Investigation of dodecylammonium adsorption on mica,albite and quartz surfaces by QM/MM simulation

The absorption mechanisms of collector and mineral surface structures play important roles in studies of lepidolite flotation. In this work, quantum mechanics (QM) and hybrid quantum mechanics/molecular mechanics (MM) methods were implemented to investigate the flotation mechanisms of lepidolite from muscovite, quartz and albite. The crystal structures, electron density distributions, bonds and the densities of states of lepidolite were calculated and compared with those of muscovite. The adsorption structures and energies of monomer dodecylammonium (DDA) on the three different minerals were also calculated. The headgroup of the DDA cation was found to adsorb on the surface of minerals, with its hydrophobic tail stretching into the vacuum slab, approximately perpendicular to the surface. Simulation results indicate that the purity of fine lepidolite is limited by the existence of muscovite, due to their similarities in surficial structure and properties. Other gangues were found to be removed efficiently with the use of acidic conditions. The results are in good agreement with other experiments. Compared with simple MM simulations, the use of the QM/MM methods to investigate the adsorption on minerals without specific forcefield parameters was concluded to be a more accurate method to attain monomer surfactant–mineral adsorption energies.     

Nondestructive Raman and atomic force microscopy measurement of molecular structure for individual diphenylalanine nanotubes

Polarized Raman microspectroscopy and atomic force microscopy were used to measure molecular orientation in individual diphenylalanine nanotubes (diameters ranging from 100 nm to 1000 nm). Analysis of the amide I Raman bands (1686 cm(-1)) indicated that the C=O side chains have a parallel alignment with the nanotube axis. The amide III Raman band (1249 cm(-1)) associated with the peptide backbone C-N vibrations showed that these bonds are preferentially aligned perpendicular to the nanotube axis. However, the Raman band corresponding to the symmetric breathing mode of the aromatic rings (1002 cm(-1)) indicated a rather random orientation. These results support the theoretical molecular structure models proposed recently.     

人乳腺癌组织的显微拉曼光谱研究

研究了人类正常与癌变乳腺组织的显微拉曼光谱特性。与正常乳腺组织相比,癌变组织的核酸骨架磷酸离子vs(PO^-2)特征谱线由1082移到1097cm^-1、强度加强,位于817cm^-1的RNA主链vs(O-P-O)的谱线强度增加;蛋白质酰胺Ⅰ和酰胺Ⅲ两个特征谱带从1657,1273cm^-1分别位移到1662和1264cm^-1,其中1264cm^-1谱线的宽度和强度均增加,某些氨基酸残基的C—O谱线向高波数位移,色氨酸特征峰1368cm^-1在癌变组织中几乎观察不到;脂类特征谱线减少。上述谱线变化表明,癌变组织中核酸的相对含量增加、主链结构发生变化;蛋白质结构同时呈现α-螺旋、无规卷曲、卢．折叠以及β-回折4种构象特征,其分子间的氢键近乎断裂,蛋白质变得松散和无序,色氨酸残基的吲哚环呈现“暴露式”;脂类含量减少。研究表明,显微拉曼光谱可以为乳腺癌变的生化机理研究以及活体诊断提供有力的实验依据。     

Raman signatures of strong and weak hydrogen bonds in binary mixtures of phenol with acetonitrile,benzene and orthodichlorobenzene

The present study aims at investigating the effect of hydrogen bonds of phenol in binary mixtures of phenol with three solvents viz. acetonitrile, orthodichlorobenzene and benzene respectively in order of decreasing hydrogen bond strength. Raman spectroscopy in correlation with density functional theory (DFT) calculations has led to a profound understanding of changes in structure, energy, dipole moment and other physical and chemical properties of phenol pertaining to hydrogen bond formation in solution. The spectral variation in wavenumber and linewidth of ring deformation, ring stretching, C≡N stretching and C―H stretching modes have been analyzed in detail. The breaking of self association of phenol in solution and formation of strong or weak hydrogen bonds depending on the nature of the solvent has been discussed by comparing the Raman and DFT results for three different solvents. Copyright © 2016 John Wiley & Sons, Ltd.     

High pressure Raman study on the local structure of 1-ethyl-3-methylimidazolium tetrafluoroborate

We have investigated the pressure-induced Raman spectral changes of 1-ethyl-3-methylimidazolium tetrafluoroborate ([emim][BF₄]). We found that [emim][BF₄] did not crystallize up to 1.2 GPa. The Raman CH stretching spectra arising from the CH₃ groups of the ethyl-chain and the CH₃ group adjacent to the imidazolium-ring in [emim]⁺ cation largely changed against pressure. Moreover, the Raman intensity of the CH₂ (N) bending band arising from the alkyl-chain drastically changes with increasing pressure, but that of the imidazolium-ring in-plane bending band arising from the imidazolium-ring is independent of pressure. Our results show that the environment around the alkyl-chain of [emim][BF₄] is largely perturbed rather than that around the imidazolium-ring upon compression.     

Investigating the formation of an adduct of formamide with dioxane by means of Raman spectroscopy

Raman experiments of formamide (FA) and p‐dioxane (DX) mixtures at different compositions were carried out. A red shift of the C O stretching band of DX was observed upon dilution, while blue shifts were observed for the C H stretching and C O C bending bands. In this latter region, the new band at ∼441 cm⁻¹, whose intensity shows large dependence on the FA concentration, has been assigned to an FA–DX adduct and it is reported for the first time in the literature. The spectral changes observed in the C O C bending region allowed to determine a proportion of 4:1 FA–DX and this experimental evidence is also presented for the first time by Raman spectroscopy. The present work shows an excellent agreement with our previous investigation, where the 2:1 FA—THF (tetrahydrofuran) adduct was characterized. Copyright © 2008 John Wiley & Sons, Ltd.     

Solvent effects on optical excitations of poly <Emphasis Type="Italic">para</Emphasis> phenylene ethynylene studied by QM/MM simulations based on many-body Green's functions theory

Electronic excitations in dilute solutions of poly para phenylene ethynylene (poly-PPE) are studied using a QM/MM approach combining many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation with polarizable force field models. Oligomers up to a length of 7.5?nm (10 repeat units) functionalized with nonyl side chains are solvated in toluene and water, respectively. After equilibration using atomistic molecular dynamics (MD), the system is partitioned into a quantum region (backbone) embedded into a classical (side chains and solvent) environment. Optical absorption properties are calculated solving the coupled QM/MM system self-consistently and special attention is paid to the effects of solvents. The model allows to differentiate the influence of oligomer conformation induced by the solvation from electronic effects related to local electric fields and polarization. It is found that the electronic environment contributions are negligible compared to the conformational dynamics of the conjugated PPE. An analysis of the electron-hole wave function reveals a sensitivity of energy and localization characteristics of the excited states to bends in the global conformation of the oligomer rather than to the relative of phenyl rings along the backbone.     

Vibrational spectroscopy and density functional theory calculations of poly‐D‐mannuronate and heteropolymeric fractions from sodium alginate

The tetrasaccharide of 1 → 4β‐D‐mannopyranuronate (MM) and the alternating tetrasaccharide of 1 → 4 b‐D‐mannopyranuronate and 1 → 4α‐L‐gulopyranuronate (MG) were analyzed based on density functional theory (DFT) by employing the Gaussian 03 W package. The molecular geometries were fully optimized by using the Becke's three‐parameter hybrid exchange functional combined with Lee–Yang–Parr correlation functional (B3LYP) and using a 6‐31G(d,p) basis set. The calculated IR spectrum of MM presents a band at 1093 cm⁻¹ for C C stretching vibration, which is in good agreement with the experimental observation (1096 cm⁻¹) for the polymannuronate fraction obtained by partial hydrolysis of sodium alginate extracted from the hybrid brown seaweed Lessonia–Macrocystis. The calculated value at 826 cm⁻¹for MM is in close agreement with the experimental value and confirms that this band is characteristic of polymannuronate blocks. Most of the bands in the IR spectrum are also present in the observed Raman spectrum of the polymannuronate fraction. The experimental IR spectrum of heteropolymeric fraction obtained by partial hydrolysis of sodium alginate shows absorbances similar to those calculated for the model tetrasaccharide (MG). Surface‐enhanced Raman scattering (SERS) allows differentiation between the homopolymeric and heteropolymeric fractions of sodium alginate. The SERS spectrum of the heteropolymeric fraction shows an enhanced signal at 731 cm⁻¹which is present in the calculated Raman spectrum of the tetrasaccharide MG at 729 cm⁻¹. This band is assigned to the ring‐breathing deformation of the β‐D‐mannopyranuronate and α‐L‐gulopyranuronate residues. Copyright © 2010 John Wiley & Sons, Ltd.     

Vibrational spectroscopic studies of the structure of di‐amino acid peptides. Part II: cyclo(L‐Asp‐L‐Asp) in the solid state and in aqueous solution

Solid‐state protonated and N,O‐deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di‐amino acid peptide cyclo(L ‐Asp‐L ‐Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3‐LYP/cc‐pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L ‐Asp‐L ‐Asp), assuming C₂ symmetry, predicts a boat conformation for the DKP ring with both the two L ‐aspartyl side chains being folded slightly above the ring. The CO stretching vibrations have been assigned for the side‐chain carboxylic acid group (e.g. at 1693 and 1670 cm⁻¹ in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm⁻¹ in the Raman spectrum). The presence of two bands for the carboxylic acid CO stretching modes in the solid‐state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm⁻¹ in the solid‐state Raman spectrum, which is in agreement with results for cyclic di‐amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C^α atom is increased, the amide II band wavenumber decreases to below 1500 cm⁻¹; this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm⁻¹), which indicates that this band has a smaller N H bending contribution than the trans amide II vibrational band observed for linear peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

PolyA,PolyU及双链复合物PolyA·PolyU的拉曼光谱研究

测试了PolyA,PolyU及其双链复合物Po1yA·PolyU的拉曼光谱,研究了双链形成前后的光谱变化.结果显示:(1)15℃下,在pH 7.0的0.14 mol.L-1 NaCl,1 mmol·L-1 Tris水溶液中,PolyU, PolyA,PolyA·PolyU分别以无规卷曲、A型单螺旋和A型双螺旋结构存在.后两种结构区别于前者的主 要光谱标志之一是有序结构在814 cm-1附近出现的拉曼峰.另一光谱标志则是1 100cm-1附近的谱峰半高宽的大小.PolyA,PolyA·PolyU在该处有着相同的半高宽,而PolyU在该处的谱峰则有明显的展宽.此外,还发现PolyA的有序程度不及PolyA·PolyU,这可以从(813±2)cm-1与1 100 cm-1的峰强比推知;(2)PolyU,PolyA形成双螺旋复合物之后,多聚核苷酸碱基-碱基堆积力大为增强,主链构象变得更为有序化,从而产生了明显的拉曼减色效应并伴随着相关谱带的频移.在这个过程中,PolyU链比PolyA链所产生的光谱变化更为显著.该研究表明,从这类实验结果中提取特征光谱标志有望实现基因芯片的拉曼光谱检测.     

几种哌嗪类抗肿瘤化合物的拉曼光谱

几种哌嗪类抗肿瘤化合物的拉曼光谱刘社文１梁二军１李祥杰２（１郑州大学河南省激光应用技术重点实验室，２郑州大学化学化工学院，郑州４５００５２）ＲａｍａｎＳｐｅｃｔｒａｏｆＳｅｖｅｒａｌＡｎｔｉｔｕｍｏｒＰｉｐｅｒａｚｉｎｅｓＣｏｍｐｏｕｎｄｓＬｉｕＳｈ...     

Cysteine‐linked aromatic nitriles as UV resonance Raman probes of protein structure

Nitriles introduced into peptides and proteins can serve as useful vibrational spectroscopic probes, because the nitrile C ≡ N stretch is well isolated from backbone and sidechain vibrational bands. Aromatic nitriles offer large νC ≡ N absorption intensity in infrared spectra and resonance enhancement in Raman spectra with ultraviolet excitation. We report the ultraviolet resonance Raman spectra of cyanophenylalanine attached to cysteine, through linkage reactions that are applicable to cysteine residues in proteins. Excitation profiles are reported, and the νC ≡ N detection limit is estimated to be 5 µ m . The band position is sensitive to solvent polarity and especially to strong H‐bonding. The derivatization of mastoparan X peptide at introduced cysteine residues demonstrated the effectiveness of a cyanophenylcysteine probe in reporting the lowered environmental polarity when the peptide was incorporated into liposomes. For an asymmetrical cyanophenyl derivative, 2‐CBCys, the intensity ratio of asymmetric and symmetric ring modes, ν8_b and ν8_a, was found to respond to solvent polarity and not to H‐bonding. Copyright © 2012 John Wiley & Sons, Ltd.     

卵黄低密度脂蛋白结构的红外光谱和激光拉曼光谱分析

低密度脂蛋白是把胆固醇运输到肝脏合成胆酸一种重要的脂蛋白。低密度脂蛋白结构的研究对弄清动脉硬化发病机理有着非常重要的意义。用硫酸铵分离法快速分离鸡蛋黄中各种蛋白成分,用Sephadex G-200柱层析分离、纯化获得纯度很高的低密度脂蛋白,对其进行SDS-聚丙烯酰胺凝胶电泳(SDS-PAGE)检测,结果显示低密度脂蛋白主要包含5种脱辅基蛋白。激光拉曼和红外光谱测定,检测出低密度脂蛋白中对称CH2以及不对称CH2的伸缩振动。红外光谱还检测到脂蛋白肽键中C=O伸缩振动、脂链中P=O的伸缩振动和磷脂中胆碱聚集体的N+(CH3)3的不对称振动。两种光谱分析为研究低密度脂蛋白的结构提供了有效信息。     

Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons of membrane-bound fusion peptides

Clean MAS observation of 13C-labeled carbons in membrane-bound HIV-1 and influenza fusion peptides was made by using a rotational-echo double-resonance spectroscopy (REDOR) filter of directly bonded 13C-15N pairs. The clean filtering achieved with the REDOR approach is superior to filtering done with sample difference spectroscopy. In one labeling approach, the peptide had labels at a single 13C carbonyl and its directly bonded 15N. The resulting chemical shift distribution of the filtered signal is used to assess the distribution of local secondary structures at the labeled carbonyl. For the influenza peptide, the Leu-2 carbonyl chemical shift distribution is shown to vary markedly with lipid and detergent composition, as well as peptide:lipid ratio, suggesting that the local peptide structure also has a strong dependence on these factors. Because most carboxylic- and amino-labeled amino acids are commercially available, this REDOR approach should have broad applicability to chemically synthesized peptides as well as bacterially synthesized proteins. In a second labeling approach, the HIV-1 fusion peptide had U-13C, 15N labeling over three sequential residues. When a 1.6 ms REDOR dephasing time is used, only backbone 13C signals are observed. The resulting spectra are used to determine spectral linewidths and to assess feasibility of assignment of uniformly labeled peptide.     

Vibrational Spectroscopic Characterization of the Arsenate Mineral Barahonaite: Implications for the Molecular Structure

The mineral barahonaite is in all probability a member of the smolianinovite group. The mineral is an arsenate mineral formed as a secondary mineral in the oxidized zone of sulphide deposits. We have studied the barahonaite mineral using a combination of Raman and infrared spectroscopy. The mineral is characterized by a series of Raman bands at 863 cm^?1 with low wavenumber shoulders at 802 and 828 cm^?1. These bands are assigned to the arsenate and hydrogen arsenate stretching vibrations. The infrared spectrum shows a broad spectral profile. Two Raman bands at 506 and 529 cm^?1 are assigned to the triply degenerate arsenate bending vibration (F ₂, ν₄), and the Raman bands at 325, 360, and 399 cm^?1 are attributed to the arsenate ν₂ bending vibration. Raman and infrared bands in the 2500–3800 cm^?1 spectral range are assigned to water and hydroxyl stretching vibrations. The application of Raman spectroscopy to study the structure of barahonaite is better than infrared spectroscopy, probably because of the much higher spatial resolution.     

激光诱导荧光水体污染遥测数据定量分析方法

在紫外光的激发下,污染水体中的溶解有机物(DOM)会产生特定的荧光光谱,因此利用激光诱导荧光(LIF)可对水体中的溶解有机物的含量进行定量分析,从而可估计出水体富营养化的程度。提出了一种用于对水质遥测数据进行定量分析的方法,这是一种基于遗传算法(GA)的光谱分离算法。首先确定拉曼散射信号和溶解有机物的荧光在404nm波段的信号强度,然后再利用拉曼散射信号对DOM荧光光谱进行归一化处理。根据浓度校准曲线可得到水体中的溶解有机物的浓度。     

Water–ice phase transition probed by Raman spectroscopy

Raman spectroscopy was used to study the liquid–solid water phase transition. Special attention was devoted to the OH stretching band of the Raman spectrum, which shows monotonous changes in the temperature range between 10 and − 15 °C. The interpretation of this spectral change, as well as a careful analysis of its integrated scattered intensity, led to a spectral marker that allows the determination of the water phase (liquid or solid), and the efficient identification of the liquid–solid phase transition itself. Copyright © 2011 John Wiley & Sons, Ltd.