Ab Initio Study Research Articles

The Analysis of Vibrational Spectra: Past, Present and Future.

Vibrational spectroscopy can be said to have started with the seminal work of Coblentz in the 1900s, who recorded the first recognisable infrared spectra. Today, vibrational spectroscopy is ubiquitous and there are many ways to measure a vibrational spectrum. But this is usually only the first step, almost always there is a need to assign the resulting spectra: "what property of the system results in a feature at this energy"? How this question has been answered has changed over the last century, as our understanding of the fundamental physics of matter has evolved. In this Perspective, I will present my view of how the analysis of vibrational spectra has evolved over time. The article is divided into three sections: past, present and future. The "past" section consists of a very brief history of vibrational spectroscopy. The "present" is centered around ab initio studies, particularly with density functional theory (DFT) and I will describe how this has become almost routine. For the "future", I will extrapolate current trends and also speculate as to what might come next.

Improved Estimates of Folding Stabilities and Kinetics with Multiensemble Markov Models.

Markov State Models (MSMs) have been widely applied to understand protein folding mechanisms by predicting long time scale dynamics from ensembles of short molecular simulations. Most MSM estimators enforce detailed balance, assuming that trajectory data are sampled at an equilibrium. This is rarely the case for ab initio folding studies, however, and as a result, MSMs can severely underestimate protein folding stabilities from such data. To remedy this problem, we have developed an enhanced-sampling protocol in which (1) unbiased folding simulations are performed and sparse tICA is used to obtain features that best capture the slowest events in folding, (2) umbrella sampling along this reaction coordinate is performed to observe folding and unfolding transitions, and (3) the thermodynamics and kinetics of folding are estimated using multiensemble Markov models (MEMMs). Using this protocol, folding pathways, rates, and stabilities of a designed α-helical hairpin, Z34C, can be predicted in good agreement with experimental measurements. These results indicate that accurate simulation-based estimates of absolute folding stabilities are within reach, with implications for the computational design of folded miniproteins and peptidomimetics.

Tuning the structural and mechanical properties of SiC-Li and SiC-Na alloys for aerospace application: an ab initio study

Aluminum (Al) and its alloys are popular in the aerospace industry due to their high strength-to-weight ratio, corrosion resistance, and ductility. However, these properties (extreme ductility and malleability) can compromise corrosion resistance, making them susceptible to dents and scratches. Silicon Carbide (SiC) is a promising alternative to Al and it alloys due to its higher Youngs modulus and excellent wear resistance, although it has the drawbacks of brittleness and higher density. This study investigated the structural and mechanical properties of SiC alloyed with lithium (SiC-Li) or sodium (SiC-Na) using ab initio calculations with the aim of tuning the structural and mechanical properties of SiC. Modeling was done using Burai software, which offers a friendly graphical user interface for Quantum ESPRESSO, thus facilitating the creation of input files, visualization of crystal structures and analysis of results. The results from this study showed that the addition of Li and Na lowered the density as well as the mechanical properties of SiC but still being favorably better than those of Al and its alloys, suggesting that the modeled alloys could potentially replace the traditional Al and its alloys in the aerospace industry. Further experimental studies are needed to validate these findings and to explore the possibility of simultaneous alloying of SiC with both Li and Na for enhanced performance.

Strain induced nitrobenzene sensing performance of MoSi2N4 monolayer: Investigation from density functional theory

The observing of environmental contaminant of Nitrobenzene (NB), from effluent discharges is a critical component of the surveillance to be conducted by public authorities and private sectors. By the way, the present work examines the NB adsorption behaviour of recently synthesized two-dimensional (2D) material MoSi2N4 through density functional theory (DFT). We observed that when increasing the percentage of strain (2, 4, 6 and 10 %) the adsorption energy also increasing reasonably compared to the unstrained case. The bandgap reduction was observed when gas molecule interacts with the strained MoSi2N4 and also the Bader charge calculation claims that the quantity of charge transferred between orbitals of N 2p of MoSi2N4 and the O 2p of NB. 4 % strain shows reasonable binding energy of 1.0201 eV with recovery time of 3.15 min. Moreover, there is strong bonding between N of MoSi2N4 and O of NB as evidenced from wavefunction analysis. 10 % strained system is stable at 600 K, which is examined through ab initio molecular dynamics study. The present theoretical investigation validates the 4 % strained MoSi2N4 can be fabricated as a sensor to detect the NB gas molecule.

Ab Initio Molecular Dynamics Studies of Stacked Adenine–Thymine and Guanine–Cytosine Nucleic Acid Base Pairs in Aqueous Solution

Ab initio MD studies have been performed on stacked adenine–thymine (A–T) and guanine–cytosine (G–C) nucleobase pairs solvated in water using Born–Oppenheimer molecular dynamics. These two systems have been analyzed using RDF, SDF, angle–distance CDF (combined distribution functions), plane projection analysis, hydrogen bond analysis, and non–covalent interaction (NCI) plots. The stacking property studies have shown that the molecular orientation of the A–T pair is completely opposite to that of the G–C pair though the center of mass distance between the two molecules is similar. The G–C pair shows significantly more stability in water than the A–T system does. RDF analyses show that the –NH– group and carbonyl groups show predominant interaction with water molecules. Water molecules are found to be most in numbers around the cytosine molecule and least around the adenine molecule. Hydrogen bonding studies show that the guanine molecule forms the highest number of hydrogen bonds with water molecules. On the other hand, the hydrogen atom attached to the –NH– group of adenine molecule shows the longest mean H–bond lifetime with water oxygen atoms. NCI interactions calculated through the ab initio method help us to visualize the [Formula: see text]-electron stacking and H–bonding between aromatic nucleobases and water molecules. A great shift in bond polarity and interaction intensity in different functional groups is observed for the nucleobases going from individually solvated molecules to paired states.

Protein Quakes in Redox Metalloenzymes: Clues to Molecular Enzyme Conductivity Triggered by Binding of Small Substrate Molecules.

Multicentre redox metalloproteins undergo conformational changes on electrochemical surfaces, or on enzyme substrate binding. The two-centre copper enzymes, laccase (Type I and TypeII/III Cu) and nitrite reductase (CuNIR) (Type I and Type II Cu) are examples. With some exceptions, these enzymes show no non-turnover voltammetry on Au(111)-surfaces modified by thiol based self-assembled molecular monolayers, but dioxygen or nitrite substrate triggers strong electrocatalytic signals. Scanning tunnelling microscopy also shows high conductivity only when dioxygen or nitrite is present. Atomic force microscopy shows constant CuNIR height but pronounced structural expansion in the electrocatalytic range on nitrite binding. We have recently offered a rationale, based on ab initio quantum chemical studies of water/nitrite substitution in a 740-atom CuNIR fragment. Presently we provide much more detailed structural assignment mapped to single-residue resolution. NO2 --binding induces both a 2 Å Cu-Cu distance increase, and pronounced frontier orbital delocalization strongly facilitating ET between the Cu regions. The conformational changes transmit from the catalytic Type II centre to the electron inlet Type I centre, via the His129-Cys130 ligands, and via Type I-Cys130 or Type I-His129 ending at Type II Asp92. The ET patterns are reflected in different atomic Mulliken charges in the water and nitrite CuNIR fragment.

Dynamical stability, electronic structure and optical absorption of strained penta-graphene monolayer: an ab-initio study

Dynamical stability, electronic structure and optical absorption of strained penta-graphene monolayer: an ab-initio study

Efficacy of Green and Chemically Synthesized Nano Boron Nitride on Sunflower Germination

ABSTRACTThis study explores the eco‐friendly synthesis of nanoparticles using natural sources, specifically employing Cassia fistula leaf extract for the production of boron nitride nanoparticles. Characterization of the synthesized nanoparticles was performed using Raman spectroscopy and UV‐visible spectroscopy to identify functional groups. Ab initio studies were conducted to investigate the electronic properties of the boron nitride nanostructures. The structural analysis through powder x‐ray diffraction confirmed a hexagonal configuration of the nanoparticles. Scanning electron microscopy and transmission electron microscopy revealed particle sizes below 100 nm. Laboratory experiments demonstrated that sunflower seeds treated with 1500 ppm of green‐synthesized nano boron nitride achieved the highest germination rate of 98.2%, surpassing other concentrations and chemically synthesized nanoparticles, which reached 93.9% at 2000 ppm. The control treatment yielded a germination rate of 76.2%. The eco‐friendly synthesized nanoparticles exhibited superior efficacy compared to both chemically synthesized nanoparticles and conventional fertilizers.

Ab initio study of LiMn2O4 cathode: electrochemical and optical properties for li-ion batteries and optoelectronic devices

Ab initio study of LiMn2O4 cathode: electrochemical and optical properties for li-ion batteries and optoelectronic devices

Ab Initio Study of the Influence of Spin and Orbital Magnetic Moments on the Stability of Magnetic and Charge Distribution in Co:ZnO Monolayer.

The development of ultrathin magnets with tunable magnetic properties is essential for advancing quantum computing technologies. In this study, density functional theory (DFT) calculations were employed to investigate the atomic and electronic structures of a ZnO monolayer embedded with cobalt atoms. The impact of spin dynamics on charge transfer within the Co:ZnO system was thoroughly examined. Results revealed that the orbital magnetic moment of the cobalt atoms plays a crucial role in stabilizing the magnetic and charge distributions across the system. These findings offer valuable insights for the design and fabrication of quantum devices, thereby highlighting the potential of Co-doped ZnO monolayers in quantum computing applications.

An ab-initio study of nodal-arcs, axial strain’s effect on nodal-lines and Weyl nodes and Weyl-contributed Seebeck coefficient in TaAs class of Weyl semimetals

An ab-initio study of nodal-arcs, axial strain’s effect on nodal-lines and Weyl nodes and Weyl-contributed Seebeck coefficient in TaAs class of Weyl semimetals

Ab initio Study of the Structural and Photoelectric Properties of γ-GeSe with B, C and N Adsorption

Ab initio Study of the Structural and Photoelectric Properties of γ-GeSe with B, C and N Adsorption

Theoretical Hints to Optimize Energy Dissipation and Cell–Cell Response in Quantum Cellular Automata Based on Tetrameric and Bidimeric Cells

This article is largely oriented towards the theoretical foundations of the rational design of molecular cells for quantum cellular automata (QCA) devices with optimized properties. We apply the vibronic approach to the analysis of the two key properties of such molecular cells, namely the cell–cell response and energy dissipation in the course of the non-adiabatic switching of the electric field acting on the cell. We consider two kinds of square planar cells, namely cells represented by a two-electron tetrameric mixed valence (MV) cluster and bidimeric cells composed of two one-electron MV dimeric half-cells. The model includes vibronic coupling of the excess electrons with the breathing modes of the redox sites, electron transfer, intracell interelectronic Coulomb repulsion, and also the interaction of the cell with the electric field of polarized neighboring cells. For both kinds of cells, the heat release is shown to be minimal in the case of strong delocalization of excess electrons (weak vibronic coupling and/or strong electron transfer) exposed to a weak electric field. On the other hand, such a parametric regime proves to be incompatible with a strong nonlinear cell–cell response. To reach a compromise between low energy dissipation and a strong cell–cell response, we suggest using weakly interacting MV molecules with weak electron delocalization as cells. From this point of view, bidimeric cells are advantageous over tetrameric ones due to their smaller number of electron transfer pathways, resulting in a lower extent of electron delocalization. The distinct features of bidimeric cells, such as their two possible mutual arrangements (“side-by-side” and “head-to-tail”), are discussed as well. Finally, we briefly discuss some relevant results from a recent ab initio study on electron transfer and vibronic coupling from the perspective of the possibility of controlling the key parameters of molecular QCA cells.

Effect of cations on the structural, optoelectronic, and thermoelectric properties of AMg2N2 (A = Yb, Sm, Eu) Zintl compounds; An ab-initio study

Zintl phases are prominent for their attribution to optical and thermoelectric meeds. AMg2N2 (A = Yb, Sm, Eu) compounds of the zintl family were investigated through first-principles studies for structural, electronic, optical, and thermoelectric properties. Potential functionals; PBE-GGA, TB-mBJ, and Hybrid (YS-PBE0) were used to study these compounds. The behavior of all compounds YbMg2N2, SmMg2N2, and EuMg2N2 was semiconducting with band gaps 3.75 eV, 2.22 eV, and 2.67 eV respectively through YS-PBE0. The density of states (DOS) study reveals that the leading role was offered by A-d orbitals to construct conduction bands and by A-f orbitals to form valence bands. The optical nature of these materials was studied from the optical parameters like; dielectric function ε(ω), refractive index n(ω), energy loss function L(ω), absorption coefficient α(ω), extension coefficient k(ω), reflectivity R(ω), and optical conductivity σ(ω). From this study, it is revealed that these samples are active in the visible and ultra-violet (UV) regions, due to which these materials are supposed to be suitable candidates for optoelectronic applications. Furthermore, the thermoelectric character of the titled compounds was scrutinized through the BoltzTraP2 code. The thermoelectric efficiency in the form of thermoelectric figure of merit(ZT) of AMg2N2 (A = Yb, Sm, Eu) compounds are achieved 1.17, 0.64, and 0.43 respectively at somehow high temperature 950 K. From ZT and optimized level of carriers’ concentrations, these materials are considered to be efficient thermoelectric.

Temperature and pressure effects on the decomposition mechanisms of 2,6-diamino-3,5-dinitropyrazine-1-oxide crystal: ab initio molecular dynamics study.

The decomposition process of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) crystal at high temperatures (2500 and 3390K) and detonation pressure of 33.4 GPa coupled with temperatures were studied by ab initio molecular dynamics simulations. The results show that the initial decomposition mechanism of LLM-105 is the same under different conditions. The product analysis indicates that high temperature is conducive to the formation of N2 and CO2, but inhibited the formation of H2O. It is found that the formation mechanism of H2O is the same under different conditions, which involves the reaction between OH radical and H radical. Although the detailed processes of the formation of N2 are different, they all involve the reaction between nitrogen-containing fragments, and its core is the formation of intermediates with R1-NN-R2 structure. The core of the formation of CO2 under different conditions is to form the intermediate R1-CO-R2 with carbonyl structure, and then generate the fragment with -OCO- structure, and finally generate CO2. This research may provide new insights into the initiation and subsequent decomposition mechanisms of energetic materials under extreme conditions. The LLM-105 supercell was constructed using the Materials Studio 7.0 package. AIMD simulations were performed in the CASTEP package. AIMD simulations adopted NVT and NPT ensemble, and the temperature was controlled by Nosé thermostat, while the pressure was controlled by Andersen barostat. Besides, DFT calculations were carried out at the B3LYP/6-311 + G(d,p) level using the Gaussian 09 package.

Ab initio study of iron-doped zinc oxide for efficient dye degradation

First principle calculations were performed on iron doped zinc oxide (Fe-ZO) to reduce its bandgap to optimize its visible light absorption. The doping of iron in the ZO is done via supercells of Zn1-xFexO. The doped systems are analyzed using generalized gradient approximation plane wave pseudopotential on density functional theory, or local density approximation and LDA + U with PBE. The computational analysis reveals that the bandgap reduced with increasing dopant concentration. Furthermore, a robust absorption is observed toward the visible region of the spectrum. This enhances its ability as a photochemical material to increase degradation rates of industrial grade dyes.

Theoretical and experimental investigation on newly synthesized pyrazolopyridine derivatives: Insight into the compound activity, NLO response, and molecular dynamics

Pyrazolopyridine derivatives exhibiting biological activity are widely present in drug molecules. The title compound, ethyl 3-amino-6-methyl-4-(thiophen-2-yl)-1H-pyrazolo[3,4-b]pyridine-5-carboxylate (II), was designed and synthesized and the structure characterized by spectroscopic techniques and confirmed by single-crystal X-ray diffraction. The pyrazolopyridine moiety is not quite planar and the thiophene and ester groups are rotated well out of the mean plane of the pyridine ring. N—H···N and C—H···O hydrogen bonds plus π-stacking interactions form thick layers of molecules parallel to (001). Based on structural activity relationship studies, II exhibits potent activity against fibroblast collagenase-1 complexed to a diphenyl-ether sulphone-based hydroxamic acid or Matrix Metalloproteinase (MMP-1). Theoretical simulations were performed to probe the reactivity and electronic properties of II where the quantum theory of atoms in molecules and NBO analysis was used to describe the bonding nature and charge transfer excitation. The optical and nonlinear characteristics of II are also evidenced by its hyperpolarizability response. The kinetic and thermodynamic stability of II was monitored through a computed ab-initio molecular dynamics study. In addition, a Hirshfeld surface analysis was performed to assess the intermolecular interactions. Efficient binding of II in the MMP-1 complex system has been achieved through classical molecular dynamics and molecular docking calculations. An ADMET analysis was also carried out to explore the potential future drug candidacy of II.

C-C Bonding in Molecular Systems via Cross-Coupling-like Reactions Involving Noncovalently Bound Constituent Ions.

Carbon-based molecules are of universal importance for a huge variety of chemical and biological processes. The complication of the structure of such molecules proceeds via the bonding of carbon atoms. An efficient mechanism for such reactions proceeds via cross-coupling, related to the association of bond-terminating counter-ions. Here, an uncommon version of such a process is investigated, with at least some ions bound in the system noncovalently and/or switching the bonding mode in due course. The analyzed sample reactions involve a single C-C bond formation in environmentally relevant halocarbon species and involve alkali-halide ion-pair components. A consistent ab initio computational study predicts the related energy barriers to alter significantly in the presence of the ion pair. Different channels are checked, with the carbon-halogen bond cleavage preceding or following the actual C-C bonding and with the counter-ions located closely or farther apart. The relative heights of the corresponding energy barriers are found to be switched by the ion pair. The above results suggest a possibility of facilitating such reactions without expensive catalysts.

Electronic excitation-induced amorphization in GaN and β-Ga2O3: an ab initio molecular dynamics study

Electronic excitation-induced amorphization in GaN and β-Ga2O3: an ab initio molecular dynamics study

The ab initio study of n-type nitrogen and gallium co-doped diamond

Abstract In order to better understand the influence of different complexes on the diamond co-doping system, N and Ga are chosen as co-dopants in diamond. The properties of several substitutional NmGan (m+n <= 3) complexes with vacancy (Va) in the bulk diamond have been investigated by ab initio density functional technique, including their optimized lattice structures, formation energies, binding energies and thermodynamic transition levels. The calculational results show that NmGan complexes in the donor-acceptor-donor (DAD) configuration can provide ionization energies similar to phosphorus-doped diamond. All other complexes provide deep impurity levels. For the DAD configuration, the adsorption process on the diamond surface has been studied to demonstrate the feasibility of growing diamonds containing N-Ga-N in experiments. The desired complex configuration is not uniquely present in the co-doped system. Investigating these properties of different complexes beyond NGaN provides insight into the N and Ga codoped diamond system, yielding a more comprehensive understanding of its potential and limitations. Our research ideas can also be extended to other co-doped systems and help to evaluate other potential co-dopants for diamond.