Bulk Molecules Research Articles

A DFT-D Study on Structural, Electronic, Thermodynamic, and Mechanical Properties of HMX/MPNO Cocrystal under High Pressure

ABSTRACTAn investigation on the structural, electronic, thermodynamic, and mechanical properties of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/2-methylpyridine-N-oxide (MPNO) cocrystal was carried out from 0 to 100 GPa by using a dispersion-corrected density functional theory (DFT-D) method. Our calculated crystal structure is in excellent agreement with experimental results at ambient pressure. Based on the analysis of lattice parameters, lattice angles, bond lengths, bond angles, and dihedral angles under high pressure, we observe that HMX molecules in the cocrystal bulk are seriously distorted but MPNO molecules remain relatively unchanged. Hydrogen bond lengths are greatly shortened under high pressure. In addition, with the increase in pressure, the bandgap decreases gradually. However, it increases suddenly at 70 GPa. Some important hydrogen bonds between HMX and MPNO are also observed in the density of states spectrum. According to the thermodynamic analysis, this cocrystal is more easily prepared under low pressure. Finally, we characterized its mechanical properties and the results show that this cocrystal is malleable in nature. We expect that this research can provide a fundamental basis for further HMX cocrystal design and preparation.

Light-harvesting Complexes (LHCs) Cluster Spontaneously in Membrane Environment Leading to Shortening of Their Excited State Lifetimes

The light reactions of photosynthesis, which include light-harvesting and charge separation, take place in the amphiphilic environment of the thylakoid membrane. The light-harvesting complex II (LHCII) is the main responsible for light absorption in plants and green algae and is involved in photoprotective mechanisms that regulate the amount of excited states in the membrane. The dual function of LHCII has been extensively studied in detergent micelles, but recent results have indicated that the properties of this complex differ in a lipid environment. In this work we checked these suggestions by studying LHCII in liposomes. By combining bulk and single molecule measurements, we monitored the fluorescence characteristics of liposomes containing single complexes up to densely packed proteoliposomes. We show that the natural lipid environment per se does not alter the properties of LHCII, which for single complexes remain very similar to that in detergent. However, we show that LHCII has the strong tendency to cluster in the membrane and that protein interactions and the extent of crowding modulate the lifetimes of the excited state in the membrane. Finally, the presence of LHCII monomers at low concentrations of complexes per liposome is discussed.

Optofluidic FRET Lasers and Their Applications in Novel Photonic Devices and Biochemical Sensing

Incorporating fluorescence resonance energy transfer (FRET) into a laser cavity can increase the sensitivity of FRET-based biochemical sensors due to the nonlinear dependence of the lasing output on the FRET parameters. Here, we carry out a comprehensive theoretical analysis of optofluidic FRET lasers based on a Fabry–Perot microcavity using a rate equation model. We compare conceptually distinct cases of donor and acceptor molecules diffusing freely in a bulk solution versus molecules connected by a fixed-length linker and show that the latter arrangement is especially well suited for sensing of low-concentration analytes. By comparing FRET lasing-based sensors with conventional FRET sensors, we show that for optimal pump fluence and FRET-pair concentration, FRET lasing can lead to more than 100-fold enhancement in detection sensitivities of conformational changes in the Forster radius range. We also show that for optimal experimental conditions, donor and acceptor emission intensities become over 20-fold more sensitive to FRET-pair concentration changes in the presence of FRET lasing. We study the dependence of the sensitivity enhancement on the cavity Q-factor. We show that the highest enhancements can be obtained for Q-factors between $10^4\text{--}10^6$ , and enhancement values decrease for Q-factors above $10^6$ due to the radiative energy transfer in the cavity.

Removal of nuclease contamination during purification of recombinant prototype foamy virus integrase

Retroviral infection requires integration of the viral genome into the host genome. Recombinant integrase proteins may be purified following bacterial expression. A bulk biochemical assay of integrase function relies on the conversion of supercoiled plasmids to linear or relaxed circles. Single molecule molecular tweezer assays of integrase also evaluate the conversion of supercoiled DNA to nicked and broken species. A bacterial nuclease that co-purifies with retroviral integrase may affect the quantitation of integration activity in bulk or single molecule assays. During purification of retroviral integrase from bacteria, fractions may be screened for contaminating nuclease activity. In order to efficiently separate the nuclease from integrase, the binding affinities of each protein must differ. We find that a co-purifying nuclease may be efficiently separated from integrase based on heparin affinity, but not ionic affinity.

Surface-Bulk Vibrational Correlation Spectroscopy.

Homo- and heterospectral correlation analysis are powerful methods for investigating the effects of external influences on the spectra acquired using distinct and complementary techniques. Nonlinear vibrational spectroscopy is a selective and sensitive probe of surface structure changes, as bulk molecules are excluded on the basis of symmetry. However, as a result of this exquisite specificity, it is blind to changes that may be occurring in the solution. We demonstrate that correlation analysis between surface-specific techniques and bulk probes such as infrared absorption or Raman scattering may be used to reveal additional details of the adsorption process. Using the adsorption of water and ethanol binary mixtures as an example, we illustrate that this provides support for a competitive binding model and adds new insight into a dimer-to-bilayer transition proposed from previous experiments and simulations.

Design and Development of a Telomere Sensor Based on Fluorescence Energy Transfer

A 200 nm in-diameter single-bead sensor for detecting single unlabeled DNA molecules in solution based on fluorescence resonance energy transfer is presented. Both bulk and single molecule fluorescence experiments were carried out at room temperature. The G-rich telomere forming a G-quadruplex structure in the presence of ZnTCPP showed two strong donor and acceptor signals. DNA-bound Alexa 488 and crimson 625 loaded in a commercial bead serve as the donor and acceptor, respectively. When Binding of the target DNA to the single bead sensor induces G-quadruplex stretching, resulting in a decrease in fluorescence energy transfer. The limit of sensor's sensitivity can reach 1 fM. Under optimized conditions using a Polydimethylsiloxane (PDMS) microfluidic device direct bead-sensor counting is used to measure the number of beads by control of the flow rate through the probe volume and finish one experiment in 5 minutes. A new parameter based on the ratio of donor and acceptor fluorescence signal from 0.1 to 100 was proposed and used to define the sensitivity and selectivity of bio-sensor.

Mechanical Unfolding of E. Coli RNase H Reveals an Intermediate with a Force-Induced Shift in the Rate-Limiting Barrier

Previous observations of the mechanical unfolding of E. coli RNase H∗ (ecRNH∗) indicated a single, cooperative transition from the native, folded state to the unfolded polypeptide. However, higher resolution single molecule optical tweezers experiments now demonstrate an obligate unfolding intermediate. Moreover, we find that with increasing force the transition from the native state to the unfolding intermediate becomes the rate-limiting barrier to complete unfolding of the protein. That is, under low force, the unfolding of the protein is kinetically limited by the transition from the intermediate to the completely unfolded state. We sought to determine the region of the protein that unfolds in the intermediate. Unfolding of the C-terminal E-helix is consistent with the measured extension change (∼33 amino acids), and the optical tweezers pulling geometry from the N- and C-termini. We utilize mutational analysis in the E-helix and other locations within ecRNH∗ to probe the unfolding kinetics. We dovetail our single molecule experiments with bulk, zero-force denaturant unfolding to quantify the effects on the energy landscape by the amino acid substitutions. The bulk kinetic and thermodynamic parameters are also used to understand the rate-limiting barrier to unfolding by these complementary methods. Our results show that destabilizing mutations in the core of the protein have no effect on the unfolding kinetics. In contrast, destabilizing mutations in the E-helix and periphery of the protein increase the rate of unfolding both in bulk and single molecule experiments. These results further corroborate that the E-helix is unfolded in the unfolded intermediate state of the protein.

Low-temperature and alkali-free dual template synthesis of micro-mesoporous aluminosilicates based on precursors of zeolite ZSM-5

The aim of this study was to determine the influence of the conditions of low-temperature sequential dual template synthesis of micro-mesoporous aluminosilicates based on precursors of ZSM-5 on their phase composition, structure, sorption properties, and acidity. The methods of X-ray powder diffraction and volumetric adsorption (N2, 77 K) analysis, dynamic light scattering (for characterization of sol-precursors), IR-spectroscopy, energy-dispersive X-ray spectroscopy, scanning and transmission electron microscopy, solid-state 29Si MAS NMR and 29Si{1H} cross-polarization MAS NMR spectroscopy, temperature-programmed desorption of ammonia, ad(de)sorption of pyridine and 2,6-di-tert-butylpyridine with IR-spectral control were used for characterization of the obtained micro-mesoporous aluminosilicates. It was shown that the convergence of compositions of the reaction mixtures and conditions of formation of zeolites and mesoporous molecular sieves, in particular, the use of alkali-free reaction medium and relatively low temperature of hydrothermal treatment (100 °C) allowed to obtain the X-ray amorphous and partially zeolitized micro-mesoporous aluminosilicates. Such aluminosilicates have appropriate structural and sorption properties and the acidity inherent to ZSM-5 and MCM-41, including the Bronsted and Lewis acid sites which are accessible for bulk molecules of organic substances. The possibility of purposeful regulation of characteristics of micro-mesoporous aluminosilicates depending on the conditions of their preparation was confirmed. Herewith the investigated aluminosilicates possess the sorption and acidic properties which are different from the mechanical mixture of two phases.

Fluorescent Nanoconjugate Derivatives with Enhanced Photostability for Single Molecule Imaging.

Fluorescence-based imaging techniques critically rely on bright and photostable probes for precise detection of biological molecules. Recently, a new class of multichromophoric probes based on fluorescent dendrimer nanoconjugates (FDNs) was developed for single molecule fluorescence microscopy (SMFM). FDNs are generated by covalent conjugation of multiple fluorescent dyes onto macromolecular polymeric scaffolds and show marked increases in brightness and long-term photostability relative to their single organic dye constituents. Multichromophoric probes, however, are generally known to suffer from transient fluorescence emission intensities and long excursions into dark states. To overcome these issues, photostabilizers can be added to bulk solution, though some small molecule additives may exhibit poor aqueous solubility or biological toxicity. In this work, we develop enhanced FDN derivatives by covalently linking a redox-active photostabilizer (Trolox) directly onto FDN molecular scaffolds. In one approach, multiple organic dyes (Cy5) and Trolox molecules are randomly distributed on dendritic scaffolds in tunable stoichiometric amounts, and in a second approach, Cy5 dyes are covalently linked to Trolox in a precise 1:1 stoichiometry followed by covalent attachment of Cy5-Trolox conjugates onto dendrimers. In all cases, FDN-Trolox conjugates show increases in photostability, brightness, and reduced fluctuations in transient fluorescent intensity relative to FDN probes. Bulk and single molecule photophysical data for FDN probes are compared to single self-healing dye systems such as Cy5-Trolox, and as a proof-of-principle demonstration, we use FDN-Trolox derivatives for bulk immunofluorescence imaging. Overall, our work suggests that self-healed multichromophoric systems such as FDN-Trolox probes present a useful strategy for increasing fluorescent probe photostability.

Structural, hydrogen bonding and in situ studies of the effect of hydrogen dilution on the passivation by amorphous silicon of n-type crystalline (1 0 0) silicon surfaces

Hydrogenated amorphous silicon (a-Si : H) layers deposited by chemical vapour deposition provide an attractive route to achieve high-performance crystalline silicon (c-Si) solar cells due to their deposition at low temperatures and their superior passivation quality. Hydrogen certainly plays an additional crucial role by passivating the dangling bonds, and thus improving the electrical and optical properties.In this work, we present the variation of the effective lifetime with the hydrogen dilution ratio R = (H2/SiH4). We find that at lower hydrogen dilution rates (R < 2), the polymerization reaction of silane molecules in the plasma bulk as well as the excess of dihydride (Si–H2) incorporation in as-deposited layers result in higher microvoid density and worse passivation quality. In contrast, the deposition at higher hydrogen dilution rates (R > 5) leads to a degradation in the film quality with very low hydrogen content and crystalline epitaxial growth at the a-Si/c-Si interface. Thus, the best material quality is obtained just below the onset of amorphous-to crystalline transition (R = 3), which favours further improvement of the passivation during a post-deposition annealing.

Quantum-Chemical Research of Fluoro Containing Hydrocarbons, That Have Fire Extinguishing Effect

Through quantum-chemical calculations, a study was conducted to find the probable products of the destruction of molecules of extinguishing agents. The formation of atomic fluorine and trifluoromethane radical has been shown to contribute to the retardation of elementary reactions in the flame. It has been shown that active inhibitory components are more easily dissociated from the silica surface than in the case of bulk molecules.

Modeling transient flow behavior of a multiscale triple porosity model for shale gas reservoirs

Gas flow in shales is a complex process from nanoscale to macroscale which includes diffusion of dissolved gas molecules in kerogen bulk, desorption from the pore walls, Knudsen diffusion and slip flow in nanopores, and conventional flow in natural fracture network according to recent studies. However, little work has been done in literature to simultaneously incorporate all these complex storage and flow mechanisms in well testing models for shale gas reservoirs. This paper presents a new tri-porosity model for shale gas reservoirs to describe that gas flows from formation to wellbore with consideration of all the mechanisms mentioned above. Compared with current well testing models for shale gas reservoirs, this model will be more close to the actual reservoir situation by simulating the physics behind the actual process. Partial differential equations of this tri-porosity model are derived and Laplace transform is employed to solve these equations analytically. The analytical solution of the transient pressure is obtained in real space with Stehfest numerical inversion method, and standard bi-logarithmic type curves are plotted. The characteristics of transient pressure behavior are analyzed thoroughly and different flow regimes are observed in type curves for shale gas reservoirs. Effects of relevant parameters are analyzed as well, which has important significance to understand the transient flow behavior for shale gas reservoirs.

The energy landscape of glassy dynamics on the amorphous hafnium diboride surface.

Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB2 glass surface, two-state hopping of 1-2 nm diameter cooperatively rearranging regions or "clusters" occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB2 has a very high bulk glass transition temperature Tg, and we observe no three-state hopping or sequential two-state hopping previously seen on lower Tg glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how "mixed" features can show up in surface dynamics of glasses.

Sub-zeolite of FER topology derived from an interlayer modification of PLS-3 lamellar precursor

A simple HCl–EtOH solution treatment has been conducted to modify the structure of Al-PLS-3, a kind of FER lamellar precursor with various Si/Al ratios (60–∞). With prolonging the treatment time from 15min to 24h at 443K, the precursors underwent a variety of structural changes, including removal of occluded organic species, loss of layer stacking order and restoration of an ordered structure by interlayer pillaring. The post structural modification gave rise to a sub-zeolite of FER topology within a short time of 40min, which possessed disordered stacking of FER sheets, named as ECNU-8. The physicochemical properties of ECNU-8 were characterized by means of various techniques and in comparison to those of conventional FER topology. Still composed of a collection of FER sheets but without an ordered stacking manner along (100) direction, the structure of ECNU-8 was constructed by a reorientation of interlayer hydrogen bond moieties caused by partial removal of interlayer organic structure directing agent. The ECNU-8 materials with different Al contents possessed external surface areas enlarged by 23.1–36.8% in comparison to corresponding three-dimensional FER zeolites. Containing the FER laminates and tetrahedral Al in framework, but mitigating the spatial restrictions in particular for the bulk molecule reactions, ECNU-8 proved to be a promising solid acid catalyst for processing larger substrates.

Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.

Structure and Dynamics of the Liquid–Liquid Interface of an Aqueous NaCl Solution with Liquid Carbon Tetrachloride from First-Principles Simulations

The present work deals with a first-principles theoretical study of the liquid–liquid interfacial system of an aqueous NaCl solution with the hydrophobic liquid of carbon tetrachloride (CCl4). Various structural and electronic properties of the system such as the inhomogeneous density profiles of ions and water molecules, hydrogen bond distributions, orientational profiles, vibrational frequency distributions, and also dipole moments of water at the bulk and interface are investigated. It is found that the chloride ions have a higher propensity for the interface and the sodium ions have a tendency to reside in the inner side of the aqueous medium. The dynamical aspects of the interfaces are analyzed in terms of the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion and are compared with those of the bulk regions. It is found that the interfacial molecules have a faster diffusion and orientation relaxation with respect to the bulk molecules. The interfacial wate...

An Ultra-low-cost Route to Mesostructured TS-1 Zeolite for Efficient Catalytic Conversion of Bulk Molecules

Developing a low-cost route to synthesize mesoporous TS-1 (MTS-1) is of great importance because of its practical application in industry. Herein, we first synthesized a copolymer containing quaternary ammonium groups by a mesoporous template comprising inexpensive starting materials. Subsequently, waterglass (sodium metasilicate), TiCl3, and copolymer were dispersed in the preformed seeds emulsion, resulting in a gel for synthesizing MTS-1. The counterpart material (CTS-1) was also synthesized by the same procedure except for the absence of the copolymer. Compared with CTS-1, the MTS-1 exhibits good crystallinity and well-defined tetrahedral coordinated Ti species (TiIV) in the framework as well as excellent catalytic activity in the oxidation of bulky molecules, such as dibenzothiophene and benzyl phenyl sulfide. This feature may be attributed to the fact that the quaternary ammonium groups on copolymer facilitates the formation of the MFI structure and energetically incorporates the Ti species into the framework.

Surface-Enhanced Raman Scattering of 4-Aminobenzenethiol on Au Nanorod Ordered Arrays

A droplet evaporation/stamping method was employed to fabricate closely packed arrays of Au nanorods aligned parallel or perpendicular to a support. The potential as SERS substrates was investigated using model molecule 4-aminobenzenethiol (4-ABT), for which enhanced signals where obtained compared to the signals of the bulk molecule. Enhancement factors of the order of 104 and 105 were calculated for parallel and perpendicular arrays, respectively. Quantitative Raman detection of 4-ABT was obtained with detection limits in the nM concentration range. Fabricated arrays displayed good stability and uniformity, showing their potential as sensing platforms for plasmon-induced optical molecular detection.

An ab Initio Molecular Dynamics Study of Water-Carbon Tetrachloride Liquid-Liquid Interface: Nature of Interfacial Structure, Hydrogen Bonds and Dynamics

We present a theoretical study of the structure and dynamics of water-carbon tetrachloride liquid-liquid interface by means of ab initio molecular dynamics simulations. We have studied the density profiles, orientational profiles, hydrogen bond distributions, vibrational power spectra, diffusion, orientational relaxation, hydrogen bond dynamics and vibrational spectral diffusion of bulk and interfacial molecules. We have also provided an analysis of vacancies present in the interfacial system using Voronoi polyhedra method. The hydrogen bonding interaction is found to be weakened at the interface compared to that in the bulk phase of water. Weakly hydrogen bonded and non-hydrogen bonded water molecules at the interface give rise to peaks at different positions of the vibrational power spectrum. Diffusion and orientational relaxation of water molecules are also found to be faster at the interface, which can be correlated with the vacancies present in the system. The dynamics of vibrational spectral diffusion is studied by means of frequency-time correlations calculated through a time-series analysis using the wavelet method and the results of spectral diffusion are correlated with the dynamics of hydrogen bond fluctuations and that of non-hydrogen bonded hydroxyl modes in the bulk and interfacial regions.

Molecular Dynamics Study of Conserved Water Molecules in PrPc and Pathological Point Mutation T188R

The secondary conformational change of cellular prion protein (PrPc) into scrapie prion protein (PrPsc) is critical important for prion disease including bovine spongiform encephalopathy and Creutzfeldt-Jakob disease.This study performed molecular dynamics simulations of both human prion protein (WT-PrPc) and pathogenic mutant prion protein (T188R) and analyze its conserved water molecules in equilibrium state.Although the secondary structure is not dramatically different, increase of Cα- RMSF occurs not only around mutation point but also in a wide range. This increase of intensity may result from the instability caused by point mutation.Next, we calculated mean residence time for each protein atoms to find conserved water molecules. Residence time is defined that the time from when the water molecule get into the sphere whose center is a protein atom to the evacuation of water molecule from the sphere. We found four conserved water molecule sites in WT-PrPc. Conserved water molecules also keep the higher rotational correlation than water molecules in bulk. These results shows that conserved water molecules are not only wrapped but also fixed by hydrogen bond between conserved water molecule and amino acids.On the other hand, every residence time of T188R decrease compared by WT-PrPc and the rotational relaxation is also faster than WT-PrPc although secondary structure is almost not different. These results show that conserved water molecules cannot survive related to the wide range fluctuation caused by point mutation.