On topological form in structures

This paper begins with a review of the Euler relation for the polyhedra and presents the corresponding Schläfli relation in n, the polygonality, and p, the connectivity of the polyhedra. The use of ordered pairs as given by (n, p), the Schläfli symbols, to organize the mapping of the polyhedra and its extension into the two-dimensional (2D) and three-dimensional (3D) networks is described. The topological form index, represented by l, is introduced and is defined as the ratio of the polygonality, n, to the connectivity, p, in a structure, it is given by l = n/p. Next a discussion is given of establishing a conventional metric of length in order to compare topological properties of the polyhedra and networks in 2D and 3D. A fundamental structural metric is assumed for the polyhedra. The metric for the polyhedra is, in turn, used to establish a metric for tilings in the Euclidean plane. The metrics for the polyhedra and 2D plane are used to establish a metric for networks in 3D. Once the metrics have been established, a conjecture is introduced, based upon the metrics assumed, that the area of the elementary polygonal circuit in the polyhedra and 2D and 3D networks is proportional to a function of the topological form index, l, for these structures. Data of the form indexes and the corresponding elementary polygonal circuit areas, for a selection of polyhedra and 2D and 3D networks is tabulated, and the results of a least squares regression analysis of the data plotted in a Cartesian space are reported. From the regression analysis it is seen that a quadratic in l, the form index, successfully correlates with the corresponding elementary polygonal circuit area data of the polyhedra and 2D and 3D networks. A brief discussion of the evident rigorousness of the Schläfli indexes (n, p) over all the polyhedra and 2D and 3D networks, based upon the correlation of the topological form index with elementary polygonal circuit area in these structures, and the suggestion that an Euler–Schläfli relation for the 2D and 3D networks, is possible, in terms of the Schläfli indexes, concludes the paper.     

食品中维生素D与25-羟基维生素D检测技术及含量分布研究进展

维生素D是一种对于维持人体健康具有重要作用的脂溶性维生素,25-羟基维生素D是其在人体内循环和存储的主要形式。食品中维生素D和25-羟基维生素D前处理的通常采用碱皂化、有机溶剂提取、固相萃取或者半制备色谱净化;其测定方法多为放射免疫法和液相色谱法。液相色谱串联质谱凭借高灵敏度和高准确度,目前在食品中维生素D和25-羟基维生素D测定中发挥重要作用。近年来二维液相色谱和超高效超临界流体色谱由于其强大的分离能力,在食品中维生素D和25-羟基维生素D的分析中表现出强大的潜力。该文综述了近年来食品中维生素D和25-羟基维生素D的检测方法及二者在动物食品和植物食品中的含量分布研究,以期为建立适合不同食物样品的测定方法,指导居民合理膳食,进行膳食摄入量评估等研究工作提供参考。     

ReverseScreen3D: a structure-based ligand matching method to identify protein targets

Ligand promiscuity, which is now recognized as an extremely common phenomenon, is a major underlying cause of drug toxicity. We have developed a new reverse virtual screening (VS) method called ReverseScreen3D, which can be used to predict the potential protein targets of a query compound of interest. The method uses a 2D fingerprint-based method to select a ligand template from each unique binding site of each protein within a target database. The target database contains only the structurally determined bioactive conformations of known ligands. The 2D comparison is followed by a 3D structural comparison to the selected query ligand using a geometric matching method, in order to prioritize each target binding site in the database. We have evaluated the performance of the ReverseScreen2D and 3D methods using a diverse set of small molecule protein inhibitors known to have multiple targets, and have shown that they are able to provide a highly significant enrichment of true targets in the database. Furthermore, we have shown that the 3D structural comparison improves early enrichment when compared with the 2D method alone, and that the 3D method performs well even in the absence of 2D similarity to the template ligands. By carrying out further experimental screening on the prioritized list of targets, it may be possible to determine the potential targets of a new compound or determine the off-targets of an existing drug. The ReverseScreen3D method has been incorporated into a Web server, which is freely available at http://www.modelling.leeds.ac.uk/ReverseScreen3D .     

二代树状碳硅烷液晶研究I.端基含36个丁氧基偶氮苯介晶基元

用发散法合成周边含36个丁氧基偶氮苯介晶基元（M5）端基新的二代树状碳硅 烷液晶（D_2），并用元素分析，氢谱，激光质谱，红外，紫外，偏光显微镜，DSC和WAXD法表 征D2为向列相，与M5相同，二代树状物相态由介晶基定．D2液晶态相行为是 K85N107I103N69K，其熔点比M5降低27-41℃，清亮点比M5降低17-18宽10-23℃．二 代碳硅烷（D2）与一代碳硅烷（D1）相比熔点增加2-3℃，清亮点降低26-29℃，液 晶态温区减少℃．在二代树状物中观察到S＝＋3／2的高强向错．     

Active site acidic residues and structural analysis of modelled human aromatase: A potential drug target for breast cancer

Summary This study sheds new light on the role of acidic residues present in the active site cavity of human aromatase. Eight acidic residues (E129, D222, E245, E302, D309, E379, D380 and D476) lining the cavity are identified and studied using comparative modeling, docking, molecular dynamics as well as statistical techniques. The structural environment of these acidic residues is studied to assess the stability of the corresponding carboxylate anions. Results indicate that the environment of the residues E245, E302 and D222 is most suitable for carboxylate ion formation in the uncomplexed form. However, the stability of D309, D222 and D476 anions is seen to increase on complexation to steroidal substrates. In particular, the interaction between D309 and T310, which assists proton transfer, is found to be formed following androgen/nor-androgen complexation. The residue D309 is found to be clamped in the presence of substrate which is not observed in the case of the other residues although they exhibit changes in properties following substrate binding. Information entropic analysis indicates that the residues D309, D222 and D476 have more conformational flexibility compared to E302 and E245 prior to substrate binding. Interaction similar to that between D476 and D309, which is expected to assist androgen aromatization, is proposed between E302 and E245. The inhibition of aromatase activity by 4-hydroxy androstenedione (formestane) is attributed to a critical hydrogen bond formation between the hydroxy moiety and T310/D309 as well as the large distance from D476. The results corroborate well with earlier site directed mutagenesis studies.     

Density functional theory calculation of (29)Si NMR chemical shifts of organosiloxanes

Density functional theory at the B3LYP/6-311++G(d,p) level is applied to calculate the (29)Si NMR chemical shifts of a variety of organosiloxane moieties including monomers or precursors for polymerization and representative segments of organosiloxane polymers or thin films. The calculated shifts of two linear dimethylsiloxane compounds, hexamethylcyclotrisiloxane (D3) and octamethylcyclotetrasiloxane (D4), compare well with their known values, having an average error of 3.4 ppm. The same method is applied to structures believed to occur in organosilicate glass thin films deposited using hot-filament chemical vapor deposition (HFCVD) from D3 and D4. The chemical shift at -15 ppm is identified as a cross-linking Si-Si bond between two strained D groups and has not previously been reported. Retention of the strained ringed structure in HFCVD films deposited from D3 is confirmed. The rings are bonded to the matrix through either Si-O or Si-Si bonds, with the latter only becoming prevalent when higher filament temperatures are employed. The strained ring structure is also observed in films deposited from a precursor with a larger unstrained ring structure, D4. These observations suggest that the known gas-phase conversion pathways of D4 to D3 and dimethylsilanone as well as the methyl abstraction reaction from D3 operate in the HFCVD reaction chemistry.     

Energy disposal during desorption of D2 from the surface and subsurface region of Ni(111)

The recombination of surface and subsurface D atoms on Ni(111) has been studied using resonance-enhanced multiphoton ionisation (REMPI) to measure the internal state and translational energy distributions of the desorbing product. By detecting D2 formed during temperature-programmed desorption we were able to examine the reaction between subsurface and surface D atoms, and the recombination of two D atoms chemisorbed on the surface. Translational energy distributions for D2 formed by recombination of surface D are very sensitive to coverage. Desorption from a low coverage surface produced a translational energy release of 2.6 kT, but a thermal rotational distribution, reflecting an entrance channel barrier to dissociative chemisorption on the clean Ni(111) surface. Sticking probabilities predicted from detailed balance are consistent with molecular beam adsorption measurements. Desorption from D coverages above 0.5 ML resulted in a sub-thermal energy release, desorption being mediated by a molecular precursor state with D2 dissociation occurring via a non-activated, trapping-dissociation channel. In contrast, the reaction of subsurface D produces translationally hot D2, with a mean energy approaching 8 kTs at 180 K. This is consistent with the energetics for direct recombination of a chemisorbed D atom with a metastable subsurface D atom, which overcomes an activation barrier to resurface of between 0.35 and 0.47 eV depending on D concentration. The energy release decreases at higher temperature, probably as a result of a reduction in the energy of resurfacing D as the subsurface D concentration drops. This low energy component is attributed to accommodation of resurfacing D which is unable to react directly, followed by slow thermal desorption via the high coverage, surface D recombination channel. No internal rotational or vibration excitation was found in D2 formed by reaction of subsurface D.     

The shape of a flexible polymer in a cylindrical pore

We calculate the mean end-to-end distance R of a self-avoiding polymer encapsulated in an infinitely long cylinder with radius D. A self-consistent perturbation theory is used to calculate R as a function of D for impenetrable hard walls and soft walls. In both cases, R obeys the predicted scaling behavior in the limit of large and small D. The crossover from the three-dimensional behavior (D --> infinity) to the fully stretched one-dimensional case (D --> 0) is nonmonotonic. The minimum value of R is found at D approximately 0.46R(F), where R(F) is the Flory radius of R at D --> infinity. The results for soft walls map onto the hard wall case with a larger cylinder radius.     

Scaled second-order perturbation corrections to configuration interaction singles: efficient and reliable excitation energy methods

Two modifications of the perturbative doubles correction to configuration interaction with single substitutions (CIS(D)) are suggested, which are excited state analogues of ground state scaled second-order M?ller-Plesset (MP2) methods. The first approach employs two parameters to scale the two spin components of the direct term of CIS(D), starting from the two-parameter spin-component scaled (SCS) MP2 ground state, and is termed SCS-CIS(D). An efficient resolution-of-the-identity (RI) implementation of this approach is described. The second approach employs a single parameter to scale only the opposite-spin direct term of CIS(D), starting from the one-parameter scaled opposite-spin (SOS) MP2 ground state, and is called SOS-CIS(D). By utilizing auxiliary basis expansions and a Laplace transform, a fourth-order algorithm for SOS-CIS(D) is described and implemented. The parameters that describe SCS-CIS(D) and SOS-CIS(D) are optimized based on a training set that includes valence excitations of various organic molecules and Rydberg transitions of water and ammonia, and they significantly improve upon CIS(D) itself. The accuracy of the two methods is found to be comparable. This arises from a strong correlation between the same-spin and the opposite-spin portions of the excitation energy terms. The methods are successfully applied to the zincbacteriochlorin-bacteriochlorin charge-transfer transition, for which time-dependent density functional theory, with presently available exchange-correlation functionals, is known to fail. The methods are also successfully applied to describe various electronic transitions outside of the training set. The efficiency of the SOS-CIS(D) and the auxiliary basis implementation of CIS(D) and SCS-CIS(D) are confirmed with a series of timing tests.     

Melting behavior of an idealized membrane model

The melting behavior of an idealized model giving rise to two-dimensional (2D) structures at low temperature and low density is investigated by Monte Carlo simulations. The system is made of particles carrying a spin of constant length and variable orientation, whose potential energy is the sum of a repulsive spherical pair interaction, and of a spin-spin contribution, reminiscent of but essentially different from the electrostatic dipole-dipole interaction. The simulation results show that the model phase diagram is determined by the interplay of a ferro- to paraelectric transition in the spin part and of the solid to fluid transition found in simple pair-potential models. The 2D solid melts into a three-dimensional (3D) fluid when the spin-spin interaction is weak. Strong spin-spin interactions give rise to two transitions, the first one corresponding to the melting of the 2D solid into a 2D fluid, and the second one corresponding to the crossover from a 2D to a 3D fluid. The fluid phase stable in between these two transitions provides a model for the liquid state arising in organic and biological membranes across their main transition.     

Two-dimensional molecular layers: interplay of H-bonding and van der waals interactions in the self-assembly of N,N'-dialkylsulfamides

N,N'-Dialkylsulfamide molecules assemble into solid-state structures consisting of 2D layers. The 2D layers are based on a hydrogen-bonded network of the sulfamide groups and the close-packing of alkyl groups on both sides of the 2D H-bonded network. The thickness of a 2D layer is proportional to the size of the alkyl substituents. The interplay of H-bonding and van der Waals interactions leads to stable 2D layers that pack into 3D structures.     

The dimensionality of chromatographic separations

The box-counting or capacity dimension algorithm, known from the fractal mathematics literature, is used to measure the dimensionality D of chromatographic separation techniques for any number of dimensions. It is shown that D has limit properties that match Giddings' sample dimensionality s. D values are shown to be sensitive to the uniformity of peak spacing. A number of examples are given where D is calculated for various limits in one- and two-dimensional separations and for heart-cutting separations. The use of D as a quantitative measure of multidimensional orthogonality is suggested as D, due to the scale-free nature, is not dependent on the effective separation area. The connection to statistical peak overlap theory is discussed.     

Interactions of D2O with methane and fluoromethane surfaces

TOF-SIMS is used to investigate the interactions between D2O and hydrophobic molecules, such as CH4, CH3F, CH2F2, CHF3, and CF4, at cryogenic temperatures (15 K). By irradiation with a 1.5-keV He+ beam, the D(+)(D2O)n ions are ejected efficiently from the D2O nanoclusters physisorbed on the CF4 layer due to Coulomb explosion: the ion yields are by about two orders of magnitude higher than those from a thick D2O layer via the kinetic sputtering. The D(+)(D2O)n yields decrease on the CHnF(4-n) layer with increasing the number of the C-H group. This is because the Coulombic fission is quenched due to the delocalization of valence holes through the C-H...H-C and C-H...D2O contacts. A pure D2O film is hardly grown on the CH4 layer as a consequence of intermixing whereas the D2O molecules basically adsorb on the surfaces of fluoromethanes, suggesting the attractive (water-repellent) interactions in the C-H...D2O (C-F...D2O) contacts. The C-H...O bond behaves like a conventional O-H...O hydrogen bond as far as the collision-induced proton transfer reaction is concerned.     

Studies of translational diffusion in the smectic A phase of a Gay-Berne mesogen using molecular dynamics computer simulation

Molecular dynamics computer simulations are used to determine the self-diffusion coefficients for a Gay-Berne model mesogen GB (4.4,20,1,1) in the isotropic, nematic and smectic A phases along two isobars. The values of the parallel and perpendicular diffusion coefficients, D(parallel) and D(perpendicular), are calculated and compared in the different phases. For the phase sequence isotropic-smectic A, D(perpendicular)*> or =D(parallel)* over the whole smectic A range with the ratio D(parallel)*/D(perpendicular)* decreasing with decreasing temperature. At a higher pressure, a nematic phase is observed between these two phases and we find that D(parallel)*>D(perpendicular)* throughout the nematic region and the inequality D(parallel)*>D(perpendicular)* remains on entering the smectic A phase. However, the ratio D(parallel)*/D(perpendicular)* decreases with decreasing temperature within the smectic A range and eventually this ratio inverts such that D(perpendicular)*>D(parallel)* at low temperatures. The temperature dependence of the parallel diffusion coefficient in the smectic A phase for this model mesogen is compared to that predicted by a theoretical model for diffusion subject to a cosine potential.     

Groundstate dispersion interaction between pi-conjugated polymers

The line-dipole approximation is used to investigate the scaling of the groundstate dispersion interaction, EW, between parallel conjugated polymers of length L and transverse separation D. Both a second-order perturbation theory calculation using the Mott-Wannier exciton model of excited states and a semiclassical analysis of distributed dipoles indicate that at L approximately D there is a crossover from the point-dipole approximation result of EW approximately L2/D6 for LD.     

Synthesis, structure, and magnetism of three azido-bridged Co2+ compounds with a flexible coligand 1,2-(tetrazole-1-yl)ethane

By utilizing suitable coligand endi (1,2-(tetrazole-1-yl)ethane)) with variable conformations, we synthesized three new azido-bridged Co(2+) compounds with molecular formulas Co(endi)(N3)2 (1, 3) and Co(endi)2(N3)2 (2) by tuning the stoichiometric ratio of ligand/metal and the concentration of the solution. All of the compounds have been characterized structurally and magnetically. In all three structures, the azide ions use the end-to-end mode to link the Co(2+) centers to the 1D chain (1) and 2D (4,4) layers (2 and 3). The endi coligands adopt a trans conformation in compound 1 and a gauche conformation in compounds 2 and 3. Linked by bridging endi, the 1D chains in compound 1 and 2D layers in compound 3 are extended, resulting in the final 2D layer for compound 1 and the 3D network for compound 3, whereas in compound 2, the endi acts as only a terminal ligand to separate the 2D layers. Compound 1 consists of dual end-to-end azido-bridged 1D Co(2+) chains that are linked by trans endi into a 2D layer and are further extended to a 3D framework through H bonds. Compound 2 is a 2D (4,4) layer that is connected by end-to-end azido ions. The gauche endi ligands act as terminal ligands to separate the neighboring layers thoroughly. Compound 3 has a (4,4) 2D layer that is similar to that of compound 2, and these layers are further extended to a 3D network through gauche endi. The magnetic investigation shows that compound 3 is antiferromagnetically coupled and compound 2 is a weak ferromagnet with a critical temperature of 22 K, which is quite high compared with that of the previously reported 2D azido-bridged Co(2+) compounds.     

Time-dependent diffusion coefficients in periodic porous materials

We derive an approximate solution for the Laplace transform of the time-dependent diffusion coefficient, D(t), of a molecule diffusing in a periodic porous material. In our model, the material is represented by a simple cubic lattice of identical cubic cavities filled with a solvent and connected by small circular apertures in otherwise reflecting cavity walls, the thickness of which can be neglected. The solution describes the decrease of D(t) from its initial value, D(0) = D, where D is the diffusion constant in the free solvent, to its asymptotic value, D(infinity) = D(eff), which is much smaller than D. A simple heuristic formula for the mean-squared displacement of the diffusing molecule is suggested. The theoretically predicted results are in good agreement with the data obtained from Brownian dynamics simulations.     

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.     

A New Interpretation of Apparent Induction Period in Ring‐Opening Polymerization of Octamethylcyclotetrasiloxane in Acid Emulsion

A following new interpretation of apparent induction period is proposed considering the experimental results obtained: octamethylcyclotetrasiloxane (D4) is activated by the reaction with acid to generate an activated derivative (A4). A4 reacts with D4 to generate A8, an active species containing eight dimethylsiloxane units. A8 backbites to generate mostly A4 and D4, which causes retardation in polymerization, but occasionally to form A3 and D5. A3 is highly reactive, and when the concentration of A3 exceeds a certain limit, much Ai where i is large enough is formed and promotes fast growth of chain at the interfacial area due to high concentration of D4. The interpretation assumes that A3 accelerates growth of chain faster than other species, and that A8 tends to backbite rather than grow. The interpretation is supported by the experimental results of polymerization conducted with D4 and D3, or D5 and D3 charged.