Chemical Physics Letters (v.390, #4-6)
Editorial board (IFC).
Partially and fully deprotonated sulfuric acid in H2SO4(H2O) n (n=6–9) clusters by Chang-Geng Ding; Kari Laasonen (307-313).
We have studied the deprotonation of sulfuric acid in small water clusters containing up to nine water molecules. Our main interest was to find out if the sulfuric acid can be completely deprotonated in such small clusters. Our results show that the fully deprotonated clusters are energetically very close to the partially deprotonated clusters. Thus, in clusters containing eight or more waters the sulfuric acid can be completely deprotonated.
The role of the 11Bu − state in carotenoid-to-bacteriochlorophyll singlet-energy transfer in the LH2 antenna complexes from Rhodobacter sphaeroides G1C, Rhodobacter sphaeroides 2.4.1, Rhodospirillum molischianum and Rhodopseudomonas acidophila by Ferdy S. Rondonuwu; Kyosuke Yokoyama; Ritsuko Fujii; Yasushi Koyama; Richard J. Cogdell; Yasutaka Watanabe (314-322).
Subpicosecond time-resolved absorption spectra were recorded, in the visible and near-infrared regions, for the LH2 antenna complexes from Rhodobacter sphaeroides G1C, Rhodobacter sphaeroides 2.4.1, Rhodospirillum molischianum, and Rhodopseudomonas acidophila. The efficiencies of carotenoid-to-bacteriochlorophyll singlet-energy transfer through the 11Bu +, 11Bu −, and 21Ag − channels in the LH2 complex were determined to be 48%, 19% and 22% in Rhodobacter sphaeroides G1C; 46%, 18% and 20% in Rhodobacter sphaeroides 2.4.1; 48%, ∼2% and ∼1% in Rhodospirillum molischianum; and 48%, ∼2%, ∼4% in Rhodopseudomonas acidophila. Sums of efficiencies through the three channels in the four LH2 complexes, 88%, 84%, 51% and 54%, nicely correlate with the efficiencies that were determined by comparison of the absorption and fluorescence-excitation spectra, 92%, 89%, 53% and 56%.
Energy distributions of CO produced in an acetone-containing discharge by Peng Li; Wai Yip Fan (323-327).
Tunable infrared diode laser absorption (TDLAS) and Fourier transform infrared absorption spectroscopies (FTIR) have been utilized to characterize the translational, rotational and vibrational distributions of CO in an acetone/argon DC plasma at total pressures ranging from 4 to 5 Torr and currents of 0.1–0.3 A. A broad vibrational distribution of CO was observed with gradually decreasing intensities from the fundamental band to v=12←11. When nitrogen was added to the plasma, the distribution is narrower, due to the efficient energy transfer between CO and N2 molecules. The measured translational temperature in such plasmas ranged from 400–550 K. The rotational distribution can generally be fitted to a Boltzmann distribution within each vibrational level although the rotational temperature is highest for the lowest vibrational quantum number.
Switching dynamics of the photochromic 1,1-dicyano-2-(4-cyanophenyl)-1,8a-dihydroazulene probed by sub-30 fs spectroscopy by Vincent De Waele; Matthias Beutter; Uli Schmidhammer; Eberhard Riedle; Jörg Daub (328-334).
We report the first time resolved investigation of the ring opening dynamics of the 1,1-dicyano-2-(4-cyanophenyl)-1,8a-dihydroazulene (CN-DHA) towards its vinylheptafulvene (CN-VHF) isomer. The kinetics are measured by sub-30 fs transient absorption spectroscopy for numerous probe wavelengths from 485 to 690 nm. The ring opening takes place within 1.2 ps on the CN-DHA-VHF S1 potential energy surface. It is followed by the internal conversion from CN-VHF-S1 to CN-VHF-S0 in 13 ps. We observe coherent oscillations of low frequency modes (150, 190, 330 and 500 cm−1) that are closely associated with the skeleton motions driving the CN-DHA structural changes immediately after the 30 fs UV excitation.
A periodic first principle study to design microporous crystal 12MO, 7Al2O3 for selective and active O− radicals encaging by Abhijit Chatterjee; Masateru Nishioka; Fujio Mizukami (335-339).
Periodic first principle calculation correlates the role of metal substitution (Sr and Ba in place of Ca) on selective encaging of active O− radicals inside the microporous 12MO, 7Al2O3 crystal structure. We have exchanged Ca by Sr and Ba and as well extracted electron stepwise to monitor selectivity of different anion encaging inside the same structure type. Ca favors O2− encaging and shows no electron transition when neutral, whereas Sr shows no transition in absence of unpaired electron and can successfully trap O−, Ba though less active than the other metal substituents shows oxygen encaging at its zero and mono-positive state.
Near infrared absorptions of CH4/He plasma: the Phillips band system of C2 by Man-Chor Chan; Shun-Hin Yeung; Yuen-Yee Wong; Yongfang Li; Wang-Ming Chan; Kan-Hing Yim (340-346).
Zero-background laser absorption spectroscopy using concentration modulation has been applied to study the near infrared absorption spectrum of the discharge of CH4 and He at a ratio of about 1:170. In the 10 300–14 250 cm−1 region, a total of 13 vibronic bands have been observed with 11 of them assigned to the very weak Phillips band system of C2. Combining these transitions with those observed in emission by Douay et al. [J. Mol. Spectrosc. 131 (1988) 250], a set of spectroscopic constants with high accuracy have been obtained.
Evidence for two light-induced metastable states in Cl3[Ru(NH3)5NO]H2O by D. Schaniel; T. Woike; C. Boskovic; H.-U. Güdel (347-351).
Differential Scanning Calorimetry measurements on irradiated Cl3[Ru(NH3)5NO]H2O reveal the existence of two light-induced long-lived metastable states SI, SII. Irradiation with light in the spectral range 400–500 nm leads to the excitation of SI. For the first time we report experimental evidence for the state SII in this compound, which can be excited by transferring SI into SII with irradiation of light in the spectral range 1000–1200 nm. The excitation and transfer of the metastable states is described and the exponential decays are evaluated according to Arrhenius' law yielding activation energies of E A(SI)=0.73(3) eV, E A(SII)=0.66(3) eV and frequency factors of Z(SI)=1 × 1012 s−1, Z(SII) = 5 × 1012 s−1.
A new alligator-clip compound for molecular electronics by Timo Jacob; Mario Blanco; William A. Goddard (352-357).
We used the B3LYP flavor of density functional calculations to study new alligator-clip compounds for molecular electronics with platinum electrodes. First, with commonly used S-based linkage molecule 3-methyl-1,2-dithiolane (MDTL) we find that after chemisorption on Pt(1 1 1) the most stable structure is ring-opened with a binding energy of 32.44 kcal/mol. Among several alternative alligator-clip compounds we find that P-based molecules lead to much higher binding energies. For the ring-closed structure of 3-methyl-1,2-diphospholane (MDPL) a binding energy of 47.72 kcal/mol was calculated and even 54.88 kcal/mol for the ring-opened molecule. Thus, MDPL provides a more stable link to the metal surface and might increase the conductance.
Towards the understanding of the spectroscopic behaviour of the C–H oscillator in C–H⋯O hydrogen bonds: the effect of solvent polarity by Paulo J.A. Ribeiro-Claro; Pedro D. Vaz (358-361).
The effect of solvent polarity versus specific C–H⋯O contacts on the vibrational νC–H mode is studied using CHCl3 as a model system. Ab initio SCI–PCM calculations show that the overall shift of the νC–H band, sometimes ascribed to the C–H⋯O hydrogen bonding, can in fact be explained by the electrostatic interaction with a dielectric environment. The presence of a new νC–H band – assigned to the C–H⋯O bonded forms – remains as the most reliable evidence of C–H⋯O hydrogen bonding.
Theoretical calculational studies on the mechanism of thermal dissociations for RN3 (R=CH3, CH3CH2, (CH3)2CH, (CH3)3C) by Yanli Zeng; Qiao Sun; Lingpeng Meng; Shijun Zheng; Dianxun Wang (362-369).
Mechanisms of RN3 (R=CH3, CH3CH2, (CH3)2CH, (CH3)3C) dissociations are proposed based on CAS, MP2 and B3LYP methods. The energy gaps between the ground-state reactants RN3 and the intersystem crossing (ISC) points are only a little lower than respective potential energy barriers of the spin-allowed reactions, 1RN3 → 1RN + 1N2. The ISC point, therefore, is considered as a transition state of the spin-forbidden reactions, 1RN3 → 3RN + 1N2. The methods of IRC and topological analysis of electron density are used to explain and predict the thermal dissociation pathways of the reactions studied.
State-to-state dissociation rate coefficients in electronically excited diatomic gases by A. Aliat; Elena V. Kustova; A. Chikhaoui (370-375).
In the present Letter, state dependent dissociation rate coefficients in diatomic gases with non-equilibrium vibrational and electronic excitation and chemical reactions are studied. A widely used Treanor–Marrone model is generalized to take into account state-to-state vibrational and electronic distributions. The influence of electronic excitation on the rate of dissociation from various electronic states of CO molecules is estimated.
Determination of the first ionization energy of furan (C4H4O) from an extrapolation of two nd Rydberg series observed in the mass-resolved (2 + 1) resonance enhanced multiphoton ionization spectrum by Trevor Ridley; Kenneth P. Lawley; Mohamed H.S.N. Al-Kahali; Robert J. Donovan (376-379).
The first ionization energy of furan (C4H4O) has been determined from a short extrapolation of two nd (n=6–22) Rydberg series observed in the mass-resolved (2 + 1) resonance enhanced multiphoton ionization spectrum as IE=71673 ± 3 cm−1. This value confirms the higher of the two values in the literature.
Force acting on the microparticles in electrorheological solids under the application of a nonuniform ac electric field by J.P. Huang (380-383).
Under the application of electric fields, the structure of electrorheological (ER) solids can be changed from the body-centered tetragonal lattice to other lattices. We have derived the dipole factor for the lattice by taking into account the local-field effect through the Ewald–Kornfeld formulation, and expressed it in the spectral representation exactly. It is found that when the ER solid is subject to a nonuniform ac electric field, the force acting on the microparticle can be affected by the structure transformation, and local-field effect as well as field frequency. Our results are very well understood in the spectral representation theory.
Solvent-mediated tautomerization of purine: single to quadruple proton transfer by Doo-Sik Ahn; Sungyul Lee; Bongsoo Kim (384-388).
We present calculations for the structures and the tautomerization reaction of purine and purine – (H2O) n (n=1–3) clusters. We find two pathways (via the carbene and the sp3-type intermediate) for the 9 ↔ 7 tautomerization of bare purine. The barrier heights for the 9 → 3 and 9 → 7 tautomerization of bare purine are calculated to be large (60–70 kcal/mol). Hydrogen bonding with the water molecule(s), however, dramatically lowers the 9 → 3 barrier by the concerted multiple proton transfer mechanism, favoring the formation of the conformer 3(H)- relative to the 7(H)-purine in the microsolvated environment, in contrast to the gas phase or the aqueous solution.
In situ characterization of surface physicochemical properties of carbon nanofibers using 1-naphthol as a fluorescent probe by Hiromasa Nishikiori; Nobuaki Tanaka; Satoshi Kubota; Morinobu Endo; Tsuneo Fujii (389-393).
1-Naphthol has been used as an in situ fluorescent probe to characterize the surface physicochemical properties of carbon nanofibers (CNFs). The fluorescence of 1-naphthol adsorbed on untreated CNFs originates from the 1Lb state and its peaks are shifted by the polarity of the surrounding media, indicating that there is a relatively non-polar area on the CNF surface. 1-Naphthol interacting with oxidized sites on the surface of nitric acid-treated CNFs exhibited an ion-pair fluorescence. This shows that there are some functional groups, interacting with 1-naphthol, on the treated CNF surface. The surface physicochemical properties of the CNFs can be characterized by this fluorescent probe.
An efficient algorithm for calculating whole-profile functions in crystal structure solution from powder diffraction data by Scott Habershon; Eugene Y. Cheung; Kenneth D.M. Harris; Roy L. Johnston (394-398).
A method for calculation of the whole-profile powder diffraction R-factor R wp, adapted specifically for use in direct-space structure solution, is shown to be faster by a factor of approximately 20 than standard methods for calculating R wp.
Charge separation at the rutile/anatase interface: a dominant factor of photocatalytic activity by Takahira Miyagi; Masayuki Kamei; Takefumi Mitsuhashi; Takamasa Ishigaki; Atsushi Yamazaki (399-402).
Epitaxial and polycrystalline anatase films were grown by pulse-powered magnetron sputtering. The photoreduction of Ag ions showed the difference in the distribution of the photocatalytic active sites in these films. The polycrystalline anatase film was covered with an Ag layer. In contrast, discrete Ag particles were interspatially deposited on the epitaxial anatase film. Evaluation of the epitaxial film by micro-Raman spectrometry revealed that the rutile coexisted at only the site where the Ag particle was precipitated. These results suggest that the rutile/anatase interface is the active site for photocatalysis and is one of the dominant factors of the photocatalytic activity.
Yb3+ ion as a sensitizer for the upconversion luminescence in nanocrystalline Gd3Ga5O12:Ho3+ by J.C. Boyer; F. Vetrone; J.A. Capobianco; A. Speghini; M. Bettinelli (403-407).
The effect of Yb3+ co-doping on the upconversion luminescence in nanocrystalline Gd3Ga5O12:Ho3+ was examined. Strong and efficient NIR to green anti-Stokes luminescence was noted in nanocrystalline Gd3Ga5O12:Ho3+, Yb3+ after excitation into the 2F5/2 level of Yb3+ with 978 nm radiation. Weaker blue, red and NIR anti-Stokes luminescence was also observed after 978 nm excitation. An enhancement of the red 5F5 → 5I8 luminescence was observed in the anti-Stokes spectrum compared to the Stokes emission spectrum. This enhancement was attributed to two distinct energy transfer upconversion (ETU) mechanisms which preferentially populate the (5F4, 5S2) and 5F5 levels.
Nuclear magnetic resonance shielding tensors calculated with kinetic energy density-dependent exchange-correlation functionals by Sergey N. Maximoff; Gustavo E. Scuseria (408-412).
Exchange-correlation functionals that depend on the non-interacting kinetic energy density (τ) break gauge invariance in the presence of a magnetic field. This yields incorrect results for molecular magnetic properties. We propose a simple generalization of the kinetic energy density that resolves this problem. Our modification is validated by computing NMR absolute isotropic shielding constants and shielding anisotropies with τ-dependent functionals for a representative set of molecules. The accuracy of τ-dependent approximations is found to surpass that of common generalized gradient approximations (GGA) and hybrid functionals for strongly deshielded nuclei.
The role of vacancy defects and holes in the fracture of carbon nanotubes by Steven L. Mielke; Diego Troya; Sulin Zhang; Je-Luen Li; Shaoping Xiao; Roberto Car; Rodney S. Ruoff; George C. Schatz; Ted Belytschko (413-420).
We present quantum mechanical calculations using density functional theory and semiempirical methods, and molecular mechanics (MM) calculations with a Tersoff–Brenner potential that explore the role of vacancy defects in the fracture of carbon nanotubes under axial tension. These methods show reasonable agreement, although the MM scheme systematically underestimates fracture strengths. One- and two-atom vacancy defects are observed to reduce failure stresses by as much as ∼26% and markedly reduce failure strains. Large holes – such as might be introduced via oxidative purification processes – greatly reduce strength, and this provides an explanation for the extant theoretical–experimental discrepancies.
A density functional theory study applied for carbon and oxygen isotope effects in the system Ni(CO)4/CO by Yuriko Ono; Yasuhiko Fujii; Takanobu Ishida (421-426).
DFT calculations were carried out on the carbon and oxygen isotopomers of CO and Ni(CO)4 and results compared with (Spindel's) experimental results on the carbon and oxygen isotope exchange equilibria between CO and Ni(CO)4. The isotopic equilibrium constants, K B, of carbon and oxygen exchange reactions between CO and Ni(CO)4 complexes were theoretically calculated as the ratio of the reduced partition function ratios (RPFRs) of the 13C/12C and 18O/16O isotopic pairs for CO and Ni(CO)4 on the assumption of the internal harmonic vibrations. The agreement between calculated separation factor and Spindel's experimental data are surprisingly good, including the temperature dependence.
Time resolved resonance Raman studies on triplet excited state of 2-methoxy-naphthalene by photo-sensitization by Himansu Mohapatra; Siva Umapathy (427-432).
We report on the resonance Raman spectrum of the triplet excited state of 2-methoxy-naphthalene (3ROMe) generated by benzophenone (BP) triplet sensitization. A comparison of the time resolved resonance Raman (TR3) spectra of 3ROMe obtained by energy transfer with that of the spectrum obtained in the absence of BP reveals no change in vibrational frequencies due to weak charge transfer interaction, as expected for a triplet exciplex. It is observed from our computational studies and the experimental data that the unpaired electron in the * orbital of triplet state is more localized on the aromatic ring attached to the methoxy group.
Two-photon absorption properties of star-shaped molecules containing peripheral diarylthienylamines by Sean Liu; Kuen Shen Lin; Victor M. Churikov; Yi Zhen Su; Jiann T'suen Lin; Tzer-Hsiang Huang; Chia Chen Hsu (433-439).
Two-photon absorption (TPA) properties of several novel donor–acceptor–donor (D–A–D) quadrupolar and octupolar star-shaped molecules containing peripheral diarylthienylamines were investigated and are discussed in this Letter. The effects of donor–acceptor strength, conjugation length, and molecular symmetry on the effective TPA cross-section of these novel molecules were studied. It was found that incorporation of a triazine acceptor center in octupolar molecules can effectively enhance TPA response. This provides a strategy for designing novel octupolar molecules with a large TPA response but without red-shifting their linear absorption wavelengths.
Nano-scale effects in electrochemistry by J. Meier; J. Schiøtz; P. Liu; J.K. Nørskov; U. Stimming (440-444).
We report combined scanning tunneling microscopy and electrochemical reactivity measurements on individual palladium nanoparticles supported on a gold surface. It is shown that the catalytic activity towards electrochemical proton reduction is enhanced by more than two orders of magnitude as the diameter of the palladium particles parallel to the support surface decreases from 200 to 6 nm. Density functional theory (DFT) calculations combined with molecular dynamics (MD) simulations have been used to investigate the origin of the effect. It is concluded that the size effect is given by the thickness-variation of the support-induced strain at the surface of the palladium nanoparticles.
Impedance spectroscopy of the electrode-tissue interface of living heart with isoösmotic conductivity perturbation by Marc Ovadia; Daniel H. Zavitz (445-453).
Impedance spectroscopy was used to solve the Pt electrode interface with metabolically active perfused living heart. Three impedance spectra were observed: the Warburg impedance (Z W∞), a single high angle constant-phase-element, and a thin-film impedance (Z D). When characterized again after cyclic change of ionic strength (and hence conductivity κ) each interface had one of only two spectra, with exclusion of Z W∞. The in vivo interfacial impedance spectrum is thus neither single-valued nor stable in time. Because metal|living tissue interfaces are obligatory circuit elements in biosensors and electrodes in heart and brain, the multiple-valued and thin-film character of its impedance are significant.
Comparison between semiclassical and composite absorbing potentials by J.G. Muga; B. Navarro (454-457).
We compare the absorption of (a) an absorbing potential proposed recently by Manolopoulos based on semiclassical arguments and (b) complex potentials composed by contiguous square barriers. The latter use more parameters and provide better absorption, but the potential by Manolopoulos is simple and robust with respect to numerical discretization, and can be very efficient if its only effective parameter is optimized.
Identification of the point defects in diamond as measured by Raman spectroscopy: comparison between experiment and computation by S. Prawer; Irina Rosenblum; J.O. Orwa; Joan Adler (458-461).
Raman spectroscopy and molecular dynamics (MD) simulations are used to identify the vibrational spectrum of simple point defects in diamond. Two local mode frequencies are found in ion irradiated diamond. The first (with an energy of 185 meV) is clearly identified as arising from the vacancy defect, whereas a mode at 202 meV is demonstrated to be due to the [1 0 0] split interstitial.
Structural evolutions of carbon nano-peapods under electron microscopic observation by Alexandre Gloter; Kazutomo Suenaga; Hiromichi Kataura; Ryosuke Fujii; Takeshi Kodama; Hiroyuki Nishikawa; Isao Ikemoto; Koichi Kikuchi; Shinzo Suzuki; Yohji Achiba; Sumio Iijima (462-466).
Supramolecular assemblages made of single wall carbon nanotubes (SWNT) filled with fullerenes or metal doped fullerenes exhibit promising electronic structure variations at a nanometer scale. Nevertheless, the knowledge about the structural defects of these systems is still very limited. Here, we report structural evolutions under high-resolution electron microscopic observation at the sensitivity of a single atom detection for Ca@C82 molecules encapsulated within SWNT.
Intermediate phase upon alloying Au–Ag nanoparticles under laser exposure of the mixture of individual colloids by A.T. Izgaliev; A.V. Simakin; G.A. Shafeev; F. Bozon-Verduraz (467-471).
The dynamics of Au–Ag alloy formation under laser irradiation of a mixture of the monometallic colloidal solutions are experimentally investigated and the factors influencing the alloy genesis are determined. Ag or Au nanoparticles are obtained by laser ablation of the corresponding metals in water or ethanol. Evidence is presented for the formation of an intermediate Au–Ag phase characterized by a transient red-shifted absorption peak. The changes in absorption spectrum and morphology of the colloidal particles are studied as a function of exposure time to laser radiation. It is found that the rate of alloying depends on both the concentration of nanoparticles and the presence of surface-active substances.
Endohedral complexes of C58 cage with H2 and CO by Yun Hang Hu; Eli Ruckenstein (472-474).
Ab initio Hartree–Fock (HF) calculations were carried out to determine the structures and energies of the endohedral complexes of C58 cage with H2 or CO. It was demonstrated that the formation of these complexes is endothermic with destabilization energies of 3.3 kcal/mol for H2 and 18.6 kcal/mol for CO. Furthermore, the H2 and CO molecules have different orientations in the C58 cage, namely, the orientation of the molecular axis of the former is normal to the face of the 7-member ring, while that of the latter is parallel to that face. In addition, the H–H bond of the H2 molecule is shortened inside the cage, whereas the length of the C–O bond remains unchanged.
Electron-ion recombination in dense gaseous and liquid argon: effects due to argon cation clusters allow to explain the experimental data by Mariusz Wojcik; M. Tachiya (475-480).
The role of cation clusters in the bulk electron-ion recombination in dense gaseous and liquid argon is investigated. The size and structure of cation clusters in those systems are determined by a Monte Carlo simulation. Then, the rate constants of electron-ion recombination are calculated by another simulation method that takes into account the presence of cation clusters in the considered systems. A good agreement with experiment for both dense gaseous and liquid argon is obtained.
Degradation of vitamin C by low-energy electrons by Hassan Abdoul-Carime; Eugen Illenberger (481-484).
We report on the degradation of gas phase vitamin C (ascorbic acid, AA) induced by low-energy electrons. In the energy range of (0–12) eV, different negatively charged fragments, attributed to the dehydro-ascorbic acid anion ((AA–H)−), OH−, O− and H−, are observed. The yield functions indicate that these ions are formed via dissociative electron attachment, DEA. While the formation of (AA–H)− is exclusively observed at sub-excitation energies (<1.5 eV), the other fragments arise from resonance features at higher energies. Possible implications of these observations for radiation damage and food treatment by high energy radiation are considered.
Newly developed ab initio fitted potentials for molecular dynamics simulations of n-pentane in the zeolite silicalite-1 by A Loisruangsin; S Fritzsche; S Hannongbua (485-490).
Ab initio fitted potentials representing n-pentane/n-pentane and n-pentane/silicalite-1 interactions were newly developed at the second-order Møller-Plesset perturbation (MP2) level with the 6-31G* basis set. Characteristics of the functions were illustrated in comparison with available force field models. They were, then, applied for the molecular dynamics simulation of n-pentane in silicalite-1. The diffusion coefficients are in satisfactory agreement with the results of PFG-NMR experiments. The effect of the box size was also examined. It was found that the components of the diffusion tensor are very sensitive to this parameter. The structure of the n-pentane in the silicalite-1 pore was analyzed in terms of radial distribution functions. The first peak at 4.1 Å indicates the optimal diffusion route of the n-pentane along the central line of the channel of the silicalite-1.
The entry pathway of O2 into human ferritin by Lucio Colombi Ciacchi; Mike C Payne (491-495).
We study the entry pathway of dioxygen into human ferritin by means of both first principles and classical molecular dynamics techniques. Oxygen molecules, which behave hydrophobically in the water solvent, are found to interact with the Tyr 29 residue of human ferritin both directly via weak interactions and indirectly via hydrophobic forces. These interactions drive O2 toward a narrow hydrophobic channel which connects the ferroxidase site of ferritin with the external environment. Diffusion of O2 through the channel is observed using locally enhanced sampling techniques, and the enthalpy barrier to diffusion is calculated from first principles.
CCSDT and CCSD(T) calculations on model H-bonded and stacked complexes by Jiřı́ Pittner; Pavel Hobza (496-499).
The CCSD(T) and CCSDT interaction energies were determined for model planar H-bonded complexes (formamide…formamide, formamidine…formamidine) and stacked complexes (ethylene…ethylene, formaldehyde…formaldehyde). Various basis sets from the 6-31G*(0.25) to aug-cc-pVDZ were used. Difference between CCSD(T) and CCSDT interaction energies were small and become negligible (bellow 0.1 kcal/mol) if the aug-cc-pVDZ (or aug-cc-pVDZ/cc-pVDZ) basis set was applied. This result strongly supports the use of the CCSD(T) method for determination of true stabilization energies of extended complexes.
Impact of receptor conformation on in silico screening performance by H. Merlitz; B. Burghardt; W. Wenzel (500-505).
We report on results for the in silico screening of a database of 10 000 flexible compounds against various crystal structures of the thymidine kinase enzyme complexed with 10 known inhibitors. We provide a quantitative analysis of the deviations in the ranking of the inhibitors depending on the choice of receptor conformation and imply that the inclusion of side-chain degrees of freedom to the receptor would significantly improve the predictive power of the screening approach. We suggest a consensus score that, in the case of several known native structures of the receptor, enables the evaluation of scoring functions without the requirement of explicit receptor-flexibility.
Two-photon absorption investigation in reduced and oxidized cytochrome c solutions by A.A. Andrade; N.M. Barbosa Neto; L. Misoguti; L. De Boni; S.C. Zilio; C.R. Mendonça (506-510).
Here we present, a two-photon absorption (2PA) study in Fe2+ and Fe3+ oxidation states of cytochrome c molecule in water solution, using the femtosecond Z-scan technique with pulses from 560 to 850 nm. No qualitative difference was observed in the 2PA process for the two Fe oxidation states. The 2PA cross-sections, for both samples, increase as the wavelength approaches the absorption band, in agreement with the resonant denominator in the sum-over states model, presenting a maximum value of approximately 1000 GM at about 600 nm.
A molecular dynamics study on the conformational stability of PrP 180–193 helix II prion fragment by M. Pappalardo; D. Milardi; C. La Rosa; C. Zannoni; E. Rizzarelli; D. Grasso (511-516).
Molecular dynamics of PrP 180–193 has allowed us to investigate the stability of the α-helical conformation of the zwitterionic peptide (L1) and the neutralized (L2). In water, the helical structure of L1 is unstable; in L2, the α-helix breaks up in the middle at Gln186, and the two resulting connected helices are stable. The hydrophobic enviroment decreases the stability of the helical structure of L1, this effect is more evident for L2 for which the unfolding of the C-terminus is followed by the formation of an intramolecular hydrogen bond connecting His187 with Thr191.
Complexes of cationic coinage metal clusters M n + (M=Cu, Ag, Au; n=1–4) and H2S: a theoretical study by I.P. Hamilton (517-521).
Geometries and vibrational frequencies of complexes of cationic coinage metal clusters M n + (M=Cu, Ag, Au; n=1–4) and H2S are computed using density functional theory. Thermochemical values for M n +H2S decomposition channels involving loss of an H atom, H2 molecule, M atom, or M2 molecule are also computed. Significantly different results are obtained for closed-shell (n odd) and open-shell (n even) complexes.
Author index (522-530).