DFT Data Research Articles

Cluster-MLP: An Active Learning Genetic Algorithm Framework for Accelerated Discovery of Global Minimum Configurations of Pure and Alloyed Nanoclusters.

Structural characterization of nanoclusters is one of the major challenges in nanocluster modeling owing to the multitude of possible configurations of arrangement of cluster atoms. The genetic algorithm (GA), a class of evolutionary algorithms based on the principles of natural evolution, is a commonly employed search method for locating the global minimum configuration of nanoclusters. Although a GA search at the DFT level is required for the accurate description of a potential energy surface to arrive at the correct global minimum configuration of nanoclusters, computationally expensive DFT evaluation of the significantly larger number of cluster geometries limits its practicability. Recently, machine learning potentials (MLP) that are learned from DFT calculations gained significant attention as computationally cheap alternative options that provide DFT level accuracy. As the accuracy of the MLP predictions is dependent on the quality and quantity of the training DFT data, active learning (AL) strategies have gained significant momentum to bypass the need of large and representative training data. In this application note, we present Cluster-MLP, an on-the-fly active learning genetic algorithm framework that employs the Flare++ machine learning potential (MLP) for accelerating the GA search for global minima of pure and alloyed nanoclusters. We have used a modified version the Birmingham parallel genetic algorithm (BPGA) for the nanocluster GA search which is then incorporated into distributed evolutionary algorithms in Python (DEAP), an evolutionary computational framework for fast prototyping or technical experiments. We have shown that the incorporation of the AL framework in the BPGA significantly reduced the computationally expensive DFT calculations. Moreover, we have shown that both the AL-GA and DFT-GA predict the same global minima for all the clusters we tested.

A machine-learning interatomic potential to understand the anisotropic fracture behavior of BaZrO3 material

The complex operating environment severely tests the mechanical stability of the electrolyte material BaZrO3 (BZO), which affects the performance of solid oxide fuel cells(SOFCs). Molecular dynamics (MD) simulation provides an efficient method to research the mechanical behavior of nanocrystalline materials. In the interest of researching the mechanical behavior of BZO materials utilizing a machine learning (ML) MD approach, this article has established the most effective ML potential with DFT reliability. By contrasting the lattice constants and elastic constants with the DFT data, the precision of the potential was confirmed. By simulating the uniaxial tensile mechanical behavior of the BZO models without crack and with a central crack in the crystal orientation of [100] and [110], we found that the BZO material has a significant anisotropic property. In the crack-free model, the BZO crack propagation mode in the [100] crystal orientation is a shear fracture. The central microcrack tilts downward and expands symmetrically in the [110] crystal-oriented BZO model. When the initial structure with a central crack, the fracture mode changes significantly, and in both crystal orientations, the crack fracture along the BaO plane, the crack expands horizontally in the BZO model in the [100] crystal orientation and the crack expands zigzag in the BZO model in the [110] crystal orientation. The calculations of fracture strength, critical energy release rate, and fracture toughness show that the [110] crystal-oriented BZO has a stronger resistance to fracture than the [100] crystal-oriented BZO model.

Ab initio calculations and empirical potential assessments of the energy and structure of symmetric tilt grain boundaries in tungsten

Molecular statics/dynamics (MS/MD) based on empirical interatomic potentials (IAPs) is an effective means for conducting grain boundary (GB) related studies. The accuracy of these MS/MD simulations, however, can be greatly affected by the IAP used. Unfortunately, the large discrepancies between the ab-initio values make it difficult to evaluate, improve and further develop IAPs. Motivated by this issue, in the present work we perform a systematic investigation of 〈100〉 and 〈110〉 symmetric tilt GBs in tungsten (W) via atomistic simulations, including the stable structure, GB energy, work of separation, excess volume, and vacancy formation energy. We here use a two-step relaxation process, initially obtaining the candidate structures from MS and then performing DFT validation of these structures to determine the ground state structure, where six empirical IAPs and four exchange–correlation (xc) functionals are used. And the step-like feature is revealed that can be used to reduce the cost of time-consuming optimization processes. Taking the results yielded by PBEsol xc-functional as a benchmark, it is shown that for the same xc-functional, the relative errors of GB energy and work of separation are almost identical, independent of the GB character. The performance of six typical empirical IAPs considered for W is also evaluated by comparing it with the DFT data. The quantities chosen for the comparison include the structure and energetic properties of GBs, as mentioned before. We demonstrate that these empirical IAPs tend to better describe only part of the properties of GBs; for example, some IAPs can predict the energetic properties well, while others can better describe the structure. This suggests that a fully reliable description of GBs remains an elusive objective, requiring further efforts in the development and optimization of the IAP.

Exploring Configurations of Nanocrystal Ligands Using Machine-Learned Force Fields.

Semiconducting nanocrystals passivated with organic ligands have emerged as a powerful platform for light harvesting, light-driven chemical reactions, and sensing. Due to their complexity and size, little structural information is available from experiments, making these systems challenging to model computationally. Here, we develop a machine-learned force field trained on DFT data and use it to investigate the surface chemistry of a PbS nanocrystal interfaced with acetate ligands. In doing so, we go beyond considering individual local minimum energy geometries and, importantly, circumvent a precarious issue associated with the assumption of a single assigned atomic partial charge for each element in a nanocrystal, independent of its structural position. We demonstrate that the carboxylate ligands passivate the metal-rich surfaces by adopting a very wide range of "tilted-bridge" and "bridge" geometries and investigate the corresponding ligand IR spectrum. This work illustrates the potential of machine-learned force fields to transform computational modeling of these materials.

Biological interaction of Pt complex with imidazole derivative as an anticancer compound with DNA: Experimental and theoretical studies

This investigation is applied to find out interesting information on DNA binding mode with Pt(II) derivative of two N, N bidentate ligands in treating cancer. Thus, one new water-soluble platinum complex with FIP and phen with a new formula of [Pt(phen)(FIP)](NO3)2 was prepared and specified. DFT data can be used to evaluate geometry parameters. Based on the ADMET prediction, this complex can be considered a drug-like agent. Cytotoxicity property was evaluated against some human cancerous MCF7, A549, and HCT116 cell lines. Accumulation of Pt complex, cisplatin, and oxaliplatin in each cancerous cell was determined, which is probably related to their lipophilicity and solubility properties. The binding mode of the complex to ct-DNA was investigated by fluorescence spectroscopy, circular dichroism, and molecular docking simulation. The viscosity of DNA by different concentrations of EB and Pt complex titration shows Pt complex interacts with DNA via groove binding like the spectroscopic binding result. In the MD study, DNA helix, RMSD, and RMSF analysis showed that DNA stability decreased and that the majority of residues left the initial state. DNA increased residual deviations and flexibility are linked to an increase in its gyratory radius, which is consistent with the findings of the experiments.

Fluorine spillover for ceria- vs silica-supported palladium nanoparticles: A MD study using machine learning potentials.

Supported metallic nanoparticles play a central role in catalysis. However, predictive modeling is particularly challenging due to the structural and dynamic complexity of the nanoparticle and its interface with the support, given that the sizes of interest are often well beyond those accessible via traditional abinitio methods. With recent advances in machine learning, it is now feasible to perform MD simulations with potentials retaining near-density-functional theory (DFT) accuracy, which can elucidate the growth and relaxation of supported metal nanoparticles, as well as reactions on those catalysts, at temperatures and time scales approaching those relevant to experiments. Furthermore, the surfaces of the support materials can also be modeled realistically through simulated annealing to include effects such as defects and amorphous structures. We study the adsorption of fluorine atoms on ceria and silica supported palladium nanoparticles using machine learning potential trained by DFT data using the DeePMD framework. We show defects on ceria and Pd/ceria interfaces are crucial for the initial adsorption of fluorine, while the interplay between Pd and ceria and the reverse oxygen migration from ceria to Pd control spillover of fluorine from Pd to ceria at later stages. In contrast, silica supports do not induce fluorine spillover from Pd particles.

Interaction of pristine and novel graphene allotropes with copper nanoparticles: Coupled density functional and molecular dynamics study

We combined the density functional theory and classical molecular dynamics to study the time evolution and thermal stability of copper nanoparticles wrapped in graphene flakes. We observed a strong attraction between nanoparticles and flakes, which was underestimated in many previous simulations. We found that the two-parameter Lennard-Jones potential with parameters ε = 0.074 eV and r0 = 3.310 Å reproduces DFT data better than other empirical potentials. We confirmed that a nanoparticle could be held reliable inside a graphene flake. The graphene-coated copper system remains stable over the temperature range of 300–1000 K. In addition to pristine graphene, we considered several strained allotropes containing pentagons, as well as heptagons, octagons, and nanometer-sized pores. Strained allotropes interact with copper nanoparticles approximately twice more strongly as compared to pristine graphene. Molecular dynamics revealed nanoparticle flattening due to strong interaction with graphene allotropes at elevated temperatures. The wettability of graphene with respect to copper strongly depends on the sheet structure and can vary significantly for different allotropes. The results may be useful for further research on copper-graphene composites, which are suitable for catalytic and biomedical applications.

A Series of Non-Oxido VIV Complexes of Dibasic ONS Donor Ligands: Solution Stability, Chemical Transformations, Protein Interactions, and Antiproliferative Activity.

A series of mononuclear non-oxido vanadium(IV) complexes, [VIV(L1-4)2] (1-4), featuring tridentate bi-negative ONS chelating S-alkyl/aryl-substituted dithiocarbazate ligands H2L1-4, are reported. All the synthesized non-oxido VIV compounds are characterized by elemental analysis, spectroscopy (IR, UV-vis, and EPR), ESI-MS, as well as electrochemical techniques (cyclic voltammetry). Single-crystal X-ray diffraction studies of 1-3 reveal that the mononuclear non-oxido VIV complexes show distorted octahedral (1 and 2) or trigonal prismatic (3) arrangement around the non-oxido VIV center. EPR and DFT data indicate the coexistence of mer and fac isomers in solution, and ESI-MS results suggest a partial oxidation of [VIV(L1-4)2] to [VV(L1-4)2]+ and [VVO2(L1-4)]-; therefore, all these three complexes are plausible active species. Complexes 1-4 interact with bovine serum albumin (BSA) with a moderate binding affinity, and docking calculations reveal non-covalent interactions with different regions of BSA, particularly with Tyr, Lys, Arg, and Thr residues. In vitro cytotoxic activity of all complexes is assayed against the HT-29 (colon cancer) and HeLa (cervical cancer) cells and compared with the NIH-3T3 (mouse embryonic fibroblast) normal cell line by MTT assay and DAPI staining. The results suggest that complexes 1-4 are cytotoxic in nature and induce cell death in the cancer cell lines by apoptosis and that a mixture of VIV, VV, and VVO2 species could be responsible for the biological activity.

Density functional analysis of molecular crystal: bis-l-Phenyl alanine mandelate

A novel organic nonlinear four component molecular crystal bis-l-phenylalanine mandelate (BLPAMA) has been synthesized and single crystal has been grown by slow evaporation method in an aqueous solution at ambient temperature. The characterization studies support the formation of the neutral novel organic molecular crystal containing 68 atoms in a molecule. The experimental and theoretical density functional analysis (DFT) have been compared for the vibrational changes, dipolar interactions, 1H and 13C NMR values, UV-Vis absorption pattern, HOMO-LUMO interactions, hyperconjugation effects, Natural Bond Orbital (NBO) and Natural Hybridisation Orbital (NHO) analysis. The molecular structure obtained from the solid state experimental data using ORTEP diagram has been compared with the gaseous state optimized stucture obtained from DFT data using Gaussian 98 software with MO6-31++(d,p) basis set. The DFT study of the title compound has confirmed the crystal formation through charge transfer mechanism, hydrogen bonding interactions and van der Waals forces of attraction. The stress and strain in the title compound leads to the low energy gap nonlinear molecular sheet formation. The title compound shows electrochemical activity due to the highly reactive and relatively unstable structure.

Synthesis, characterization of dialkylated erythrosin B derivatives and their utility as a propitious anti-microbial agent

The development of small molecule based drugs as an antimicrobial agent is an important area of research nowadays. In the present work, two new molecular entities based on dialkylated erythrosin B has been synthesized via Arbuzov type of rearrangement using dialkyl sulphite as a reagent in the presence of Et3N. Ethyl and methyl based dialkylated derivatives of erythrosin B were characterized using 1H NMR, 13C NMR and HRMS data. Keeping in mind the biological safety of erythrosin B, synthesized derivatives were checked for their antimicrobial activity against the microbial strains Escherichia coli (E.coli). The two were found to be effective against the E. coli with the antimicrobial activity similar to that of Ampicillin. Further, the trend of antimicrobial activity has been supported by DFT data analysis and it was observed that compound, B with low HOMO (–5.93 eV) and LUMO (–3.11 eV) energies is a better antimicrobial agent than compound A.

Monometallic complexes of novel dihydrazone‐oxime ligand: Synthesis, structure, spectral, DFT, and in vitro bioactivity investigation against fungal, bacterial, and tumor cells

In the current study, uni‐metallic Cu2+, Ni2+, Mn2+, Co2+, and Zn2+ complexes of ONN‐tridentate dihydrazone‐oxime incorporating indolin‐2‐one moiety (HL,1) were synthesized and structurally characterized employing elemental, spectral, thermo‐gravimetric, magnetic, and molar conductivity measurements, to investigate the structure and composition of these new uni‐metallic complexes. According to the results of several analyses, the dihydrazone‐oxime behaved as a mono‐negative or neutral tridentate ONN chelator bound the metal cations in molar ratio (1M:1L) through the isatinic carbonylic oxygen, azomethine nitrogen, and nitrogen atom of deprotonated/protonated oximatic moiety forming uni‐metallic complexes with formulae [M(L)XYZ(H2O)].nH2O (where M = Cu2+ (2–4), Ni2+, Mn2+, Co2+, or Zn2+, X = Cl, CH3COO, or NO3, Y = H2O or 0, Z = H2O or 0, n = 2, 0) and [Cu (HL)(SO4)(H2O)]. The Cu2+ complexes were found to have a tetragonally distorted octahedral or square pyramidal geometry, whereas those of Mn2+, and Ni2+, exhibited a tetrahedral geometry but Co2+ complex demonstrated a distorted octahedral geometry. Based on DFT‐B3LYP technique and 6‐311G++(d,p) basis set, The DFT data confirmed the structural investigation of dihydrazone‐oxime and its complexes, revealing that the complexes reactivity is more than un‐complexed dihydrazone‐oxime. Moreover, quantum chemical parameters of dihydrazone‐oxime and its uni‐metallic complexes like the energies of both lowest unoccupied molecular orbital (ELUMO) and highest occupied molecular orbital (EHOMO), separation energy (ΔE = ELUMO − EHOMO), chemical potential, absolute electronegativity, absolute hardness, and absolute softness were obtained. According to the thermogravimetric analysis, the complexes breakdown in two to four disintegrating phases in range of temperature 25°C to 575°C leaving the oxide of metal or metal oxide contaminated with carbon. In vitro microbicide effect of the un‐complexed dihydrazone‐oxime and its uni‐metallic complexes toward various bacterial and fungal strains was tested by agar‐well diffusion method. It is demonstrated that the complexes are more effective than free dihydrazone‐oxime. The antitumor activity has been also analyzed against three cell lines including prostate adenocarcinoma (PC‐3), ovarian adenocarcinoma (SKOV3), and cervical cancer (HeLa) cell lines. Studies showed that all complexes have greater inhibition activity against the above three cell lines than the free dihydrazone oxime and the most effective compound was the Zn2+ complex (9) with IC50, 27.42, 35.16, and 46.77 μg/ml, respectively.

Preparation of zwitterionic ionic surfactants-based sulphonyl for steel protections: Experimental and theoretical insights

Abstract Designating an organic inhibitor with a specific chemical structure that actively participates in steel protection by increasing adsorption on the steel surface. Based on that, we synthesized three zwitterionic surfactants based on azomethine with different hydrophobic chain lengths labeled ZWSO, ZWSD, and ZWSH. The presence of azomethine group, electrons, and heteroatoms in the zwitterionic surfactant’s amphipathic structure helped to improve C-steel protection. Their inhibitory activity toward steel corrosion was investigated utilizing electrochemical impedance spectroscopy (EIS), gravimetrical, and potentiodynamic polarization techniques. Importantly, the surfactant tail influenced corrosion inhibition performance; as surfactant tail length increased, so did inhibition efficiency due to increased adsorption affinity. The inhibition efficiencies of ZWSO, ZWSD, and ZWSH are 87.15, 89.82, and 91.36%, respectively. Tafel data clarified that ZWSO, ZWSD, and ZWSH inhibitors behave as mixed-type inhibitors following the modified Langmuir isotherm. The inhibitors can adsorb physiochemically on the steel surface with ∆G ads ranges from −38.48 to −44.6 kJ mol−1. The SEM confirms that the morphology of C-steel becomes smoother because of inhibitor adsorption. The DFT and MCs output data supported the experimental performance of the tested ZWSO, ZWSD, and ZWSH inhibitors and especially their dependence on surfactant tail length.

Deuteration of Pd-activated C(sp2)–H bonds in the solid state

A novel approach for deuteration of C–H bonds in a ball mill at ambient temperature using Cys-d4 as D-source is developed. In situ Raman, ex situ spectroscopic and DFT data allowed identification of intermediates and insight into the reaction course.

Synthesis and Photophysical Properties of Novel Meta-Conjugated Organic Molecules with 1,3,5-Benzene Branching Units

The synthesis and photophysical investigation of three novel meta-conjugated molecules based on 3,1,2-benzothiadiazole and thiophene-2,5-diyl derivatives linked through 1,3,5-benzene branching units are described. Each of them is a symmetrical molecule with two branching units, four identical lateral thiophene-containing fragments, and one central benzothiadiazole-containing fragment. To study the effect of the chemical structure on their photophysical properties, the molecules with different linearly conjugated lateral and central fragments due to incorporation of additional thiophene rings were synthesized and compared. It was shown that absorption spectra of the meta-conjugated molecules can be represented as a sum of absorption bands of model compounds for their peripheral and central fragments containing a common benzene ring being branched at the 1,3,5-benzene unit in the meta-conjugated molecules. Therefore, they cannot be considered simply as isolated π-conjugated systems of their peripheral and central fragments. Instead, DFT calculations showed that several transitions between the orbitals located in different regions of the meta-conjugated molecule are responsible for the formation of their absorption spectra, and they strongly depend on the degree of their overlapping. Theoretical absorption spectra reconstructed from the DFT data demonstrated a good agreement with the experimental results: the transitions with larger oscillator strength correspond to the bands with higher molar extinction coefficients and vice versa. It was shown that luminescence spectral maxima of the meta-conjugated molecules monotonically shift to the lower energy from 489 to 540 and 613 nm with increasing the number of thiophene rings in the peripheral and central fragments, respectively. However, luminescence quantum yield of the meta-conjugated molecules critically depends on the length of linearly conjugated fragments in its structure decreasing from 24% to 1.3% with increasing the number of thiophene rings in the lateral fragments but increasing to 90% in the molecule with more thiophene rings in both types of the fragments. The results obtained are well correlated to the ratio of radiative and nonradiative deactivation rate constants of the meta-conjugated molecules that indicates a high rate of internal conversion between the excited states corresponding to different fragments of the molecule. The CV measurements allowed estimating the HOMO, LUMO, and bandgap values of the target and model compounds, which confirm the presence of meta-conjugation within the molecules investigated. Thus, connection of linearly conjugated fragments through meta-positions (meta-conjugation) of a benzene ring leads to an intermediate option between fully conjugated and nonconjugated molecules due to partial delocalization of electron density through the 1,3,5-substituted benzene branching center.

A machine-learning interatomic potential to understand primary radiation damage of silicon

Harsh radiation environments cause displacement damages in semiconductor components, resulting in performance degradation. Molecular simulations provide a unique approach to study the dynamic processes of radiation-induced defect production, clustering, and evolution to design and reinforce novel semiconductor components. In this paper, we developed a more efficient machine learning (ML) potential with DFT accuracy to investigate the radiation damage in silicon material. The accuracy of the potential was verified by comparing the static properties, defect formation energy, and threshold displacement energy with experiments and DFT data. By simulating the excitation of a single PKA we found that with the ML potential PKA has an impact over a larger spatial area compared to the empirical potentials. Finally, by simulating multiple PKA excitations in sequence, we found that the first several excited PKAs produce an amorphous region. For the later excited PKAs, the energies are dissipated when they cross through the amorphous region, resulting in a 36% decrease in newly generated defects.

Ab initio thermo-elasticity of [formula omitted]-MH[formula omitted] (M[formula omitted]Zr, Ti)

In the present work, we report the results of a systematic ab initio study of the thermo-elastic properties of δ-MH1.5 (M=Zr, Ti). This investigation serves three purposes: (i) Elucidate the fully anisotropic temperature dependent elastic constants of hydrides, (ii) address discrepancies in thermal expansion data reported in the literature and (iii) provide input data for thermodynamic-based phase-transformation modelling. Due to a reduced contribution from the vibrational free energy to the strain energy, in agreement with experimental observations we find that the temperature dependent stiffness of hydrides vary to a much lesser degree than the matrix. For δ-ZrH1.5, we further find that Zener’s anisotropy ratio varies with temperature. Regarding the linear thermal expansion, our results indicate that it is highly temperature dependent. With the exception of a few outliers, our DFT data concurs well with experimental data, if the temperature range over which it was measured is taken into account.

Antimony(III) dithiocarbamates: Structural studies and exploration of the rare Sb···Sb interaction

• Synthesis and characterization of antimony(III) dithiocarbamates. • Crystal structures and supramolecular features of the metal complexes. • Exploration of the rare antimony-antimony interaction. • DFT studies. Herein, we report synthesis and spectroscopic characterization of a new piperidine-based homoleptic antimony(III) dithiocarbamate complex Sb[S 2 CN(CH 2 ) 4 CH(Bn)] 3 ) (1) and solid state crystal structure of a piperazine - based complex Sb[S 2 CN(CH 2 ) 4 N(Bn)] 3 (2) . This study identifies molecular and supramolecular features of the two compounds based on single crystal XRD data. Interestingly, complex 1 features an Sb ··· Sb (stibophilic) linkage, a rarely observed interaction in this class of compounds. To investigate the rarity of this stibophilic linkage CSD retrieved structures have been scrutinized and DFT studies conducted. XRD data unveiled that the linkage materializes in two possible ways: firstly, when monomers carrying pentagonal pyramidal coordination geometry adopt usual orientations (antiparallel alignment of the monomers attached through four-membered [Sb—S ··· ] 2 ring) and characteristically organized neighboring “anchoring molecules” influence them to substantiate the linkage, and secondly when monomers align in unusual patterns (this is observed in both usual geometries, pentagonal pyramidal and trigonal antiprismatic). Interestingly, trigonal antiprismatic geometry with usual pattern of dimeric aggregation is deprived of the Sb ··· Sb linkage. Furthermore, DFT data are well consistent with the findings, and convincingly explains the rarity of the linkage.

Influence of Proline Chirality on Neighbouring Azaproline Residue Stereodynamic Nitrogen Preorganization.

We report herein the first systematic crystal structural investigation of azaproline incorporated in homo- and heterochiral diprolyl peptides. The X-ray crystallography data of peptides 1-5 illustrates that stereodynamic nitrogen in azaproline adopted the stereochemistry of neighbouring proline residue without depending on its position in the peptide sequence. Natural bond orbital analysis of crystal structures indicates OazPro -C'Pro of peptides 4 and 5 participating in n→π* interaction with stabilization energy about 1.21-1.33 kcal/mol. Density functional theory calculations suggested that the endo-proline ring puckering favoured over exo-conformation by 6.72-7.64 kcal/mol. NBO and DFT data reveals that the n→π* interactions and proline ring puckering stabilize azaproline chirality with the neighbouring proline stereochemistry. The CD, solvent titration, variable-temperature and 2D NMR experimental results further supported the crystal structures conformation.

Tripodal 1,2,3-triazole click ligand based on the triphenylphosphine oxide platform: atrane-type lanthanide complexes in solutions

Tris[2-(1-phenyl-1,2,3-triazol-4-ylmethoxy)phenyl]-phosphine oxide, a novel tripodal polytopic ligand produces, stable complexes with La(NO3)3 and Lu(NO3)3. According, to IR, multinuclear NMR and DFT data, the complexes, have atrane-type structure with tetradentate O,N,N,Ncoordination, of ligand in MeCN solutions.

Electronic Structure of Chromium(III) Acetylacetonate Sulfenyl Chloride and Its γ-Vinyltrimethylsilane-Substituted Derivatives according to XPS and DFT Data

Electronic Structure of Chromium(III) Acetylacetonate Sulfenyl Chloride and Its γ-Vinyltrimethylsilane-Substituted Derivatives according to XPS and DFT Data