Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets,protocols, and force fields

The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 769–780, 1998     

Supramolecular structures of poly(γ-benzyl-L-glutamate) self-assembled on mica surface

This article reports the results of structural studies of poly (γ-benzyl-L -glutamate) (PBLG) layers self-assembled from dilute solutions in organic solvents on mica surface. Polarized dynamic light scattering and atomic force microscopy were used to study polymer properties in solutions and on the surface. The hierarchy of self-assembly from PBLG solutions in different solvents was investigated as a function of polymer concentration and solvent polarity. We show that the surface–polymer interaction is suppressed in polar solvents that is interpreted in terms of suppressed charge–dipole interaction. The transformation of the PBLG surface structure occurs upon addition of different amounts of trifluoroacetic acid to polymer solution in dioxane. Rigid-rod PBLG molecules experience rod–globular transition while assembling on nonmodified mica from the very dilute solutions. A scheme is proposed describing different stages of PBLG fibrogenesis on a charged surface. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 1567–1577, 1998     

Direct Growth of Aggregates on {110} Faces of Cadmium Mercury Thiocyanate Crystals

New growth phenomena ‐ direct incorporation of aggregates have been observed on the {110} faces of cadmium mercury thiocyanate CdHg(SCN)₄ crystals by atomic force microscopy. These aggregates grow in two forms: some directly cover up the steps and forms new growth layers; while others are just incorporated at the step edges. These aggregates, which are mostly oriented along [111] direction, are formed by small columnar structural units. The aggregates have the similar structure of CdHg(SCN)₄ crystals and greatly vary in nature with the variation of solution supersaturation σ and growth time t. With the increase of σ the aggregates become larger, consistent with the variation of growth units dimension with the supersaturation; and with the increase of growth time the aggregates become more structurally substantial. These observations have led to a new understanding about the crystal growth.     

The Relevance of Interactions in Nanoparticle Systems – Application to Particulate Thin Films

In the field of Particle Technology, processes cannot yet be designed from basic molecular understanding. Nanotechnology, however, begins to bridge this gap between molecules and particles and may thus open up new ways not only for the production and handling of particulate matter but also for the engineered design of advanced material properties. The visions and applications in nanoparticle technology cover a broad range, for instance quantum dots in information technology, refractory particles for advanced ceramics, highly active substances in pharmacy, catalysts or micro‐ and mesoporous adsorbents, to name only a few applications. Starting from the concept of product engineering, we investigate the basic preconditions for tailoring nanoparticulate properties, i.e. the control of the particle interactions. This concept is then applied to particulate thin film formation as an example of structure formation. The structure of dip‐coated samples, defined as the order of particles within the layer, was found to vary with the pH and the ion concentration adjusted in the sol bath. It was observed that the surface roughness scanned by an atomic force microscope increased with increasing electrolyte concentration. The structural evolution of the particulate network was studied by measuring the viscosity as a function of shear rate and solid concentration. Finally, the influence of coating structures on the transmission properties was determined. Especially in the case of LaCl₃ a strong dependence was observed. The results explicitly confirm a correlation between microscopic structure and macroscopic properties.     

基于三维离散元堆积碎石土细-宏观力学参数相关性研究

以室内三轴压缩试验为基础,运用PFC3D离散元软件生成含有不同形状碎石块的1∶1堆积碎石土数值模型,标定得到相应的细观参数(相对误差控制在10%以内)。改变细观参数,定量探讨其与宏观力学参数(粘聚力和内摩擦角)关系,得到细观参数与粘聚力、内摩擦角的细-宏观参数关系式,并对其可靠性进行了验证。研究发现,(1)粘聚力与接触粘结力、颗粒摩擦系数呈线性正相关;同时受粘结力比值M=σc/τc的影响,当M1时,粘聚力随着M的增加而线性增加;M≥4时,粘聚力趋于稳定。(2)内摩擦角与颗粒摩擦系数呈对数关系,与接触粘结力呈抛物线关系。(3)细-宏观参数关系式是在含水率为7%室内试验结果基础上研究得出,将关系式运用到含水率为9%和11%的室内试验结果进行标定验证:依据含水率为9%和11%室内试验得到的c和φ值,运用细-宏观参数关系式计算得到细观参数,经验证其数值-室内试验结果相对误差在10%以内,说明通过细-宏观力学关系式得到的细观参数符合精度要求,关系式可靠。为后续土石混合体数值试验研究者进行细观参数标定工作提供了参考依据。     

"老人"历史债务的双随机模型

为社会养老保险制度转轨过程中的“老人”历史债务建立了双随机模型，得到了“老人”历史债务的前二阶段，并对息力累积函数以Wiener过程和Ornstein-Uhlenbeck过程建模得到了的具体表达式。最后做了一个实例，以浙江省某市的实际数据，估算了该市的“老人”历史债务额。     

MMFF VI. MMFF94s option for energy minimization studies

This article describes the derivation of MMFF94s, which is the “s” (static) variant of MMFF94. MMFF94s incorporates altered out of plane bending parameters that yield planar (or nearly planar) energy-minimized geometries at unstrained delocalized trigonal nitrogen centers. Some experimental and most theoretical structures show appreciable puckering at nitrogen in isolated structures. However, condensed-phase effects or even strong intermolecular hydrogen bonding tends to reduce, but need not eliminate, such puckering; in contravention to results reported on the lower level Hartree–Fock surface, we show in the correlated LMP2/6-31G** calculations for the Watson–Crick guanine–cytosine base pair that one of the hydrogen-bonded NH₂ groups remains appreciably puckered. The resultant MMFF94s geometries emulate the “time-averaged” structures typically observed in crystallographic and most other experimental structure determinations. MMFF94s also employs modified torsion parameters for interactions that involve such centers, but is identical to MMFF94 for other systems. Isolated instances are found in which MMFF94s fails to locate a (probably shallow) local minimum found on the MMFF94 and reference MP2/6-31G* surfaces. In general, however, MMFF94s describes conformation energies for delocalized trigonal nitrogen systems nearly as well as MMFF94 does. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 720–729, 1999     

Consensus bond-charge increments fitted to electrostatic potential or field of many compounds: Application to MMFF94 training set

Bond-charge increments (BCIs) are additive parameters used to assign atomic charges for the MMFF force field. BCI parameters are classified parsimoniously according to two atom types and the bond order. We show how BCIs may be fitted rapidly by linear least squares to the calculated ab initio electrostatic potential (ESP) or to the electrostatic field. When applied simultaneously to a set of compounds or conformations, the method yields consensus values of the BCIs. The method can also derive conventional “ESP-fit” atomic charges with improved numerical stability. The method may be generalized to determine atom multipoles, multicenter charge templates, or electronegativities, but not polarizability or hardness. We determine 65 potential-derived (PD) BCI parameters, which are classified as in MMFF, by fitting the 6-31G* ESP or the electrostatic field of the 45 compounds in the original MMFF94 training set. We compare the consensus BCIs with classified BCIs that were fit to each molecule individually and with “unique-bond” BCIs (ESP-derived atom charges). Consensus BCIs give a satisfactory representation for about half of the structures and are robust to the adjustment of the alkyl CH bond increment to the zero value employed in MMFF94. We highlight problems at three levels: Point approximation: the potential near lone pairs on sulfur and to some extent nitrogen cannot be represented just by atom charges. Bond classification: BCIs classified according to MMFF atom types cannot represent all delocalized electronic effects. The problem is especially severe for bonds between atoms of equivalent MMFF type, whose BCI must be taken as zero. Consensus: discrepancies that occur in forming the consensus across the training set indicate the need for a more detailed classification of BCIs. Contradictions are seen (e.g., between acetic acid and acetone and between guanidine and formaldehydeimine). We then test the three sets of PD-BCIs in energy minimizations of hydrogen-bonded dimers. Unique-bond BCIs used with the MMFF buffered 14–7 potential reproduce unscaled quantum chemical dimer interaction energies within 0.9 kcal/mol root mean square (or 0.5, omitting two N-oxides). These energies are on average 0.7 (or 0.5) kcal/mol too weak to reproduce the scaled quantum mechanical (SQM) results that are a benchmark for MMFF parameterization. Consensus BCIs tend to weaken the dimer energy by a further 0.4–0.6 kcal/mol. Thus, consensus PD-BCIs can serve as a starting point for MMFF parameterization, but they require both systematic and individual adjustments. Used with a “harder” AMBER-like Lennard–Jones potential, unique-bond PD-BCIs without systematic adjustment give dimer energies in fairly good agreement with SQM. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1495–1516, 1999     

Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide

Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree–Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by “breaking” bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. Results from tests of the method to find relative conformational energies and geometries of alanine dipeptides and alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1468–1494, 1999     

Bis(dichlorosilyl)methylamine – Synthesis,Crystal Structure,and Conformational Analysis in the Gas Phase

A straightforward preparation has been found for bis(dichlorosilyl)methylamine, (SiHCl₂)₂NMe ( 1 ), involving reaction between H₂NMe and an excess of SiHCl₃, dissolved either in pentane or THF at 253 K. 1 and a side‐product, 1,3,5‐trichloro‐2,4,6‐trimethylcyclotrisilazane, (–SiHCl–NMe–)₃ ( 2 ), were identified by elemental analysis, mass spectrometry and ¹H‐NMR‐spectroscopy. Some physical, NMR‐ and IR spectroscopical properties of 1 were determined. The molecular and crystal structure of 1 was investigated by single crystal X‐ray diffraction. Selected structural parameters: r(Si–N) 169.7(5), r(Si–Cl) 203.1(2)–204.4(2), r(C–N) 150.0(8) pm; a(SiNSi) 123.6(3), a(SiNC) 118.3(4)/118.0(4)°. Ab initio force field data and infrared intensities were calculated for four conformers of 1 . Comparison of the observed and calculated IR spectra favours the two structures found ab initio provided that their actual abundancies are different from those calculated.