Interatomic Interaction Energy Research Articles

New 2,4-dihydro-1H-1,2,4-triazole-3-selones and 3,3′-di(4H-1,2,4-triazolyl)diselenides. Synthesis, biological evaluation, and in silico studies as antibacterial and fungicidal agents

The reaction of aromatic ring-substituted isoselenocyanates with 2-thiopheacetic and 4-pyridinecarboxylic acid hydrazides yielded selenosemicarbazides which were further converted into previously unknown 1,2,4-triazole-3-selones and 3,3′-di(4H-1, 2,4-triazolyl)diselenides. The structures of the obtained compounds were studied by NMR spectroscopy, IR spectroscopy, and high-resolution mass spectroscopy (HR-MS). The bactericidal and fungicidal activity of some obtained compounds was evaluated in molecular modeling studies such as docking and simulation studies. The compound 3ba was reported as the most promising compound to show robust binding energy with different antibacterial and antifungal compounds. The compounds were observed in strong hydrophilic and hydrophobic interactions and remained in stable binding conformation with the receptor enzymes. Furthermore, the interatomic interaction energies were dominated by Van der Waals and electrostatic energies indicating the formation of stable complexes.

The Algorithm to Predict the Grain Boundary Diffusion in Non-Dilute Metallic Systems

The analysis of grain boundary (GB) diffusion in metallic systems based on Cu, Ni, Ag and Al was made to set demonstrate the common behavior. It was shown that the slow penetration for 11 systems can be connected with negative segregation or specific interatomic interaction. Two energetic parameters such as energy of interaction with GB and energy of interatomic interaction are proposed as main characteristics. The analysis of a tendency toward segregation and tendency of intermediate phase formation in these terms allows us to divide the systems on four groups and formulate a qualitative way to predict the behavior of the diffusing elements in a non-dilute solution. Mathematical formulation of GB diffusion problem and typical solutions are presented.

General framework for interatomic interaction energy of two ground-state atoms in a thermal bath

We give a general derivation of the fourth-order DDC formalism (a formalism proposed by Dalibard, Dupont-Roc, and Cohen-Tannoudji) for calculating the interaction energy between two ground-state multilevel atoms which are coupled to electromagnetic fields in a thermal bath at temperature $T$. Both the contributions of the thermal field fluctuations and the radiation reaction of atoms are separately identified. As an application of the formalism, we revisit the interaction energy of two static ground-state two-level atoms in a free space and discover new behaviors such as the $\ensuremath{\sim}T{L}^{\ensuremath{-}2}$ behavior of the van der Waals interaction energy in the region where ${\ensuremath{\lambda}}^{3/4}{T}^{\ensuremath{-}1/4}\ensuremath{\ll}L\ensuremath{\ll}\ensuremath{\lambda}$, with $\ensuremath{\lambda}$ the transition wavelength of the atoms and $L$ the interatomic separation, and an oscillatory behavior of the Casimir-Polder interaction energy as $L$ varies which is superimposed on the monotonic $\ensuremath{\sim}T{L}^{\ensuremath{-}6}$ dependence when $L\ensuremath{\gg}\ensuremath{\lambda}\ensuremath{\gg}{T}^{\ensuremath{-}1}$.

Quantum thermal field fluctuation induced corrections to the interaction between two ground-state atoms

We generalize the formalism proposed by Dalibard, Dupont-Roc, and Cohen-Tannoudji (the DDC formalism) in the fourth order for two atoms in interaction with scalar fields in vacuum to a thermal bath at finite temperature T, and then calculate the interatomic interaction energy of two ground-state atoms separately in terms of the contributions of thermal fluctuations and the radiation reaction of the atoms and analyze in detail the thermal corrections to the van der Waals and Casimir–Polder interactions. We discover a particular region, i.e. with L, β and λ denoting the interatomic separation, the wavelength of thermal photons and the transition wavelength of the atoms respectively, where the thermal corrections remarkably render the van der Waals force, which is usually attractive, repulsive, leading to an interesting crossover phenomenon of the interatomic interaction from attractive to repulsive as the temperature increases. We also find that the thermal corrections cause significant changes to the Casimir–Polder force when the temperature is sufficiently high, resulting in an attractive force proportional to TL −3 in the λ ≪ β ≪ L region, and a force that can be either attractive or repulsive and even vanishing in the β ≪ λ ≪ L region depending on the interatomic separation.

Theoretical algorithm for fast calculation of interatomic bonds as applied to metallic hydrogen and carbon condensates

A method for calculating the potential energy of interatomic interaction, an alternative to the use of significant computer resources, is proposed. The algorithm was tested on the example of 1S-1S bonds, in particular, in hydrogen, as well as 2S-2S and 2 P-2P bonds, in particular, in carbon. It is shown that bound states can be formed in all three cases, but the interacting atoms must overcome the potential barrier. The presence of a barrier makes it possible to explain a number of known features in the formation of the corresponding condensates.

Change the state of 2D nanofilms under the substrate influence

2D films deformations under action of ferroelectric substrate by computer modeling method are performed in article. The film has a square lattice. We use harmonic law for the energy of interatomic interaction. The substrate effect on the film is simulated by the 2D Frenkel-Kontorova potential. The orientation of the film and the substrate do not match. Different cases for periods of film and substrate are considered. The Monte Carlo method is used for computer modeling. If the period of the film and the substrate coincide, the film atoms are placed at the minimum points of the substrate. The film on the substrate has a square crystal lattice. If the period of the substrate is less than the period of the film, the continuous film is converted into a film 2D nanoparticles. The substrate potential amplitude affects the filling of the space between particles. If the period of the substrate is longer than the period of the film, a superstructure in the form of a periodic lattice with an increased particle concentration is formed in the film. The distribution of atoms in the superstructure is determined by the substrate potential amplitude of the substrate potential.

TWOE Code: An Efficient Tool for Explicit Partition of Coupled Cluster and Configuration Interaction Energies into Atomic and Diatomic Contributions

The efficient implementation of the TWOE program for evaluating the atomic and interatomic energy components at post-HF level was developed. The systematic convergence of these terms up to a near full-CI limit was performed for the first time for a series of coupled cluster methods: CCSD → CCSDT → CCSDTQ → CCSDTQP. A comparison with corresponding CI approaches (up to fifth excitation level) is additionally discussed. For a set of diatomic systems, it was demonstrated that, along with a full molecular energy convergence, all its components are also converged but with different patterns. It was found that not all components are decreased in their values at increasing computational rank. For instance, atomic energy parts are decreased while interatomic (interaction) energies are increased as the limiting level is approached. Two schemes were employed for atomic partition of molecules: the Baders approach and planes dissection. Influence of dynamical correlation effects on atomic energy components was analyzed in detail. Current TWOE implementation allows one, in principle, to work with any ab initio method providing the two-particle density matrix. It is believed that the developed program will be a useful tool for a real space energy decomposition that helps to reveal the most peculiar points in the structure of the total and correlation energies of a molecule.

Bonding and Aromaticity in Electron-Rich Boron and Aluminum Clusters.

In this work bonding and aromaticity of triply bonded atoms of group 13 elements (M≡M, M = B and Al) in recently characterized B2Al3-, Na3Al2-, and Na4Al2 are studied. Here, I show that although molecular orbital-based analyses characterize triple bonds, the electropositive nature of group 13 elements gives these bonds unique characteristics. The bond orders derived from the delocalization index, topology of the electron density, and local characteristics of (3, -1) critical points, as defined within the context of quantum theory of atoms in molecules, do not conform with those of ordinary triple bonds. In Na3Al2- and Na4Al2 clusters non-nuclear attractors form between the electropositive Al atoms acting like pseudo atoms. The bond between boron atoms in B2Al3- is more similar to an ordinary triple covalent bond benefiting from the exchange-correlation component of the interatomic interaction energy as defined via interacting quantum atom theory. However, extreme electrostatic repulsion between negatively charged boron atoms attenuates this bond. Finally, current density analysis suggests that B2Al3- is a magnetic aromatic system, nearly 50% more aromatic compared to benzene.

Effect of ligand conjugation site on the micellization of Bio-Targeted PLGA-Based nanohybrids: A computational biology approach

In this study, the effect of ligand binding position on the polymeric nanoparticles (NPs) is based on poly(lactic-co-glycolic acid) (PLGA) with two different polymer chain length at the atomistic level was presented. We explored the conjugation of riboflavin (RF) ligand from the end of the ribityl chain (N-10) to the polymer strands as well as from the amine group on the isoalloxazine head (N-3). The energy interactions for all samples revealed that the NPs containing ligands from N-10 positions have higher total attraction energies and lower stability in comparison with their peers conjugated from N-3. As NPs containing RF conjugated from N-3 exhibit the lower energy level with 20% and 10% of RF-containing composition for lower and higher. The introduction of RF from the N-10 position in any composition has increased the energy level of nanocarriers. The results of Gibb's free energy confirm the interatomic interaction energies trend where the lowest Gibbs free energy level for N-3 NPs occurs at 20 and 10% of RF-containing polymer content for PLGA10- and PLGA11- based NPs. Furthermore, with N-10 samples based on both polymers, non-targeted models form the stablest particles in each category. These findings are further confirmed with molecular docking analysis which revealed affinity energy of RF toward polymer chain from N-3 and N-10 are −981.57 kJ/mole and −298.23 kJ/mole, respectively. This in-silico study paves the new way for molecular engineering of the bio-responsive PLGA-PEG-RF micelles and can be used to nanoscale tunning of smart carriers used in cancer treatment. Communicated by Ramaswamy H. Sarma

Pairwise interatomic interaction in alloys

The concepts of the physics of metallic alloys regarding the driving forces of diffusion phase transformations, the nature of solid solutions, the chemical interatomic interaction energy, the principles of plotting phase diagrams, and the principles of heat treatment of alloys are critically reviewed. The ordering–separation phase transition, which is caused by the recently detected property of alloys to change the sign of chemical interatomic interaction when temperature changes, is shown to change these concepts radically. The experimental data that fully support the ideas advanced in this review are presented (comprehensive experimental data for Ni–Cr and Co3V alloys are presented). The problem of the diffusion processes in multicomponent alloys is considered in detail. They are shown to occur according to the model of pairwise chemical interatomic interaction. The formation of diffusion couples in a multicomponent alloy begins in its liquid state. When temperature decreases, this process occurs in each diffusion couple similarly to the phase formation in the corresponding binary alloys.

Simulation of the NaGd(MoO4)2–NaEu(MoO4)2 and Na2Gd4(MoO4)7–Na2Eu4(MoO4)7 Solid Solutions by the Interatomic Potential Method

Simulation of the solid solutions in the system of double sodium–gadolinium and sodium–europium molybdates, which are promising matrices for solid state lasers and phosphors has been carried out by the method of interatomic potentials. Two types of solid solutions have been studied, one of which contains finite components corresponding to the stoichiometric NaGd(MoO4)2–NaEu(MoO4)2 compositions with statistical distribution of cations in the crystal lattice. Another object is a cation-deficient Na2Gd4(MoO4)7–Na2Eu4(MoO4)7 system, in which we have examined the variants of statistical distribution and partial ordering of cations over structural positions. Atomistic simulation has been performed using the GULP 4.0.1 software package (General Utility Lattice Program). It is shown that when we pass from sodium-gadolinium molybdate to sodium-europium molybdate, both of stoichiometric and cation-deficient compositions, an increase in the unit cell volume is observed, while the density of the crystal, the energy of interatomic interactions in the structure, the vibrational entropy and the heat capacity decrease along with increasing europium content. The energy of interatomic interactions in the structure for cation-deficient solid solutions is less than for stoichiometric ones. Other aforementioned characteristics for cation-deficient solid solutions have greater values than for stoichiometric ones. The role of cluster europium centers in concentration quenching in NaGd(MoO4)2–NaEu(MoO4)2 solid solutions has been examined.

Моделирование твердых растворов NaGd(MoO-=SUB=-4-=/SUB=-)-=SUB=-2-=/SUB=-- NaEu(MoO-=SUB=-4-=/SUB=-)-=SUB=-2-=/SUB=- и Na-=SUB=-2-=/SUB=-Gd-=SUB=-4-=/SUB=-(MoO-=SUB=-4-=/SUB=-)-=SUB=-7-=/SUB=--Na-=SUB=-2-=/SUB=-Eu-=SUB=-4-=/SUB=-(MoO-=SUB=-4-=/SUB=-)-=SUB=-7-=/SUB=- методом межатомных потенциалов

AbstractSimulation of the solid solutions in the system of double sodium–gadolinium and sodium–europium molybdates, which are promising matrices for solid state lasers and phosphors has been carried out by the method of interatomic potentials. Two types of solid solutions have been studied, one of which contains finite components corresponding to the stoichiometric NaGd(MoO_4)_2–NaEu(MoO_4)_2 compositions with statistical distribution of cations in the crystal lattice. Another object is a cation-deficient Na_2Gd_4(MoO_4)_7–Na_2Eu_4(MoO_4)_7 system, in which we have examined the variants of statistical distribution and partial ordering of cations over structural positions. Atomistic simulation has been performed using the GULP 4.0.1 software package (General Utility Lattice Program). It is shown that when we pass from sodium-gadolinium molybdate to sodium-europium molybdate, both of stoichiometric and cation-deficient compositions, an increase in the unit cell volume is observed, while the density of the crystal, the energy of interatomic interactions in the structure, the vibrational entropy and the heat capacity decrease along with increasing europium content. The energy of interatomic interactions in the structure for cation-deficient solid solutions is less than for stoichiometric ones. Other aforementioned characteristics for cation-deficient solid solutions have greater values than for stoichiometric ones. The role of cluster europium centers in concentration quenching in NaGd(MoO_4)_2–NaEu(MoO_4)_2 solid solutions has been examined.

Resonance interaction between two two-level entangled atoms in cosmic string spacetime

We investigate the influence of a cosmic string on the resonance interaction between two identical two-level entangled atoms mediated by a fluctuating electromagnetic field in the vacuum state. We separately consider two representative configurations of the system and give the corresponding analytical expressions of interatomic interaction energy for the special case of a ‘quantized string’ with integer ν. The results indicate that the resonance interatomic interaction energy depends crucially upon the relative position between the two atoms, their respective locations and polarizabilities relative to the string. As these parameters change, we show that the presence of the cosmic string can enhance or weaken and even produce or prohibit the interatomic resonance interaction. Our work suggests that the nontrivial spacetime topology due to the cosmic string can influence the field-mediated interatomic interaction significantly.

Resonance interaction between uniformly rotating two-level entangled atoms

We investigate the influence of acceleration and boundaries on the resonance interaction between two identical two-level entangled atoms in synchronous circular motions mediated by a fluctuating massless quantum scalar field. In the ultra-relativistic limit, we give the analytical results of the resonance interaction energy either in the absence or in the presence of a reflecting plane boundary. Our results indicate that the interatomic resonance interaction energy depends on the atomic intrinsic energy level spacing, the atomic acceleration, the interatomic separation, and the distance of the atoms from the boundary. By adjusting these parameters, the resonance interatomic force can be either enhanced or weakened and even its direction can be altered as compared with the case of two inertial entangled atoms in an unbounded Minkowski spacetime. Our work clearly suggests that the resonance interatomic interaction can be regulated and controlled significantly by changing the atomic motion state and the field’s boundary condition.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy.

Nearly all standard force fields employ the "sum-of-spheres" approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this "atomic-level anisotropy" can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmark MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for "next-generation" force field development.

Effect of the allotropic transition in titanium on its interatomic interaction energy

The variation of interatomic interaction energy during allotropic transition in titanium is established by analyzing the stress and temperature dependences of durability. This energy is ≈458 kJ/mol in bodycentered β-Ti at a temperature of T > 1155 K, which agrees well with the titanium sublimation heat, and ≈305 kJ/mol in hexagonal close-packed α-Ti at T < 1155 K. Literature data confirming the conclusions drawn are discussed.

A multipolar approach to the interatomic covalent interaction energy.

Interatomic exchange-correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities ρA(r) and ρB(r), we examine in this work the mp approach to approximate the interatomic exchange-correlation (xc) energies of the Interacting Quantum Atoms method. We show that the full xc mp series is quickly divergent for directly bonded atoms (1-2 pairs) albeit it works reasonably well most times for 1- n (n > 2) interactions. As with conventional perturbation theory, we show numerically that the xc series is asymptotically convergent and that, a truncated xc mp approximation retaining terms up to l1+l2=2 usually gives relatively accurate results, sometimes even for directly bonded atoms. Our findings are supported by extensive numerical analyses on a variety of systems that range from several standard hydrogen bonded dimers to typically covalent or aromatic molecules. The exact algebraic relationship between the monopole-monopole xc mp term and the inter-atomic bond order, as measured by the delocalization index of the quantum theory of atoms in molecules, is also established. © 2017 Wiley Periodicals, Inc.

The relationship between thermodynamic properties and local atomic structure of Al-TM (TM = Mn, Fe, Co, Ni, Cu) melts

ABSTRACTThe relationship between structure and thermodynamic properties of Al- transition metal (TM) (TM = Mn, Fe, Co, Ni, Cu) melts had been studied by using the results of X-ray diffraction experiments, reverse Monte Carlo simulations and the model of ideal associated solution (MIAS). It was considered that local atomic structure of melts is determined by dense non-crystalline atomic packing and energy of interatomic interactions. This allowed to choose the types of associates for the MIAS. It is shown that the prominent role of the atomic packing factor in the Al-Mn, Al-Fe melts leads to correlation between the local atomic ordering of melts and the one of relevant polytetrahedral phases and defines a set of associates. Strengthening of heteroatomic interactions in the Al-Co, Al-Ni melts leads to an increase of the energy factor role in determining their structure and properties that reduces the number of associates from three for the Al-Mn melts to one for the Al-Ni.

Geometric method for large Morse clusters formation

This paper describes a geometrically founded method for constructing the initial configuration of a complete icosahedral structure of an atomic cluster. The method finds a global minimum of the cluster energy as a result of a single local optimization procedure. The method is based on the proposed algorithm for the stratified accommodation of atom centers, that allows one to form structural configurations commonly found among the clusters with global minimum of interatomic interaction energy. This algorithm provides the ability to build a spatial configuration of the dense packing of spheres for the formation of icosahedral and decahedral structures, as well as building complete icosahedrons with a large number of atoms. With the proposed method, we have reached the global minima for large Morse clusters (N = 817, 923, and 1415), which is a record for Morse clusters with r = 6.

COMPUTER SIMULATION OF FUNCTIONALIZED CARBON NANOTUBES AND GRAPHENE

Nanomaterials based on carbon nanotubes (CNT) and graphenes attract a lot of attention of researchers as the materials capable to raise the development of various industries to the new level, and first of all, of the chemical and electronic sectors. In addition to known experimental methods, new nanosystems are widely studied using advanced tools of quantum-chemical approaches. Modern theoretical methods are of great interest due to their ability to interpret known experimental facts and predict properties of non-synthesized compounds yet. This paper reviews results of theoretical studies performed using the density functional theory (DFT) methods to obtain data on the structure and electronic properties of single-walled CNT and graphene, modified with various impurities, with covalent-ionic and non-covalent binding mechanisms. New computational methods are briefly described that are currently employed to treat the dispersion interaction and enhance possibilities of DFT tools in systems where the van der Waals forces play a significant role. Particular attention is paid to the characteristics of carbon nanomaterials containing technologically important hydroxyl, carboxyl and amino groups. It is shown that the specific peculiarity of band structures of discussed in the literature CNT functionalized by OH, COOH, NHn and CONH2 groups is the partially occupied band in the neighborhood of the Fermi level, which directly affects the CNT conductivity. Modification of graphene layers is analyzed that interact with hydrogen, fluorine, bases of nucleic acids and the metal substrate surface. We also provide accuracy estimates for the calculations of interatomic bond lengths, interaction energy and band gap carried out in the literature using a variety of DFT approximations.