纳米二氧化硅物理吸附乙醇的密度泛函研究

利用密度泛函理论, 采用周期性边界条件及簇方法研究了无定型纳米二氧化硅的表面结构以及其对小分子吸附物乙醇的吸附性质. 计算结果表明, 小簇模型在研究特定种类的吸附方面具有优势, 而周期性切片模型更能真实地反映纳米二氧化硅的表面环境; 乙醇在二氧化硅表面的吸附主要依赖于氢键作用, 并倾向于充当氢键受体的角色.     

Interaction of nucleobases with proflavine on silica surface

The adsorption of purine and pyrimidine nucleobases from aqueous solutions on silica surface modified by preliminary adsorption of proflavine has been studied as depending on pH and adsorbate concentration. It has been shown that the bases interact with proflavine, the molecules of which are attached to neutral silanol groups of silica via hydrogen bonds. The equilibrium constants of the complexation reactions between the bases and adsorbed proflavine have been calculated.     

Investigating Alanine–Silica Interaction by Means of First‐Principles Molecular‐Dynamics Simulations

In our attempts to achieve a detailed understanding of protein–silica interactions at an atomic level we have, as a first step, simulated a small system consisting of one alanine in different protonation states, and a hydroxylated silica surface, using a first‐principles molecular‐dynamics technique. The simulations are carried out in vacuo as well as in the presence of water molecules. In the case of a negatively charged surface and an alanine cation, an indirect proton transfer from the alanine carboxylic group to the surface takes place. The transfer involves several water molecules revealing an alanine in its zwitterionic state interacting with the neutral surface through indirect hydrogen bonds mediated by water molecules. During the simulation of the zwitterionic state the ammonium group eventually establishes a direct ? N? H???O? Si interaction, suggesting that the surface–amino group interaction is stronger than the interaction between the surface and the carboxylic group. In vacuum simulations, the amino group exhibits clearly stronger interactions with the surface than the carboxylic group.     

Structures of dense glycine and alanine adlayers on chiral Cu(3,1,17) surfaces

Density Functional Theory calculations have been used to predict the structures of dense glycine and alanine adlayers on Cu(3,1,17)(S). Facets of this chiral Cu surface result from adsorbate-induced surface reconstruction when glycine or alanine are adsorbed and annealed on Cu(100). We have calculated the surface energy changes associated with this surface reconstruction. Our results allow the enantiospecificity of this reconstruction following adsorption of enantiopure or racemic alanine on Cu(100) to be discussed. The overall stability of glycine and alanine adlayers on Cu(3,1,17)(S) arises from an interplay between the formation of chemical bonds with the Cu surface, deformations in the adsorbed molecules during adsorption, and intermolecular hydrogen bonds within the adlayer; none of these factors individually dominates.     

DFT Study on the Effect of Hydrogen-bond Formation on the Adsorption of Aminotriazines on Graphene

DFT calculations have been performed to explore the aminotriazine adsorption on graphene surfaces.Relative energies,equilibrium geometries and electronic structures of monomer and dimer of aminotriazine molecules adsorbed at the surface were investigated and analyzed in details.It was found that the hydrogen atoms in the NH2 group of aminotriazine molecules are directed toward the graphene surface,and the adsorption energy increases as the NH2 group is added.The adsorbed aminotriazine molecules facilely form a dimer through the hydrogen bonding interactions,and the two aromatic rings of optimized structure of 2-amino-1,3,5-triazine(B) dimmer(denoted by B2) and melamine(D) dimmer(denoted by D2) are parallel to the graphene sheet.The large deviation of the averaged adsorption energy of B2 and D2 compared to monor adsorption may reflect the increase of π-π repulsion and the effect of hydrogen bond formation.The electronic structure analyses reveal that the formation of hydrogen bonds in melamine dimer has great influence on the adsorption mode at the graphene surface.     

Studies of adsorption of 2,2′-bipyridyl on the surface of highly regulated silica matrix of the MCM-41 type by means of <Superscript>15</Superscript>N NMR spectroscopy

The study of 2,2′-bipyridyl adsorption on the surface of highly regular MCM-41 silica at 300 and 130 K was carried out by the ¹⁵N NMR spectroscopy. It was shown that at 300 K the adsorbed molecules were involved in the processes of isotropic reorientation accompanied by the formation and rupture of hydrogen bonds with the surface-located hydroxy groups. Each molecule of 2,2′-bipyridyl forms no more than one hydrogen bond at a time, and their surface density is about one molecule per 1 nm² of the surface. At 130 K 2,2′-bipyridyl forms a monolayer on the surface of silica including about 1.6 molecule per 1 nm². In this monolayer each molecule forms a hydrogen bond with one hydroxy group and prevents the interaction of the other bipyridyl molecules with one more hydroxy group.     

二水合甘氨酸两性离子复合体的结构和性能的理论研究

采用理论计算方法B3LYP, 在6-31++G**基组水平研究使甘氨酸质子化所需的最少水分子数目, 然后讨论水合两性离子复合体的结构和性能, 进而计算了二水合甘氨酸中性分子复合体(2W-GN)到二水合甘氨酸两性离子复合体(2W-GZ)的过渡态, 得到如下结论: (1)两个水分子可以使甘氨酸质子化, 能够形成稳定的二水合两性离子复合体. (2)甘氨酸与水分子之间通过氢键相互作用, 结合能较大, 复合体稳定; 在二水合甘氨酸复合体中, 水合甘氨酸中性分子比水合甘氨酸两性离子稳定. (3)由2W-GN到2W-GZ过程的反应活化能和氢键键能相近.     

Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.     

Adsorption of hydrogen peroxide on functionalized mesoporous silica surfaces

MCM-41 and MSU-H mesoporous silicas were successfully functionalized with hydrogen bonds forming organic moieties, which have been proven by elemental analysis. Both moieties, based on oxygen and nitrogen containing groups, were introduced with high efficiency—the amount of carbon in all cases exceeded 10 % and the elemental ratios suggest binding to the surface through two or three Si–O–Si bonds. Hydrogen peroxide adsorption was conducted in its aqueous solutions and the amount adsorbed was determined using the ferric thiocyanate method. Results are presented as a function of hydrogen peroxide concentration in aqueous solution from 5 to 30 %. Both functionalized silicas show increased adsorption capacity when compared with that of their unfunctionalized analogues. The surface modified with nitrogen-based organic moiety revealed better adsorption properties as well as higher resistance against oxidation. MSU-H silica, due to its larger pore diameter, provides more space to bind hydrogen peroxide molecules and thus was found to have higher adsorption capacity: it adsorbed up to four times more hydrogen peroxide than MCM-41.     

Adsorption and thermal condensation mechanisms of amino acids on oxide supports. 1. Glycine on silica

Glycine was adsorbed on the surface of a well-defined silica from aqueous solutions of variable concentrations and pHs. The adsorbed molecules were characterized using middle-IR and UV-vis-NIR spectroscopies. Except at the lowest pH (2.0), they were predominantly present on the surface as zwitterions. Two successive deposition mechanisms were evidenced with increasing glycine concentration. At low concentrations, glycine is specifically adsorbed on silica surface sites, probably through its NH3+ moiety. The pH dependence suggests that these sites may be silanolate groups (approximately equal to Si-O-). At higher concentrations, specific adsorption sites are saturated and surface-induced precipitation of beta-glycine is observed. The thermal reactivity of adsorbed/deposited glycine was then investigated by thermogravimetric analysis, in situ diffuse reflectance IR spectroscopy, and thermoprogrammed desorption coupled with mass spectrometry. Adsorbed glycine molecules react to form peptide bonds at a temperature considerably lower than that for bulk crystalline alpha-glycine. The main reaction product is the cyclic dimer diketopiperazine, with no evidence of the linear dimer. The activation mechanism is not diffusionally limited; the formation of "surface acyls", previously proposed for related systems, has not been evidenced here. These findings are of relevance for the evaluation of prebiotic peptide synthesis scenarios.     

Theoretical and experimental study of the adsorption of neutral glycine on silica from the gas phase.

The adsorption of neutral glycine onto amorphous silica was investigated both theoretically and experimentally. DFT calculations were performed at the BLYP-631++G** level using a cluster approach. Several possible configurations involving the formation of H bonds between glycine and one, two, or three silanol groups (SiOH) were considered. The most favorable bonding of glycine with one silanol group (45 kJ mol(-1)) occurs through the COOH moiety, thus forming a cycle in which the CO group is an H-bond acceptor whereas the acidic OH group is an H-bond donor. With two or three silanol groups, additional H bonds are formed between the amine moiety and the silanol groups, which leads to an increased adsorption energy (70 and 80 kJ mol(-1) for two and three silanol groups, respectively). Calculated nu(CO), delta(HNH), and delta(HCH) values are sensitive to the adsorption mode. A bathochromic shift of nu(CO) as compared to the nu(CO) of free glycine (calculated in the 1755-1790 cm(-1) range) is found for glycine in interaction with silanol(s). The more H bonds are formed between the COOH moiety and silanol groups, the higher the bathochromic shift. For delta(HNH), no shift is found for glycine adsorbed on one and two silanol groups (where the amine is either not bound or an H-bond donor), whereas a bathochromic shift is calculated with three silanols when the amine moiety is an H-bond acceptor. Experimental FTIR spectra performed at room temperature for glycine adsorbed at 160 degrees C on Aerosil amorphous silica exhibit bands at 1371, 1423, 1630, and 1699 cm(-1). The experimental/calculated frequencies have their best correspondence for glycine adsorbed on two silanol groups. It is important to note that the forms giving the best correspondence to experimental frequencies are the most stable ones.     

Adsorption of 1-octanol at the free water surface as studied by Monte Carlo simulation

The adsorption of 1-octanol at the free water surface has been investigated by Monte Carlo computer simulation. Six different systems, built up by an aqueous and a vapor phase, the latter also containing various number of octanol molecules, have been simulated. The number of the octanol molecules has been chosen in such a way that the octanol surface density varies in a broad range, between 0.27 and 7.83 micromol/m(2) in the six systems simulated. For reference, the interfacial system containing bulk liquid octanol in the apolar phase has also been simulated. The results have shown that the formation of hydrogen bonds between the interfacial water and adsorbed octanol molecules is of key importance in determining the properties of the adsorbed layer. At low octanol surface concentration values all the octanol molecules are strongly (i.e., by hydrogen bonds) bound to the aqueous phase, whereas their interaction with each other is negligibly small. Hence, they are preferentially oriented in such a way that their own binding energy (and thus their own free energy) is minimized. In this preferred orientation the O-H bond of the octanol molecule points flatly toward the aqueous phase, declining by about 30 degrees from the interfacial plane, irrespectively from whether the octanol molecule is the H-donor or the H-acceptor partner in the hydrogen bond. Hence, in its preferred orientation the octanol molecule can form at least two low energy hydrogen bonds with water: one as a H-donor and another one as a H-acceptor. Moreover, the preferred orientation of the hydrogen bonded water partners is close to one of the two preferred interfacial water alignments, in which the plane of the water molecule is parallel with the interface. When increasing the octanol surface density, the water surface gets saturated with hydrogen bonded octanols, and hence any further octanol molecule can just simply condense to the layer of the adsorbed octanols. The surface density value at which this saturation occurs is estimated to be about 1.7 micromol/m(2). Above this surface density value the hydrogen bonded octanols and their water partners are oriented in such a way that the number of the water-octanol hydrogen bonds is maximized. Hence, the preferred alignment of the O...O axes of these hydrogen bonds is perpendicular to the interface. This orientation is far from the optimal alignment of the individual octanol molecules, which is also reflected in the observed fact that, unlike in the case of many other adsorbents, the average molecular binding energy of the adsorbed octanol molecules increases (i.e., becomes less negative) with increasing octanol surface density.     

DFT Calculation of Glycine with Methanols Clusters

Density functional theory （DFT） calculations are reported for the structures of neutral and zwitterionic glycine-（CHaOH）n where n=1-6. Initial geometries of the clusters of neutral and zwitterionic glycine with 1-6 methanol molecules are fully optimized at B3LYP/6-31＋G^＊ level of theory. The lowest energy configurations are located and their hydrogen bond structures are analyzed. Theoretical prediction reveals that the methanols prefer to locate near the carboxylic acid group for the small clusters （n_〈3） with the neutral form while the configurations with the methanols bridging the acid and the amino group are favorite in the zwitterionic form clusters. When the number of the methanol molecules in the clusters reaches five and six, the two forms tend to be isoenergetic.     

Neutral and ionic hydrogen bonding in Schiff bases

Low-temperature, high-resolution X-ray studies of charge distributions in the three Schiff bases, the dianil of 2-hydroxy-5-methylisophthaldehyde, 3,5-dinitro-N-salicylidenoethylamine and 3-nitro-N-salicylidenocyclohexylamine, have been carried out. These structures exhibit interesting weak interactions, including two extreme cases of intramolecular hydrogen bonds that are ionic N(+)-H...O- and neutral O-H...N in nature. These two types of hydrogen bond reflect differences in geometrical parameters and electron density distribution. At the level of geometry, the neutral O-H...N hydrogen bond is accompanied by an increase in the length of the C(1)-O(1) bond, opening of the ipso-C(1) angle, elongation of the aromatic C-C bonds, shortening of the C(7)-N(2) bond and increased length of the C(1)-C(7) bond, relative to the ionic hydrogen bond type. According to the geometrical and critical point parameters, the neutral O-H...N hydrogen bond seems to be stronger than the ionic ones. There are also differences between charge density parameters of the aromatic rings consistent with the neutral hydrogen bond being stronger than the ionic ones, with a concomitant reduction in the aromaticity of the ring. Compounds with the ionic hydrogen bonds show a larger double-bond character in the C-O bond than appears in the compound containing a neutral hydrogen bond; this suggests that the electronic structure of the former pair of compounds includes a contribution from a zwitterionic canonical form. Furthermore, in the case of ionic hydrogen bonds, the corresponding interaction lines appear to be curved in the vicinity of the hydrogen atoms. In the 3-nitro-N-salicylidenocyclohexylamine crystal there exists, in addition to the intramolecular hydrogen bond, a pair of intermolecular O...H interactions in a centrosymmetric dimer unit.     

Study of polydimethylacrylamide- and polydiethylacrylamide-adsorbed coatings on fused silica capillaries and their application in genetic analysis

The adsorption of two polymers (polydimethylacrylamide and polydiethylacrylamide) on the inner surface of a fused silica of capillary (or wafer) was investigated by means of atomic force microscopy (AFM), multi-angle laser light scattering (MALLS) technique, and by measuring the electroosmotic flow (EOF) and contact angle. The AFM images showed that PDMA and PDEA tightly adsorbed on the fused silica surface and formed stable coatings. The contact angle data demonstrated that the polymer-adsorbed coatings have different hydrophobicities, which are related to the structures of the polymers. The adsorbing capability and stability of the adsorption coating, perhaps, were mainly dependent on the hydrogen bond force between oxygen atom on the carbonyl group of polymers and the hydroxyl group of the silica surface, and the hydrophobic nature of polymers. Our data also illustrated that the polymer-adsorbed coatings efficiently suppressed the EOF and the adsorption of DNA fragments on the capillary surface. These polymers were successfully used as sieving media in capillary electrophoresis of DNA fragments and detection of single point mutation of C677T from human methylenetetrahydrofolate reductase (MTHFR) gene.     

Theoretical study of CH…O hydrogen bond in proton transfer reaction of glycine

Density functional theory (DFT) calculations are used to study the strength of the CH…O H‐bond in the proton transfer reaction of glycine. Comparison has been made between four proton transfer reactions (ZW1, ZW2, ZW3, SCRFZW) in glycine. The structural parameters of the zwitterionic, transition, and neutral states of glycine are strongly perturbed when the proton transfer takes place. It has been found that the interaction of water molecule at the side chain of glycine is high in the transition state, whereas it is low in the zwitterionic and neutral states. This strongest multiple hydrogen bond interaction in the transition state reduces the barrier for the proton transfer reaction. The natural bond orbital analysis have also been carried out for the ZW2 reaction path, it has been concluded that the amount of charge transfer between the neighboring atoms will decide the strength of H‐bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Adsorption and desorption behaviors of DNA with magnetic mesoporous silica nanoparticles

The interaction between DNA and mesopores is one of the basic concerns when mesoporous silica nanoparticle (MSN) is used as a DNA carrier. In this work, we have synthesized a type of mesoporous silica nanoparticle that has a Fe(3)O(4) inner core and mesoporous silica shell. This magnetic mesoporous silica nanoparticle (denoted as M-MSN) offers us a convenient platform to manipulate the DNA adsorption and desorption processes as it can be easily separated from solution by applying a magnetic field. The DNA adsorption behavior is studied as a function of time in chaotropic salt solution. The maximum amount of adsorbed DNA is determined as high as 121.6 mg/g. We have also developed a method to separate the DNA adsorbed onto the external surface and into the mesopores by simply changing temperature windows. The desorption results suggest that, within the whole adsorbed DNA molecules, about 89.5% has been taken up by M-MSN mesopores. Through the dynamic light scattering experiment, we have found that the hydrodynamic size for M-MSN with DNA in its mesopores is higher than the naked M-MSN. Finally, the preliminary result of the adsorption mechanism study suggests that the DNA adsorption into mesopores may generate more intermolecular hydrogen bonds than those formed on the external surface.     

DFT study of the adsorption of microsolvated glycine on a hydrophilic amorphous silica surface

Density functional theory (DFT) periodic ab initio molecular dynamics calculations are used to study the adsorption of gaseous and microsolvated glycine on a hydroxylated, hydrophilic silica surface. The silica model is presented and the interaction of water with surface silanols is studied. The heat of interaction of water is higher with the associated silanols (be they terminal or geminal ones) studied here than with isolated silanols presented in past works. Glycine is stabilized in a parallel mode on the hydroxylated surface. Terminal silanols do not allow the stabilization of the zwitterionic form, whereas geminal silanols do. Molecular dynamics (MD) first-principle calculations show that microsolvated zwitterion glycine directly binds through the carboxylate function to a surface silanol rather than through water molecules. The adsorption mode, whether with or without additional water molecules, is parallel to the surface. The ammonium function does not interact directly with the silanol groups but rather through water molecules. Thus, the carboxylate and ammonium functions exhibit two different reactivities towards silanols. The calculated free energies, taking into account the chemical potentials of water and glycine in the gas phase, suggest the existence of a thermodynamic domain in which the glycine is present in the gas phase as well as strongly adsorbed on specific sites of the surface.     

Conformational aspects of glutathione tripeptide: electron density topological & natural bond orbital analyses

Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density $ \nabla^{2} $ ρ(r) from Bader’s atom in molecules theory. Charge transfer energies based on natural bond orbital analysis are also considered to interpret these intramolecular hydrogen bonds. Our results show that these hydrogen bonds are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the stabilization energy of hydrogen bond increases. Furthermore, the back bone and side chain (Ramachandran map) orientations of various ionic forms of glutathione have been studied and conformation of each constitution of glutathione tripeptide (i.e., Glu, Cys, and Gly moieties) was determined. In most species side chain conformation were found to be hindered gauche–gauche orientation by intramolecular hydrogen bonds.     

Role of Surface Molecular Architecture and Energetics of Hydrogen Bonding Sites in Adsorption of Polymers and Surfactants

Hydrogen bonding is generally thought to be an ubiquitous adsorption mechanism, which often foils selective adsorption schemes. Through investigation of hydrogen bonding energy and its dependence on surface molecular architecture, it may be possible to develop new methodologies to control the adsorption of surfactants and polymeric flocculants, depressants, and dispersants used in particulate processing industries. A model system using St?ber silica spheres and polyethylene oxide, a polymer known for its ability to form hydrogen bonds, was examined. The effect of two different surface treatments of the silica particles, calcination and rehydroxylation, upon the adsorption of two polymer molecular weights was studied. The adsorption behavior was then linked to the respective surface structures via characterization of the surfaces using FTIR, NMR, and Raman techniques. In this paper role of hydrogen bonding sites and surface architecture on adsorption is discussed. Copyright 2000 Academic Press.