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1.
Full- [six-dimensional (6-D)] and reduced-dimensional [five-dimensional (5-D)] quantum wave packet calculations have been performed for the title reaction to obtain reaction probabilities deriving from the ground rovibrational states of OH and CO with total angular momentum J = 0. Three potential energy surfaces (PES) are studied, namely, those of Bradley and Schatz (BS), Yu, Muckerman, and Sears (YMS), and Lakin, Troya, Schatz, and Harding (LTSH). 6-D calculations are performed only for the BS PES, while 5-D results are reported for all three PES'. The 6-D results obtained in the present work improve on those previously reported, since a larger vibrational basis and a better representation of the OH and CO bonds has been introduced. In particular, we now employ a generalized Lanczos-Morse discrete variable representation for both the OH and CO vibrations. In a further improvement, the generalized discrete variable representation of the CO vibration is based on different CO intramolecular potentials for the asymptotic and product grids employed in our projection formalism. This new treatment of the vibrational bases allows for a large reduction in computation time with respect to our previous implementation of the wave packet method, for a given level of accuracy. As a result, we have been able to extend the range of collision energies for which we can obtain converged 6-D results to a higher energy (0.8 eV) than was possible before (0.5 eV). The comparison of the new 6-D and previous 5-D results for the BS PES shows good agreement of the general trend in the reaction probabilities over all collision energies considered (0.1-0.8 eV), while our previous 6-D calculation showed reaction probabilities that differed from the 5-D results by up to 10% between 0.5 and 0.8 eV. The 5-D reaction probabilities reveal interesting trends for the different PES'. In particular, at low energies (< 0.2 eV) the LTSH PES gives rise to much larger reactivity than the other PES', while at high energies (> 0.3 eV) its reaction probability decreases with respect to the BS and YMS PES', being more than a factor of 2 smaller at 0.8 eV. A 5-D calculation on a modified version of the LTSH surface shows that the van der Waals interaction in the entrance channel, which is not correctly described in the other PES' is largely responsible for its larger reactivity at low energies. The large difference between the 5-D reaction probabilities for the YMS and LTSH PES' serves to emphasize the importance of the van der Waals interaction for the reactivity at low energies, because most of the stationary point energies on the YMS and LTSH PES are rather similar, being in line with high-level ab initio information. 相似文献
2.
Galan MC Venot AP Glushka J Imberty A Boons GJ 《Journal of the American Chemical Society》2002,124(21):5964-5973
It is demonstrated that conformationally restricted oligosaccharides can act as acceptors for glycosyltransferases. Correlation of the conformational properties of N-acetyl lactosamine (Galbeta(1-4)GlcNAc, LacNAc) and several preorganized derivatives with the corresponding apparent kinetic parameters of rat liver alpha-(2,6)-sialyltransferase-catalyzed sialylations revealed that this enzyme recognizes LacNAc in a low energy conformation. Furthermore, small variations in the conformational properties of the acceptors resulted in large differences in catalytic efficiency. Collectively, our data suggest that preorganization of acceptors in conformations that are favorable for recognition by a transferase may improve catalytic efficiencies. 相似文献
3.
A novel approach for the synthesis of various fragments of proteophosphoglycans from Leishmania major and Leishmania mexicana proteophosphoglycans has been developed. These compounds have been obtained by coupling alpha-mannosyl and alpha-N-acetyl-glucosamine phosphoramidite derivatives with the serine hydroxyl of various amino acids and peptides to give, after oxidation with tert-BuOOH, phosphotriesters exclusively as alpha-anomers in good yield. The resulting compounds could be deblocked using conventional methods. Glycophosphorylation of preassembled and properly protected peptides was found to be more efficient for the preparation of proteophosphoglycan fragments than a building block approach strategy using a phosphoglycosylserine derivative. 相似文献
4.
We report six-dimensional quantum dynamics calculations of the dissociative scattering of molecular hydrogen from the copper111 surface. Two potential energy surfaces are investigated and the results are compared with experiment. Our study completes the preliminary work of Somers et al. [Chem. Phys. Lett. 360, 390 (2002)] and focuses on the role of initial vibrational excitation and on isotopic effects. None of the two investigated potential energy surfaces is found satisfactory: the use of neither potential yields reaction and vibrational excitation probabilities and vibrational efficacies that are in close agreement with experiment. In addition to showing the shortcomings of existing potential energy surfaces we point out an inconsistency in the experimental fits for D2. 相似文献
5.
Dr. Camiel H. C. Janssen Dr. Antonio Sánchez Prof. Geert-Jan Witkamp Prof. Mark N. Kobrak 《Chemphyschem》2013,14(16):3806-3813
We present a novel mechanism for the extraction of metals from aqueous phases to room-temperature ionic liquids (ILs) by use of a high-temperature salt as an extraction agent. The mechanism capitalizes on the fact that charged metal complexes are soluble in ILs; this allows for extraction of charged complexes rather than the neutral species, which are formed by conventional approaches. The use of a well-chosen extraction agent also suppresses the competing ion-exchange mechanism, thus preventing degradation of the ionic liquid. The approach permits the use of excess extractant to drive the recovery of metals in high yield. This work presents both a thermodynamic framework for understanding the approach and experimental verification of the process in a range of different ILs. The method has great potential value in the recovery of metals, water purification and nuclear materials processing. 相似文献
6.
Yuntao Dai Jaap van Spronsen Geert-Jan Witkamp Robert Verpoorte Young Hae Choi 《Analytica chimica acta》2013
Developing new green solvents is one of the key subjects in Green Chemistry. Ionic liquids (ILs) and deep eutectic solvents, thus, have been paid great attention to replace current harsh organic solvents and have been applied to many chemical processing such as extraction and synthesis. However, current ionic liquids and deep eutectic solvents have still limitations to be applied to a real chemical industry due to toxicity against human and environment and high cost of ILs and solid state of most deep eutectic solvents at room temperature. Recently we discovered that many plant abundant primary metabolites changed their state from solid to liquid when they were mixed in proper ratio. This finding made us hypothesize that natural deep eutectic solvents (NADES) play a role as alternative media to water in living organisms and tested a wide range of natural products, which resulted in discovery of over 100 NADES from nature. In order to prove deep eutectic feature the interaction between the molecules was investigated by nuclear magnetic resonance spectroscopy. All the tested NADES show clear hydrogen bonding between components. As next step physical properties of NADES such as water activity, density, viscosity, polarity and thermal properties were measured as well as the effect of water on the physical properties. In the last stage the novel NADES were applied to the solubilization of wide range of biomolecules such as non-water soluble bioactive natural products, gluten, starch, and DNA. In most cases the solubility of the biomolecules evaluated in this study was greatly higher than water. Based on the results the novel NADES may be expected as potential green solvents at room temperature in diverse fields of chemistry. 相似文献
7.
Natali Rianika Mustafa Vincent Simon Spelbos Geert-Jan Witkamp Robert Verpoorte Young Hae Choi 《Molecules (Basel, Switzerland)》2021,26(9)
Some medicines are poorly soluble in water. For tube feeding and parenteral administration, liquid formulations are required. The discovery of natural deep eutectic solvents (NADES) opened the way to potential applications for liquid drug formulations. NADES consists of a mixture of two or more simple natural products such as sugars, amino acids, organic acids, choline/betaine, and poly-alcohols in certain molar ratios. A series of NADES with a water content of 0–30% (w/w) was screened for the ability to solubilize (in a stable way) some poorly water-soluble pharmaceuticals at a concentration of 5 mg/mL. The results showed that NADES selectively dissolved the tested drugs. Some mixtures of choline-based NADES, acid-neutral or sugars-based NADES could dissolve chloral hydrate (dissociated in water), ranitidine·HCl (polymorphism), and methylphenidate (water insoluble), at a concentration of up to 250 mg/mL, the highest concentration tested. Whereas a mixture of lactic-acid–propyleneglycol could dissolve spironolacton and trimethoprim at a concentration up to 50 and 100 mg/mL, respectively. The results showed that NADES are promising solvents for formulation of poorly water-soluble medicines for the development of parenteral and tube feeding administration of non-water-soluble medicines. The chemical stability and bioavailability of these drug in NADES needs further studies. 相似文献
8.
Muchena J. Kailemia Melvin Park Desmond A. Kaplan Andre Venot Geert-Jan Boons Lingyun Li Robert J. Linhardt I. Jonathan Amster 《Journal of the American Society for Mass Spectrometry》2014,25(2):258-268
High-field asymmetric waveform ion mobility spectrometry (FAIMS) is shown to be capable of resolving isomeric and isobaric glycosaminoglycan negative ions and to have great utility for the analysis of this class of molecules when combined with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and tandem mass spectrometry. Electron detachment dissociation (EDD) and other ion activation methods for tandem mass spectrometry can be used to determine the sites of labile sulfate modifications and for assigning the stereochemistry of hexuronic acid residues of glycosaminoglycans (GAGs). However, mixtures with overlapping mass-to-charge values present a challenge, as their precursor species cannot be resolved by a mass analyzer prior to ion activation. FAIMS is shown to resolve two types of mass-to-charge overlaps. A mixture of chondroitin sulfate A (CSA) oligomers with 4–10 saccharides units produces ions of a single mass-to-charge by electrospray ionization, as the charge state increases in direct proportion to the degree of polymerization for these sulfated carbohydrates. FAIMS is shown to resolve the overlapping charge. A more challenging type of mass-to-charge overlap occurs for mixtures of diastereomers. FAIMS is shown to separate two sets of epimeric GAG tetramers. For the epimer pairs, the complexity of the separation is reduced when the reducing end is alkylated, suggesting that anomers are also resolved by FAIMS. The resolved components were activated by EDD and the fragment ions were analyzed by FTICR-MS. The resulting tandem mass spectra were able to distinguish the two epimers from each other. Figure
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9.
Apoorva D. Srivastava Dr. Luca Unione Dr. Margreet A. Wolfert Dr. Pablo Valverde Dr. Ana Ardá Prof. Dr. Jesús Jiménez-Barbero Prof. Dr. Geert-Jan Boons 《Chemistry (Weinheim an der Bergstrasse, Germany)》2020,26(67):15605-15612
The parasitic worm, Schistosoma mansoni, expresses unusual fucosylated glycans in a stage-dependent manner that can be recognized by the human innate immune receptor DC-SIGN, thereby shaping host immune responses. We have developed a synthetic approach for mono- and bis-fucosylated LacdiNAc (LDN-F and LDN-DF, respectively), which are epitopes expressed on glycolipids and glycoproteins of S. mansoni. It is based on the use of monosaccharide building blocks having carefully selected amino-protecting groups, facilitating high yielding and stereoselective glycosylations. The molecular interaction between the synthetic glycans and DC-SIGN was studied by NMR and molecular modeling, which demonstrated that the α1,3-fucoside of LDN-F can coordinate with the Ca2+-ion of the canonical binding site of DC-SIGN allowing for additional interactions with the underlying LDN backbone. The 1,2-fucoside of LDN-DF can be complexed in a similar manner, however, in this binding mode GlcNAc and GalNAc of the LDN backbone are placed away from the protein surface resulting in a substantially lower binding affinity. Glycan microarray binding studies showed that the avidity and selectivity of binding is greatly enhanced when the glycans are presented multivalently, and in this format Lex and LDN-F gave strong responsiveness, whereas no binding was detected for LDN-DF. The data indicates that S. mansoni has developed a strategy to avoid detection by DC-SIGN in a stage-dependent manner by the addition of a fucoside to a number of its ligands. 相似文献
10.
本文探讨了几种梯度近似(GGA)密度泛函及元梯度近似(meta-GGA)密度泛函在描述甲烷在重构的Pt(110)-(2×1)上的解离化学吸附作用的适用性. 金属的体相和表面结构、甲烷的吸附能量和解离能垒等被用来评估泛函的可靠性. 另外,在从头算分子动力学计算中,采用范德瓦尔斯矫正的GGA函数(optPBE-vdW)和范德瓦尔斯矫正的meta-GGA函数(MS-PBEl-rVV10)计算粘附概率. 计算结果表明,使用这两种泛函能更好地与现有的实验结果吻合,从而为发展甲烷在Pt(110)-(2×1)表面解离的可靠机器学习势能面打下重要基础. 相似文献