Nuclear quantum effect and temperature dependency on the hydrogen‐bonded structure of base pairs

The structure of Watson–Crick‐type adenine‐thymine and guanine‐cytosine pairs has been studied by hybrid Monte Carlo (HMC) and path integral hybrid Monte Carlo (PIHMC) simulations with the use of semiempirical PM6‐DH+ method in the gas phase. We elucidated the nuclear quantum effect and temperature dependency on the hydrogen‐bonded moiety of base pairs. It was shown that the contribution of nuclear quantum effect on the hydrogen‐bonded structure is significant not only at low temperature 150 K but also at temperature as high as 450 K. The relative position of hydrogen‐bonded proton between two heavy atoms and the nuclear quantum nature of the proton are also shown. Furthermore, we have applied principal component analysis to HMC and PIHMC simulations to analyze the nuclear quantum effect on intermolecular motions. We found that the ratio of Buckle mode (lowest vibrational mode from normal mode analysis) decreases due to the nuclear quantum effect, whereas that of Propeller mode (second lowest vibrational mode) increases. In addition, nonplanar structures of base pairs were found to become stable due to the nuclear quantum effect from two‐dimensional free energy landscape along Buckle and Propeller modes. © 2013 Wiley Periodicals, Inc.     

Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm

The Transition Rapidly exploring Random Eigenvector Assisted Tree (TRREAT) algorithm is introduced to perform searches along low curvature pathways on a potential energy surface (PES). The method combines local curvature information about the PES with an iterative Rapidly exploring Random Tree algorithm (LaValle, Computer Science Department, Iowa State University, 1998, TR98–11) that quickly searches high‐dimensional spaces for feasible pathways between local minima. Herein, the method is applied to identifying conformational changes of molecular systems using Cartesian coordinates while avoiding a priori definition of collective variables. We analyze the pathway identification problem for alanine dipeptide, cyclohexane and glycine using nonreactive and reactive forcefields. We show how TRREAT‐identified pathways can be used as valuable input guesses for double‐ended methods such as the Nudged Elastic Band when ascertaining transition state energies. This method can be utilized to improve/extend the reaction databases that lie at the core of automatic chemical reaction mechanism generator software currently developed to build kinetic models of chemical reactions. © 2013 Wiley Periodicals, Inc.     

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.     

Temperature Effect on the Phase Behavior of the Systems Water/Sucrose Laurate/Ethoxylated‐mono‐di‐glyceride/Oil

The phase behavior of the systems water/sucrose laurate/ethoxylated mono‐di‐glyceride/oil was investigated as function of temperature and the weight ratio of EMDG in the mixed surfactants. The oils were R (+)‐limonene, isopropylmyristate, and caprylic‐capric triglyceride. This study demonstrates that the phase inversion temperature (PIT) decreases and the efficiency of the mixed surfactants (γ¯) increase as the weight ratio of the EMDG in the mixed surfactants increases. R (+)‐limonene gave lower phase inversion temperatures and higher efficiencies compared to isopropylmyristate, and caprylic‐capric triglyceride. The solubilization capacity of the system water/sucrose laurate/oil increased upon the addition of ethoxylated mono‐di‐ glyceride which stabilize the surfactant layer and increase the interfacial area.     

Oil-Induced Structural Change in Nonionic Microemulsions

Effect of added oil (heptane or squalane) on the microemulsion structures in polyoxyethylene dodecyl ether (C₁₂EO_n) systems was investigated by means of phase behavior and NMR diffusion experiments. In the binary water-C₁₂EO_n systems, an isotropic fluid, D₂ (or L₃), and an aqueous micellar solution, Wm, phases are successively formed with increasing the EO-chain length. Upon addition of heptane, D₂ and Wm phases are merged and a microemulsion of large solubilization is produced at a low surfactant concentration. With squalane, the solubilization of oil in D₂ phase is very low or almost zero, whereas the oil solubilization in Wm phase is relatively large. These structural changes in microemulsions are discussed based on the self-diffusion coefficients of water, oil, and surfactant measured by the PGSE-NMR method. The difference in the phase behavior may be attributed to the difference in the penetration tendency of oil in the surfactant palisade layer.     

Microstructure and Magnetic Properties of Carbon‐Coated Nanoparticles

Abstract

In the present work, microstructure and superparamagnetic properties of two types of carbon‐coated magnetic Ni and Fe nanoparticles [Ni(C) and Fe(C)] are reviewed. High‐resolution transmission electron microscopy (HRTEM), electron diffraction (SAED), and x‐ray diffraction (XRD) analyses have been used to reveal the distinct structural morphologies of Ni and Fe nanoparticles. Moreover, novel carbon‐coated Ni nanoparticle assemblies offer us great opportunities for studying the mechanism of superparamagnetism in particle assemblies. Magnetization measurements [M(T) and M(H) curves] for assemblies of Ni nanoparticles indicate that modified superparamagnetic properties at T > T _B, have been found in the assemblies of Ni(C) particles. The blocking temperature, T _B, is determined to be near 115K under a certain applied field. Above T _B, the magnetization M(H, T) can be described by the classical Langevin function L using the relation, M/M _s (T = 0) = coth (μH/kT) ? kT/μH. It is suggested that these assemblies of carbon‐coated Ni nanoparticles have typical single‐domain, field‐dependent superparamagnetic relaxation properties. Finally, Mössbauer spectra and hyperfine magnetic fields at room temperature for the assemblies of Fe(C) nanoparticles confirm their distinct nanophases that were detected by structural analysis. Modified superparamagnetic relaxation is observed in the assemblies of Fe(C) nanoparticles, which is attributed to the nanocrystalline nature of the carbon‐coated nanoparticles.     

Emulsions of Heavy Crude Oils. II. Viscous Responses and Their Influence on Emulsion Stability Measurements

The stability of 30 heavy crude oil emulsions was studied in a parallel-plate laboratory coalescer (DC field). Particularly, viscous responses and their influence on the emulsion stability measurements were investigated. In addition to highlighting previous results from the same experimental setup and discussing these based on recent experience, new results at different temperatures and volume fractions of water were presented. A new semi-empirical model for the characteristic time of the destabilization process was presented. The electrical forces were modelled with a point-dipole approximation and the hydrodynamic resistance to droplet transport was modelled with an empirical term including the logarithmic viscosity of the oil phase. The new model clearly performed much better than the previous model, particularly for very viscous crude oils. Studies of the performance of industrial electrocoalescers have showed that simple electrostatic theory can potentially explain complex separation phenomena when the resistance to the coalescence step is reduced by an efficient demulsifier. The ultimate goal is to build a model for both the laboratory setup and the industrial coalescer so that laboratory experiments can be used to predict the behavior of the industrial process.     

Experimental Validation of the Temperature-Resistant and Salt-Tolerant Xanthan Enhanced Foam for Enhancing Oil Recovery

Xanthan enhanced foam (XGF) is a newly developed chemical agent for enhanced oil recovery in high-temperature and high-salinity reservoirs. In this paper, laboratory experiments were performed to characterize the morphology and foam properties of XGF, to study its performance under different temperature and different salinity conditions, respectively. Based on simulate reservoir formation conditions of Xidaliya field, a series of research on XGF were conducted. The experimental results showed that the scanning electron microscopy of XGF reflected a more viscoelastic and stable nature of the foam system. High temperature had a great adverse impact upon the stability of XGF, and the increase of salinity in the solution helped to improve the stability of foam. The foam stability increased remarkably when XG4 is added, and an increase in ambient pressure made enhancement of foam stability became more noticeable. In the presence of crude oil, Xanthan could enhance the stability of emulsions and was more favorable to stabilize foam. XG4 enhanced foam had dramatic properties for mobility controlling and oil displacement in the porous media.     

Propylene Glycol and Ethoxylated Surfactant Effects on the Phase Behavior of Water/Sucrose Stearate/Oil System

In this work, we studied the phase behavior as function of temperature of water/sucrose stearate/propylene glycol/oil and water/sucrose stearate/ethoxylated mono‐di‐glyceride/oil systems. The oils were R (+)‐limonene, isopropylmyristate, and caprylic‐capric triglyceride. It was found that adding propylene glycol and ethoxylated mono‐di‐glyceride to the water/sucrose stearate/R (+)‐limonene and water/sucrose stearate/isopropylmyristate systems decreases the temperature and surfactants concentration needed for the formation of a microemulsion phase region and no three phase region is observed. In the case of water/sucrose stearate/caprylic‐capric triglyceride system a three phase region is observed. In the caprylic‐capric based system, it was found that increasing the propylene glycol and ethoxylated mono‐di‐glyceride contents decrease the phase inversion temperature and increases the efficiency. In the case where the mixed surfactants (sucrose stearate and ethoxylated mono‐di‐glyceride) were present in the system, the efficiencies observed are higher than those observed in the system based on the mixture of sucrose stearate and propylene glycol.     

Microwave‐Assisted Synthesis and Characterization of CuO Nanocrystals

CuO feather‐like and flower‐like crystals have been synthesized by a fast microwave‐assisted solution approach using Cu(NO₃)₂ and NaOH. The morphology transformation of CuO could be achieved by ionic liquid 1‐n‐butyl‐3‐methyl imidazolium tetrafluoroborate ([BMIM]BF₄). With [BMIM]BF₄, flower‐like CuO were obtained, whereas without [BMIM]BF₄, feather‐like CuO were obtained. The possible formation mechanism of flower‐like CuO was discussed on the basis of experimental results. The products were characterized by XRD, FESEM/EDS, and TEM/SAED. In addition, the adsorption of [BMIM]BF₄ on flower‐like CuO was confirmed by FTIR and TG/DSC, and the band gap energies of the flower‐like CuO was estimated by UV‐vis spectra.