Molecular Dynamics Simulation of Mg2+ and Ca2+ Ions in Water

Molecular dynamics simulations of single Mg²⁺ and Ca²⁺ ions in water have been carried out. Different ion-water potentials from the literature have been used, whereas the same water potential, a rigid simple point charged model, has been considered in all the simulations. Structural, thermodynamic, and dynamic properties have been calculated, and the results for different potentials have been compared with available experimental data. The study includes ion–water radial distribution functions, coordination numbers, solution enthalpies, hydration free energies, self-diffusion coefficients, and reorientational times of water molecules in the hydration shells.     

Effects of Carboxylic Acids on the Crystallization of Calcium Carbonate

The effects of seven carboxylic acids, i.e., acrylic acid, maleic acid, tartaric acid, malic acid, succinic acid, and citric acid, on CaCO(3) crystallization were studied using the unseeded pH-drift method along with a light-scattering technique. Experiments were started by mixing solutions of CaCl(2) and NaHCO(3) in the presence or absence of additives. The crystallization was studied by recording the decrease in pH resulting from the reaction Ca(2+)+HCO(3)(-)-->CaCO(3)+H(+). A given amount of carboxylic acid was added to the solution of CaCl(2) or NaHCO(3) before mixing the reactants. The pH profiles obtained in the case of the CaCl(2) solution containing an additive were similar to those for the NaHCO(3) solution containing one, and when an additive was added after the onset of crystallization, the growth of CaCO(3) immediately stopped. The light-scattering observations, in all cases, indicated that CaCO(3) nucleation occurred at 10-20 s after mixing of the reactants. The results indicated that the nucleation of CaCO(3) was not influenced by the presence of carboxylic acids, but CaCO(3) crystal growth was reduced by their adsorption to the surface of the CaCO(3) crystals. These phenomena were explained by assuming a stronger affinity of the carboxylic acids for CaCO(3) particles than for the free Ca(2+) ions in solution. The crystallization of CaCO(3) in the presence of additives was divided into three stages: nucleation, growth incubation, and growth periods. Copyright 2001 Academic Press.     

A Study of the Reaction of Phosphorus Trichloride with Paraformaldehyde in the Presence of Carboxylic Acids

Abstract

We investigated the mechanism of the reaction of paraformaldehyde with phosphorus trichloride in the presence of carboxylic acids (acetic, propanoic, and formic). Our results revealed that bisphosphonic acids were obtained without the use of water. The structures of the reaction products were studied by 1D and 2D homonuclear and heteronuclear ¹H-, ¹³C-, ³¹P- NMR spectroscopy.

[Supplementary materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfer, and Silicon and the Related Elements for the following free supplemental files: Additional tables.]     

低能氮离子诱发氨基酸前生物合成反应的初步研究

利用氮气火花放电产生离子 ,其中的正离子在阴极位降的加速下“注入”到三种羧酸盐的水溶液中 ,诱发其中的化学反应并沉积在水溶液中 .利用高效液相色谱 (HPLC)对离子注入后的样品进行分析 ,结果表明 ,氮离子注入可使氮沉积在溶液中 ,生成氨及氨基酸 ,这一结果不仅验证了低能离子注入样品时的“质量沉积”效应 ,而且还是原始地球条件下氨基酸生成的一种可能的途径     

Determination of Epoxy Groups in the Presence of Carboxylic Acids of the Acryl Series and Aromatic Amines

Selective reactions for the determination of epoxy groups in the presence of acrylic acids and aromatic amines were studied. Factors affecting results of the determination of epoxy groups were revealed. Procedures were developed for the determination of epoxy and carboxylic groups and epoxy and amine (aromatic) groups in the presence of each other. The reaction is conducted in excess HCl in the former case and in excess tetraethylammonium bromide in the latter case. Performance characteristics of the procedures were estimated.     

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

The influence of Mg²⁺, Na⁺ and temperature on the conformational state of three-stranded helical polyA/2polyU (A2U) has been studied by the thermal denaturation method. At Na⁺ concentrations of 0.01–0.1 M , on heating the transition A2U→AU+U (the 3→2 transition) and then AU→A+U transition (the 2→1 transition) are observed. (AU is double helix polyA/polyU; A and U are single-stranded polyA and polyU, respectively.) With 0.01 M and 0.03 M Na⁺ these transitions occur at Mg²⁺ concentrations within (0 ÷ 0.003) M . At these ionic concentrations, there is a narrow temperature region (3 ÷ 5°C) at which double-helical AU formed by the 3→2 transition is resistant to heating. In 0.1 M Na⁺, a rise in the Mg²⁺ concentration leads to a continuous decrease in the temperature range of this region, and above a critical concentration of Mg²⁺ (ca. 3.6×10^–5 M )_cr there is only one transition (the 3→1 transition) instead of the successive transitions 3→2→1. The constants of Mg²⁺ ion association with polyU, polyA and A2U were calculated using equilibrium binding theory. The data obtained helped explain the reasons for the different phase diagrams for A2U + Mg²⁺ complexes in solution at high and low Na⁺ concentrations.     

钙离子和镁离子浓度变化对磷脂酰乙醇胺-磷脂酰甘油双分子层膜的影响

Ca²⁺ and Mg²⁺ ions are the main divalent cations in living cells and play vital roles in the structure and function of biological membranes. To date, the differences in the effects of these two ions on the Escherichia coli (E. coli) inner membrane at various concentrations remain unknown. Here, the effects of Ca²⁺ and Mg²⁺ ions on a mixed lipid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) in a 3 : 1 ratio (mol/mol), which mimics the E. coli inner membrane, were quantitatively differentiated at different concentrations by dynamic light scattering (DLS), zeta potential measurements and all-atom molecular dynamics (AA-MD) simulations. The DLS results demonstrated that the POPE/POPG liposomes were homogeneous and monodisperse in solutions with Ca²⁺ or Mg²⁺ ion concentrations of 0 and 1 mmol∙L^-1. As the Ca²⁺ or Mg²⁺ ion concentration was increased to 5-100 mmol∙L^-1, lipid aggregation or the fusion of unilamellar liposomes occurred in the ion solutions. The zeta potential measurements showed that both the Ca²⁺ and Mg²⁺ ions had overcharging effects on the negatively charged POPE/POPG liposomes. The AA-MD simulation results indicated that the Ca²⁺ ions irreversibly adsorbed on the membranes when the simulation time was longer than 100 ns, while the Mg²⁺ ions were observed to dynamically adsorb on and desorb from the membranes at various concentrations. These results are consistent with the DLS and zeta potential experiments. The average numbers of Ca²⁺ and Mg²⁺ ions in the first coordination shell of the oxygen atoms of the phosphate, carbonyl and hydroxyl groups of POPE and POPG (i.e., the first coordination numbers) in the pure membrane and membranes containing 5 and 100 mmol∙L^-1 ions were calculated from the radial distribution functions. The results indicated that the primary binding site of these two ions on POPE and POPG at the concentrations studied was the negatively charged phosphate group. Thus, these results might explain the overcharging effects of both the Ca²⁺ and Mg²⁺ ions on the POPE/POPG liposomes. Moreover, as the Ca²⁺ concentration increased, the area per lipid of the lipid bilayers decreased, and the membrane thickness increased, while the Mg²⁺ ions had negligible effects on these membrane parameters. In addition, these ions had different effects on the orientation of the lipid head groups. These simulation results may be used to provide the possible explanations for the differences between Ca²⁺ and Mg²⁺ ions in DLS and zeta potential measurements at the atomic level. The experimental results and MD simulations provide insight into various biological processes regulated by divalent cations, such as membrane fusion.     

由二氧化碳合成长链羧酸

正CO_2是极具潜力的可再生C_1资源,由其制备高附加值化学品具有重要意义。羧酸是一类重要的化学品,由CO_2作为原料合成羧酸受到人们的广泛关注。在过去几十年,科学家们在CO_2加氢制备甲酸方面不断取得进展,而由CO_2为原料合成高级羧酸也是人们一直追求的目标。但是,目前通常需要利用昂贵的或者对空气/水敏感的底物(比如格氏试剂、不饱和烃、有机卤化物等),并且使用硅     

多聚磷酸存在下取代6-苄硫基嘧啶与羧酸的环合反应研究

以多聚磷酸(PPA)为催化剂, 对取代6-苄硫基嘧啶与羧酸的反应进行了研究. 当羧酸为脂肪酸时, 在60-80 ℃下反应, 可选择性地得到6-苄硫基嘌呤衍生物; 改用芳香酸时, 则得到硫上的苄基被脱除的6-巯基嘌呤和嘧啶并[5,4-d]噻唑; 如果将嘧啶4-位上伯胺取代基变成仲胺取代基, 只得到嘧啶并[5,4-d]噻唑. 通过双途径反应机理对上述现象进行了解释.     

Reactions of Disulfides Derived from Penicillin Sulfoxides with Tertiary Phosphines in Presence of Carboxylic Acids

A novel method for the preparation of thioesters starting from Iso-Fujisawa disulfides is reported. The presence of an acylamino group cis to the disulfide function on the β-lactam nucleus seems to be an essential requirement for this reaction. In the absence of such a cis-acylamino group, desulfurization, is the preferred course.     

Crucial Roles of Two Hydrated Mg2+ Ions in Reaction Catalysis of the Pistol Ribozyme

Pistol ribozymes constitute a new class of small self‐cleaving RNAs. Crystal structures have been solved, providing three‐dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre‐catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg²⁺ ion remains innersphere‐coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg²⁺ ion that approaches the scissile phosphate from its binding site in the pre‐cleavage state to reach out for water‐mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg²⁺ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme‐catalyzed backbone cleavage.     

Formation of y + 10 and y + 11 Ions in the Collision-Induced Dissociation of Peptide Ions

Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many cases these persist even when creating consensus spectra for inclusion in spectral libraries, where it is important to determine whether these peaks represent new fragmentation paths or arise from impurities. Using spectra from libraries and synthesized peptides, we investigate a class of fragment ions corresponding to y_n-1 + 10 and y_n-1 + 11, where n is the number of amino acid residues in the peptide. These 10 and 11 Da differences in mass of the y ion were ascribed before to the masses of [+ CO – H₂O] and [+ CO – NH₃], respectively. The mechanism is suggested to involve dissociation of the N-terminal residue at the CH-CO bond following loss of H₂O or NH₃. MS³ spectra of these ions show that the location of the additional 10 or 11 Da is at the N-terminal residue. The y_n-1 + 10 ion is most often found in peptides with N-terminal proline, asparagine, and histidine, and also with serine and threonine in the adjacent position. The y_n-1 + 11 ion is observed predominantly with histidine and asparagine at the N-terminus, but also occurs with asparagine in positions two through four. The intensities of the y_n-1 + 10 ions decrease with increasing peptide length. These data for y_n-1 + 10 and y_n-1 + 11 ion formation may be used to improve peptide identification from tandem mass spectra.     

镁离子存在下乙醇-水混合溶液中碳酸钙结晶行为的研究

通过对不同反应体系中合成样品的物相及镁含量变化规律的分析, 认为水溶液中碳酸钙的结晶遵循溶解重结晶机理, 乙醇-水溶液中则以聚集重构为主, 碳酸根阴离子的溶剂化作用对碳酸钙的沉积产生显著影响. 采用XRD, IR等手段对醇水混合溶液中合成的碳酸钙样品进行分析, 认为形成了含镁方解石及具有类白云石结构的过渡相同时存在的混合物相, 醇水溶液中含镁方解石趋于白云石化.     

Efficient and Selective Formation of Unsaturated Carboxylic and Phenylacetic Acids from Diketene

A nickel catalyst promotes the multicomponent coupling reaction of diketene, an alkyne, and Me₂Zn to provide 3‐methylene‐4‐hexenoic acids in excellent yields. Under similar conditions, the combination of the nickel catalyst and Et₂Al(OEt) promotes a cycloaddition reaction involving dimerization of an alkyne to furnish phenylacetic acids. In the presence of PPh₃, a formal [2+2+1+1] cycloaddition reaction proceeds to afford regioisomeric phenylacetic acids via cleavage of the C?C bond.     

高锰酸钾-鲁米诺反应体系中碱土金属离子Mg2+,Ca2+,Sr2+,Ba2+化学发光行为研究

将被认为没有化学发光活性的第二主族(碱土金属)离子Mg^2 ,Ca^2 ,Sr^2 ,Ba^2 溶液注入到已充分反应的高锰酸钾与鲁米诺混合液中时,又发生了新的化学发光反应,并检测到强的化学发光信号．在对有关反应的动力学性质、化学发光光谱、紫外可见光谱及其它一系列实验研究的基础上,提出了可能的化学发光反应机理．同时,优化了反应条件,评价了这一反应用于Mg^2 ,Ca^2 ,Sr^2 ,Ba^2 分析的可行性．     

Selective and Efficient Oxidation of Aldehydes to Their Corresponding Carboxylic Acids Using H2O2/HCl in the Presence of Hydroxylamine Hydrochloride

A wide variety of aldehydes were efficiently converted to their corresponding carboxylic acids in high yields using H₂O₂/HCl in the presence of hydroxylamine hydrochloride. In addition, selective oxidation of aldehydes in the presence of other functional groups such as hydroxyl group, carbon‐carbon double bond and other heteroatoms can be considered a noteworthy advantage of this method.     

Direct Synthesis of Tri-/Difluoromethyl Ketones from Carboxylic Acids by Cross-Coupling with Acyloxyphosphonium Ions

A simple and straightforward approach to the synthesis of trifluoromethyl and difluoromethyl ketones from widely available carboxylic acids is disclosed. The transformation utilizes an acyloxyphosphonium ion as the active electrophile, conveniently generated in situ from the carboxylic acid substrate by using commodity chemicals. The utility of the reaction system is exemplified by its chemoselectivity, with tolerance to a variety of important functional groups. The late-stage functionalization of carboxylic acid active pharmaceutical ingredients and pharmaceutically relevant compounds is also discussed.     

Deoxygenative Deuteration of Carboxylic Acids with D2O

We report a general, practical, and scalable means of preparing deuterated aldehydes from aromatic and aliphatic carboxylic acids with D₂O as an inexpensive deuterium source. The use of Ph₃P as an O‐atom transfer reagent can facilitate the deoxygenation of aromatic acids, while Ph₂POEt is a better O‐atom transfer reagent for aliphatic acids. The highly precise deoxygenation of complex carboxylic acids makes this protocol promising for late‐stage deoxygenative deuteration of natural product derivatives and pharmaceutical compounds.