Three centered hydrogen bonds of the type C=O...H(N)...X-C in diphenyloxamide derivatives involving halogens and a rotating CF3 group: NMR, QTAIM, NCI and NBO studies

The existence of three centered C=O...H(N)...X-C hydrogen bonds (H-bonds) involving organic fluorine and other halogens in diphenyloxamide derivatives has been explored by NMR spectroscopy and quantum theoretical studies. The three centered H-bond with the participation of a rotating CF3 group and the F...H-N intramolecular hydrogen bonds, a rare observation of its kind in organofluorine compounds, has been detected. It is also unambiguously established by a number of one and two dimensional NMR experiments, such as temperature perturbation, solvent titration, N-15-H-1 HSQC, and F-19-H-1 HOESY, and is also confirmed by theoretical calculations, such as quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) and non-covalent interaction (NCI).

Tailoring the interface in graphene/thermoset polymer composites: A critical review

With the emergence of scientific interest in graphene oxide (GO) in recent times, researchers have endeavored to incorporate GO in thermoset polymeric matrix to develop composites with extraordinary set of properties. The current state of research in graphene/thermoset polymer composites is highlighted here with a focus on the role of interface in dictating the overall properties of the composites. Different strategies like covalent and non-covalent functionalization of GO have been discussed with respect to improvement in mechanical, electrical, thermal and rheological properties. In addition, future prospects have been outlined. By assessing the current state of research in graphene/thermoset composites, it is obvious that graphene derivatives are promising materials in enhancing the structural properties of the nanocomposites at extremely low levels of filler loading. This opens new avenues in designing lightweight composites for myriad applications and by tailoring the interfacial adhesion with the polymer, ordered structure can be achieved at macroscopic processing scales. (C) 2015 Elsevier Ltd. All rights reserved.

Dissecting pi-helices: sequence, structure and function

A new procedure for the identification of regular secondary structures using a C-alpha trace has identified 659 pi-helices in 3582 protein chains, solved at high resolution. Taking advantage of this significantly expanded database of pi-helices, we have analysed the functional and structural roles of helices and determined the position-wise amino acid propensity within and around them. These helices range from 5 to 18 residues in length with the average twist and rise being 85.2 +/- 7.2 and 1.28 +/- 0.31 angstrom, respectively. A total of 546 (similar to 83%) out of 659 pi-helices occur in conjunction with alpha-helices, with 101 pi-helices being interspersed between two alpha-helices. The majority of interspersed pi-helices were found to be conserved across a large number of structures within a protein family and produce a significant bend in the overall helical segment as well as local distortions in the neighbouring a-helices. The presence of a pi-helical fragment leads to appropriate orientation of the constituent residues, so as to facilitate favourable interactions and also help in proper folding of the protein chain. In addition to intra helical 6 -> 1 N H center dot center dot center dot O hydrogen bonds, pi-helices are also stabilized by several other non-bonded interactions. pi-Helices show distinct positional residue preferences, which are different from those of a-helices.

High frequency millimetre wave absorbers derived from polymeric nanocomposites

The world has dominated by automation, wireless communication and various electronic equipments, which has led to the most undesirable offshoots like electromagnetic (EM) pollution. The rationale is environmental concern and the necessity to develop EM absorbing materials. This paper reviews the state of the art of designing polymer based nanocomposites containing nanoscopic particles with high electrical conductivity and complex microwave properties for enhanced EM attenuation. Given the brevity of this review article, herein we have summarized the high frequency millimetre wave absorbing properties of polymer nanocomposites consisting of various nanoparticles that either reflect or absorb microwave radiation like electrically conducting carbon nanotubes (CNTs) and graphene nanosheets (GNs), high dielectric constant ceramic nanoparticles that show relaxation loss in the microwave frequency and magnetic metal and ferrite nanoparticles that absorb microwave radiation through natural resonance, eddy current and hysteresis losses. Furthermore, we have stressed the necessity and impact of hybrid nanoparticles consisting of magnetic and dielectric nanoparticles along with conducting inclusions like CNT and GNs in this review. Electromagnetic interference (EMI) theory and necessary criterion for attenuation has been briefly discussed. The emphasis is made on various mechanisms towards EM attenuation controlled by these nanoparticles. Various structures developed using polymer nanocomposites like bulk, foam and layered structures and their effect on EM attenuation has been elaborately discussed. In addition, various covalent/non-covalent modifications on nanoparticles have been juxtaposed in context to EM attenuation. In addition, we have highlighted important facets and direction for enhancing the microwave attenuation. (C) 2016 Elsevier Ltd. All rights reserved.

Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores.

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks.

非特异性相互作用的断裂力与寿命测量

目的探讨量化非特异性相互作用在特异性选择素．配体分子相互作用中的贡献。方法利用光镊技术，对牛血清白蛋白（Bovine serum albumin，BSA）封闭的玻璃小球间的非特异性作用进行了系统测量，得出不同加载率下的断裂力以及不同外力作用下的寿命分布。结果实验结果表明，非特异性作用同样表现出断裂力随加载率增加而增大的趋势。在较低加载率下，非特异性断裂力与选择素-配体特异性断裂力大小、增大趋势基本一致；随着加载率增加，二者的差别逐渐显著，前者的断裂力增加速率远低于后者。同样外力作用下，非特异性作用的寿命平均值比特异性作用要小；不同外力作用下，非特异性作用的寿命随外力增大仅略有下降，与特异性作用中逆锁键-滑移键转化现象有明显不同。结论该研究结果将为正确评估非特异性相互作用对选择素-配体特异性相互作用实验结果的影响提供基础。

Studies of phonon anharmonicity in solids

Today our understanding of the vibrational thermodynamics of materials at low temperatures is emerging nicely, based on the harmonic model in which phonons are independent. At high temperatures, however, this understanding must accommodate how phonons interact with other phonons or with other excitations. We shall see that the phonon-phonon interactions give rise to interesting coupling problems, and essentially modify the equilibrium and non-equilibrium properties of materials, e.g., thermodynamic stability, heat capacity, optical properties and thermal transport of materials. Despite its great importance, to date the anharmonic lattice dynamics is poorly understood and most studies on lattice dynamics still rely on the harmonic or quasiharmonic models. There have been very few studies on the pure phonon anharmonicity and phonon-phonon interactions. The work presented in this thesis is devoted to the development of experimental and computational methods on this subject.

Modern inelastic scattering techniques with neutrons or photons are ideal for sorting out the anharmonic contribution. Analysis of the experimental data can generate vibrational spectra of the materials, i.e., their phonon densities of states or phonon dispersion relations. We obtained high quality data from laser Raman spectrometer, Fourier transform infrared spectrometer and inelastic neutron spectrometer. With accurate phonon spectra data, we obtained the energy shifts and lifetime broadenings of the interacting phonons, and the vibrational entropies of different materials. The understanding of them then relies on the development of the fundamental theories and the computational methods.

We developed an efficient post-processor for analyzing the anharmonic vibrations from the molecular dynamics (MD) calculations. Currently, most first principles methods are not capable of dealing with strong anharmonicity, because the interactions of phonons are ignored at finite temperatures. Our method adopts the Fourier transformed velocity autocorrelation method to handle the big data of time-dependent atomic velocities from MD calculations, and efficiently reconstructs the phonon DOS and phonon dispersion relations. Our calculations can reproduce the phonon frequency shifts and lifetime broadenings very well at various temperatures.

To understand non-harmonic interactions in a microscopic way, we have developed a numerical fitting method to analyze the decay channels of phonon-phonon interactions. Based on the quantum perturbation theory of many-body interactions, this method is used to calculate the three-phonon and four-phonon kinematics subject to the conservation of energy and momentum, taking into account the weight of phonon couplings. We can assess the strengths of phonon-phonon interactions of different channels and anharmonic orders with the calculated two-phonon DOS. This method, with high computational efficiency, is a promising direction to advance our understandings of non-harmonic lattice dynamics and thermal transport properties.

These experimental techniques and theoretical methods have been successfully performed in the study of anharmonic behaviors of metal oxides, including rutile and cuprite stuctures, and will be discussed in detail in Chapters 4 to 6. For example, for rutile titanium dioxide (TiO₂), we found that the anomalous anharmonic behavior of the B_1g mode can be explained by the volume effects on quasiharmonic force constants, and by the explicit cubic and quartic anharmonicity. For rutile tin dioxide (SnO₂), the broadening of the B_2g mode with temperature showed an unusual concave downwards curvature. This curvature was caused by a change with temperature in the number of down-conversion decay channels, originating with the wide band gap in the phonon dispersions. For silver oxide (Ag₂O), strong anharmonic effects were found for both phonons and for the negative thermal expansion.

Computational design of self-assembling proteins and protein-DNA nanowires

Computational protein design (CPD) is a burgeoning field that uses a physical-chemical or knowledge-based scoring function to create protein variants with new or improved properties. This exciting approach has recently been used to generate proteins with entirely new functions, ones that are not observed in naturally occurring proteins. For example, several enzymes were designed to catalyze reactions that are not in the repertoire of any known natural enzyme. In these designs, novel catalytic activity was built de novo (from scratch) into a previously inert protein scaffold. In addition to de novo enzyme design, the computational design of protein-protein interactions can also be used to create novel functionality, such as neutralization of influenza. Our goal here was to design a protein that can self-assemble with DNA into nanowires. We used computational tools to homodimerize a transcription factor that binds a specific sequence of double-stranded DNA. We arranged the protein-protein and protein-DNA binding sites so that the self-assembly could occur in a linear fashion to generate nanowires. Upon mixing our designed protein homodimer with the double-stranded DNA, the molecules immediately self-assembled into nanowires. This nanowire topology was confirmed using atomic force microscopy. Co-crystal structure showed that the nanowire is assembled via the desired interactions. To the best of our knowledge, this is the first example of a protein-DNA self-assembly that does not rely on covalent interactions. We anticipate that this new material will stimulate further interest in the development of advanced biomaterials.

Aplicação da equação de Poisson-Boltzmann modificada em sistemas biológicos: análise da partição iônica em um eritrócito

Neste trabalho, a partição iônica e o potencial de membrana em um eritrócito são analisados via equação de Poisson-Boltzmann modificada, considerando as interações não eletrostáticas presentes entre os íons e macromoléculas, assim como, o potencial β. Este potencial é atribuído à diferença de potencial químico de referência entre os meios intracelular e extracelular e ao transporte ativo de íons. O potencial de Gibbs-Donnan via equação de Poisson-Boltzmann na presença de carga fixa em um sistema contendo uma membrana semipermeável também é estudado. O método de aproximação paraboloide em elementos finitos em um sistema estacionário e unidimensionalé aplicado para resolver a equação de Poisson-Boltzmann em coordenadas cartesianas e esféricas. O parâmetro de dispersão relativo às interações não eletrostáticas écalculado via teoria de Lifshitz. Os resultados em relação ao potencial de Gibbs-Donnan mostram-se adequados, podendo ser calculado pela equação de Poisson-Boltzmann. No sistema contendo um eritrócito, quando o potencial β é considerado igual a zero, não se verifica a diferença iônica observada experimentalmente entre os meios intracelular e extracelular. Dessa forma, os potenciais não eletrostáticos calculados via teoria de Lifshitz têm apenas uma pequena influência no que se refere à alta concentração de íon K+ no meio intracelular em relação ao íon Na+

Role of transglutaminase-mediated cross-linking of protein in the temperature-dependent setting of Alaska pollack surimi

During the low temperature setting of fish paste, myosin heavy chain (MHC) is polymerized to cross-linked myosin heavy chain (CMHC), which is considered to occur by the action of endogenous transglutaminase (TGase). In this study the contribution of TGase on the setting of Alaska pollack surimi at different temperatures was studied. Alaska pollack surimi was ground with 3% NaCl, 30% h2o and with or without ethylene glycol bis (β-aminoethylether) N, N, N¹,N¹- tetra acetic acid (EGTA), an inhibitor of TGase. Among the pastes without EGTA, highest TGase activity was observed at 25°C but breaking force of the gel set at 25°C was lower than that set at 30°, 35°, and 40°C. Addition of EGTA (5m mol/kg) to the paste suppressed TGase activity at all setting temperatures from 20° to 40°C. Gelation of the pastes and cross-linking of MHC on addition of EGTA were suppressed completely at 20° and 25°C, partially at 30° and 35°C, and not at all at 40°C. The findings suggested that during the setting of Alaska pollack surimi TGase mediated cross-linking of MHC was strong at around 25°C but the thermal aggregation of MHC by non-covalent bonds was strong at above 35°C. Setting of surimi at 40°C and cross-linking of its MHC did not involve TGase.

Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks. © 2011 Elsevier B.V.

Spectroscopic characteristics and cellular compatibility of protein wrapped single wall carbon nanotubes

Non-covalent functionalization of CoMoCAT single-wall carbon nanotubes (SWNTs) by bovine serum albumin (BSA) was achieved. Photoluminescence spectra for the functionalized nanotubes showed good dispersion by BSA functionalization. Raman spectra were taken for the sonicated SWNT-BSA solution to establish the signal versus concentration correlation. Cellular uptake of functionalized carbon nanotubes by mouse macrophage (RAW264.7) was then investigated using Raman spectroscopy. For a seeding density of 50% confluence in a culture solution containing 10 μg/ml of BSA-SWNTs, uptake of 200 μg/ml by the macrophages was recorded after 23hr incubation, indicating an active uptake of SWNTs. © 2012 IEEE.

Communication: energy benchmarking with quantum Monte Carlo for water nano-droplets and bulk liquid water.

We show the feasibility of using quantum Monte Carlo (QMC) to compute benchmark energies for configuration samples of thermal-equilibrium water clusters and the bulk liquid containing up to 64 molecules. Evidence that the accuracy of these benchmarks approaches that of basis-set converged coupled-cluster calculations is noted. We illustrate the usefulness of the benchmarks by using them to analyze the errors of the popular BLYP approximation of density functional theory (DFT). The results indicate the possibility of using QMC as a routine tool for analyzing DFT errors for non-covalent bonding in many types of condensed-phase molecular system.

环糊精非共价复合物和黄芪皂甙的质谱研究

首先，由于电喷雾质谱技术已被广泛的应用于研究非共价复合物。为了深入揭示环糊精复合物和气液两相相关性，本章系统的研究了α，β两种环糊精和联苯胺的包合物，并分别用IHNMR和荧光光谱表征了其在液相中的行为，用ESI-MS，表征了他们在气相中的行为。ESI-MS检测这些复合物发现：两种环糊精都与benzidine形成较稳定的1:1复合物，-CD还能与benzidine形成2:1的复合物。这也部分证明了环糊精基于分子大小和空间结构匹配的分子识别作用。通过这些特异性复合物在气液两相中行为的相关性研究，证实了复合物离子的相对强度，相对碰撞诱导解离（CID）与其液相稳定性相一致。本文还研究了α-CD和二茂铁衍生物的非共价复合物的电喷雾质谱，实验结果表明非共价复合物的物质的量的比为1:1，通过循环伏安的电化学方法提出了两种可能存在的包合物的结构。我们对黄茂中的皂甙化合物进行了提取和分离，并成功的应用电喷雾多级串联质谱技术跟踪监测混合物中的皂贰化合物，建立混合物中便捷，实用，高效的测定皂贰的质谱方法。来用电喷雾多级串联质谱技术，研究了正负离子条件下传统中药黄茂中的有效成分黄蔑甲贰的特征质谱行为，确定了小柱梯度淋洗的条件，可以此鉴定传统黄芪中有效成分，为传统黄芪药材及相关药品的快速鉴别和质量控制具有重要意义。利用质谱技术为研究手段，深入探讨了碱金属离子对黄茂甲贰结构分析的影响，发现在相同的碰撞活化诱导解离能的条件下，锂离子的加合物能够给出更丰富的碎片离子信息。

Investigation of heptakis(2,6-di-O-methyl)-beta-cyclodextrin inclusion complexes with flavonoid glycosides by electrospray ionization mass spectrometry

The non-covalent complexes between three flavonoid glycosides (quercitrin, hyperoside and rutin) and heptakis(2,6-di-O-methyl)-beta-cyclodextrin (DM-beta-CD) were investigated by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The 1:1 complexation of each flavonoid glycoside (guest) to the DM-beta-CD (host) was monitored in the negative ion mode by mixing each guest with an up to 30-fold molar excess of the host. The binding constants for all complexes were calculated by a linear equation in the order: DM-beta-CD:quercitrin > DM-beta-CD:rutin > DM-beta-CD:hyperoside. A binding model for the complexes has also been proposed based on the binding constants and tandem mass spectrometric data of these complexes.