Formation of the magic cluster Na8 in noble gas matrixes

The sodium molecules Na(2), Na(4), and Na(8) have been isolated in argon matrixes at 15 K and characterized for the first time by Raman spectroscopy. The vibrational frequencies are compared with density functional (DFT) calculations. The Na(4) cluster possesses a rhombic structure (D(2h)) with calculated d(Na-Na) = 307.2 and 347.4 pm, respectively. For octasodium, a hypertetrahedral structure (T(d)) is predicted in which each side of an inner tetrahedron with d(Na-Na) = 331.5 pm is capped by sodium atoms with a distance of d(Na-Na) = 348.7 pm. The green octasodium cluster is the first example of a matrix-isolated magic number cluster. Its formation from blue tetrasodium is discussed on the basis of the observed sequence of cluster growth.     

Competition between Bailar and Ray-Dutt paths in conformational interconversion of tris-chelated complexes: a DFT study

Tris-chelated complexes of aluminum with α-isopropenyltropolonate and α-isopropyltropolonate ligands can be considered prototypical complexes for the study of internal rearrangements through prismatic transient structures. Such isomerization paths, known as Bailar and Ray-Dutt twists, have been suggested for these compounds on the basis of dynamic NMR study, but modern computational methodologies have never been applied to corroborate this finding. In this paper, we report a computational investigation about the internal isomerization processes of the mentioned complexes. Both the Bailar and Ray-Dutt twists have been found as possible reaction paths. The prismatic structures along each reaction path have been described as transition structures rather than intermediate and have been computationally characterized. A comparison between experimental and computational kinetic data has been performed.     

The size factor in the temperature retardation of diffusion in noble gas crystals

The times t* needed for noble gas crystals to reach the equilibrium state as a result of thermal motion of atoms upon temperature lowering during a nearly equilibrium process were calculated. The t* value was determined by solving a differential equation describing equalization of vacancy concentrations in a spherical sample of radius R. Upon temperature decrease, the t* values exponentially increase. As the sample radius R decreases, the time t* exponentially decreases. However, the tendency of t* to increase upon temperature lowering overrides the effect of decreasing sample size; therefore, there always exists a temperature range in which the diffusion is almost completely frozen.     

Pyrene: a probe to study protein conformation and conformational changes

The review focuses on the unique spectral features of pyrene that can be utilized to investigate protein structure and conformation. Pyrene is a fluorescent probe that can be attached covalently to protein side chains, such as sulfhydryl groups. The spectral features of pyrene are exquisitely sensitive to the microenvironment of the probe: it exhibits an ensemble of monomer fluorescence emission peaks that report on the polarity of the probe microenvironment, and an additional band at longer wavelengths, the appearance of which reflects the presence of another pyrene molecule in spatial proximity (~10 ?). Its high extinction coefficient allows us to study labeled proteins in solution at physiologically relevant concentrations. The environmentally- and spatially-sensitive features of pyrene allow monitoring protein conformation, conformational changes, protein folding and unfolding, protein-protein, protein-lipid and protein-membrane interactions.     

A variational coupled cluster theory for closed shells using a propagator modification procedure

A general partial summation method for including arbitrary classes of diagrams to all orders in the coupled cluster based size consistent energy functional for closed shell states is developed. Since the various reduced density matrices which appear in the energy functional are essentially the time-independent analogues of the corresponding many body Green functions, it is possible to derive Dyson-like equations for these quantities. By expanding the associated proper self energy parts in terms of the T-amplitudes, one can carry out partial summations in the reduced density matrices and thus in energy. At a higher level, higher order terms in a proper self energy can also be generated by renormalizing the internal propagators in it, and considering only the irreducible self-energy terms.     

Solvent-induced conformational changes of O-phenyl-cinchonidine: a theoretical and VCD spectroscopy study

The conformational analysis of the synthetic chiral modifier O-phenyl-cinchonidine (PhOCD) used in enantioselective hydrogenations over noble metal catalysts has been performed at a PM3 semiempirical level in vacuum. The minimum energy conformations calculated at the DFT level with a medium-size basis set have been compared to those of the parent alkaloid cinchonidine (CD). PhOCD behaves similarly to CD and shows four main conformers, denoted as Closed(1), Closed(2), Open(3), and Open(4). Open(3) is found to be the most stable in vacuum and in CH2Cl2 and CCl4 solvents. A comprehensive normal-mode analysis has been performed for these conformers, and assignment of the infrared spectrum of PhOCD in CCl4 (epsilon = 2.2) has been performed using the calculated spectrum of Open(3), which appears to be the most populated in this solvent. A combined theoretical-experimental VCD spectroscopy approach was used to increase the spectroscopic sensitivity toward changes in the distribution of conformers upon change of solvent polarity. The VCD spectra confirm that Open(3) is by far the most stable conformation in CCl4 (epsilon = 2.2) and indicate that an excess Closed(2) conformer has to be expected in CD2Cl2 (epsilon = 8.9). The possible influence of this conformational behavior is discussed on the basis of available catalytic data and in relation to the enantioselective potential of PhOCD as a chiral modifier on supported metal catalysts.     

pH-dependent protein conformational changes in albumin:gold nanoparticle bioconjugates: a spectroscopic study

The conformational changes of bovine serum albumin (BSA) in the albumin:gold nanoparticle bioconjugates were investigated in detail by various spectroscopic techniques including UV-vis absorption, fluorescence, circular dichroism, and Fourier transform infrared spectroscopies. Our studies suggested that albumin in the bioconjugates that was prepared by the common adsorption method underwent substantial conformational changes at both secondary and tertiary structure levels. BSA was found to adopt a more flexible conformational state on the boundary surface of gold nanoparticles as a result of the conformational changes in the bioconjugates. The conformational changes at pH 3.8, 7.0, and 9.0, which corresponded to different isomeric forms of albumin, were investigated, respectively, to probe the pH effect on the conformational changes of BSA in the bioconjugates. The results showed that the pH of the medium influenced the changes greatly and that fluorescence and circular dichroism studies further indicated that the changes were larger at higher pH.     

Silica sputtering by noble gas projectiles: elucidating the effect of cluster species with molecular dynamic simulation

Plasma Chemistry and Plasma Processing - The interaction of gas cluster projectiles with the surface of the inorganic compounds is still not a fully understood issue. To clarify the features of...     

An approximate method in using molecular mechanics simulations to study slow protein conformational changes

The broad range of characteristic motions in proteins has limited the applicability of molecular dynamics simulations in studying large-scale conformational transitions. We present an approximate method, making use of standard MD simulations and using a much larger integration time step, to obtain the structural changes for slow systematic motions of large complex systems. We show the applicability of this method by simulating the open to closed Calmodulin calcium binding domain conformational changes. Starting with the Ca2+-bound X-ray structure, and after the removal of the Ca2+ ions, our calculation yielded intermediate conformations during the rearrangement of helices in each Ca2+ binding pocket, leading to a structure with a lowest rmsd of 1.56 A compared to the NMR apo-calmodulin structure.     

The conformational flexibility of nucleic acid bases paired in gas phase: a Car-Parrinello molecular dynamics study

The flexibilities of pyrimidine and imidazole rings in the paired nucleobases are investigated using Car-Parrinello molecular dynamics simulation in gas phase. The pairing influence on the stiffness of rings is analyzed based on the molecular structure of the nucleobases and constraints caused by pairing. We prove that the flexibilities of pyrimidine rings in isolated state have subtle correlation with the degree of aromaticity of the rings. The pairings in nucleic base pairs cause the rings to be more rigid for G, T, and U but more flexible for A and the same for C.     

Neutron activation analysis of some noble metals with preconcentration procedure using a new type of cation chelating resin

The characteristic properties of the chelating resin-3926(II) and the advantage of using it in the preconcentration procedure was described. The chemical recoveries determined by the trace technique were presented. The preconcentration procedure put forward in this paper may be used satisfactorily in neutron activation analysis.     

Application of scaling and kinetic equations to helium cluster size distributions: Homogeneous nucleation of a nearly ideal gas

A previously published model of homogeneous nucleation [Villarica et al., J. Chem. Phys. 98, 4610 (1993)] based on the Smoluchowski [Phys. Z. 17, 557 (1916)] equations is used to simulate the experimentally measured size distributions of 4He clusters produced in free jet expansions. The model includes only binary collisions and does not consider evaporative effects, so that binary reactive collisions are rate limiting for formation of all cluster sizes despite the need for stabilization of nascent clusters. The model represents these data very well, accounting in some cases for nearly four orders of magnitude in variation in abundance over cluster sizes ranging up to nearly 100 atoms. The success of the model may be due to particularities of 4He clusters, i.e., their very low coalescence exothermicity, and to the low temperature of 6.7 K at which the data were collected.     

Insertion of noble gas atoms into cyanoacetylene: an ab initio and matrix isolation study

A computational and experimental matrix isolation study of insertion of noble gas atoms into cyanoacetylene (HCCCN) is presented. Twelve novel noble gas insertion compounds are found to be kinetically stable at the MP2 level of theory, including four molecules with argon. The first group of the computationally studied molecules belongs to noble gas hydrides (HNgCCCN and HNgCCNC), and we found their stability for Ng = Ar, Kr, and Xe. The HNgCCCN compounds with Kr and Xe have similar stability to that of previously reported HKrCN and HXeCN. The HArCCCN molecule seems to have a weaker H-Ar bond than in the previously identified HArF molecule. The HNgCCNC molecules are less stable than the HNgCCCN isomers for all noble gas atoms. The second group of the computational insertion compounds, HCCNgCN and HCCNgNC, are of a different type, and they also are kinetically stable for Ng = Ar, Kr, and Xe. Our photolysis and annealing experiments with low-temperature cyanoacetylene/Ng (Ng = Ar, Kr, and Xe) matrixes evidence the formation of two noble gas hydrides for Ng = Kr and Xe, with the strongest IR absorption bands at 1492.1 and 1624.5 cm(-1), and two additional absorption modes for each species are found. The computational spectra of HKrCCCN and HXeCCCN fit most closely the experimental data, which is the basis for our assignment. The obtained species absorb at quite similar frequencies as the known HKrCN and HXeCN molecules, which is in agreement with the theoretical predictions. No strong candidates for an Ar compound are observed in the IR absorption spectra. As an important side product of this work, the data obtained in long-term decay of KrHKr+ cations suggest a tentative assignment for the CCCN radical.     

Average cluster size determination in supersonic beams from angular distribution measurements after scattering by a buffer gas

A method for the determination of average cluster size in supersonic beams is presented. Based on angular distribution broadening of the beams caused by passing through a buffer gas, this method is well suited for in situ determination of the mean cluster size when the apparatus contains a movable detector with sufficient spatial resolution. The shape and width of the beam profile after scattering by a buffer gas are evaluated theoretically as functions of buffer gas pressure and atom-cluster collision cross-section. Experimental results are presented for an argon beam, yielding average cluster sizes between 300 and 7000 atoms depending on the stagnation pressure. Simple criteria to assess the applicability of the method to a given experimental situation are discussed. The average cluster sizes determined in this work agree quite satisfactorily with previously published values for similar beam generation conditions.     

Modifying the fullerene surface using endohedral noble gas atoms: density functional theory based molecular dynamics study of C70O3

We have performed a series of ab initio molecular orbital and molecular dynamics calculations to ascertain the influence of an endohedral noble gas atom on the reactivity of the surface of the model system C(70)O(3). Our simulations show that the minimum energy pathways for the ozone ring-opening reaction are influenced by the presence of the endohedral atom. The effect is isomer dependent, with the enthalpy of the reaction increasing for a,b-C(70)O(3) and decreasing for e,e-C(70)O(3) when doped with the heavy noble gas atoms Xe and Rn.     

Screening procedure for detecting butyrophenone and bisfluorophenyl neuroleptics in urine using a computerized gas chromatographic-mass spectrometric technique

A method for the identification of butyrophenone and bisfluorophenyl neuroleptics and their predominant basic metabolites in urine after acid hydrolysis is described. The acetylated extract is analysed by computerized gas chromatography-mass spectrometry. An on-line computer allows rapid detection using mass fragmentography with the masses m/e 112, 123, 134, 148, 169, 257, 321 and 189, 191, 223, 233, 235, 245, 287, 297. The identity of positive signals in the reconstructed mass fragmentograms is established by a comparison of the entire mass spectra with those of standards. The mass fragmentograms and the underlying mass spectra are documented.     

Characterization of conformational adsorbate changes on a tissue-derived substrate using Fourier transform infrared spectroscopy

Fourier transform infrared (FT-IR) spectroscopy is utilized to observe adsorbate interactions with a tissue-derived collagen scaffold extracted from the Bruch's membrane of pig eyes. The characterization includes conformational changes in isoleucine, polyisoleucine, collagen-binding peptide, RGD-tagged collagen-binding peptide, and laminin after adsorption onto the substrate. Isotopically labeled isoleucine is further utilized to understand changes in the biomolecular structure upon binding to a tissue-derived surface. The adsorbates associated with the collagen scaffold predominately through hydrophobic interactions and hydrogen bonding. The results of this study can be used to improve our understanding of surface chemistry changes during the engineering of biomimetic scaffolds before and after biomolecule adsorption.     

T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles

T-Analyst is a user-friendly computer program for analyzing trajectories from molecular modeling. Instead of using Cartesian coordinates for protein conformational analysis, T-Analyst is based on internal bond-angle-torsion coordinates in which internal torsion angle movements, such as side-chain rotations, can be easily detected. The program computes entropy and automatically detects and corrects angle periodicity to produce accurate rotameric states of dihedrals. It also clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. Correlated motions between selected dihedrals can also be observed from the correlation map. T-Analyst focuses on showing changes in protein flexibility between different states and selecting representative protein conformations for molecular docking studies. The program is provided with instructions and full source code in Perl.     

Correlating cluster size and NLO response of complexes aggregated with bifurcated metal bonds: a DFT study

In the present work, the cooperativity effect on the NLO response of clusters aggregated with bifurcated metal bonds is reported by DFT calculations at the CAM-B3LYP/6-311++G(d,p) level. Linear clusters of (LiN(CHO)₂)_1-5 and (NaN(CHO)₂)_1-5 which are connected with bifurcated metal bonds have been selected as model systems. Stabilization energies, polarizability, first hyperpolarizability, energy gap of HOMO and LUMO, and charge transfer (CT) were obtained at the same level of optimization. In the studied clusters, first hyperpolarizability is increased by cluster size and its values were obtained in ranges of 606.1–1327.4 and 1239.4–2071.1 a.u. for (LiN(CHO)₂)_1-5 and (NaN(CHO)₂)_1-5 clusters, respectively. The many-body analysis was carried out to determine two-body and many-body contributions in total interaction-induced properties. TD-DFT calculations were performed to compute the crucial electronic transitions of the related clusters. UV–vis spectra exhibit red shift due to cooperativity effects.