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The sputtering of tungsten surfaces caused by hot plasma particles is an important process in fusion reactors where divertors are typically made of tungsten sheets. In this study, we present a molecular dynamics simulation strategy to investigate the sputtering yields of tungsten surfaces with geometrical defects. This should serve as a model for non-monocrystalline surfaces in general and could also be a rough model for nanoscale "fuzzy" layers, which are known to be formed by surface bombardment with energetic particles. Using a non-cumulative approach, we simulate the irradiation of tungsten surfaces with cone-shaped, cylindrical, and spherical defects by argon atoms. We analyze the sputtering yields as functions of particle energy and defect sizes. As a result, we find that surfaces with distinctly shaped defects always exhibit reduced sputtering yields, compared to smooth ones. We also investigate the angular distributions of sputtered particles and find them mostly to be in accordance with prior experimental and computational results. [ABSTRACT FROM AUTHOR]

Sputtering from plasma-facing surfaces upon particle impact is an important process in material science. It is especially relevant in the diverter region of fusion devices, which nearly always consist of tungsten. Besides the main plasma components, argon is used in fusion devices to improve energy confinement. As a consequence, hot Ar atoms interact with W surfaces and can cause sputtering and other material degrading events. Atomistic simulations of the plasma-wall interactions make it possible to carry out a detailed analysis of sputtering, reflection, and retention processes. We report the results of molecular dynamics simulations with neural network potential energy expressions modelling the bombardment of tungsten samples by argon atoms in the energy range from 100 to 800 eV. The obtained sputtering results are in good agreement with available literature data. Furthermore, our data provide additional insight into atomic details of the processes involved in sputtering. We also investigate the effect of surface temperature on sputtering and reflection probabilities, which significantly affects the irradiation process at higher impact energies. [ABSTRACT FROM AUTHOR]

A two-dimensional quantum-mechanical vibrational model has been used to calculate the anharmonic OH vibrational frequencies in the layered Mg(OH)2 (brucite) crystal. The underlying potential energy surface was generated by density functional theory (DFT) calculations. The resulting OH frequencies are upshifted (blueshifted) by about +75 cm-1 with respect to the gas-phase OH frequency (+120 cm-1 in experiments; the discrepancy is mainly due to inadequacies in the DFT and pseudopotential models). The Raman-IR split is about 50 cm-1, both in the calculations and in experiments. We find that the blueshift phenomenon in brucite can qualitatively be explained by a parabolalike “OH frequency versus electric field” correlation curve pertaining to an OH- ion exposed to an electric field. We also find that it is primarily the neighbors within the Mg(OH)2 layer that induce the blueshift while the interlayer interaction gives a smaller (and redshifting) contribution. [ABSTRACT FROM AUTHOR]

Our initial study on the performance of molecular polarization methods close to a positive point charge [M. Masia, M. Probst, and R. Rey, J. Chem. Phys. 121, 7362 (2004)] is extended to the case in which a molecule interacts with a real cation. Two different methods (point dipoles and shell model) are applied to both the ion and the molecule. The results are tested against high-level ab initio calculations for a molecule (water or carbon tetrachloride) close to Li+, Na+, Mg2+, and Ca2+. The monitored observable is in all cases the dimer electric dipole as a function of the ion-molecule distance for selected molecular orientations. The moderate disagreement previously obtained for point charges at intermediate distances, and attributed to the linearity of current polarization methods (as opposed to the nonlinear effects evident in ab initio calculations), is confirmed for real cations as well. More importantly, it is found that at short separations the phenomenological polarization methods studied here substantially overestimate the dipole moment induced if the ion is described quantum chemically as well, in contrast to the dipole moment induced by a point-charge ion, for which they show a better degree of accord with ab initio results. Such behavior can be understood in terms of a decrease of atomic polarizabilities due to the repulsion between electronic charge distributions at contact separations. It is shown that a reparametrization of the Thole method for damping of the electric field, used in conjunction with any polarization scheme, allows to satisfactorily reproduce the dimer dipole at short distances. In contrast with the original approach (developed for intramolecular interactions), the present reparametrization is ion and method dependent, and corresponding parameters are given for each case. [ABSTRACT FROM AUTHOR]

The three main methods to implement molecular polarization (point dipoles, fluctuating charges, and shell model) are tested against high level ab initio calculations for a molecule (water, carbon tetrachloride) close to a point charge (at the distance of a lithium or magnesium ion). The goal is to check whether an approximation (linear polarization) strictly valid at large intermolecular distances is sufficiently accurate for liquid state molecular dynamics simulations, where strong polarization effects are to be expected at short separations. The monitored observable is the molecular dipole moment as a function of the charge-molecule distance for selected molecular orientations. Analytic formulas are derived for the components of the molecular polarization tensor, facilitating the optimization of the performance for each polarization method as a function of its underlying parameters. Overall, the methods studied provide a remarkably good representation of the induced dipole, with no divergences appearing even at the shortest distances. For water close to a monovalent point charge the point dipole model, implemented with one or three dipoles, accurately reproduces the water dipole moment at all distances. Deficiencies appear as the molecular polarizability and/or charge increase: basically, the ab initio induced moments grow faster at intermediate distances than the linear increase characteristic of the phenomenological polarization methods, suggesting that nonlinear effects (hyperpolarizability) cannot be neglected in these cases. Regarding the capabilities of each method, the point dipole method is the one that performs best overall, with the shell model achieving acceptable results in most instances. The fluctuating charge method shows some noticeable limitations for implementations of comparable complexity (in terms of the number of sites required). © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Ab initio calculations of force constants up to fourth order and anharmonic frequencies for the uncoupled O–H stretching vibration in hydrates of the ions Li+, Na+, Mg2+, and Al3+ have been performed at the Hartree–Fock level for Mn+(H2O)m and Mn+(H2O)m···(H2O)2 complexes, with m=5–7. The dependence of force constants and frequency shifts on ion type, cation–water distances, second hydration shell, hydrogen bonding and coordination number is discussed. In the optimized Li+(H2O)6 system, the OH frequency is downshifted 20 cm-1 compared to the free water molecule, whereas, in the optimized Li+(H2O)6···(H2O)2 complex, the downshift is 120 cm-1. The corresponding numbers for the Al3+ hexaaqua complexes are -250 and -1215 cm-1. Frequency shifts with respect to bulk water for the cation–coordinated water molecules have been estimated from the difference between the frequencies of Mn+ (H2O)6···(H2O)2 and a (H2O)2···H2O···(H2O)2 complex. The values are +85 cm-1 for Li+ and Na+, -150 cm-1 for Mg2+, and -1000 cm-1 for Al3+, to be compared with the infrared frequency shifts of +50 for Li+ and Na+, -155 for Mg2+ and -500 cm-1 for Al3+ (experimental aqueous solution values from the literature). The activation energies for water exchange between the hydration shells in the hexaaqua complexes have been calculated for dissociative and associative exchange processes and suggest a dissociative mechanism to be dominant. [ABSTRACT FROM AUTHOR]

High-accuracy molecular force field models suited for hot gases and plasmas are not as abundant as those geared toward ambient pressure and temperature conditions. Here, we present an improved version of our previous electron-density based force field model that can now account for polarization effects by adjusting the atomic valence electron contributions to match ab initio calculated Mulliken partial charges. Using a slightly modified version of the Hohenberg–Kohn theorem, we also include an improved theoretical formulation of our model when applied to systems with degenerate ground states. We present two variants of our polarizable model, fitted from ab initio reference data calculated at CCSD(T)/cc-pVTZ and CCSD(T)/CEP-31G levels of theory, that both accurately model water dimer interaction energies. Further improvements include the additional interaction components with fictitious non-spherically symmetric, yet atom-centered, electron densities and fitting the exchange and correlation coefficients against analytical expressions. The latter removes all unphysical oscillations that are observed in the previous non-polarizable variant of our force field. [ABSTRACT FROM AUTHOR]

Highlights: [•] We model the interaction of fusion-relevant molecules with graphite. [•] Coronene serves as a cluster model for the graphite(0001) surface. [•] We calculate energy barriers upon permeation of a molecule through coronene. [•] Energy barriers for (closed-shell) molecules are much higher than for atoms. [•] Barrier heights can be diminished by temporary bonding. [Copyright &y& Elsevier]

Highlights: [•] Equilibrium geometries and associated electronic and energetic properties of PCBM n (n =1–5). [•] The maximally stable structures identified tend to include a PCBM dimer motif. [•] The significance of van-der-Waals effects for the prevailing bonding mechanism is demonstrated. [•] OPLS force fields turn out to be effective stability predictors for PCBM n . [•] The KS HOMO–LUMO gaps obtained may be useful to diagnose PCBM clustering in organic photocells. [Copyright &y& Elsevier]

We report the energy-dependent fragmentation patterns upon protonation of eight sulfides (organosulfur compounds) in Proton Transfer Reaction-Mass Spectrometry (PTR-MS). Studies were carried out, both, experimentally with PTR-MS, and with theoretical quantum-chemical methods. Charge retention usually occurred at the sulfur-containing fragment for short chain sulfides. An exception to this is found in the unsaturated monosulfide allylmethyl sulfide (AMS), which preferentially fragmented to a carbo-cation at m/z 41, C3H5+. Quantum chemical calculations (DFT with the M062X functional 6-31G(d,p) basis sets) for the fragmentation reaction pathways of AMS indicated that the most stable protonated AMS cation at m/z 89 is a protonated (cyclic) thiirane, and that the fragmentation reaction pathways of AMS in the drift tube are kinetically controlled. The protonated parent ion MH+ is the predominant product in PTR-MS, except for diethyl disulfide at high collisional energies. The saturated monosulfides R-S-R' (with R

Abstract: The solvation structure around the dicyanoaurate(I) anion (Au(CN)2 −) in a dilute nitromethane (CH3NO2) solution is presented from X-ray diffraction measurements and molecular dynamics simulation (NVT ensemble, 460 nitromethane molecules at room temperature). The simulations are based on a new solute–solvent force-field fitted to a training set of quantum-chemically derived interaction energies. Radial distribution functions from experiment and simulation are in good agreement. The solvation structure has been further elucidated from MD data. Several shells can be identified. We obtain a solvation number of 13–17 nitromethane molecules with a strong preference to be oriented with their methyl groups towards the solute. [Copyright &y& Elsevier]

Abstract: Volatile sulphur compounds (VSCs) are key compounds in many fields of basic and applied science and technology, such as environmental sciences, food science, geochemistry, petrochemistry, agriculture, biology and medicine. Proton transfer reaction mass spectrometry (PTR-MS) allows for on-line monitoring of volatile organic compounds (VOCs) and, in particular, of VSCs with ultra low detection limits and a fast response time. In principle, with PTR-MS, absolute quantification of VOC concentrations without calibration is possible, provided the branching ratios are known. However, for this, the reaction rate coefficients between VOCs and the hydronium ion have also to be known. Several well-established theories may be used to determine ion-neutral molecule reaction rate coefficients. In the case of H3O+–VOC reactions proceeding in a PTR-MS drift tube, a key factor to be considered is the centre-of-mass energy, which is generally much higher than the thermal energy, due to the additional translational (drift) energy of the ion. Nevertheless, it is common practice to employ collision theories that do not show an explicit dependence on the centre-of-mass energy. First we review basic aspects of ion-neutral reactions in the PTR-MS drift tube and various methods to calculate reaction rate coefficients. Next, we calculate, on the basis of quantum chemical methods and different theoretical approaches for ion-molecule collisions, reaction rate coefficients between selected sulphur compounds and H3O+. Finally, we discuss proper methods for the calculations of ion-neutral molecule reaction rate coefficients in the context of PTR-MS and the corresponding experimental parameters involved. [ABSTRACT FROM AUTHOR]

We report the results of molecular dynamics (MD) simulations using a new semi-empirical intermolecular interaction potential on the adsorption and diffusion of hexane in siliceous MCM-41 at 300 K. The potential function is tuned to give an adsorption energy of - 9.1 kcal/mol, reproducing the experimental value for a corresponding pore size. We investigated MCM-41 models with four different pore sizes and studied loadings from one molecule of hexane up to a loading corresponding to the density of liquid hexane. As a result of confinement in MCM-41, the free energy of adsorption of hexane increases when the pore sizes decrease; for example, the adsorption energy increases from - 9.1 to 13.7 kcal/mol for the largest to the smallest pore size for a loading of one molecule. Also, the adsorption energy increases by 3-4 kcal/mol for all pore sizes when the loading is increased from one hexane molecule to the density of liquid hexane. The calculated self-diffusion coefficients of hexane in MCM-41 with a pore diameter of 27 Å are in the order of 1 × 10-5 cm2/s, depending on the loading, which is in reasonable agreement with available experimental data. The self-diffusion coefficients decrease with increasing loadings and when the pore sizes decrease. The average distance between the centers of the mass of hexane molecules in the smallest pores is only marginally less than in the larger pores and in the liquid phase. For low loadings the hexane molecules lie parallel to the pore channel for every pore size. When the loading is increased, they build up concentric rings. These rings of hexane molecules are less well separated from each other in the larger models, and thus their structure more resembles the liquid phase. [ABSTRACT FROM AUTHOR]

Electron-molecule reactions and interactions are of increasing importance in science and technology. This already includes wide areas of environmental physics, technological plasmas, astrophysics, electron-driven chemistry, and fusion research. In this work we give a short overview of the topic and turn to two specific examples that show how synergies between experiments and calculations can lead to progress in the field. The first example concerns fragmentation of an ionized species. It has been found that hydrogen atoms are ejected from a specific position if an electron interacts with an adenine molecule. This process is prototypical for many electron-driven reactions and its understanding—which has not yet been fully achieved—is very important for a variety of processes in fundamental physics, biophysics, chemistry, and technology. The second example concerns mixtures of adenine and thymine and their ionization. Binding energies and structures of neutral and ionic nucleic acid dimers AA, AT, and TT (A = adenine, T = thymine), which are formed in such mixtures, have been calculated. The results predict which of the species will occur preferably in a comparable experimental situation and show for which cases the geometries of charged dimers differ from the neutral ones. [ABSTRACT FROM AUTHOR]

Abstract: The adsorption properties of pyridine on H-ZSM-5 zeolites have been investigated by cluster calculations with the ONIOM scheme and with an embedded-ONIOM scheme. The active site has been modeled with cluster sizes of up to 46 tetrahedra. Two different types of pyridine adsorption complexes on the zeolite models are found. If Zeolite is modeled by a small 3T quantum cluster, the adsorption energy of the hydrogen-bonded pyridine complex (Py-Hz), is found to be −18.5kcal/mol. When a larger cluster or the ONIOM models are employed, the optimized geometries show the formation of pyrdinium cation [PyH+] bound as an ion-pair complex [PyH+][Z−]. The calculated energy of formation for this ion-pair complex is −36.8kcal/mol in the ONIOM (B3LYP/6–31G(d,p):UFF) model. Both values are considerably lower than the experimentally estimated heat of adsorption of pyridine in ZSM-5 zeolite of −47.6kcal/mol. Inclusion of the electrostatic effects of the zeolite crystal lattice via the embedded ONIOM model increases the adsorption energy to −44.4kcal/mol. Performing the quantum-chemical treatment at the MP2/6–31G(d,p) level instead of the B3LYP/6–31G(d,p) leads to a slightly lower adsorption energy to −45.9kcal/mol. These data suggest that the embedded ONIOM scheme provides an accurate method of studying the interaction of small organic molecules with zeolites. [Copyright &y& Elsevier]

Abstract: High level ab initio calculations show that the self-induced dipole moment of a halide–water dimer deviates from the usually employed point dipole model, with a substantial nonlinear damping at separations corresponding to the first hydration shell. The total dipole moment is rather similar along the halide series, with the maximum value decreasing as anionic polarizability increases. A new implementation of the Thole damping method satisfactorily reproduces the dipole moment at all separations for the most probable configurations. [Copyright &y& Elsevier]

Density-functional theory (B3LYP/6-31G(d,p)) and the ONIOM (Our-own-N-layer Integrated molecular Orbital+molecular Mechanics) approach utilizing two-layer ONIOM schemes (B3LYP/6-31G(d,p):UFF) have been employed to investigate structures of Na-exchanged zeolite-encapsulated formaldehyde (HCHO@Na-zeolite) and their interactions with propylene. The carbonyl-ene reaction of propylene and formaldehyde was studied on three model systems: (1) formaldehyde in Na-exchanged zeolite: HCHO@Na-zeolite/CH3CH2; (2) naked Na(I) as catalyst: Na(I)/HCHO/CH3CH=CH2; (3) a bare model where only the reactants are present: HCHO/CH3CH=CH2. It is found that inclusion of the extended zeolite framework has an effect on the structure and energetics of the adsorption complexes and leads to a lower energy barrier (25.1 kcal/mol) of the reaction as compared to the bare model system (34.4 kcal/mol). If the naked Na(I) interacts with the HCHO/CH3CH=CH2 complex the energy barrier of the system is even lower than HCHO@Na-zeolite/CH3CH=CH2, due to the large electrostatic field generated by the naked Na(I) cation (17.5 kcal/mol). The carbonyl-ene reaction of propylene using HCHO@Na-faujasite takes place in a single concerted reaction step. [Copyright &y& Elsevier]

[Display omitted] • We used DFT calculations to study n-hexane cracking over zeolites. • Trends in activation barriers and transition state energies relate to zeolite acidities. • Simple SISSO descriptors predicts Ea and E TS , avoiding time-consuming calculations. Significant computational cost arises in calculating the pathways for heterogeneous catalyzed cracking reactions by quantum chemical means. This can prevent the screening of catalysts and thus the identification of potent ones. To reduce this computational cost, we investigate if recently developed nonlinear regression methods can be employed to predict transition state and activation energies of species arising along the reaction pathways. Cracking of n-hexane catalyzed by the zeolites ZSM-5, FAU, FER, and MOR isomorphously substituted with B, Al, Ga, and Fe serves as an example. We first derive the relevant quantities by density functional theory (DFT) calculations. The trend in activation barriers (Ea) and transition state energies (E TS) is found to be closely related to their acidities. Standard regression analysis already shows that transition state energies can be well reproduced by linear functions of the energies of the final states, while activation barriers can be moderately well predicted from deprotonation energy and dipole moment of the zeolite cluster. In order to enhance the prediction accuracy, especially for Ea, we use the sure-independence screening and sparsifying operator (SISSO) method. This machine-learning method can search a large pool of combinations of physical descriptors and select the best ones. We derive a simple mathematical expression that predicts E TS and Ea values with reasonable accuracy, thus making it possible to avoid the time-consuming calculation of the reaction pathway. Statistical tests indicate that the expressions suggested by SISSO are reasonably robust as well, at least within the limited data set. [ABSTRACT FROM AUTHOR]

Provides information on a study that assesses the significance of body size estimation in eating disorders. Relationship of body size estimation with clinical and psychological variables; Methodology of the study; Statistical analysis.

The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl2−. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of chlorine atom positions around the aromatic ring, and compared our results with those using ortho-, meta- and para-dichlorobenzene molecules. This was achieved by combining gas-phase experiments to determine the reaction threshold by means of mass spectrometry together with quantum chemical calculations. We also observed that Cl2− formation can only occur in 1,2-C6H4Cl2, where the two closest C–Cl bonds are cleaved while the chlorine atoms are brought together within the ring framework due to excess energy dissipation. These results show that a strong coupling between electronic and C–Cl bending motion is responsible for a positional isomeric effect, where molecular recognition is a determining factor in chlorine anion formation. [ABSTRACT FROM AUTHOR]

The spin‐dependent transmission properties of (0,8) graphene nanoribbons (GNRs) with two substitutional Fe atom impurities (2Fe‐aGNRs) have been studied by the non‐equilibrium Green's function (NEGF) method in conjunction with density functional theory (DFT). Emphasis is placed on the spin‐filtering activity of current transmission elements derived from these structures. In particular, it is shown that devices based on 2Fe‐aGNR approach the limit of half‐metallicity, where the magnitude and the sign of the current spin polarization is controlled by the bias across the device as well as the spin state of the 2Fe subsystem. This effect is rationalized by electronic structure and partial‐density‐of‐states (PDOS) analysis of the transmission element. An occupied spin minority state, induced by the Fe‐atom moiety and close to the Fermi energy of 2Fe‐aGNR, accounts for the predominance of minority spin polarization. Comparison with nanosystems obtained from 2Fe‐aGNR, involving vacancies rather than impurities, or both types of defects, reveals that substantial degrees of current spin polarization prevail across a wide variety of device types. [ABSTRACT FROM AUTHOR]

After a general discussion of neural networks potential energy functions and their standing within the various approaches of representing the potential energy function of a system, we describe a new interface between the open source atomistic library aenet of Artrith and Urban and the DL_POLY 4 code. As an application example, the training of a neural network for liquid water is described and the network is used in a molecular dynamics simulation. The resulting thermodynamic properties are compared with those from a reference simulation with the same SPC/E model that has been used in the training. [ABSTRACT FROM AUTHOR]

• Attachment of low energy electrons to 2-chlorotoluene is followed by dissociation. • The cross-section for the dissociation of Cl– decreases with temperature. • Such negative temperature dependence has only rarely been observed before. • Calculations show a low barrier where neutral and anionic dissociation curves cross. • Therefore non-Arrhenius effects take over and lead to the observed T-dependence. Dissociative electron attachment to 2-chlorotoluene has been studied experimentally. The formed Cl− fragment appears in the energy range from 0 to 2 eV. Increasing the temperature of the target molecule results in a decrease of the height of the threshold peak (∼0 eV) but in a considerable increase of the height of the second peak at 0.78 eV. Such behaviour was observed only rarely and does not occur in similar molecules. We have analysed the out-of-plane vibrations and calculated approximate potential energy curves for the neutral and anionic states. Possible explanations of the observed temperature dependence are discussed. [ABSTRACT FROM AUTHOR]

We report total electron-impact ionisation cross sections (EICSs) of cisplatin, its hydrolysis products and transplatin in the energy range from threshold to 10 keV using the binary-encounter-Bethe (BEB) and its relativistic variant (RBEB), and the Deutsch-Märk (DM) methods. We find reasonable agreement between all three methods, and we also note that the RBEB and the BEB methods yield very similar (almost identical) results in the considered energy range. For cisplatin, the resulting EICSs yield cross section maxima of 22.09 × 10−20 m2 at 55.4 eV for the DM method and 18.67 × 10−20 m2 at 79.2 eV for the (R)BEB method(s). The EICSs of monoaquated cisplatin yield maxima of 12.54 × 10−20 m2 at 82.8 eV for the DM method and of 9.74 × 10−20 m2 at 106 eV for the (R)BEB method(s), diaquated cisplatin yields maxima of 7.56 × 10−20 m2 at 118.5 eV for the DM method and of 5.77 × 10−20 m2 at 136 eV for the (R)BEB method(s). Molecular geometry does not affect the resulting EICS significantly, which is also reflected in very similar EICSs of the cis- and trans-isomer. Limitations of the work as well as desirable future directions in the research area are discussed. [ABSTRACT FROM AUTHOR]

Low-energy electrons effectively decompose the isomers 2-nitroimidazole and 4(5)-nitroimidazole by dissociative electron attachment (DEA) into a variety of fragment anions and radicals. The present study shows that a distinct selectivity for the two isomers occurs in the DEA reactions. Several new decay channels are observed for 2-nitroimidazole, including a dominant one leading to the loss of molecular H2O by attachment of a low-energy electron. In contrast, the loss of a single hydrogen atom is a much more efficient reaction in DEA to 4(5)-nitroimidazole. Quantum chemical calculations were carried out to explain the pronounced isomer effect found in the DEA experiment. Although the free energies of the reactions are similar for the different isomers, the very different natures of the dipole-bound states and valence-bound anions lead to preference for or hindrance of a particular dissociation channel. Nitroimidazolic compounds are considered as radiosensitizing compounds in tumor radiation therapy. The enhanced formation of fragments, including the highly reactive hydroxyl radical, in DEA to 2-nitroimidazole suggests that it may be a more efficient radiosensitizing agent than 4(5)-nitroimidazoles. [ABSTRACT FROM AUTHOR]

We report calculations of total (and absolute) electron-impact ionization cross sections (EICSs) for the fusion-relevant diatomic molecular species BeH, BeN, BeO, WH, WBe, WN, WO, O2, and N2 by means of the Deutsch-Märk and the binary-encounter-Bethe methods in the energy range from threshold to 10 keV. In addition, we discuss an empirical scheme to estimate partial cross sections from the total ones based on reaction energetics and empirical threshold laws and explore its accuracy by assessing available experimental data on total and partial EICSs. Finally, we also report parameters obtained by fitting the calculated cross sections to an expression commonly used in fusion edge plasma modeling. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to an article published in the December 1, 1994 issue pertaining to the molecular diagnosis of neoplasms.

We present a theoretical study of a range of surface defects for the most abundant polar ZnO(0001)/(0001) surfaces using a tight binding approach with self-consistent charges (SCC-DFTB). We find that a combination of triangular pits at the Zn-terminated surface and a strongly ordered hexagonal defect pattern at the O-terminated surface constitutes a very stable reconstruction, in excellent agreement with experimental findings. On the whole, the SCC-DFTB method describes the polar surfaces of ZnO very well, and at a low computational cost which allows for the investigation of larger - and more realistic - surface structures compared to previous studies. Such large-scale calculations show that, at the Zn-terminated surface, the reconstruction results in a high density of one-layer deep triangular pit-like defects and surface vacancies which allow for a high configurational freedom and a vast variety of defect motifs. We also present extensive tests of the performance of the SCC-DFTB method in comparison with DFT results. [ABSTRACT FROM AUTHOR]

Energetic and geometric aspects of the permeation of the atoms hydrogen to neon neutral atoms through graphene sheets are investigated by investigating the associated energy barriers and sheet deformations. Density functional theory calculations on cluster models, where graphene is modeled by planar polycyclic aromatic hydrocarbons (PAHs), provide the energies and geometries. Particularities of our systems, such as convergence of both energy barriers and deformation curves with increasing size of the PAHs, are discussed. Three different interaction regimes, adiabatic, planar and vertical, are investigated by enforcing different geometrical constraints. The adiabatic energy barriers range from 5 eV for hydrogen to 20 eV for neon. We find that the permeation of oxygen and carbon into graphene is facilitated by temporary chemical bonding while for other, in principle reactive atoms, it is not. We discuss implications of our results for modeling chemical sputtering of graphite. [ABSTRACT FROM AUTHOR]

Weexplore solvent dynamics effects in interfacial bond breakingelectron transfer in terms of a multimode approach and make an attemptto interpret challenging recent experimental results (the nonmonotonousbehavior of the rate constant of electroreduction of S2O82–from mixed water–EG solutionswhen increasing the EG fraction; see Zagrebin, P.A. et al. J. Phys. Chem. B2010, 114, 311). The exact expansion of the solvent correlation function (calculatedusing experimental dielectric spectra) in a series predicts the splittingof solvent coordinate in three independent modes characterized bydifferent relaxation times. This makes it possible to construct a5D free-energy surface along three solvent coordinates and one intramoleculardegree of freedom describing first electron transfer at the reductionof a peroxodisulphate anion. Classical molecular dynamics simulationswere performed to study the solvation of a peroxodisulphate anion(S2O82–) in oxidized and reducedstates in pure water and ethylene glycol (EG) as well as mixed H2O–EG solutions. The solvent reorganization energy ofthe first electron-transfer step at the reduction of S2O82–was calculated for several compositionsof the mixed solution. This quantity was found to be significantlyasymmetric. (The reorganization energies of reduction and oxidationdiffer from each other.) The averaged reorganization energy slightlyincreases with increasing the EG content in solution. This findingclearly indicates that for the reaction under study the static solventeffect no longer competes with solvent dynamics. Brownian dynamicssimulations were performed to calculate the electron-transfer rateconstants as a function of the solvent composition. The results ofthe simulations explain the experimental data, at least qualitatively. [ABSTRACT FROM AUTHOR]

We report on a previously unknownreaction mechanism involvingwater in the fragmentation reaction following chemical ionization.This result stems from a study presented here on the humidity-dependentand energy-dependent endoergic fragmentation of allyl methyl sulfide(AMS) upon protonation in a proton transfer reaction-mass spectrometer(PTR-MS). The fragmentation pathways were studied with experimental(PTR-MS) and quantum chemical methods (polarizable continuum model(PCM), microhydration, studied at the MP2/6-311+G(3df,2p)//MP2/6-31G(d,p)level of theory). We report in detail on the energy profiles, reactionmechanisms, and proton affinities (G4MP2 calculations). In the discoveredreaction mechanism, water reduces the fragmentation of protonatedspecies in chemical ionization. It does so by direct interaction withthe protonated species via covalent binding (C3H5+) or via association (AMS·H+). This stabilizesintermediate complexes and thus overall increases the activation energyfor fragmentation. Water thereby acts as a reusable inhibitor (anticatalyst)in chemical ionization. Moreover, according to the quantum chemical(QC) results, when water is present in abundance it has the oppositeeffect and enhances fragmentation. The underlying reason is a concentration-dependentchange in the reaction principle from active inhibition of fragmentationto solvation, which then enhances fragmentation. This amphoteric behaviorof water is found for the fragmentation of C3H5+to C3H3+, and similarlyfor the fragmentation of AMS·H+to C3H5+. The results support humidity-dependent quantificationefforts for PTR-MS and chemical ionization mass spectrometry (CIMS).Moreover, the results should allow for a better understanding of ion-chemistryin the presence of water. [ABSTRACT FROM AUTHOR]

We report simulations of the elastic scattering of atomic hydrogen isotopes and helium beams from graphite (0001) surfaces in an energy range of 1-4 eV. To this aim, we numerically solve a time-dependent Schrödinger equation using a split-step Fourier method. The hydrogen- and helium-graphite potentials are derived from density functional theory calculations using a cluster model for the graphite surface. We observe that the elastic interaction of tritium and helium with graphite differs fundamentally. Whereas the wave packets in the helium beam are directed to the centers of the aromatic cycles constituting the hexagonal graphite lattice, they are directed toward the rings in case of the hydrogen beams. These observations emphasize the importance of swift chemical sputtering for the chemical erosion of graphite and provide a fundamental justification of the graphite peeling mechanism observed in molecular dynamics studies. Our investigations imply that wave packet studies, complementary to classical atomistic molecular dynamics simulations open another angle to the microscopic view on the physics underlying the sputtering of graphite exposed to hot plasma. [ABSTRACT FROM AUTHOR]

Proton transfer reaction - mass spectrometry (PTR-MS) has become a reference technique in environmental science allowing for VOC monitoring with low detection limits. The recent introduction of time-of-flight mass analyzer (PTR-ToF-MS) opens new horizons in terms of mass resolution, acquisition time, and mass range. A standard procedure to perform quantitative VOC measurements with PTR-ToF-MS is to calibrate the instrument using a standard gas. However, given the number of compounds that can be simultaneously monitored by PTR-ToF-MS, such a procedure could become impractical, especially when standards are not readily available. In the present work we show that, under particular conditions, VOC concentration determinations based only on theoretical predictions yield good accuracy. We investigate a range of humidity and operating conditions and show that theoretical VOC concentration estimations are accurate when the effect of water cluster ions is negligible. We also show that PTR-ToF-MS can successfully be used to estimate reaction rate coefficients between H3O+ and VOC at PTR-MS working conditions and find good agreement with the corresponding nonthermal theoretical predictions. We provide a tabulation of theoretical rate coefficients for a number of relevant volatile organic compounds at various energetic conditions and test the approach in a laboratory study investigating the oxidation of alpha-pinene. [ABSTRACT FROM AUTHOR]

Abstract: Molecular dynamics simulations were performed for ethane, propane, and n-butane in siliceous faujasite for different numbers of molecules per unit cell (loadings) at 300K. Both the adsorbed molecules and the zeolite framework were modeled as flexible entities. A new semiempirical analytical potential function for the systems was constructed. From the mean-square displacement of the molecules, self-diffusion coefficients of 18.7×10−5, 13.3×10−5, and 4.3×10−5 cm2/s were calculated for ethane, propane, and n-butane, respectively at a loading of 8 molecules/unit cell. They compare well with experimental values from pulsed-field gradient NMR measurements (10×10−5, 9×10−5, and 6×10−5 cm2/s, respectively). Besides depending on the size of the hydrocarbon, the heats of adsorption and self-diffusion coefficients also strongly depend on the loading of adsorbate molecules. The results suggest that the new intermolecular force field can reasonably describe the adsorption and diffusion behavior of ethane, propane, and n-butane in faujasite zeolite. [Copyright &y& Elsevier]

Abstract: Molecular dynamics (MD) simulations of benzene in siliceous zeolites (FAU, ZSM-5, and MCM-22) were performed at loadings of 1, 2, 4, 8, and 16 molecules per supercell. The potential energy functions for these simulations were constructed in a semi-empirical way from existing potentials and experimental energetic data. The MD simulations were employed to analyze the dynamic properties of the benzene–zeolite systems. The adsorption energies of benzene/siliceous zeolite complexes increase with increasing loading number, due to the intermolecular attraction between benzene molecules. The self-diffusion coefficient of benzene in siliceous zeolites decreases with increasing loading due to the steric hindrance between the sorbates passing each other. From the zeolite–benzene radial distribution functions it was found that the benzene molecules are relatively far from each other, about 5.2Å for siliceous FAU, 5.2Å for siliceous ZSM-5, and 4.8Å for siliceous MCM-22. In the case of FAU, the benzene molecules prefer to be adsorbed parallel to the surface of the sodalite cage above the six-membered-ring. In ZSM-5, we found a T-structure of the benzene molecules at loadings 2, 4, and 8 molecules per supercell. At loadings of 16 molecules per supercell, the molecules are lined up along the straight channel and their movement is highly correlated. For MCM-22 we found adjacent benzene molecules at a loading of 4 molecules with an orientation similar to the stacked conformation of benzene dimer in the gas phase. [Copyright &y& Elsevier]

Calculations on cluster models of infinite systems require less computational effort and are technically simpler than periodic calculations, but they neglect, among other contributions, the effect of long-range electrostatic interaction from the infinite crystal lattice. In the case of zeolites, such contributions can be important for adsorption processes and surface reactions. We test a simple method for including this effect into the calculation by generating a finite number of point charges placed on the lattice sites. These point charges reproduce the infinite electrostatic potential at the chemically important region of the zeolite. We apply this method to the adsorption of pyridine on H-Faujasite zeolite. The embedding method gives an adsorption energy of -42.8 kcal/mol, which agrees well with the experimental value of -43.1 ± 1 kcal/mol. Without the electrostatic effect of the crystal field, the value is ∼9 kcal/mol higher. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [ABSTRACT FROM AUTHOR]

Abstract: The interaction of PO4 3− with water has been investigated by ab initio calculations. Geometry optimizations of the orthophosphate anion complex with one or two water molecules (PO4 3−/H2O) show that the most stable conformations have C2v symmetry and symmetrical hydrogen bonds as part of one or two six-membered rings. Intermolecular potential functions and an intramolecular force field were derived from ab initio calculated energies. They were used in molecular dynamics simulations of aqueous solutions of K3PO4, K2HPO4 and KH2PO4. The simulations were performed in the NVT ensemble with systems consisting of one anion and about 500 water molecules. The main results of the simulations are a pronounced first hydration shell consisting of about 16 water molecules for orthophosphate and about 20 water molecules for mono- and dihydrogenphosphate and a partially ordered second hydration shell. The results are in good agreement with recent experimental data. [Copyright &y& Elsevier]

Abstract: Adsorption of the halide ions X (X=Cl−, Br−, I−) at a cadmium monocrystalline face (0001) from aqueous solutions has been studied by the impedance spectroscopy. Analysis of the impedance data does not predict specific adsorption for Cl− and shows that the Gibbs adsorption energy increases from Br− to I− in accordance with the decrease of the hydration energy of anions. The adsorption of halide ions and their atomic forms on a Cd(0001) electrode at the potential of zero charge (pzc) has been studied with the use of the cluster model. The quantum chemical calculations were performed at the DFT and the SCF levels involving the hydrated species X−(H2O)3 and X−(H2O)6 besides the bare anions. The effective distance-dependent solvation energy of halide ions constructed on the basis of molecular dynamics simulations was used to build the adsorption terms. For all three halides contact adsorption was found to be the most favourable state. The partial charge transfer (PCT) from the adsorbed species to the metal was analysed in terms of the Anderson–Newns model. A combined consideration of the solvation and PCT effects enables prediction of the experimentally observed metal–ion interaction order (Cl− <Br− <I−). [Copyright &y& Elsevier]

Short-term pollution events via runoff are typical of streams in agricultural areas. Existing runoff models that simulate pesticide loss from agricultural fields require extensive input of information. There is thus a need for a simple model that can predict runoff-related pesticide concentrations in many streams on a landscape level when only limited data are available.To validate such a model, the runoff-related pesticide load of 18 small lowland streams was predicted with an extended version of the model “simplified formula for indirect loadings caused by runoff” (available from the Organisation for Economic Cooperation and Development, OECD). The authors suggest that the model presented here is suitable for use in routine exposure assessment of pesticides on a landscape level, as all input data (soil, slope, precipitation, pesticide application) are readily available from public authorities or could be generated by simple regional flood hydrograph curves.The predicted concentrations were compared with measured concentrations obtained by runoff-triggered sampling. Fungicides, insecticides and herbicides were detected in 17 streams, with max. concentrations measuring up to 29.7 μg/l for the fungicide azoxystrobin and 0.3 μg/l for the insecticide parathion-ethyl. Herbicides were detected in 16 streams, with max. concentrations between 13.7 and 1.2 μg/l. The linear regression between the predicted and measured concentrations (log-values) shows significant correlations for the following pesticides: azoxystrobin: r2=0.43; p=0.03; epoxiconazole: r2=0.71; p⩽0.01; tebuconazole: r2=0.77; p⩽0.01. The present model successfully explains the pesticide concentrations associated with single entry events caused by runoff, especially at concentration levels above (⩾0.5 μg/l). [Copyright &y& Elsevier]

Dehydration reactions are important in the petroleum and petrochemical industries, especially for the feedstock production. In this work, the catalytic activity of zeolites with different acidities for the dehydration of ethanol to ethylene and diethylether is investigated by density functional calculations on cluster models of three isomorphous B, Al, and Ga substituted H-ZSM-5 zeolites. Both unimolecular and bimolecular mechanisms are investigated. Detailed reaction profiles for the dehydration reaction, assuming either a stepwise or a concerted mechanism, were calculated by using the ONIOM(MP2:M06-2X) + SCREEP method. The adsorption energies of ethanol are −21.6, −28.1, and −27.7 kcal mol−1 on H-[B]-ZSM-5, H-[Al]-ZSM-5, and H-[Ga]-ZSM-5 zeolites, respectively. The activation energies for the rate-determining step of the unimolecular concerted mechanism for the ethylene formation are 48.5, 42.6, and 43.6 kcal mol−1 on H-[B]-ZSM-5, H-[Al]-ZSM-5, and H-[Ga]-ZSM-5 zeolites, respectively. The activation energies for the ethoxy formation as the rate-determining step for the bimolecular formation of diethylether are 42.3, 40.0, and 41.1 kcal mol−1 on H-[B]-ZSM-5, H-[Al]-ZSM-5, and H-[Ga]-ZSM-5 zeolites, respectively. The results indicate that the catalytic activities for the dehydration of ethanol decrease in the order H-[Al]-ZSM-5 ~ H-[Ga]-ZSM-5 > H-[B]-ZSM-5. Besides the acid strength, the zeolite framework affects the reaction by stabilizing the reaction intermediates, leading to more stable adsorption complexes and lower activation barriers. [ABSTRACT FROM AUTHOR]

Dissociative electron attachment (DEA) to acetic acid in the energy range between about 0 and 13 eV generates as much as nine different fragment ions. The dominant products are CH3COO− and CH2O2− which appear from two closely spaced low energy resonances peaking at 0.75 and 1.5 eV. In view of our ab initio calculation we assign these states as single particle shape resonances associated with the first and second virtual MO, respectively. The electronic and geometrical structure of CH2O2− remains under question, the thermodynamics of the associated DEA reaction, however, predict an exceptionally high stability of this anion. [Copyright &y& Elsevier]

Sputtering from plasma-facing surfaces upon particle impact can limit the lifetime of components in fusion devices, especially in the diverter region. Atomistic simulations of the processes associated with plasma–wall interactions allow for a detailed analysis of sputtering, reflection and adsorption. Most former works of beryllium sputtering by hydrogen isotopes were aimed mostly on the sputtering yield. We investigate the influence of impact energy and angle on sputtering, and analyze these quantities also for the outgoing particle. We model the sputtering by non-cumulative molecular dynamics simulations with a large number of trajectories for the various parameters. The underlying forces and energies are obtained from high-dimensional neural networks fitted to density functional calculations. We find a good agreement with the previously reported sputtering yields for perpendicular impact and a qualitative accordance with experimental data. In detail, the sputtering yield increases with increasing impact energy for angles of incidence larger than 45° with respect to the surface normal, while smaller angles show a maximal yield up to 100 eV. In cases where D reflection rather than sputtering occurs, a similar pattern is found for all angles, with the maximal reflection rate at 80°. [ABSTRACT FROM AUTHOR]

Tirapazamine (TP) has been shown to enhance the cytotoxic effects of ionizing radiation in hypoxic cells, thus making it a candidate for a radiosensitizer. This selective behavior is often directly linked to the abundance of O2. In this paper, we study the electronic properties of TP in vacuum, micro-hydrated from one up to three molecules of water and embedded in a continuum of water. We discuss electron affinities, charge distribution, and bond dissociation energies of TP, and find that these properties do not change significantly upon hydration. In agreement with its large electron affinity, and bond breaking triggered by electron attachment requires energies higher than 2.5 eV, ruling out the direct formation of bioactive TP radicals. Our results suggest, therefore, that the selective behavior of TP cannot be explained by a one-electron reduction from a neighboring O2 molecule. Alternatively, we propose that TP's hypoxic selectivity could be a consequence of O2 scavenging hydrogen radicals. [ABSTRACT FROM AUTHOR]

Purpose: Right ventricular (RV) dysfunction in acute pulmonary embolism (PE) is a critical determinant of outcome. Obstructive sleep apnea (OSA) is a common comorbidity of PE and might also affect RV function. Therefore, we sought to investigate RV dysfunction in PE patients in proportion to the severity of OSA by evaluating the right-to-left ventricular (RV/LV) diameter ratio on computed tomographic pulmonary angiography (CTPA). Materials and Methods: 197 PE patients were evaluated for sleep-disordered breathing by portable monitoring and nocturnal polysomnography. RV dilatation was defined as an RV/LV diameter ratio of ⩾ 1.0. Results: RV dilatation was significantly more frequent in OSA patients compared to study participants without OSA (66.4% vs 49.1%, P =.036). Elevated troponin I values, indicating myocardial injury due to acute, PE-related RV strain, were significantly more frequent in OSA patients with an apnea-hypopnea index (AHI) ⩾ 15/h compared to those with an AHI < 15/h (62.1% vs 45.8%, P =.035). However, RV dysfunction documented by the RV/LV diameter ratio on CTPA was not significantly associated with the severity of OSA in multivariable regression analysis. Conclusion: Patients with moderate or severe OSA might compensate acute, PE-related RV strain better, as they are adapted to repetitive right heart pressure overloads during sleep. [ABSTRACT FROM AUTHOR]

Purpose: Right ventricular (RV) dysfunction in acute pulmonary embolism (PE) is a critical determinant of outcome. Obstructive sleep apnea (OSA) is a common comorbidity of PE and might also affect RV function. Therefore, we sought to investigate RV dysfunction in PE patients in proportion to the severity of OSA by evaluating the right-to-left ventricular (RV/LV) diameter ratio on computed tomographic pulmonary angiography (CTPA). Materials and Methods: 197 PE patients were evaluated for sleep-disordered breathing by portable monitoring and nocturnal polysomnography. RV dilatation was defined as an RV/LV diameter ratio of ⩾ 1.0. Results: RV dilatation was significantly more frequent in OSA patients compared to study participants without OSA (66.4% vs 49.1%, P =.036). Elevated troponin I values, indicating myocardial injury due to acute, PE-related RV strain, were significantly more frequent in OSA patients with an apnea-hypopnea index (AHI) ⩾ 15/h compared to those with an AHI < 15/h (62.1% vs 45.8%, P =.035). However, RV dysfunction documented by the RV/LV diameter ratio on CTPA was not significantly associated with the severity of OSA in multivariable regression analysis. Conclusion: Patients with moderate or severe OSA might compensate acute, PE-related RV strain better, as they are adapted to repetitive right heart pressure overloads during sleep. [ABSTRACT FROM AUTHOR]

Dissociative electron attachment to dialanine and alanine anhydride has been studied in the gas phase utilizing a double focusing two sector field mass spectrometer. We show that low-energy electrons (i.e., electrons with kinetic energies from near zero up to 13 eV) attach to these molecules and subsequently dissociate to form a number of anionic fragments. Anion efficiency curves are recorded for the most abundant anions by measuring the ion yield as a function of the incident electron energy. The present experiments show that as for single amino acids (M), e.g., glycine, alanine, valine, and proline, the dehydrogenated closed shell anion (M-H)- is the most dominant reaction product. The interpretation of the experiments is aided by quantum chemical calculations based on density functional theory, by which the electrostatic potential and molecular orbitals are calculated and the initial electron attachment process prior to dissociation is investigated. [ABSTRACT FROM AUTHOR]