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Journal articles on the topic 'Systems biology, density functional theory, computational modeling'

Author: Grafiati

Published: 9 March 2023

Last updated: 19 July 2025

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1

Koch, Robert J., Guangfang Li, Shubham Pandey, Simon R. Phillpot, Hui Wang, and Scott T. Misture. "Complex modeling for the quantification of nanoscale disorder using genetic algorithms, density functional theory and line-profile analysis." Journal of Applied Crystallography 53, no. 4 (2020): 1087–100. http://dx.doi.org/10.1107/s1600576720008225.

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A new, computationally efficient, complex modeling approach is presented for the quantification of the local and average atomic structure, nanostructure and microstructure of an Au0.25Cu0.75 alloy. High-resolution X-ray powder diffraction and whole pattern fitting show that the sample is phase pure, with isotropic lattice strain and a distribution of equiaxed crystallites of mean size 144 (11) nm, where each crystallite has on average four twin boundaries and an average of three deformation faults per four crystallites. Both small- and large-box model optimizations were used to extract local a

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Czernek, Jiří, and Jiří Brus. "Reliable Dimerization Energies for Modeling of Supramolecular Junctions." International Journal of Molecular Sciences 25, no. 1 (2024): 602. http://dx.doi.org/10.3390/ijms25010602.

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Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respect

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Arora, Yashika, Pushpinder Walia, Mitsuhiro Hayashibe, et al. "Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans." PLOS Computational Biology 17, no. 10 (2021): e1009386. http://dx.doi.org/10.1371/journal.pcbi.1009386.

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Transcranial direct current stimulation (tDCS) has been shown to evoke hemodynamics response; however, the mechanisms have not been investigated systematically using systems biology approaches. Our study presents a grey-box linear model that was developed from a physiologically detailed multi-compartmental neurovascular unit model consisting of the vascular smooth muscle, perivascular space, synaptic space, and astrocyte glial cell. Then, model linearization was performed on the physiologically detailed nonlinear model to find appropriate complexity (Akaike information criterion) to fit functi

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Pandey, Anoop Kumar, Vijay Singh, and Apoorva Dwivedi. "Quantum chemical calculations of a novel Specie – Boron Nano Bucket (B16) and the interaction of its complex (B15-Li) with drug Resorcinol." Journal of Computational Methods in Sciences and Engineering 20, no. 3 (2020): 1017–28. http://dx.doi.org/10.3233/jcm-200032.

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At Nano-scale level, innovative biomedical techniques are developed in advanced drug delivery systems and targeted Nano-therapy. Ultrathin needles provide a low invasive and highly selective means for molecular delivery and cell manipulation. This article studies the geometry and the stability of Boron Nano-Bucket (B16 Cluster of Bucket Shape) and B15-Li complex by using computational modeling methods. The equilibrium geometry of Boron Nano-Bucket and BNB-Li complex in the ground state have been determined and analyzed by Density functional theory (DFT) employing 6-311 G (d, p) as the basis se

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Cruz-Cabeza, Aurora J., та Frank H. Allen. "Conformation and geometry of cyclopropane rings having π-acceptor substituents: a theoretical and database study". Acta Crystallographica Section B Structural Science 67, № 1 (2010): 94–102. http://dx.doi.org/10.1107/s0108768110049517.

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The 3e′ orbitals of cyclopropane have the correct symmetry to interact with low-lying unoccupied orbitals of π-acceptor substituents and maximum overlap occurs when the two orbital systems are parallel, i.e. when the π-acceptor bisects the ring in projection down the substituent bond. Since the cyclopropyl group is a common component of active pharmaceutical and agrochemical ingredients, it is important that these strong conjugative interactions are well modelled by computational techniques, and clearly represented in experimental crystal structures. Here we show that torsion angle distributio

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Czernek, Jiří, and Jiří Brus. "On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions." International Journal of Molecular Sciences 24, no. 17 (2023): 13349. http://dx.doi.org/10.3390/ijms241713349.

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There have been attempts, both experimental and based on density-functional theory (DFT) modeling, at understanding the factors that govern the electronic conductance behavior of single-stacking junctions formed by pi-conjugated materials in nanogaps. Here, a reliable description of relevant stacked configurations of some thiophene-cored systems is provided by means of high-level quantum chemical approaches. The minimal structures of these configurations, which are found using the dispersion-corrected DFT approach, are employed in calculations that apply the coupled cluster method with singles

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Kersen, David E. Chen, Gaia Tavoni, and Vijay Balasubramanian. "Connectivity and dynamics in the olfactory bulb." PLOS Computational Biology 18, no. 2 (2022): e1009856. http://dx.doi.org/10.1371/journal.pcbi.1009856.

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Dendrodendritic interactions between excitatory mitral cells and inhibitory granule cells in the olfactory bulb create a dense interaction network, reorganizing sensory representations of odors and, consequently, perception. Large-scale computational models are needed for revealing how the collective behavior of this network emerges from its global architecture. We propose an approach where we summarize anatomical information through dendritic geometry and density distributions which we use to calculate the connection probability between mitral and granule cells, while capturing activity patte

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Kostrobij, P. P., B. M. Markovych, and I. A. Ryzha. "Semi-infinite metallic system: QST versus DFT." Mathematical Modeling and Computing 9, no. 1 (2022): 178–85. http://dx.doi.org/10.23939/mmc2022.01.178.

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Modeling and investigation of thermodynamic characteristics of spatially-finite metallic systems is an essential task of modern nanophysics. We show that the widely used DFT (density functional theory) is less efficient than the QST (quantum-statistical theory) approach.

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9

Söderlind, Per, G. Kotliar, K. Haule, P. M. Oppeneer, and D. Guillaumont. "Computational modeling of actinide materials and complexes." MRS Bulletin 35, no. 11 (2010): 883–88. http://dx.doi.org/10.1557/mrs2010.715.

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In spite of being rare, actinide elements provide the building blocks for many fascinating condensed-matter systems, both from an experimental and theoretical perspective. Experimental observations of actinide materials are difficult because of rarity, toxicity, radioactivity, and even safety and security. Theory, on the other hand, has its own challenges. Complex crystal and electronic structures are often encountered in actinide materials, as well as pronounced electron correlation effects. Consequently, theoretical modeling of actinide materials and their 5f electronic states is very diffic

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10

KOLB, BRIAN, and T. THONHAUSER. "MOLECULAR BIOLOGY AT THE QUANTUM LEVEL: CAN MODERN DENSITY FUNCTIONAL THEORY FORGE THE PATH?" Nano LIFE 02, no. 02 (2012): 1230006. http://dx.doi.org/10.1142/s1793984412300063.

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Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical

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11

Guan, Haoyue, Huimin Sun, and Xia Zhao. "Application of Density Functional Theory to Molecular Engineering of Pharmaceutical Formulations." International Journal of Molecular Sciences 26, no. 7 (2025): 3262. https://doi.org/10.3390/ijms26073262.

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This review systematically examines the pivotal applications of the Density Functional Theory (DFT) in drug formulation design, emphasizing its capability to elucidate molecular interaction mechanisms through quantum mechanical calculations. By solving the Kohn–Sham equations with precision up to 0.1 kcal/mol, DFT enables accurate electronic structure reconstruction, providing theoretical guidance for optimizing drug–excipient composite systems. In solid dosage forms, DFT clarifies the electronic driving forces governing active pharmaceutical ingredient (API)–excipient co-crystallization, pred

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Palos, Etienne, Saswata Dasgupta, Eleftherios Lambros, and Francesco Paesani. "Data-driven many-body potentials from density functional theory for aqueous phase chemistry." Chemical Physics Reviews 4, no. 1 (2023): 011301. http://dx.doi.org/10.1063/5.0129613.

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Density functional theory (DFT) has been applied to modeling molecular interactions in water for over three decades. The ubiquity of water in chemical and biological processes demands a unified understanding of its physics, from the single molecule to the thermodynamic limit and everything in between. Recent advances in the development of data-driven and machine-learning potentials have accelerated simulation of water and aqueous systems with DFT accuracy. However, anomalous properties of water in the condensed phase, where a rigorous treatment of both local and non-local many-body (MB) intera

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13

Plass, Winfried. "Vanadium haloperoxidases as supramolecular hosts: Synthetic and computational models." Pure and Applied Chemistry 81, no. 7 (2009): 1229–39. http://dx.doi.org/10.1351/pac-con-08-10-19.

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In the active-site cavity of vanadium haloperoxidases vanadate as the prosthetic group is solely fixed by one covalent bond to a histidine residue and embedded in a supramolecular environment of extensive hydrogen bonds. Structural aspects of relevant vanadium complexes with supramolecular interactions, including assemblies with chiral hosts, are presented. The importance of hydrogen-bonding relays is presented together with relevant examples. The reactivity of related functional mimics containing vanadium and molybdenum toward the oxidation of thioethers is described. Computational modeling b

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Borrego-Sánchez, Ana, Mahmoud Awad, and Claro Sainz-Díaz. "Molecular Modeling of Adsorption of 5-Aminosalicylic Acid in the Halloysite Nanotube." Minerals 8, no. 2 (2018): 61. http://dx.doi.org/10.3390/min8020061.

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Halloysite nanotubes are becoming interesting materials for drug delivery. The knowledge of surface interactions is important for optimizing this application. The aim of this work is to perform a computational study of the interaction between 5-aminosalicylic acid (5-ASA) drug and halloysite nanotubes for the development of modified drug delivery systems. The optimization of this nanotube and the adsorption of different conformers of the 5-ASA drug on the internal surface of halloysite in the presence and absence of water were performed using quantum mechanical calculations by using Density Fu

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Champagne, Aurélie, Samuel Dechamps, Simon M. M. Dubois, Aurélien Lherbier, Viet-Hung Nguyen, and Jean-Christophe Charlier. "Computational Atomistic Modeling in Carbon Flatland and Other 2D Nanomaterials." Applied Sciences 10, no. 5 (2020): 1724. http://dx.doi.org/10.3390/app10051724.

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As in many countries, the rise of nanosciences in Belgium has been triggered in the eighties in the one hand, by the development of scanning tunneling and atomic force microscopes offering an unprecedented possibility to visualize and manipulate the atoms, and in the other hand, by the synthesis of nano-objects in particular carbon nanostructures such as fullerene and nanotubes. Concomitantly, the increasing calculating power and the emergence of computing facilities together with the development of DFT-based ab initio softwares have brought to nanosciences field powerful simulation tools to a

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Badu, Shyam, Roderick Melnik, and Sundeep Singh. "Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models." Applied Sciences 10, no. 19 (2020): 6821. http://dx.doi.org/10.3390/app10196821.

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In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formul

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17

Ferretti, Alfonso, Laura Canal, Robert A. Sorodoc, Sourab Sinha, and Giuseppe Brancato. "Fine Tuning the Intermolecular Interactions of Water Clusters Using the Dispersion-Corrected Density Functional Theory." Molecules 28, no. 9 (2023): 3834. http://dx.doi.org/10.3390/molecules28093834.

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Dispersion-inclusive density functional theory (DFT) methods have unequivocally demonstrated improved performances with respect to standard DFT approximations for modeling large and extended molecular systems at the quantum mechanical level. Yet, in some cases, disagreements with highly accurate reference calculations, such as CCSD(T) and quantum Monte Carlo (MC) calculations, still remain. Furthermore, the application of general-purpose corrections, such as the popular Grimme’s semi-classical models (DFT-D), to different Kohn–Sham exchange–correlation functionals sometimes leads to variable a

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18

Holmberg-Kasa, Jacob, Pär A. T. Olsson, and Martin Fisk. "Investigating Elastic Deformation of Ordered Precipitates by Ab Initio-Informed Phase-Field Crystal Modeling." Metals 14, no. 12 (2024): 1399. https://doi.org/10.3390/met14121399.

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Ni-based superalloys, essential for high-temperature applications, derive strength from coherent second-order precipitates that impede dislocation motion through coherency misfit and elastic mismatch. This study employs multi-component phase-field crystal (PFC) simulations to explore the elastic deformation of such precipitates. Using a binary ordered square structure for the precipitate and a single species square structure for the matrix, elastic properties and lattice parameters are fitted to data from ab initio density functional theory calculations for Ni and Ni3Ti systems. Simulations re

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19

Sokurov, Aslan A. "Numerical calculation of integrals in the density functional theory in the electron gas approximation using CUDA technology." Vestnik of Saint Petersburg University. Applied Mathematics. Computer Science. Control Processes 20, no. 3 (2024): 335–49. http://dx.doi.org/10.21638/spbu10.2024.303.

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The expression for the potential energy of interaction of two neutral atoms in the absence of a chemical bond consists of the sum of multiple and improper integrals. Due to the cumbersome nature of the functions, finding these integrals in explicit form is not possible. Software systems widely used in practice based on standard methods of computational mathematics are also not capable of providing satisfactory accuracy in their numerical calculations in a short time. In quantum chemistry and computational physics, the above greatly limits approaches to modeling the properties and structures of

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20

Huang, Liang-Feng, John R. Scully, and James M. Rondinelli. "Modeling Corrosion with First-Principles Electrochemical Phase Diagrams." Annual Review of Materials Research 49, no. 1 (2019): 53–77. http://dx.doi.org/10.1146/annurev-matsci-070218-010105.

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Understanding and predicting materials corrosion under electrochemical environments are of increasing importance to both established and developing industries and technologies, including construction, marine materials, geology, and biomedicine, as well as to energy generation, storage, and conversion. Owing to recent progress in the accuracy and capability of density functional theory (DFT) calculations to describe the thermodynamic stability of materials, this powerful computational tool can be used both to describe materials corrosion and to design materials with the desired corrosion resist

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21

Gusarov, Sergey, Yuri Yu Dmitriev, Stanislav R. Stoyanov, and Andriy Kovalenko. "Koopmans’ multiconfigurational self-consistent field (MCSCF) Fukui functions and MCSCF perturbation theory." Canadian Journal of Chemistry 91, no. 9 (2013): 886–93. http://dx.doi.org/10.1139/cjc-2012-0526.

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Prediction of chemical reactivity has become one of the highest priority tasks of computational chemistry since the development of the methods of modeling electronic structure. Despite the general simplicity of the physical concept of reactivity and the rapid development of modern density functional theory (DFT) methods, this task remains state-of-the-art for systems with wavefunctions that have a multiconfigurational character. In such cases, for the accurate description of reactivity one needs to use multiconfigurational approaches that are much heavier computationally then ordinary single-d

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22

Donà, Lorenzo, Jan Gerit Brandenburg, and Bartolomeo Civalleri. "Metal–organic frameworks properties from hybrid density functional approximations." Journal of Chemical Physics 156, no. 9 (2022): 094706. http://dx.doi.org/10.1063/5.0080359.

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The chemical versatility and modular nature of Metal–Organic Frameworks (MOFs) make them unique hybrid inorganic–organic materials for several important applications. From a computational point of view, ab initio modeling of MOFs is a challenging and demanding task, in particular, when the system reaches the size of gigantic MOFs as MIL-100 and MIL-101 (where MIL stands for Materials Institute Lavoisier) with several thousand atoms in the unit cell. Here, we show how such complex systems can be successfully tackled by a recently proposed class of composite electronic structure methods revised

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23

GUN'KO, VLADIMIR M. "MODELING OF INTERFACIAL BEHAVIOR OF WATER AND ORGANICS." Journal of Theoretical and Computational Chemistry 12, no. 07 (2013): 1350059. http://dx.doi.org/10.1142/s0219633613500594.

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Modeling of water structure at a surface of different adsorbents, as well as an influence of dissolved compounds or co-adsorbates on bound water, is of importance to understand the temperature dependence of the characteristics of bound water, especially at T < 273 K, in comparison with bulk water. 1 H NMR spectra giving useful information on the water structure can be obtained using different ways such as experimental measurements, direct ab initio and density functional theory (DFT) calculations or estimation using semiempirical calculations and appropriate calibration functions. Here, app

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Flores-Holguín, Norma, Joaquín Ortega-Castro, Juan Frau, and Daniel Glossman-Mitnik. "Conceptual DFT-Based Computational Peptidology, Pharmacokinetics Study and ADMET Report of the Veraguamides A–G Family of Marine Natural Drugs." Marine Drugs 20, no. 2 (2022): 97. http://dx.doi.org/10.3390/md20020097.

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As a continuation of our research on the chemical reactivity, pharmacokinetics and ADMET properties of cyclopeptides of marine origin with potential therapeutic abilities, in this work our already presented integrated molecular modeling protocol has been used for the study of the chemical reactivity and bioactivity properties of the Veraguamides A–G family of marine natural drugs. This protocol results from the estimation of the conceptual density functional theory (CDFT) chemical reactivity descriptors together with several chemoinformatics tools commonly considered within the process of deve

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Saleev, Vladimir, and Alexandra Shipilova. "Ab initio study of optical and bulk properties of cesium lead halide perovskite solid solutions." Modern Physics Letters B 33, no. 31 (2019): 1950386. http://dx.doi.org/10.1142/s021798491950386x.

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The first-principles calculations of band gaps and bulk moduli of cesium lead halide perovskite solid solutions, [Formula: see text] and [Formula: see text], are performed at the level of general gradient approximation of the density functional theory. We use supercell approach for computational modeling of disordered systems, which gives a description of the properties of the structure baasing on the average over a set of multiple configurations, namely distributions of different species over a given set of atomic positions. The calculations were performed with the CRYSTAL14 program package.

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Drosou, Maria, Christiana A. Mitsopoulou, Maylis Orio, and Dimitrios A. Pantazis. "EPR Spectroscopy of Cu(II) Complexes: Prediction of g-Tensors Using Double-Hybrid Density Functional Theory." Magnetochemistry 8, no. 4 (2022): 36. http://dx.doi.org/10.3390/magnetochemistry8040036.

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Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for all chemical systems. Among transition metal ions, Cu(II) centers in inorganic chemistry and biology, and their associated EPR properties such as hyperfine coupling and g-tensors, pose exceptional difficulties for all levels of quantum chemistry. In the pres

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Qian, Zhao, Guanzhong Jiang, Yingying Ren, Xi Nie, and Rajeev Ahuja. "Atomistic Modeling of Various Doped Mg2NiH4 as Conversion Electrode Materials for Lithium Storage." Crystals 9, no. 5 (2019): 254. http://dx.doi.org/10.3390/cryst9050254.

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In this work, we have compared the potential applications of nine different elements doped Mg2NiH4 as conversion-type electrode materials in Li-ion batteries by means of state-of-the-art Density functional theory calculations. The electrochemical properties, such as specific capacity, volume change and average voltage, as well as the atomic and electronic structures of different doped systems have been investigated. The Na doping can improve the electrochemical capacity of the pristine material. Si and Ti doping can reduce the band gap and benefit the electronic conductivity of electrode mater

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Deng, Xingyi, Dominic Alfonso, Dan C. Sorescu, Thuy Duong Nguyen Phan, and Douglas Kauffman. "(Invited) Coupling of Electrochemistry with Surface Science and Computational Modeling to Understand Nanoparticle Electrocatalysts." ECS Meeting Abstracts MA2023-02, no. 48 (2023): 2414. http://dx.doi.org/10.1149/ma2023-02482414mtgabs.

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We investigated nanoparticle electrocatalysts in oxygen evolution reaction (OER) and CO2 reduction reaction (CO2RR) via an approach coupling electrochemistry with ultra-high vacuum (UHV) surface science and computational modeling. Well-defined nanoparticle electrocatalysts such as Fe2O3, NiFeOx, and Ag, were prepared in the UHV chamber via physical vapor deposition (PVD) and characterized with surface science techniques including X-ray photoelectron spectroscopy (XPS) and scanning tunneling microscopy (STM), followed by electrochemistry measurements to establish the structure-property relation

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Matanovic, Ivana, Megan Christina Davis, Wilton Kort-Kamp, et al. "Computational Modeling and Machine Learning Approaches for Accelerated Materials Design." ECS Meeting Abstracts MA2024-01, no. 45 (2024): 2530. http://dx.doi.org/10.1149/ma2024-01452530mtgabs.

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A substantial part of research in energy storage and conversion systems concerns the discovery and characterization of novel materials with improved performance, but most advancements are still generally attributed to costly and time-consuming trial-and-error experimentation. Computational chemistry methods combined with machine learning techniques offer paradigm shift in how materials are fundamentally understood and designed. Namely, high-throughput calculations combined with machine learning can help evaluate different properties of complex materials and efficiently screen millions of candi

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Markovic, Milica, Shimon Ben-Shabat, Shahar Keinan, Aaron Aponick, Ellen M. Zimmermann, and Arik Dahan. "Molecular Modeling-Guided Design of Phospholipid-Based Prodrugs." International Journal of Molecular Sciences 20, no. 9 (2019): 2210. http://dx.doi.org/10.3390/ijms20092210.

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The lipidic prodrug approach is an emerging field for improving a number of biopharmaceutical and drug delivery aspects. Owing to their structure and nature, phospholipid (PL)-based prodrugs may join endogenous lipid processing pathways, and hence significantly improve the pharmacokinetics and/or bioavailability of the drug. Additional advantages of this approach include drug targeting by enzyme-triggered drug release, blood–brain barrier permeability, lymphatic targeting, overcoming drug resistance, or enabling appropriate formulation. The PL-prodrug design includes various structural modalit

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Tang, Michael T., Michal Bajdich, and Frank Ablid-Pedersen. "Contrasting Theories of Electrode Models in Electrocatalysis Under Aqueous Alkaline Solutions." ECS Meeting Abstracts MA2024-02, no. 61 (2024): 4089. https://doi.org/10.1149/ma2024-02614089mtgabs.

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The computational hydrogen electrode (CHE) model has been a mainstay tool for understanding electrochemical reactions over electrocatalytic surfaces. While the electrode model has seen success in modeling catalysis under highly acidic solutions, over recent years, focus has shifted towards electrochemistry under neutral or alkaline solutions. In such cases, various correction schemes have been applied onto the computational hydrogen electrode in order to address its inability to describe pH dependent effects. Many of these schemes are often computationally cumbersome and not very transferrable

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Petrone, Alessio, Fulvio Perrella, Federico Coppola, et al. "Ultrafast photo-induced processes in complex environments: The role of accuracy in excited-state energy potentials and initial conditions." Chemical Physics Reviews 3, no. 2 (2022): 021307. http://dx.doi.org/10.1063/5.0085512.

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Light induces non-equilibrium time evolving molecular phenomena. The computational modeling of photo-induced processes in large systems, embedded in complex environments (i.e., solutions, proteins, materials), demands for a quantum and statistical mechanic treatment to achieve the required accuracy in the description of both the excited-state energy potentials and the choice of the initial conditions for dynamical simulations. On the other hand, the theoretical investigation on the atomistic scale of times and sizes of the ultrafast photo-induced reactivity and non-equilibrium relaxation dynam

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Marino, Tiziana, Maria Grazia Fortino, Nino Russo, Marirosa Toscano, and Marta Erminia Alberto. "Computational Mechanistic Insights on the NO Oxidation Reaction Catalyzed by Non-Heme Biomimetic Cr-N-Tetramethylated Cyclam Complexes." International Journal of Molecular Sciences 20, no. 16 (2019): 3955. http://dx.doi.org/10.3390/ijms20163955.

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The conversion reaction of NO to NO3− ion catalyzed by the end-on [Cr(III)(n-TMC)(O2)(Cl)]+ superoxo and side-on [Cr(IV)(n-TMC)(O2)(Cl)]+ peroxo non-heme complexes (n = 12, 13, 14 and 15), which are biomimetic systems of nitric oxide dioxygenases (NODs), has been explored using a computational protocol in the framework of density functional theory. Results show that the potential energy profiles for the studied reactions lie above the reagent energies, regardless of the used catalyst. Both the O-O bond breaking in the biomimetics and the NO3− ion formation require low energy barriers suggestin

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Woo, Mino, Lubow Maier, Steffen Tischer, Olaf Deutschmann, and Martin Wörner. "A Qualitative Numerical Study on Catalytic Hydrogenation of Nitrobenzene in Gas-Liquid Taylor Flow with Detailed Reaction Mechanism." Fluids 5, no. 4 (2020): 234. http://dx.doi.org/10.3390/fluids5040234.

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While the number of computational studies considering two-phase flows in microfluidic systems with or without mass transfer is increasing, numerical studies incorporating chemical reactions are still rare. This study aims to simulate the catalytic hydrogenation of nitrobenzene in gas-liquid Taylor flow by combining interface-resolving numerical simulations of two-phase flow and mass transfer by a volume-of-fluid method with detailed modeling of the heterogeneous chemical reaction by software package DETCHEMTM. Practically relevant physical properties are utilized for hydrodynamic and mass tran

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Numin, Mohd Sofi, Khairulazhar Jumbri, Kee Kok Eng, et al. "Effect of Alkyl Chain Length of Quaternary Ammonium Surfactant Corrosion Inhibitor on Fe (110) in Acetic Acid Media via Computer Simulation." ChemEngineering 9, no. 1 (2025): 7. https://doi.org/10.3390/chemengineering9010007.

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Density functional theory (DFT) and molecular dynamics (MD) simulations were employed to investigate the inhibition mechanism of cationic quaternary ammonium surfactant corrosion inhibitors (CIs) with varying chain lengths in 1.0 M HCl and 500 ppm acetic acid on Fe (110) surfaces. DFT calculations demonstrated that all surfactant CI molecules possess favorable inhibition properties, with the cationic quaternary ammonium groups (N+) and alpha carbon serving as electron-donating reactive centers, characterized by a low band-gap energy of 1.26 eV. MD simulations highlighted C12, with a 12-alkyl c

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Anita, Sahu, Sarathi Sengupta Partha, and Biswas Bhaskar. "Synthesis, spectroscopic characterization with computational modeling and epoxidation activity of two iron(III)-Schiff base complexes." Journal of Indian Chemical Society Vol. 95, May 2018 (2018): 507–15. https://doi.org/10.5281/zenodo.5642722.

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Department of Chemistry, Surendranath College, Kolkata-700 009, India E-mail: mr.bbiswas@rediffmail.com, icbbiswas@gmail.com Department of Chemistry, Vivekananda Mahavidyalaya, Burdwan-713 104, West Bengal, India <em>Manuscript received 25 March 2018, revised 29 March 2018, accepted 02 April 2018</em> Two non-heme mononuclear iron(III) complexes, [Fe(L)Cl] (1) and [Fe(L)Br] (2) containing a (N,O)-donor Schiff base ligand, (H<sub>2</sub> L = 2-((5-((2-hydroxyphenylimino)methyl)furan-2-yl)methyleneamino)phenol), have been synthesized and isolated in pure state. The structural formulation for iro

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Duan, Na, Zisen Gao, Baichun Hu, et al. "Computational insights into the binding pattern of mitochondrial calcium uniporter inhibitor through homology modeling, molecular dynamics simulation, binding free energy prediction and density functional theory calculation." Journal of Biomolecular Structure and Dynamics 38, no. 17 (2019): 5095–107. http://dx.doi.org/10.1080/07391102.2019.1695674.

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Lin, Yin-Pai, Sergei Piskunov, Laima Trinkler, Mitch Ming-Chi Chou, and Liuwen Chang. "Electronic and Optical Properties of Rocksalt Mg1−xZnxO and Wurtzite Zn1−xMgxO with Varied Concentrations of Magnesium and Zinc." Materials 15, no. 21 (2022): 7689. http://dx.doi.org/10.3390/ma15217689.

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The structural, electronic and optical properties of rocksalt Mg1−xZnxO and wurtzite Zn1−xMgxO with the concentration of Zn and Mg varying from 0.125 to 0.875 were investigated using density functional theory (DFT), DFT+U, linear response theory and the Bethe–Salpeter equation. According to the experimental band gap for varied concentrations of magnesium and zinc, modeling the supercell was utilized for the varied concentrations of Mg/Zn/O compounds in order to not only avoid constructing the complicated interface systems that are observed in the experiments but also take into account the exci

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Abramyan, Ara, Zhiwei Liu, and Vojislava Pophristic. "An ab-initio study of pyrrole and imidazole arylamides." Journal of the Serbian Chemical Society 78, no. 11 (2013): 1789–95. http://dx.doi.org/10.2298/jsc130929104a.

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Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD) simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we

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Armaković, Stevan, Đorđe Vujić, and Boris Brkić. "Computational Multiscale Study of the Interaction Between the PDMS Polymer and Sunscreen-Related Pollutant Molecules." Molecules 29, no. 20 (2024): 4908. http://dx.doi.org/10.3390/molecules29204908.

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Sunscreen molecules play a critical role in protecting skin from ultraviolet radiation, yet their efficient detection and separation pose challenges in environmental and analytical contexts. In this work, we employ a multilevel modeling approach to investigate the molecular interactions between representative sunscreen molecules and the polydimethylsiloxane (PDMS) polymer, a material widely recognized for its sorbent properties. Our goal is to explore how these interactions can be fine-tuned to facilitate the effective separation of sunscreen molecules in portable membrane inlet mass spectrome

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Armaković, Stevan, Đorđe Vujić, and Boris Brkić. "Computational Multiscale Study of the Interaction Between the PDMS Polymer and Sunscreen-Related Pollutant Molecules." Molecules 29, no. 20 (2024): 4908. https://doi.org/10.3390/molecules29204908.

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Sunscreen molecules play a critical role in protecting skin from ultraviolet radiation, yet their efficient detection and separation pose challenges in environmental and analytical contexts. In this work, we employ a multilevel modeling approach to investigate the molecular interactions between representative sunscreen molecules and the polydimethylsiloxane (PDMS) polymer, a material widely recognized for its sorbent properties. Our goal is to explore how these interactions can be fine-tuned to facilitate the effective separation of sunscreen molecules in portable membrane inlet mass spectrome

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Biaggne, Austin, Lawrence Spear, German Barcenas, et al. "Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates." Molecules 27, no. 11 (2022): 3456. http://dx.doi.org/10.3390/molecules27113456.

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Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M−1cm−1) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations,

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Oprea, Corneliu, and Mihai Gîrțu. "Structure and Electronic Properties of TiO2 Nanoclusters and Dye–Nanocluster Systems Appropriate to Model Hybrid Photovoltaic or Photocatalytic Applications." Nanomaterials 9, no. 3 (2019): 357. http://dx.doi.org/10.3390/nano9030357.

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We report the results of a computational study of TiO2 nanoclusters of various sizes as well as of complex systems with various molecules adsorbed onto the clusters to set the ground for the modeling of charge transfer processes in hybrid organic–inorganic photovoltaics or photocatalytic degradation of pollutants. Despite the large number of existing computational studies of TiO2 clusters and in spite of the higher computing power of the typical available hardware, allowing for calculations of larger systems, there are still studies that use cluster sizes that are too small and not appropriate

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Cindrić, Maja, Irena Sović, Marija Mioč, et al. "Experimental and Computational Study of the Antioxidative Potential of Novel Nitro and Amino Substituted Benzimidazole/Benzothiazole-2-Carboxamides with Antiproliferative Activity." Antioxidants 8, no. 10 (2019): 477. http://dx.doi.org/10.3390/antiox8100477.

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We present the synthesis of a range of benzimidazole/benzothiazole-2-carboxamides with a variable number of methoxy and hydroxy groups, substituted with nitro, amino, or amino protonated moieties, which were evaluated for their antiproliferative activity in vitro and the antioxidant capacity. Antiproliferative features were tested on three human cancer cells, while the antioxidative activity was measured using 1,1-diphenyl-picrylhydrazyl (DPPH) free radical scavenging and ferric reducing antioxidant power (FRAP) assays. Trimethoxy substituted benzimidazole-2-carboxamide 8 showed the most promi

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Ching, Wai-Yim, Puja Adhikari, Bahaa Jawad, and Rudolf Podgornik. "Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory." Biomedicines 11, no. 2 (2023): 517. http://dx.doi.org/10.3390/biomedicines11020517.

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The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations

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Pourrahmani, Hossein. "Analyzing the Roles of Copper in Carbon Capture and Sequestration Using Mean Field Density Functional Theory and Scanning Transmission Electron Microscopy." ECS Meeting Abstracts MA2024-02, no. 62 (2024): 4254. https://doi.org/10.1149/ma2024-02624254mtgabs.

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Exploring the role of Copper (Cu) in carbon capture and sequestration presents a rich area for research, including but not limited to Nanostructure copper materials, Copper-based hybrid materials, Copper-based electrocatalysts, copper in biomimetic systems, Copper-based membranes for gas separation, Copper in carbon mineralization, Copper in photochemical conversion, and copper-based direct air capture technologies that can enhance the capture and conversion. In this regard, efficient methods to characterize the role of Cu in carbon sequestration processes should be developed computationally a

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Cocchi, Caterina, and Holger-Dietrich Saßnick. "Ab Initio Quantum-Mechanical Predictions of Semiconducting Photocathode Materials." Micromachines 12, no. 9 (2021): 1002. http://dx.doi.org/10.3390/mi12091002.

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Ab initio Quantum-Mechanical methods are well-established tools for material characterization and discovery in many technological areas. Recently, state-of-the-art approaches based on density-functional theory and many-body perturbation theory were successfully applied to semiconducting alkali antimonides and tellurides, which are currently employed as photocathodes in particle accelerator facilities. The results of these studies have unveiled the potential of ab initio methods to complement experimental and technical efforts for the development of new, more efficient materials for vacuum elec

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Labus, Karolina, Lukasz Radosinski, and Piotr Kotowski. "Functional Properties of Two-Component Hydrogel Systems Based on Gelatin and Polyvinyl Alcohol—Experimental Studies Supported by Computational Analysis." International Journal of Molecular Sciences 22, no. 18 (2021): 9909. http://dx.doi.org/10.3390/ijms22189909.

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The presented research is focused on an investigation of the effect of the addition of polyvinyl alcohol (PVA) to a gelatin-based hydrogel on the functional properties of the resulting material. The main purpose was to experimentally determine and compare the properties of hydrogels differing from the content of PVA in the blend. Subsequently, the utility of these matrices for the production of an immobilized invertase preparation with improved operational stability was examined. We also propose a useful computational tool to predict the properties of the final material depending on the propor

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Trappe, Martin-I., and Ryan A. Chisholm. "A density functional theory for ecology across scales." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-023-36628-4.

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AbstractEcology lacks a holistic approach that can model phenomena across temporal and spatial scales, largely because of the challenges in modelling systems with a large number of interacting constituents. This hampers our understanding of complex ecosystems and the impact that human interventions (e.g., deforestation, wildlife harvesting and climate change) have on them. Here we use density functional theory, a computational method for many-body problems in physics, to develop a computational framework for ecosystem modelling. Our methods accurately fit experimental and synthetic data of int

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Della Sala, Fabio. "Orbital-Free Methods for Plasmonics: Linear Response." Journal of Chemical Physics, August 3, 2022. http://dx.doi.org/10.1063/5.0100797.

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Plasmonic systems, such as metal nanoparticles, are widely used in different application areas, going from biology to photovoltaics.The modeling of the optical response of such systems is of fundamental importance to analyze their behavior and to design new systems with required properties.When the characteristic sizes/distances reach a few nanometers, non-local and spill-out effects become relevant and conventional classical electrodynamics models are no more appropriate. Methods based on the Time-Dependent Density-Functional Theory (TD-DFT) represent the current reference for the description

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