CONTEXT: The potential of graphene derivatives for theranostic applications depends on their compatibility with cellular and biomolecular components. Lysophosphatidylcholine (LPC), a lipid component present in oxidized low-density lipoproteins, microvesicles and free circulation in blood, plays a critical role in the pathophysiology of various diseases. Using density functional theory-based methods, we systematically investigated the interaction of atherogenic LPC molecule with different derivatives of graphene, including pristine graphene, graphene with defect, N-doped graphene, amine-functionalized graphene, various graphene oxides and hydroxylated graphene oxides. We observed that the adsorption of LPC on graphene derivatives is highly selective based on the orientation of the functional groups of LPC interacting with the surface of the derivatives. Hydroxylated graphene oxide exhibited the strongest interaction with LPC with adsorption energy of - 2.1 eV due to the interaction between the hydroxyl group on graphene and the phosphate group of LPC. The presence of aqueous medium further enhanced this interaction indicating favourable adsorption of LPC and graphene oxide in biological systems. Such strong interaction leads to substantial change in the electronic structure of the LPC molecule, which results in the activation of this molecule. In contrast, amine-modified graphene showed the least interaction. These theoretical results are in line with our experimental fluorescence spectroscopic data of LPC/1-anilino-8-napthalene sulfonic acid complex. Our present comprehensive investigation employing both theoretical and experimental methods provides a deeper understanding of graphene-lipid interaction, which holds paramount importance in the design and fabrication of graphene-based nanomaterials for biomedical applications. METHODS: In this study, we employed the density functional theory-based methods to investigate the electronic and structural properties of graphene derivatives and LPC molecule using the Quantum Espresso package. The exchange-correlation functional was described within generalized gradient approximation (GGA) as parameterized by Perdew, Burke and Ernzerhof (PBE). The valence electrons were represented using plane wave basis sets. `The Grimme's dispersion method was used to include the van der Waals dispersion correction.

CONTEXT: N-Nitrosamine is one of the highly toxic carcinogenic compounds that are found almost in the entire environment. In the present work, novel penta-silicene (penta-Si) and penta-silicane (penta-HSi) are utilised to sense the N-nitrosamine in the air environment. Initially, structural firmness of penta-Si and penta-HSi is confirmed using cohesive energy. Subsequently, the electronic properties of penta-Si and penta-HSi are discussed with the aid of electronic band structure and projected density of states (PDOS) maps. The calculated band gap of penta-Si and penta-HSi is 0.251 eV and 3.117 eV, correspondingly. Mainly, the adsorption property of N-nitrosamine on the penta-Si and penta-HSi is studied based on adsorption energy, Mulliken population analysis along with relative energy gap changes. The computed adsorption energy range is in physisorption (- 0.101 to - 0.619 eV), which recommends that the proposed penta-Si and penta-HSi can be employed as a promising sensor to detect the N-nitrosamine in the air environment. METHODS: The structural, electronic and adsorption behaviour of N-nitrosamine on penta-Si and penta-HSi are studied based on the density functional theory (DFT) approach. The hybrid generalized gradient approximation (GGA) with Becke's three-parameter (B3) + Lee-Yang-Parr (LYP) exchange correlation functional is used to optimise the base material. All calculations in the present work are carried out in Quantum-ATK-Atomistic Simulation Software.

CONTEXT: Mercaptopurine is an effective anticancer medicine yet known with serious adverse reactions, thus requiring further attempts to enhance its biological targeting. Small gold clusters Aun (n = 2-10) were used as model reactants to simulate the surface of gold nanoparticles. The computed results show that the drug molecules tend to anchor on the gold clusters at the S atom with the associated binding energies varying from -50 to -34 kcal mol-1 (in vacuum) and from -42 to -28 kcal mol-1 (in aqueous solution). Furthermore, the adsorption of the drug onto the gold surface is considered as a reversible process, and the mechanism of drug releasing was found to be triggerable by internal factors, such as a pH change or the concentrated presence of thiol amino acids in cancerous protein structures. METHOD: Calculations based on density functional theory (DFT) were performed to probe the nature of interactions between the drug and gold nanoparticles. Structural features, thermodynamic parameters, bonding characteristics, and electronic properties of the resulting complexes were investigated at the PBE//cc-pVTZ/cc-pVDZ-PP level.

CONTEXT: Two-dimensional borophene can be used in rechargeable batteries due to its high specific surface area. In this paper, the performance of borophene as an anode material for calcium ion batteries is predicted based on density functional theory calculations. The calculation results show that P doping enhances the calcium storage properties of borophene. The maximum adsorption number of calcium atoms in the P-doped system is 7, with a theoretical capacity of 964 mAh/g. DOS analysis showed that borophene exhibited metallic properties after adsorbing calcium atoms, which improved the electrical conductivity of the electrode material. Calculation of the diffusion energy barrier shows that strain has an effect on calcium diffusion in monolayer borophene, and compressive strain promotes calcium diffusion through borophene. The findings suggest that borophene may be a promising electrode material for calcium-ion batteries. METHODS: In this paper, the intrinsic model and doping model of borophene are constructed by Material Studio 8.0, and the first-principles calculation is carried out by CASTEP module.

CONTEXT: A large number of manganese and rhenium tricarbonyl complexes are known in literature along with various applications in different fields. CO-releasing molecules (CORMs) got recent research attention because CO can act as a prodrug for different diseases. CORMs offer the promising prospect of a safe and controllable amount of CO release. In this research work, we have explored the electronic properties of compounds such as bipyridine-related [Mn(CO)3] and [Re(CO)3] and we have compared the electronic properties of both manganese and rhenium tricarbonyl complexes in the light of carbon monoxide releasing tendency. The chosen Mn and Re metals have enough possibility to vary or play with ligands and design a new and novel CORM molecule. In this context, we have taken a range of 4,4'-disubstituted 2,2' bipyridyl ligands (Rbpy, where R = NH2, tBu, OCH3, H, CF3, CN, NO2) to investigate CO's liberation ability to identify and study such molecules. The calculated absorbance of designed complexes (1-14) shows visible/near-IR region (350-850 nm). The HOMO-LUMO energy gap of 7 (ΔE=2.40 eV) complex and for complex 14 (ΔE=2.28 eV) which is lesser in all complexes but the MLCT percentage is greater in Mn tricarbonyl complexes in comparison to Re tricarbonyl complexes. The calculated results of the FMO approach revealed that complex 7 and 14 have the lowest energy gap which is also in good agreement with DOSs and TDM results. The theoretically calculated results revealed that the both Mn and Re tricarbonyl complexes have a tendency for labialization of CO, but Mn tricarbonyl complexes are more prone to CO release because they have higher MLCT percentage. METHODS: In this research work, we have performed density functional theory (DFT) calculations to explore the physical properties of compounds such as bipyridine-related [Mn(CO)3] and [Re(CO)3] and we have compared the physical properties of both manganese and rhenium tricarbonyl complexes in the light of carbon monoxide releasing tendency. DFT-based calculations were performed by using B3LYP/LANL2DZ basis set followed by acetonitrile solvent using the conductor-like polarizable continuum model (CPCM) for different calculations. Various geometrical calculations were performed using the Gaussian16 suite of programs and the output results obtained from Gaussian16 were visualized using GaussView 5.0.16. The same level of theory was used for various calculations, including frontier molecular orbital (FMO) analysis, metal to ligand charge transfer (MLCT), density of state (DOS) calculations, and transition density of matrix (TDM) calculations. For specific calculations, GaussSum 2.2 software package was used to calculate the density of states, and the Multiwfn 3.8 program was used to analyze the transition density matrix, which is presented using heat maps for both electrons and holes.

Adsorption of 1 and 2 H2O molecules for hydrogen production and storage on the surface of pristine, carbamic acid and 2-amino 3-acetylpyridine functionalized SWCNTs with the dimensionality of (2, 4), (5, 5), and (6, 0) at various positions, i.e., center and edges were investigated by using computational DFT calculations. Adsorption energies and structural and electronic parameters were determined for pristine and functionalized SWCNTs with four different H2O orientations. Functionalization of 2-amino 3-acetylpyridine resulted in more favorable adsorption energies for 1 and 2 H2O molecules splitting as compared to spitting on pristine and carbamic acid functionalized SWCNT. Calculated adsorption constant, Kad confirmed greater binding interactions of functionalized SWCNTs with 1 and 2 H2O molecules as compared to pristine SWCNT. Isosurface for the adsorption of 1 and 2 H2O molecules on pristine and functionalized SWCNTs elaborated altered electrophilic and nucleophilic character. Effect of H2O concentration was monitored to determine hydrogen storage capacity which was found to be 7.17 wt.% for thirty molecules. An important finding of study is production of Stone-Wales (SW) defect upon H2O adsorption leading to increase in hydrogen production and its storage capacity. The functionalization of topological defected SWCNTs provides distinctive applications of CNTs for gas storage purposes.t: METHODS: In the current study, First Principal Density Functional Theory (DFT) calculations were carried which provides greater computational efficiency as compared to many traditional quantum mechanical methods. SCME: ADF (2018) modeling suite software with in framework of DFT approach using exchange correlation (XC) LDA-GGA (Generalized Gradient Approximation) with PBE (Perdew, Burke and Ernzerhof) functional and DZ (Double beta) basis set was employed to investigate structural, energetic and electronic aspects of adsorption on the surface of pristine, carbamic acid and 2-amino 3-acetly pyridine functionalized SWCNTs. (2, 4), (5, 5) and (6, 0) SWCNTs were designed using Avogadro's software and were imported to SCM: ADF graphical interface and were optimized as adsorbent. Single point energy (SPE), geometry optimization and high accuracy frequency calculations were performed to determine energetic, electronic and thermodynamic characteristics and feasibility of adsorption using XC of GGA-PBE functional & DZ basis set.

CONTEXT: Using transition state theory, acetone sensing by pristine and rhodium-doped tin dioxide is discussed. The Evans-Polanyi principle is modified from its original formulation commensurate with the Arrhenius equation to be more suitable for transition state theory. The new formalism for the activation energy replaces enthalpy with Gibbs free energy in the original Evans-Polanyi principle. The new formalism considers reaction entropy, which is not considered previously in Evans-Polanyi principle. Response and response time of interaction of acetone with both pristine and Rh-doped SnO2 clusters is calculated. Variations of response in terms of acetone concentration and temperature are calculated and compared to the experiment. Acceptable agreement between theory and experiment that calls for more comparisons to demonstrate the modified approach. METHODS: The pristine and Rh-doped clusters and their interaction with acetone are simulated using density functional theory at the B3LYP level. 6-311G** and SDD (for heavy atoms) basis sets are used to optimize the structures examined in the present work. Gaussian 09 program and accompanying software performed the current tasks.

CONTEXT: The irradiation of water solution of cytosine with UV light (λmax = 254 nm) shows oxo-hydroxy tautomerism with a rate constant of 6.297 × 10-3 min-1. The order of the reaction implies a tautomeric conversion. After removing the UV light source, we observed a dark reaction with a rate constant of 1.473 × 10-3 min-1 which leads to a restoration of the initial tautomer as before the irradiation. The mechanism of oxo-hydroxy tautomerism of cytosine in water solution was studied in the excited state. It was found that the transformations occur along the 1πσ* excited-state reaction paths which link the Franck-Condon geometries of the tautomers and the conical intersections S0/S1 connected with the H-detachment processes of the corresponding bonds. Furthermore, we established that the conical intersections S0/S1 are also mutually accessible along the 1πσ* excited-state reaction paths. METHODS: The ground-state equilibrium geometries were optimized at the B3LYP/aug-cc-pVDZ level of theory in water environment according to PCM as well as at the CC2/aug-cc-pVDZ level in the gas phase. The TD B3LYP and CC2 methods were applied for the study of the excited states. The tautomerization mechanisms were studied with the use of the linear interpolation in internal coordinates approach using the optimized geometries of tautomers minima and conical intersections S0/S1 at the CASSCF(6,6)/6-31G* level. All calculations were performed with the GAUSSIAN 16 commercial software.

Owing to the devise applications of molecules in industries, the bound state solution of the non-relativistic wave equation with a molecular potential function has been obtained in a closed-form using the Nikiforov-Uvarov method. The solutions of the bound state are then applied to study the information-theoretic measures such as the one-dimensional Shannon and Renyi entropic densities. The expectation values for the position and momentum spaces were obtained to verify the Heisenberg's uncertainty principle. Utilizing the energy spectrum equation, the thermodynamic vibrational partition function is obtained via the Poisson summation. Other thermodynamic function variations with absolute temperature have been obtained numerically for four diatomic molecules (H2, N2, O2, and HF) using Maple 18 software. The Shannon global entropic sum inequality has also been verified. The Renyi sum for constrained index parameters satisfies the global entropic inequality. The thermodynamic properties of the four molecules are similar and conform to works reported in the existing literature. The obtained vibrational energies are in fair agreement with the ones obtained using other forms of potential energy. The result further indicates that the lowest bounds for the Shannon, Renyi, and Heisenberg inequalities are ground states phenomena.