Interaction mechanisms between poly(amido‐amine) and nano‐silicon dioxide

To gain insight into the attachment of ?Si⁺ (SC) and ?SiO^? (SOA) ions (regarded as guests) to the lowest generation, ? NH₂‐terminated poly(amidoamine) (PAMAM) dendrimers (regarded as host) in the gas phase, density functional theory is used to investigate the structures and energetics of the complexes with B3LYP/6‐31+G (d) and HF/6‐31G basis sets. The initial parameters are obtained through the initial optimizations at the HF level using the most basic STO‐3G basis set. Various initial configurations of the ions bound to PAMAM are tested, and four stable conformers are found, i.e., types A to D. Types 1A and 2C are the most stable due to the chemical bond formations of Si? N° and Si? O, respectively. For type B, SC coordination to amide O sites occurs via electrostatic induction. For type D, SOA coordination to amide hydrogen and amine hydrogen sites occurs via hydrogen bond interaction. Spatial hindrance, electrostatic induction force, and hydrogen‐bond interaction play important roles in the complexation process. © 2013 Wiley Periodicals, Inc. This article was published online on 5 July 2012. An error was subsequently identified. This notice is included in the online and print version to indicate that both have been corrected on 3 August 2012.     

The Geometric Structure of Silver‐Doped Silicon Clusters

Cationic silver‐doped silicon clusters, Si_nAg⁺ (n=6–15), are studied using infrared multiple photon dissociation in combination with density functional theory computations. Candidate structures are identified using a basin‐hopping global optimizations method. Based on the comparison of experimental and calculated IR spectra for the identified low‐energy isomers, structures are assigned. It is found that all investigated clusters have exohedral structures, that is, the Ag atom is located at the surface. This is a surprising result because many transition‐metal dopant atoms have been shown to induce the formation of endohedral silicon clusters. The silicon framework of Si_nAg⁺ (n=7–9) has a pentagonal bipyramidal building block, whereas the larger Si_nAg⁺ (n=10–12, 14, 15) clusters have trigonal prism‐based structures. On comparing the structures of Si_nAg⁺ with those of Si_nCu⁺ (for n=6–11) it is found that both Cu and Ag adsorb on a surface site of bare Si_n⁺ clusters. However, the Ag dopant atom takes a lower coordinated site and is more weakly bound to the Si_n⁺ framework than the Cu dopant atom.     

脯氨酸与Cu、Cu+和Cu2+配位体系的计算研究

运用M06-2X和ωB97XD方法分别在6-311++G（2d,p）和TZVP基组水平上,对脯氨酸（Pro）的15种构象与Cu、Cu⁺和Cu²⁺形成的多种配合物的几何结构、能量学特征、振动光谱和电子结构等进行计算研究. 四种水平得到20种[Pro-Cu]、16种[Pro-Cu]⁺和16种[Pro-Cu]²⁺稳定结构. [Pro-Cu]和[Pro-Cu]⁺体系中出现12种Pro构象,而[Pro-Cu]²⁺体系中出现11种Pro构象,三种体系中最稳定的结构都不是由能量最低的Pro构象生成的. 在结构CI3、CI4、CII7和CII8中,Pro的羧基氢转移到亚氨基氮形成两性离子与Cu双配位结合. [Pro-Cu]^0/1+/2+体系四种水平计算相对能差范围逐渐增加,结合能分别在-60.0 --5.0 kJ·mol^-1、-340.0 --170.0 kJ·mol^-1和-1100.0 --860.0 kJ·mol^-1范围,配位体系中Pro的变形能逐渐增加. N―H和O―H键伸缩振动频率普遍发生红移,配位体系中部分电荷从Pro转移到Cu上,在[Pro-Cu]²⁺体系中单配位结构中电荷转移最多,约为单位负电荷.     

Electron capture dissociation and collision-induced dissociation of metal ion (Ag+, Cu2+, Zn2+, Fe2+, and Fe3+) complexes of polyamidoamine (PAMAM) dendrimers

The electron capture dissociation (ECD) and collision-induced dissociation (CID) of complexes of polyamidoamine (PAMAM) dendrimers with metal ions Ag⁺, Cu²⁺, Zn²⁺, Fe²⁺, and Fe³⁺ were determined by Fourier transform ion cyclotron resonance mass spectrometry. Complexes were of the form [PD + M + mH]⁵⁺ where PD = generation two PAMAM dendrimer with amidoethanol surface groups, M = metal ion, m = 2−4. Complementary information regarding the site and coordination chemistry of the metal ions can be obtained from the two techniques. The results suggest that complexes of Fe³⁺ and Cu²⁺ are coordinated via both core tertiary amines, whereas coordination of Ag⁺ involves a single core tertiary amine. The Zn²⁺ and Fe²⁺ complexes do not appear to involve coordination by the dendrimer core.     

The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Molecular dynamics (MD) is an essential tool for correlating collision cross-section data determined by ion mobility spectrometry (IMS) with candidate (calculated) structures. Conventional methods used for ion structure determination rely on comparing the measured cross-sections with the calculated collision cross-section for the lowest energy structure(s) taken from a large pool of candidate structures generated through multiple tiers of simulated annealing. We are developing methods to evaluate candidate structures from an ensemble of many conformations rather than the lowest energy structure. Here, we describe computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH₂-Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI, and compare the structures of MIFAGIK derivatives to test the ‘sensitivity’ of the cluster analysis method. Cluster analysis suggests that [MIFAGIK + H]⁺ ions formed by MALDI have a predominantly turn structure even though the low-energy ions prefer partial helical conformers. Although the ions formed by ESI have collision cross-sections that are different from those formed by MALDI, the results of cluster analysis indicate that the ions backbone structures are similar. Chemical modifications (N-acetyl, methylester as well as addition of Boc or Fmoc groups) to MIFAGIK alter the distribution of various conformers; the most dramatic changes are observed for the [M + Na]⁺ ion, which show a strong preference for random coil conformers owing to the strong solvation by the backbone amide groups.     

Ab initio Study of Complexation Process between Poly(amido-amine) and Nano-Silicon Dioxide

To understand better the molecular-level details of ≡Si⁺(SC) or ≡SiO^-(SOA) ion group to -NH₂ teminated poly(amido-amine) dendrimers in the gas phase, density functional theory is used to optimize the minimum energy and transition state structures with UB3LYP/6-311G(d) and HF/6-31G levels. The tertiary amine nitrogen and the amide oxygen are found to be the most favorable binding sites. The activation energies of the different active sites and the reaction steps of SC and/or SOA ion group and the amide sites are also analyzed. The stable compounds are formed via the electrostatic interaction and the coordination effect. The orientation of the amide O and the rotation of the branches minimizes the energy of the whole system.     

Amine side arm effect on the ion selectivity of 12-crown-O3N derivatives with an amine arm in aqueous and acetonitrile solutions

Molecular geometries of crown ether derivatives play an important role in capturing and transporting alkali metal ions such as Li⁺ and Na⁺. As selectivity of the ions is observed in solution, it is necessary to know their molecular structures in solutions. Recently, we investigated stable conformations of 12-crown-O₃N and its alkali ion complexes in aqueous and acetonitrile solutions. In the present study, we applied a procedure similar to that in previous papers to investigate the side arm effect of 12-crown-O₃N with an amine arm for capturing Li⁺ and Na⁺ in the two solutions. It was confirmed that the stable structures of Li⁺ and Na⁺ complexes in solutions, especially the geometry of the amine side arm, are highly solvent-dependent. This conformational difference is the key to understanding the high Li⁺ selectivity of 12-crown-O₃N derivatives with an amine side arm in acetonitrile.     

脯氨酸与Zn~(2+/1+/0)相互作用及性质

运用M062X和X3LYP两种密度泛函理论(DFT)方法在TZVP和6-311++G(2d,p)+LANL2DZ基组水平上,对已报道的15种脯氨酸(Pro)构象分别与Zn2+、Zn+及Zn进行不同方式配位体系的几何结构、能量学特征、振动光谱和电子结构性质进行了计算研究.Pro-Zn2+、Pro-Zn+和Pro-Zn三种体系分别得到19、21和24种稳定结构.Pro-Zn2+体系中Zn2+与Pro两性离子的氧端(OO)配位形成的四元环结构能量最低,其次是与Pro羧羰基氧和亚氨基氮配位形成的五元环结构,而Pro-Zn+体系与之相反.Pro-Zn2+/1+/0体系的相对能差逐渐降低,结合能分别位于-620--936,-139--325和-1.5--22 kJ·mol-1范围,配位Pro的变形能随价态降低而减小.ProZn2+体系受方法和基组影响较大,离子体系中Zn均获得少量负电荷,所有配位化合物的前线轨道能差均比相应两个碎片要低.     

Chemical ionization mass spectrometry of halogenoalkanes with tetramethylsilane as reagent gas

Chemical ionization mass spectra of halogenoalkanes (RX) obtained using tetramethylsilane as reagent gas show two major peaks corresponding to the cluster ion RX⁺SiMe₃ and alkyl ion R⁺. Iodides exhibit the highest affinity toward the trimethylsilyl ion and produce the most stable silylated molecular ions, whereas bromides and especially chlorides are less reactive toward Me₃Si⁺ ions and form less stable [M + SiMe₃]⁺ ions.     

Alkali and Alkaline Earth Metal Ions Complexes with a Partial Peptide of the Selectivity Filter in K+ Channels Studied by a Cold Ion Trap Infrared Spectroscopy

The infrared (IR) spectra of alkali and alkaline earth metal ion complexes with the Ac-Tyr-NHMe (GYG) peptide have been measured by laser photodissociation in a cold ion trap coupled with an electrospray mass spectrometer. The GYG peptide corresponds to a portion of the ion selectivity filter in the KcsA K⁺ channel that allows K⁺ to pass, but blocks Na⁺ even though it has a smaller ionic radius than K⁺. This current study extends a previous investigation on Na⁺ and K⁺ to the entire set of alkali metaI ions and alkaline earth dications. IR-IR hole-burning (IR² dip) spectroscopy has established the coexistence of several conformers of the GYG-metal ion complexes. The structures of the conformers were assigned by comparison between the isomer-selected IR spectra and theoretical IR spectra obtained from quantum chemical calculations. It was found that the structure of the dominant conformer correlates with the ability of the ion to permeate through the K⁺ channel.     

A structural study of Si6‐ring‐containing [Si6Cl14]2− chlorosilicates

The crystal structures of four substituted‐ammonium dichloride dodecachlorohexasilanes are presented. Each is crystallized with a different cation and one of the structures contains a benzene solvent molecule: bis(tetraethylammonium) dichloride dodecachlorohexasilane, 2C₈H₂₀N⁺·2Cl⁻·Cl₁₂Si₆, (I), tetrabutylammonium tributylmethylammonium dichloride dodecachlorohexasilane, C₁₆H₃₆N⁺·C₁₃H₃₀N⁺·2Cl⁻·Cl₁₂Si₆, (II), bis(tetrabutylammonium) dichloride dodecachlorohexasilane benzene disolvate, 2C₁₆H₃₆N⁺·2Cl⁻·Cl₁₂Si₆·2C₆H₆, (III), and bis(benzyltriphenylphosphonium) dichloride dodecachlorohexasilane, 2C₂₅H₂₂P⁺·2Cl⁻·Cl₁₂Si₆, (IV). In all four structures, the dodecachlorohexasilane ring is located on a crystallographic centre of inversion. The geometry of the dichloride dodecachlorohexasilanes in the different structures is almost the same, irrespective of the cocrystallized cation and solvent. However, the crystal structure of the parent dodecachlorohexasilane molecule shows that this molecule adopts a chair conformation. In (IV), the P atom and the benzyl group of the cation are disordered over two sites, with a site‐occupation factor of 0.560 (5) for the major‐occupied site.     

Isomerization Energy Decomposition Analysis for Highly Ionic Systems: Case Study of Starlike E5Li7+ Clusters

The most stable forms of E₅Li₇⁺ (E=Ge, Sn, and Pb) have been explored by means of a stochastic search of their potential‐energy surfaces by using the gradient embedded genetic algorithm (GEGA). The preferred isomer of the Ge₅Li₇⁺ ion is a slightly distorted analogue of the D_5h three‐dimensional seven‐pointed starlike structure adopted by the lighter C₅Li₇⁺ and Si₅Li₇⁺ clusters. In contrast, the preferred structures for Sn₅Li₇⁺ and Pb₅Li₇⁺ are quite different. By starting from the starlike arrangement, corresponding lowest‐energy structures are generated by migration of one of the E atoms out of the plane with the a corresponding rearrangement of the Li atoms. To understand these structural preferences, we propose a new energy decomposition analysis based on isomerizations (isomerization energy decomposition analysis (IEDA)), which enable us to extract energetic information from isomerization between structures, mainly from highly charged fragments.     

Study on structures and electron affinities of small potassium–silicon clusters Si n K (n = 2–8) and their anions with Gaussian-3 theory

The neutral Si _n K (n = 2–8) clusters and their anions have been systematically studied by means of the higher level of Gaussian-3 schemes. Equilibrium geometries and electron affinities have been calculated and are discussed for each considered size. For neutral Si _n K clusters, the ground state structure is found to be “attaching structure”, in which the K atom is bound to Si _n clusters. The most stable isomer for their anions, however, is found to be “substitutional structures”, which is derived from Si_(n+1) by replacing the Si atom with a K. The dissociation energies of K atom from the lowest energy structures of Si _n K have also been estimated to examine relative stabilities.     

Universality of the Sodium Ion Binding Mechanism in Class A G‐Protein‐Coupled Receptors

The allosteric modulation of G‐protein‐coupled receptors (GPCRs) by sodium ions has received significant attention as crystal structures of several receptors show Na⁺ ions bound to the inactive conformations at the conserved Asp^2.50. To date, structures from 24 families of GPCRs have been determined, though mechanistic insights into Na⁺ binding to the allosteric site are limited. We performed hundreds‐of‐microsecond long simulations of 18 GPCRs and elucidated their Na⁺ binding mechanism. In class A GPCRs, the Na⁺ ion binds to the conserved residue 2.50 whereas in class B receptors, it binds at 3.43b, 6.53b, and 7.49b. Using Markov state models, we obtained the free energy profiles and kinetics of Na⁺ binding to the allosteric site, which reveal a conserved mechanism of Na⁺ binding for GPCRs and show the residues that act as major barriers for ion diffusion. Furthermore, we also show that the Na⁺ ion can bind to GPCRs from the intracellular side when the allosteric site is inaccessible from the extracellular side.     

Dependence of Property of Silver Nanoparticles within Dendrimer-template on Molar Ratios of Ag+ to PAMAM Dendrimers

G5.0‐OH PAMAM dendrimers were used to prepare fluorescent silver clusters with weaker ultraviolet irradiation reduction method, in which the molar ratio of Ag⁺ to PAMAM dendrimers was the key factor to determine the geometry and properties of silver nanoparticles. The results showed that because of G5.0‐OH PAMAM dendrimers as strong encapsulatores, when the molar ratios of Ag⁺ to PAMAM dendrimers was smaller than 5, the obtained Ag_n clusters (n<5) had line structures and "molecular‐like" properties, which were highly fluorescent and quite stable in aqueous solution. Whereas when the molar ratios were between 5 and 8, the obtained Ag_n clusters were 2D structures and their fluorescence was weaker. When the molar ratio was larger than 8, the structure of silver nanoparticles was 3D and no fluorescence was observed from the obtained silver nanoparticles.     

Hydration of gas-phase ytterbium ion complexes studied by experiment and theory

Hydration of ytterbium (III) halide/hydroxide ions produced by electrospray ionization was studied in a quadrupole ion trap mass spectrometer and by density functional theory (DFT). Gas-phase YbX₂ ⁺ and YbX(OH)⁺ (X?=?OH, Cl, Br, or I) were found to coordinate from one to four water molecules, depending on the ion residence time in the trap. From the time dependence of the hydration steps, relative reaction rates were obtained. It was determined that the second hydration was faster than both the first and third hydrations, and the fourth hydration was the slowest; this ordering reflects a combination of insufficient degrees of freedom for cooling the hot monohydrate ion and decreasing binding energies with increasing hydration number. Hydration energetics and hydrate structures were computed using two approaches of DFT. The relativistic scalar ZORA approach was used with the PBE functional and all-electron TZ2P basis sets; the B3LYP functional was used with the Stuttgart relativistic small-core ANO/ECP basis sets. The parallel experimental and computational results illuminate fundamental aspects of hydration of f-element ion complexes. The experimental observations??kinetics and extent of hydration??are discussed in relationship to the computed structures and energetics of the hydrates. The absence of pentahydrates is in accord with the DFT results, which indicate that the lowest energy structures have the fifth water molecule in the second shell.     

Modeling of magic water clusters (H2O)20 and (H2O)21H+ with the PM3 quantum-mechanical method

The PM3 quantum-mechanical method is able to model the magic water clusters (H₂O)₂₀ and (H₂O)₂₁H⁺. Results indicate that the H₃O⁺ ion is tightly bound within the (H₂O)₂₀ cluster by multiple hydrogen bonds, causing deformation to the symmetric (H₂O)₂₀ pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H₂O)₂₁H⁺ clusters are presented. © John Wiley & Sons, Inc.     

In situ XPS and SIMS analysis of O2+ beam‐induced silicon oxidation

The chemical composition variation of silicon under 4 keV O₂⁺ ion beam bombardment at different incident angles was studied by in situ small‐area XPS. The changes in secondary ion profile (³⁰Si⁺, ⁴⁴SiO⁺, ⁵⁶Si₂⁺, ⁶⁰SiO₂⁺) during oxygen ion beam bombardment also have been monitored. We present a direct correlation of the changes in secondary ion depth profile with surface composition during sputtering. Evolution of the secondary ion profile obtained from SIMS shows similar trends with variation of oxygen concentration in the crater surface measured by XPS. It is shown that when the oxygen ion beam incidence angle is < 40° silicon dioxide is the dominant species on the crater surface and the matrix ion species ratio (MISR) value for ⁴⁴SiO⁺/⁵⁶Si₂⁺ is higher than for ³⁰Si⁺/⁵⁶Si₂⁺. For incidence angles of >40°, the formation of sub‐oxide is favoured and thus the MISR value for ⁴⁴SiO⁺/⁵⁶Si₂⁺ is lower than for ³⁰Si⁺/⁵⁶Si₂. At 40° bombardment there are similar amounts of SiO₂ and sub‐oxides present on the crater surface and the MISR values for ⁴⁴SiO⁺/⁵⁶Si₂⁺ and ³⁰Si⁺/⁵⁶Si₂⁺ are also similar. Copyright © 2004 John Wiley & Sons, Ltd.     

Study of metal ions (Na+, K+) interaction with different conformations of glycine molecule

Interaction of metal ions (Na⁺, K⁺) with different binding sites, such as amino nitrogen, hydroxyl oxygen, and carbonyl oxygen for all gaseous conformers of glycine molecule were investigated using Density Functional Theory (B3LYP/6‐311++G**, B3PW91/6‐311++G**) methods. It was found that the order of stability of the conformers was changed due to the binding of the metal ion. The relative energy values show that the 7p conformer is more stable than the 1p conformer when a metal ion binds with the carbonyl oxygen. The intensity of interaction on hydroxyl oxygen is very low due to the low basicity of hydroxyl oxygen. The binding affinities of the complexes were calculated using the thermochemical properties. The relative energy and chemical hardness values predicted the most stable complex. The calculated condensed Fukui functions predict the favorable reactive site among the three binding sites. It is concluded that the reactivity of each binding site varies for each conformation due to the presence of intramolecular hydrogen bonding. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study on structures and vibrational spectra of M+(H2O)Ar (M = Cu,Ag, Au)

A theoretical study on the structures and vibrational spectra of M⁺(H₂O)Ar_0‐1 (M = Cu, Ag, Au) complexes was performed using ab initio method. Geometrical structures, binding energies (BEs), OH stretching vibrational frequencies, and infrared (IR) absorption intensities are investigated in detail for various isomers with Ar atom bound to different binding sites of M⁺(H₂O). CCSD(T) calculations predict that BEs are 14.5, 7.5, and 14.4 kcal/mol for Ar atom bound to the noble metal ion in M⁺(H₂O)Ar (M = Cu, Ag, Au) complexes, respectively, and the corresponding values have been computed to be 1.5, 1.3, and 2.1 kcal/mol when Ar atom attaches to a H atom of water molecule. The former structure is predicted to be more stable than the latter structure. Moreover, when compared with the M⁺(H₂O) species, tagging Ar atom to metal cation yields a minor perturbation on the IR spectra, whereas binding Ar atom to an OH site leads to a large redshift in OH stretching vibrations. The relationships between isomers and vibrational spectra are discussed. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011