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     

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.     

Atomic force microscopy imaging of novel macromolecular species,nanosponges, and their clusters

Atactic polystyrene of M = 330,000 Da and M_w/M_n = 1.04 was subjected to a complete chloromethylation. By heating the chloromethyl polystyrene with SnCl₄ in a very dilute solution in ethylene dichloride, the polymeric coils were converted into intramolecularly hypercrosslinked macromolecules, called “nanosponges.” These species have a molecular weight of about 370,000 Da and a diameter of about 17 nm. When in solution, the nanosponges display a tendency to reversibly self‐assemble into regular clusters. Preparative size‐exclusion chromatography isolates a fraction consisting predominantly of spherical clusters that are composed of 13 subunits and acquire a molecular weight of approximately 5.0 × 10⁶ Da and a diameter of 45 nm. Scanning atomic force microscopy (AFM) provides images of individual nanosponges, N = 13 clusters, as well as higher spherical clusters. The regular spherical species most probably belong to the cluster series N = 1 + ∑(10n² + 2), where n is the number of shells around the central nanosponge. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1451–1455, 1999     

高功率微波在等离子体填充波导中的传播特性

 在考虑有质动力情况下对高功率微波在等离子体填充波导中的传播特性进行了理论分析和数值计算,研究了高功率微波在等离子体中的传播特性和微波场强与等离子体密度分布之间的关系。结果表明高功率微波的有质动力将影响微波色散特性,使微波场强分布偏离Bessel分布,并对等离子体有排开作用,当场强足够大时可将波导中心处等离子体排空形成低密度通道。     

Details of surface features in aromatic polyamide reverse osmosis membranes characterized by scanning electron and atomic force microscopy

In the present article, some new events on the surface morphology of the aromatic polyamide thin‐film‐composite (TFC) membranes were demonstrated in conjunction with their inherent chemical nature. In addition, the detailed, quantitative understanding of the microscopic surface features was shown to be essential in controlling the water permeability and eventually developing the high performance membranes. The surface roughness and the surface area were mainly affected by the existence or nonexistence of the crosslinking and/or the free amide groups not pertinent to the formation of the hydrogen bonding, which in turn contributed to the water permeability. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1429–1440, 1999     

The Anthelmintic Quassinoids Ailanthone and Bruceine a Induce Infertility in the Model Organism Caenorhabditis elegans by an Apoptosis-like Mechanism Induced in Gonadal and Spermathecal Tissues

In continuation of the search for new anthelmintic natural products, the study at hand investigated the nematicidal effects of the two naturally occurring quassinoids ailanthone and bruceine A against the reproductive system of the model nematode Caenorhabditis elegans to pinpoint their anthelmintic mode of action by the application of various microscopic techniques. Differential Interference Contrast (DIC) and the epifluorescence microscopy experiments used in the presented study indicated the genotoxic effects of the tested quassinoids (c _ailanthone = 50 µM, c _{bruceine A} = 100 µM) against the nuclei of the investigated gonadal and spermathecal tissues, leaving other morphological key features such as enterocytes or body wall muscle cells unimpaired. In order to gain nanoscopic insight into the morphology of the gonads as well as the considerably smaller spermathecae of C. elegans, an innovative protocol of polyethylene glycol embedding, ultra-sectioning, acridine orange staining, tissue identification by epifluorescence, and subsequent AFM-based ultrastructural data acquisition was applied. This sequence allowed the facile and fast assessment of the impact of quassinoid treatment not only on the gonadal but also on the considerably smaller spermathecal tissues of C. elegans. These first-time ultrastructural investigations on C. elegans gonads and spermathecae by AFM led to the identification of specific quassinoid-induced alterations to the nuclei of the reproductive tissues (e.g., highly condensed chromatin, impaired nuclear membrane morphology, as well as altered nucleolus morphology), altogether implying an apoptosis-like effect of ailanthone and bruceine A on the reproductive tissues of C. elegans.     

单原子作为保护基团实现石墨双炔纳米线的表面合成

由于在贵金属表面的双炔单元具有高反应活性,表面合成半导体性质的石墨双炔纳米线通常会受到副反应的严重影响,难以分立的纳米线的高质量制备.本文利用化学气相沉积1,4-bis(4-bromophenyl)-1,3-butadiyne分子到表面发生Ullmann偶联反应,可实现无支链的石墨双炔纳米线[-C≡C-Ph_2-C≡C-]_n (PYP)的高产率合成.进一步的单化学键分辨的非接触原子力显微镜表征揭示了单个金增原子与双炔键之间形成了π-ligand键,有效地充当了反应过程中双炔单元的保护基团,避免了偶联过程中的副反应,从而实现了分立的超长石墨双炔纳米线的合成.这项研究将启发对在表面反应中各类表面增原子所起保护作用的更深入研究.     

Polarized Debye Sheath in Degenerate Plasmas

The force on a charged dust grain in a plasma due to polarization of thermal ions and degenerate electrons around the grain is derived in the limits of weakly relativistic and ultra-relativistic degeneracy of electrons. It is found that in both these cases, the magnitude of the polarization force is enhanced compared to that in classical plasmas. The influence of this force on dust-acoustic(DA) modes is examined and discussed. It is shown that the DA wave frequency in degenerate plasmas is significantly reduced compared to the classical DA mode.     

Impacts of neutral shadowing force on dust particle dynamics in cryogenic plasma

Recently, it was shown that the neutral shadowing force can have a strong impact on the structural properties of the charged dust particles in cryogenic dusty plasmas. Therefore, in this work, we have investigated the impact of the neutral shadowing force on the dynamical properties by means of molecular dynamics simulations. By computing the velocity auto‐correlation function of particles and their spectrum, we found that the neutral shadowing force has a strong impact on the dust particle dynamics if the mean free path of neutrals exceeds the mean inter‐dust particle distance.