Chemical Physics Letters (v.590, #C)

Contents (iii-xiv).

Display OmittedThe structure of water confined in MCM41 silica cylindrical pores is studied to determine whether confined water is simply a version of the bulk liquid which can be substantially supercooled without crystallisation. A combination of total neutron scattering from the porous silica, both wet and dry, and computer simulation using a realistic model of the scattering substrate is used. The water in the pore is divided into three regions: core, interfacial and overlap. The average local densities of water in these simulations are found to be about 20% lower than bulk water density, while the density in the core region is below, but closer to, the bulk density. There is a decrease in both local and core densities when the temperature is lowered from 298 K to 210 K. The radical proposal is made here that water in hydrophilic confinement is under significant tension, around −100 MPa, inside the pore.

Ion imaging studies of the photodissociation dynamics of CH2I2 at 248 nm by Julia H. Lehman; Hongwei Li; Marsha I. Lester (16-21).
The photodissociation of CH2I2 at 248 nm is investigated using velocity map ion imaging with photoionization detection of the I (2 P 1/2) products. The velocity distribution of the I products reveals that only a small fraction of the available energy is released as translational energy, consistent with a simple impulsive model. Most of the excess energy is channeled into internal excitation with 〈 E int 〉 = 36.3 kcal mol−1 for CH2I radical fragments produced with I atoms. The anisotropy angular distribution of the I fragments and corresponding positive anisotropy parameter are indicative of prompt dissociation and electronic state mixing.

Spontaneous ion-pair formation in the gas phase induced by Beryllium bonds by Manuel Yáñez; Otilia Mó; Ibon Alkorta; José Elguero (22-26).
Display OmittedThe changes in the structure and bonding of the hydrogen bonded complexes between hydrogen halides and ammonia, phosphine and water, when the hydrogen halides form beryllium bonds with BeCl2 have been investigated by CCSD(T)/aug-cc-pVTZ ab initio calculations. Although the experimental evidence showed that a spontaneous proton transfer (PT) from hydrogen halides toward ammonia does not occur, and only is observed for HI when interacting with trimethylamine, we have found that a spontaneous PT does occur when the halide forms beryllium bonds with BeCl2. The complexes so formed are the result of the interaction of Cl2BeX with NH4 +, PH4 +, H3O+, respectively.

Display OmittedAs the first example of a mixed metal amidoborane, Na2Mg(NH2BH3)4 (DSMAB) contains both alkali and alkaline earth metals, has been demonstrated excellent properties of dehydrogenation. This is the first systematically study on its dehydrogenation mechanism. First, both the periodic and molecular structure have been studied. As for the kinetic study, the energy barrier of the possible dehydrogenation pathway is 57.99 kcal/mol, and the rate of the reaction is 6.0 × 10−3  min−1, which is consistent with the experiment result and provides evidence that oligomerization is the primary pathway based on the motion of Na+.

Oxidation by OH radicals: final product structures unraveled by IRMPD spectroscopy.Although the first steps of the oxidation of methionine containing peptides by OH radicals have been very well documented, not much is known about the final products. They have been characterized and unraveled by mass spectrometry and IR Multiple Photon Dissociation (IRMPD) spectroscopy carried out with model dipeptides and methionine enkephalin, often involving the transformation of residues other than methionine. Several products were found, in addition to methionine sulfoxide, which is omnipresent. Thus IRMPD proved to be very useful in oxidative proteomics.

The Pt site reactivity of the molecular graphs of Au6Pt isomers by Tianlv Xu; Samantha Jenkins; Chen-Xia Xiao; Julio R. Maza; Steven R. Kirk (41-45).
Within the framework of the theory of atoms in molecules (QTAIM), in an exploratory study we propose a new measure of site reactivity equivalent to the atomic coordination number based purely on the electronic structure. It was found that the number of ring critical points (NNRCPs) positioned on the boundary of the atomic basin of the dopant (Pt) nucleus correlated very well with the relative zero point energy (ZPE) corrected energies. A weaker condition (i.e. than the number of associated bond paths) for the association of the dopant Pt nucleus with the Au6Pt molecular graph is found for NNRCP  = 0.

The experimental free ion 4f 2 energy level data sets comprising 12 or 13 J-multiplets of La+, Ce2+, Pr3+ and Nd4+ have been fitted by a semiempirical atomic Hamiltonian comprising 8, 10, or 12 freely-varying parameters. The root mean square errors were 16.1, 1.3, 0.3 and 0.3 cm−1, respectively for fits with 10 parameters. The fitted inter-electronic repulsion and magnetic parameters vary linearly with ionic charge, i, but better linear fits are obtained with (4−i)2, although the reason is unclear at present. The two-body configuration interaction parameters α and β exhibit a linear relation with [ΔE(bc)]−1, where ΔE(bc) is the energy difference between the 4f 2 barycentre and that of the interacting configuration, namely 4f6p for La+, Ce2+, and Pr3+, and 5p 54f 3 for Nd4+. The linear fit provides the rationale for the negative value of α for the case of La+, where the interacting configuration is located below 4f 2.

Interfaces between metal atoms and organic molecules are key units of many important metal–organic systems. Presented are results of ab initio calculations for a series of complexes of 2nd-row metal atoms sandwiched between small unsaturated hydrocarbon molecules. Evolution of the system structure and stability is studied for different metal atoms, as well as upon excitation, ionization and electron attachment. Predicted interesting features include cooperative stabilization, unusual geometries, reversible charge- or excitation-governed geometry alterations. The observed variety of properties suggests potential applications of such species as intermolecular junctions and units with charge- or spin-controlled shapes in molecular devices and/or machines.

Ab initio study of nonlinear optical properties of aromatic fused rings by Radhakrishnan Balu; Prakashan Korambath; Ravindra Pandey; Shashi P. Karna (58-62).
The nonlinear optical properties of benzene, naphthalene, anthracene, and pyrene are investigated. Static and dynamic polarizability, α(−ω;  ω), and second hyperpolarizability, corresponding to dc electric-field-induced Kerr effect (DCKE), intensity dependent refractive index (IDRI), dc electric field-induced second harmonic generation (EFISHG), and third harmonic generation (THG) have been calculated. The calculated α and γ show good agreement with the available theoretical and gas-phase experimental data. The second hyperpolarizabilities exhibit the following trend: γ(THG) >  γ(EFISHG) >  γ(IDRI) ∼  γ(DCKE) >  γ(static). We find that the second hyperpolarizabilities increase as the number of rings in the system increases in either dimension, but the magnitude of increase is more pronounced along the molecular chain axis.

Gas-phase reactivity of aluminum cluster anions with ethanethiol: Carbon–sulfur bond activation by Zhixun Luo; Jordan C. Smith; Cüneyt Berkdemir; A.W. Castleman (63-68).
Display OmittedWe report a joint experimental and theoretical study of the gas-phase reactivity of Al cluster anions with ethanethiol (EtSH) in a fast-flow tube reactor. Nearly all Al n - clusters observed are reactive at the presence of sufficient EtSH molecules with minor exceptions. Sulfide species Al n S m - dominate the observed reaction products, indicating C–S bond activation of EtSH. By using DFT calculations we provide an in-depth analysis on the interesting cluster reactivity of Al n - with EtSH. It is demonstrated that the desulfurization leading to Al n S m - products is associated with the dehydrogen processes successively initiated by S–H bond cleavage and C–H bond cracking.

Dynamical profiles of the reactive components in direct and revert Liesegang patterns by Leen Kalash; Hiba Farah; Amal Zein Eddin; Rabih Sultan (69-73).
This Letter traces the experimental profiles of Cu2+ and CrO4 2− in a CuCrO4 Liesegang pattern with direct spacing, and Pb2+ and CrO4 2− in a PbCrO4 Liesegang pattern.Display OmittedIn periodic precipitation (Liesegang banding), the overwhelmingly common trend is the increase in spacing between consecutive bands as we move away from the interface. Revert spacing is a rare trend observed in a few systems, wherein the spacing decreases with distance from the interface. In this Letter, we compare the spatial profiles of the aqueous components in two chromate Liesegang precipitates: CuCrO4 and PbCrO4, displaying direct and revert spacing, respectively. The profiles are measured using UV–Vis spectrophotometry. The formation of a Pb2+–PbCrO4 complex in equilibrium with the free Pb2+, seems to play a key role in the revert spacing scenario.

High pressure X-ray photochemical studies of carbon tetrachloride: Cl2 production and segregation by Michael Pravica; Daniel Sneed; Quinlan Smith; Ligang Bai (74-76).
We report on two experiments on carbon tetrachloride. CCl4 was pressurized to 4.9 GPa and irradiated with 20 keV hard X-rays for 4 h and 8 h respectively. We observed a greenish yellow material form in the irradiated regions. In the second experiment, the same irradiated sample was left pressurized for 4 weeks. The irradiated regions consolidated and Raman spectra of these spots displayed strong Cl2 lines.

Nature of SnO6 octahedron in bulk and nanoparticles of Y2Sn2O7 probed by experimental and theoretical methods by Sandeep Nigam; Amresh I. Prasad; V. Sudarsan; C. Majumder; R.K. Vatsa (77-82).
Based on XRD, 119Sn MAS NMR and Luminescence studies it is confirmed that in very fine nanoparticles of Y2Sn2O7, tin environment is significantly distorted with respect to bulk Y2Sn2O7. NMR studies revealed that electron density around Sn4+ is significantly high in nanoparticles in comparison to bulk. Theoretical studies under DFT formalism has further confirmed that electron density around Sn4+ ions is enriched, as well as distorted in Y2Sn2O7 nanoparticles compared to bulk. The higher electron density around Sn4+ ions has been attributed to elongation in Sn–O bond distance which results in relatively poor charge transfer from tin site to oxygen.

Controlled antioxidative steps of the cell. The concept of chalcogenicity by Béla Fiser; Zoltán Mucsi; Béla Viskolcz; Svend J. Knak Jensen; Imre G. Csizmadia (83-86).
The removal of reactive oxygen species by glutathione peroxidase involves reactions where the chalcogens O, S, and Se play a central role. The thermodynamics of the steps in the removal are investigated by electron structure calculations on a series of reactions involving these chalcogens. Analysis of the free energy- and enthalpy changes for the reactions shows a universal linear relationship, called the chalcogenicity, which may be useful in estimating thermodynamic properties in related reactions.

Optical waveguiding and temperature dependent photoluminescence of nanotubulars grown from molecular building blocks by C. Maibohm; M. Rastedt; F. Kutscher; O.N. Frey; R. Beckhaus; H.-G. Rubahn; K. Al-Shamery (87-91).
Optical waveguiding of blue light after UV-excitation is demonstrated in bundles of organic nanotubulars obtained via template assisted aggregation of the small π-conjugated non planar molecules 17H-Tetrabenzo[a,c,g,i]fluorene (17H-Tbf) and 17-Trimethylsilyltetrabenzo[a,c,g,i]fluorene (TMS-Tbf). The propagating blue light is strongly attenuated due to self-absorption. Vibronic spectra for both nanotubulars and macroscopic crystallites for temperatures between 5 and 300 K show a behavior of TMS-Tbf that resembles that of long chained molecules while 17H-TbF resembles that of small organic molecules. For both molecular species crystallites and nanostructures have large average Huang–Rhys factors indicating strong phononic coupling promoted by the polycrystallinity of the samples.

CuO reduction induced formation of CuO/Cu2O hybrid oxides by Lu Yuan; Qiyue Yin; Yiqian Wang; Guangwen Zhou (92-96).
Reduction of CuO nanowires results in the formation of a unique hierarchical hybrid nanostructure, in which the parent oxide phase (CuO) works as the skeleton while the lower oxide (Cu2O) resulting from the reduction reaction forms as partially embedded nanoparticles that decorate the skeleton of the parent oxide. Using in situ transmission electron microscopy observations of the reduction process of CuO nanowires, we demonstrate that the formation of such a hierarchical hybrid oxide structure is induced by topotactic nucleation and growth of Cu2O islands on the parent CuO nanowires.

On determining the entrance size of cage-like pores in mesoporous silica films by positron annihilation lifetime spectroscopy by Chunqing He; Bangyun Xiong; Wenfeng Mao; Yoshinori Kobayashi; Toshitaka Oka; Nagayasu Oshima; Ryoichi Suzuki (97-100).
Pore entrance size of cage-like pores in mesoporous silica films is difficult to be determined by conventional techniques. A simple expedient is proposed by using positron annihilation lifetime spectroscopy (PALS) based on a slow positron beam. Because of the nature of positronium (Ps, the bound state of a positron and an electron) in mesoporous silica, almost no Ps annihilates in the smaller connecting channels of cages. By trimethylsilylation of the silica, an appreciable fraction of Ps can be trapped and annihilate in the channels, which renders the possibility to estimate the pore entrance size from Ps lifetime in it.

Atomistic multiscale simulation of the structure and properties of an amorphous OXD-7 layer by Svetlana Emelyanova; Vladimir Chashchikhin; Alexander Bagaturyants (101-105).
The structure and properties of an amorphous 1,3-bis(2-(4-tert-butylphenyl)-1,3,4-oxadiazol-5-yl)benzene (OXD-7) layer are investigated by atomistic multiscale simulation combining quantum chemical (DFT, TDDFT) and molecular dynamics (MD, Amber force field) calculations. Three stable OXD-7 conformers are found on its ground-state DFT potential energy surface. The force-field parameters of torsion angles lacking in the Amber force field are determined by fitting to the results of MP2 calculations for a model oxadiazole derivative. The OXD-7 absorption band shape and HOMO and LUMO energy distributions in an amorphous film are found by TDDFT/DFT calculations for sample points obtained by MD calculations.

In organic materials, triplet–triplet annihilation (TTA) can be dominated by triplet diffusion or triplet-to-triplet energy transfer. Here, we discuss the diffusion and transfer dominated mechanisms in the context of photoluminescence (PL) transient measurements from thin films of archetype phosphorescent organic light emitters based on Ir and Pt complexes. We find that TTA in these emitters is controlled by diffusion due to a Dexter-type exchange interaction, suggesting triplet radiative decay and TTA are independent processes. Minimizing the PL and absorption spectral overlap in phosphorescent emitters can lead to a significantly decreased TTA rate, and thus suppressed efficiency roll-off in phosphorescent organic light emitting diodes at high brightness.

Spin-polarized transport properties of Mn@Au6 cluster by Jing Huang; Weiyi Wang; Shangfeng Yang; Qunxiang Li; Jinlong Yang (111-115).
Display OmittedWe explore the spin-polarized electronic structures and transport properties of Mn@Au6 cluster. The ab initio modeling is performed by combining the spin-polarized density functional theory with nonequilibrium Green’s function formalism. Theoretical results clearly reveal that the central Mn atom anti-ferromagnetically couples with the Au6 ring and the cluster magnetic moment is 3.0 μB. The spin-resolved transmission spectra of Mn@Au6 sandwiched between two Li (1 0 0) electrodes exhibit robust spin filtering effect. The conductance of Mn@Au6 at the small bias voltage is mainly determined by the spin-up electrons. The findings indicate that Mn@Au6 cluster holds promise in molecular spintronics applications.

Optical property theoretical study and mild-temperature synthesis of (Ga,Zn)N nanocrystals by Naifeng Zhuang; Lin Wei; Yinhua Li; Yongfan Zhang; Xiaolin Hu; Jianzhong Chen; Junqian Li (116-120).
Wurtzite GaN and (Ga,Zn)N nanocrystals about 8–20 nm were synthesized at mild temperature. Optical properties were analyzed theoretically by means of quantum chemical method. Zn dopant increases activity of GaN in visible region. White light can be produced by mixing the strong blue and yellow emission lines.Wurtzite GaN and (Ga,Zn)N nanocrystals with the size of 8–20 nm were synthesized by the solid-phase thermal decomposition method at mild temperature of 350–650 °C. This synthesis method is a simple and low cost method. From the further study on the luminescence mechanism, Zn dopant introduces new energy levels in the band gap of GaN nanocrystals, which effectively induces the fluorescence emission in the visible region. In addition, the VN-H defect significantly affects the optical properties of nanocrystals. Moreover, GaN nanocrystals with a proper Zn-doping concentration will produce a white light.

Graphene–carbon nanotube composite aerogel for selective detection of uric acid by Feifei Zhang; Jie Tang; Zonghua Wang; Lu-Chang Qin (121-125).
Graphene and single-walled carbon nanotube (SWNT) composite aerogel has been prepared by hydrothermal synthesis. The restacking of graphene is effectively reduced by SWNTs inserted in between graphene layers in order to make available more active sites and reactive surface area. Electrochemical experiments show that the graphene–SWNT composite electrode has superior catalytic performance in selective detection of uric acid (UA).

The effect of carbon nanotubes and graphene on the mechanical properties of multi-component polymeric composites by Enkeleda Dervishi; Festus Hategekimana; Laurent Boyer; Fumiya Watanabe; Thikra Mustafa; Abhijit Biswas; Alexandru R. Biris; Alexandru S. Biris (126-130).
Two types of nano-materials (nanotubes and graphene) were incorporated at different concentrations into a bio-compatible polymer matrix, and the mechanical properties of the composite films were studied. Although both nanomaterials improved the mechanical attributes of the polymer, it was found that the composites containing the nanotube–graphene mixture exhibited significantly superior elasto-plastic properties. This work presents a facile technique of fabricating nano-composites that could be scaled up and applied to various types of polymers. These multi-component films have the potential to be used in a wide range of applications including bio-medicine and photovoltaics, as well as the military and automotive industry.

Despite significant progress in single walled carbon nanotube (SWCNT) production by plasma enhanced chemical vapor deposition (PECVD), the growth mechanism in this method is not clearly understood. We employ reactive molecular dynamics simulations to investigate how plasma-based deposition allows growth at low temperature. We first investigate the SWCNT growth mechanism at low and high temperatures under conditions similar to thermal CVD and PECVD. We then show how ion bombardment during the nucleation stage increases the carbon solubility in the catalyst at low temperature. Finally, we demonstrate how moderate energy ions sputter amorphous carbon allowing for SWCNT growth at 500 K.

Display OmittedPolyyne oligomers (H2C n H2), with CH2 group at each end of the oligomer, have been found to give helical molecular orbitals for the HOMO and LUMO and other molecular orbitals around the HOMO and LUMO when the two CH2 groups are tilted from their equilibrium positions. This can be explained by the changes in the symmetry of H2C2 m +1H2 from D2d to D2, the former having degenerate molecular orbitals but the latter having non-degenerate orbitals. These helical molecular orbitals have been pointed out as being a kind of molecular device through which electrons pass.

Potential dependence of SERS spectra of reduced graphene oxide adsorbed on self-assembled monolayer at gold electrode by Ieva Matulaitienė; Jurgis Barkauskas; Romualdas Trusovas; Gediminas Račiukaitis; Regina Mažeikienė; Olegas Eicher-Lorka; Gediminas Niaura (141-145).
The reduced graphene oxide was prepared at interface of Au electrode modified by positive charge bearing self-assembled monolayer of N-(6-mercapto)hexylpyridinium. Surface-enhanced Raman spectroscopy (SERS) was employed to probe in situ the potential induced changes in parameters of D- and G-bands. We demonstrated that both D- and G-band wavenumbers linearly depend on the potential with slopes of 4.7 ± 0.3 and 5.9 ± 0.3 cm−1/V, respectively. The decrease in width of both bands was detected at more positive potentials. The effect was explained in terms of changes in the C–C bond length induced by the electrochemical doping.

A simple synthesis and characterization procedure for graphene growth on Ru(0 0 0 1) is demonstrated. Only a sample heating setup and mass spectrometer (or residual gas analyzer) are required. In addition, sample stability at ambient conditions (in air) was tested. Furthermore, benzene adsorption on graphene/Ru(0 0 0 1) was characterized by thermal desorption spectroscopy and compared with earlier experiments and theory on carbon nanotubes and highly-oriented pyrolytic graphite (HOPG). In addition, Auger and X-ray photoelectron spectroscopy were used.

Raman spectroscopy experiments on multiwall carbon nanotube (MWCNTs), carbon black (CB) and on a styrene–butadiene rubber (SBR) filled either with MWCNTs or CB and also with a mixture of both particles (MWCNTs + CB) are reported. Emphasis is given on the dispersive effects of the Raman D band with laser energy that are shown for the first time to differ in each type of composites revealing a different polymer–filler interface. In addition, an upshift of the G band is observed when CB particles are incorporated into the polymer matrix.

Bias-dependent conductance of Si2 cluster by Fu-ti Liu; Yan Cheng; Fu-Bin Yang; Xiang-Rong Chen (160-164).
The conductance of Si2 cluster coupled to Au electrodes at the equilibrium positions as a function of voltage: (a) top–top parallel configuration, (b) top–top perpendicular configuration, (c) top–hollow configuration, and (d) hollow–hollow configuration.Conductance of Si2 cluster sandwiched between Au electrodes is investigated by the density functional theory combined with the non-equilibrium Green’s function method. We simulate the Au–Si2–Au junctions breaking process, calculate the corresponding cohesion energy in four different anchoring geometries, and obtain the equilibrium conductance and the projected density of states of junctions in optimal position, and find that all junctions have large conductance. In addition, we calculate the relationship of conductance with external bias voltage, and find that the conductance of hollow–hollow configuration is more stable than other three configurations when the applied bias voltage increases. The calculated results proved that the distance, coupling morphology of Si2 cluster connected with electrodes and external bias voltage have an important effect on the conductance of nanoscale junctions.

Large magneto-optical birefringence of colloidal suspensions of α-FeOOH goethite nanocrystallites by Jian Li; Xiaoyan Qiu; Yueqiang Lin; Longlong Chen; Xiaodong Liu; Decai Li (165-168).
A large magnetic-field induced birefringence (reduced value of approximately 10−2), was observed at 40 kA/m field strength for colloid suspensions of spherical goethite nanocrystallite. We ascribe this behavior of these suspensions to long-range orientation of optically equivalent ellipsoids, rather than long-ranged spatial ordering of building blocks (as liquid crystals) or interparticle interaction (as ferrofluids) from the magnetic field. Comparing experimental and theoretical results based on bulk properties, goethite nanocrystallites have refractive index approximately 103 times larger than that of the bulk; accordingly, dielectric constant is approximately 106 times larger in the optical-frequency regime.

Vibronic couplings in C 60 derivatives for organic photovoltaics by Naoya Iwahara; Tohru Sato; Kazuyoshi Tanaka; Hironori Kaji (169-174).
Display OmittedVibronic coupling constants (VCCs) and reorganisation energies of C 60 derivative anions including [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) are evaluated. The results are analysed in terms of the vibronic coupling density. As long as the electronic state is conserved, the VCCs are similar to those in C 60 - . The VCCs are large when (1) the distribution of LUMO is large around the substituent or (2) the structure of the orbital is significantly changed by the symmetry lowering, which would be unsuitable for an organic photovoltaic material from the viewpoint of vibronic couplings.

Lithium-doped endohedral single-walled carbon nanotubes can arise during tube growth by E.Y. Matsubara; C.A. Luengo; J.M. Rosolen (175-179).
This Letter shows that it is possible to dope single-walled carbon nanotubes (SWCNT) with lithium during SWCNT growth in an arc reactor. Depending on the oxygen and lithium concentrations in the reactor, one can obtain endohedral Li@SWCNT after rinsing the product in water. Oxygen plays a decisive role in Li insertion during SWCNT growth and in the diameter distribution of the samples. Doping the tubes with Li produces end-closed SWCNT bundles that afford more stable dispersion in water as compared with non-doped tubes.

Theoretical study of the superoxide anion assisted firefly oxyluciferin formation by Luís Pinto da Silva; Joaquim C.G. Esteves da Silva (180-182).
This a theoretical Letter based on density functional theory, on the role of superoxide anion in firefly chemiluminescence in DMSO. We have found that this anion can attack luciferin radical molecules, thus forming a luciferin-like trianion. This latter molecule transfers an oxygen atom, which results in the formation of oxyluciferyl radical dianion and carbon dioxide molecules. Oxyluciferin is finally formed after an electron transfer from oxyluciferyl radical dianion to tert-BuO radical molecules. Thus, we have found evidence that firefly oxyluciferin can be formed in a energetically favorable superoxide anion-assisted reaction, without the need for the formation of firefly dioxetanone.

Display OmittedWe have derived an equation, based on Helfrich’s curvature elasticity, describing the equilibrium shape of membrane vesicles in the presence of magnetic fields. We have solved this equation with and without the constraint of constant vesicle area. For vesicles with constant area, an exact calculation using our model confirms Helfrich’s estimate (Helfrich, 1973) [20] and predicts a magnetic field induced surface tension. Without the constant area constraint, our model predicts that vesicles with positive diamagnetic susceptibility anisotropy will swell in magnetic fields. It also predicts the anharmonic magnetic deformation of self-assembled nanocapsules of bola-amphiphilic molecules and the linear birefringence observed by Manyuhina et al. (2007) [22] .

How acidic are monomeric structural units of heparin? by Milan Remko; Ria Broer; Piet Th. Van Duijnen (187-191).
Density functional theory methods with the B3LYP functional have been used to study the acidity of carboxylate, O-sulfate and N-sulfate groups in six basic monomeric structural units of heparin (1-OMe ΔUA-2S, 1-OMe GlcN-S6S, 1,4-DiOMe GlcA, 1,4-DiOMe GlcN-S3S6S, 1,4-DiOMe IdoA-2S, and 1,4-DiOMe GlcN-S6S).Density functional theory methods with the B3LYP functional have been used to letter the acidity of carboxyl, O-sulfo and N-sulfo groups in six basic monomeric structural units of heparin (1-OMe ΔUA-2S, 1-OMe GlcN-S6S, 1,4-DiOMe GlcA, 1,4-DiOMe GlcN-S3S6S, 1,4-DiOMe IdoA-2S, and 1,4-DiOMe GlcN-S6S). The predicted gas-phase acidity of the acidic functional groups in the monomeric structural units of heparin is: O-sulfo >  N-sulfo > carboxyl. The computed pKa values provide the same order of acidity as was observed in water solution. This implies that hydration does not change ordering of acidity of major acidic groups of monomeric structural units of heparin.

This approach presents a 3D amino acid adjacency matrix based on the 2D amino acid adjacency matrix which was proposed by Randić et al. (2008) [1]. Furthermore, a novel numerical method is proposed to measure the degree of similarity based on 2D and 3D adjacency matrices. This new method is applied to nine ND5 proteins of different species. To prove the efficiency of the presented work a correlation with ClustalW and significance analyses are provided. The results show that our work is the most significant among other related works.

A mean field theory is developed to quantify the simulated fraction N 1/N of hard spheres (diameter σ) around the rim region (V 1) against the size of spherical cavity R cav for packing fraction η  = 0.3 (open circles) and 0.15 (solid circles) with the characteristic length of depletion forces for rim particles (dotted circle) z c as an adjustable parameter. For large R cav , N 1/N obeys a power law: N 1 / N ∼ R cav - 1 . Investigated densities are similar to crowded biological cells.Display OmittedWe investigate a mean filed theory to elucidate the fraction of hard spheres in the rim of rigid spherical cavities for densities similar to crowded cellular nuclei. Rims are one hard sphere thickness from the interior surface of cavities. We theoretically interpret the particle fraction around the rim by considering entropies from inter-particle excluded volume interactions and depletion forces under confined cavities. By adapting the characteristic length of depletion forces as a single tunable parameter, the proposed theory is successfully applied to understand simulation data, which provides a simple but general picture on confinement effects including cavity curvature and density.

To account for frequently documented low-temperature deviations from Arrhenius rate law, the proposed expansion of inverse activation energy against inverse temperature is shown to yield a first order linearizing parameter which is formally correlated with Tsallis non-extensive classical statistical mechanics. Its sign provides a heuristic criterion, especially appealing in biochemistry, for assigning deviations as due either: (i) to quantum mechanical under-barrier tunneling, or (ii) to ‘classical’ collective phenomena. For (i), an explicit relationship is here derived in terms of barrier features. Case (ii) typically occurs in enzymatic or heterogeneous catalysis, in membrane mediated processes and in those controlled by diffusion or by transport in general.

Artifacts due to trivial unavoided crossings in the modeling of photoinduced energy transfer dynamics in extended conjugated molecules by Tammie Nelson; Sebastian Fernandez-Alberti; Adrian E. Roitberg; Sergei Tretiak (208-213).
Display OmittedA previously developed algorithm to identify potential energy surface crossings involving interacting or noninteracting states during nonadiabatic excited-state molecular dynamics simulations, allows the diabatic pathway to be followed through the crossing region so that there is no experienced change in the states identity. In this Letter, we investigate the transition from interacting/delocalized states to noninteracting/localized states in oligomers of poly-phenylene vinylene separated by varying distances. We demonstrate that the appearance of trivial unavoided crossings during nonadiabatic dynamics leads to artifacts in the state population analysis. Consequently, changes in the localization of the electronic transition density must be followed instead.

Replica exchange with Smart Monte Carlo and Hybrid Monte Carlo in manifolds by R. Jenkins; E. Curotto; Massimo Mella (214-220).
Display OmittedSeveral Smart Monte Carlo (SMC) and Hybrid Monte Carlo (HMC) simulations coupled with the Replica Exchange (RE) strategy are compared in multidimensional flat and curved manifolds characterized by extremely rugged potential energy surfaces, to quantify their convergence properties with respect to walk length and overall cost. We learn that the HMC coupled with a sampling enhancing method is much more efficient in manifolds mapped with unconventional coordinates than SMC. This is due to an inherent difficulty in conserving energy in curved spaces directly mapped, and the lack of such strict requirement for HMC.

Kinetic study of the reaction of chlorine atoms with hydroxyacetone in gas-phase by Clara Stoeffler; Lilian Joly; Georges Durry; Julien Cousin; Nicolas Dumelié; Aurélien Bruyant; Estelle Roth; Abdelkhaleq Chakir (221-226).
Display OmittedIn this letter the kinetics of the reaction of hydroxyacetone CH3C(O)CH2OH with Cl atoms is investigated using the relative rate technique. Experiments are carried out in a 65 L multipass photoreactor in the temperature range of 281–350 K. A mid-infrared spectrometer based on a quantum cascade laser in external cavity emitting at 9.5 μm is used to analyze the reactants. The determined rate coefficient for the investigated reaction is (1.7 ± 0.3) × 10−11exp(381.5 ± 57.3/T). The results are presented and discussed in terms of precision and compared with those obtained previously. The impact of Cl atoms on the atmospheric life time of hydroxyacetone is also discussed.

Display OmittedThe structural parameters and relative energies of the minimum-energy crossing points (MECPs) of eight small molecules are calculated using five different representative density functional theory approximations as well as MP2, MP4, and CCSD(T) as a reference. Compared to high-level wavefunction methods, the main structural features of the MECPs of the systems included in this Letter are reproduced reasonably well by density functional approximations, in agreement with previous works. Our results show that when high-level wavefunction methods are computationally prohibitive, density functional approximations offer a good alternative for locating and characterizing the MECP in spin-forbidden chemical reactions.

A novel approach for preparation of aligned electrospun polyacrylonitrile nanofibers by Iman Heidari; Mahmoud Mosavi Mashhadi; Ghader Faraji (231-234).
Display OmittedIn this Letter, a new type of collector named ‘rotating grid collector’ was introduced and its capability in aligning the nanofibers was examined. The results showed that electrospinning using rotating grid collector could produce well aligned fibers with fiber alignment percent of 76%. It was found that in a constant solution flow rate increasing collector rotation speed and eccentric distance improved the fiber alignments. Having prepared the fiber textiles, we found that increasing the rotation speed improved the tensile strength of the fiber textile. This new collector is promising for future application in aligning nanofibers.

Optically tailored access to metastable electronic states by David L. Andrews; David S. Bradshaw (235-238).
Display OmittedOn irradiating a molecular system with a laser beam of ultraviolet or visible frequency, photon absorption occurs when an electronic state is at a suitable energy level relative to an initial state. Despite meeting this criterion, interesting metastable states can remain inaccessible because of symmetry constraints. In this Letter a mechanism, based on the input of an off-resonant beam, is shown to enable the population of such states. This is achievable because the laser-modified process involves different selection rules compared to conventional photon absorption. The effects of applying the stimulus beam to either a one- or two-photon process are examined.

In these curves, if the points are all round the trend line, this shows that the correlation is better. Observing these curves, our method possesses higher correlation with Clustal W than other seven methods.We use the occurrence frequency of 20 amino acids and take the new numerical characteristic of 2D graphical representation based on three physicochemical properties indexes as pseudo amino acid components. After a protein sequence is converted into a 23 dimensional vectors. Finally, based on the Euclidean distance, the similarities of ND5 proteins of nine species are used to demonstrate the effectiveness and rationality of our method. And correlation analysis has been provided to compare both our results and the results basing on the other graphical representation with the Clustal W’s results in order to show the utility of our method.