New functionals for correlation energy deduced in the framework of the correlation factor approach

The general characteristics of two-body density functionals (TBDF) are explored and two new correlation energy functionals are derived using the correlation factor approach. The optimization of the parameters entering the above functionals requires exact and accurate atomic correlation energies (ACE). We revised the ACE values in the literature and obtained a new set of “exact” ACE for atoms with 2 ≤ Z ≤ 10. Unfortunately, there exist some inaccuracies in the ACE values of the second-row atoms, which make unsuitable the inclusion of them in the optimization. The ACE calculated for the first period with the above functionals, using the optimized sets of parameters, are in excellent agreement with the exact ones, while the corresponding values calculated for the second-row atoms are between the precision margins estimated by us for the exact values. © 1997 John Wiley & Sons, Inc.     

Gas hydrate equilibria for CO2-N2 and CO2-CH4 gas mixtures—Experimental studies and thermodynamic modelling

In this paper, a set of experimental data on the phase equilibrium of gas hydrates in the presence of binary gas mixtures comprising CO₂ is presented. The procedure established allows for the determination of both the composition of the gas phase as well as the hydrate phase without the need to sample the hydrate. The experimental results obtained in these measurements have been described by means of the classical model of van der Waals and Platteeuw. The values of internal parameters of the reference state and the Kihara parameters have been re-discussed and their interdependency is pointed. Finally the new set of parameters is validated against experimental data from other sources available in the literature, or invalidated against other sources. Finally, we conclude on the difference of experimental data between laboratories. The differences are not on the classical (pressure, temperature, gas composition) data which appear equivalent between laboratories. The difference stands on the measurement composition of the hydrate phase.     

一组和AMBER力场配合的普适波恩模型参数

提出了一套和AMBER力场相匹配的普适波恩模型参数.新的参数集包含21种原子类型的初始半径和屏蔽因子.参数通过遗传算法拟合359个小分子水合自由能的实验值得到.采用新的参数，预测了44个小分子的水合自由能，预测值和实验值能很好地吻合，而且大大优于采用Jayaram参数得到的结果.此外，采用新的参数，还预测了15个蛋白质的水合自由能，预测值和PB/SA预测得到的结果能很好地吻合.     

The limitations of Slater's element-dependent exchange functional from analytic density-functional theory

Our recent formulation of the analytic and variational Slater-Roothaan (SR) method, which uses Gaussian basis sets to variationally express the molecular orbitals, electron density, and the one-body effective potential of density-functional theory, is reviewed. Variational fitting can be extended to the resolution of identity method, where variationality then refers to the error in each two-electron integral and not to the total energy. However, a Taylor-series analysis shows that all analytic ab initio energies calculated with variational fits to two-electron integrals are stationary. It is proposed that the appropriate fitting functions be charge neutral and that all ab initio energies be evaluated using two-center fits of the two-electron integrals. The SR method has its root in Slater's Xalpha method and permits an arbitrary scaling of the Slater-Gàspàr-Kohn-Sham exchange-correlation potential around each atom in the system. The scaling factors are Slater's exchange parameters alpha. Of several ways of choosing these parameters, two most obvious are the Hartree-Fock (HF) alpha(HF) values and the exact atomic alpha(EA) values. The former are obtained by equating the self-consistent Xalpha energy and the HF energies, while the latter set reproduces exact atomic energies. In this work, we examine the performance of the SR method for predicting atomization energies, bond distances, and ionization potentials using the two sets of alpha parameters. The atomization energies are calculated for the extended G2 set of 148 molecules for different basis-set combinations. The mean error (ME) and mean absolute error (MAE) in atomization energies are about 25 and 33 kcal/mol, respectively, for the exact atomic alpha(EA) values. The HF values of exchange parameters alpha(HF) give somewhat better performance for the atomization energies with ME and MAE being about 15 and 26 kcal/mol, respectively. While both sets give performance better than the local-density approximation or the HF theory, the errors in atomization energy are larger than the target chemical accuracy. To further improve the performance of the SR method for atomization energies, a new set of alpha values is determined by minimizing the MAE in atomization energies of 148 molecules. This new set gives atomization energies half as large (MAE approximately 14.5 kcal/mol) and that are slightly better than those obtained by one of the most widely used generalized-gradient approximations. Further improvements in atomization energies require going beyond Slater's functional form for exchange employed in this work to allow exchange-correlation interactions between electrons of different spins. The MAE in ionization potentials of 49 atoms and molecules is about 0.5 eV and that in bond distances of 27 molecules is about 0.02 A. The overall good performance of the computationally efficient SR method using any reasonable set of alpha values makes it a promising method for study of large systems.     

普通有机分子或药物热分解稳定性的理论预测

采用密度泛函理论方法, 在B3LYP/6-31+G(d,p)水平上, 对任意选定的32个有机化合物或药物进行最低能量构象优化和结构参数理论计算. 建立了四极矩参数Q_ii与半数摩尔热分解函数Y_d(1/2)的相关方程, 其定量构性关系(QSPR)方程为Y_d(1/2)=-8.65747-3.8954Q_ii, 相关系数为r²=-0.99297, 交叉验证相关系数为XV-r²=0.99188, F检验结果为4237.343321. 训练集化合物的半数分解温度T_d(1/2)的平均绝对预测误差(AVEDEV)为14.70 K. 进一步利用该方程对测试集中43个分子进行预测验证, T_d(1/2)的预测值与实验值的相关系数为0.92304, Y_d的预测值与实验值的相关系数为0.99345, 证实了所建立方法的可靠性. 结构差异性分析表明, 训练集和测试集中的化合物均较均匀地分布在结构参数的3D空间中, 化合物结构具有较好的多样性和差异性.     

Comprehensive parameter set for the prediction of the 13C-NMR chemical shifts of sp3-hybridized carbon atoms in organic compounds

A parameter set is described for prediction of the carbon-13 chemical shifts of sp³-hybridized carbon atoms based on a simple linear additivity relationship. It was tested against 88 692 known chemical shift values. Many of the previously reported parameters were amended and new parameters added. With this parameter set, the chemical shifts in 99.7% of the 88 692 cases can be estimated with an overall standard deviation of 5.6 ppm for the predicted values relative the the experimental ones. The additivity parameters reported here can be used per se or in connection with a recent computer program for the estimation of carbon-13 chemical shifts, which automatically selects and applies additivity rules appropriate for the individual carbon atoms of the chemical constitution entered.     

Solvation parameters Part 1. Mutual improvements of several approaches and determination of two first sets of optimized values

An improvement in the characterization and the determination of the solvation parameters allows, not only a better knowledge of solutions, but also of some biological phenomena. In this paper, we test several published data and approaches in the field of solubility and solvation parameters in two ways: (i) the mutual independence of the parameters and (ii) their ability to take into account recently published gas-liquid chromatographic data. From this enquiry it arises that the most suitable published values are those of Abraham concerning 314 solutes. It also arises that the parameters of dispersion and orientation of this published data set are appreciably improved using two simple equations. In addition, a new set of optimized values for 133 solutes is given, by derivation from retention indices in gas-liquid chromatography (GLC) on five selected stationary phases, published by Kováts and co-workers and in the present study. The two sets have a total of 373 defined compounds.     

Consistent valence force-field parameterization of bond lengths and angles with quantum chemical ab initio methods applied to some heterocyclic dopamine D3-receptor agonists

To secure a broad utilization of molecular mechanics in medicinal chemistry appropriate parameters (e.g., reference values and force constants) are required to describe correctly all possible atomic interactions. For this purpose parameters for bond lengths and bond angles were derived for some heterocyclic dopamine D₃-receptor agonists. Some new atom types were introduced and consistent valence force-field (CVFF) was supplied with several bond-stretching and angle-bending force constants as well as reference values. Representative fragments containing these missing parameters were minimized at the HF/6-31G* level of theory using Gaussian-92. After frequency calculation, corresponding force constants were extracted from the Hessian matrix. The values were then appropriately converted and scaled. Also, reference values were taken from quantum mechanically minimized structures, applying the same basis set. The transferability of the calculated force constants to CVFF was investigated using fragments with already known parameters. The quality of the extended force field was checked in comparison with “automatic parameters” and ab initio-minimized structures. Finally, the evaluated procedure was applied successfully to related structures. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 935–946, 1998     

pKa prediction for acidic phosphorus‐containing compounds using multiple linear regression with computational descriptors

Ninety‐six acidic phosphorus‐containing molecules with pK_a 1.88 to 6.26 were collected and divided into training and test sets by random sampling. Structural parameters were obtained by density functional theory calculation of the molecules. The relationship between the experimental pK_a values and structural parameters was obtained by multiple linear regression fitting for the training set, and tested with the test set; the R² values were 0.974 and 0.966 for the training and test sets, respectively. This regression equation, which quantitatively describes the influence of structural parameters on pK_a, and can be used to predict pK_a values of similar structures, is significant for the design of new acidic phosphorus‐containing extractants. © 2016 Wiley Periodicals, Inc.     

Rotationally invariant ab initio evaluation of Coulomb and exchange parameters for DFT+U calculations

Conventional density functional theory (DFT) fails for strongly correlated electron systems due to large intra-atomic self-interaction errors. The DFT+U method provides a means of overcoming these errors through the use of a parametrized potential that employs an exact treatment of quantum mechanical exchange interactions. The parameters that enter into this potential correspond to the spherically averaged intra-atomic Coulomb (U) and exchange (J) interactions. Recently, we developed an ab initio approach for evaluating these parameters on the basis of unrestricted Hartree-Fock (UHF) theory, which has the advantage of being free of self-interaction errors and does not require experimental input [Mosey and Carter, Phys. Rev. B 76, 155123 (2007)]. In this work, we build on that method to develop a more robust and convenient ab initio approach for evaluating U and J. The new technique employs a relationship between U and J and the Coulomb and exchange integrals evaluated using the entire set of UHF molecular orbitals (MOs) for the system. Employing the entire set of UHF MOs renders the method rotationally invariant and eliminates the difficulty in selecting unambiguously the MOs that correspond to localized states. These aspects overcome two significant deficiencies of our earlier method. The new technique is used to evaluate U and J for Cr(2)O(3), FeO, and Fe(2)O(3). The resulting values of U-J are close to empirical estimates of this quantity for each of these materials and are also similar to results of constrained DFT calculations. DFT+U calculations using the ab initio parameters yield results that are in good agreement with experiment. As such, this method offers a means of performing accurate and fully predictive DFT+U calculations of strongly correlated electron materials.     

ANN-MATOPT hybrid algorithm: determination of kinetic and non-kinetic parameters in different reaction mechanisms

In this work we have applied the computational methodology based on Artificial Neural Networks (ANN) to the kinetic study of distinct reaction mechanisms to determine different types of parameters. Moreover, the problems of ambiguity or equivalence are analyzed in the set of parameters to determine in different kinetic systems when these parameters are from different natures. The ambiguity in the set of parameters show the possibility of existence of two possible set of parameter values that fit the experimental data. The deterministic analysis is applied to know beforehand if this problem occurs when rate constants of the different stages of the mechanism and the molar absorption coefficients of the species participating in the reaction are obtained together. Through the deterministic analysis we will analyze if a system is identifiable (unique solution or finite number of solutions) or if it is non-identifiable if it possesses infinite solutions. The determination of parameters of different nature can also present problems due to the different magnitude order, so we must analyze in each case the necessity to apply a second method to improve the values obtained through ANN. If necessary, an optimization mathematical method for improving the values of the parameters obtained with ANN will be used. The complete process, ANN and mathematical optimizations constitutes a hybrid algorithm ANN-MATOPT. The procedure will be applied first for the treatment of synthetic data with the purpose of checking the applicability of the method and after, it will be used in the case of experimental kinetic data.

     

A New Software to Show the Behaviour of the PID Controller. Influence of the setting parameters of DSCs. Part I

Some DSC calorimeters such as the model Setaram DSC 111 allow the user to set the parameters of temperature programming. Default values furnished by the constructor are often used, but it is very interesting to study the thermal behaviour of the regulation of the calorimeter under different conditions and kinds of set point temperatures. For this research we have developed in C a set of softwares in order to show the behaviour of the proportional integral derivative (PID) controller of the DSC. It can help the user to choose correct values for P, I and D parameters according to the kind of experiment conducted. The software allows studies for extra parameters such as the sampling rate of the computerized PID controller or the determination of filtering of the correction. This revised version was published online in July 2006 with corrections to the Cover Date.     

A New Software to Show The Behaviour of The PID Controller. Part II. Influence of the setting parameters of DSCs

Some DSC calorimeters, such as the model DSC 111, built by the society Setaram, allow the user to set the temperature programming parameters. Usually default values furnished by the constructor are often used, but it is very interesting to study the thermal behaviour of the regulation of the calorimeter under different conditions and with different kinds of set point temperatures. For this research, we have developed in C language a set of software in order to demonstrate the behaviour of the (proportional integral derivative) PID controller of the DSC. It can help the user to choose correct values for P, I and D parameters according to the kind of experiment conducted. The software allows studies of extra parameters, such as the sampling rate of the computerized PID controller or the determination of filtering of the correction. This revised version was published online in August 2006 with corrections to the Cover Date.     

A method for analysis of DMFC performance curves

Our recent analytical model of direct methanol fuel cell is used to fit experimental performance curves. Based on evolutionary genetic algorithm, a new fitting procedure is developed. The idea is to fit simultaneously a set of performance curves, which have several common fitting parameters. On the first stage of evolution all parameters are determined independently. Starting from certain step a mean values of common parameters are calculated and further evolution corrects the mean values. For different sets of experimental curves the method gives well reproducible results. The physical parameters resulted from fitting and the effect of crossover on cell performance are discussed.     

支持向量机法用于4-芳基-4氢-苯并比喃化合物的凋亡诱导活性研究

通过计算获得了39个4-芳基-4氢.苯并吡喃化合物的11个结构特征参数,应用逐步线性回归方法对参数进行筛选.并用支持向量回归(SVR)算法,对4-芳基-4氢-苯并吡喃化合物与其凋亡诱导活性进行定量构效关系(QSAR)研究.通过核函数参数的优化,建立了预测模型,训练集和预测集的实验值与计算值的平方相关系数R2分别为0.997和0.893.研究结果表明,支持向量回归算法可用于小样本数的药物分子设计研究,以合成具有更高生物活性的新药物.     

Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery

The ability to accurately predict biological affinity on the basis of in silico docking to a protein target remains a challenging goal in the CADD arena. Typically, "standard" scoring functions have been employed that use the calculated docking result and a set of empirical parameters to calculate a predicted binding affinity. To improve on this, we are exploring novel strategies for rapidly developing and tuning "customized" scoring functions tailored to a specific need. In the present work, three such customized scoring functions were developed using a set of 129 high-resolution protein-ligand crystal structures with measured Ki values. The functions were parametrized using N-PLS (N-way partial least squares), a multivariate technique well-known in the 3D quantitative structure-activity relationship field. A modest correlation between observed and calculated pKi values using a standard scoring function (r2 = 0.5) could be improved to 0.8 when a customized scoring function was applied. To mimic a more realistic scenario, a second scoring function was developed, not based on crystal structures but exclusively on several binding poses generated with the Flo+ docking program. Finally, a validation study was conducted by generating a third scoring function with 99 randomly selected complexes from the 129 as a training set and predicting pKi values for a test set that comprised the remaining 30 complexes. Training and test set r2 values were 0.77 and 0.78, respectively. These results indicate that, even without direct structural information, predictive customized scoring functions can be developed using N-PLS, and this approach holds significant potential as a general procedure for predicting binding affinity on the basis of in silico docking.     

Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents.

Recently, the GROMOS biomolecular force field parameter set 53A6--which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexane of amino acid side-chain analogs--was presented. To investigate the transferability of the new parameter set, we calculated free enthalpies of solvation of a range of polar and apolar compounds in different solvents (methanol, dimethyl sulfoxide (DMSO), acetonitrile, and acetone) from molecular dynamics simulations using the GROMOS 53A6 force field. For methanol and DMSO, parameters were used that are available in the 53A6 parameter set. For acetonitrile, a recently developed model was taken and for acetone, two models available in literature were used. We found that trends in and values for the solvation free enthalpies are in satisfactory agreement with experiment, except for the solvation in acetone for which deviations from experiment can be explained in terms of the properties of the models used.