First Principles Analysis of the Electrocatalytic Oxidation of Methanol and Carbon Monoxide

The strong drive to commercialize fuel cells for portable as well as transportation power sources has led to the tremendous growth in fundamental research aimed at elucidating the catalytic paths and kinetics that govern the electrode performance of proton exchange membrane (PEM) fuel cells. Advances in theory over the past decade coupled with the exponential increases in computational speed and memory have enabled theory to become an invaluable partner in elucidating the surface chemistry that controls different catalytic systems. Despite the significant advances in modeling vapor-phase catalytic systems, the widespread use of first principle theoretical calculations in the analysis of electrocatalytic systems has been rather limited due to the complex electrochemical environment. Herein, we describe the development and application of a first-principles-based approach termed the double reference method that can be used to simulate chemistry at an electrified interface. The simulations mimic the half-cell analysis that is currently used to evaluate electrochemical systems experimentally where the potential is set via an external potentiostat. We use this approach to simulate the potential dependence of elementary reaction energies and activation barriers for different electrocatalytic reactions important for the anode of the direct methanol fuel cell. More specifically we examine the potential-dependence for the activation of water and the oxidation of methanol and CO over model Pt and Pt alloy surfaces. The insights from these model systems are subsequently used to test alternative compositions for the development of improved catalytic materials for the anode of the direct methanol fuel cell.     

Surface Functionalization with Phosphazene Substrates. Part II. Theoretical and Experimental Investigations of the Interactions of Hexachlorocyclophosphazene with Hydroxylated Silicon-based Surfaces

The interaction of hexachlorocyclophosphazene (HCCP) with the hydroxylated silicon-based surfaces is studied by a combination of XPS experimental analysis and theoretical ab initio simulations, including the estimate of the energy barriers via CI-NEB method to determine the minimum energy reaction paths. Several possible, stable chemisorbed configurations are found to exist, whose structural, energetic, and electronic properties have been analyzed in detail. The theoretical results are in good qualitative agreement with available experimental data. In particular, we get indications that water plays a crucial role in the surface functionalization with HCCP, although the presence of a suitable solvent (e.g. tetrahydrofuran, THF) seems to be essential. This paper is dedicated to Prof. Harry R. Allcock and the pioneering discoveries of his research group particularly in polyphospazenes and generally in materials science.     

S2分子的激发态与X3Σ-g→B3Σ-u吸收谱研究

S₂分子是一种在能源和激光领域有应用前景的物质,几十年来,人们对S₂分子的电子结构与光谱的研究不断深入。应用量子化学从头算方法(完全活性空间多组态自洽场方法和多参考二阶微扰方法)计算了S₂分子的11个电子态,并与其他文献结果作了比较,得到了与其他文献符合较好的结果;讨论了不同方法对激发态计算的适用性的问题:完全活性空间多组态自洽场方法适用于分子平衡态几何构形的优化,考虑到电子的动力学相关,能量的计算多参考二阶微扰方法更好。计算了S₂分子X³Σ^-_g(v)→B³Σ^-_u的垂直吸收谱,给出了速度规范下基态电子态各振动级X³Σ^-_g(v)垂直跃迁到B³Σ^-_u的振子强度,结果表明S₂分子是一种泵浦范围较宽(350~600 nm)的良好的激光工作物质。     

Insights from ab initio molecular dynamics simulations for a multicomponent oxide glass

It remains a challenge to establish structural models of multicomponent oxide glass systems. In this study, we have investigated 68.3SiO₂–16.1B₂O₃–4.2Al₂O₃–11.4Na₂O glass and melt structures by ab initio molecular dynamics (AIMD) simulations. The atomic configurations obtained from AIMD simulations were validated against ¹⁷O solid‐state NMR spectrum under 24.0 T and neutron diffraction data, and excellent agreement was achieved. The bond lengths, angles, and coordination geometries were statistically analyzed for each atomic species. Here we particularly address the role of minor atomic species such as five‐coordinate Si (Si^V) and Al (Al^V). The Si^V–O bond lengths and O–Si^V–O angle distribution in the glass indicated 1.718 Å and three peaks at 90°, 120°, and 175°, which are assigned to a coordination geometry of the trigonal bipyramidal structure. Ring statistic analysis revealed that Si^V and Al^V were found to preferentially contribute to the formation of small ring sizes.     

<Emphasis Type="Italic">Ab initio</Emphasis> studies on [bmim][PF<Subscript>6</Subscript>]-CO<Subscript>2</Subscript> mixture and CO<Subscript>2</Subscript> clusters

Ab initio molecular dynamics studies have been carried out on the room temperature ionic liquid, 1,n-butyl,3-methylimidazolium hexafluorophosphate ([bmim][PF₆]) and supercritical carbon dioxide mixture at room temperature and experimental density. Partial radial distribution functions (RDF) for different sites have been computed to see the organization of CO₂ molecules around the ionic liquid. Several partial RDFs around the carbon atom of CO₂ molecule are compared to find out that the CO₂ has specific interaction with a carbon atom present in the imidazolium ring. The CO₂ is also found to be very well organized around the terminal carbon atom of the butyl chain. The partial RDFs for the oxygen atoms around oxygen and carbon atoms of the CO₂ suggests that there is very good organization of CO₂ molecules around themselves even in the [bmim][PF₆]-CO₂ mixture. The instantaneous quadrupole moment tensor has been calculated for the anion and the cation. The ensemble average of diagonal components of quadrupole moment tensor of the cation have finite values, whereas the off-diagonal components of the cation and both the diagonal and off-diagonal components of the anion have the value of zero with a large standard deviation. The CPMD studies performed on CO₂ clusters reveals the greater tendency of the clusters with more CO₂ units, to deviate from the linear geometry.     

Friction and a Tribochemical Reaction between Ice and Hexagonal Boron Nitride: A Theoretical Study

Friction between ice-Ih and hexagonal boron nitride (h-BN) has been determined by periodic ab initio calculations. Surfaces of ice-Ih and h-BN were brought into sliding contact, and the interaction energies were calculated as a function of interplanar distance and lateral displacement of the surfaces. The friction between the surfaces was calculated from the interaction energies, producing a friction coefficient of 0.140. Friction is further influenced at high loads by a tribochemical reaction between ice-Ih and h-BN.     

A comparative study of the reported performance of ab initio protein structure prediction algorithms

Protein structure prediction is one of the major challenges in bioinformatics today. Throughout the past five decades, many different algorithmic approaches have been attempted, and although progress has been made the problem remains unsolvable even for many small proteins. While the general objective is to predict the three-dimensional structure from primary sequence, our current knowledge and computational power are simply insufficient to solve a problem of such high complexity.Some prediction algorithms do, however, appear to perform better than others, although it is not always obvious which ones they are and it is perhaps even less obvious why that is. In this review, the reported performance results from 18 different recently published prediction algorithms are compared. Furthermore, the general algorithmic settings most likely responsible for the difference in the reported performance are identified, and the specific settings of each of the 18 prediction algorithms are also compared.The average normalized r.m.s.d. scores reported range from 11.17 to 3.48. With a performance measure including both r.m.s.d. scores and CPU time, the currently best-performing prediction algorithm is identified to be the I-TASSER algorithm. Two of the algorithmic settings--protein representation and fragment assembly--were found to have definite positive influence on the running time and the predicted structures, respectively. There thus appears to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.     

光学元件吸收测量

采用量热法测量了光学元件的吸收,分析了元件表面反射对测量的影响,并测量了GaAs基片和GaAs高反镜的吸收,分析了测量误差。     

Ab initio molecular orbital calculations of the NMR chemical shieldings for mannose and mannobiose

The ¹³C and ¹H NMR shielding constants for -methylmannose and -methylmannobiose have been calculated using the ab initio gauge-including atomic orbital (GIAO) method to study the conformational dependencies of the NMR chemical shifts of the sugars. The molecular structures were fully optimized using B3LYP/6-31G^* and the NMR shielding constants were calculated at both Hartree–Fock (HF) and density functional (DF) levels of theory with various kinds of basis sets. The values determined using the B3LYP hybrid functional were a little closer to those obtained experimentally than those determined at the HF level. Both, HF and B3LYP with the 6-311+G(2d,p) basis were found to give a very good correlation between the experimental and calculated shielding constants, especially for ¹³C.     

Impact of polymer structure and confinement on the kinetics of Zdol 4000 bonding to amorphous‐hydrogenated carbon

The bonding of molecularly‐thin (10 Å) Zdol 4000 films to amorphous, hydrogenated carbon (CH_x) was investigated as a function of the Zdol structure, i.e., the ratio of the perfluoromethylene oxide (C₁) to perfluoroethylene oxide (C₂) monomer units in the backbone. The influence of the C₁/C₂ ratio on the intrinsic mobility of the Zdol polymer was also investigated by computing the energetic barriers to internal rotation about the C–O and C–C bonds in model compounds by both ab initio and molecular mechanics methods. The calculations indicate that increasing the C₁/C₂ ratio increases the relative flexibility of the Zdol polymer. The kinetic results demonstrate that the rate at which submonolayer Zdol films bond to CH_x is non‐classical (time‐dependent) regardless of the Zdol chain stiffness. The Zdol bonding rate can best be described by a kinetic equation of the form, dB/dt=k(t)A, where the rate coefficient, k(t) can be expressed as a power function in time: k(t)= k_B t ^-h. The values of the initial bonding rate constant, k _B, and the functional form of the time dependence, t ^-h, are both strongly dependent on the Zdol backbone flexibility. The magnitude of the initial bonding rate constants generally increase with increasing Zdol chain mobility. A discontinuous change in both the magnitude of k _B and the functional form of the time dependence is, however, observed at 64°C when the C₁/C₂ ratio is increased from 0.97 to 1.08. The bonding rate coefficient scales as t ^-0.5 for the relatively rigid Zdol backbone structures with C₁/C₂ < 1, while a t ^-1.0 time‐dependent bonding rate is observed for the more flexible Zdol backbones with C₁/C₂ < 1. The initial rate constant, k _B, also changes abruptly near C₁/C₂ ≈ 1, with k _B of the flexible Zdol chains (samples with C₁/C₂) being approximately an order of magnitude greater than the more rigid chains (C₁/C₂ < 1). These results indicate that the physical state of the confined Zdol film can be either liquidlike or solidlike depending upon the molecular stiffness of the backbone employed. The t ^-0.5 time‐dependent bonding rate is shown to be consistent with a one‐dimensional, diffusion‐limited reaction from a solidlike Zdol structure, whereas the t ^-1.0 bonding rate results when bonding occurs from a liquidlike Zdol film structure. The temperature dependence of the Zdol 4000 bonding rate coefficient for the Zdol backbone characterized by C₁/C₂ = 0.97 (solidlike at T = 64°C) was found to undergo a transition from a t ^-0.5 time dependence for T < 150°C, to a t ^-1.0 time dependence at T > 180. This transition occurs over relatively narrow temperature range (150 < T < 180°C) and is attributed to a 2D melting of the confined Zdol film.