含羧酸镁(钙)官能团的多孔芳香骨架材料储氢性能的预测

用MP2方法,TZVPP基组以及基组重叠误差(BSSE)校正计算了氢分子与修饰在多孔芳香骨架(PAF)上的羧酸镁、羧酸钙官能团的相互作用,并建立了描述这一相互作用的分子力学力场.在此基础上用巨正则系综蒙特卡洛(GCMC)模拟预测了氢气在该种新型PAF材料上的吸附等温线.量子化学计算结果表明,每个羧酸镁、羧酸钙官能团分别可以提供13、14个氢分子吸附位点,与每个氢分子的平均结合能在8kJ·mol-1左右.通过比较不同温度和压力下材料的绝对吸附量和超额吸附量发现,在PAF骨架中引入羧酸镁、羧酸钙官能团可以显著提高材料的综合储氢性能,达到并超过了美国能源部提出的2015年储氢标准.同时该工作还揭示了氢吸附量与材料的表面积、空腔体积和分子作用强度间的复杂关系.     

Role of the uranyl oxo group as a hydrogen bond acceptor

Density functional theory calculations have been used to evaluate the geometries and energetics of interactions between a number of uranyl complexes and hydrogen bond donor groups. The results reveal that although traditional hydrogen bond donors are repelled by the oxo group in the [UO(2)(OH(2))(5)](2+) species, they are attracted to the oxo groups in [UO(2)(OH(2))(2)(NO(3))(2)](0), [UO(2)(NO(3))(3)](-), and [UO(2)Cl(4)](2-) species. Hydrogen bond strength depends on the equatorial ligation and can exceed 15 kcal mol(-1). The results also reveal the existence of directionality at the uranyl oxo acceptor, with a weak preference for linear U═O---H angles.     

Designing novel materials through functionalization of carbon nanotubes for application in nuclear waste management: speciation of uranyl

Understanding the behavior of radioactive nuclide elements in different environmental conditions is an active area of research. In this work, we have investigated the possible interaction mechanism between carbon nanotubes and uranyl using density functional theory. It is shown that functionalized carbon nanotubes can be used to bind uranyl ions much more efficiently as compared to their unfunctionalized counterpart. The uranyl binding energies are sensitive to the nature of the functional groups rather than the carbon nanotube itself. The binding takes place preferably at the functionalized sites, although pH could determine the strength of uranyl binding. Our predicted results correlate well with the recent experimental uranyl sorption studies on carbon nanotubes. These finding are new and can open up a new era for actinide speciation and separation chemistry using carbon nanotubes.     

Can functionalized cucurbituril bind actinyl cations efficiently? A density functional theory based investigation

The feasibility of using cucurbituril host molecule as a probable actinyl cation binders candidate is investigated through density functional theory based calculations. Various possible binding sites of the cucurbit[5]uril host molecule to uranyl are analyzed and based on the binding energy evaluations, μ(5)-binding is predicted to be favored. For this coordination, the structure, vibrational spectra, and binding energies are evaluated for the binding of three actinyls in hexa-valent and penta-valent oxidation states with functionalized cucurbiturils. Functionalizing cucurbituril with methyl and cyclohexyl groups increases the binding affinities of actinyls, whereas fluorination decreases the binding affinities as compared to the native host molecule. Surprisingly hydroxylation of the host molecule does not distinguish the oxidation state of the three actinyls.     

Theoretical study of the uranyl complexation by hydroxamic and carboxylic acid groups

A theoretical study on the complexation of uranyl cation (UO2(2+)) by three different functional groups of a calix[6]arene cage, that is, two hydroxamic and a carboxylic acid function, has been carried out using density functional theory calculations. In particular, interaction energies between the uranyl and the functional groups have been used to determine their affinity toward uranyl, whereas pKa calculations give some information on the availability of the functional groups in the extraction conditions. On the one hand, calculations of the interaction energies have pointed out clearly a better affinity with the hydroxamic groups. The stabilization of this complex was rationalized in terms of a stronger electrostatic interaction between the uranyl cation and the hydroxamic groups. The presence of a water molecule in the first coordination sphere of uranyl does not destabilize the complex, and the most stable complex is obtained with two functional groups and two water molecules, leading to a coordination number of 8 for the central uranium atom. On the other hand, pKa theoretical evaluation shows that both hydroxamic (deprotonated on the oxygen site) and carboxylic groups are potential extractants in aqueous medium with a preference for carboxylic functions at low pH. Moreover, these data allowed to unambiguously identify the oxygen of the alcohol function as the favored deprotonation site on the hydroxamic function.     

Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study

Trivalent lanthanide cations are extensively being used in biochemical experiments to probe various dication-binding sites in proteins; however, the factors governing the binding specificity of lanthanide cations for these binding sites remain unclear. Hence, we have performed systematic studies to evaluate the interactions between La3+ and model Ca2+ - and Mg2+ -binding sites using density functional theory combined with continuum dielectric methods. The calculations reveal the key factors and corresponding physical bases favoring the substitution of trivalent lanthanides for divalent Ca2+ and Mg2+ in holoproteins. Replacing Ca2+ or Mg2+ with La3+ is facilitated by (1) minimizing the solvent exposure and the flexibility of the metal-binding cavity, (2) freeing both carboxylate oxygen atoms of Asp/Glu side chains in the metal-binding site so that they could bind bidentately to La3+, (3) maximizing the number of metal-bound carboxylate groups in buried sites, but minimizing the number of metal-bound carboxylate groups in solvent-exposed sites, and (4) including an Asn/Gln side chain for sites lined with four Asp/Glu side chains. In proteins bound to both Mg2+ and Ca2+, La3+ would prefer to replace Ca2+, as compared to Mg2+. A second Mg2+-binding site with a net positive charge would hamper the Mg2+ --> La3+ exchange, as compared to the respective mononuclear site, although the La3+ substitution of the first native metal is more favorable than the second one. The findings of this work are in accord with available experimental data.     

DFT studies of uranyl acetate,carbonate, and malonate,complexes in solution

The aim of this work is to demonstrate that theoretical chemistry can be used as a complementary tool in determining geometric parameters of a number of uranyl complexes in solution, which are not observable by experimental methods. In addition, we propose plausible structures with partial geometric data from experimental results. A gradient corrected DFT methodology with relativistic effects is used employing a COSMO solvation model. The theoretical calculations show good agreement with experimental X-ray and EXAFS data for the triacetato-dioxo-uranium(VI) and tricarbonato-dioxo-uranium(VI) complexes and are used to assign possible geometries for dicalcium-tricarbonato-dioxo-uranium(VI) and malonato-dioxo-uranium(VI) complexes. The results of this exercise indicate that carbonate bonding in these complexes is mainly bidentate and that hydroxo bridging plays a critical role in the stabilization of the polynuclear uranyl complexes.     

Complexation of the carbonate, nitrate, and acetate anions with the uranyl dication: density functional studies with relativistic effective core potentials

The structures and vibrational frequencies of uranyl carbonates, [UO2(CO3)n](2-2n) and [(UO2)3(CO3)6]6-, uranyl nitrates, [UO2(NO3)n](2-n), and uranyl acetates, [UO2(CH3COO)n](2-n) (n = 1,2,3) have been calculated by using local density functional theory (LDFT). Only bidentate ligand coordination modes to the uranyl dication have been modeled. The calculated structures and frequencies are compared to available experimental data, including IR, Raman, X-ray diffraction, and EXAFS solution and crystal structure data. The energetics of ligand binding have been calculated using the B3LYP hybrid functional. In general, the structural and vibrational results at the LDFT level are in good agreement with experimental results and provide realistic pictures of solution phase and solid-state behavior. For the [UO2(CO3)3]6- anion, calculations suggest that complexity in the CO3(2-) stretching signature upon complexation is due to the formation of C=O and C-O domains, the latter of which can split by as much as 300 cm(-1). Assessment of the binding energies indicate that the [UO2(CO3)2]2- anion is more stable than the [UO2(CO3)3]4- anion due to the accumulation of excess charge, whereas the tri-ligand species are the most stable in the nitrate and acetate anions.     

Interaction of atrazine with Laurentian fulvic acid: binding and hydrolysis

Ultrafiltration fractionation and liquid chromatography (LC) have been applied to the study of the binding and hydrolysis of the polar herbicide atrazine on a stoichiometrically well characterized fulvic acid. Binding requires extensive carboxylate site protonation but the binding sites represent a very small fraction of total carboxylate. The data show that binding of atrazine is not competitive with binding of the hydrolytic product hydroxyatrazine. However, smaller molecular weight fractions of the fulvic acid mixture compete with atrazine for sites on the larger molecular weight fraction. Binding equilibrium is not rapid. A model of binding involving hydrogen bonding and/or charge-transfer complexing to specific sites created dynamically by the conformational equilibria of the higher molecular weight polymeric fulvic acid fractions is proposed as the best accommodation of the variety of observed facts.     

General molecular mechanics method for transition metal carboxylates and its application to the multiple coordination modes in mono- and dinuclear Mn(II) complexes

A general molecular mechanics method is presented for modeling the symmetric bidentate, asymmetric bidentate, and bridging modes of metal-carboxylates with a single parameter set by using a double-minimum M-O-C angle-bending potential. The method is implemented within the Molecular Operating Environment (MOE) with parameters based on the Merck molecular force field although, with suitable modifications, other MM packages and force fields could easily be used. Parameters for high-spin d (5) manganese(II) bound to carboxylate and water plus amine, pyridyl, imidazolyl, and pyrazolyl donors are developed based on 26 mononuclear and 29 dinuclear crystallographically characterized complexes. The average rmsd for Mn-L distances is 0.08 A, which is comparable to the experimental uncertainty required to cover multiple binding modes, and the average rmsd in heavy atom positions is around 0.5 A. In all cases, whatever binding mode is reported is also computed to be a stable local minimum. In addition, the structure-based parametrization implicitly captures the energetics and gives the same relative energies of symmetric and asymmetric coordination modes as density functional theory calculations in model and "real" complexes. Molecular dynamics simulations show that carboxylate rotation is favored over "flipping" while a stochastic search algorithm is described for randomly searching conformational space. The model reproduces Mn-Mn distances in dinuclear systems especially accurately, and this feature is employed to illustrate how MM calculations on models for the dimanganese active site of methionine aminopeptidase can help determine some of the details which may be missing from the experimental structure.     

Unusual co-ordination behaviour of imidazole-4-acetic acid. Synthesis, crystal structure and vibrational studies of one-dimensional co-ordination polymer of zinc(II) with two different ligand forms

This work is devoted to structural and vibrational studies of novel 1D polymeric zinc(II) complex [ZnCl(ia)(Hia)]·H₂O (infinity) [Hia=imidazole-4-acetic acid]. It has been found for the first time that the ia anion is acting as bidentate bridging ligand with N1 and carboxylate oxygen atoms as binding centres. The quasi-tetrahedral coordination polyhedron is completed by one chloride anion and monodentate Hia ligand bonded with zinc(II) cation via carboxylate oxygen atom. The compound crystallise in the triclinic P space group with Z=2. The polymer chains are held together by hydrogen bonding network involving the N---H and carboxylate groups, chloride ions and water molecules. The differences between normal vibrations of two ligand forms present in the complex are discussed on the basis of the density functional calculations (DFT) performed for natural and N-deuterated isotopomers. The assignment of the observed MIR and Raman bands is given in terms of potential energy distribution (PED).     

Complexation of uranium(VI) with aromatic acids in aqueous solution: a combined computational and experimental study

The complexes of uranium(VI) with salicylhydroxamate, benzohydroxamate, and benzoate have been investigated in a combined computational and experimental study using density functional theory methods and extended X-ray absorption fine structure spectroscopy, respectively. The calculated molecular structures, relative stabilities, as well as excitation spectra from time-dependent density functional theory calculations are in good agreement with experimental data. Furthermore, these calculations allow the identification of the coordinating atoms in the uranium(VI)-salicylhydroxamate complex, i.e. salicylhydroxamate binds to the uranyl ion via the hydroxamic acid oxygen atoms and not via the phenolic oxygen and the nitrogen atom. Carefully addressing solvation effects has been found to be necessary to bring in line computational and experimental structures, as well as excitation spectra.     

Effect of the TBP and water on the complexation of uranyl nitrate and the dissolution of nitric acid into supercritical CO2. A Theoretical Study

We report theoretical studies on the complexation of uranyl nitrate and the dissolution of nitric acid in supercritical CO2 by TBP. According to quantum mechanical calculations, TBP (modeled by trimethyl phosphate TMP) displays stronger hydrogen-bonding interactions with HNO3 than with H2O, and this has been modeled in force-field calculations. Different combinations of water, TBP, and acid are compared in SC-CO2 and simulated by molecular dynamics (MD), demonstrating the importance of TBP and water concentrations. In MD simulations, which started from "random" mixtures of water, TBP, nitric acid, and uranyl nitrate, complexation of uranyl by TBP is observed and the yield increases with the TBP concentration. TBP molecules are also necessary to dissolve nitric acid in the supercritical phase. Indeed, without TBP, nitric acid alone self aggregates via hydrogen-bonding interactions. Adding water to this solution leads to the formation of water microdomains containing the acid and uranyl salts. The simulations show that a high TBP/nitric acid ratio is needed to fully dissolve the acid in the supercritical phase and to form CO2-philic UO2(NO3)2(TBP)2 complexes. The resulting hydrogen-bonding and solvation patterns are analyzed. The results are consistent with experimental observations and provide microscopic views of this important extraction system.     

Structural features of humic acid of the coastal sediment in Ariake Sea tidelands: use of humic acid as an environmental indicator for river basins and coastal regions.

The structural features of humic acid (HA) at the sediment surface of the tideland at the Hayatsuegawa-river mouth at the Ariake Sea were investigated for the utilization of HA toward an environmental indicator of the features of the river basin and coastal region. 1H NMR analysis revealed a high-content hydrocarbon residue with a similar type of terrigenous HA. Direct and methylation-pyrolysis-GC analysis suggested the incorporation of long-chain carboxylate in HA in the tidelands. The incorporation of branched-chain carboxylate residues in HA is the result of the microbial decomposition of detritus; these residues could be one of the characteristic structural features of HA in this area, which is rich in biodiversity and microbial activity. Because the structural features of coastal zone HA appear to reveal the characteristics and activities of the biological environment, these findings suggest the possibility of becoming an indicator of the detailed analysis of the structural features of coastal zone HA.     

Interactions of 1-methylimidazole with UO2(CH3CO2)2 and UO2(NO3)2: structural, spectroscopic, and theoretical evidence for imidazole binding to the uranyl ion

The first definitive high-resolution single-crystal X-ray structure for the coordination of the 1-methylimidazole (Meimid) ligand to UO2(Ac)2 (Ac = CH3CO2) is reported. The crystal structure evidence is confirmed by IR, Raman, and UV-vis spectroscopic data. Direct participation of the nitrogen atom of the Meimid ligand in binding to the uranium center is confirmed. Structural analysis at the DFT (B3LYP) level of theory showed a conformational difference of the Meimid ligand in the free gas-phase complex versus the solid state due to small energetic differences and crystal packing effects. Energetic analysis at the MP2 level in the gas phase supported stronger Meimid binding over H2O binding to both UO2(Ac)2 and UO2(NO3)2. In addition, self-consistent reaction field COSMO calculations were used to assess the aqueous phase energetics of combination and displacement reactions involving H2O and Meimid ligands to UO2R2 (R = Ac, NO3). For both UO2(NO3)2 and UO2(Ac)2, the displacement of H2O by Meimid was predicted to be energetically favorable, consistent with experimental results that suggest Meimid may bind uranyl at physiological pH. Also, log(Knitrate/KAc) calculations supported experimental evidence that the binding stoichiometry of the Meimid ligand is dependent upon the nature of the reactant uranyl complex. These results clearly demonstrate that imidazole binds to uranyl and suggest that binding of histidine residues to uranyl could occur under normal biological conditions.     

New theoretical insight on the acid sites distribution,their local structures and acid strength of the SAPO‐11 molecular sieve

ONIOM(DFT:PM3) calculations were carried out to investigate and characterize possible acid sites of SAPO‐11 molecular sieve. Two functionals were employed: B3LYP and ωB97X‐D. This last functional includes dispersion effects that are absent in the former. Benzene, pyridine, and ammonia interaction energies as well as the OH stretching frequencies of the POH, SiOH, and bridged Si(OH)Al groups were used to characterize the acid sites. This work shows that the adsorption of benzene on the surface is as strong as the adsorptions inside main channel of SAPO‐11. Pyridine adsorption on the surface is weaker than the one corresponding to the main channel. NH₃ molecule interacts strongly with all OH groups or acid sites present in SAPO‐11. Moreover, the results reveal that it is possible to adsorb two NH₃ molecules at only one Brønsted site. The adsorption of the second NH₃ molecule is energetically favorable mainly due to the hydrogen bond formation between the NH₃ molecules. In general the interaction energy increases with the type of functional used, according to the trend ωB97X‐D > B3LYP. The results show that ONIOM methodology seems to be suited to investigate the acid sites in SAPO‐11.     

Determination of fusaric acid in maize using molecularly imprinted SPE clean‐up

A new LC method to detect fusaric acid (FA) in maize is reported based on a molecularly imprinted SPE clean‐up using mimic‐templated molecularly imprinted polymers. Picolinic acid was used as a toxin analog for imprinting polymers during a thermolytic synthesis. Both acidic and basic functional monomers were predicted to have favorable binding interactions by MP2 ab initio calculations. Imprinted polymers synthesized with methacrylic acid or 2‐dimethylaminoethyl methacrylate exhibited imprinting effects in SPE analysis. FA levels were determined using RP ion‐pairing chromatography with diode‐array UV detection and tetrabutylammonium hydrogen sulfate in the mobile phase. A method was developed to detect FA in maize using molecularly imprinted SPE analysis within the range of 1–100 μg/g with recoveries between 83.9 and 92.1%.     

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of ferulic acid by density functional study

Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of ferulic acid (FA) (4-hydroxy-3-methoxycinnamic acid) were carried out by using density functional (DFT/B3LYP/BLYP) method with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the FA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of FA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT-IR and FT-Raman spectra for the title molecule have been constructed.     

Energetics and structural elucidation of mechanisms for gas phase H/D exchange of protonated peptides

Hydrogen/deuterium exchange reactions involving protonated triglycine and deuterated ammonia (ND(3)) have been examined in the gas phase using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Ab initio and density functional theory (DFT) calculations have been carried out to model the exchanges and to obtain energetics and vibrational frequencies for molecules involved in the proposed exchange mechanisms. Structural optimization and frequency calculations have been performed at the B3LYP level of theory with the 6-311+G(d,p) basis set. Transition states have been calculated at the same level of theory and basis set as above using the QST2 and QST3 methods. Single-point energy calculations have been performed at the MP2/6-311+G(d,p) level. Six labile sites of protonated triglycine were found to undergo H/D exchange. Of these six labile hydrogens, two are amide, three are ammonium, and one is carboxyl. Detailed mechanisms for each of these transfers are proposed. Qualitative onium ion and tautomer mechanisms for the exchanges of ammonium and amide hydrogens, respectively, using semiempirical calculations were suggested in previous studies by Beauchamp et al. As shown by the current ab initio and DFT calculations completed during this study, the mechanisms proposed in that study are notionally correct; however, the tautomer mechanisms are shown here to be the result of the fact that a second stable isomer of protonated triglycine exists in which the amide1 carbonyl oxygen is protonated. The exchange of the carboxyl hydrogen is found to proceed via a transition state resembling an ammonium ion interacting with a carboxylate moiety via two hydrogen bonds. The current work thus provides significant mechanistic and structural detail for a considerably more in-depth understanding of the processes involved in gas phase H/D exchange of peptides.     

Binding constant of thorium with gray humic acid

Humic acid sample was separated from the bottom sediments of Lake Quarun, in Egypt. It was purified and characterized by elemental analysis, potentiometric titration, IR, UV-visible and ¹³C NMR spectroscopies. The product of humic acid was very low (0.009%), gray in color and has low carboxylate capacity (2.4 meq/g). The first derivative of the titration curve indicated one maximum only, which implies one kind of carboxylate groups. The binding constant of ²³⁴Th with Lake Quarun humic acid was determined by solvent extraction. Only one parameter, β ₁, was required to fit the binding as a function of carboxylate concentration: the Th⁴⁺ bound to the carboxylate sites in the gray humic acid forming 1:1 complex only. The binding constant increased with the degree of ionization and with the pK_a of the humic acid.