Atom In Question Research Articles

Interlayer Biatomic Pair Bridging the van der Waals Gap for 100% Activation of 2D Layered Material.

2D layered materials are regarded as prospective catalyst candidates due to their advantageous atomic exposure ratio. Nevertheless, the predominant population of atoms residing on the basal plane with saturated coordination, exhibit inert behavior, while a mere fraction of atoms located at the periphery display reactivity. Here, a novel approach is reported to attain complete atom activation in 2D layered materials through the construction of an interlayer biatomic pair bridge. The atoms in question have been strategically optimized to achieve a highly favorable state for the adsorption of intermediates. This optimization results from the introduction of new gap states around the Fermi level. Moreover, the presence of the interlayer bridge facilitates the electron transfer across the van der Waals gap, thereby enhancing the reaction kinetics. The hydrogen evolution reaction exhibits an impressive ultrahigh current density of 2000mA cm-2 at 397mV, surpassing the pristine MoS2 by approximately two orders of magnitude (26mA cm-2 at 397mV). This study provides new insights for enhancing the efficacy of 2D layered catalysts.

Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA.

The early DNA damage induced by ionizing radiation depends on how ionizing particles transfer energy to this molecule and the surrounding medium, mostly water. In preliminary studies, we found that the energy transferred by a 4 keV proton to a cytosine-guanine base pair in a classical simulation collision using the ReaxFF potential is much smaller than that obtained by a quantum calculation using time-dependent density functional theory (TDDFT). We observed that there are two main reasons for that: no accurate force-field for this situation and problems while dealing with the proton charge during the collision. Here, we only focus on the interaction potential. We calibrated the van der Waals energy term of the ReaxFF potential using TDDFT calculations and a genetic algorithm, specifically for the interaction of a proton with the DNA constituent atoms (carbon, hydrogen, phosphorus, nitrogen, and oxygen). We obtained a significant improvement in the interaction potential and, consequently, in the scattering angle of the proton colliding with the target atoms in question. However, we conclude that despite the improvement for the force-field and scattering angle, the classical charge equilibration method should also be improved to properly describe the proton-DNA collision process.

Atoms do exist in molecules: analysis using electrostatic potentials at nuclei

We have shown in the past that the electrostatic potential at the nucleus of a given atom A is relatively insensitive to that atom’s molecular environment. However, the separate nuclear and electronic contributions to it can be quite different. For a free atom, the electrostatic potential at the nucleus is due entirely to its electrons. If this were to be subtracted from the total electronic potential at the nucleus of a molecule or polyatomic ion, this would yield the potential due to the electrons in the remainder of the molecule or ion, not including those of the atom in question itself. In this paper, we show results for ten atoms in a variety of molecules and polyatomic ions. We find that the potentials created by other electrons are almost identical in magnitude with the potentials due to the other nuclei. This is a significant finding because it demonstrates that an atom in a molecule or polyatomic ion is only very slightly affected by the nuclei and electrons of the other atoms. It supports the concept that individual atoms retain their characteristic identities in molecules and ions. The electrostatic potentials created by other electrons are almost identical with the potentials due to the other nuclei. This is a most significant finding because it demonstrates that an atom in a molecule or polyatomic ion is only very slightly affected by the nuclei and electrons of the other atoms. Their effects can truly be considered as no more than a minor perturbation.

Causation, electronic configurations and the periodic table

The article examines a recent interventionist account of causation by Ross, in which electronic configurations of atoms are considered to be the cause of chemical behavior. More specifically I respond to the claim that a change in electronic configuration of an atom, such as occurs in the artificial synthesis of elements, causes a change in the behavior of the atom in question. I argue that chemical behavior is governed as much by the nuclear charge of an atom as it is by its electronic structure. It is suggested that an adequate analysis requires attention to the dynamical interactions between nuclear charges and those of electrons, as typically carried out through the application of the Schrodinger equation. It is concluded that electronic configurations can only be said be causal in a weak sense that is somewhat analogous to the causal arguments that are invoked in folk physics.

Analysis of double-slit interference experiment at the atomic level

I argue that the marquis characteristics of the quantum-mechanical double-slit experiment (point detection, random distribution, Born rule) can be explained using Schroedinger's equation alone, if one takes into account that, for any atom in a detector, there is a small but nonzero gap between its excitation energy and the excitation energies of all other relevant atoms in the detector (isolated-levels assumption). To illustrate the point I introduce a toy model of a detector. The form of the model follows common practice in quantum optics and cavity QED. Each detector atom can be resonantly excited by the incoming particle, and then emit a detection signature (e.g., bright flash of light) or dissipate its energy thermally. Different atoms have slightly different resonant energies per the isolated-levels assumption, and the projectile preferentially excites the atom with the closest energy match. The toy model permits one easily to estimate the probability that any atom is resonantly excited, and also that a detection signature is produced before being overtaken by thermal dissipation. The end-to-end detection probability is the product of these two probabilities, and is proportional to the absolute-square of the incoming wavefunction at the atom in question, i.e. the Born rule. I consider how closely a published neutron interference experiment conforms to the picture developed here; I show how this paper's analysis steers clear of creating a scenario with local hidden variables; I show how the analysis steers clear of the irreversibility implicit in the projection postulate; and I discuss possible experimental tests of this paper's ideas. Hopefully, this is a significant step toward realizing the program of solving the measurement problem within unitary quantum mechanics envisioned by Landsman, among others.

A Simple Correction for Nonadditive Dispersion within Extended Symmetry-Adapted Perturbation Theory (XSAPT).

Extended symmetry-adapted perturbation theory (XSAPT), in conjunction with empirical "+ aiD" potentials fit to ab initio dispersion data, is a low-scaling approach to compute intermolecular interaction energies in noncovalent clusters. One shortcoming is that the aiD atom-atom dispersion potentials are independent of the chemical environment of the atoms in question and therefore neglect nonadditive dispersion effects. These can be significant in large systems, so to account for them we test a simple correction to XSAPT(KS)+ aiD, where "KS" indicates the use of Kohn-Sham orbitals. This correction, which can be evaluated at fourth-order cost using double-ζ basis sets, is based on comparing second-order SAPT dispersion with and without a self-consistent charge embedding for the monomer wave functions. The correction amounts to ∼1.4 kcal/mol in (H2O)6 but ∼5.5 kcal/mol in (H2O)20. With the nonadditive dispersion correction, XSAPT(KS)+ aiD affords errors of ∼1 kcal/mol for isomers of F-(H2O)10 and (H2O)20, where the benchmarks are complete-basis CCSD(T) energies, as well as for ion-water clusters X(H2O) n where n ≤ 6 and X = F-, Cl-, SO42-, Li+, Na+, or K+. We also test the MP2 method and a variety of density-functional methods that have been specifically recommended for noncovalent interactions. Among the latter, only ωB97X-V and ωB97M-V can be recommended for ion-water clusters, as mean errors for other popular approaches (including ωB97X-D3 and several Minnesota functionals) exceed 1 kcal/mol. Lastly, we examine clathrate-hydrate host/guest complexes whose mixture of hydrogen bonding and dispersion make them challenging tests for noncovalent quantum chemistry. Although the B97-D2 functional performs best for clathrate hydrates and has been previously recommended in other studies of these inclusion complexes, its performance for other systems examined here is quite poor. We are unable to find a functional whose accuracy is ≲1 kcal/mol accuracy for both clathrate hydrates and ion-water clusters. However, the XSAPT(KS)+ aiD method with the nonadditive dispersion correction can achieve this, with a mean error for the clathrate hydrates of 0.3 kcal/mol.

Combination of large and small basis sets in electronic structure calculations on large systems.

Two basis sets-a large and a small one-are associated with each nucleus of the system. Each atom has its own separate one-electron basis comprising the large basis set of the atom in question and the small basis sets for the partner atoms in the complex. The perturbed atoms in molecules and solids model is at core of the approach since it allows for the definition of perturbed atoms in a system. It is argued that this basis set approach should be particularly useful for periodic systems. Test calculations are performed on one-dimensional arrays of H and Li atoms. The ground-state energy per atom in the linear H array is determined versus bond length.

Buckling analysis of graphene nanosheets by the finite element method

The paper is devoted to the problems related to buckling analysis of graphene sheets without and with vacancies in the structure under different boundary conditions. The analysis was performed by the classical numerical treatment – the finite element method (FEM). The graphene sheets were modelled by beam elements. Interatomic relations between carbon atoms in the structure were represented by the beams connecting individual atoms. The behaviour of the beam as structural element was based on the properties that were established from relations of molecular mechanics. The vacancies in single layer graphene sheets (SLGSs) were created by elimination of randomly chosen atoms and corresponding beam elements connected to the atoms in question. The computations were accomplished for different percentage of atom vacancies and the results represent an obvious fact that the critical buckling force decreases for increased percentage of vacancies in the structure. The numerical results are represented in form of graphs.

Polder maps: improving OMIT maps by excluding bulk solvent.

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available in PHENIX.

Metastable Aluminum Atoms Floating on the Surface of Helium Nanodroplets.

Metal atoms have proved to be sensitive probes of the properties of superfluid helium nanodroplets. To date, all experiments on the doping of helium droplets have concentrated on the attachment of metal atoms in their ground electronic states. Here we report the first examples of metal atoms in excited states becoming attached to helium nanodroplets. The atoms in question are aluminum, and they have been generated by laser ablation in a metastable quartet state, which attaches to and remains on the surface of helium droplets. Evidence for a surface location comes from electronic spectra, which consist of very narrow absorption profiles that show very small spectral shifts. Supporting abinitio calculations show there to be an energy incentive for a metastable Al atom to remain on the surface of a helium droplet rather than move to the interior. The results suggest that helium droplets may provide a method for the capture and transport of metastable excited atomic and molecular species.

Effects of Collisional and Vibrational Velocity on Proton and Deuteron Transfer in the Reaction of HOD+ with CO

Reaction of HOD(+) with CO was studied over the collision energy (E(col)) range between 0.18 and 2.87 eV, for HOD(+) in its ground state and with one quantum in each of its vibrational modes: (001)--predominantly OH stretch; (010)--bend, and (100)--predominately OD stretch. In addition to integral cross sections, product recoil velocity distributions were also measured for each initial condition. The dominant reactions are near-thermoneutral proton and deuteron transfer, generating HCO(+) and DCO(+) product ions by a predominantly direct mechanism. The HCO(+) and DCO(+) channels occur with a combined efficiency of 76% for ground state HOD(+) at our lowest E(col), increasing to 94% for E(col) around 0.33 eV, then falling at high E(col) to ~40%. The HCO(+) and DCO(+) channels have a complicated dependence on the HOD(+) vibrational state. Excitation of the OH or OD stretch modes enhances H(+) or D(+) transfer, respectively, and inhibits D(+) or H(+) transfer. Bend excitation preferentially enhances H(+) transfer, with no effect on D(+) transfer. There is no coupling of energy initially in any HOD(+) vibrational mode to recoil velocity of either of the product ions, even at low E(col) where vibrational excitation doubles or triples the energy available to products. The results suggest that transfer of H or D atoms is enhanced if the atom in question has a high vibrational velocity, and that this effect offsets what is otherwise a general inhibition of reactivity by added energy. HOCO(+) + D and DOCO(+) + H products are also observed, but as minor channels despite being barrierless and exoergic. These channels appear to be complex mediated at low E(col), essentially vanish at intermediate E(col), then reappear with a direct reaction mechanism at high E(col).

A Bond Path and an Attractive Ehrenfest Force Do Not Necessarily Indicate Bonding Interactions: Case Study on M2X2(M=Li, Na, K; X=H, OH, F, Cl)

Interactions in dimers of model alkali metal derivatives M(2)X(2) (M = Li or Na or K; X = H or F, Cl, OH) are studied in the frame of the quantum theory of atoms in molecules (QTAIM) using the interacting quantum atoms approach (IQA). Contrary to opinion prevalent in QTAIM studies, the interaction between two anions linked by a bond path is demonstrated to be strongly repulsive. One may therefore say that a bond path does not necessarily indicate bonding interactions. The interactions between two anions or two cations that are not linked by a bond path are also strongly repulsive. The repulsive anion-anion and cation-cation interactions are outweighed by much stronger attractive anion-cation interactions, and the model molecules are therefore in a stable state. The attractive Ehrenfest forces (calculated in the frame of the QTAIM) acting across interatomic surfaces shared by anions in the dimers do not reflect the repulsive interactions between anions. Probable reasons of this disagreement are discussed. The force exerted on the nucleus and the electrons of a particular atom by the nucleus and the electrons of any another atom in question is proposed. It is assumed that this force unambiguously exposes whether basins of two atoms are attracted or repelled by each other in a polyatomic molecule.

How do weak Z–X–X and stronger X–Z–X interactions affect NMR chemical shifts of chalcogenide dihalides, R2Z·X2? Theoretical background on the structural prediction of R2Z·X2 through chemical shifts in solutions

AbstractThe mechanism is clarified for the high applicability of criteria to distinguish molecular complexes (MC) from pseudo‐trigonal bipyramidal adducts (TBP) of chalcogenide dihalogens in solutions, based on the NMR chemical shifts. The criteria are theoretically investigated employing MC and TBP of MeSeMe (1), EtSeEt (3), PhSePh (7), PhSPh (8), and PhSeH (22) with chlorine and/or bromine. The adducts of (CH2CH)2Se (26), H2C(CHCH)2Se (27), and H2C(CHCH)2S (28) are also investigated. Behaviors of total absolute magnetic tensors (σt) for the atoms in question are analyzed separately by the diamagnetic and paramagnetic terms, which well support the observed NMR chemical shifts of the MC and TBP adducts in solutions. As a result, the criteria are thoroughly supported on the basis of theoretical background and the mechanism of criteria is clarified with the diamagnetic and paramagnetic terms. The results shed light on the specific effect of weak ZXX and stronger XZX interactions on the NMR chemical shifts of the adducts, R2Z·X2. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:446–456, 2011; View this article online at wileyonlinelibrary.com. DOI 10.1002/hc.20707

Material Properties and Structural Characterization of M3Si6O12N2:Eu2+ (M=Ba, Sr)—A Comprehensive Study on a Promising Green Phosphor for pc‐LEDs

The efficient green phosphor Ba(3)Si(6)O(12)N(2):Eu(2+) and its solid-solution series Ba(3-x)Sr(x)Si(6)O(12)N(2) (with x approximately = 0.4 and 1) were synthesized in a radio-frequency furnace under nitrogen atmosphere at temperatures up to 1425 degrees C. The crystal structure (Ba(3)Si(6)O(12)N(2), space group P3 (no. 147), a = 7.5218(1), c = 6.4684(1) A, wR2 = 0.048, Z = 1) has been solved and refined on the basis of both single-crystal and powder X-ray diffraction data. Ba(3)Si(6)O(12)N(2):Eu(2+) is a layer-like oxonitridosilicate and consists of vertex-sharing SiO(3)N-tetrahedra forming 6er- and 4er-rings as fundamental building units (FBU). The nitrogen atoms are connected to three silicon atoms (N3), while the oxygen atoms are either terminally bound (O1) or bridge two silicon atoms (O2) (numbers in superscripted square brackets after atoms indicate the coordination number of the atom in question). Two crystallographically independent Ba(2+) sites are situated between the silicate layers. Luminescence investigations have shown that Ba(3)Si(6)O(12)N(2):Eu(2+) exhibits excellent luminescence properties (emission maximum at approximately 527 nm, full width at half maximum (FWHM) of approximately 65 nm, low thermal quenching), which provides potential for industrial application in phosphor-converted light-emitting diodes (pc-LEDs). In-situ high-pressure and high-temperature investigations with synchrotron X-ray diffraction indicate decomposition of Ba(3)Si(6)O(12)N(2) under these conditions. The band gap of Ba(3)Si(6)O(12)N(2):Eu(2+) was measured to be 7.05+/-0.25 eV by means of X-ray emission spectroscopy (XES) and X-ray absorption near edge spectroscopy (XANES). This agrees well with calculated band gap of 6.93 eV using the mBJ-GGA potential. Bonding to the Ba atoms is highly ionic with only the 4p(3/2) orbitals participating in covalent bonds. The valence band consists primarily of N and O p states and the conduction band contains primarily Ba d and f states with a small contribution from the N and O p states.

Understanding the NMR chemical shifts for 6-halopurines: role of structure, solvent and relativistic effects

A prototypical study of NMR chemical shifts in biologically relevant heteroaromatic compounds containing a heavy halogen atom is presented for two isomers of halogen-substituted purines. Complete sets of (1)H-, (13)C- and (15)N-NMR chemical shifts are determined experimentally in solution. Experimental results are complemented by quantum-chemical calculations that provide understanding of the trends in the chemical shifts for the studied compounds and which show how different physical effects influence the NMR parameters. Chemical shifts for isolated molecules are calculated using density-functional theory methods, the role of solvent effects is studied using polarised continuum models, and relativistic corrections are calculated using the leading-order Breit-Pauli perturbation theory. Calculated values are compared with the experimental data and the effects of structure, solvent and relativity are discussed. Overall, we observe a good agreement of theory and experiment. We find out that relativistic effects cannot be neglected even in the chlorine species when aiming at high precision and a good agreement with the experimental data. Relativity plays a crucial role in the bromine and iodine species. Solvent effects are of smaller importance for (13)C shifts but are shown to be substantial for particular (15)N shifts. The test of method performance shows that the BLYP and B3LYP functionals provide the most reliable computational results after inclusion of the solvent and relativistic effects while BHandHLYP may--depending on atom in question--slightly improve but mostly deteriorate the data. Ab initio Hartree-Fock suffers from triplet instability in the Breit-Pauli relativistic part while MP2 provides no clear improvement over DFT in the nonrelativistic region. This work represents the first full application of the Breit-Pauli perturbation theory to an organic chemistry problem.

A hypercube queueing loss model with customer-dependent service rates

Abstract This paper is concerned with the solution of a specific hypercube queueing model. It extends the work that was described in a related paper by Atkinson et al. [Atkinson, J.B., Kovalenko, I.N., Kuznetsov, N., Mykhalevych, K.V., 2006. Heuristic methods for the analysis of a queuing system describing emergency medical services deployed along a highway. Cybernetics & Systems Analysis, 42, 379–391], which investigated a model for deploying emergency services along a highway. The model is based on the servicing of customer demands that arise in a number of distinct geographical zones, or atoms. Service is provided by servers that are positioned at a number of bases, each having a fixed geographical location along the highway. At each base a single server is available. Demands arising in any atom have a first-preference base and a second-preference base. If the first-preference base is busy, service is provided by the second-preference base; and, if both bases are busy, the demand is lost. In practice, because of differences in travel times from the first and second-preference bases to the atom in question, the service rate may be significantly different in the two cases. The model studied here allows for such customer-dependent service rates to occur, and the corresponding hypercube model has 3 n states, where n is the number of bases. The computational intractability of this model means that exact solutions for the long-run proportion of lost demands ( p loss ) can be obtained only for small values of n . In this paper, we propose two heuristic methods and a simulation approach for approximating p loss . The heuristics are shown to produce very accurate estimates of p loss .

A deformation gradient tensor and strain tensors for atomistic simulations

A kinematical algorithm is proposed for the construction of strain tensors from atomistic simulation data. Local strain tensors such as the Almansi and Green strain tensors suitable for use in large deformation molecular dynamics/statics simulations are computed directly from a discrete form of the deformation gradient. The discrete, incremental form of the deformation gradient emerges from a weighted least squares minimization that includes a length scale relating the distance from the atom in question with a particular radius. This region defines the nonlocal domain of the strain at that atom. The local atomic strain tensors are then computed using continuum definitions in terms of the deformation gradient. The results of molecular dynamics simulations are presented that compare the Almansi and Green strain tensors under inhomogeneous deformation and indicate that the small-strain approximation should not be used to determine large atomic strains.

The use of softer X-rays in the structure elucidation of microporous materials

Microporous materials, such as zeolites and aluminophosphates, have many applications as molecular sieves and shape-selective catalysts. This is due to their three-dimensional frameworks, which contain regular pores and channels, to their high acidity, arising from Brønsted and Lewis acid active sites, and to the incorporation of transition metal atoms into framework sites. This review firstly provides an introduction into the nature and properties of these materials, and their important applications; the difficulties in their full characterization and possible methods of elucidating their structures are then outlined; finally, methods of characterization, utilizing 'softer X-rays' are introduced. The first method is the determination of low concentrations of transition metals, incorporated into the frameworks using single crystal anomalous dispersion crystallography; synchrotron radiation is used to tune to the absorption edge of the metal atom in question, in order to change its signal relative to that of the rest of the structure, thereby allowing the pinpointing of its positions and the determination of its concentration at each site in the framework. Secondly, the use of longer wavelengths in powder diffraction studies is described, which, by stretching out the powder pattern, thereby reduces the overlapping of the diffraction peaks, thus allowing the structure to be solved by conventional direct methods. Finally, the use of X-ray absorption spectroscopy to determine the metal incorporation and the nature of coordination at the metal atom sites, in Mn silicalite-1 and FAPO-36, are described.

Magnetic susceptibility: Further insights into macroscopic and microscopic fields and the sphere of Lorentz

AbstractTo make certain quantitative interpretations of spectra from NMR experiments carried out on heterogeneous samples, such as cells and tissues, we must be able to estimate the magnetic and electric fields experienced by the resonant nuclei of atoms in the sample. Here, we analyze the relationships between these fields and the fields obtained by solving the Maxwell equations that describe the bulk properties of the materials present. This analysis separates the contribution to these fields of the molecule in which the atom in question is bonded, the “host” fields, from the contribution of all the other molecules in the system, the “external” fields. We discuss the circumstances under which the latter can be found by determining the macroscopic fields in the sample and then removing the averaged contribution of the host molecule. We demonstrate that the results produced by the, so‐called, “sphere of Lorentz” construction are of general validity in both static and time‐varying cases. This analytic construct, however, is not “mystical” and its justification rests not on any sphericity in the system but on the local uniformity and isotropy, i.e., spherical symmetry, of the medium when averaged over random microscopic configurations. This local averaging is precisely that which defines the equations that describe the macroscopic fields. Hence, the external microscopic fields, in a suitably averaged sense, can be estimated from the macroscopic fields. We then discuss the calculation of the external fields and that of the resonant nucleus in NMR experiments. © 2003 Wiley Periodicals, Inc. Concepts Magn Reson Part A 18A: 72–95, 2003

Teaching Chemistry with Electron Density Models. 2. Can Atomic Charges Adequately Explain Electrostatic Potential Maps?

Electrostatic potential maps generated from quantum mechanical calculations are widely used to teach students about molecular polarity and assign atomic charges (Shusterman, G. P.; Shusterman, A. J. J. Chem. Educ. 1997, 74, 771–776; Hehre, W. J.; Shusterman, A. J.; Nelson, J. E. The Molecular Modeling Workbook for Organic Chemistry: Wavefunction: Irvine, CA, 1998). The assumption that potential equals charge is only valid, however, when comparing atoms of similar size. The proper use of potential maps requires consideration of atomic charge, atomic radius, and the electron configuration (orbital occupancy) of the atom in question. These points are illustrated through the analysis of the potential maps of various halogen-containing molecules.