Theoretical investigation of the structure and coverage of the Si(111)-OCH3 surface

The surface structure, strain energy, and charge profile of the methoxylated Si(111) surface, Si(111)-OCH3, has been studied using quantum mechanics, and the results are compared to those obtained previously for Si(111)-CH3 and Si(111)-C2H5. The calculations indicate that 100% coverage is feasible for Si(111)-OCH3 (similar to the methylated surface), as compared to only approximately 80% coverage for the ethylated surface. These differences can be understood in terms of nearest-neighbor steric and electrostatic interactions. Enthalpy and free energy calculations indicate that the formation of the Si(111)-OCH3 surface from Si(111)-H and methanol is favorable at 300 K. The calculations have also indicated the conditions under which stacking faults can emerge on Si(111)-OCH3, and such conditions are contrasted with the behavior of Si(111)-CH3 and Si(111)-CH2CH3 surfaces, for which stacking faults are calculated to be energetically feasible when etch pits with sufficiently long edges are present on the surface.     

Two-, three-, and four-coordinate Ag(I) coordination polymers formed by the novel phosphinite PPh2(3-OCH2C5H4N)

The novel phosphinite PPh(2)(3-OCH(2)C(5)H(4)N) (1) has been synthesized, and its coordination properties to Ag(I) have been studied. When reacted in a 1:1 ratio with Ag(I), coordination polymers with different coordination numbers about the Ag are found depending on the anion. For PPh(2)(3-OCH(2)C(5)H(4)N)AgBF(4) (2), a two-coordinate Ag is observed with a P-Ag-N angle of 167 degrees. Mixed three and four coordination about Ag is observed for PPh(2)(3-OCH(2)C(5)H(4)N)AgOTf (3), and for the trifluoroacetate derivative, PPh(2)(3-OCH(2)C(5)H(4)N)Agtfa (4), only a four-coordinate Ag is produced. X-ray crystal-structure determinations for compounds 2-4 have been carried out. The X-ray structures show a wide range of Ag-Ag distances in the polymers, which are dependent on the conformation of the bridging ligand.     

Molecular analysis of water clusters: Calculation of the cluster structures and vibrational spectrum using density functional theory

Density functional theory (DFT) is applied to obtain absorption spectra at THz frequencies for molecular clusters of H₂O. The vibrational modes of the clusters are calculated. Coupling among molecular vibrational modes explains their spectral features associated with THz excitation. THz excitation is associated with vibrational frequencies which are here calculated within the DFT approximation of electronic states. This is done for both isolated molecules and collections of molecules in a cluster. The principal result of the paper is that a crystal-like cluster of 38 water molecules together with a continuum solvent background is sufficient to replicate well the experimental vibrational frequencies.     

Planar bilayer studies reveal multiple conductance states for synthetic anion transporters

Compounds of the general type R(1)(2)NCOCH(2)OCH(2)CO-(Gly)(3)-Pro-(Gly)(3)-OCH(2)Ph insert in phospholipid bilayers and conduct ions. Different levels of activity were observed when R(1) was either decyl or octadecyl, as judged either by Cl(-) release, detected by ion selective electrodes, or carboxyfluorescein dequenching, detected by fluorescence. Either method reports average behavior for all ionophores over all liposomes. These methods also show that at least two ionophores are involved in the formation of each pore. Planar bilayer experiments reported here confirm pore formation by these compounds but identify more than one conductance state for each. The pseudo-dimer, in which two molecules of the type shown above are covalently linked, shows only two conductance states, of which one is dominant. This state has been characterized by use of a current-voltage plot.     

Synthesis of silver molybdate clusters driven by laser-annealing

The synthesis of silver rich molybdate clusters is achieved by laser induced chemical reaction of coadsorbed MoO(3) and O(2) molecules on free silver clusters. The reactants MoO(3) and/or O(2) molecules condensed at low temperature (77 K-175 K) on free silver clusters. Then, the silver clusters together with their adsorbed molecules are flashed either ionized with a discharge or ionized and heated by a laser. Then they are cooled down by evaporation. The synthesized chemical compounds are analyzed by a high-resolution time-of-flight mass spectrometer. If only one type of reactant is adsorbed on the cluster, only one oxide molecule is stabilized on the metallic core after the heating and cooling cycle. On the contrary, the coadsorption of the two types of molecules MoO(3) and O(2) on Ag(n) (+), at 77 K, leads to complex aggregates that transform, after laser heating, into a molybdate rich metal clusters. These synthesized species cool down by evaporating silver atoms showing evidence of a binary oxide that is more stable than the metallic core. Moreover we demonstrate that for small size molybdate clusters, a stoichiometric composition may differ from the bulk one.     

Mechanistic studies of La3+ and Zn2+-catalyzed methanolysis of O-ethyl O-aryl methylphosphonate esters. An effective solvolytic method for the catalytic destruction of phosphonate CW simulants

The kinetics of methanolysis of six O-ethyl O-aryl methylphosphonates (6a-f) promoted by methoxide, La3+ and 1,5,9-triazacyclododecane complex of Zn2+(-OCH3) (5:Zn2+(-OCH3)) were studied as simulants for chemical warfare (CW) agents, and analyzed through the use of Br?nsted plots. The beta(lg) values are, respectively, -0.76, -1.26 and -1.06, pointing to significant weakening of the P-OAr bond in the transition state. For the metal-catalyzed reactions the data are consistent with a concerted process where the P-OAr bond rupture has progressed to the extent of 84% in the La3+ reaction and ca. 70% in the Zn2+ catalyzed reaction. The catalysis afforded by the metal ions is remarkable, being about 10(6)-fold and 10(8)-fold for poor and good leaving groups, respectively, relative to the background reactions at pH 9.1. Solvent deuterium kinetic isotope studies for two of the substrates promoted by 5:Zn2+(-OCH3) give kH/kD = 1.0 +/- 0.1, consistent with a nucleophilic mechanism. A unified mechanism for the metal-catalyzed reactions is presented which involves pre-equilibrium coordination of the substrate to the metal ion followed by intramolecular delivery of a coordinated methoxide.     

The dinuclear Zn(II) complex catalyzed cyclization of a series of 2-hydroxypropyl aryl phosphate RNA models: progressive change in mechanism from rate-limiting P-O bond cleavage to substrate binding

A methoxide-bridged dinuclear Zn(II) complex of 1,3-[N,N'-bis(1,5,9-triazacyclododecane)]propane (1-Zn(II)2:(-OCH3)) was prepared, and its catalysis of the cyclization of a series of 2-hydroxypropyl aryl phosphates (4a-g) was investigated in methanol at pH 9.8, T = 25degreesC by stopped-flow spectrophotometry. An X-ray diffraction structure of the hydroxide analogue of 1-Zn(II)2:(-OCH3), namely 1-Zn(II)2:(-OH), reveals that each of the Zn(II) ions is coordinated by the three N's of the triazacyclododecane units and a bridging hydroxide. The cyclizations of substrates 4a-g reveal a progressive change in the observed kinetics from Michaelis-Menten saturation kinetics for the poorer substrates (4-OCH3 (4g); 4-H (4f); 3-OCH3 (4e); 4-Cl (4d); 3-NO2, (4c)) to second-order kinetics (linear in 1-Zn(II)2:(-OCH3)) for the better substrates (4-NO2,3-CH3 (4b); 4-NO2, (4a)). The data are analyzed in terms of a multistep process whereby a first formed complex rearranges to a reactive complex with a doubly activated phosphate coordinated to both metal ions. The kinetic behavior of the series is analyzed in terms of change in rate-limiting step for the catalyzed reaction whereby the rate-limiting step for the poorer substrates (4g-c) is the chemical step of cyclization of the substrate, while for the better substrates (4b,a) the rate-limiting step is binding. The catalysis of the cyclization of these substrates is extremely efficient. The kcat/KM values for the catalyzed reactions range from 2.75 x 10(5) to 2.3 x 10(4) M-1 s-1, providing an acceleration of 1 x 10(8) to 4 x 10(9) relative to the methoxide reaction (k2OCH3, which ranges from 2.6 x 10(-3) to 5.9 x 10(-6) M-1 s-1 for 4a-g). At a pH of 9.8 where the catalyst is maximally active, the acceleration for the substrates ranges from (1 - 4) x 10(12) relative to the background reaction at the same pH. Detailed energetics calculations show that the transition state for the catalyzed reaction comprising 1-Zn(II)2, methoxide, and 4 is stabilized by about -21 to -23 kcal/mol relative to the transition state for the methoxide reaction. The pronounced catalytic activity is attributed to a synergism between a positively charged catalyst that has high affinity for the substrate and for the transition state for cyclization, and a medium effect involving a reduced polarity/dielectric constant that complements a reaction where an oppositely charged reactant and catalyst experience charge dispersal in the transition state.     

Structural and electric field effects of ions in aqueous nanodrops

Ensemble infrared photodissociation (IRPD) spectra in the hydrogen stretch region (～2950-3800 cm(-1)) are reported for M(H(2)O)(35-37), with M = I(-), Cl(-), HCO(3)(-), OH(-), tetrabutyl-, tetrapropyl-, and tetramethylammonium, Cs(+), Na(+), Li(+), H(+), Ba(2+), Ca(2+), Co(2+), Mg(2+), La(3+), and Tm(3+), at 133 K. A single, broad feature is observed in the bonded-OH region of the spectra that indicates that the water network in these clusters is bulk-like and likely resembles liquid water more strongly than ice. The free-OH region for all of these clusters is dominated by peaks corresponding to water molecules that accept two and donate one hydrogen bond (AAD water molecules), indicating that AAD water molecules are more abundant at the surface of these ions than AD water molecules. A-only water molecules are present in significant abundance only for the trivalent metal cations. The frequency of the AAD free-OH stretch band shifts nearly linearly with the charge state of the ion, consistent with a Stark shift attributable to the ion's electric field. From these data, a frequency range of 3704.9-3709.7 cm(-1) is extrapolated for the free-OH of AAD water molecules at the (uncharged) bulk liquid water surface, consistent with sum-frequency generation spectroscopy experiments. Differences in both the bonded- and the free-OH regions of the spectra for these ions are attributable to ion-induced patterning of the water network that extends to the surface of the clusters, which includes water molecules in the third and fourth solvation shells; that is, these ions pattern water molecules at long distance to various extents. These spectra are simulated using two different electrostatic models previously used to calculate OH-stretch spectra of bulk water and aqueous solutions and parametrized for bonded-OH frequencies. These models qualitatively reproduce a number of features in the experimental spectra, although it is evident that more sophisticated treatment of water molecule and ion polarizability and vibrational coupling is necessary for more quantitative comparisons.     

Computer simulation of quantum melting in hydrogen clusters.

We introduce a new criterion, based on multipole dynamical correlations calculated within reptation quantum Monte Carlo, to discriminate between a melting versus freezing behavior in quantum clusters. This criterion is applied to small clusters of para-hydrogen molecules (both pristine and doped with a CO chromophore), for cluster sizes of around twelve molecules. This is a magic size at which para-hydrogen clusters display an icosahedral structure and a large stability. Despite the similar geometric structure of CO@(pH2)12 and (pH2)13, the first system has a rigid, crystalline, behavior; the second behaves more like a superfluid (or, possibly, a supersolid).     

Comprehensive study on the solvation of mono- and divalent metal cations: Li+, Na+, K+, Be2+, Mg2+ and Ca2+

Hydration of mono- and divalent metal ions (Li(+), Na(+), K(+), Be(2+), Mg(2+) and Ca(2+)) has been studied using the DFT (B3LYP), second-order M?ller-Plesset (MP2) and CCSD(T) perturbation theory as well as the G3 quantum chemical methods. Double-zeta and triple-zeta basis sets containing both (multiple) polarization and diffuse functions were applied. Total and sequential binding energies are evaluated for all metal-water clusters containing 1-6 water molecules. Total binding energies predicted at lower levels of theory are compared with those from the high level G3 calculations, whereas the sequential binding energies are compared with available experimental values. An increase in the quality of the basis set from double-zeta to triple-zeta has a significant effect on the sequential binding energies, irrespective of the geometries used. Within the same group (I or II), the sequential binding energy predictions at the MP2 and B3LYP vary appreciably. We noticed that, for each addition of a water molecule, the change of the M-O distance in metal-water clusters is higher at the B3LYP than at the MP2 level. The charge of the metal ion decreases monotonically as the number of water molecules increase in the complex.     

Chemical pathways in the interactions of reactive metal atoms with organic surfaces: vapor deposition of Ca and Ti on a methoxy-terminated alkanethiolate monolayer on Au

In situ time-of-flight secondary ion mass spectrometry, infrared spectroscopy, and X-ray photoelectron spectroscopy measurements have been used to characterize the interfacial chemistry that occurs upon physical vapor deposition of Ti and Ca atoms onto a -OCH(3) terminated alkanethiolate self-assembled monolayer (SAM) on Au{111}. While the final result for both metals is near-exhaustive degradation of the methoxy terminal group and partial degradation of the alkyl chains to inorganic products such as carbides, hydrides, and oxides, the reaction mechanisms differ significantly. Titanium reacts in parallel with the -OCH(3) and -CH(2)- units, extensively degrading the latter until a metallic overlayer forms preventing further degradation. At this point, there is a cessation of the Ti-SAM reactions. In contrast, Ca is initially consumed by the -OCH(3) terminal group via a reaction mechanism involving two -OCH(3) groups; subsequent depositions lead to alkyl chain degradation, but at a rate slower than that for Ti deposition. These results demonstrate the subtle differences in chemistry that can arise in the vapor deposition of reactive metals, and have important implications for the behavior of electrical interfaces in organic and molecular devices made with Ti or Ca top contacts.     

Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide

(13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction.     

Laser induced fluorescence spectroscopy of tetracene with large Ar, Ne, and H2 clusters in superfluid He nanodroplets

Clusters of tetracene molecules with different numbers of attached (Ar)(N), (Ne)(N) and (H(2))(N) particles (N = 1-2000) are assembled inside superfluid He nanodroplets and studied via laser-induced fluorescence. The frequency shift of the fluorescence spectrum of the tetracene molecules is studied as a function of cluster size and pickup order of tetracene and cluster species. For (Ar)(N) and (Ne)(N) clusters, our results indicate that the tetracene molecules reside inside the clusters when tetracene is captured by the He nanodroplet before the cluster species; conversely, the tetracene molecules stay on the surface of the clusters when tetracene is captured after the cluster species. In the case of (H(2))(N) clusters, however, tetracene molecules reside inside the (H(2))(N) clusters irrespective of the pickup order. We conclude that (Ar)(N) and (Ne)(N) clusters are rigid at T = 0.38 K, while (H(2))(N) clusters of up to N = 2000 remain fluxional at the same temperature. The results may also indicate the occurrence of heterogeneous nucleation of the (H(2))(N) clusters, which is induced by the interaction with tetracene chromophore molecules.     

Insights into the control of magnetic coupling in the Mn4(III) complex: from ferromagnetic to antiferromagnetic

Magnetic coupling interactions of a Mn(III)(4) system are investigated by calculations based on density functional theory combined with a broken-symmetry approach (DFT-BS). Three different interactions including ferromagnetic and antiferromagnetic coupling are concomitant in this complex. This magnetic phenomenon of the complex is due to the different bridging angles between the Mn(III) centers in the three different models and the orbital complementarity of the μ-pzbg and μ-OCH(3) bridging ligands, which is proven by the analyses of the molecular orbitals. According to the analyses of the magneto-structural correlation, it is revealed that the magnetic coupling interaction switches from ferromagnetic to antiferromagnetic at the point of the bridging angle Mn-(μ-OCH(3))-Mn = 99°, which is equal to the value in the origin crystal. Significant correlation between the magnetic properties and the component of the d orbitals in these systems shows that the larger contribution of the d(z(2)) orbital corresponds to the larger ferromagnetic coupling interaction. These results should provide a means to control the magnetic coupling of the polynuclear Mn systems, which is instructive for the design of new molecular magnetic materials.     

Structures and dissociation channels of protonated mixed clusters around a small magic number: infrared spectroscopy of ((CH3)3N)n-H(+)-H2O (n = 1-3)

The magic number behavior of ((CH(3))(3)N)(n)-H(+)-H(2)O clusters at n = 3 is investigated by applying infrared spectroscopy to the clusters of n = 1-3. Structures of these clusters are determined in conjunction with density functional theory calculations. Dissociation channels upon infrared excitation are also measured, and their correlation with the cluster structures is examined. It is demonstrated that the magic number cluster has a closed-shell structure, in which the water moiety is surrounded by three (CH(3))(3)N molecules. The ion core (protonated site) of the clusters is found to be (CH(3))(3)NH(+) for n = 1-3, but coexistence of an isomer of the H(3)O(+) ion core cannot be ruled out for n = 3. Large rearrangement of the cluster structures of n = 2 and 3 before dissociation, which has been suggested in the mass spectrometric studies, is confirmed on the basis of the structure determination by infrared spectroscopy.     

How Many Methanol Molecules Can Solvate a Glycine: a PBE1PBE Approach

Microsolvation of glycine in methanol clusters is explored by the use of DFT calculation method. The lowest energy conformations within 16.72 kJ·mol-1 of the glycine clustering with one to six methanol molecules, which are obtained at the B3LYP/6-31+G(d) level of theory, are reoptimized at PBE1PBE/6-311+G(d,p). The calculated results agree with our previous results with B3LYP (Chin. J. Chem. Phys. 22 (2009) 577) that the clusters of two forms (Z-and N-form) tend to be isoenergetic when the number of the solvate molecules reaches six. Furthermore, this result is in good agreement with the experiment of the tryptophan-methanol clusters, implying that the present treatments are reasonable and reliable. The results also indicate that nine methanol molecules are not enough to fully solvate a glycine molecule, and a tentative estimation is obtained that ten methanol molecules may fully solvate a glycine molecule, which consists with the experiment results.     

Shape resonances in molecular clusters: the 2t(2g) shape resonances in S 2p-excited sulfur hexafluoride clusters

Sulfur hexafluoride clusters are investigated in the S 2p excitation regime. For the first time special emphasis is put on high-energy resolution spectroscopy of shape resonances in free clusters. We have investigated the 2t(2g)-shape resonance occurring above the S 2p threshold as one typical example to study size effects that are related to shape resonances. A small redshift of this resonance of 30 +/- 5 meV occurs in clusters relative to the free molecule and changes in line shape are observed. A double-barrier optical potential model is applied for the analysis of intra- and intermolecular effects occurring in SF6 clusters, which is suitable for rationalizing the experimentally observed spectral changes. The experimental and theoretical results are briefly discussed in comparison to previous work on core-excited van der Waals clusters containing diatomic molecules.     

Mechanistic studies of La3+- and Zn2+-catalyzed methanolysis of aryl phosphate and phosphorothioate triesters. Development of artificial phosphotriesterase systems

The methanolyses of a series of O,O-diethyl O-aryl phosphates (2,5) and O,O-diethyl S-aryl phosphorothioates (6) promoted by methoxide and two metal ion systems, (La3+)2(-OCH3)2 and 4:Zn2+:-OCH3 (4 = 1,5,9-triazacyclododecane) has been studied in methanol at 25 degrees C. Br?nsted plots of the logk2 values vs. pKa for the phenol leaving groups give beta(lg) values of -0.70, -1.43 and -1.12 for the methanolysis of the phosphates and -0.63, -0.87 and -0.74 for the methanolysis of the phosphorothioates promoted by the methoxide, La3+ and Zn2+ systems respectively. The kinetic data for the metal-catalyzed reactions are analyzed in terms of a common mechanism where there is extensive cleavage of the P-XAr bond in the rate-limiting transition state. The relevance of these findings to the mechanism of action of the phosphotriesterase enzyme is discussed.     

钒、铬团簇的电子亲合能、硬度与原子数的关系

根据静电球形液滴模型理论和离子极化、屏蔽效应对团簇的影响, 推导适合钒、铬团簇电子亲合能、硬度与原子数关系符合的普遍公式: Y=ae2/R+b/R2+c, R=rsN1/3, 从而更方便地预测大尺寸团簇的性质参数, 并发现和分析结构和性质异常的小团簇, 如Vn(n=5, 7, 9, 13)和Crn(n=6, 10, 17)的性质.     

Analysis of the substituent effect on the reactivity modulation during self-protonation processes in 2-nitrophenols

A voltammetric and spectroelectrochemical ESR study of the reduction processes of five substituted 4-R-2-nitrophenols (R = -H, -OCH(3), -CH(3), -CN, -CF(3)) in acetonitrile was performed. In the potential range considered here (-0.2 to -2.5 V vs Fc+/Fc), two reduction signals (Ic and IIc) were detected; the first one was associated with the formation of the corresponding hydroxylamine via a self-protonation pathway. The voltammetric analysis at the first reduction signal showed that there are differences in the reduction pathway for each substituted 4-R-2-nitrophenol, being the E1/2 values determined by the inductive effect of the substituent in the meta position with respect to the nitro group, while the electron-transfer kinetics was determined by the protonation rate (k(1)+ ) of the anion radical electrogenerated. However, at potential values near the first reduction peak, no ESR signal was recorded from stable radical species, indicating the instability of the radical species in solution. Nevertheless, an intense ESR spectrum generated at the second reduction peak was detected for all compounds, indicating the monoelectronic reduction of the corresponding deprotonated 4-R-2-nitrophenols. The spin-coupling hyperfine structures revealed differences in the chemical nature of the electrogenerated radical; meanwhile, the -CF(3) and -CN substituents induced the formation of a dianion radical structure, and the -H, -CH(3), and -OCH(3) substituents provoked the formation of an anion radical structure due to protonation by acetonitrile molecules of the initially electrogenerated dianion radical. This behavior was confirmed by analyzing the ESR spectra in deuterated acetonitrile and by performing quantum chemical calculations of the spin densities at each site of the electrogenerated anionic radicals.