Atomic Potentials Research Articles

Phenomenological description of the acidity of the citric acid and its deprotonated species: informational-theoretical study.

In spite of the fact that molecular acidity is a fundamental physicochemical property of molecular systems, the vast majority of theoretical studies have focused attention on monoprotic acids and on the prediction of pKa's. Polyprotic acids, represent a challenge for electronic structure calculations since the multiple acidic sites result in a vast group of species with different conformations and reactivities. In this work, Information-theoretic (IT) concepts of localizability, order and uniformity are applied to the Citric Acid and its deprotonated species through the one-electron density functionals: Shannon entropy (S), Fisher information (I) and Disequilibrium (D), respectively. We pursue the goal of characterizing the acidity of the aforementioned species with the aim to associate the IT concepts to chemical features such as the polarizability of the protonated/deprotonated species, the liability of the acidic sites, atomic electrostatic potentials, covalent bonding. IT analyses looks very promising for future studies on the acidity of specific deprotonation-sites of polyprotic acids. Density functional theory (DFT) calculations were performed with Gaussian 09 program. A sensitivity analysis of the IT-measures was performed for the citric acid and the citrate using B3LYP, B3PW91, BPW91, M05-2X, M06-2X and PBEPBE functionals with the 6-311++g(3df,2p), 6-311++g(d,p), 6.311+g(d,p) and aug-cc-pVDZ basis sets. The rest of the analysis was performed with the M05-2X/6-311+G(d,p) level of theory. Additionally, aqueous media was considered by use of the SMD solvent model. The IT-measures were calculated using a suite of programs developed in our laboratory jointly with the DGRID software package.

Quantum computational, Spectroscopic investigations on benzofuranylcarbonylpyrazolopyridine by DFT/TD-DFT: Synthesis, Structure, NBO and NLO research

Reaction of 4-methoxy-5-oxo-5H-furo[3,2-g] chromene-6-carboxaldehyde (1) with 5-amino-2,4-dihydro-3H-pyrazol-3-one (2) afforded the novel 5-(6-hydroxy-4-methoxy-1-benzofuran-5-ylcarbonyl)-3-hydroxy-1H-pyrazolo[3,4-b]pyridine (3, BFCPP). The experimental and theoretical quantum computations (optimized structure, IR, NMR and UV-Vis.) investigation of the current compound were performed using DFT theory at B3LYP functional and 6–311++G(d,p) basis set. The complete analysis of the vibrational spectra was taken with the aid of normal coordinate analysis followed by scaled quantum mechanical force field methodology. The theoretical NMR was achieved in DMSO-d6 as a solvent, while the IR and optimized calculations were done in the gas phase. A kind of solutions were used to discover the UV-Visible spectrum using the TD-DFT method. The stability of the current molecule occurred from hyper conjugative interactions leading to its nonlinear optical activity. Also, the charge delocalization was analyzed using natural bond orbital technique. Mulliken atomic charge and molecular electrostatic potential (MEP) are also calculated. HOMO–LUMO energy gap value indicates the probability of charge transfer within the molecule. The thermodynamic properties at different temperatures are also analyzed.

Etching Kinetics of Nanodiamond Seeds in the Early Stages of CVD Diamond Growth.

We present an experimental study on the etching of detonation nanodiamond (DND) seeds during typical microwave chemical vapor deposition (MWCVD) conditions leading to ultra-thin diamond film formation, which is fundamental for many technological applications. The temporal evolution of the surface density of seeds on the Si(100) substrate has been assessed by scanning electron microscopy (SEM). The resulting kinetics have been explained in the framework of a model based on the effect of the particle size, according to the Young-Laplace equation, on both chemical potential of carbon atoms in DND and activation energy of the reaction with atomic hydrogen. The model describes the experimental kinetics of seeds' disappearance by assuming that nanodiamond particles with a size smaller than a "critical radius," r*, are etched away while those greater than r* can grow. Finally, the model allows to estimate the rate coefficients for growth and etching from the experimental kinetics.

Energy reemission and possible radiosensitizing effect caused by the cascade decay of single vacancies in the K, L, M, and N shells of atomic silver

Cascade decays of single vacancies in the K, L, M, and N shells of the silver atom are studied using the method of straightforward construction and analysis of the cascade de-excitation trees with inclusion of additional shake-off ejections of outer-shell electrons caused by the change of atomic core potential due to cascade transitions. The spectra of the cascade-produced electrons and photons emitted upon the decay of single vacancies in 1s1/2 to 4p3/2 subshells are calculated. For each initial vacancy, the energies absorbed by the silver atom itself, and those carried away by cascade electrons and photons, are calculated. Absorption of energy by the silver atom itself is only significant upon N- and M-shell ionization (49–66% and 18–36%, respectively), i.e. in the UV to soft X-ray range. After L- to N-ionization, most of the acquired energy is reemitted with cascade electrons, respective portions making 81–85% during L-ionization, 62–82% during M-ionization, and 34–51% during N-ionization. Reemission of energy with cascade photons is dominant after K-ionization (76%). When silver atoms are used as radiosensitizing agents in radiotherapy, cascade electrons play the principal role in the energy transfer to organism tissues. Due to small free paths in the organic medium, they give their energy to the environment in rather small volumes inside a particular cell where they are placed. As for the photons emitted after K-ionization, they transfer energy to the medium in much larger volumes, and with much smaller absorbed doses.

Optimized Quantum Drude Oscillators for Atomic and Molecular Response Properties.

The quantum Drude oscillator (QDO) is an efficient yet accurate coarse-grained approach that has been widely used to model electronic and optical response properties of atoms and molecules as well as polarization and dispersion interactions between them. Three effective parameters (frequency, mass, and charge) fully characterize the QDO Hamiltonian and are adjusted to reproduce response properties. However, the soaring success of coupled QDOs for many-atom systems remains fundamentally unexplained, and the optimal mapping between atoms/molecules and oscillators has not been established. Here we present an optimized parametrization (OQDO) where the parameters are fixed by using only dipolar properties. For the periodic table of elements as well as small molecules, our model accurately reproduces atomic (spatial) polarization potentials and multipolar dispersion coefficients, elucidating the high promise of the presented model in the development of next-generation quantum-mechanical force fields for (bio)molecular simulations.

Dynamic interaction between dislocations and obstacles in bcc iron based on atomic potentials derived using neural networks

Dynamic interaction between dislocations and obstacles in bcc iron based on atomic potentials derived using neural networks

Study the change of some physical and chemical properties of TiN under high pressure

The pressure equation of state of Titanium nitrate TiN was investigated in the current work using two equations of state (EOS) from the literature, including the Barden EOS and the Birch-Murnaghan EOS, whereas the Bardeen EOS, which is based on interstellar atomic potentials, and the Birch-Murnaghan EOS, which is based on the solid mechanics notion of finite strain. The EOSs were processed to identify the impacts of high pressure on the bulk modulus B, Debye temperature θD and lattice constant a, which are characterizations of TiN. Ultimately, a fair comparison of the current findings with the first principle approximation and the generalized gradient approximation approach was conducted, and a perfect agreement was found. It was demonstrated that TiN EOS can be used to calibrate high pressure for chemical compound TiN .

Mesomorphic and computational evaluation of C[tbnd]N‧‧‧I halogen bonded complexes of 4-alkoxy-4′-cyanobiphenyls systems with 1,6- diiodoperfluorohexane

Thermotropic halogen bonded (XB) liquid crystalline complex (A-n XB) of 4-alkoxy-4′- cyano biphenyls (A-n) systems containing nitrile (-CN) group with variable alkoxy chain length (-CnH2n+1, where n = 3 to 10) acting as halogen bond acceptor with 1,6-diiodoperfluorohexane, (I-atom) acting as halogen bond donor were prepared by the liquid-assisted grinding method. The A-n XB complex formations, through CN‧‧‧I XB interactions, were established by the FTIR, Raman, PXRD, polarizing optical microscope (POM) with hot stage, DSC and TGA techniques. Further, POM study of these homologous XB complex series showed liquid crystalline phases with a alteration of (1–10 °C) compared to their respective parent mesogenic molecules. The computational study was carried out using Frontier Molecular Orbitals (FMOs), Molecular Electrostatic Potential (MEP), Non-covalent interactions (NCI) and Quantum theory of atoms in molecule (QTAIM) analysis to evaluate the reactivity parameters and strength of XB in the complexes.

Investigating the Hydroxyl Reorientation in Hydroxyapatite Using Machine Learning Potentials

The chain or network of hydroxyl groups (OH–) is crucial in determining the structure and function of materials, especially in hydroxyapatite (HAP), a mineral essential for human bones. HAP exhibits a linear arrangement of OH– along the c-axis, which determines its phase transition, dielectric, and piezoelectric properties. However, the mechanism underlying OH– reorientation with temperature remains elusive using traditional experimental and theoretical methods. To address this, we developed a machine learning atomistic potential for HAP using an active learning algorithm, which achieved density functional theory-level accuracy in describing OH– of HAP. The machine learning molecular dynamics simulations revealed that the reorientation of OH– in HAP with temperature occurs through ″flip-flop″ motion, rather than proton transfer. This process starts at about 473 K and accelerates with increasing temperature, consistent with the experimentally observed transformation from the monoclinic to hexagonal phase. At 973 K and above, the rapid “flip-flop” reorientation process leads to an undetermined orientation of OH– along the c-axis. These findings highlight the potential of machine learning-accelerated molecular dynamics simulations in unraveling the microscopic mechanisms underlying the hydrogen bond network in complex multicomponent materials at the atomic level.

Superexchange-induced Pt-O-Ti3+ site on single photocatalyst for efficient H2 production with organics degradation in wastewater

Efficient photocatalytic H2 production from wastewater instead of pure water is a dual solution to the environmental and energy crisis, but due to the rapid recombination of photoinduced charge in the photocatalyst and inevitable electron depletion caused by organic pollutants, a significant challenge of dual-functional photocatalysis (simultaneous oxidative and reductive reactions) in single catalyst is designing spatial separation path for photogenerated charges at atomic level. Here, we designed a Pt-doped BaTiO3 single catalyst with oxygen vacancies (BTPOv) that features Pt-O-Ti3+ short charge separation site, which enables excellent H2 production performance (1519 μmol·g-1·h-1) while oxidizing moxifloxacin (k = 0.048 min-1), almost 43 and 98 times than that of pristine BaTiO3 (35 μmol·g-1·h-1 and k = 0.00049 min-1). The efficient charge separation path is demonstrated that the oxygen vacancies extract photoinduced charge from photocatalyst to catalytic surface, and the adjacent Ti3+ defects allow rapid migration of electrons to Pt atoms through the superexchange effect for H* adsorption and reduction, while the holes will be confined in Ti3+ defects for oxidation of moxifloxacin. Impressively, the BTPOv shows an exceptional atomic economy and potential for practical applications, a best H2 production TOF (370.4 h-1) among the recent reported dual-functional photocatalysts and exhibiting excellent H2 production activity in multiple types of wastewaters.

Engineering single Pt Atoms on hybrid amorphous/crystalline CoFe layered double hydroxide accelerates the charge transfer for solar water splitting

Owing to the sluggish kinetics suppressing the oxygen evolution reaction, developing single atoms (SAs) catalyst oxygen evolution reaction catalysts on photoelectrodes is challenging for accelerating charge separation and transfer on photoelectrochemical water splitting. Herein, we elaborately demonstrate the decoration of platinum SAs on hybrid crystalline/amorphous CoFe LDH, and assess the role of SAs on the photogenerated charge carrier separation and transport of photoelectrode. The crystalline/amorphous CoFe LDH is capable of embedding the platinum SAs in its structure by modulating the electronic structure. The single atoms platinum in catalyst enables the effective charge transfer and suppress the charge recombination of the BiVO4 photoelectrode. The SAs Pt/AC-CoFe catalyst delivers an overpotential of 230 mV at 10 mA cm−2, obviously lower than those of AC-CoFe without the introduction of SAs Pt. The SAs Pt/AC-CoFe/BiVO4 exhibits an excellent PEC performance, a current density of 5.14 mA cm−1 obtained at 1.23 VRHE in 1 M KBi under one sun illumination with a stability of 20 h. This work proposes a rational design of single atoms catalysts decorated on semiconductors and reveals the potential of the single atoms to boost charge carrier kinetics.

An artificial neural network potential for uranium metal at low pressures

Based on machine learning, the high-dimensional fitting of potential energy surfaces under the framework of first principles provides density-functional accuracy of atomic interaction potential for high-precision and large-scale simulation of alloy materials. In this paper, we obtained the high-dimensional neural network (NN) potential function of uranium metal by training a large amount of first-principles calculated data. The lattice constants of uranium metal with different crystal structures, the elastic constants, and the anisotropy of lattice expansion of alpha-uranium obtained based on this potential function are highly consistent with first-principles calculation or experimental data. In addition, the calculated formation energy of vacancies in alpha- and beta-uranium also matches the first-principles calculation. The calculated site of the most stable self-interstitial and its formation energy is in good agreement with the findings from density functional theory (DFT) calculations. These results show that our potential function can be used for further large-scale molecular dynamics simulation studies of uranium metal at low pressures, and provides the basis for further construction of potential model suitable for a wide range of pressures.

Coulomb distorted plane wave-Volkov ansatz for strong-field ionization

In the strong-field ionization of atomic and molecular systems, the photoelectron is exposed to the long-range Coulomb force which is neglected in the standard theories based on the strong-field approximation (SFA). We introduce an ansatz which takes into account the Coulomb effects and at the same time is as simple as the standard SFA. Our Coulomb distorted plane wave-Volkov approximation provides analytical expressions for the relevant matrix elements. We also present a generalization of this approximation taking into account first-order term of an expansion in the atomic potential. Similarly as in the standard improved SFA, this generalized approximation describes well the rescattering plateau and the cutoff observed in the photoelectron spectra. Our new approximation is illustrated with numerical examples of strong-field ionization of the hydrogen atom exposed to linearly and circularly polarized laser pulses. The spectra obtained are slightly flatten in comparison with the SFA spectra and this effect is stronger for shorter laser wavelengths.

Evolution of large Aβ16-22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events.

Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from β-rich aggregates of Y and elongated topologies predicted by coarse-grained simulations and consisting of more than 100 Aβ16-22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 μs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta-strand structuring with a dominance of antiparallel beta-sheets over parallel beta-sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aβ sequences.

Interaction Potential of Protons and Hydrogen Atoms with Metals

Interaction Potential of Protons and Hydrogen Atoms with Metals

ænet-PyTorch: A GPU-supported implementation for machine learning atomic potentials training.

In this work, we present ænet-PyTorch, a PyTorch-based implementation for training artificial neural network-based machine learning interatomic potentials. Developed as an extension of the atomic energy network (ænet), ænet-PyTorch provides access to all the tools included in ænet for the application and usage of the potentials. The package has been designed as an alternative to the internal training capabilities of ænet, leveraging the power of graphic processing units to facilitate direct training on forces in addition to energies. This leads to a substantial reduction of the training time by one to two orders of magnitude compared to the central processing unit implementation, enabling direct training on forces for systems beyond small molecules. Here, we demonstrate the main features of ænet-PyTorch and show its performance on open databases. Our results show that training on all the force information within a dataset is not necessary, and including between 10% and 20% of the force information is sufficient to achieve optimally accurate interatomic potentials with the least computational resources.

Crystal effects in the vibrational spectra of one-dimensional molecular spin crossover crystals using molecular dynamics simulations

We use molecular dynamics simulations to model the iron phonon density of states (pDOS) of a spin crossover (SCO) crystal built from 39-nuclear [Fe(atrz)_3Cl_2] chains (atrz = 4-amino-1,2,4-triazole). This is possible by using an atomistic potential that depends on the spin state of the Fe atoms. While quantum-chemical methods are able to provide data on isolated SCO molecules, the computational costs necessitate the use of classical simulations to calculate crystal effects on the spectra. Data are provided for a high-spin (HS) crystal, in which all Fe atoms are in their HS state, and a low-spin (LS) crystal. HS and LS crystals show distinctively different spectra that are in agreement with experimental data. Compared to the single-molecule spectra, the crystal spectra show several distinctive features: (i) The spectra are smoother, and the main peaks are slightly reduced in amplitude. (ii) The effect of intermolecular interactions shows up in additional structure at long-wavelengths. Good agreement between experimental and simulated phonon spectra is observed. The lattice-dynamics analysis of the low-energy pDOS allows to extract the temperature dependence of the vibrational entropy of the LS and HS crystals. Our study thus provides novel information about the crystal effects in SCO crystals.

Unraveling the Vibrational Spectral Signatures of a Dislocated H Atom in Model Proton-Coupled Electron Transfer Dyad Systems.

Phenol-benzimidazole and phenol-pyridine proton-coupled electron transfer (PCET) dyad systems are computationally investigated to resolve the origins of the asymmetrically broadened H-bonded OH stretch transitions that have been previously reported using cryogenic ion vibrational spectroscopy in the ground electronic state. Two-dimensional (2D) potentials describing the strongly shared H atom are predicted to be very shallow along the H atom transfer coordinate, enabling dislocation of the H atom between the donor and acceptor groups upon excitation of the OH vibrational modes. These soft H atom potentials result in strong coupling between the OH modes, which exhibit significant bend-stretch mixing, and a large number of normal mode coordinates. Vibrational spectra are calculated using a Hamiltonian that linearly and quadratically couples the H atom potentials to over two dozen of the most strongly coupled normal modes treated at the harmonic level. The calculated vibrational spectra qualitatively reproduce the asymmetric shape and breadth of the experimentally observed bands in the 2300-3000 cm-1 range. Interestingly, these transitions fall well above the predicted OH stretch fundamentals, which are computed to be surprisingly red-shifted (<2000 cm-1). Time-dependent calculations predict rapid (<100 fs) relaxation of the excited OH modes and instant response from the lower-frequency normal modes, corroborating the strong coupling predicted by the model Hamiltonian. The results highlight a unique broadening mechanism and complicated anharmonic effects present within these biologically relevant PCET model systems.

Comprehensive structural changes in nanoscale-deformed silicon modelled with an integrated atomic potential

In spite of remarkable developments in the field of advanced materials, silicon remains one of the foremost semiconductors of the day. Of enduring relevance to science and technology is silicon's nanomechanical behaviour including phase transformation, amorphization and dislocations generation, particularly in the context of molecular dynamics and materials research. So far, comprehensive modelling of the whole cycle of events in silicon during nanoscale deformation has not been possible, however, due to the limitations inherent in the existing interatomic potentials. This paper examines how well an unconventional combination of two well-known potentials - the Tersoff and Stillinger-Weber - can perform in simulating that complexity. Our model indicates that an irreversible deformation of silicon (Si-I) is set in motion by a transformation to a non-diamond structure (Si-nd), and followed by a subsequent transition to the Si-II and Si-XII phases (Si-1→Si-nd→Si-II→Si-XII). This leads to the generation of dislocations spreading outwards from the incubation zone. In effect, our simulations parallel the structural changes detected experimentally in the deformed material. This includes both the experimentally observed sequence of phase transitions and dislocation activity, which - taken together - neither the Tersoff nor Stillinger-Weber, or indeed any other available Si interatomic potential, is able to achieve in its own right. Notably, the Si-XII phase was not discerned by any of the previous computational models, which points towards the effectiveness of our integrated approach to forecasting novel phenomena discovered by advanced structure examinations. Last not least, our method satisfies the demand for a quick means to construct potentials by opening up the huge library of existing models to new applications in various branches of materials science.

New approaches to study of mismatched interfaces structure on low-index surfaces by molecular dynamics simulation

We used molecular dynamics simulations to study the structure of mismatched Al/Ni and Ag/Cu interfaces, considering low-index surfaces of the substrate. Embedded Atom Potentials are being employed to mimic atomic interactions between the different elements. The effect of the substrate orientation on the adlayer structure is investigated. The results showed that, on the (111) substrate, the adlayer presents a coincidence site lattice characterized by a rotation (labeled α) with respect to the substrate. This coincidence site lattice may contain dislocations and twin boundary that can be produced by the occurrence of a twin spirals (with opposite directions). To accommodate the adlayer deposition on the substrate, a slight shuffling of some atoms occurs in the substrate and leads to a rectangular structures producing a dislocation. Furthermore, on the (001) substrate, the accommodation of the triangular structure on the square lattice (substrate) is produced by a shift of some atomic rows producing a dislocation. But, the agglomeration of several square structures of 2d shape gives rise to a polycrystal delimited by a disclination forming grain boundaries and vacancies. However, the inward adsorption on the (110) substrate restricts the space of extension of adsorbed atoms, producing linear cracks. The relaxation of atoms adsorbed on these cracks change the linear shape of vacancies towards a staircase structure.