Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study.

Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.

Water Depletion Enhanced by Halogenation of Benzene.

The pressure dependence of the solubility of hydrophobic solutes in aqueous solutions is equivalent to volume changes upon hydrophobic hydration. This phenomenon has been attributed to the packing effects induced by the van der Waals volume difference between the solute and water. However, the volume changes may also be related to the chemical properties of the solute. In this study, we investigated hydrophobic hydration using a series of halogenated benzenes. Solution density measurements revealed negative volume changes for benzene, fluorobenzene, and chlorobenzene, whereas those for bromobenzene and iodobenzene were positive. Subsequent volumetric analyses demonstrated that the relationship between the excess particle number for hydration water and the van der Waals volume for bromobenzene and iodobenzene significantly deviated from the universal line for hydrophobic solutes. This behavior suggests that the volume changes are due to factors other than the packing effect with bromo and iodine functional groups acting as modulators of the hydration structure, resulting in enhanced water depletion.

Water fluctuation in methanol, ethanol, and 1-propanol aqueous-mixture probed by Brownian motion.

The origin of the driving force in Brownian motion is the collision between the colloidal particle and the molecules of the surrounding fluid. Therefore, Brownian motion contains information on the local solvent structures of the surrounding colloid. The mean square displacement in a water-ethanol mixture is greater than that anticipated from the macroscopic shear viscosity, indicating that the microscopic movement of Brownian motion involves the local information on the water-ethanol mixture on a molecular level, i.e., an inhomogeneity in the Brownian particle size (∼1 µm). Here, the Brownian motion of mixtures of water and methanol, ethanol, and 1-propanol are systematically investigated. Similar discrepancies between the microscopic and macroscopic viscosities are observed at low alcohol molar concentrations, for all the alcohol mixtures. This means that inhomogeneity with water fluctuation is important in explanation of the unusual Brownian diffusions of alcohol aqueous solutions. The Brownian motion also reveals a thermal energy conversion mechanism between translation and rotation.

Brownian motion probe for water-ethanol inhomogeneous mixtures.

Brownian motion provides information regarding the microscopic geometry and motion of molecules, insofar as it occurs as a result of molecular collisions with a colloid particle. We found that the mobility of polystyrene beads from the Brownian motion in a water-ethanol mixture is larger than that predicted from the liquid shear viscosity. This indicates that mixing water and ethanol is inhomogeneous in micron-sized probe beads. The discrepancy between the mobility of Brownian motion and liquid mobility can be explained by the way the rotation of the beads in an inhomogeneous viscous solvent converts the translational movement.

Anion and cation effects on the size control of Au nanoparticles prepared by sputter deposition in imidazolium-based ionic liquids.

The sputter deposition of metals in an ionic liquid (IL) capture medium is a simple and elegant method for preparing nanoparticles without any chemical reaction. Although there have been some reports on the size determination factors for Au nanoparticles (AuNPs) prepared using this method, the effects with respect to the type of IL used have not been clearly elucidated. This is because there are some complicating factors, some of which have been revealed by our previous systematic studies. In the present study, we prepare AuNPs in nine types of imidazolium-based IL to examine the size determination effects of the type of anion involved, the length of the alkyl chain of the cation, and the preparation temperature for each IL, while keeping other factors constant. For most of the capture media ILs, the sizes of the AuNPs increase with an increase in temperature. The AuNPs prepared in ILs containing different types of anions exhibit distinctly different particle sizes and temperature dependences. Conversely, the alkyl chain is regarded as a secondary stabilizer that works only at higher preparation temperatures. We conclude that the sizes of AuNPs prepared by this method may be determined by the competition between the collision frequency of the ejected Au atoms and the stabilizing capability of the anions that form the first coordination shell around the AuNPs. The AuNP sizes are closely related to the volume of anions.

Temperature effects on prevalent structures of hydrated Fe⁺ complexes: infrared spectroscopy and DFT calculations of Fe⁺(H2O)n (n = 3-8).

Hydrated Fe(+) ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe(+)(H2O)n (n = 3-8) complexes are mass-selected and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region. Density functional theory (DFT) calculations are also carried out for analyzing the experimental IR spectra and for evaluating thermodynamic quantities of low-lying isomers. Solvation through H-bonding instead of direct coordination to Fe(+) is observed already at n = 3, indicating the completion of the first hydration shell with two H2O molecules. Size dependent variations in the spectra for n = 5-7 provide evidence for the second-shell completion at n = 6, where a linearly coordinated Fe(+)(H2O)2 subunit is solvated with four H2O molecules. Overall spectral features for n = 3-8 agree well with those predicted for 2-coordinated structures. DFT calculations predict that such 2-coordinated structures are lowest in energy for smaller n. However, 4-coordinated isomers are predicted to be more stable for n = 7 and 8; the energy ordering is in conflict with the IR spectroscopic observation. Examination of free energy as a function of temperature suggests that the ordering of the isomers at warmer temperatures can be different from the ordering near 0 K. For n = 7 and 8, the 4-coordinated isomers should be observed at low temperatures because they are lowest in enthalpy. Meanwhile, outer-shell waters in the 2-coordinated structures are bound less rigidly; their contribution to entropy is rather large. The 2-coordinated structures become abundant at warmer temperatures, owing to the entropy effect.

Weak ferromagnetism and strong spin-spin interaction mediated by the mixed-valence ethynyltetrathiafulvalene-type ligand.

A new chromium complex with ethynyltetrathiafulvalene (TTF)-type ligands, [CrCyclam(C≡C-5-methyl-4'5'-ethylenedithio-TTF)(2)]OTf ([1]OTf), was synthesized. The cyclic voltammetry of the complex shows two reversible oxidation waves owing to the first and second oxidation of the TTF unit. The electrochemical oxidation of [1]OTf in a Bu(4)NClO(4) or Bu(4)NBF(4) solution of a 1:1 acetonitrile-chlorobenzene mixture gave isostructural crystals of [1][ClO(4)](2)(PhCl)(2)(MeCN) and [1][BF(4)](2)(PhCl)(2)(MeCN), where two mixed-valence TTF units of adjacent complexes form a dimer radical cation. The crystal structures are characterized by an alternating chain of S = 3/2 Cr(3+)Cyclam units and S = ½ (TTF)(2)(+) dimers. These two paramagnetic components are connected directly by an ethynyl group, resulting in a strong intrachain spin-spin interaction of 2J/k(B) = -30 and -28 K for [ClO(4)](-) and [BF(4)](-) salts, respectively (H = -2J∑(i)S(i)·S(i+1)). Both salts show a weak ferromagnetic transition at 23 K thanks to interchain antiferromagnetic interaction between TTF dimers. The remanent magnetizations and coercive forces of nonoriented samples at 1.8 K are 0.016 µ(B) and 90 mT for the [ClO(4)](-) salt and 0.010 µ(B) and 50 mT Oe for the [BF(4)](-) salt, respectively. The weak ferromagnetism is attributed to the Dzyaloshinsky-Moriya interaction between adjacent TTF dimers and/or the single-ion anisotropy of [1](2+).

Infrared photodissociation spectroscopy of Co(+)(NH(3))(n) and Ni(+)(NH(3))(n): preference for tetrahedral or square-planar coordination.

Coordination structures of the Co(+)(NH(3))(n) and Ni(+)(NH(3))(n) ions are probed by infrared (IR) photodissociation spectroscopy with the aid of density functional theory (DFT) calculations. The IR spectra of N(2)-tagged Co(+)(NH(3))(n) (n = 1-4) exhibit two distinct bands assignable to the symmetric and antisymmetric NH stretches of the NH(3) molecules binding directly to Co(+). Size-dependent changes in the spectra of Co(+)(NH(3))(n) (n = 4-8) indicate that the first shell of Co(+) is filled with four NH(3) molecules and the resulting 4-coordinated structure forms the central core of further solvation. The spectra of Ni(+)(NH(3))(n) (n = 3-8) suggest that the coordination number of Ni(+) is also four, although a minor 3-coordinated isomer is identified for Ni(+)(NH(3))(4). Despite the same coordination number, the DFT calculations predict a distorted square-planar coordination for Ni(+)(NH(3))(4) and a distorted tetrahedral coordination for Co(+)(NH(3))(4). The coordination of Ni(+)(NH(3))(4) is explainable by using a simple model based on the geometry of a half-filled 3d orbital in Ni(+). This suggests that the Ni(+) ion gives priority to the minimization of the metal-ligand repulsion in accommodating four ligands in the first shell. On the other hand, the same model fails to explain the coordination of Co(+)(NH(3))(4). An interpretation for this is that the Co(+) ion gives priority to the minimization of the ligand-ligand repulsion.

Chromium acetylide complex based ferrimagnet and weak ferromagnet.

The crystal structures and magnetic properties of new molecule-based magnets, [CrCyclam(C[triple bond]C-3-thiophene)(2)][Ni(mdt)(2)] (1) and [CrCyclam(C[triple bond]C-Ph)(2)][Ni(mdt)(2)](H(2)O) (2) (Cyclam = 1,4,8,11-tetraazacyclotetradecane, mdt = 1,3-dithiole-4,5-dithiolate), are reported. The crystal structures of both compounds are characterized by ferrimagnetic chains of alternately stacked [CrCyclam(C[triple bond]C-R)](+) cations and [Ni(mdt)(2)](-) anions with intrachain exchange interactions of 2J = -6.1 K in 1 and -5.7 K in 2 (H = -2J Sigma(i) S(i) x S(i+1)). The material 1 exhibits ferrimagnetic transition at 2.3 K owing to weak interchain antiferromagnetic interactions between cations and anions. In the case of 2, cations in adjacent ferrimagnetic chains are bridged by a water molecule, resulting in an interchain antiferromagnetic coupling. Despite a centrosymmetry of a whole crystal of 2, one bridging water molecule occupies only one of the two centrosymmetric sites and breaks a local centrosymmetry between adjacent cations. The interchain antiferromagnetic interaction and Dzyaloshinsky-Moriya interaction originated from the local symmetry breakdown of 2 bring a weak-ferromagnetic transition at 3.7 K with a coercive force of less than 0.8 mT, followed by the second magnetic phase transition at 2.9 K. Below this temperature, the coercive force rapidly increases from 1 to 11.8 mT as the temperature decreases from 2.9 to 1.8 K, while the remanent magnetization monotonically increases from 0.008 mu(B) at 3.6 K to 0.12 mu(B) at 1.8 K.

Coordination structures of the silver ion: infrared photodissociation spectroscopy of Ag(+)(NH(3))(n) (n = 3-8).

Infrared (IR) spectra are measured for Ag(+)(NH(3))(n) with n = 3-8 in the NH-stretch region using photodissociation spectroscopy. The spectra of n = 3 and 4 exhibit absorption features only near the frequencies of the isolated NH(3), indicating that every NH(3) molecule is coordinated individually to Ag(+). For n >or= 5, the occupation of the second shell is evidenced by lower-frequency features characteristic of hydrogen bonding between NH(3) molecules. Density functional theory and MP2 calculations are carried out in support of the experiments. A detailed comparison of the experimental and theoretical IR spectra reveals the preference for a tetrahedral coordination in the n = 5 and 6 ions. Likewise, most of the features observed in the spectra of n = 7 and 8 can be assigned to isomers containing a tetrahedrally coordinated inner shell as the basic structural motif. These results signify that the ammonia-solvated Ag(+) ion has a propensity toward a coordination number of four and the resulting tetrahedral Ag(+)(NH(3))(4) complex forms the central core of further solvation process.

Coordination and solvation of copper ion: infrared photodissociation spectroscopy of Cu(+)(NH(3))(n) (n = 3-8).

Coordination and solvation structures of the Cu(+)(NH(3))(n) ions with n = 3-8 are studied by infrared photodissociation spectroscopy in the NH-stretch region with the aid of density functional theory calculations. Hydrogen bonding between NH(3) molecules is absent for n = 3, indicating that all NH(3) molecules are bonded directly to Cu(+) in a tri-coordinated form. The first sign of hydrogen bonding is detected at n = 4 through frequency reduction and intensity enhancement of the infrared transitions, implying that at least one NH(3) molecule is placed in the second solvation shell. The spectra of n = 4 and 5 suggest the coexistence of multiple isomers, which have different coordination numbers (2, 3, and 4) or different types of hydrogen-bonding configurations. With increasing n, however, the di-coordinated isomer is of growing importance until becoming predominant at n = 8. These results signify a strong tendency of Cu(+) to adopt the twofold linear coordination, as in the case of Cu(+)(H(2)O)(n).

Cluster chemistry: size-dependent reactivity induced by reverse spill-over.

In the present work, the CO oxidation rate on size-selected Pd clusters supported on thin MgO films is investigated in pulsed molecular beam experiments. By varying the cluster coverage independent of the cluster size, we were able to change the ratio of direct and diffusion flux (reverse spill-over) of CO onto the cluster catalyst and thus probe the influence of reverse spill-over on the reaction rate for different cluster sizes (Pd(8) and Pd(30)). The experimental results show that the change in reaction rate as a function of cluster coverage is different for Pd(8) and Pd(30). In order to explain these findings, the CO flux onto the clusters is modeled utilizing the collection zone model for the given experimental conditions. The results indicate that, for small clusters (Pd(8)), the reaction probability of an impinging CO molecule is independent of whether it is supplied by diffusion or direct flux. By contrast, for larger clusters (Pd(30)) a reduced reaction probability is found for CO supplied by reverse spill-over compared to CO supplied by direct flux.

Infrared photodissociation spectroscopy of Al(+)(CH(3)OH)(n) (n = 1-4).

Infrared photodissociation spectra of Al(+)(CH(3)OH)(n) (n = 1-4) and Al(+)(CH(3)OH)(n)-Ar (n = 1-3) were measured in the OH stretching region, 3000-3800 cm(-1). For n = 1 and 2, sharp absorption bands were observed in the free OH stretching region, all of which were well reproduced by the spectra calculated for the solvated-type geometry with no hydrogen bond. For n = 3 and 4, there were broad vibrational bands in the energy region of hydrogen-bonded OH stretching vibrations, 3000-3500 cm(-1). Energies of possible isomers for the Al(+)(CH(3)OH)(3),4 ions with hydrogen bonds were calculated in order to assign these bands. It was found that the third and fourth methanol molecules form hydrogen bonds with methanol molecules in the first solvation shell, rather than a direct bonding with the Al(+) ion. For the Al(+)(CH(3)OH)(n) clusters with n = 1-4, we obtained no evidence of the insertion reaction, which occurs in Al(+)(H(2)O)(n). One possible explanation of the difference between these two systems is that the potential energy barriers between the solvated and inserted isomers in the Al(+)(CH(3)OH)(n) system is too high to form the inserted-type isomers.

Infrared spectroscopy of Cu+(H2O)(n) and Ag+(H2O)(n): coordination and solvation of noble-metal ions.

M(+)(H(2)O)(n) and M(+)(H(2)O)(n)Ar ions (M=Cu and Ag) are studied for exploring coordination and solvation structures of noble-metal ions. These species are produced in a laser-vaporization cluster source and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region using a triple quadrupole mass spectrometer. Density functional theory calculations are also carried out for analyzing the experimental IR spectra. Partially resolved rotational structure observed in the spectrum of Ag(+)(H(2)O)(1) x Ar indicates that the complex is quasilinear in an Ar-Ag(+)-O configuration with the H atoms symmetrically displaced off axis. The spectra of the Ar-tagged M(+)(H(2)O)(2) are consistent with twofold coordination with a linear O-M(+)-O arrangement for these ions, which is stabilized by the s-d hybridization in M(+). Hydrogen bonding between H(2)O molecules is absent in Ag(+)(H(2)O)(3) x Ar but detected in Cu(+)(H(2)O)(3) x Ar through characteristic changes in the position and intensity of the OH-stretch transitions. The third H(2)O attaches directly to Ag(+) in a tricoordinated form, while it occupies a hydrogen-bonding site in the second shell of the dicoordinated Cu(+). The preference of the tricoordination is attributable to the inefficient 5s-4d hybridization in Ag(+), in contrast to the extensive 4s-3d hybridization in Cu(+) which retains the dicoordination. This is most likely because the s-d energy gap of Ag(+) is much larger than that of Cu(+). The fourth H(2)O occupies the second shells of the tricoordinated Ag(+) and the dicoordinated Cu(+), as extensive hydrogen bonding is observed in M(+)(H(2)O)(4) x Ar. Interestingly, the Ag(+)(H(2)O)(4) x Ar ions adopt not only the tricoordinated form but also the dicoordinated forms, which are absent in Ag(+)(H(2)O)(3) x Ar but revived at n=4. Size dependent variations in the spectra of Cu(+)(H(2)O)(n) for n=5-7 provide evidence for the completion of the second shell at n=6, where the dicoordinated Cu(+)(H(2)O)(2) subunit is surrounded by four H(2)O molecules. The gas-phase coordination number of Cu(+) is 2 and the resulting linearly coordinated structure acts as the core of further solvation processes.

Charging effects on bonding and catalyzed oxidation of CO on Au8 clusters on MgO.

Gold octamers (Au8) bound to oxygen-vacancy F-center defects on Mg(001) are the smallest clusters to catalyze the low-temperature oxidation of CO to CO2, whereas clusters deposited on close-to-perfect magnesia surfaces remain chemically inert. Charging of the supported clusters plays a key role in promoting their chemical activity. Infrared measurements of the stretch vibration of CO adsorbed on mass-selected gold octamers soft-landed on MgO(001) with coadsorbed O2 show a red shift on an F-center-rich surface with respect to the perfect surface. The experiments agree with quantum ab initio calculations that predict that a red shift of the C-O vibration should arise via electron back-donation to the CO antibonding orbital.

Acetylene trimerization on Ag, Pd and Rh atoms deposited on MgO thin films.

The acetylene trimerization on the group VIII transition metal atoms, Rh and Pd, as well as on Ag atoms supported on MgO thin films has been studied experimentally and theoretically. The three metal atoms with the atomic configurations 4d(8)5s1 (Rh), 4d10s0 (Pd) and 4d(10)5s1 (Ag) behave distinctly differently. The coinage metal atom silver is basically inert for this reaction, whereas Pd is active at 220 and 320 K, and Rh produces benzene in a rather broad temperature range from 350 to ca. 430 K. The origins of these differences are not only the different electronic configurations, leading to a weak interaction of acetylene with silver due to strong Pauli repulsion with the 5s electron but also the different stability and dynamics of the three atoms on the MgO surface. In particular, Rh and Pd atoms interact differently with surface defects like the oxygen vacancies (F centers) and the step edges. Pd atoms migrate already at low temperature exclusively to F centers where the cyclotrimerization is efficiently promoted. The Rh atoms on the other hand are not only trapped on F centers but also at step edges up to about 300 K. Interestingly, only Rh atoms on F centers catalyze the trimerization reaction whereas they are turned inert on the step edges due to strong steric effects.

Low-temperature cluster catalysis.

Free and supported metal clusters reveal unique chemical and physical properties, which vary as a function of size as each cluster possesses a characteristic electron confinement. Several previous experimental results showed that the outcome of a given chemical reaction can be controlled by tuning the cluster size. However, none of the examples indicate that clusters prepared in the gas phase and then deposited on a support material are indeed catalytically active over several reaction cycles nor that their catalytic properties remain constant during such a catalytic process. In this work we report turn-over frequencies (TOF) for Pd(n) (n = 4, 8, 30) clusters using pulsed molecular beam experiments. The obtained results illustrate that the catalytic reactivity for the NO reduction by CO (CO + NO --> 1/2N(2) + CO(2)) is indeed a function of cluster size and that the measured TOF remain constant at a given temperature. More interestingly, the temperature of maximal reactivity is at least 100 K lower than observed for palladium nanoparticles or single crystals. One reason for this surprising observation is the character of the binding sites of these small clusters: N(2) forms already at relatively low temperatures (400 and 450 K) and therefore poisoning by adsorbed nitrogen adatoms is prevented. Thus, small clusters not only open the possibility of tuning a catalytic process by changing cluster size, but also of catalyzing chemical reactions at low temperatures.

Cluster size-dependent mechanisms of the CO + NO reaction on small Pdn (n < or = 30) clusters on oxide surfaces.

The CO + NO reaction (2CO + 2NO --> N(2) + 2CO(2)) on small size-selected palladium clusters supported on thin MgO(100) films reveals distinct size effects in the size range Pd(n) with n < or = 30. Clusters up to the tetramer are inert, while larger clusters form CO(2) at around 300 K, and this main reaction mechanism involves adsorbed CO and an adsorbed oxygen atom, a reaction product from the dissociation of NO. In addition, clusters consisting of 20-30 atoms reveal a low-temperature mechanism observed at temperatures below 150 K; the corresponding reaction mechanism can be described as a direct reaction of CO with molecularly adsorbed NO. Interestingly, for all reactive cluster sizes, the reaction temperature of the main mechanism is at least 150 K lower than those for palladium single crystals and larger particles. This indicates that the energetics of the reaction on clusters are distinctly different from those on bulklike systems. In the presented one-cycle experiments, the reaction is inhibited when strongly adsorbed NO blocks the CO adsorption sites. In addition, the obtained results reveal the interaction of NO with the clusters to show differences as a function of size; on larger clusters, both molecularly bonded and dissociated NO coexist, while on small clusters, NO is efficiently dissociated, and hardly any molecularly bonded NO is detected. The desorption of N(2) occurs on the reactive clusters between 300 and 500 K.