The location of transition states: A comparison of Cartesian,Z-matrix,and natural internal coordinates

A comparison is made between geometry optimization in Cartesian coordinates, in Z-matrix coordinates, and in natural internal coordinates for the location of transition states. In contrast to the situation with minima, where all three coordinate systems are of comparable efficiency if a reliable estimate of the Hessian matrix is available at the starting geometry, results for 25 different transition states covering a wide range of structural types demonstrate that in practice Z-matrix coordinates are generally superior. For Cartesian coordinates, the commonly used Hessian update schemes are unable to guarantee preservation of the necessary transition state eigenvalue structure, while current algorithms for generating natural internal coordinates may have difficulty handling the distorted geometries associated with transition states. The widely used Eigenvector Following (EF) algorithm is shown to be extremely efficient for optimizing transition states. © 1996 by John Wiley & Sons, Inc.     

T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles

T-Analyst is a user-friendly computer program for analyzing trajectories from molecular modeling. Instead of using Cartesian coordinates for protein conformational analysis, T-Analyst is based on internal bond-angle-torsion coordinates in which internal torsion angle movements, such as side-chain rotations, can be easily detected. The program computes entropy and automatically detects and corrects angle periodicity to produce accurate rotameric states of dihedrals. It also clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. Correlated motions between selected dihedrals can also be observed from the correlation map. T-Analyst focuses on showing changes in protein flexibility between different states and selecting representative protein conformations for molecular docking studies. The program is provided with instructions and full source code in Perl.     

Geometry optimization in Cartesian coordinates: Constrained optimization

An efficient algorithm for constrained geometry optimization in Cartesian coordinates is presented. It incorporates mode-following techniques within both the classical method of Lagrange multipliers and the penalty function method. Both constrained minima and transition states can be located and, unlike the standard Z-matrix using internal coordinates, the desired constraints do not have to be satisfied in the initial structure. The algorithm is as efficient as a Z-matrix optimization while presenting several additional advantages.     

Further links between the maximum hardness principle and the hard/soft acid/base principle: insights from hard/soft exchange reactions

Ayers, Parr, and Pearson recently showed that insight into the hard/soft acid/base (HSAB) principle could be obtained by analyzing the energy of reactions in hard/soft exchange reactions, i.e., reactions in which a soft acid replaces a hard acid or a soft base replaces a hard base [J. Chem. Phys., 2006, 124, 194107]. We show, in accord with the maximum hardness principle, that the hardness increases for favorable hard/soft exchange reactions and decreases when the HSAB principle indicates that hard/soft exchange reactions are unfavorable. This extends the previous work of the authors, which treated only the "double hard/soft exchange" reaction [P. K. Chattaraj and P. W. Ayers, J. Chem. Phys., 2005, 123, 086101]. We also discuss two different approaches to computing the hardness of molecules from the hardness of the composing fragments, and explain how the results differ. In the present context, it seems that the arithmetic mean of fragment softnesses is the preferable definition.     

Elucidating the hard/soft acid/base principle: a perspective based on half-reactions

A comprehensive analysis is presented for the acid-base double-exchange reaction as well as the associated acid-displacement and base-displacement "half-reactions" with the goal of elucidating the meaning of the hard/soft acid/base (HSAB) principle and the conditions for its validity. When electron-transfer effects are important and other effects are negligible, the HSAB principle is driven by the surpassing stability of the soft acid/soft base product. When electrostatic effects dominate the reactivity, the HSAB principle is driven by the surpassing stability of the hard acid/hard base product. Because electron-transfer effects favor soft/soft interactions, while electrostatic effects favor hard/hard interactions, acid-base exchange reactions may be used to determine whether a reagent's reactivity is dominated by electron-transfer or by electrostatic effects. Because electron-transfer and electrostatic considerations separately favor the HSAB principle whenever the electronic chemical potentials of the acids and bases involved in the reaction are similar, our analysis provides strong support for the HSAB principle. The electronic chemical potential measures the intrinsic strength of acids and bases.     

Poly(urea)urethanes based on amorphous quaternizable hard segments and a crystalline polyol derived from castor oil

A set of poly(urea)urethanes (PUU), with different contents of amorphous hard segment and castor oil-derived crystalline polyol as soft segment, was prepared combining bulk and solution polymerizations. It is shown that both the soft segment crystallinity and hard segment glassy nature control the stiffness of the materials and that phase mixing at intermediate hard segment compositions produces softer materials. Upon yielding, PUU developed large plasticity associated to the nature of soft segments. At longer strains, PUU presented strain-induced crystallization related both to soft segments alignment and crystallization, leading to strong and tough materials, especially with high hard segment content compositions. Despite the hydrophobicity of the soft segments, the PUU with 65 wt% hard segment content was dispersable in water after quaternization with acetic acid. The high amount of urea groups in this quaternized PUU makes one think of these types of polymers as promising water soluble environmentally friendly strong adhesives, coatings, or water soluble polymeric electrolites.     

Dynamic light scattering study of the dynamics of a gelled polymeric micellar system

The dynamics of the E(92)B(18)/water system are studied by dynamic light scattering (DLS) in the liquid, soft gel, and hard gel phases. Both the liquid and the soft gel phases are micellar phases, although the structural order is higher in the soft gel phase than in the liquid phase. The hard gel phase corresponds to a face-centered cubic arrangement of micelles. DLS results show that the dilute liquid phase is characterized by a single characteristic time tau(1) associated with the diffusion of the micelles. In addition, a second characteristic time tau(2) associated with the presence of micellar clusters in the system is identified in the concentrated liquid and in the soft gel phases. According to these results, DLS suggests that the structure of the soft gel phase comprises micellar clusters coexisting with micellar fluid, in good agreement with hypotheses from our previous work. The dynamics of the system slows down as the hard gel phase is approached and a plateau is observed in the DLS correlation function. The structure of the hard gel is "softened" upon increasing temperature and/or decreasing concentration.     

Spectroscopic linear dichroism FT-IR studies of synthetic spider silk

This work deals with the analysis of the orientation behavior of different segments of synthetic spider silk samples containing hard and soft segments. Two different types of spider silk were examined, one with an aliphatic hard segment (hexamethylene-diisocyanate) and an amorphous soft segment (polytetramethylene oxide) (A40) and the other with an aromatic hard segment (4,4′-methylene bisphenyl diisocyanate) and a semicrystalline soft segment (polyethylene oxide-polypropylene oxide- polyethylene oxide) (A143). In order to observe the orientation behavior of the hard and the soft segments it was necessary to define marker bands. While for both samples the chosen marker bands for the hard segments were the same, the marker bands for the soft segments were different. FT-IR spectra were recorded while strain was applied to the material at the same time. Two parameters, the dichroic ratio R and the order Parameter f were used to evaluate the behavior of these materials under conditions of strain. It was found that sample A143 broke at a strain level of 37,5 %, while sample A40 showed a high dynamic range up to a strain level of 307 %.     

聚酯-聚酯多嵌段共聚物序列结构研究

利用对苯二甲酸乙二酯-己内酯多嵌段共聚物质子谱中各官能团的特征共振吸收峰计算证明两种吸收强度关系式反映了软链段和硬链段中相应官能团的数量关系,从而进一步肯定了所提出的链化学结构,在此基础上又直接利用各种官能团对其质子谱中特征吸收峰的强度贡献,计算得到多嵌段共聚物中软硬链段数,软硬链段平均长度,分子量和硬链段重量百分数的表示式。本文最后一部分用三素组的几率计算方法对多嵌段共聚物的质子谱和~(13)C谱分析讨论,所得有关链结构的数量关系是合理的,进一步证实了质子谱的直接计算法。     

The first bis(phosphine) monoxide (BPMO) complexes of copper(I)

Copper(I) complexes of bis(phosphine) monoxide ligands, bis(diphenylphosphino)ethane monoxide (dppeo) and bis(diphenylphosphino)methane monoxide (dppmo) have been prepared and characterized. One of the complexes with dppeo was characterized by X-ray crystal structure analysis confirming Cu(I) coordination to hard and soft donors. The stability of these complexes in solution was probed via spectroscopic and electrochemical studies. Copper(I) is more readily oxidized in the presence of the hard O donor ligands. In solution, they readily exchange the hard donor O, for soft ligands. Although copper(I) prefers soft ligands and is more stable towards oxidation in their presence, it coordinates to hard donors when there is electrostatic or an entropy driven advantage.     

Study of the drying behavior of model latex blends during film formation: influence of carboxyl groups

Latex blending is a strategy used to eliminate volatile organic compounds from latex coatings formulations. This paper focuses on the study of the drying kinetics of model hard/soft latex blends and the influence of the presence of carboxyl groups on these particles as well as the extent of neutralization of the carboxyl groups with different bases. The model latex blend was comprised of clean, well‐defined polystyrene hard and poly(n‐butyl methacrylate‐co‐n‐butyl acrylate) soft latex particles with monodisperse particle sizes, homogeneous copolymer composition, and independent control of particle size and carboxyl group content. Drying models are discussed. It was found that the presence of carboxyl groups in the latex particles retarded the drying rate of the model latex blends. When the carboxyl groups present in the latex blends with low carboxyl group coverage on polystyrene particles were neutralized by using ammonium hydroxide or sodium hydroxide, the drying rate increased. When the carboxyl groups present in the latex blends with a high carboxyl group coverage on polystyrene particles were neutralized by sodium hydroxide, potassium hydroxide, or cesium hydroxide, the drying rate first decreased and then increased as the extent of the neutralization increased. However, the neutralization of these carboxyl groups with ammonium hydroxide increased the drying rate of the latex blends within a broad range of neutralization conditions (from 0 to 100%). A cluster model was proposed to explain these phenomena.     

Substituent effects in acid-catalyzed hydration of alkenes, measured under consistent reaction conditions

A set of convenient conditions for the title reaction is used to determine directly relative reactivities of alkenes with widely-varying steric requirements. Previous determinations did not use one set of conditions for all alkenes, but developed parameters in order to compare alkene reaction rates run in different solvents and in different concentrations; such an indirect reactivity comparison can introduce errors. Relative rates established under this common set of reaction conditions are compared to those previously calculated by using correction parameters. Comparison reveals that the approximate method overestimated effects of some groups attached to CC, such as methyl and chloro.     

Cationic gel-phase liposomes with "decorated" anionic SPIO nanoparticles: morphology, colloidal, and bilayer properties

The assembly and complexation of oppositely charged colloids are important phenomena in many natural and synthetic processes. Liposome-nanoparticle assemblies (LNAs) represent an interesting hybrid system that combines "soft" and "hard" colloidal materials. This work describes the formation and characterization of gel-phase LNAs formed by the binding of anionic superparamagnetic iron oxide (SPIO) nanoparticles to cationic dipalmitoylphosphatidylcholine (DPPC)/dipalmitoyltrimethylammonium propane (DPTAP) liposomes. Particles were examined with hydrodynamic diameters below (16 nm) and above (30 nm) the cutoff reported for supported lipid bilayer formation. LNA formation with 16 nm particles was entropically driven and particles bound individually to yield "decorated" structures. In this case, increasing nanoparticle concentration yielded colloidal LNA aggregates and eventual charge inversion. In contrast, LNA formation with 30 nm particles was enthalpically driven, and the nanoparticles aggregated at the bilayer interface. These aggregates led to significant LNA aggregation and large bilayer sheets due to liposome rupture despite minimal charge screening of the liposome surface. In this case SLBs were present, but these structures were not dominant. Differences in LNA structure were also revealed through the lipid phase transition behavior. This work infers size-dependent nanoparticle binding and LNA formation mechanisms that can be used to tailor colloidal and bilayer properties. Analogies are made to polyelectrolyte patch charge heterogeneities and DNA complexation with cationic liposomes.     

New space warping method for the simulation of large-scale macromolecular conformational changes

A space warping method, facilitating the modeling of large-scale conformational changes in mesoscopic systems, is presented. The method uses a set of "global (or collective) coordinates" that capture overall behavior, in conjunction with the set of atomic coordinates. Application of the space warping method to energy minimization is discussed. Several simulations where the method is used to determine the energy minimizing structures of simple central force systems are analyzed. Comparing the results and behavior of the space warping method to simulations involving atomic coordinates only, it is found that the space warping method scales better with system size and also finds lower minima when the potential energy surface has multiple minima. It is shown that the transformation of [Ala16]+ in vacuo from linear to globular is captured efficiently using the space warping method.     

Self‐assembly and morphology of polydimethylsiloxane supramolecular thermoplastic elastomers

Functionalization of polydimethylsiloxanes (PDMS) polymers with hydrogen‐bonding ureidopyrimidinone (UPy) groups leads to supramolecular thermoplastic elastomers. In previous studies, no lateral stacking of UPy dimers was observed in UPy‐functionalized polymers, unless additional urethane or urea groups were built into the hard block. However, we have shown that when PDMS is used as the soft block, this lateral aggregation of UPy dimers does take place, since long fibers could be observed in the atomic force microscopy (AFM) phase image. Also in bulk, the presence of these interactions was proven by oscillatory shear experiments. We attribute this aggregation to the incompatibility of soft block and hard block, leading to phase separation. Moreover, we have shown that additional urethane or urea groups in the hard block do lead to materials with more fibers and higher melting points. For the UPy‐urea functionalized PDMS even single fibers are observed with AFM when dropcasted from a very diluted solution. When the length of the soft block is increased, the morphology changes from fibrous to spherical. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 3877–3885, 2008     

Preparation and characterization of waterborne poly(urethane urea) with well‐defined hard segments

A series of polyester‐based poly(urethane urea) (PUU) aqueous dispersions with well‐defined hard segments were prepared from polyester polyol, 4,4′‐diphenylmethane diisocyanate, dimethylolpropionic acid, 1,4‐butanediol, isophorone diisocyanate, and ethylenediamine. These anionic‐type aqueous dispersions had good dispersity in water and were stable at the ambient temperature for more than 1 year. For these aqueous dispersions, the particle size decreased as the hard‐segment content increased, and the polydispersity index was very narrow (<1.10). Films prepared with the PUU aqueous dispersions exhibited excellent waterproof performance: the amount of water absorption was as low as 5.0 wt %, and the contact angle of water on the surface of this kind of film was as high as 103° (this led to a hydrophobic surface). The water‐resistant property of these waterborne PUU films could be well correlated with some crystallites and ordered structures of the well‐defined hard segments formed by hydrogen bonding between the urethane/urethane groups and urethane/ester groups, as well as the degree of microphase separation between the hard and soft segments in the PUU systems. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2606–2614, 2005     

Evolved gas analysis (EGA) in TG and DSC with single photon ionisation mass spectrometry (SPI-MS): molecular organic signatures from pyrolysis of soft and hard wood,coal, crude oil and ABS polymer

A combined thermogravimetry/differential scanning calorimetry device (TG/DSC) was coupled to single photon ionisation mass spectrometry (SPI-MS) for evolved gas analysis (EGA). Single photon ionisation (SPI) was performed with a new type of VUV light source, the so called electron beam pumped rare gas excimer lamp (EBEL). SPI does not fragment molecules upon the ionisation process. Thus the molecular mass signature of the evolving gases from thermal composition of carbonaceous material can be directly on-line recorded. In this work the thermo-analytical data and the SPI-MS information on the released organics is presented and discussed for various samples. Namely biomass (soft and hard wood), fossil fuel (crude oil and coal) as well as a complex polymer (ABS) are investigated. The general potential of hyphenating thermal analysis and soft photo ionisation mass spectrometry (EBEL-SPI-MS) for fundamental and applied research and material analysis is discussed.     

卤化物中化学键的稳定度与硬软酸的定量分类

本文提出卤化物化学键的稳定度的概念,用于衡量卤化物化学键的稳定性。给出了键稳定度公式S_(AB)=E_(AE)/(r_(AB)|x_A—x_B|),S_(AB)为键稳定度,E_(AB)为键能,r_(AB)为键长,x_A和x_B为两原子的电负性。卤化物建稳定度的物理意义是:在平衡状态下,卤化物单键上两原子的单位电负性差、单位键长的键能。用公式计算了52个金属离子卤化物的键稳定度,得到260个数据,用于硬软酸的定量分类。结果表明,用其中的(S_F—S_1)值能有效地把硬酸、交界酸、软酸分开,S_F—S_I>10为硬酸,-10Cl>Br>I,软酸的S值为F相似文献   

Complexing properties of ambidentate benzo-15-crown-5-substituted azomethine ligands

Crown-containing azomethines and their zinc complexes were prepared. Examination of their structure by ¹H and ⁷Li NMR and electronic spectroscopy showed that, in accordance with the concept of hard and soft acids and bases, the hard lithium cation coordinates to the crown ether fragment with the formation of mono-(Li) and binuclear (Li, Zn) complexes.