A method for creating a non-equilibrium NT(P1-P2) ensemble in molecular dynamics simulation

A method is proposed for creating a non-equilibrium ensemble with a constant number of molecules, constant temperature and constant pressures with different target values in two reservoirs [referred to as NT(P(1)-P(2)) ensemble] that are connected by a finite length nanopore. This method includes two steps. The first step places a partition between the two reservoirs and then creates a static pressure field and a proper system volume by using two self-adjusting plates on which two external forces/pressures with different target values are exerted. The second step removes the partition and the two self-adjusting plates and the pressure difference between the two reservoirs is maintained by a "pump" designed to simultaneously create a periodic boundary condition between the two reservoirs and supply the necessary force (work) to a subset of molecules for a steady state flow. To examine this method, several cases using liquid argon with a truncated and shift Lennard-Jones potential under different target pressures and pump sizes were studied. Results show that the method proposed in this paper works well. In addition, the method proposed in this paper was compared with the other external force field methods. The results show that as long as the external force is applied to a restricted set of molecules away from the channel a constant pressure difference between two reservoirs is maintained. The advantage of the algorithm proposed here also sets the absolute pressures with different target levels in two reservoirs instead of it being arbitrary. Studies show that the fluid flow rate or permeability through a nanopore depends not only on the pressure difference between two reservoirs, but also on the absolute pressures in two reservoirs.     

Interaction of Adjacent Amino Acids

Ramachandran plots display the dihedral angles of a single protein residue. We propose a crossed torsion angle plot called SSY‐plot between two neighboring amino acids and demonstrate that a special coherence motion can exist between some very special amino acid pairs leading to spontaneous unusual structures. A 6mer was extracted from a BBA polypeptide chain which in this plot shows two diagonal domains for the Ser‐Arg pair after some induction time. Other amino acid pairs in general do not show this kind of split domain. This shows that a special pair is required for stabilizing two distinct native structures in protein folding. We suggest that the existence of these two domains corresponds to a bifurcation between two different protein structures and that the special pair is the key to producing these two structures. These two different structures are produced spontaneously without an external agent.     

Computer-assisted optimization of pesticides separation by two-dimensional high-performance thin-layer chromatography

Summary A computer-assisted method is presented for optimization of two mobile phase selection for separation of a mixture of eight pesticides in two-dimensional TLC. Optimization of the separation over the experimental region is based on two special polynomial estimations from preliminary runs of two groups. Using D (distance of two spots) as the selection criterion with a two factor statistical scanning technique excellent agreement is obtained between predicted and experimental results.     

MOLECULAR RIBBONS COMPOSED OF CALCIUM(II) IONS BRIDGED BY CARBOXYLATE AND WATER OXYGEN ATOMS IN THE CRYSTALS OF Ca(II) COMPLEX WITH 5-METHYLPYRAZINE-2-CARBOXYLATE LIGANDS

Abstract

Crystals of monoaquo(μ-5-methylpyrazine-2-carboxylato-N,O,O′), (5-methylpyrazine-2-carboxyato-N,O)di(μ-aquo-O,O)calcium(II) contain molecular ribbons in which two adjacent calcium(II) ions are bridged by two bidentate oxygen atoms donated by two ligand molecules on one side and bidentate oxygen atoms of two water molecules on the other. The coordination polyhedron around the Ca(II) ion is a pentagonal bipyramid. The vertices of its pentagonal base are composed of two bridging water oxygen atoms, two carboxylate oxygen atoms of two ligand molecules and a nitrogen atom belonging to one of the bridging ligands. A coordinated water molecule constitutes the apex of the pyramid on one side of the base, while the N, O bonding moiety of a second ligand molecule makes two apices on the other side of the base. The ribbons are held together by a system of hydrogen bonds.     

Formation of molecular ladder elements with macrocyclic platforms via linear bifunctional ligands

Reaction between 4-aminopyridine and a dinuclear zinc(II) component of a Robson macrocyclic ligand has resulted in the formation of a molecular ladder element motif. X-ray single crystal structural analysis indicates that two pyridine rings are assembled at the same direction of the macrocycle, which are placed in a nearly parallel way via pi-pi interactions, forming a concavity structure with a macrocyclic base. It is significantly noted that one hydrogen-bond cycle generated from hydrogen atoms of two amino groups with two perchlorate anions has sustained such an assembly of two 4-aminopyridine species to stand in a face to face pattern through a weak molecular interaction on the macrocyclic platform by one-end coordination bonding. The self-assembly of 4-carboxylic pyridine acid and the same macrocyclic component in the presence of sodium hydroxide has yielded an interesting wheel-like complex. Two macrocyclic dinuclear zinc(II) components have been linked through coordination bonding with two pyridine derivatives situated on the same direction of a macrocycle. X-ray structural results suggest that the compound has a unique sandwich-like structure consisting of two macrocyclic covers with two inversely positioned bridging pyridine carboxylic groups in the middle.     

吸附树脂和活性炭对气体中苯的吸附研究

采用了动态吸附实验方法研究了吸附树脂NDA-201和椰壳型活性炭C1对苯蒸汽的吸附行为.对吸附平衡数据采用Dubinill-Astakov方程进行了拟合分析,并根据吸附剂孔结构特征探讨了吸附机理.实验结果表明,两种吸附剂的苯吸附等温线存在交叉现象,对高浓度苯蒸汽吸附治理可采用NDA-201树脂,低浓度则采用椰壳型活性炭C1;Dubinin-Astakov方程能用来对两种吸附剂的等温线进行拟合,表明吸附剂的微孔区域对吸附起着重要作用.微孔体积计算值的比较和特征曲线叠合的程度说明了.Polanyi吸附势理论更适合于描述椰壳型活性炭C1对苯的吸附,这可能是由于椰壳型活性炭C1的孔分布集中于微孔区,而NDA-201树脂除了微孔外还有一定量的中孔和大孔.     

Syntheses and crystal structures of 3-tert-butyl-4-cyano pyrazole and its complexes with cobalt(II), manganese(II), and copper(II)

A new pyrazole ligand, 3-tert-butyl-4-cyano pyrazole (Hpz^t-Bu,4CN), has been synthesized. The crystal structure of this pyrazole, along with the syntheses and crystal structures of Co, Cu, and Mn complexes of this ligand, are reported. The uncoordinated pyrazole shows the formation of a cyclic hydrogen-bound dimer. The Co complex is octahedral, with four coordinated pyrazoles and two coordinated waters. The Mn complex is octahedral, with two coordinated pyrazoles, two coordinated triflates and two coordinated waters. A hydrogen bonding network involving the triflates and waters results in a linear double chain of Mn complexes. The Cu complex has two coordinated pyrazoles and two coordinated chlorides in a slightly distorted square-planar geometry, with a long bond to the cyano N atom of a neighboring Cu complex, forming a pseudodimer.     

二维泡沫稳定性与拓扑学性质的关系研究

研究了二维泡沫形成、进化及其拓扑学性质随时间的变化关系以及影响其稳定性的因素.探索了二维泡沫初始有序化的气泡进化和完全无序化的气泡进化的两种过程,并分析在无序化气泡的进化过程中,平均气泡面积随时间的变化呈现出α=1.5的幂指数关系,以及该指数大于VonNeumann定律的时间指数的可能原因.讨论了气泡的边数分布及其二阶矩.     

Dendrimer with rotaxane-like mechanical branching

[reaction: see text] A dendrimer wherein the branching points are mechanical in nature has been synthesized. It contains two identical covalently linked bis-dendrons and a core unit fused to two rings that encircle the two bis-dendrons. A "threading-followed-by-stoppering" approach is used in the template-directed synthesis of a precursor bis[2]rotaxane, which undergoes stopper exchange four times to yield the dendrimer in which the two bis-dendrons act as stoppers within the two [2]rotaxane subunits.     

Synthesis of an S-linked glycopeptide analog derived from human Tamm-Horsfall glycoprotein

Direct base catalyzed S-glycosylation of a cysteine and a homocysteine containing peptide with O-acetyl protected bromides in DMF-water solution furnished two glycopeptide fragments. The two glycopeptide fragments were linked to the target glycopeptide with two S-glycosyl residues mimicking a part of Tamm-Horsfall glycoprotein.     

A Dipolar Anthracene Dye: Synthesis,Optical Properties and Two‐photon Tissue Imaging

Two‐photon microscopy is a powerful tool for studying biological systems. In search of novel two‐photon absorbing dyes for bioimaging, we synthesized a new anthracene‐based dipolar dye (anthradan) and evaluated its two‐photon absorbing and imaging properties. The new anthradan, 9,10‐bis(o‐dimethoxy‐phenyl)‐anthradan, absorbs and emits at longer wavelengths than acedan, a well‐known two‐photon absorbing dye. It is also stable under two‐photon excitation conditions and biocompatible, and thus used for two‐photon imaging of mouse organ tissues to show bright, near‐red fluorescence along with negligible autofluorescence. Such an anthradan thus holds promise as a new class of two‐photon absorbing dyes for the development of fluorescent probes and tags for biological systems.     

Carbonic acid: from polyamorphism to polymorphism

Layers of glassy methanolic (aqueous) solutions of KHCO3 and HCl were deposited sequentially at 78 K on a CsI window, and their reaction on heating in vacuo in steps from 78 to 230 K was followed by Fourier transform infrared (FTIR) spectroscopy. After removal of solvent and excess HCl, IR spectra revealed formation of two distinct states of amorphous carbonic acid (H2CO3), depending on whether KHCO3 and HCl had been dissolved in methanol or in water, and of their phase transition to either crystalline alpha- or beta-H2CO3. The main spectral features in the IR spectra of alpha- and beta-H2CO3 are observable already in those of the two amorphous H2CO3 forms. This indicates that H-bond connectivity or conformational state in the two crystalline phases is on the whole already developed in the two amorphous forms. The amorphous nature of the precursors to the two crystalline polymorphs is confirmed using powder X-ray diffraction. These diffractograms also show that alpha- and beta-amorphous H2CO3 are two distinct structural states. The variety of structural motifs found within a few kJ/mol in a computational search for possible crystal structures provides a plausible rationalization for (a) the observation of more than one amorphous form and (b) the retention of the motif observed in the amorphous form in the corresponding crystalline form. The polyamorphism inferred for carbonic acid from our FTIR spectroscopic and powder X-ray diffraction studies is special since two different crystalline states are linked to two distinct amorphous states. We surmise that the two amorphous states of H2CO3 are connected by a first-order-like phase transition.     

萘氧乙酸及咪唑构筑的锌(Ⅱ)和铜(Ⅱ)配合物的水热合成、晶体结构及荧光性质

通过水热的方法合成得到2个由萘氧乙酸及咪唑配体构筑的配合物Zn(2-naph)₂(imi)₂ (1)和2Cu(2-naph)₂(imi)₂(H₂O)·Cu(2-naph)₂(imi)₂(H₂O) (2)(2-naph=2-naphthoxyacetate,imi=imidazole),它们的结构通过X射线晶体衍射、红外光谱和元素分析得到确定。在配合物1中,锌原子与来自不同2-萘氧乙酸配体中的2个羧酸氧原子和不同的咪唑分子中的2个氮原子形成了变形的四面体的几何构型。单个分子通过N-H…O氢键连接形成了一维链,然后在C-H…π弱作用下形成了三维结构。配合物2有2个独立的铜中心,它们有几乎相同的配位环境。每个铜中心都是变形的四方锥的配位构型。来自不同的2-萘氧乙酸配体中的2个羧酸氧原子和不同的咪唑分子中的2个氮原子形成了一个相对规则的四方锥赤道平面,配位水分子位于平面上方。配合物2的分子通过N-H…O和O-H…O氢键连接形成了二维结构。2个配合物的热稳定和固体荧光性质在本文中也得到了研究和讨论。     

Balancing framework densification with charged, halogen-bonded-pi-conjugated linkages: [PPh4]2{[E-TTF-I2][Re6Se8(CN)6]} versus [PPh4]2[EDT-TTF-I]2{[EDT-TTF-I][Re6Se8(CN)6]}

The ionic character of a set of two redox linkages and strong, directional halogen bonding at the organic-inorganic interface compromise to produce two materials sharing a common two-dimensional net, eventually extended in a third dimension, although two of the six symmetrical halogen bond acceptors ultimately remain uninvolved as a result of charge densification.     

UV band Splitting of chromogenic azo-coupled calix[4]crown upon cation complexation

Calixcrown-6 compounds carrying a pair of phenylazo moieties on the upper rim and two OH groups, one OH group, and two OR groups on the lower rim have been prepared in both the cone and partial cone conformations. UV/vis spectral measurements showed a red shift upon the addition of Ca2+ to the calixcrown carrying two OH groups and a blue shift for the calixcrown carrying two OR groups. For the compounds with two OR groups on the lower rim and a fixed partial cone conformation, a blue shift caused by electrostatic interaction between the oxygen atoms of OR and the metal ion as well as a red shift caused by the pi-metal complexation between the rotated calix benzene and the metal ion were observed.     

Comparison of two methods of detection,determination, and library search of the substances present in gas chromatography—mass spectrometry data

A comparison is made of two different methods, LIANAL and MSSMET, for the analysis of a g.c.—m.s. data matrix for the purpose of detecting and determining the metabolic profiles of the substances present. The parameters of the methods and the profiles determined on two different data matrices are compared. The two methods agree in 92 out of a possible 103 instances as to the presence or absence of the 103 substances for which they both made determinations. Ratios of the metabolic profiles for the two samples are highly correlated (0.9954) for the two methods.     

Synthesis and Crystal Structure of a Novel 2-Fold Interpenetrating Three-dimensional Coordination Polymer, {[Co3(byip)2(bix)3(H20)2]·H2O}n

T The title coordination polymer including two crystallographically independent Co<'2+> ions is hydrothermally synthesized, in which the Co(1)<'2+> ion is four-coordinated by two carboxylate oxygen atoms from two different 5-(benzoic acid-4-yldiazenyl)isophthalate(byip<'3->)anions and two nitrogen atoms from two distinct 1,4-bis(imidazol-1-ylmethyl)benzene(bix)ligands displaying a tetrahedral geometry. The Co(2)<'2+> ion is six-coordinated by two water molecules at the apical positions, and two carboxylate oxygen atoms and two nitrogen atoms at the equatorial positions, affording a slightly distorted octahedron. Two Co(1)<'2+> and two Co(2)<'2+> ions are linked together by four byip<'3-> anions forming a 44-membered motif and these motifs are further arranged into a three-dimensional framework through bix ligands along the a axis with a larger channel(ca.22.70(A)×11.01(A)). Each individual network interpenetrates with the other identical network in a parallel fashion to generate a 2-fold interpenetrating array with the {6<'2>.8<'4>} {6<'3>}<,2> {6<'4>.8<'2>}<,2> topology.     

Synthesis and conformational analysis of azacyclophanes from l-tyrosine

The synthesis of a new azacyclophane formed by two l-tyrosine units joined by two methylene bridges is presented. The structural and conformational characteristics are briefly discussed. Spectroscopic and theoretical data reveal a syn structure with two intramolecular hydrogen bonds.     

吡啶-3-甲醛缩氨基硫脲合镍(Ⅱ)、锌(Ⅱ)配合物的合成、晶结构及生物活性

本文合成并表征了吡啶-3-甲醛缩氨基硫脲(HL)合镍(Ⅱ)、锌(Ⅱ)配合物.在配合物[NiL2(1)中,镍(Ⅱ)离子与来自2个脱氢配体的2个氮原子和2个硫原子配位.形成四配位的平面正方形构型.在配合物[Zn(HL)2(C2H5OH)2(H2O)2](NO3)2(2)中,锌(Ⅱ)离子与2个中性配体、2个乙醇分子和2个水分子配位,配位原子在锌(Ⅱ)离子周围形成畸变的八面体构型.通过荧光吸收法研究了配合物1、2与小牛胸腺DNA的作用机理.结果表明,这2个配合物均以插入形式进入DNA的碱基对.此外,还研究了配体及2个配合物对金黄色葡萄球菌、乙型溶血性链球菌、肺炎链球菌、炭疽杆菌的抗菌活性.结果表明,配体及配合物1对上述测试菌种无抑制作用.配合物2对前面3种有弱的抑菌作用.     

A novel parallel interpenetrating two‐dimensional (4,4) network: poly[[μ2‐1,4‐bis(imidazol‐1‐ylmethyl)benzene](μ2‐naphthalene‐1,4‐dicarboxylato)zinc(II)]

In the title coordination compound, [Zn(C₁₂H₆O₄)(C₁₄H₁₄N₄)]_n, the two Zn^II centers exhibit different coordination environments. One Zn^II center is four‐coordinated in a distorted tetrahedral environment surrounded by two carboxylate O atoms from two different naphthalene‐1,4‐dicarboxylate (1,4‐ndc) anions and two N atoms from two distinct 1,4‐bis(imidazol‐1‐ylmethyl)benzene (1,4‐bix) ligands. The coordination of the second Zn^II center comprises two N atoms from two different 1,4‐bix ligands and three carboxylate O atoms from two different 1,4‐ndc ligands in a highly distorted square‐pyramidal environment. The 1,4‐bix ligand and the 1,4‐ndc anion link adjacent Zn^II centers into a two‐dimensional four‐connected (4,4) network. The two (4,4) networks are interpenetrated in a parallel mode.