On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter

The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.     

FTIR study of the mode of binding of the reactants on the Pd nanoparticle surface during the catalysis of the Suzuki reaction

In the Suzuki reaction between phenylboronic acid and iodobenzene catalyzed by palladium nanoparticles, our previous studies suggested that the phenylboronic acid adsorbs on the nanoparticle surface and then interacts with the iodobenzene that is present in solution. In the present study, FTIR is used to examine the change in the vibrational frequencies of phenylboronic acid in films with and without the addition of palladium nanoparticles. The large change in the B-O stretching frequency of phenylboronic acid from 1348 to 1376 cm(-1) in the presence of sodium acetate and palladium nanoparticles strongly suggests that the mode of binding of phenylboronic acid to the Pd nanoparticle surface involves a B-O-Pd type of bonding. Shifts in the B-C stretching mode and the out-of-plane phenyl C-C ring deformation bands associated with phenylboronic acid provide additional confirmations of the binding process. It is also shown that the phenylboronic acid needs to be in the deprotonated form in the presence of sodium acetate (phenylboronate anion) to bind to the palladium nanoparticle surface. No changes in the characteristic bands of iodobenzene were observed in films made in the presence of the palladium nanoparticles. The FTIR studies provide proof of the mode of binding that occurs in the nanoparticle surface for the first time and also confirms the mechanism of the Suzuki reaction that we proposed previously.     

Correlation Analysis of the Runoff of the Rivers and the Seisms in China

In recent hundred years the annual discharge variations of the Changjiang River (represented by the Yichang station) and the Huanghe River (represented by Shanxian and Tangnaihe, respectively) have closely related to the geographical distribution of the earthquakes coming about in China in the same year, Both the occurrence of the destructive seism or seismic swarm in the river basins and the disappearance of the shocks in the east and south of the basins are the conditions that the Changjiang and Huanghe Rivers are the high flow while that the strong earthquake of magnitude 7 or more occurred in North China is the condition for the Changjiang low flow year and that of 6 or more in the Qilian Mountains area is for the Huanghe River. In the latter part of this paper, a 2-year sample is given to explain that the conditions of the 2 rivers being high flow years are that the north-south seismic belt is active and in the meanwhile no seism occurred in South China, and those of the low flow year are that the     

On the adequacy of modeling the concentration dependences of the activity coefficients for the components of solutions

An analysis of the accepted methods for calculating the activity coefficients for the components of binary aqueous solutions was performed. It was demonstrated that the use of the osmotic coefficients in auxiliary calculations decreases the accuracy of estimates of the activity coefficients. The possibility of calculating the activity coefficient of the solute from the concentration dependence of the water activity was examined. It was established that, for weak electrolytes, the interpretation of data on heterogeneous equilibria within the framework of the standard assumption that the dissociation is complete encounters serious difficulties.     

5-Hydroxymethylcytosine, the sixth base of the genome

5-Hydroxymethylcytosine (hmC) was recently discovered as a new constituent of mammalian DNA. Besides 5-methylcytosine (mC), it is the only other modified base in higher organisms. The discovery is of enormous importance because it shows that the methylation of cytosines to imprint epigenetic information is not a final chemical step that leads to gene silencing but that further chemistry occurs at the methyl group that might have regulatory function. Recent progress in hmC detection--most notably LC-MS and glucosyltransferase assays--helped to decipher the precise distribution of hmC in the body. This led to the surprising finding that, in contrast to constant mC levels, the hmC levels are strongly tissue-specific. The highest values of hmC are found in the central nervous system. It was furthermore discovered that hmC is involved in regulating the pluripotency of stem cells and that it is connected to the processes of cellular development and carcinogenesis. Evidence is currently accumulating that hmC may not exclusively be an intermediate of an active demethylation process, but that it functions instead as an important epigenetic marker.     

Features of the ESI mechanism that affect the observation of multiply charged noncovalent protein complexes and the determination of the association constant by the titration method

Several factors, attributable to the ESIMS mechanism, that can affect the assumptions of the titration method are examined: (1) The assumption that the concentrations in solution of the protein P, the ligand L, and the complex PL are proportional to the respective ion intensities observed with ESIMS, is examined with experiments in which ion intensities of two non-interacting proteins are compared with the respective concentrations. The intensities are found to be approximately proportional to the concentrations. The proportionality factors are found to increase as the mass of the protein is decreased. Very small proteins have much higher intensities. The results suggest that it is preferable to use only the intensity ratio of PL and P, whose masses are very close to each other when L is small, to determine the association constant KA in solution. (2) From the charge residue model (CRM) one expects that the solution will experience a very large increase of concentration due to evaporation of the precursor droplets, before the proteins P and PL are produced in the gas phase. This can shift the equilibrium in the droplets: P + L = PL, towards PL. Analysis of the droplet evaporation history shows that such a shift is not likely, because the time of droplet evolution is very short, only several micros, and the equilibrium relaxation time is much longer. (3) The droplet history shows that unreacted P and L can be often present together in the same droplet. On complete evaporation of such droplets L will land on P leading to PL and this effect will lead to values of KA that are too high. However, it is argued that mostly accidental, weakly bonded, complexes will form and these will dissociate in the clean up stages (heated transfer capillary and CAD region). Thus only very small errors are expected due to this cause. (4) Some PL complexes may have bonding that is too weak in the gas phase even though they have KA values in solution that predict high solution PL yields. In this case the PL complexes may decompose in the clean up stages and not be observed with sufficient intensity in the mass spectrum. This will lead to KA values that are too low. The effect is expected for complexes that involve significant hydrophobic interaction that leads to high stability of the complex in solution but low stability in the gas phase. The titration method is not suited for such systems.     

All-trans-retinal is the chromophore bound to the photoreceptor of the alga Chlamydomonas reinhardtii.

Rhodopsin is the general name for a family of visual pigments that receive light and transmit this signal to the rest of an organism. Chlamydomonas reinhardtii is a unicellular eukaryote whose light-tracking system consists of a single eye. Through spectral studies of Chlamydomonas' reaction to light of different wavelengths (action spectroscopy), it has been shown in vivo that the photoreceptor of Chlamydomonas is functionally similar to vertebrate rhodopsin. We seek to characterize the photoreceptor further by identifying the molecule that is incorporated into the rhodopsin of Chlamydomonas forming the chromophore. High performance liquid chromatography analysis of organic extracts of retinaloximes from membrane fractions enriched in eye-spots and in cells virtually free of interfering carotenoids identified syn-all-trans as the existing retinaloxime isomer. We conclude that all-trans-retinal is the native molecule that is available to be incorporated into the rhodopsin of Chlamydomonas and therefore forms the functioning chromophore on binding.     

Unexpected photolysis of the sunscreen octinoxate in the presence of the sunscreen avobenzone

A major concern raised about photostability studies of sunscreen products is that the photodegradation of sunscreens does not readily translate into changes in product performance. This study examines the correlation between photochemical degradation of sunscreen agents and changes in protection provided by sunscreen films. Films of a commercial sunscreen product containing avobenzone, oxybenzone and octinoxate were irradiated using a fluorescent UV-A phototherapy lamp with additional UV-B blocking filter. Periodically, during irradiation the transmittances of the films were measured and samples collected for chemical analysis of the sunscreen agents using high-performance liquid chromatography techniques. The results show that UV-induced changes in UV transmittance of sunscreen films correlate with changes in concentration of sunscreen agents. In a parallel experiment, we also irradiated a thin film of the same product in the cavity of an electron spin resonance (ESR) spectrometer. We report the concomitant photolysis of avobenzone and octinoxate that predominates over expected E/Z photoisomerization and that irradiation of a film of this product produced free radicals detected by ESR spectroscopy that persisted even after exposure had ended.     

On the origin of the redshift of the OH stretch in Ice Ih: evidence from the momentum distribution of the protons and the infrared spectral density

Recent measurements of the momentum distribution in water and ice have shown that the proton is in a considerably softer potential in ice Ih than in water or the free monomer. This is broadly consistent with the large red shift observed in the vibrational spectrum. We show that existing water models, which treat the intramolecular potential as unchanged by the hydrogen bonding are unable to reproduce the momentum distribution. In addition, even if they can substantially explain the red shift they are unable to explain the large increase in intensity observed in the infrared spectrum in going from the monomer to ice Ih. We show that the inclusion of a bond dipole derivative term is essential to explain the observed intensities in the infrared spectrum. Though this term is partially responsible for the softening of the effective potential of the proton we show that best agreement with the observed momentum distribution requires a further softening of the harmonic component of the intramolecular potential. We introduce an efficient normal-mode molecular dynamics algorithm for calculating the momentum distribution with path-integrals.     

Modeling the stability and the motion of DNA nucleobases on the gold surface

We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol(-1), and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considered.     

Effect of the geometric phase on the dynamics of the hydrogen-exchange reaction

A recent puzzle in nonadiabatic quantum dynamics is that geometric phase (GP) effects are present in the state-to-state opacity functions of the hydrogen-exchange reaction, but cancel out in the state-to-state integral cross sections (ICSs). Here the authors explain this result by using topology to separate the scattering amplitudes into contributions from Feynman paths that loop in opposite senses around the conical intersection. The clockwise-looping paths pass over one transition state (1-TS) and scatter into positive deflection angles; the counterclockwise-looping paths pass over two transition states (2-TS) and scatter into negative deflection angles. The interference between the 1-TS and 2-TS paths thus integrates to a very small value, which cancels the GP effects in the ICS. Quasiclassical trajectory (QCT) calculations reproduce the scattering of the 1-TS and 2-TS paths into positive and negative deflection angles and show that the 2-TS paths describe a direct insertion mechanism. The inserting atom follows a highly constrained "S-bend" path, which allows it to avoid both the other atoms and the conical intersection and forces the product diatom to scatter into high rotational states. By contrast, the quantum 2-TS paths scatter into a mainly statistical distribution of rotational states, so that the quantum 2-TS total ICS is roughly twice the QCT ICS at 2.3 eV total energy. This suggests that the S-bend constraint is relaxed by tunneling in the quantum system. These findings on H+H(2) suggest that similar cancellations or reductions in GP effects are likely in many other reactions.     

On the factors influencing the dispersion of radioiodines

Radioactivities dispersed from 0.1 N sodium hydroxide solutions of 123I, 125I, or 131I were measured, and the factors influencing dispersion of radioiodines were analyzed. The radioiodines dispersed were trapped by glass fiber filters, charcoal filters, and separable paint. The factors influencing the dispersion of radioiodines are discussed in terms of the dispersal rate, which defined as the ratio of total activity of three kinds of traps in a unit time to whole activity. In order to clarify the factors influencing the dispersal rate, we carried out the experiments; on the effect of reducing agent, that of radioactive concentration of radioiodine, that of mixing the 125I solution with 131I, and that of scavenging hydrated electrons and hydroxyl radicals. It could be concluded from experimental results that the principal factors influencing dispersion of radioiodines are the number of atoms of radioiodine per volume and the energy absorbed in solution from radioiodines. In regard to the absorbed energy, we thought that the dispersion of radioiodines is influenced mainly by hydrated electron, not markedly by hydroxyl radical.     

On the origin of the unusual behavior in the stretching of single-stranded DNA

Force-extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force (f), are often quantitatively fit using worm-like chain (WLC) or freely jointed chain (FJC) models. These models predict that the chain extension, x, normalized by the contour length increases linearly at small f and at high forces scale as x ~ (1 - f(-α)), where α = 0.5 for WLC and unity for FJC. In contrast, experiments on single-stranded DNA (ssDNA) show that over a range of f and ionic concentration, x scales as x ~ ln f, which cannot be explained using WLC or FJC models. Using theory and simulations we show that this unusual behavior in FEC in ssDNA is due to sequence-independent polyelectrolyte effects. We show that the x ~ ln f arises because in the absence of force the tangent correlation function, quantifying chain persistence, decays algebraically on length scales on the order of the Debye length. Our theory, which is most appropriate for monovalent salts, quantitatively fits the experimental data and further predicts that such a regime is not discernible in double-stranded DNA.     

Regarding the theory of the Zeno line

The line of thermodynamic states with a unit value of the compressibility factor was calculated for a Lennard-Jones system using four different approaches. We show that all four approaches give rise to a straight line on the density-temperature plane. Thus, we theoretically confirm that the Lennard-Jones system satisfies Zeno line regularity.     

Influence of the wettability on the boiling onset

Experimental investigation of pool boiling is conducted in stationary conditions over very smooth bronze surfaces covered by a very thin layer of gold presenting various surface treatments to isolate the role of wettability. We show that even with surfaces presenting mean roughness amplitudes below 10 nm the role of surface topography is of importance. The study shows also that wettability alone can trigger the boiling and that the boiling position on the surface can be controlled by chemical grafting using for instance alkanethiol. Moreover, boiling curves, that is, heat flux versus the surface superheat (which is the difference between the solid surface temperature and the liquid saturation temperature), are recorded and enabled to quantify, for this case, the significant reduction of the superheat at the onset of incipient boiling due to wettability.     

A priori resolution of the intermediate spectra in the bacteriorhodopsin photocycle: the time evolution of the L spectrum revealed

Resolution of the spectra of the intermediates in the photocycle of wild-type bacteriorhodopsin (BR) was achieved by singular value decomposition with exponential-fit-assisted self-modeling (SVD-EFASM) treatment of multichannel difference spectra measured at 5 degrees C during the course of the photocycle. New is the finding that two spectrally distinct L intermediates, L(1) and L(2), form sequentially. Our conclusion is that the photocycle is more complex than most published schemes. The dissection of the spectrally different L forms eliminates stoichiometric discrepancies usually appearing as systematically varying total intermediate concentrations before the onset of BR recovery. In addition, our analysis reveals that the red tails in the spectra of K and L(1) are more substantial than those of L(2) and BR. We suggest that these subtle differences in the shapes of the spectra reflect torsional and/or environmental differences in the retinyl chromophore.     

Reconstruction of the free energy in the metastable region using the path ensemble

By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent distributions from which we reconstruct the free energy as a function of the magnetic field, temperature, and system size. From the reconstructed free energy, we obtain the free-energy barrier that is associated with the transition from a metastable state to the stable equilibrium state. Although mean-field theory predicts a sharp transition between the metastable and the unstable region where the free-energy barrier is zero, the results for the nearest-neighbor Ising model show that the free-energy barrier does not go to zero.     

On the Nature of the Positronic Bond

Recently it has been proposed that the positron, the anti-particle analog of the electron, is capable of forming an anti-matter bond in a composite system consists of two hydride anions and a positron [Angew. Chem. Int. Ed. 57 , 8859–8864 (2018)]. In order to dig into the nature of this novel bond the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) is applied to this positronic system. The topological analysis reveals that this species is composed of two atoms in molecules, each containing a proton and half of the electronic and the positronic populations. Further analysis elucidates that the electron exchange phenomenon is virtually non-existent between the two atoms and no electronic covalent bond is conceivable in between. On the other hand, it is demonstrated that the positron density enclosed in each atom is capable of stabilizing interactions with the electron density of the neighboring atom. This electrostatic interaction suffices to make the whole system bonded against all dissociation channels. Thus, the positron indeed acts like an anti-matter glue between the two atoms.     

A study of the correlation effects upon the modelization of the double exchange phenomenon

A previous work by the authors has shown that the usual spin Hamiltonian used to model the magnetic spectra of mixed valence compounds was not sufficient to reproduce the magnetic spectrum of the molecule [Fe(2)(OH)(3)(NH(3))(6)](2+). In the present paper, the spin Hamiltonian is confronted to correlated ab initio calculations. The discrepancy between this Hamiltonian and the calculations is investigated and explained. It is pointed out that the multiconfigurational nature of the transition metal is responsible for this discrepancy. However, we show that this effect can easily be treated at the complete active space self-consistent field (CASSCF) level and that no further correlation treatment is needed. The spin Hamiltonian, which reproduces very well the minimal CASSCF results, could not be improved to recover the multireference effects.