Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to that seen in ab initio data. Intrinsic torsional energy is modeled as a sum over pairs of adjacent torsion angles of 2-dimensional Fourier series. Hydrophobic energy is that of a hydration shell model. The remainder of hydration free energy is obtained as the energetic effect of a continuous dielectric medium. Parameters are adjusted to reproduce the following data: a complete set of ab initio energy surfaces, meaning one for each pair of adjacent torsion angles of each blocked amino acid; experimental crystal structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds. All ab initio data is at the Hartree–Fock/6–31G* level. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 548–573, 1998     

Excess Heat Capacity in Yttria Stabilized Zirconia

The heat capacity of 9.70 and 11.35 mol% yttria stabilized zirconia ((ZrO₂)_1–x(Y₂O₃)_x; x=0.0970, 0.1135) was measured by adiabatic calorimetry between 13 and 300 K, and some thermodynamic functions were calculated and given in a table. A large excess heat capacity extending from the lowest temperature to room temperature with a broad maximum at about 75 K was found in comparison with the heat capacity calculated from those of pure zirconia and yttria on the basis of simple additivity rule. The shape of the excess heat capacity is very similar to the Schottky anomaly, which may be attributed to a softening of lattice vibration. The amount of the excess heat capacity decreased with increasing yttria doping, while the maximum temperature did not vary. The relationships among the excess heat capacity, defect structure and interatomic force constants, and also the role of oxygen vacancy were discussed.This revised version was published online in November 2005 with corrections to the Cover Date.     

Valence p functions for alkali and alkaline-earth atoms

Contracted Gaussian-type function (CGTF) basis sets are reported for valence p orbitals of the six alkali and alkaline-earth atoms Li, Be, Na, Mg, K, and Ca for molecular applications. These sets are constructed by Roothaan–Hartree–Fock calculations for the ns → np excited states of atoms, in which both linear and nonlinear parameters of CGTFs are variationally optimized. The present CGTF sets reproduce well the numerical Hartree–Fock ns → np excitation energies: the largest error is 0.0009 hartrees for Li. New CGTFs are tested with diatomic Li₂, Na₂, K₂, and MH molecules, where M = Li, Be, Na, Mg, K, and Ca, by self-consistent-field (SCF) and multiconfiguration SCF calculations. The resultant spectroscopic constants compare well with those of more elaborate calculations and are sufficiently close to experimental values, supporting the efficiency of the present set for the valence p orbitals. Received: 9 July 1998 / Accepted: 17 September 1998 / Published online: 1 February 1999     

Zur Theorie der Chiralitätsfunktionen

The Algebraic Theory of Chirality Functions is derived by means of exclusively qualitative considerations. Hence, the significance of quantitative results is questionable. Moreover the construction of “Näherungsansätze” (”Approximation-Ansatz”), which may be interpreted as semiempirical methods, is achieved on the basis of plausibility and mathematical simplicity. Since physical arguments are not included, the consistency or inconsistency of “Näherungsansätze” with experimental results do not justify direct physical conclusions.     

A six-dimensional quadrature procedure

An account is given of the use of Gaussian quadrature product formulae in the evaluation of certain six-dimensional, two-centre integrals involving one-electron Green's functions. These integrals occur in a new molecular variational principle recently proposed by Hall, Hyslop and Rees [1] from which an approximate energy may be derived which can be shown to be at least as good as that obtained from the Rayleigh-Ritz principle. Reductions in computing time are realized by removing certain singularities using a subtraction technique and also by using an empirically determined Richardson-type extrapolation formula.This paper was presented during the session on numerical integration methods for molecules of the 1970 Quantum Theory Conference in Nottingham. It has been revised in the light of the interesting discussion which followed.     

A process–structure–property study of anisotropic PMDA-ODA films

A practical methodology for the correlation and prediction of the process–property performance of advanced materials is developed. The model polymer studied is PMDA-ODA polyimide. The connecting link between the process and the properties is the structural state of the polymer. An essential ingredient for a quantitative characterization of the system is a knowledge of its phase state and intrinsic molecular properties. The intrinsic molecular properties define the limiting performance properties available to the polymer. Anisotropic films and sheets produced by five different fabrication processes are examined. Maps of the molecular symmetry axis, the orientation function, and the thickness distributions of two 50-in.-wide sheets fabricated differently are measured nondestructively for process comparison. Four other film fabrication processes are examined and their three-dimensional orientation states determined and correlated. A three-dimensional orientation function triangular plot permits simultaneous representation of the different fabrication processes on the same figure and allows the investigator to choose the most economic and efficient fabrication route. The structure–property study includes the structural correlation and intrinsic molecular property determination of the anisotropic coefficient of thermal expansion (CTE), the anisotropic mechanical moduli and compliances, and the anisotropic dielectric constants. 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 777–788, 1997     

System Zn–Rh–O: heat capacity and Gibbs free energy of formation using differential scanning calorimeter and electrochemical cell

The standard molar Gibbs free energy of formation of ZnRh₂O₄(s) has been determined using an oxide solid-state electrochemical cell wherein calcia-stabilized zirconia (CSZ) was used as an electrolyte. The oxide cell can be represented by: . The electromotive force was measured in the temperature range from 943.9 to 1,114.2 K. The standard molar Gibbs energy of formation of ZnRh₂O₄(s) from elements in their standard state using the oxide electrochemical cell has been calculated and can be represented by: . Standard molar heat capacity C ^o _p,m(T) of ZnRh₂O₄(s) was measured using a heat flux-type differential scanning calorimeter in two different temperature ranges, from 127 to 299 and 307 to 845 K. The heat capacity in the higher temperature range was fitted into a polynomial expression and can be represented by: . The heat capacity of ZnRh₂O₄(s), was used along with the data obtained from the oxide electrochemical cell to calculate the standard enthalpy and entropy of formation of the compound at 298.15 K.     

样条变换集成罚函数偏最小二乘方法用于光谱数据重构和定量分析

针对高维小样本光谱数据所显现的函数型数据(Functional data)特性、与性质参数的非线性关系及变量间存有的严重共线性,采用了样条变换集成罚函数偏最小二乘回归新技术.它首先以三次B基样条变换实现非线性光谱数据的线性化重构,随后将重构的新光谱矩阵交由罚函数偏最小二乘法(Penalized PLS)构建其与性质参变量间的校正模型,其中罚函数中的光滑因子由交叉验证优化确定以调控模型的拟合精度.最后,通过小麦样品水分含量的近红外光谱定量分析,结果显示该技术光谱数据重构稳健,去噪明显,并有效解决高维小样本的过拟合和变量间的共线性,而预测集的均方根误差(RMSEP)为0.1808%,方法的非线性校正模型预测能力得到了明显提高.