Ab Initio Calculations Research Articles

Sulfur isotopic fractionation during hydrolysis of carbonyl sulfide

Carbonyl Sulfide (OCS) is the most abundant sulfur-containing gas in the atmosphere, and it is used as a proxy for terrestrial gross primary productivity (GPP). Oceans are the major source of OCS to the atmosphere, produced by photochemical and “dark” reactions. Hydrolysis to H2S and CO2 is the major removal process of OCS from the ocean's surface. Measuring the sulfur isotope values (δ34S) and the isotopic fractionation (ε) associated with these major OCS sources and sinks could decrease the uncertainties in its fluxes. In the current study, we aim to determine the ε during the hydrolysis process of OCS (εh). We used a purge and trap system coupled to a GC/MC-ICPMS to measure δ34S values during hydrolysis under different temperatures (4–40 °C), salinities (0.2–40 g/L), and pH (4–9), representing various natural environmental conditions. In addition, we use the quantum chemical method to calculate the equilibrium εh and compare it to the empirical results. Our results for the low salinity (0.2 g/L; pH 8.0) water show a temperature dependency of the εh from −3.9 ‰ ± 0.2 ‰ (4 °C,) to −2.2 ± 0.6 ‰ (40 °C (. The higher fractionation at low temperatures has implication for ice-core data interpretation. However, in natural seawater at 4°C and 22 °C (S = 40 g/L, pH 8.2) there was no such temperature dependency and the εh averaged −2.6 ± 0.3 ‰. Thus, it seems that salinity cancels the temperature effect close to the freezing temperature of water. Varying the pH between 4 and 9 (at 22 °C) did not result in any εh trend. Ab-initio calculations suggest that OCS hydrolysis is not controlled by equilibrium. The εh values we report will aid in quantifying the impact of OCS's hydrolysis on the observable sulfur isotopic signature of OCS in oceanic and in freshwater environments. This in turn will facilitate more accurate mass-balance calculations for the OCS budget from the ocean to the atmosphere.

Elucidating Charge Transfer Processes and Enhancing Electrochemical Performance of Laser-Induced Graphene via Surface Engineering with Sustainable Hydrogel Membranes: An Electrochemist's Perspective

Laser-induced graphene (LIG) has emerged as a promising solvent-free strategy for producing highly porous, 3D graphene structures, particularly for electrochemical applications. However, the unique character of LIG and hydrogel membrane (HM) coated LIG requires accounting for the specific conditions of its charge transfer process. This study investigates electron transfer kinetics and the electroactive surface area of LIG electrodes, finding efficient kinetics for the [Fe(CN)6]3-/4- redox process, with a high rate constant of 4.89 x 10-3 cm/s. The impact of polysaccharide HM coatings (cationic chitosan, neutral agarose and anionic sodium alginate) on LIG's charge transfer behavior is elucidated, considering factors like ohmic drop across porous LIG and Coulombic interactions/permeability affecting diffusion coefficient (D), estimated from amperometry.It was found that D of redox species is lower for HM-coated LIGs, and is the lowest for chitosan HM. Chitosan coating results in increased capacitive share in the total current while does not apparently reduce Faradaic current. Experimental findings are supported by ab-initio calculations showing an electrostatic potential map’s negative charge distribution upon chitosan chain protonation, having an effect in over a two-fold redox current increase upon switching the pH from 7.48 to 1.73. This feature is absent for other studied HMs. It was also revealed that the chitosan's band gap was reduced to 3.07 eV upon acetylation, due to the introduction of a new LUMO state. This study summarizes the operating conditions enhanced by HM presence, impacting redox process kinetics and presenting unique challenges for prospective LIG/HM systems’ electrochemical applications.

Stable potassium isotope ratios in human blood serum towards biomarker development in Alzheimer's disease.

The Alzheimer's disease (AD)-affected brain purges K with concurrently increasing serum K, suggesting brain-blood K transferal. Here, natural stable K isotope ratios-δ41K-of human serum samples were characterized in an AD biomarker pilot study (plus two paired Li-heparin and potassium ethylenediaminetetraacetic acid [K-EDTA] plasma samples). AD serum was found to have a significantly lower mean δ41K relative to controls. To mechanistically explore this change, novel ab initio calculations (density functional theory) of relative K isotope compositions between hydrated K+ and organically bound K were performed, identifying hydrated K+ as isotopically light (lower δ41K) compared to organically bound K. Taken together with literature, serum δ41K and density functional theory results are consistent with efflux of hydrated K+ from the brain to the bloodstream, manifesting a measurable decrease in serum δ41K. These data introduce serum δ41K for further investigation as a minimally invasive AD biomarker, with cost, scalability, and stability advantages over current techniques.

Trifluoroacetyl peroxynitrate (CF3C(O)O2NO2, FPAN) degradation in wet atmosphere

Trifluoroacetyl peroxynitrate (FPAN) is the fluorinated analogue of PAN, proposed as a degradation intermediate of fluorinated compounds like CFC (chlorofluorocarbons) and their replacements. FPAN presents a longer atmospheric lifetime in comparison with the hydrogenated PAN. On the other hand, participation of water in atmospheric processes have received significant attention due to its potential impact on the stability of pollutants and chemical reactions. For example, the interaction between PAN and water by van der Waals interactions can lead to an increase in the degradation rate of PAN. The present work expands the knowledge about the stability of fluorinated peroxynitrates in wet atmosphere.The interaction between FPAN and water was studied from mixtures containing FPAN/H2O and FPAN/H2O/NO2 and monitored by infrared spectroscopy. The analysis of spectra reveals formation of CF3C(O)OH in both systems. Ab initio calculations were performed to explore the interactions at molecular level.Finally, a reaction mechanism is proposed considering the experimental evidence and theoretical calculations results. Rate coefficients for the formation of CF3C(O)OH were estimated using a kinetic software.

Ab Initio Study of the Crystalline Structure of HgS under Low and High Pressure

This study analyzes the lattice dynamics of HgS under various pressures using ab initio self-consistent calculations based on the plane-wave method (PW) and generalized gradient approximation (GGA). The static study, performed by enthalpy calculations, predicts that the transition from the cinnabar phase (α-HgS) to the zinc-blende B3 (β-HgS) or wurtzite (2H) structures occurs at very low pressures, at 0.65 or 0.70 GPa, respectively. Furthermore, the transition from β-HgS to the rocksalt (B1) phase occurs at 7 GPa, and at high pressure, specifically at 110 GPa, HgS can adopt the CsCl (B2) phase. The mechanical study confirms the stability of the β and 2H phases at 0 GPa. Phonon calculations corroborate the results of the static and mechanical studies regarding stability (α→0.7GPa2H→0.9GPaβ), and the results indicate that the instabilities of the transverse acoustic (TA) modes, induced by the application of pressures of 10.5 GPa, 21 GPa, and 190 GPa, are responsible for the observed phase transitions in part of the Brillouin.

Excitonic signatures of ferroelectric order in parallel-stacked MoS2

Interfacial ferroelectricity, prevalent in various parallel-stacked layered materials, allows switching of out-of-plane ferroelectric order by in-plane sliding of adjacent layers. Its resilience against doping potentially enables next-generation storage and logic devices. However, studies have been limited to indirect sensing or visualization of ferroelectricity. For transition metal dichalcogenides, there is little knowledge about the influence of ferroelectric order on their intrinsic valley and excitonic properties. Here, we report direct probing of ferroelectricity in few-layer 3R-MoS2 using reflectance contrast spectroscopy. Contrary to a simple electrostatic perception, layer-hybridized excitons with out-of-plane electric dipole moment remain decoupled from ferroelectric ordering, while intralayer excitons with in-plane dipole orientation are sensitive to it. Ab initio calculations identify stacking-specific interlayer hybridization leading to this asymmetric response. Exploiting this sensitivity, we demonstrate optical readout and control of multi-state polarization with hysteretic switching in a field-effect device. Time-resolved Kerr ellipticity reveals direct correspondence between spin-valley dynamics and stacking order.

A semiempirical model for low energy electron–atom transport cross sections: The case of noble gases

A semiempirical approach to describe low energy electron–atom transport cross sections of easy implementation and reproduction is presented. The heart of the model is an energy independent two-parameter potential that was adjusted to reproduce the accurate total cross sections for He, Ne, Ar and Kr, measured with a threshold photoelectron source technique from meV up to 20 eV. Once the potential was conceived, the model was validated by comparing the values obtained for the calculated scattering lengths and phase shifts with the respective quantities previously reported in the literature. We close the article by presenting the momentum transfer and viscosity cross sections. Good agreement is found when compared to the similar data obtained from swarm experiments, from phase shifts according to differential cross section measurements and to the cross sections reported by sophisticated ab initio relativistic many-body calculations. Tables for the phase shifts and cross sections are provided for direct use and applications.

Quantum Chemical Stability Analysis of Phthalocyanine Metal One-Dimensional Polymers with Bidentate Ligands.

The combination of metal-phthalocyanine complexes and axially coordinated organic molecules into polymer chains presents a significant challenge in the synthesis of hybrid materials. A calculated structure for one-dimensional coordinate polymers with N-donor ligands using ab initio (PM6) and DFT (LanL2Dz) methods is presented. DFT methods have shown that there is a linear, one-dimensional structure without distorted geometry for the two bipyridine ligands. The components of the proposed polymers consist of square-planar Zn complexes of phthalocyanine (PcZn) connected via bridging ligands (L). Electronic properties of the monomer PcZnL of zinc phthalocyanine with bidentate ligands have been analyzed using calculations based on density functional theory (B3LYP6-31G(d,p)). Molecular orbital calculations show that this connection between the metallomacrocycle and the conjugated ligand results in a small energy gap, promising molecularly active materials as conductors. The crystallographic reports indicate that obtaining this kind of polymer with the participation of Pc Zn and bidentate ligands is possible.

Synergistic effects of nitrogen-containing functionalized copolymer and silicon-doped DLC for friction and wear reduction

We present a strategy to enhance the tribological performances of diamond-like carbon (DLC) films based on synergistic chemical modifications in the polymer lubricant additives and in the carbon film. Our experiments revealed that the polymer functionalization with nitrogen-containing groups and the DLC doping with silicon atoms result in significant friction and wear reduction under severe boundary lubrication conditions. Atomic Force Microscopy revealed the formation of a lubricious tribofilm. Ab initio calculations highlighted the key role of N-Si interactions in promoting the polymer chemisorption on the film, which represents the first, essential step for the tribofilm formation. Our findings suggest that targeted chemical modifications in lubricants and films can substantially advance the tribological performances of DLC films for various industrial applications.

Breaking the size limitation of nonadiabatic molecular dynamics in condensed matter systems with local descriptor machine learning

Nonadiabatic molecular dynamics (NA-MD) is a powerful tool to model far-from-equilibrium processes, such as photochemical reactions and charge transport. NA-MD application to condensed phase has drawn tremendous attention recently for development of next-generation energy and optoelectronic materials. Studies of condensed matter allow one to employ efficient computational tools, such as density functional theory (DFT) and classical path approximation (CPA). Still, system size and simulation timescale are strongly limited by costly ab initio calculations of electronic energies, forces, and NA couplings. We resolve the limitations by developing a fully machine learning (ML) approach in which all the above properties are obtained using neural networks based on local descriptors. The ML models correlate the target properties for NA-MD, implemented with DFT and CPA, directly to the system structure. Trained on small systems, the neural networks are applied to large systems and long timescales, extending NA-MD capabilities by orders of magnitude. We demonstrate the approach with dependence of charge trapping and recombination on defect concentration in MoS2. Defects provide the main mechanism of charge losses, resulting in performance degradation. Charge trapping slows with decreasing defect concentration; however, recombination exhibits complex dependence, conditional on whether it occurs between free or trapped charges, and relative concentrations of carriers and defects. Delocalized shallow traps can become localized with increasing temperature, changing trapping and recombination behavior. Completely based on ML, the approach bridges the gap between theoretical models and realistic experimental conditions and enables NA-MD on thousand-atom systems and many nanoseconds.

Ab inito investigation on structural, electronic, and optical characteristics of HfClI Janus monolayer

Utilizing ab initio calculations based on density functional theory, this study delves into the structural, electronic, and optical properties of the HfClI Janus monolayer. Our comprehensive analysis demonstrates the monolayer's dynamical stability, evident from the absence of negative modes in its phonon dispersion spectra. Furthermore, structural analysis reveals no significant bond disruptions or reconstructions, thereby confirming the monolayer's ability to sustain its configuration even at elevated temperatures up to 600 K. In terms of electronic structure, HSE calculations reveal an indirect band gap of 1.359 eV, which undergoes a reduction to 1.281 eV upon inclusion of spin-orbit coupling (SOC). Particularly, the HfClI Janus monolayer exhibit ultrahigh carrier mobilities, ranging from 1257 cm2/sV to 3125 cm2/sV, displaying ultrahigh carrier mobilities. Notably, the monolayer exhibits remarkable absorption capabilities spanning the visible and ultraviolet spectra, hinting at its potential for nano-optoelectronic applications, especially in the realm of electromagnetic radiation absorption and detection. These findings underscore the promising characteristics of the HfClI Janus monolayer, positioning it as a viable candidate for future technological advancements and advancements in nano-optoelectronics.

Electronic Structure of a Neodymium(III) Tris(oxidiacetate) Complex from Luminescence Data and Ab Initio Calculations.

Neodymium(III) is a near-infrared emissive and magnetic ion, which has found use in various high-technology applications. Yet, accurate predictions of the luminescent and magnetic properties of neodymium(III) based on the coordination environment remain to be done. Guidelines exist, but to build structure-property relationships for this element, more data are needed. Herein, we present a high-symmetry starting point. The tris(oxidiacetate) complex of neodymium(III) was prepared and crystallized, and access to the experimentally determined structure allowed us to quantify the symmetry of the compound and to perform calculations directly on the same structure that is investigated experimentally. The luminescent properties were determined and the electronic structure was computed using state-of-the-art ab initio methods. All electronic transitions in the range from 490 to 1400 nm were mapped experimentally. Using a Boltzmann population analysis, the combination of the excitation and emission spectra revealed the crystal field splitting of the 18 lowest-energy Kramers levels that experimentally could be unambiguously resolved. This assignment was supported by ab initio calculations, and the crystal field splitting was well reproduced. The electronic structure reported for the tris(oxidiacetate) complex was used to deduce the coordination structure in aqueous solution. Finally, the results are compared to empirical trends in the literature for the electronic structure of neodymium(III).

First-Principle Study on Tailoring the Martensitic Transformation of B2 Nb50−xTixRu50 Shape-Memory Alloy for Structural Applications

NbRu has a potential as a high-temperature shape-memory alloy (HTSMA) because it has a martensitic transformation temperature above 1000 °C. However, its shape-memory properties could be improved for consideration in the aerospace and automotive industry. The unsatisfactory shape-memory properties could be associated with the presence of a brittle tetragonal L10 martensitic phase. Therefore, in an attempt to modify the transformation path from B2→L10 in preference of either B2→orthorhombic or B2→monoclinic (MCL), an addition of B2 phase stabiliser, titanium (Ti), has been considered in this study to partially substitute niobium (Nb) atoms. The ab initio calculations have been conducted to investigate the effect of Ti addition on the thermodynamic, elastic, and electronic properties of the Nb50−xTixRu50 in B2 and L10 phases. The results showed that the B2 and L10 phases had comparable stability with increasing Ti content. The simulated data presented here was sufficient for the selection of suitable compositions that would allow the L10 phase to be engineered out. The said composition was identified within 15–30 at.% Ti. These compositions have a potential to be considered when designing alloys for structural application at high temperatures above 200 °C.

Magnetic and electronic properties of double perovskite Sr2CrMoO6 for spintronic applications: Insights from first-principles and Monte Carlo approaches

Abstract In this work, we studied the electronic and magnetic properties of the double perovskite Sr2CrMoO6 using ab initio calculations with Generalized Gradient Approximation (GGA) and Monte Carlo (MC) simulations. The compound has two magnetic sublattices: one occupied by Mo5+ with spin (S = 1/2) and the other by Cr3+ with spin (σ = 3/2). The results showed half-metallic behavior with a total magnetic moment of 2.0 μB. Using Monte Carlo simulations, we investigated the phase transitions and observed interesting phenomena such as a critical endpoint and both second-order and first-order phase transitions. Additionally, the results revealed compensation points for specific values of the crystal field.

Structural characterization of DNA-binding domain of essential mammalian protein TTF 1.

Transcription Termination Factor 1 (TTF1) is a multifunctional mammalian protein with vital roles in various cellular processes, including Pol I-mediated transcription initiation and termination, pre-rRNA processing, chromatin remodelling, DNA damage repair, and polar replication fork arrest. It comprises two distinct functional regions; the N-terminal regulatory region (1-445 aa), and the C-terminal catalytic region (445-859 aa). The Myb domain located at the C-terminal region is a conserved DNA binding domain spanning from 550 to 732 aa (183 residues). Despite its critical role in various cellular processes, the physical structure of TTF1 remains unsolved. Attempts to purify the functional TTF1 protein have been unsuccessful till date. Therefore, we focused on characterizing the Myb domain of this essential protein. We started with predicting a 3-D model of the Myb domain using homology modelling, and ab-initio method. We then determined its stability through MD simulation in an explicit solvent. The model predicted is highly stable, which stabilizes at 200ns. To experimentally validate the computational model, we cloned and expressed the codon optimized Myb domain into a bacterial expression vector and purified the protein to homogeneity. Further, characterization of the protein shows that, Myb domain is predominantly helical (65%) and is alone sufficient to bind the Sal Box DNA. This is the first-ever study to report a complete in silico model of the Myb domain, which is physically characterized. The above study will pave the way towards solving the atomic structure of this essential mammalian protein.

Microsolvation of a Proton by Ar Atoms: Structures and Energetics of ArnH+ Clusters.

We present a computational investigation on the structural arrangements and energetic stabilities of small-size protonated argon clusters, Ar nH +. Using high-level ab initio electronic structure computations, we determined that the linear symmetric triatomic ArH +Ar ion serves as the molecular core for all larger clusters studied. Through harmonic normal-mode analysis for clusters containing up to seven argon atoms, we observed that the proton-shared vibration shifts to lower frequencies, consistent with measurements in gas-phase IRPD and solid Ar-matrix isolation experiments. We explored the sum-of-potentials approach by employing kernel-based machine-learning potential models trained on CCSD(T)-F12 data. These models included expansions of up to two-body, three-body, and four-body terms to represent the underlying interactions as the number of Ar atoms increases. Our results indicate that the four-body contributions are crucial for accurately describing the potential surfaces in clusters with n> 3. Using these potential models and an evolutionary programming method, we analyzed the structural stability of clusters with up to 24 Ar atoms. The most energetically favored Ar nH + structures were identified for magic size clusters at n = 7, 13, and 19, corresponding to the formation of Ar-pentagon rings perpendicular to the ArH +Ar core ion axis. The sequential formation of such regular shell structures is compared to ion yield data from high-resolution mass spectrometry measurements. Our results demonstrate the effectiveness of the developed sum-of-potentials model in describing trends in the nature of bonding during the single proton microsolvation by Ar atoms, encouraging further quantum nuclear studies.

Exploring structural and optical properties of iodine-doped TiO2 nanoparticles in Rhodamine-B dye degradation: Experimental and theoretical investigation

Energy conversion and pollutant degradation are critical for advancing sustainable technologies, yet they often encounter challenges related to charge recombination and efficiency limitations. This study explores iodine-doped TiO2 nanoparticles as a potential solution for enhancing both energy conversion and pollutant degradation. The nanoparticles were synthesized via the sol-gel method with varying iodine precursor concentrations (0.025–0.1 M) and were characterized for their structural, compositional, and optical properties, particularly in relation to their photocatalytic performance in Rhodamine-B dye degradation. X-ray diffraction confirmed a tetragonal anatase crystal structure, with the average crystallite size decreasing from 10.06 nm to 8.82 nm with increase in iodine concentration. Selected area electron diffraction patterns verified the polycrystalline nature of the nanoparticles. Dynamic light scattering analysis showed hydrodynamic radii ranging from 95 to 125 nm. Fourier-transform infrared spectroscopy identified metal-oxygen vibrations at 441 cm⁻1, and electron microscopy confirmed the spherical morphology of the nanoparticles. Elemental analysis detected the presence of Ti, O, and I in the samples. Diffuse reflectance spectroscopy indicated the optical absorption edges for the doped samples in the visible region from which the corresponding band gap values were deduced. Photoluminescence spectroscopy revealed that the sample with 0.1 M iodine exhibit the lowest emission intensity, suggesting reduced charge recombination. Notably, 0.1 M iodine doped TiO2 samples demonstrated the highest photocatalytic efficiency, achieving 82.36% degradation of Rhodamine-B dye within 140 min under visible light. Additionally, ab-initio density functional theory calculations were performed to investigate the structural, optical, and adsorption properties of TiO2, iodine-doped TiO2, Rhodamine-B, and their composites, providing further insight into the enhanced photocatalytic activity observed in the experiments.

Ab initio extended Hubbard model of short polyenes for efficient quantum computing.

We propose introducing an extended Hubbard Hamiltonian derived via the abinitio downfolding method, which was originally formulated for periodic materials, toward efficient quantum computing of molecular electronic structure calculations. By utilizing this method, the first-principles Hamiltonian of chemical systems can be coarse-grained by eliminating the electronic degrees of freedom in higher energy space and reducing the number of terms of electron repulsion integral from O(N4) to O(N2). Our approach is validated numerically on the vertical excitation energies and excitation characters of ethylene, butadiene, and hexatriene. The dynamical electron correlation is incorporated within the framework of the constrained random phase approximation in advance of quantum computations, and the constructed models capture the trend of experimental and high-level quantum chemical calculation results. As expected, the L1-normof the fermion-to-qubit mapped model Hamiltonians is significantly lower than that of conventional abinitio Hamiltonians, suggesting improved scalability of quantum computing. Those numerical outcomes and the results of the simulation of excited-state sampling demonstrate that the abinitio extended Hubbard Hamiltonian may hold significant potential for quantum chemical calculations using quantum computers.

Studying hcp-bcc transition of Be via anisotropy of modulus and sound velocity

Abstract Based on ab initio calculations, we utilize the mean-field potential approach with the quantum modification in conjunction with stress-strain relation to investigate the elastic anisotropies and sound velocities of hcp and bcc Be at high-temperature (0-6000 K) and high-pressure (0-500 GPa) conditions. We propose the general defintion of anisotropy for elastic moduli and sond velocities. Results suggest that the elastic anisotropy of Be is more significantly influenced by pressure than by temperature. The pressure induced increase of c/a ratio makes the anisotropy of hcp Be significantly strengthen. Whereas the hcp Be still exhibits smaller anisotropy than bcc Be in terms of elastic moduli and sound velocities. We suggest that measuring the anisotropy in shear sound velocity may be an approach to distinguishing the hcp-bcc phase transition under extreme conditions.

FP-LMTO simulation of the physical properties of arsenic-based binary XAs(X = Sc, and Al) compounds

This paper presents a simulation of the structural and optoelectronic properties of Scandium Arsenide (ScAs) and Aluminum Arsenide (AlAs) compounds. Theoretical modeling was performed using ab initio first-principles calculations, specifically the density functional theory (DFT), and the Mindlab numerical software. The software used two methods: the full-potential muffin-tin orbital method (FP-LMTO) and the full-potential plane-wave method (FP-LAPW). These two methods are employed to solve the Schrödinger equation. The exchange correlation effects have been computed using two different approximations: the generalized gradient approximation (GGA) and the local density approximation (LDA). Our findings indicate that the zinc blende structure (B3) is the stable phase, while the Wurtzite phase (B4) is metastable for the AlAs compound. On the other hand, the ScAs compound crystallizes in the NaCl phase (B1). The AlAs compounds undergo three phase transitions: [Formula: see text], [Formula: see text] and [Formula: see text]. In contrast, ScAs does not undergo any transition. The obtained results for equilibrium energies, lattice parameters and gap energies are in closer agreement with the experimental and theoretical data. The AlAs compound exhibits a semiconducting character, while ScAs exhibits a semi-metallic character. Additionally, the refractive index of these two compounds is similar to that of silicon, which is crucial for their application in photovoltaic cells.