用密度泛函方法研究质子化苯基丙酮-水团簇

The structure and growth trend of the protonated acetophenone-water clusters have been investigated using the DFT-B3LYP method combined with the standard 6-31+G(d,p) basis set. In order to obtain more accurate single-point energy the B3LYP/6-311++G(3df,2p) method was adapted. The results show that the formation of H+C8H8O-H2O is a barrierless reaction process and the equilibrium distance between the proton and the O atom in C8H8O molecule is 1.015 A. For H+C8H8O-(H2O)n(n=1,2,3) clusters, the proton lies between the acetophenone molecule C8H8O and the water molecule H2O. The distance between the proton and the O atom of the C8H8O molecule increased from n=1 to n=3; C8H8O-H+-H2O can be regarded as an solvation shell. For H+C8H8O (H2O)n (n=4,5,6,7,8) clusters, the proton lies between the two H2O molecules forming a H5O2+ structure, C8H8O-H5O2+ is an important structure, which the other H2O molecules will attack from different sides.     

Nonempirical conformational analysis of oubaine molecule chelate complexes with Ca2+ and possible mechanism of modulation of transductor function of Na+,K+-ATPhase

Complete conformational analysis of chelate complex of oubaine molecule with Ca²⁺ in 1:1 stoichiometry is carried out. Complete ab initio optimization of geometric parameters of all possible structures of the complexes is performed in the framework of restricted Hartree-Fock method with 6–31G* basis using GAMESS program. Influence of the complex formation on the steric structure and electronic structure of oubaine molecule is analyzed. Oubaine molecule is found capable of binding Ca²⁺ by two modes. Mechanism of binding of oubaine molecule with transductor site of Na⁺,K⁺-ATPhase is proposed: ligand-receptor interaction is assumed to be realized in account of formation of trial complex oubaine-Ca²⁺-Na⁺,K⁺-ATPhase, with main contribution to the interaction energy of ion-ion bonds formation between Ca²⁺ and nucleophilic functional groups in the composition of the mentioned binding site of Na⁺,K⁺-ATPhase.     

Crystallization-controlled dynamic self-assembly and an on/off switch for equilibration using boronic ester formation

Macrocyclic boronic esters of different sizes can be prepared selectively from the same starting diboronic acid and 1,2-diol by means of an interesting dynamic self-assembly phenomena. More specifically, two kinds of macrocyclic boronic esters could be formed diastereoselectively and nearly quantitatively under neutral conditions by the addition of an appropriate guest molecule that acts as a template. Although a mixture of tetrol 1 and di(boronic acid) 2 in methanol gave only insoluble polymeric boronic esters, a soluble macrocyclic boronic ester, homo-[2+2], was obtained selectively in the presence of toluene as a guest molecule. Furthermore, when benzene was employed as a guest molecule, the selective formation of another macrocyclic boronic ester, hetero-[3+3], occurred. Interestingly, each of these macrocycles could be converted into the other in the presence of methanol and the appropriate guest molecule; however, under aprotic conditions, guest molecules encaged by the macrocyclic boronic ester could be exchanged without affecting its structure. Thus the presence or absence of a protic solvent could be used as a regulator to switch on or off the dynamic equilibrium of the system. In addition, investigation of the effect of reaction time, direct observation of the reaction mixture by NMR spectroscopy, and carrying out the reaction using optically active tetrol suggested that precipitation plays an essentially important role in the selective formation of the macrocyclic boronic esters. Thus, although both of [2+2] and [3+3] were present as solutes in the reaction mixture, the type of added guest molecule induced the selective precipitation of only one form of macrocyclic boronic ester, hence displacing the equilibrium of the system.     

Gas phase attachment of water and methanol to Ag(I) complexes with alpha-amino acids in an ion trap mass spectrometer

Electrospray ionization was used to generate gas phase complexes of Ag+ with selected alpha-amino acids. Following storage (isolation without collisional activation) in an ion trap mass spectrometer, the mass spectra produced from the complexes of Ag+ with alpha-amino acids such as alanine, valine and tert-leucine contained peaks consistent with the formation of water or methanol molecule adduct ions. The same adduct ions were not present, however, in the mass spectra generated from the Ag+ complexes with phenylalanine, tyrosine and tryptophan following isolation and storage under similar conditions. For those complexes that showed reactivity, the uptake of water and methanol increased with longer storage times in the ion trap. A preliminary molecular modeling study using phenylalanine demonstrated that the aromatic ring coordinates the Ag+ ion, and the interaction between the metal ion and pi-system, in part, is assumed to prohibit the binding of water or methanol during isolation in the gas phase. This conclusion is supported by a comparison of the adduct formation by the Ag+ complexes with phenylalanine, 4-fluorophenylalanine and alpha-aminocyclohexanepropionic acid. In addition, collision induced dissociation experiments involving the Ag+ complexes of phenylalanine, tyrosine and tryptophan suggest that limiting the coordination of the Ag ion by the complexing molecule (i.e. by loss of a coordinating functional group and/or change in structure due to dissociation) results in the binding of a water or methanol molecule during storage in the ion trap. Surprisingly, the bare Ag+ ion, when trapped and stored under identical experimental conditions, formed neither adduct species, suggesting that the attachment of water or methanol may be due to interactions with a molecular orbital within the Ag+/molecule complex.     

The kinetics study of the S + S2 → S3 reaction by the chaperone mechanism

The recombination of S atoms has been found to be stepwise from the smallest unit, the elemental S atom, to the most abundant molecule S(8). The reaction between S + S(2) → S(3) has not been reported either experimentally or by theory, but may be a key intermediate step in the formation of sulfur aerosols in low-O(2) atmospheres. In this work, the kinetics of this reaction is reported with Ar gas used as the chaperone molecule in the production of S(3) via two complex intermediates: SAr + S(2) and S(2)Ar + S. Quasi-classical and classical trajectory methods are used. The rate constant of the S + S(2) + Ar → S(3) + Ar reaction is determined to be 2.66 × 10(-33) cm(6) mol(-1)?s(-1) at 298.15 K. The temperature dependence of the reaction is found to be 2.67 × 10(-33) exp[143.56(1∕T-1∕298.15)]. The second-order rate constant of S + S(2) → S(3) is 6.47 × 10(-14) cm(3)?molecule(-1)?s(-1) at 298.15 K and the Arrhenius-type rate constant is calculated to be 6.25 × 10(-14) exp[450.15(1∕T-1∕298.15)] cm(3)?molecule(-1)?s(-1). This work provides a rate coefficient for a key intermediate species in studies of sulfur formation in the modern Venus atmosphere and the primitive Earth atmosphere, for which assumed model rate coefficients have spanned nearly 4 orders of magnitude. Although a symmetry-induced mass-independent isotope effect is not expected for a chaperone mechanism, the present work is an important step toward evaluating whether mass-independence is expected for thiozone formation as is observed for ozone formation.     

Structure and decompression melting of a novel, high-pressure nanoconfined 2-D ice

Molecular dynamics (MD) simulations of water confined in nanospaces between layers of talc (system composition Mg(3)Si(4)O(10)(OH)(2) + 2H(2)O) at 300 K and pressures of approximately 0.45 GPa show the presence of a novel 2-D ice structure, and the simulation results at lower pressures provide insight into the mechanisms of its decompression melting. Talc is hydrophobic at ambient pressure and temperature, but weak hydrogen bonding between the talc surface and the water molecules plays an important role in stabilizing the hydrated structure at high pressure. The simulation results suggest that experimentally accessible elevated pressures may cause formation of a wide range of previously unknown water structures in nanoconfinement. In the talc 2-D ice, each water molecule is coordinated by six O(b) atoms of one basal siloxane sheet and three water molecules. The water molecules are arranged in a buckled hexagonal array in the a-b crystallographic plane with two sublayers along [001]. Each H(2)O molecule has four H-bonds, accepting one from the talc OH group and one from another water molecule and donating one to an O(b) and one to another water molecule. In plan view, the molecules are arranged in six-member rings reflecting the substrate talc structure. Decompression melting occurs by migration of water molecules to interstitial sites in the centers of six-member rings and eventual formation of separate empty and water-filled regions.     

Search of nature of planar chirality for pendent benzodiazacoronands in the solid state: NMR, X-ray, and DFT studies

In this work, we report the structural studies on the solid state of two benzodiazacoronads that form chiral and achiral crystals. Crystals have to be considered as a two-component system consisting of an organic unit and a water molecule in 1:1 ratio. Both components play an important role in the crystal structure. The strong (O-H...O, N-H...O) and weak (C-H...O) intermolecular hydrogen bonds are responsible for phase organization and, in consequence, formation of chiral or achiral crystals. The alignment of the water molecule with respect to the macrocycle is different for samples 1 and 2. Removal of water from the crystal lattice of 1 is reversible. Formation of chiral cocrystals from two different achiral molecules by self-assembly is well-known. However, in this paper, we show that the water molecule can be an important achiral cofactor responsible for chiral crystallization.     

Speed Tuning of the Formation/Dissociation of a Metallorotaxane

Switching between the formation/dissociation of rotaxanes is important to control the function of various types of rotaxane-based materials. We have developed a convenient and simple strategy, the so-called “accelerator addition”, to make a static rotaxane dynamic without apparently affecting the chemical structure. As an interlocked molecule that enables tuning of the formation/dissociation speed, a metallorotaxane was quantitatively generated by the complexation of a triptycene-based dumbbell-shaped mononuclear complex, [PdL₂]²⁺ (L=2,3-diaminotriptycene), with 27C9. As a result of the inertness of the Pd²⁺-based coordination structure, the metallorotaxane was slowly formed (the static state). This rotaxane formation was accelerated 27 times simply by adding Br⁻ as an accelerator (the dynamic state). A similar drastic acceleration was also demonstrated during the dissociation process when Cs⁺ was added to the metallorotaxane to form the free axle [PdL₂]²⁺ and the 27C9-Cs⁺ complex.     

An atomistic level description of guest molecule effect on the formation of hydrate crystal nuclei by <Emphasis Type="Italic">ab initio</Emphasis> calculations

In the present study, we report the results of a systematic investigation of cage-like water structures using the first-principles calculations. These results show that, in the case of methane hydrate, the following nucleation mechanism can be revealed. The formation of small water cavities filled with methane is the first step of the formation of methane hydrate. It is not necessary to occupy all dodecahedral cages by guest molecules. After that small cavities start to form the H-bonding network with surrounding water molecules and a small number of water molecules is enough for the formation of a stable hydrogen-bonding network. The structural information contained in such nuclei is conserved in the forming crystal. Moreover, the presence of a methane molecule between small cages is also important to prevent the adhesion of cavities. It found that the ozone molecule can also stabilize the small cage since the value of the interaction energy between the ozone guest and the water host framework is very close to that obtained for the methane case. However, ozone affects the structure of large cavities and hence, the second guest is necessary to stabilize the hydrate structure.     

Water-catalyzed gas-phase hydrogen abstraction reactions of CH3O2 and HO2 with HO2: a computational investigation

The gas-phase hydrogen abstraction reactions of CH(3)O(2) and HO(2) with HO(2) in the presence and absence of a single water molecule have been studied at the CCSD(T)/6-311++G(3d,2p)//B3LYP/6-311G(2d,2p) level of theory. The calculated results show that the process for O(3) formation is much faster than that for (1)O(2) and (3)O(2) formation in the water-catalyzed CH(3)O(2) + HO(2) reaction. This is different from the results for the non-catalytic reaction of CH(3)O(2) + HO(2), in which almost only the process for (3)O(2) formation takes place. Unlike CH(3)O(2) + HO(2) reaction in which the preferred process is different in the catalytic and non-catalytic conditions, the channel for (3)O(2) formation is the dominant in both catalytic and non-catalytic HO(2) + HO(2) reactions. Furthermore, the calculated total CVT/SCT rate constants for water-catalyzed and non-catalytic title reactions show that the water molecule doesn't contribute to the rate of CH(3)O(2) + HO(2) reaction though the channel for O(3) formation in this water-catalyzed reaction is more kinetically favorable than its non-catalytic process. Meanwhile, the water molecule plays an important positive role in increasing the rate of HO(2) + HO(2) reaction. These results are in good agreement with available experiments.     

Komplexe mit makrocyclischen Liganden I. Mechanismus der Komplexbildung zwischen Ni2+ und 1,4,8,11-Tetraazacyclotetradecan

The kinetics of the formation of the Ni^II-complex with 1,4,8,11-tetraazacyclotetradecan (Cyclam) are studied by spectrophotometric and potentiostatic methods. The reaction of Ni²⁺ with the cyclic ligand is about 30000 times slower than with the open chain triethylenetetraamine (Trien). Therefore the rate determining step with Cyclam can not be the dissociation of the first coordinated water molecule, as it is usually in complexation reactions, but it must be the formation of the second coordinative bond. This is considered to be due to the more rigid structure of Cyclam in comparison with Trien.     

Matrix-isolated diglycolic anhydride: vibrational spectra and photochemical reactivity

The structure of diglycolic anhydride (1,4-dioxane-2,6-dione; DGAn) isolated in a low-temperature argon matrix at 10 K was studied by means of FTIR spectroscopy. Interpretation of the experimental vibrational spectrum was assisted by theoretical calculations at the DFT(B3LYP)/aug-cc-pVTZ level. The optimized structure of the isolated DGAn molecule adopts an envelope conformation, which was found to resemble closely the structure of DGAn in a crystal. The UV-induced (lambda > 240 nm) photolysis of the matrix-isolated compound was also investigated. In order to identify the main species resulting from irradiation of the monomeric DGAn, a comparison between the DFT(B3LYP)/aug-cc-pVTZ calculated spectra of the putative products and the experimental data was carried out. The observed photoproducts can be explained by a model involving four channels: (a) 1,3-dioxolan-4-one + CO; (b) CO2 + CO + oxirane; (c) formaldehyde + ketene + CO2; (d) oxiran-2-one + oxiran-2-one. As a whole, the experiments indicated that the C-O-C bridge, connecting the two C=O groups, is the most reactive fragment in the molecule excited with UV light. This observation was confirmed by the natural bond orbital (NBO) analysis revealing that the most important NBO interactions are those between the carbonyl groups and the adjacent C-O and C-C bonds.     

含甲硫氨酸二肽的单电子氧化反应：激光闪光光解研究

运用248nm激光光解瞬态吸收光谱研究了中性水溶液中丙氨酰甲硫氨酸(Ala-Met)和N-甲酰甲硫氨酰色氨酸(N-Formyl-Met-Trp)的单电子氧化反应过程,分别观察到+和含硫三电子键的生成,但在N-甲酰甲硫氨酰色氨酸体系中没有观察到\+的生成。提出了+和含硫三电子键的生成机理,认为N-甲酰甲硫氨酰色氨酸体系不能生成+三电子键是源于其本身的分子结构。     

Further studies on the origins of asymmetric charge partitioning in protein homodimers

Dissociation of gas-phase protonated protein dimers into their constituent monomers can result in either symmetric or asymmetric charge partitioning. Dissociation of alpha-lactalbumin homodimers with 15+ charges results in a symmetric, but broad, distribution of protein monomers with charge states centered around 8+/7+. In contrast, dissociation of the 15+ heterodimer consisting of one molecule in the oxidized form and one in the reduced form results in highly asymmetric charge partitioning in which the reduced species carries away predominantly 11+ charges, and the oxidized molecule carries away 4+ charges. This result cannot be adequately explained by differential charging occurring either in solution or in the electrospray process, but appears to be best explained by the reduced species unfolding upon activation in the gas phase with subsequent separation and proton transfer to the unfolding species in the dissociation complex to minimize Coulomb repulsion. For dimers of cytochrome c formed directly from solution, the 17+ charge state undergoes symmetric charge partitioning whereas dissociation of the 13+ is asymmetric. Reduction of the charge state of dimers with 17+ charges to 13+ via gas-phase proton transfer and subsequent dissociation of the mass selected 13+ ions results in a symmetric charge partitioning. This result clearly shows that the structure of the dimer ions with 13+ charges depends on the method of ion formation and that the structural difference is responsible for the symmetric versus asymmetric charge partitioning observed. This indicates that the asymmetry observed when these ions are formed directly from solution must come about due either to differences in the monomer conformations in the dimer that exist in solution or that occur during the electrospray ionization process. These results provide additional evidence for the origin of charge asymmetry that occurs in the dissociation of multiply charged protein complexes and indicate that some solution-phase information can be obtained from these gas-phase dissociation experiments.     

On the spectacular structural isomorphism between CnHs monoradical and Cn+sHs+3 diradical benzenoid hydrocarbons: from reactive intermediates to vacancy (Hole) defects in graphite

The formula/structure informatics of monoradical and diradical benzenoid hydrocarbons that are potential reactive intermediates is studied. Some new enumeration and structural results with analytical expressions are presented. The topological paradigm and one-to-one correspondence between the monoradical and diradical constant-isomer series is demonstrated. Constant-isomer benzenoid monoradicals of the formula CnHs have a one-to-one correspondence in isomer number and topology to constant-isomer diradicals of the formula Cn+sHs+3. Some electronic properties of benzenoid radicals are delineated. Excising out a monoradical or diradical benzenoid carbon molecule from a perfect hexagonal graphite layer leaves a matching monoradical or diradical vacancy hole defect called an antimolecule; this observation can be generalized to include excising out all nondisjoint and obvious benzenoid polyradicals from a perfect (Kekuléan) hexagonal graphite layer. It is shown that the characteristics of graphite vacancies (antimolecules) can be deduced from knowledge about the carbon molecules removed in their formation.     

潮湿空气微波放电离子形成动力学

利用微波放电电离质谱装置，通过水蒸气与空气混合气体（潮湿空气）的微波放电，同时获得了化学电离质谱探测技术中常用的三种重要母体离子H3O＋、NO＋和.结合潮湿空气中主要成分N2、O2以及水蒸气各自微波放电后的质谱探测结果，对潮湿空气微波放电后上述三种离子产生的动力学过程进行了分析，并给出了各种离子的形成机制.这些离子 分子反应过程在计算机模拟中得到了进一步的证实.     

Ion trap tandem mass spectrometric identification of thiabendazole phototransformation products on titanium dioxide

The purpose of this study is to artificially produce degradation intermediates of thiabendazole, which could be reasonably similar to those really present in the environment. The formation of by-products from thiabendazole transformation has been evaluated by adopting irradiated titanium dioxide as a photocatalyst. Several species more hydrophilic than the thiabendazole have been identified and characterized by HPLC-multiple MS. A pattern of reactions accounting for the observed intermediates is proposed. Two different parallel pathways are operating (and through these pathways the transformation of the molecule proceeds) leading to several intermediate compounds. The main steps involved are: (1) the hydroxylation of the molecule on the aromatic ring with the formation of a species having [M+H]+ 218; a further oxidation leads to the ring-opening and to the formation of aldehydic and alcoholic structures ([M+H]+ 270, 268 and 152); and (2) the cleavage of a C-C bond and the formation of a species having [M+H]+ 119.     

Topochemical 3D polymerization of C60 under high pressure at elevated temperatures

Fullerene C60 monomer crystals were compressed to a face-centered cubic (fcc) phase with a lattice parameter of a = 11.93(5) A and a micro-Vickers hardness of 4500 kg/mm2 using high-pressure and high-temperature conditions of 15 GPa at 500-600 degrees C. The hardness is compatible with that of cubic boron nitride (c-BN), suggesting the formation of a 3D C60 polymer. The single-crystal X-ray structural analysis revealed that each C60 molecule in the polymer was linked to the 12 nearest neighbors by [2+2] cycloaddition between the common pentagon-hexagon (56) edges. However, ab initio geometry optimization and molecular dynamics calculations suggested that the 3D polymer should have a rhombohedral structure with the space group of R containing [3+3] cycloaddition between the pentagons of C60 molecules within the plane perpendicular to the 3-fold axis. The higher apparent symmetry of fcc was observed as an averaged structure of different orientations of the rhombohedral structure. The R structure can be derived by only a slight rotation of each C60 unit in the (111) plane of the fcc structure. The band-structure calculation suggested that the 3D polymer (R) was a semiconductor; the activation energy for the electrical conductivity was experimentally determined to be 0.25 eV at 550 K.     

The surface dependence of CO adsorption on Ceria

An understanding of the interaction between ceria and environmentally sensitive molecules is vital for developing its role in catalysis. We present the structure and energetics of CO adsorbed onto stoichiometric (111), (110), and (100) surfaces of ceria from first principles density functional theory corrected for on-site Coulomb interactions, DFT+U. DFT+U is applied because it can describe consistently the properties of both the stoichiometric and reduced surfaces. Our major finding is that the interaction is strongly surface dependent, consistent with experiment. Upon interaction of CO with the (111) surface, weak binding is found, with little perturbation to the surface or the molecule. For the (110) and (100) surfaces, the most stable adsorbate is that in which the CO molecule bridges two oxygen atoms and pulls these atoms out of their lattice sites, with formation of a (CO(3)) species. This results in a strong modification to the surface structure, consistent with that resulting from mild reduction. The electronic structure also demonstrates reduction of the ceria surface and consequent localization of charge on cerium atoms neighboring the vacancy sites. The surface-bound (CO(3)) species is identified as a carbonate, (CO(3))(2-) group, which is formed along with two reduced surface Ce(III) ions, in good agreement with experimental infrared data. These results provide a detailed investigation of the interactions involved in the adsorption of CO on ceria surfaces, allowing a rationalization of experimental findings and demonstrate further the applicability of the DFT+U approach to the study of systems in which reduced ceria surfaces play a role.     

Inhibition mechanism of lanthanum ion on the activity of horseradish peroxidase in vitro

In order to understand the inhibition mechanism of lanthanum ion (La³⁺) on the activity of horseradish peroxidase (HRP), the effects of La³⁺ on the activity, electron transfer and conformation of HRP in vitro were investigated by using cyclic voltammetry (CV), atomic force microscopy (AFM), circular dichroism (CD), high performance liquid chromatography (HPLC), matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF/MS) and inductively coupled plasma mass spectrometry (ICP-MS). It was found that La³⁺ can combine with the amide groups of the polypeptide chain in HRP molecule, forming the complex of La³⁺ and HRP (La-HRP). The formation of the La-HRP complex causes the destruction of the native structure of HRP molecule, leading to the decrease in the non-planarity of the porphyrin ring in the heme group of HRP molecule, and then in the exposure extent of active center, Fe(III) of the porphyrin ring of HRP molecule. Thus, the direct electrochemical and catalytic activities of HRP are decreased. It is a possible inhibition mechanism of La³⁺ on the activity of peroxidase.