a proneness to continually absorb externally supplied energy. This enables it to ascend from its momentary energy minimum state to one of its myriad barriers only to subsequently descend to a new minimum with a potentiality to perform new functions or processes, in the while exuding energy (mainly in the form of heat). As in studies of molecular intersystem crossing, the jumping processes are describable in terms of quantum states. In this work we derive the low energy quantum states for those three templated self-assembling processes, self-replication, metabolism and self-repair that are commonly regarded as distinguishing animate from inanimate substance. The outcome of each process is a new, long-living, stable molecular aggregate characterized by its specific conformation, comprising a host of micro-states associated with sub-conformations and patterned upon the template. The provenance of these newly-formed states is obtained here by a unified formalism for all three processes, based on a Hamiltonian, constructed in an abstract Hilbert-space framework, whose essences are bilinear coupling terms in the Hamiltonian between the template and the bath, as well as between the reactants and the bath. Treating these terms by second order perturbation, one finds in low lying quantum states an alignment between the template and the product, somewhat analogous to the Kramers-Anderson superexchange mechanism, with the bath replacing the bridging anion and by exploitation of the decohering due to the randomness of the bath. The idea underlying this work, recurrent in the biological literature and here expressed in a Physics, Hamiltonian framework, is the correlative unity of the whole biological system comprising multiple organs.

Improving the accuracy of pose prediction in molecular docking via structural fltering and conformational clustering

Structure-based virtual screening（molecular docking）is now one of the most pragmatic techniques to leverage target structure for ligand discovery.Accurate binding pose prediction is critical to molecular docking.Here,we describe a general strategy to improve the accuracy of docking pose prediction by implementing the structural descriptor-based fltering and KGS-penalty function-based conformational clustering in an unbiased manner.We assessed our method against 150 high-quality protein–ligand complex structures.Surprisingly,such simple components are suffcient to improve the accuracy of docking pose prediction.The success rate of predicting near-native docking pose increased from 53%of the targets to 78%.We expect that our strategy may have general usage in improving currently available molecular docking programs.

Molecular mechanism of crystal nucleation from solution

Nucleation from solution is fundamental to many natural and industrial processes.The understanding of molecular mechanism of nucleation from solution is conducive to predict crystal structure,control polymorph and design desired crystal materials.In this review,the nucleation theories,including classical nucleation theory(CNT),nonclassical nucleation theory,as well as other new proposed theories,were reprised,and the molecular mechanism of these theories was compared.Then,the molecular process of nucleation,including the current study techniques,the effect of molecular self-assembly in solutions,desolvation process,as well as the properties of solvent and crystal structure on nucleation from solution were summarized.Furthermore,the relationship of molecular conformation in solution and in crystal,and the effect of solute molecular flexibility on nucleation were discussed.Finally,the current challenges and future scopes of crystal nucleation from solution were discussed.

Cholesterol modulating the orientation of His17 in hepatitis C virus p7 (5a) viroporin--A molecular dynamic simulation study

Protein p7 of HCV is a 63 amino acid channel forming membrane protein essential for the progression ofviral infection and the sensitivity of this channel to small-molecule inhibitors renders p7 a potentialtarget for novel therapies against HCV infection. Previous biochemical experiments suggested that theHis17 of p7 is a pore-lining residue and solvated-exposed to participate in channel gating. However, arecent NMR structural identification of the p7 hexamer in dodecylphosphocholine （DPC） micellesindicated that the His17 is embedded into the protein matrix. In this work, we performed moleculardynamic simulations to bridge the controversial observations. Our results illustrated that byincorporating the cholesterol into DOPC membranes to mimic an actual membrane-like composition,the orientation of His17 in the hexameric bundles spontaneously access to the central pore region,indicating a versatile property of the p7 viroporin conformation that could be voluntarily influenced byits surrounding environments.

Exploring the influence of crystal packing on the optical-physical property of quercetin-based binary and ternary solid forms

The co-crystallization of quercetin(Qur)with a flexible molecule 4-(4-pyridinyldisulfanyl)pyridine(DPDS)in different solvents and conditions was investigated,yielded five multi-component crystalline phases and characterized with X-ray diffractions and thermal analysis.Although the crystal system of Qur-DPDSMe OH and Qur-DPDS-Dioxane is the same,the desolvation results revealed that Qur-DPDS-Me OH transformed to Qur-DPDS when Me OH solvent molecules escape from the lattice,while Qur-DPDS-Dioxane transformed to Qur-DPDS-II through a similar process,which is same with Qur-DPDS-THF.These two cocrystal polymorphs Qur-DPDS and Qur-DPDS-II obey an enantiotropic relationship.Moreover,the formation of cocrystal solvates improves the packing efficiency of crystals.Crystal structure analysis showed that hydrogen bonds and conformations of the corresponding parent molecules play a major role in molecular assembly and crystal packing patterns,thus bring different physicochemical properties.Finally,the fluorescence spectra and quantum-chemical calculations were carried out to explore the difference in the optical-physical properties.