Types Of Interatomic Interactions Research Articles

STUDY OF STABLE STRUCTURES OF THE PENTAPEPTIDE MOLECULE

Low-energy conformational states of the CREKA molecule, a new drug with an antitumor effect, have been studied by the method of theoretical conformational analysis. Geometric parameters and energy contributions of various types of interatomic interactions to the stabilization of the calculated structures have been established.

Lone pairs vs. covalent bonds: conformational effects in bicyclo[3.3.1]nonane derivatives

Investigations on the relative energy of two least-strain conformers for bicyclo[3.3.1]nonane 1, bicyclo[3.3.1]nonan-9-one 2, and their heteroanalogues: 3,7-dimethyl-3,7-diazabicyclo[3.3.1]nonane 3, 3,7-dimethyl-3,7-diazabicyclo[3.3.1]nonan-9-one 4 were performed using the calculations from the first principles (ab initio, DFT) as well as by semiempirical (NDDO, DFTB) and empirical (molecular mechanics, MM) techniques. For these quite simple structures, serious discrepancies in results of modeling between methods of different origins were revealed. Nonempirical calculations state that the “double chair” (CC) form is the most favorable for carbobicyclic structures 1 and 2, while 3,7-dimethyl-3,7-diaza compounds 3 and 4 are in general more prone to adopt the “chair-boat” (CB) conformation. The classical rationalization of these quantum chemistry results leads to the hypothesis similar to one that underlies the Gillespie VSEPR concept, namely that the 3,7-repulsion of lone electron pairs is stronger than the corresponding interaction of hydrogen atoms of C–H bonds. The semiempirical NDDO calculations retain the qualitative correspondence of the results to those of the ab initio calculations, while the results of more recent DFTB approaches are closer to MM in their qualitative inconsistency with high-level ab initio methods. In particular, for 4 the relative energy of CC is severely underestimated, erroneously predicting the predominance of this form over CB. The origin of this failure could lie in the relatively coarse parameterization of common force fields when concerning the subtle interplay between different types of interatomic interactions and could be recovered, although only partially, by the proper choice of the charge scheme to use the atomic-centered charges in the explicit account for the non-valency interactions in the Coulombic form.

Interplay of Structural and Bonding Characters in Thermal Conductivity and Born-Effective Charge of Transition Metal Dichalcogenides

Thermal transport in a material is governed by anharmonicity of crystal potential, which depends on the type of interatomic interaction. Using first-principles calculations, we report that lattice thermal conductivity (κlatt) and its anisotropy (κx,y – κz) of transition metal dichalcogenides (TMDs) increase by orders of magnitude with the change of constituent metal atom from Zr/Hf to Mo/W. This unprecedented difference in κlatt is substantiated by lower phonon group velocity, and 4 times larger anharmonicity of Zr/Hf based TMDs compared to Mo/W based TMDs. The sign and the absolute value of the Born effective charges, which emerges from the ionicity of the bonds, are found to be different for these two classes of materials. This leads to a significant difference in their interlayer van der Waals (vdW) interaction strengths, which are shown to be inversely related to the anisotropy in κlatt.

An X-ray spectral and theoretical study of the electronic structure and features of interatomic interactions in phenoxysilanes

The electronic structure and features of interatomic interactions providing the Si–O–C6H5 bonds in H4-nSi(OC6H5)n (n = 1–4) were studied by a combined analysis of the X-ray emission and photoelectron spectroscopic data and the results of quantum-chemical calculations. Theoretical calculations were carried out using the density functional theory. The distributions of the density of states were constructed, the correlation energy diagrams were presented, and the main types of interatomic interactions in phenoxysilanes were revealed.

Structural, atomic Hirschfeld surface, magnetic and magnetocaloric properties of SmNi5 compound

The SmNi5 intermetallic compound has been investigated by arc-melting. Powder X-ray diffraction analysis and Rietveld refinement revealed that the sample crystallized in the hexagonal CaCu5-type structure P6/mmm space group with the following lattice parameters: a = 4.9203 (1) Å, c = 3.9662 (1) Å. These lattice parameters for the compound are in good agreement with previous theoretical result and experimental data. The EDX analysis has been performed to confirm the composition of this compound. The chemical bonding in SmNi5 was analyzed using atomic Hirshfeld surfaces, and this analysis supports the presence of the structural elements and the coordination of Sm (1a), Ni (2c) and Ni (3 g). This study indicates the different types of interatomic interactions between the Sm and Ni atoms and the weak interactions between Sm–Sm atoms were also observed along the c axis. The magnetic properties and magnetocaloric effect (MCE) have been established by the magnetization and isothermal magnetization of different temperature measurements. The magnetization curve as a function of temperature shows a magnetic transition from ferromagnetic to paramagnetic state at the Curie temperature TC = 29 K. We have studied the MCE phenomena in the vicinity of magnetic phase transitions in terms of magnetic entropy change. The temperature dependence of the magnetization, the magnetic entropy changeΔSM, as well as the relative cooling power around the second-order magnetic transition and the Arrott plots for the alloys are reported.

Molecular Dynamics Study of Ni/YSZ Systems Based on Improved Interatomic Model

Porous nickel/yttria-stabilized zirconia (YSZ) composite is a common choice as an anode material for solid oxide fuel cells (SOFCs). Because of its complicated structure, there are several processes occurring in the anode that affect total performance of SOFCs. For instance, oxygen ion diffusion provides oxygen transport to triple phase boundaries (TPBs) where fuel is oxidized. Another important process is nickel sintering, which causes decreasing of the active TPB length and thus leads to degradation of SOFCs. Understanding the mechanism of each individual phenomenon in Ni/YSZ anodes can contribute to improving total performance and stability of SOFCs. Atomistic simulations can provide a deep insight into the processes taking place in Ni/YSZ anodes. While the density functional theory method is one of the most rigorous atomistic approaches used in materials science, its applicability is limited to small systems of hundreds of atoms. Larger systems can be studied by molecular dynamics (MD) and Monte-Carlo simulations, which are based on empirical potentials. However, most of the potentials for YSZ are based on simple pairwise interactions and designed in the way to reproduce specific bulk properties. Unfortunately, their validity for studying surface and interface properties of Ni/YSZ systems is usually only presumed [1], which can lead to questionable results for such processes as nickel sintering and oxygen surface diffusion. Thus, in the present paper we develop a DFT-based model that purposefully aims for studying a wide range of processes in Ni/YSZ systems, including oxygen diffusion in bulk and surface regions of YSZ, yttrium surface segregation, and nickel sintering. Our model combines three types of interatomic interactions. The first one is based on the dipole model [2] and was parameterized for bulk and surface YSZ regions in our previous work [3]. It reproduces with a good accuracy not only bulk but also surface properties of YSZ. The second describes nickel by the embedded atom method [4]. The third is for interactions between Ni and YSZ and is described by a pairwise Buckingham potential, which was parameterized individually for different Ni/YSZ interfaces. Having confirmed that the model well reproduces the bulk properties of YSZ, we employed the developed model to demonstrate that it reproduces with good accuracy the surface structures and bulk conductivity of YSZ. This allowed us to use the model to further study oxygen ion diffusion near (111) and (110) YSZ surfaces where YSZ structure can be very much distorted [5], and thus oxygen diffusion can be affected. Obtained results suggest suppressed oxygen diffusion along (111) because of the lower oxygen vacancy concentration near the surface. In contrast, oxygen vacancies tend to migrate to the (110) surface, which, together with activation of jumps along <110> directions, facilitates diffusion along the surface. This indicates that it can be easier for oxygen ions to migrate to TPBs near the (111) surfaces from bulk regions than along the surface, while near the (110) surface ions prefers to migrate along the surface. We also demonstrate how the model performs for the nickel sintering problem, based on the structures consisting of two Ni particles being 30 Å in diameter and placed on a YSZ slab. We studied the effect of binding energy between the particles and the slab by considering different interfaces at the contact areas and using corresponding interactions. Simulations at 1250 K indicate that a relatively low binding energy of 0.5 J/m2, which corresponds to the Ni(111)/YSZ(111) interface, allows the nanoparticles to slide over the YSZ support and coalesce. When the binding energy is above 1.0 J/m2, the sliding is restricted and particle migration may occur only by means of nickel atom diffusion on nickel surface. [1] H. Lee et al., Acta Materialia 58 (2010) 2197. [2] P. Tangney et al., J. Chem. Phys. 117 (2002) 8898. [3] A. Iskandarov et al., J. Phys.: Condens. Matter 25 (2015) 015005. [4] Y. Mishin et al., Phys. Rev. B 59 (1999) 3393. [5] G. Ballabio et al., Phys. Rev. B. 70 (2004) 075417.

Lattice Dynamics at Zone-Center of Sulphide and Selenide Spinels

A rigid-ion model is used to calculate the force constants and effective dynamical charges of sulphide and selenide spinels. The Raman and infrared phonon modes of normal cubic sulphide spinels MCr2S4 (M = Mn, Co, Fe, Hg, Zn, and Cd) and selenide spinels MCr2Se4 (M = Hg, Zn, and Cd) are calculated at the first Brillouin zone-centre using above model. The significant outcome of the present work is (i) the interatomic interaction between Cr-S (Se) dominates over the Cr-S(Se) and S-S(Se-Se) type of interatomic interactions, (ii) the effective dynamical charges of the bivalent metal ions are nearly zero, and (iii) the selenide spinels are less ionic than the sulphide spinels and the ionicity decreases as MnCr2S4 > FeCr2S4 > CoCr2S4 > and CdCr2C4 > ZnCr2C4 > HgCr2C4 (C = S and Se). The zone-center phonon frequencies, calculated using these parameters, are found to be in very good agreement with the observed results.

Further Understanding of the Thermal Motions of Atoms in Aspirin and Acetaminophen Crystals with Conceptual Density Functional Theory

Following up on a previous report, further correlations between force constants of thermal motions of atoms in aspirin and acetaminophen single crystals and nuclear Fukui functions have been identified. It is believed that the energy barrier of the thermal vibration of one atom in an organic crystal is mainly dominated by the soft–soft type of interatomic interactions, which may be characterized by the nuclear Fukui functions.

Ionization, atomization, and bond energies as functions of distances in inorganic molecules and crystals

The ionization potentials and dissociation energies of diatomic molecules are determined as functions of bond length, and the atomization energies of metals and crystalline compounds are determined as E = a/d n functions. In most cases, n ≥ 1; but for a number of metals and compounds, n < 1, as distinct from all known types of interatomic interactions. It is shown that the ratios of the bond energies and bond lengths of Group 1A and 1B metals to the respective molecular parameters have similar values, proving the identical valence states of the atoms of these metals in crystal structures.

Types of inter-atomic interactions at the MHC-peptide interface: Identifying commonality from accumulated data

BackgroundQuantitative information on the types of inter-atomic interactions at the MHC-peptide interface will provide insights to backbone/sidechain atom preference during binding. Qualitative descriptions of such interactions in each complex have been documented by protein crystallographers. However, no comprehensive report is available to account for the common types of inter-atomic interactions in a set of MHC-peptide complexes characterized by variation in MHC allele and peptide sequence. The available x-ray crystallography data for these complexes in the Protein Databank (PDB) provides an opportunity to identify the prevalent types of such interactions at the binding interface.ResultsWe calculated the percentage distributions of four types of interactions at varying inter-atomic distances. The mean percentage distribution for these interactions and their standard deviation about the mean distribution is presented. The prevalence of SS and SB interactions at the MHC-peptide interface is shown in this study. SB is clearly dominant at an inter-atomic distance of 3Å.ConclusionThe prevalently dominant SB interactions at the interface suggest the importance of peptide backbone conformation during MHC-peptide binding. Currently, available algorithms are developed for protein sidechain prediction upon fixed backbone template. This study shows the preference of backbone atoms in MHC-peptide binding and hence emphasizes the need for accurate peptide backbone prediction in quantitative MHC-peptide binding calculations.

Hydrogen bond in 3-acetyl-4-hydroxycoumarin: X-ray diffraction study and quantum-chemical calculations

The proton transfer and the character of the strong intramolecular O--H...O hydrogen bond (O...O 2.442 A) in 3-acetyl-4-hydroxycoumarin were analyzed based on the results of X-ray diffraction study in the temperature range from 100 to 353 K and quantum-chemical B3LYP/6-31G(d,p) calculations. The barrier to proton transfer along the H-bond line is low (2 kcal mol–1). However, no proton transfer was observed in the crystal at 100 K. Bader's topological analysis of the electron density distribution both in the crystal and in the isolated molecule demonstrated that the hydrogen bond corresponds to an intermediate type of interatomic interactions (E(r) 0 at the critical point (3, –1)).

Solid solution domains in equilibrium phase diagrams: Our concepts and reality

According to the model of interatomic pair interaction, there are two possible types of interaction between components of binary metallic substitutional alloys: the attraction between the A and B atoms, resulting eventually in the formation of chemical compound A m B n (the mixing energy E mix = u AA + u AB — 2 u AB is negative), and the repulsion between A and B atoms, giving rise to a mixture of crystals formed by pure components (the mixing energy is positive). In thermodynamics, these two types of interatomic interactions are related to the tendency of a system to ordering (the sign of deviations from the Raoult law is negative) and to phase separation (the sign of deviations is positive), respectively. These two types of interatomic interactions correspond to two basic types of equilibrium phase diagrams: for the case E mix 0, the phase diagrams consist of the regions corresponding to the mechanical mixture of crystals formed by components of the alloy. However, there exists a large number of equilibrium phase diagrams involving domains (bounded and unbounded) in which, as expected, solid solutions are formed. The presence of the solid solution domains in the phase diagrams means that these solid solutions are equilibrium phases. If the solid solution is an equilibrium phase at temperatures for which the diffusion of components is sufficient for its decomposition, it is possible to say that such a solid solution is ideal. Such a conclusion is in striking contrast with thermodynamic data which suggest that the overwhelming majority of solid solutions are nonideal and exhibit either positive or negative deviations from the Raoult law. As a consequence, they demonstrate the tendency either to phase separation or to ordering, which should certainly lead to the decomposition of the solid solution when the system approaches equilibrium.

Properties of the Experimental Crystal Charge Density of Methylammonium Hydrogen Maleate. A Salt with a Very Short Intramolecular O−H−O Hydrogen Bond

The experimental crystal charge density of deuterated methylammonium hydrogen maleate has been determined from neutron and X-ray diffraction data collected at 122.4 K. Refinements of the neutron diffraction data showed that the very short intramolecular O−H−O hydrogen bonds found in the two independent anions are symmetric with D(H) on crystallographic mirror planes. The experimental charge density was subjected to a topological analysis. It is positive throughout the unit cell and constitutes a topological space that fulfills the Poincare−Hopf relation. The topological analysis enabled us to characterize different types of interatomic interactions in the crystal and showed that the two very short intramolecular hydrogen bonds have covalent character. Newly developed algorithms made it possible to determine the atomic basins in the crystal charge density, which were used to calculate integrated properties such as volume, charge, and the integrated Laplacian. Those of the methylammonium ion have been compa...

Investigation of the electron energy spectrum in some phases of CsCl‐type

AbstractThe results of X‐ray spectral investigations of some phases of the CsCl‐type composed by alloying of a series of transition metals of the first, second, and the third main periods are presented. The K, L, and M emission bands of the atoms constituting the alloys are investigated. Some conclusions about the type of interatomic interaction and the nature of bonding in the considered compounds are presented.