From orientation disordered to ordered—An ab initio simulation on ammonia borane phase transition within van der Waals corrections

In this work, we report a detailed theoretical investigation of the phase transition of ammonia borane (NH₃BH₃; AB), from a tetragonal I4mm ( ) phase with disordered orientation of hydrogen to an orthorhombic phase with Pmn2₁ ( ) symmetry, as a function of temperature based on Density Functional Theory calculations with semiempirical dispersion potential correction. We define a series of substructures with the NH₃BH₃ moiety always in C_3v symmetry and the partially occupied high temperature state can be described as a continuous transformation between these substructures. To understand the role of the van der Waals corrections to the physical properties, we use the empirical Grimme's dispersion potential correction (PBE‐D2). Both Perdew–Burke–Emzerhof (PBE) and PBE‐D2 functional yield almost the same energy sequence along the transition path. However, PBE‐D2 functional shows obvious advantage in describing the lattice parameters of AB. The rigid rotor harmonic oscillator approximation is used to compute the free energy and the entropies contribution along the transition pathway. With knowledge of free energy surfaces along rotations of the ? [NH₃] and ? [BH₃] groups, complete transformation paths are mapped out. The phase transition is found to follow the sequence of partially occupied tetragonal system (I4mm) of a mixture of states with monoclinic (Cc), (CM) and orthorhombic (Pmn2₁) symmetries to fully occupied quasitetragonal system (the intermediate phase, Pmn2₁) to fully occupied orthorhombic system (Pmn2₁). © 2014 Wiley Periodicals, Inc.     

How does a hydrocarbon staple affect peptide hydrophobicity?

Water is essential for the proper folding of proteins and the assembly of protein–protein/ligand complexes. How water regulates complex formation depends on the chemical and topological details of the interface. The dynamics of water in the interdomain region between an E3 ubiquitin ligase (MDM2) and three different peptides derived from the tumor suppressor protein p53 are studied using molecular dynamics. The peptides show bimodal distributions of interdomain water densities across a range of distances. The addition of a hydrocarbon chain to rigidify the peptides (in a process known as stapling) results in an increase in average hydrophobicity of the peptide–protein interface. Additionally, the hydrophobic staple shields a network of water molecules, kinetically stabilizing a water chain hydrogen‐bonded between the peptide and MDM2. These properties could result in a decrease in the energy barrier associated with dehydrating the peptide–protein interface, thereby regulating the kinetics of peptide binding. © 2015 Wiley Periodicals, Inc.     

Calculation of the stability of nonperiodic solids using classical force fields and the method of increments: N2o as an example

Combining classical force fields for the Hartree–Fock (HF) part and the method of increments for post‐HF contributions, we calculate the cohesive energy of the ordered and randomly disordered nitrous oxide (N₂O) solid. At 0 K, ordered N₂O is most favorable with a cohesive energy of ?27.7 kJ/mol. At temperatures above 60 K, more disordered structures become compatible and a phase transition to completely disordered N₂O is predicted. Comparison with experiment in literature suggests that experimentally prepared N₂O crystals are mainly disordered due to a prohibitively high activation energy of ordering processes. © 2015 Wiley Periodicals, Inc.     

[DBU‐H]+ and H2o as effective catalyst form for 2,3‐dihydropyrido[2,3‐d]pyrimidin‐4(1H)‐ones: A DFT Study

DFT investigations are carried out to explore the effective catalyst forms of DBU and H₂O and the mechanism for the formation of 2,3‐dihydropyrido[2,3‐d]‐pyrimidin‐4(1H)‐ones. Three main pathways are disclosed under unassisted, water‐catalyzed, DBU and water cocatalyzed conditions, which involves concerted nucleophilic addition and H‐transfer, concerted intramolecular cyclization and H‐transfer, and Dimroth rearrangement to form the product. The results indicated that the DBU and water cocatalyzed pathway is the most favored one as compared to the rest two pathways. The water donates one H to DBU and accepts H from 2‐amino‐nicotinonitrile ( 1 ), forming [DBU‐H]⁺‐H₂O as effective catalyst form in the proton migration transition state rather than [DBU‐H]⁺‐OH^?. The hydrogen bond between [DBU‐H]⁺···H₂O··· 1 ^? decreases the activation barrier of the rate‐determining step. Our calculated results open a new insight for the green catalyst model of DBU‐H₂O. © 2015 Wiley Periodicals, Inc.     

Revisiting the extrapolation of correlation energies to complete basis set limit

The extrapolation scheme of correlation energy is revisited to evaluate the complete basis set limit from double‐zeta (DZ) and triple‐zeta levels of calculations. The DZ level results are adjusted to the standard asymptotic behavior with respect to the cardinal number, observed at the higher levels of basis sets. Two types of adjusting schemes with effective scaling factors, which recover errors in extrapolations with the DZ level basis set, are examined. The first scheme scales the cardinal number for the DZ level energy, while the second scheme scales the prefactor of the extrapolation function. Systematic assessments on the Gaussian‐3X and Gaussian‐2 test sets reveal that these calibration schemes successfully and drastically reduce errors without additional computational efforts. © 2015 Wiley Periodicals, Inc.     

The PyPES library of high quality semi‐global potential energy surfaces

In this article, we present a Python‐based library of high quality semi‐global potential energy surfaces for 50 polyatomic molecules with up to six atoms. We anticipate that these surfaces will find widespread application in the testing of new potential energy surface construction algorithms and nuclear ro‐vibrational structure theories. To this end, we provide the ability to generate the energy derivatives required for Taylor series expansions to sixth order about any point on the potential energy surface in a range of common coordinate systems, including curvilinear internal, Cartesian, and normal mode coordinates. The PyPES package, along with FORTRAN, C, MATLAB and Mathematica wrappers, is available at http://sourceforge.net/projects/pypes-lib . © 2015 Wiley Periodicals, Inc.     

表面形貌控制增强铁基载氧体与褐煤化学链燃烧反应活性

为探究载氧体形貌控制获取适用于化学链燃烧的高活性表面结构载氧体的可行性,以Fe2O3作为模型载氧体,从理论上对比研究Fe2O3的高弥勒指数晶面(104)和Fe2O3自然裸露的最主要晶面之一(001)的表面电子特性,结果表明,Fe2O3(104)的电子结构更有利于表面与煤模型分子的相互作用.基于理论分析结果,从实验上控制制备了单晶载氧体Fe2O3(104)/Al2O3,研究了该载氧体与褐煤的化学链燃烧反应特性.Fe2O3(104)/Al2O3比传统浸渍法制备的载氧体Fe2O3/Al2O3具有更高的反应活性,与理论计算结果一致.元素分析表明,Fe2O3(104)/Al2O3与褐煤反应的积碳量远少于Fe2O3/Al2O3与褐煤反应的积碳量.对比新鲜载氧体及再生后载氧体的结构发现,Fe2O3(104)/Al2O3在反应过程中不断进行氧化还原反应而发生结构弛豫后,仍然能通过氧化再生.这表明形貌控制制备可为化学链燃烧技术开发新型高效载氧体提供新思路.     

氧化石墨超声时间对三维还原氧化石墨烯结构及超级电容性能的影响

将氧化石墨凝胶超声不同时间制备氧化石墨烯(GO)溶胶,再以GO溶胶为前驱体采用一步水热法制备了三维还原氧化石墨烯(3DRGO),采用X射线衍射(XRD)、拉曼光谱、原子力显微镜(AFM)、扫描电子显微镜(SEM)和电化学测试等研究了不同超声时间对3DRGO的形貌、结构及超级电容性能的影响.结果表明,当超声时间不超过120 min时,经水热反应后还原氧化石墨烯均能形成稳定的三维结构,但随着超声时间的延长,三维结构尺寸不断减小,强度增加,样品的内部结构也由片状逐渐向多孔网状转化;当超声时间超过120 min时,还原氧化石墨烯虽具有网状结构,但在宏观上不利于形成稳定的三维结构.电化学测试结果表明,经不同超声时间所制备的还原氧化石墨烯均表现出较好的超级电容性能,其中超声时间为120 min时制备的3DRGO具有更均匀的多孔网状结构,表现出了最佳的超级电容性能,在1 A/g电流密度下其比电容可达328 F/g,即使在20 A/g的大电流密度条件下,其比电容仍可高达240 F/g.     

荧光标记法研究鱼类GABA受体与Ro7-1986/1和Fipronil的相互作用

以苯二氮卓类化合物Ro7-1986/1和氟虫腈(Fipronil)分别与异硫氰酸荧光素(FITC)反应合成了2种γ-氨基丁酸(GABA)受体的配体荧光复合物,即FITC-Ro7-1986/1(简称FITC-Ro7)和FITC-Fipronil;利用傅里叶变换红外光谱(FTIR)和核磁共振氢谱(1H NMR)等手段对其结构进行了表征.以2种荧光配体为探针,采用荧光标记法研究了Ro7-1986/1和Fipronil与鳙鱼(Hypophthalmichthys nobilis)脑内GABA受体的相互作用,得到了亲和常数Kd和最大结合量[RT].同时考察了GABA对Ro7-1986/1与受体相互作用的影响.研究结果表明,Ro7-1986/1和Fipronil与受体的亲和常数Kd分别为(67±5)nmol/L和(346±6)nmol/L;最大结合量[RT]分别为(13.8±1.8)pmol/mg protein和(40.6±3.5)pmol/mg protein;GABA促进了Ro7-1986/1与受体的结合,进一步的研究结果表明,鱼类与哺乳动物脑中GABA受体结构相似;相对于哺乳动物,苯吡唑类杀虫剂Fipronil对鱼类GABA的亲和力较高.