Pair Potential Calculations Research Articles

CO2 ultrathin film growth on a monolayer of CO2 adsorbed on the NaCl(100) surface: sticking coefficient and IR-optical signatures in the ν3 region.

CO2 ultrathin molecular films were grown onto a preadsorbed monolayer NaCl(100)/p(2 × 1)-CO2 at 40 K. Polarization infrared spectroscopy (PIRS) reveals that so-prepared films have better quality than directly grown films. A sticking probability of 0.74 ± 0.1 was deduced from the integrated IR absorption. The presence of the monolayer doublet in the film spectra suggests a Stranski-Krastanov film growth with locally varying film thicknesses on the surface. In the region of the ν3(12C16O2) band, fine structure was observed between the well-known transverse-optical (TO) and longitudinal optical (LO) bands. Two independent computational models were applied to analyze the nature of the observed fine structure. Both pair potential calculations in combination with a vibrational exciton model as well as plane-wave density functional theory (DFT) in combination with phonon calculations of IR intensities at the Γ-point reveal that a weak mode visible in s-polarization and p-polarization originates from a vibrational film excitation located near the substrate interface. A series of p-polarized weak bands appearing and partly disappearing upon film-growth is assigned to film stacks of unique local thickness.

DNA-protamine condensates under low salt conditions: molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions.

Protamine, a small, strongly positively-charged protein, plays a key role in achieving chromatin condensation inside sperm cells and is also involved in the formulation of nanoparticles for gene therapy and packaging of mRNA-based vaccines against viral infection and cancer. The detailed mechanisms of such condensations are still poorly understood especially under low salt conditions where electrostatic interaction predominates. Our previous study, with a refined coarse-grained model in full consideration of the long-range electrostatic interactions, has demonstrated the crucial role of electrostatic interaction in protamine-controlled reversible DNA condensation. Therefore, we herein pay our attention only to the electrostatic interaction and devise a coarser-grained bead-spring model representing the right linear charge density on protamine and DNA chains but treating other short-range interactions as simply as possible, which would be suitable for real-scale simulations. Effective pair potential calculations and large-scale molecular dynamics simulations using this extremely simple model reproduce the phase behaviour of DNA in a wide range of protamine concentrations under low salt conditions, again revealing the importance of the electrostatic interaction in this process and providing a detailed nanoscale picture of bundle formation mediated by a charge disproportionation mechanism. Our simulations also show that protamine length alters DNA overcharging and in turn redissolution thresholds of DNA condensates, revealing the important role played by entropies and correlated fluctuations of condensing agents and thus offering an additional opportunity to design tailored nanoparticles for gene therapy. The control mechanism of DNA-protamine condensates will also provide a better microscopic picture of biomolecular condensates, i.e., membraneless organelles arising from liquid-liquid phase separation, that are emerging as key principles of intracellular organization. Such condensates controlled by post-translational modification of protamine, in particular phosphorylation, or by variations in protamine length from species to species may also be responsible for the chromatin-nucleoplasm patterning observed during spermatogenesis in several vertebrate and invertebrate species.

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue.

Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 106-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.

Computational simulation of al-based alloy surface structure dislocation: the first-principles calculation and atomic pair-potential lattice dynamics calculation

In this paper, the first-principles calculation methods are used to obtain the generalized stacking fault (GSF) energy of Al and Al alloy surface structures. At the same time, after obtaining the atomic pair potential, GSF energy is calculated by the means of atomic simulation simultaneously. By comparison, the calculation of GSF energy at different scales is consistent and the study of GSF energy from different scale level with an acceptable accuracy is realized. For the study of surface structure dislocation defects, the calculation of antiphase boundary (APB) energy is pretty significant. By means of the atomic pair potential, we calculate the APB energy of surface structure of the NiAl, FeAl and CoAl binary Al-based alloys. Therefore, in this paper, the surface structural dislocation of Al-base binary alloys was studied on different scales.

Two-dimensional growth of dendritic islands of NTCDA on Cu(001) studied in real time.

The success of future organic electronic devices distinctively depends on the electronic and geometric properties of thin organic films. Although obviously these properties are strongly influenced by the growth mechanisms, real time growth studies are relatively rare since not many experimental techniques exist that allow in situ studies in ultra high vacuum. In this context, we investigated the prototypical system 1,4,5,8-naphtalene-tetracarboxylic-dianhydride (NTCDA) on Cu(001). We used low-energy electron microscopy (LEEM) for the real-time growth study, and a variety of other techniques for investigating the geometric and electronic structure. While for similar model systems well known and well characterized growth modi occur (e.g., compact, well ordered islands or disordered, gas-like layers), for NTCDA/Cu(001) we observe the growth of dendrite-like, fractal structures. The dendritic structures arise from a strongly preferred one-dimensional growth mode forming a long-range ordered network of thin molecular chains spanning over the entire surface already at small coverages. Later in the growth process, the voids in the network structure are incrementally filled. These results are very unexpected for such a simple adsorbate system consisting of well investigated components, the properties of which were believed to be already well understood. We explain this unexpected behavior by a dendritic growth model that is supported by energetic arguments based on pair-potential calculations. These calculations give reason for the experimentally observed growth of one-dimensional structures, and therefore represent the key to a semi-quantitative understanding of this dendritic growth mode.

Strain relaxation and epitaxial relationship of perylene overlayer on Ag(110).

We present a room temperature STM study of perylene self-assembly on Ag(110) beyond the monolayer coverage regime. Coupling of the perylene aromatic boards yields π-π bonded stacks. The perylene stacks self-assemble into a continuous three-dimensional epitaxial overlayer of (3 × 5) symmetry. The self-assembly is driven by thermodynamic balance established under coupling of the intra- and intermolecular interactions and the molecule-substrate interaction all accommodating the short-range thermal motion of the constituent molecules. The balance bestows to the overlayer the unique ability to accommodate the underlying substrate morphology and to spread over the surface steps as a single structure preserving its lateral order and keeping epitaxial relationship with every surface terrace. The complete epitaxy is driven by (i) anchoring of half of the perylene stacks into specific adsorption sites on each terrace, (ii) interlacing of the perylene stacks across the steps within the entire H-bonded network, and (iii) relaxation of the overlayer strain via enhancement of the overlayer-specific vibrational modes and short-range thermal motion of the constituent molecules. This complete epitaxy phenomenon is described via (i) structural and statistical analysis of the molecularly resolved STM topographies, (ii) monitoring of the short-range molecular displacements under the strain relaxation, (iii) highlighting of specific intra-molecular and inter-molecular vibration modes through detailed analysis of HREELS spectra, and (iv) parametrization of the intermolecular interaction via pair potential calculation.

Calculating particle pair potentials from fluid‐state pair correlations: Iterative ornstein–zernike inversion

An iterative Monte Carlo inversion method for the calculation of particle pair potentials from given particle pair correlations is proposed in this article. The new method, which is best referred to as Iterative Ornstein-Zernike Inversion, represents a generalization and an improvement of the established Iterative Boltzmann Inversion technique (Reith, Pütz and Müller-Plathe, J. Comput. Chem. 2003, 24, 1624). Our modification of Iterative Boltzmann Inversion consists of replacing the potential of mean force as an approximant for the pair potential with another, generally more accurate approximant that is based on a trial bridge function in the Ornstein-Zernike integral equation formalism. As an input, the new method requires the particle pair correlations both in real space and in the Fourier conjugate wavenumber space. An accelerated iteration method is included in the discussion, by which the required number of iterations can be greatly reduced below that of the simple Picard iteration that underlies most common implementations of Iterative Boltzmann Inversion. Comprehensive tests with various pair potentials show that the new method generally surpasses the Iterative Boltzmann Inversion method in terms of reliability of the numerical solution for the particle pair potential. © 2018 Wiley Periodicals, Inc.

Submonolayer and multilayer growth of titaniumoxide-phthalocyanine on Ag(111)

For exploiting the full potential of organic materials for future organic electronic devices it is of crucial importance to understand structural and electronic properties of metal-organic interfaces and adsorbate systems, in particular electronic interactions and growth mechanisms. Phthalocyanine molecules represent one class of materials which are very frequently discussed in this context. They feature an appealing tunability in terms of structural, electronic and magnetic properties, simply by exchanging the central (metal) atom or group of atoms. Here we present a comprehensive study of one of the model systems in this field, TiOPc on Ag(111). We discuss structure formation and growth from submonolayer to multilayer films, based on results obtained by electron diffraction, scanning tunneling microscopy, electron energy loss spectroscopy, x-ray standing waves, photoelectron spectroscopy and pair potential calculations. Similar to related metal-phthalocyanine adsorbate systems we find three distinct phases in the submonolayer regime, a disordered gas-like ‘g-phase’, a commensurate ‘c2-phase’ at low temperature, and a ‘p.o.l.-phase’ consisting of a series of point-on-line structures with continuously shrinking unit cells. For the latter a uniform TiO-up configuration (Ti–O group pointing towards vacuum) was found. Hence, the first-layer molecules form a strong dipole layer, the dipole moment of which is compensated by molecules adsorbing in the second layer at hollow-sites in TiO-down geometry (Ti-O group pointing towards the surface). The Coulomb interaction between the dipole moments in the first and second layer stabilizes this bilayer structure and causes a bilayer-by-bilayer growth mode of molecular films above a thickness of 2 ML. We report the structural properties (vertical adsorption heights, inter-layer distances, inplane orientations and positions) of the molecules in all phases in detail, and discuss the effect of inelastic dynamical charge transfer. Our results contribute to a comprehensive understanding of this interesting adsorbate system and, in comparison with earlier studies on CuPc, H2Pc and SnPc on Ag(111), we shine new light on the interesting interplay of molecule-molecule and molecule-substrate interactions.

Oxygen diffusion in ThO2-CeO2 and ThO2-UO2 solid solutions from atomistic calculations.

We elucidate oxygen diffusivity in ThO2-CeO2 and ThO2-UO2 solid solutions across their whole concentration ranges in the phase diagram using static pair-potential calculations and molecular dynamics simulations. Between pure CeO2 (and UO2) and pure ThO2, oxygen diffusivity is higher in CeO2 (and UO2) due to lower oxygen migration barriers. With the addition of Th to CeO2 (and UO2) in the phase diagram, the diffusivity decreases due to the increase in the migration barriers introduced by a larger ionic radius of Th. On the other side of the phase diagram, with the addition of Ce to ThO2 oxygen diffusion decreases due to oxygen vacancy binding with Ce, even though the migration barriers decrease due to the smaller size of Ce than the host Th. Using these calculations, we provide a schematic of high oxygen diffusivity regions in the phase diagram. We also compare the impact of tetravalent dopants (e.g. actinides) on oxygen vacancy energetics to that of trivalent dopants (e.g. lanthanides). We find that trivalent dopants bind much more strongly with oxygen vacancy than the tetravalent dopants. We also find that the tetravalent dopants that have larger radii than the host cation have negative oxygen vacancy binding energy, whereas all trivalent dopants have positive binding energy irrespective of their ionic radii. This work thus highlights key differences in the oxygen vacancy energetics between the trivalent and tetravalent cations.

Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd2Ti2O7.

The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd2Ti2O7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. In view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.

Electrostatic Interaction and Commensurate Registry at the Heteromolecular F16CuPc–CuPc Interface

Tailoring the properties of molecular thin films and interfaces will have decisive influence on the success of future organic electronic devices. This is equally true for metal–organic and hetero–organic contacts as they occur, for example, in donor–acceptor systems. Here, we report on the structure formation and interaction across such a heteromolecular interface. It is formed by monolayers of F16CuPc and CuPc stacked on a Ag(111) surface. We investigated the lateral and vertical structure using spot-profile analysis low energy electron diffraction and normal incidence X-ray standing waves, and performed pair potential calculations to understand the driving forces for the structure formation. Most surprisingly, for one phase we found a commensurate registry between the two organic layers, usually a sign for a strong (chemisorptive) interaction often involving metallic states of the surface. However, because the organic bilayer is not commensurate with the underlying Ag substrate in our case, the dominating factor must be the intermolecular interaction. Pair potential calculations suggest a site-specific adsorption that leads to a commensurate registry at the heteromolecular interface. The adsorbate system was further characterized by measuring adsorption heights, indicating flat-lying molecules and a CuPc–F16CuPc layer spacing of 3.06 Å.

Implementation of pseudoreceptor-based pharmacophore queries in the prediction of probable protein targets: explorations in the protein structural profile of Zea mays.

Molecular docking plays an important role in the protein target identification by prioritizing probable druggable proteins using docking energies. Due to the limitations of docking scoring schemes, there arises a need for structure-based approaches to acquire confidence in theoretical binding affinities. In this direction, we present here a receptor (protein)-based approach to predict probable protein targets using a small molecule of interest. We adopted a reverse approach wherein the ligand pharmacophore features were used to decipher interaction complementary amino acids of protein cavities (a pseudoreceptor) and expressed as queries to match the cavities or binding sites of the protein dataset. These pseudoreceptor-based pharmacophore queries were used to estimate total probabilities of each protein cavity thereby representing the ligand binding efficiency of the protein. We applied this approach to predict 3 experimental protein targets among 28 Zea mays structural data using 3 co-crystallized ligands as inputs and compared its effectiveness using conventional docking results. We suggest that the combination of total probabilities and docking energies increases the confidence in prioritizing probable protein targets using docking methods. These prediction hypotheses were further supported by DrugScoreX (DSX) pair potential calculations and molecular dynamic simulations.

Density functional theory investigations of titanium γ-surfaces and stacking faults

Bulk properties of hcp-Ti, relevant for the description of dislocations, such as elastic constants, stacking faults and γ-surface, are computed using density functional theory (DFT) and two central force embedded atom interaction models (Zope and Mishin 2003 Phys. Rev. B 68 024102, Hammerschmidt et al 2005 Phys. Rev. B 71 205409). The results are compared with previously published calculations, except pair potential calculations, which are not appropriate for the description of the metallic bond. The comparison includes N-body central force (NB-CF) and N-body angular (NB-A) empirical potentials, tight-binding approximation to the electronic structure (TB), DFT pseudopotential (DFT-P) and all electron (DFT-A) calculations. None of the considered interaction models are fully satisfactory for the description of these properties. In particular, NB-CF, NB-A and TB interaction models are unable to describe the softening of the easy prismatic γ-surface leading to the appearance of a metastable stacking fault, as evidenced in all the DFT calculations. Most often, when the basal stacking fault excess energy is underevaluated, this leads to an inversion of the energetic stability between the I2 basal and the prismatic easy stacking faults. Even the DFT-pseudopotential calculations need to be improved regarding the description of the shear elastic constants. The implications of these results on the core structure and gliding properties of the screw dislocation are analyzed. The calculated dissociation lengths into Shockley partials in both the basal and prismatic planes for the different models compare well with the measured ones in the corresponding simulations of the dislocation core structure when available. Finally, the Peierls stress is also evaluated using the Peierls–Nabarro model and compared with the experimentally measured one.

Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

Segregation of xenon to dislocations and grain boundaries in uranium dioxide

It is well known that Xe, being insoluble in UO${}_{2}$, segregates to dislocations and grain boundaries (GBs), where bubbles may form resulting in fuel swelling. Less well known is how sensitive this segregation is to the structure of the dislocation or GB. In this work we employ pair potential calculations to examine Xe segregation to dislocations (edge and screw) and several representative grain boundaries (\ensuremath{\Sigma}5 tilt, \ensuremath{\Sigma}5 twist, and random). Our calculations predict that the segregation trend depends significantly on the type of dislocation or GB. In particular we find that Xe prefers to segregate strongly to the random boundary as compared to the other two boundaries and to the screw dislocation rather than the edge. Furthermore, we observe that neither the volumetric strain nor the electrostatic potential of a site can be used to predict its segregation characteristics. These differences in segregation characteristics are expected to have important consequences for the retention and release of Xe in nuclear fuels. Finally, our results offer general insights into how atomic structure of extended defects influence species segregation.

Studying soft matter with “soft” potentials: fast lattice Monte Carlo simulations and corresponding lattice self-consistent field calculations

We introduce fast lattice Monte Carlo (FLMC) simulations, where multiple occupancy of lattice sites is allowed with a proper Boltzmann weight and thus the evaluation of nearest-neighbor interactions can also be avoided. FLMC simulations (with multiple occupancy of lattice sites and Kronecker δ-function interactions) are much more efficient, in the study of equilibrium properties of soft matter such as polymers, than both conventional lattice MC simulations (with self- and mutual-avoiding walks and nearest-neighbor interactions) and fast off-lattice MC simulations (with pair-potential calculations). When compared with the corresponding lattice field theories based on the same Hamiltonian, FLMC simulations further provide a powerful means for unambiguously and quantitatively revealing the effects of long-wavelength correlations/fluctuations. Using confined homopolymers as an example, we report for the first time FLMC simulation data ranging from the single-chain case all the way to the lattice self-consistent field limit.

Thermodynamics of liquid Fe-Ni alloys: Calculations at different temperatures

For the description of the ion-ion interaction in a transition metal the method of pair potential calculation introduced by Wills and Harrison is used. The potential is represented as a sum of the s-electron and d-electron contributions. The first is calculated in the framework of the Bretonnet and Silbert local model pseudopotential. On the basis of this approximation the thermodynamic properties are calculated by using the variational method of the thermodynamic perturbation theory. The formalism is applied to calculate the free energy of mixing for the Fe-Ni liquid system at different compositions and temperatures. An agreement with the available experimental data is quite satisfactory.

Deformation mechanisms leading to auxetic behaviour in theα-cristobaliteand α-quartz structures of both silica and germania

Analytical expressions have been developed in which the elastic behaviour of theα-quartzand α-cristobalite molecular tetrahedral frameworks of both silica and germania are modelledby rotation, or dilation or concurrent rotation and dilation of the tetrahedra.Rotation and dilation of the tetrahedra both produce negative Poisson’s ratios(auxetic behaviour), whereas both positive and negative values are possible whenthese mechanisms act concurrently. Concurrent rotation and dilation of thetetrahedra reproduces with remarkable accuracy both the positive and negativeν31 Poisson’s ratiosobserved for silica α-quartz and α-cristobalite, respectively, when loaded in thex3 direction. A parametric fit of the concurrent model to the germaniaα-quartz experimentalν31 Poisson’s ratiois used to predict ν31 for germania α-cristobalite, for which no experimental value exists. This is predicted to be+0.007.Strain-dependent ν31 trends, due to concurrent rotation and dilation in the silica structures, are inbroad agreement with those predicted from pair-potential calculations, althoughsignificant differences do occur in the absolute values. With the model of concurrentdilation and rotation of the tetrahedra we predict that an alternative uniaxial stress(σ3)-induced phase existsfor both silica, α-quartzand α-cristobalite,and germania, α-cristobalite, having geometries in reasonable agreement withβ-quartz andidealized β-cristobalite, respectively.

Elasticity and lattice vibrational properties of transparent polycrystalline yttrium–aluminium garnet: Experiments and pair potential calculations

Brillouin light scattering, Raman light scattering and visible–infrared reflectometry techniques have been used to investigate, respectively, the elastic properties, the phonons and the optical properties of bulk textured polycrystalline yttrium–aluminum garnet doped with 2 at% neodymium obtained by the sintering of commercial oxides. From the analysis of the observed bulk longitudinal and transverse acoustic modes with the knowledge of the refractive index 1.81 inferred from the visible reflectometry, the two independent effective elastic constants of the isotropic polycrystal C 11 = 362 GPa and ( C 11 − C 12)/2 = 121 GPa are determined leading to the value of the bulk modulus B = ( C 11 + 2 C 12)/3 = 200 GPa. The ratio ɛ 0/ ɛ ∞ = 3.1 and the optic permittivity ɛ ∞ = 3.46 are derived from the infrared reflectivity data. Pair potential calculations of the three single crystal elastic constants c 11 = 340, c 12 = 127 and c 44 = 112 GPa, of the bulk modulus B = ( c 11 + 2 c 12)/3 = 198 GPa, of the zone-center (Γ) phonons and of the permittivity function provide good comparison with our experimental results.

Quantum Monte Carlo, density functional theory, and pair potential studies of solid neon

We report quantum Monte Carlo (QMC), plane-wave density-functional theory (DFT), and interatomic pair-potential calculations of the zero-temperature equation of state (EOS) of solid neon. We find that the DFT EOS depends strongly on the choice of exchange-correlation functional, whereas the QMC EOS is extremely close to both the experimental EOS and the EOS obtained using the best semiempirical pair potential in the literature. This suggests that QMC is able to give an accurate treatment of van der Waals forces in real materials, unlike DFT. We calculate the QMC EOS up to very high densities, beyond the range of values for which experimental data are currently available. At high densities the QMC EOS is more accurate than the pair-potential EOS. We generate a different pair potential for neon by a direct evaluation of the QMC energy as a function of the separation of an isolated pair of neon atoms. The resulting pair potential reproduces the EOS more accurately than the equivalent potential generated using the coupled-cluster CCSD(T) method.