We present the atomistica.online, a web application for generating input files for the ORCA molecular modelling package. atomistica.online is entirely made with the Anvil platform, which allows the ...development of web applications using only Python programming language. ORCA is one of the most, if not the most, powerful molecular modelling tools covering a wide range of possibilities for atomistic calculations on molecules. Speed, ease of installation and use, and clear and intuitive syntax for input files are some of ORCA's characteristics that make it one of the most cited modelling tools in the last several years. Nevertheless, although tools for generating input files for ORCA exist, they are not available as online applications. In this work, we demonstrate how the combination of Python programming language and the Anvil platform makes the development of scientific web applications available to all scientists. All tools within atomistica.online are freely available at the project's official website -
https://atomistica.online
Titanium dioxide (TiO2), one of the most frequently used materials in general, has emerged as an excellent photocatalytic material for environmental applications. In this review, principles and ...mechanisms of the photocatalytic activity of TiO2 have been analyzed. Structural and physical specificities of TiO2 nanoparticles, such as morphology, crystal structure, and electronic and optical properties, have been considered in the context of photocatalytic applications. A review of the influence of several factors, such as the type and dimensions of photocatalyst particles, pH of the solution, the influence of oxidants/electron acceptors, and light intensity on photocatalytic properties of TiO2, has been provided. Superhydrophilicity as an intrinsic property of the TiO2 surface was discussed through surface reconstruction on TiO2 during the reversible hydrophilic changes. Additionally, attention was paid to improving the photocatalytic properties of TiO2 particles through aggregation and agglomeration.
This study investigated the potential of zeolites (NH4BETA, NH4ZSM-5, and NaY) to remove two frequently used dyes, methylene blue (MB) and rhodamine B (RB), from an aqueous environment. The removal ...of dyes with zeolites was performed via two mechanisms: adsorption and photocatalysis. Removal of dyes through adsorption was achieved by studying the Freundlich adsorption isotherms, while photocatalytic removal of dyes was performed under UV irradiation. In both cases, the removal experiments were conducted for 180 min at two temperatures (283 K and 293 K), and dye concentrations were determined spectrophotometrically. Additionally, after photodegradation, mineralization was analyzed as chemical oxygen demand. A computational analysis of the structures of MB and RB was performed to gain a deeper understanding of the obtained results. The computational analysis encompassed density functional theory (DFT) calculations and analysis of two quantum-molecular descriptors addressing the local reactivity of molecules. Experimental results have indicated that the considered zeolites effectively remove both dyes through both mechanisms, especially NH4BETA and NH4ZSM-5, due to the presence of active acidic centers on the outer and inner surfaces of the zeolite. The lowest efficiency of dye removal was achieved in the presence of NaY zeolite, which has a lower SiO2/Al2O3 ratio. A more efficient reduction was completed for RB dye, which agrees with the computationally obtained information about reactivity.
This article represents the spectroscopic and computational studies of two new pyrazine compounds. In order to establish the structure and functional nature of the compounds, we have employed Fourier ...transformed infrared (FT-IR) and Raman spectra, nuclear magnetic resonance (NMR) spectra, and ultraviolet (UV) absorptions and have compared them with the simulated computational spectra and found that they are in the agreeable range. Simulated hyperpolarisability values are used to obtain the nonlinear optic (NLO) activity of the compound, to be used in organic electronic materials. The charge transfer and related properties was investigated by the simulation of electronic spectrum with time dependent density functional theory (TD-DFT). Natural transition orbitals (NTO) provides information about which region of the molecules are more involved in the electronic transitions and the charge transfer properties for the lowest energy excitation have been analyzed on the basis of electron density variation. Molecular dynamics simulations provide information about the behavior of the molecule in solutions. Frontier orbital analysis and study of various reactivity descriptors like ALIE and Fukui provided deep knowledge on the reactivity side. Molecular docking has been also performed to investigate the interaction between title molecules and exhibits inhibitory activity against Pseudomonas aeruginosa Enoyl-Acyl carrier protein reductase (Fabl).
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•Reports spectral analysis and computational studies of two new cyanopyrazine-2-carboxamide derivatives•Details physico-chemical property studies attempted•Compounds show excellent NLO property.•Docking results suggest about activity towards Pseudomonas aeruginosa Enoyl-Acyl carrier protein reductase.
Systematic investigation of optoelectronic properties of curved carbon systems has been performed and the results have been compared with the representatives of flat carbon systems. Moreover, the ...application of third order dispersion corrected density functional tight binding method (with third order corrections of self-consistent charges) including Becke-Johnson dumping (DFTB3-D3(BJ)) has been validated in order to obtain reliable dimer structures for the calculations of charge transfer rates. Optoelectronic properties encompassed calculations of reorganization energies, energy difference between the singlet and triplet state, first hyperpolarizabilities, whereas the charge transfer rates have been calculated according to the equation of Marcus semi-empiric approach. The obtained results indicate that a wide list of outstanding features of buckybowls could be expanded for optoelectronic properties as well. Furthermore, it has also been shown that correlation in the form of the second order exponential decay between electron transfer rates and the specific structural property of buckybowls exists. This allows for computationally inexpensive assessment of electron hopping rates.
In this paper, we introduce our development of both online and desktop graphical user interfaces (GUIs) for the xtb programme to enhance accessibility and user-friendliness. The field of molecular ...modelling has been profoundly transformed by the advent of modern semiempirical calculations, with the xtb programme from Prof. Stefan Grimme's group emerging as an exceptionally powerful tool in this domain. xtb programme operates through a command prompt interface, necessitating a certain level of technical proficiency from its users. The need to use a command prompt might be repealing for some users, such as beginners or users who are not dedicated to computational techniques. This was the primary motivation to develop GUIs for this programme, considering that experienced molecular modellers would also appreciate a user-friendly GUI application that helps them automate their modelling tasks. The online GUI represents a significant leap forward, allowing users to execute xtb calculations directly from their web browsers. Complementing the online version, our desktop GUI extends the functionalities available to users, harnessing the more extensive capabilities of the xtb programme. As all other tools of atomistica.online project, xtb GUIs are freely available at the project's official website -
https://atomistica.online
.
In this work we report spectroscopic characterization and reactivity study by density functional theory (DFT) and molecular dynamics (MD) simulations of two quinoline derivatives. Collected ...computational results for the two new derivatives have been compared with the pristine quinoline in order to investigate the consequences of modifications by introduction of chlorine atoms and methyl and OH groups. Potential energy distribution (PED) analysis has been performed in order to assign principal vibrational numbers. DFT calculations have been used to obtain global and local quantum-molecular descriptors including frontier molecular orbitals, charge distribution by molecular electrostatic potential (MEP) surface, average local ionization energy (ALIE) surface, and Fukui functions. Natural bond order (NBO) analysis has been performed in order to investigate hyper-conjugative properties. To investigate sensitivity towards autoxidation and hydrolysis we have calculated bond dissociation energies (BDE) and radial distribution functions (RDF). Molecular docking study has also been performed in order to initially assess the potential of target molecules to bind with dehydrogenase inhibitor and these quinoline derivatives can be a lead compounds for developing new anti-malarial drug.
2-N-(carboxymethyl)anilino acetic acid (PIDAA) molecule has been spectroscopically characterized and computationally investigated for its fundamental reactive properties by a combination of density ...functional theory (DFT) calculations, molecular dynamics (MD) simulations and molecular docking procedure. A comparison drawn between the simulated and experimentally attained spectra by FT-Raman and FT-IR showed concurrence. The natural bond orbital (NBO) analysis enabled in comprehending the stability and charge delocalization in the title molecule. The first hyperpolarizability which is an important parameter for future studies of nonlinear optics (NLO) was calculated to check the potential of the molecule to be an NLO material. Besides, frontier molecular orbitals (FMO), electron localization function (ELF) and localized orbital locator (LOL) analysis were performed. Energy gap (ΔE), electronegativity (χ), chemical potential (μ), global hardness (η), softness (S), Mulliken population analysis on atomic charges and thermodynamic properties of the title compound at different temperatures have been calculated. The local reactive properties of PIDAA have been addressed by MEP and ALIE surfaces, together with bond dissociation energy for hydrogen abstraction (H-BDE). MD simulations have been used in order to identify atoms with pronounced interactions with water molecules. The pharmaceutical potential of PIDAA has been considered by the analysis of drug likeness parameters and molecular docking procedure. The biological activity of the molecule in terms of molecular docking has been analyzed theoretically for the treatment of SARS and minimum binding energy calculated. The Ramachandran plot was used to check the stereochemistry of the protein structure. In addition, a comparison of the physiochemical parameters of PIDAA and commercially available drugs (Yu et al., 2004; Tan et al., 2004; Elshabrawy et al., 2014; Chu et al., 2004; Gopal Samy and Xavier, 2015) were carried out.
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•CHELPG, NBO and NHO analyses of PIDAA were carried out.•NLO properties, local reactivity parameters (MEP and ALIE), electron localization function and localized orbital locator were analysed.•The bond dissociation energy for hydrogen abstraction (H-BDE) and interactions with water are accounted for.•The bond dissociation energy for hydrogen abstraction (H-BDE) and interactions with water are accounted for.•Suitable excipient substance to improve the properties was analyzed•Molecular docking of PIDAA with SARS protein 4APH.
Due to the inability of conventional wastewater treatment procedures to remove organic pharmaceutical pollutants, active pharmaceutical components remain in wastewater and even reach tap water. In ...terms of pharmaceutical pollutants, the scientific community focuses on β-blockers due to their extensive (over)usage and moderately high solubility. In this study, the photocatalytic activity of V2O5 was investigated through the degradation of nadolol (NAD), pindolol (PIN), metoprolol (MET), and their mixture under ultraviolet (UV) irradiation in water. For the preparation of V2O5, facile hydrothermal synthesis was used. The structural, morphological, and surface properties and purity of synthesized V2O5 powder were investigated by scanning electron microscopy (SEM), X-ray, and Raman spectroscopy. SEM micrographs showed hexagonal-shaped platelets with well-defined morphology of materials with diameters in the range of 10–65 µm and thickness of around a few microns. X-ray diffraction identified only one crystalline phase in the sample. The Raman scattering measurements taken on the catalyst confirmed the result of XRPD. Degradation kinetics were monitored by ultra-fast liquid chromatography with diode array detection. The results showed that in individual solutions, photocatalytic degradation of MET and NAD was relatively insignificant (<10%). However, in the PIN case, the degradation was significant (64%). In the mixture, the photodegradation efficiency of MET and NAD slightly increased (15% and 13%). Conversely, it reduced the PIN to the still satisfactory value of 40%. Computational analysis based on molecular and periodic density functional theory calculations was used to complement our experimental findings. Calculations of the average local ionization energy indicate that the PIN is the most reactive of all three considered molecules in terms of removing an electron from it.
Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic ...pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding their fundamental reactive properties. In this study we have theoretically investigated reactive properties of LOR using both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT study is used for collecting information related to the molecule stability, structure, frontier molecular orbitals, quantum molecular descriptors, charge distribution, molecular electrostatic potential surfaces, charge polarization, and local reactivity properties according to average local ionization energy surfaces. Based on these results, N24 atom of pyridine ring and oxygen atom O1 were identified with nucleophilic nature. In order to collect the information necessary for the proposition of degradation compounds we also calculated bond dissociation energies (BDE) for hydrogen abstraction and single acyclic bonds as well. According to BDE, the oxidation is likely to occur in the piperidine and cycloheptane rings. MD simulations were used in order to understand the interactions with water through radial distribution functions (RDF). Based on RDFs the most important interactions with solvent are determined for carbon atom C5, chlorine atom Cl15, and oxygen atom O1. Collected results based on DFT calculations and MD simulations provided information important for suggestion of possible degradation compounds. Covalent and noncovalent interactions between LOR and
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OH have also been investigated.
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