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Holmes, John L., Karl J. Jobst, and Johan K. Terlouw. "Small (Poly)Unsaturated Oxygen Containing Ions and Molecules: A Brief Assessment of Their Thermochemistry Based on Computational Chemistry." European Journal of Mass Spectrometry 15, no. 2 (April 2009): 261–73. http://dx.doi.org/10.1255/ejms.959.
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The CBS-QB3, CBS-APNO and Gaussian-3 model chemistries have been used to determine the ionic and neutral heats of formation and the adiabatic ionization energies ( IEa) derived therefrom, for the ca 30 principal isomers of the C3H2O•+ and the C4H4O•+ families of radical cations. Theory and experiment are in excellent agreement for those molecules whose experimental IEa has been accurately measured. In contrast, large deviations from the computed values were found for a great many ionic heats of formation reported in the literature. These deviations largely arise from the uncertainty in the heat of formation of the corresponding neutral species for which often only a rough estimate is available. A useful by-product of this study is that it permits the evaluation of new Benson-type group additivity ( GA) terms appropriate for highly unsaturated oxygen containing molecules. Several new GA terms are proposed but it is also argued that a single GA term for the ketene function cannot be defined.
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Chesnut, D. B. "Localization function study of excitation processes in a set of small isoelectronic molecules." Journal of Computational Chemistry 22, no. 14 (2001): 1702–11. http://dx.doi.org/10.1002/jcc.1125.
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NAKANO, MASAYOSHI, RYOHEI KISHI, HITOSHI FUKUI, TAKUYA MINAMI, HIROSHI NAGAI, KYOHEI YONEDA, SEAN BONNESS, and HIDEAKI TAKAHASHI. "THEORETICAL STUDY ON OPEN-SHELL NONLINEAR OPTICAL MOLECULAR SYSTEMS AND A DEVELOPMENT OF A NOVEL COMPUTATIONAL SCHEME OF EXCITON DYNAMICS." International Journal of Nanoscience 08, no. 01n02 (February 2009): 123–29. http://dx.doi.org/10.1142/s0219581x09005803.
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This contribution firstly elucidates a structure–property relationship in third-order nonlinear optical molecular systems with singlet diradical characters. It turns out that the second hyperpolarizabilities (γ) of the singlet open-shell molecules with intermediate diradical characters are significantly enhanced as compared with those of closed-shell and pure diradical molecules. The hybrid density functional theory method, i.e. UBHandHLYP, is applied to the calculations of γ of dimer models composed of singlet diradical diphenalenyl molecules, which show a remarkable enhancement of γ per monomer as decreasing the intermolecular distance. The second contribution is concerned with a development of ab initio molecular orbital configuration-interaction-based quantum master equation (QME) approach. This is found to provide both coherent processes, e.g. dynamic polarization and exciton (electron–hole pair) recurrence motion, and incoherent processes, e.g. exciton migration, in molecular systems. Using this approach, the electron/hole dynamics for dynamic polarizabilities α(ω) are examined for several π-conjugated linear chain systems, and the structural dependences of α(ω) are elucidated.
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Abe, Shigeaki, Yoshinori Nagoya, Fumio Watari, and Hiroto Tachikawa. "Evaporation processes of water molecules from graphene edge: DFT and MD study." Computational Materials Science 50, no. 9 (July 2011): 2640–43. http://dx.doi.org/10.1016/j.commatsci.2011.04.009.
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Pilling, S., G. A. Carvalho, H. A. de Abreu, B. R. L. Galvão, C. H. da Silveira, and M. S. Mateus. "Understanding the Molecular Kinetics and Chemical Equilibrium Phase of Frozen CO during Bombardment by Cosmic Rays by Employing the PROCODA Code." Astrophysical Journal 952, no. 1 (July 1, 2023): 17. http://dx.doi.org/10.3847/1538-4357/acdb4a.
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Abstract Within the cold regions of space, ices that are enriched with carbon monoxide (CO) molecules are exposed to ionizing radiation, which triggers new reactions and desorption processes. Laboratory studies on astrochemical ices employing different projectiles have revealed the appearance of several new species. In this study, we employed the upgraded PROCODA code, which involves a calculation phase utilizing thermochemistry data, to map the chemical evolution of pure CO ice irradiated by cosmic-ray analogs. In the model, we have considered 18 different chemical species (six observed: CO, CO2, C3, O3, C2O, and C5O3; 12 unobserved: C, O, C2, O2, CO3, C3O, C4O, C5O, C2O2, C2O3, C3O2, and C4O2) coupled at 156 reaction routes. Our best-fit model provides effective reaction rates (effective rate constants, (ERCs)), branching ratios for reactions within reaction groups, several desorption parameters, and the characterization of molecular abundances at the chemical equilibrium (CE) phase. The most abundant species within the ice at the CE phase were atomic oxygen (68.2%) and atomic carbon (18.2%), followed by CO (11.8%) and CO2 (1.6%). The averaged modeled desorption yield and rate were 1.3e5 molecules ion−1 and 7.4e13 molecules s−1, respectively, while the average value of ERCs in the radiation-induced dissociation reactions was 2.4e-1 s−1 and for the bimolecular reactions it was 4.4e-24 cm3 molecule−1 s−1. We believe that the current kinetics study can be used in future astrochemical models to better understand the chemical evolution of embedded species within astrophysical ices under the presence of an ionizing radiation field.
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Wohlwend, Jennifer L., Cosima N. Boswell, Simon R. Phillpot, and Susan B. Sinnott. "A computational study of SrTiO3 thin film deposition: Morphology and growth modes." Journal of Materials Research 24, no. 6 (June 2009): 1994–2000. http://dx.doi.org/10.1557/jmr.2009.0229.
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The growth of SrTiO3 (STO) thin films is examined using classical molecular dynamics simulations. First, a beam of alternating SrO and TiO2 molecules is deposited on the (001) surface of STO with incident kinetic energies of 0.1, 0.5, or 1.0 eV/atom. Second, deposition of alternating SrO and TiO2 monolayers, where both have incident energies of 1.0 eV/atom, is examined. The resulting thin film morphologies predicted by the simulations are compared to available experimental data. The simulations indicate the way in which the incident energy, surface termination, and beam composition influence the morphology of the thin films. On the whole, some layer-by-layer growth is predicted to occur on both SrO- and TiO2-terminated STO for both types of deposition processes, with the alternating monolayer approach yielding thin films with compositions that are much closer to that of bulk STO.
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Abplanalp, Matthew J., Samer Gozem, Anna I. Krylov, Christopher N. Shingledecker, Eric Herbst, and Ralf I. Kaiser. "A study of interstellar aldehydes and enols as tracers of a cosmic ray-driven nonequilibrium synthesis of complex organic molecules." Proceedings of the National Academy of Sciences 113, no. 28 (July 5, 2016): 7727–32. http://dx.doi.org/10.1073/pnas.1604426113.
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Complex organic molecules such as sugars and amides are ubiquitous in star- and planet-forming regions, but their formation mechanisms have remained largely elusive until now. Here we show in a combined experimental, computational, and astrochemical modeling study that interstellar aldehydes and enols like acetaldehyde (CH3CHO) and vinyl alcohol (C2H3OH) act as key tracers of a cosmic-ray-driven nonequilibrium chemistry leading to complex organics even deep within low-temperature interstellar ices at 10 K. Our findings challenge conventional wisdom and define a hitherto poorly characterized reaction class forming complex organic molecules inside interstellar ices before their sublimation in star-forming regions such as SgrB2(N). These processes are of vital importance in initiating a chain of chemical reactions leading eventually to the molecular precursors of biorelevant molecules as planets form in their interstellar nurseries.
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Ormachea, Carla M., María Nélida Kneeteman, and Pedro M. E. Mancini. "Diels–Alder Polar Reactions of Azaheterocycles: A Theoretical and Experimental Study." Organics 3, no. 2 (May 22, 2022): 102–10. http://dx.doi.org/10.3390/org3020008.
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A number of azaheterocycles (pyridines, pyrroles and indoles) have been properly functionalized so that they can act as dienophiles in cycloaddition Diels–Alder processes. This work analyzed the reactive behavior of these molecules through mechanistic analysis and the regioselectivity of the process using computational calculation tools. Based on this knowledge, a study was conducted on the influences of reaction variables, in particular solvent, catalyst and microwave irradiation, to achieve favorable changes—shorter reaction times, more acceptable temperatures and better yields. Theoretical calculations allowed the development of predictive approaches, which were later experimentally corroborated. This analysis allowed us to make reasonable assumptions related to reaction mechanisms, which allowed—through the analysis of corresponding transition states—us to consider such reactions at the boundary between pericyclic and polar processes.
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Filion, Renee J., and Aleksander S. Popel. "Intracoronary administration of FGF-2: a computational model of myocardial deposition and retention." American Journal of Physiology-Heart and Circulatory Physiology 288, no. 1 (January 2005): H263—H279. http://dx.doi.org/10.1152/ajpheart.00205.2004.
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This study uses a computational model to characterize the myocardial deposition and retention of basic fibroblast growth factor (FGF-2) at the cellular level after intracoronary (IC) administration of exogenous FGF-2. The model is applied to the in situ conditions present within the myocardium of a dog for which the plasma pharmacokinetics resulting from IC injection of FGF-2 were recorded. Our estimates show that the processes involved in FGF-2 signaling are not diffusion limited; rather, the response time is determined by the reaction time of FGF-2 binding to cell surface receptors. Additionally, the processes of receptor secretion and internalization are found to play crucial roles in the FGF-2 dynamics; future experiments are required to quantify these processes. The model predictions obtained in this study suggest that IC administration of FGF-2 via either a single bolus or repetitive injections causes a transient increase (time scale of hours) in myocardial FGF-2 concentration if the endogenous level of free interstitial FGF-2 is low enough to allow permeation of FGF-2 molecules from the microvascular to the interstitial spaces. The model shows that the majority (64%) of the extracellular FGF-2 ligands are located within the interstitium, and similar fractions are found in the basement membrane and extracellular matrix. Among the FGF-2 molecules found within the interstitium, 2% are free and 98% are bound to interstitial heparan sulfate proteoglycans. These results support the theory of extracellular control of the bioavailability of FGF-2 via dynamic storage of FGF-2 within the basement membrane and extracellular matrix.
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Shafranyosh, M., and D. Kish. "Processes of formation of positive ions at the electron - thymine molecule interactions." Bulletin of Taras Shevchenko National University of Kyiv. Series: Physics and Mathematics, no. 2 (2019): 104–7. http://dx.doi.org/10.17721/1812-5409.2019/2.14.
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The work is aimed to solve the key problems of modern biophysics related to the study of fundamental mechanisms of interaction of ionizing radiation on living cells and stability of biological systems to its influence. The obtained data and their generalizations create a basis for understanding the interaction mechanisms and stability of biological systems to its influence. Investigation is aimed on the obtaining the new priority data about the characteristics of the life important biological molecules, establishing the mechanisms and features of dissociative capture, excitation and ionization under the slow electrons; the study of the influence of intermolecular interactions on these processes and solution of some applications concerning the definition of physical stability of biomolecules in different states of aggregation. The AM1 method that was used in research is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the neglect of differential diatomic overlap integral approximation and investigates the processes of formation of positive ions, which are formed during the interaction of thymine molecules with slow electrons. Fragmentation model of thymine molecules under electron ipmpact is proposed. Six most likely bond breaks in the cyclic structure of thymine molecular ion are identified. The obtained results are in good agreement with experimental data.
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Moreno, Miquel, José M. Lluch, and Ricard Gelabert. "On the Computational Design of Azobenzene-Based Multi-State Photoswitches." International Journal of Molecular Sciences 23, no. 15 (August 4, 2022): 8690. http://dx.doi.org/10.3390/ijms23158690.
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In order to theoretically design multi-state photoswitches with specific properties, an exhaustive computational study is first carried out for an azobenzene dimer that has been recently synthesized and experimentally studied. This study allows for a full comprehension of the factors that govern the photoactivated isomerization processes of these molecules so to provide a conceptual/computational protocol that can be applied to generic multi-state photoswitches. From this knowledge a new dimer with a similar chemical design is designed and also fully characterized. Our theoretical calculations predict that the new dimer proposed is one step further in the quest for a double photoswitch, where the four metastable isomers could be selectively interconverted through the use of different irradiation sequences.
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Chen, Tao, Yi Luo, and Aigen Li. "Fragmentation and isomerization of polycyclic aromatic hydrocarbons in the interstellar medium: Coronene as a case study." Astronomy & Astrophysics 633 (January 2020): A103. http://dx.doi.org/10.1051/0004-6361/201936873.
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Aims. Due to the limitations of current computational technology, the fragmentation and isomerization products of vibrationally-excited polycyclic aromatic hydrocarbon (PAH) molecules and their derivatives have been poorly studied. In this work, we investigate the intermediate products of PAHs and their derivatives as well as the gas-phase reactions relevant to the interstellar medium, with coronene as a case study. Methods. Based on the semi-empirical method of PM3 as implemented in the CP2K program, molecular dynamics simulations were performed to model the major processes (e.g., vibrations, fragmentations, and isomerizations) of coronene and its derivatives (e.g., methylated coronene, hydrogenated coronene, dehydrogenated coronene, nitrogen-substituted coronene, and oxygen-substituted coronene) at temperatures of 3000 K and 4000 K. Results. We find that the anharmonic effects are crucial for the simulation of vibrational excitation. For the molecules studied here, H2, CO, HCN, and CH2 are the major fragments. Following the dissociation of these small units, most of the molecules could maintain their ring structures, but a few molecules would completely break into carbon chains. The transformation from a hexagon to a pentagon or a heptagon may occur and the heteroatomic substitutions (e.g., N- or O-substitutions) would facilitate the transformation.
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Satoh, Akira. "Stability of Computational Algorithms Used in Molecular Dynamics Simulations." Journal of Fluids Engineering 117, no. 3 (September 1, 1995): 531–34. http://dx.doi.org/10.1115/1.2817296.
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The present study focuses on a three-dimensional Lennard-Jones system in a thermodynamic equilibrium in order to discuss divergence processes, the relationship between time intervals and divergence times, and the influence of time intervals on thermodynamic quantities and transport coefficients under various number density and temperature. It is found that the velocities of molecules in a system gradually increase with time until the system suddenly diverges exponentially. The time interval-divergence time relationship can be expressed in approximate terms as linear functions if the data are plotted on logarithmic scales, and the system diverges more easily as temperature or number density increases. Thermodynamic quantities show the influence of large time intervals more clearly than do transport coefficients.
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Izumi, Yukihiro, Ken-ichi Saitoh, Tomohiro Sato, Masanori Takuma, and Yoshimasa Takahashi. "Shear Deterioration of the Hierarchical Structure of Cellulose Microfibrils under Water Condition: All-Atom Molecular Dynamics Analysis." Applied Mechanics 4, no. 1 (February 19, 2023): 230–47. http://dx.doi.org/10.3390/applmech4010013.
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This study aims to understand the mechanical properties of cellulose nanofibers (CNFs), a nano-sized material element of woods or plants. We develop all-atom (AA) molecular dynamics models of cellulose microfibrils (CMFs), which are the smallest constituent of CNFs. The models were designed for the process of structural failure or the degradation of a hierarchical material of multiple CMF fibers, due to shear deformation. It was assumed that two CMFs were arranged in parallel and in close contact, either in a vacuum or in water. The CMF models in water were built by surrounding AA-modeled water molecules with a few nanometers. Shear deformation was applied in the axial direction of the CMF or in the direction parallel to molecular sheets. Shear moduli were measured, and they agree with previous experimental and computational values. The presence of water molecules reduced the elastic modulus, because of the behavior of water molecules at the interface between CMFs as a function of temperature. In the inelastic region, the CMF often broke down inside CMFs in a vacuum condition. However, in water environments, two CMFs tend to slip away from each other at the interface. Water molecules act like a lubricant between multiple CMFs and promote smooth sliding.
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Budziak, Iwona, Marta Arczewska, and Daniel M. Kamiński. "Structure and Physical Properties of Cardamonin: A Spectroscopic and Computational Approach." Molecules 25, no. 18 (September 6, 2020): 4070. http://dx.doi.org/10.3390/molecules25184070.
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This is the first study of the crystal structure of cardamonin (CA) confirmed using single-crystal XRD analysis. In the crystal lattice of CA, two symmetry independent molecules are linked by hydrogen bonds within the layers and by the π···π stacking interactions in the columns which lead to the occurrence of two types of conformations among the CA molecules in the crystal structure. To better understand the stability of these arrangements in both crystals and the gaseous phase, seven different CA dimers were theoretically calculated. The molecular structures were optimized using density functional theory (DFT) at the B3LYP/6–311G+(d,p) level and the spectroscopic results were compared. It was found that the calculated configurations of dimer I and III were almost identical to the ones found in the CA crystal lattice. The calculated UV-Vis spectra for the CA monomer and dimer I were perfectly consistent with the experimental spectroscopic data. Furthermore, enhanced emissions induced by aggregated CA molecules were registered in the aqueous solution with the increase of water fractions. The obtained results will help to further understand the relation between a variety of conformations and the biological properties of CA, and the results are also promising in terms of the applicability of CA as a bioimaging probe to monitor biological processes.
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Rahmawati, Sitti, Cynthia Linaya Radiman, Muhamad Abdulkadir Martoprawiro, Siti Nuryanti, Pathuddin, and Ahmad Ma'ruf. "Hydration and Proton Transfer Processes in Sulfonated Nata De Coco Membrane with Density Functional Theory." Key Engineering Materials 874 (January 2021): 58–66. http://dx.doi.org/10.4028/www.scientific.net/kem.874.58.
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Direct Methanol Fuel Cells (DMFCs) is one of the most promising alternative energy resources to meet human energy needs. DMFCs is fuel cells that use polymer membranes as the electrolytes to transfer the protons from anode to cathode. The characteristics of those two types of membranes in ion exchange capacity (IEC) and degree of swelling (swelling) have shown a very important role of water in the proton transfer. However, the mechanism of interaction between the repeating units of the polymer with water molecules has not been studied in depth. Computational methods can be used to study such interactions as well as the transfer of protons. To examine the transfer of protons in the membrane, studies of computing via electronic structure calculations, geometry optimization, interaction inter/intra molecular, as well as the hydration process and transfer of protons in the sulfonated nata-de-coco membranes (NDCS) has been conducted in this work. All calculations were performed using DFT with B3LYP functional and basis set 6-311G(d). The repeating units of the membranes were optimized (n=1,2,...,5), to obtain the structure with minimum energy. The optimized structure was then interacted with one water molecule in the same position to study the effect of chain length on its interaction strength with water molecules. The thermodynamic and proton dissociation parameters was calculated by adding n water molecules (n=1,2, …,10) to determine the hydration process and the proton transfer on the membranes. The calculations showed that for interactions with water, the polymer structure in NDCS can be represented/modeled by two repeating units. Therefore, the hydration process and transfer of protons in the membranes were studied by adding n water molecules gradually into the two repeating units. The results showed that the proton dissociation process in NDCS membrane started with the addition of two molecules of water. The presence of water molecules promoted the proton dissociation in the -SO3H groups to form SO3- and H3O+ ions, which further formed Zundel ions and Eigen ions. The energy profile of proton transfer showed that the barrier energy was 58.13 kcal/mol for NDCS-5(H2O). Its thermodynamic parameters, the calculation showed that the interaction energy (ΔE), the enthalpy change (ΔH) and the Gibbs free energy (ΔG) to its interaction with n water molecules (n=1,2,…,10) in NDCS are getting more negative. This indicated that the interaction with water molecule is stronger. So, based on these results, it can be concluded that the computational calculations using DFT method at B3LYP functional and 6-311G(d) basis set can be used to describe the process of hydration and proton transfer in the interactions in the polymer electrolyte membrane (NDCS membrane)
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Cipriani, Maicol, and Oddur Ingólfsson. "HF Formation through Dissociative Electron Attachment—A Combined Experimental and Theoretical Study on Pentafluorothiophenol and 2-Fluorothiophenol." International Journal of Molecular Sciences 23, no. 5 (February 23, 2022): 2430. http://dx.doi.org/10.3390/ijms23052430.
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In chemoradiation therapy, dissociative electron attachment (DEA) may play an important role with respect to the efficiency of the radiosensitizers used. The rational tailoring of such radiosensitizers to be more susceptive to DEA may thus offer a path to increase their efficiency. Potentially, this may be achieved by tailoring rearrangement reactions into the DEA process such that these may proceed at low incident electron energies, where DEA is most effective. Favorably altering the orbital structure of the respective molecules through substitution is another path that may be taken to promote dissociation up on electron capture. Here we present a combined experimental and theoretical study on DEA in relation to pentafluorothiophenol (PFTP) and 2-fluorothiophenol (2-FTP). We investigate the thermochemistry and dynamics of neutral HF formation through DEA as means to lower the threshold for dissociation up on electron capture to these compounds, and we explore the influence of perfluorination on their orbital structure. Fragment ion yield curves are presented, and the thermochemical thresholds for the respective DEA processes are computed as well as the minimum energy paths for HF formation up on electron capture and the underlying orbital structure of the respective molecular anions. We show that perfluorination of the aromatic ring in these compounds plays an important role in enabling HF formation by further lowering the threshold for this process and through favorable influence on the orbital structure, such that DEA is promoted. We argue that this approach may offer a path for tailoring new and efficient radiosensitizers.
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Barone, Vincenzo, and Cristina Puzzarini. "Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry." EPJ Web of Conferences 246 (2020): 00021. http://dx.doi.org/10.1051/epjconf/202024600021.
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The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.
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Lungu, Claudiu N., Violeta Mangalagiu, Ionel I. Mangalagiu, and Mihaela C. Mehedinti. "Benzoquinoline Chemical Space: A Helpful Approach in Antibacterial and Anticancer Drug Design." Molecules 28, no. 3 (January 20, 2023): 1069. http://dx.doi.org/10.3390/molecules28031069.
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Benzoquinolines are used in many drug design projects as starting molecules subject to derivatization. This computational study aims to characterize e benzoquinone drug space to ease future drug design processes based on these molecules. The drug space is composed of all benzoquinones, which are active on topoisomerase II and ATP synthase. Topological, chemical, and bioactivity spaces are explored using computational methodologies based on virtual screening and scaffold hopping and molecular docking, respectively. Topological space is a geometrical space in which the elements composing it can be defined as a set of neighbors (which satisfy a particular axiom). In such space, a chemical space can be defined as the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. In this chemical space, the potentially pharmacologically active molecules form the bioactivity space. Results show a poly-morphological chemical space that suggests distinct characteristics. The chemical space is correlated with properties such as steric energy, the number of hydrogen bonds, the presence of halogen atoms, and membrane permeability-related properties. Lastly, novel chemical compounds (such as oxadiazole methybenzamide and floro methylcyclohexane diene) with drug-like potential, active on TOPO II and ATP synthase have been identified.
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Agamennone, Mariangela, and Fabiana Superti. "Broad-Spectrum Activity of Small Molecules Acting against Influenza a Virus: Biological and Computational Studies." Pharmaceuticals 15, no. 3 (February 28, 2022): 301. http://dx.doi.org/10.3390/ph15030301.
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Influenza still represents a problematic disease, involving millions of people every year and causing hundreds of thousands of deaths. Only a few drugs are clinically available. The search for an effective weapon is still ongoing. In this scenario, we recently identified new drug-like compounds with antiviral activity toward two A/H1N1 Influenza virus strains, which were demonstrated to interfere with the processes mediated by hemagglutinin (HA). In the present work, the compound’s ability to act against the A/H3N2 viral strain has been evaluated in hemagglutination inhibition (HI) assays. Two of the five tested compounds were also active toward the A/H3N2 Influenza virus. To validate the scaffold activity, analogue compounds of two broad-spectrum molecules were selected and purchased for HI testing on both A/H1N1 and A/H3N2 Influenza viruses. Forty-three compounds were tested, and four proved to be active toward all three viral strains. A computational study has been carried out to depict the HA binding process of the most interesting compounds.
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Luksys, Gediminas, Matthias Fastenrath, David Coynel, Virginie Freytag, Leo Gschwind, Angela Heck, Frank Jessen, et al. "Computational dissection of human episodic memory reveals mental process-specific genetic profiles." Proceedings of the National Academy of Sciences 112, no. 35 (August 10, 2015): E4939—E4948. http://dx.doi.org/10.1073/pnas.1500860112.
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Episodic memory performance is the result of distinct mental processes, such as learning, memory maintenance, and emotional modulation of memory strength. Such processes can be effectively dissociated using computational models. Here we performed gene set enrichment analyses of model parameters estimated from the episodic memory performance of 1,765 healthy young adults. We report robust and replicated associations of the amine compound SLC (solute-carrier) transporters gene set with the learning rate, of the collagen formation and transmembrane receptor protein tyrosine kinase activity gene sets with the modulation of memory strength by negative emotional arousal, and of the L1 cell adhesion molecule (L1CAM) interactions gene set with the repetition-based memory improvement. Furthermore, in a large functional MRI sample of 795 subjects we found that the association between L1CAM interactions and memory maintenance revealed large clusters of differences in brain activity in frontal cortical areas. Our findings provide converging evidence that distinct genetic profiles underlie specific mental processes of human episodic memory. They also provide empirical support to previous theoretical and neurobiological studies linking specific neuromodulators to the learning rate and linking neural cell adhesion molecules to memory maintenance. Furthermore, our study suggests additional memory-related genetic pathways, which may contribute to a better understanding of the neurobiology of human memory.
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Mathur, Melina, Joy S. Xiang, and Christina D. Smolke. "Mammalian synthetic biology for studying the cell." Journal of Cell Biology 216, no. 1 (December 8, 2016): 73–82. http://dx.doi.org/10.1083/jcb.201611002.
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Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.
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Williams, David, and Serena Viti. "Modelling interstellar physics and chemistry: implications for surface and solid-state processes." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371, no. 1994 (July 13, 2013): 20110587. http://dx.doi.org/10.1098/rsta.2011.0587.
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We discuss several types of regions in the interstellar medium of the Milky Way and other galaxies in which the chemistry appears to be influenced or dominated by surface and solid-state processes occurring on or in interstellar dust grains. For some of these processes, for example, the formation of H 2 molecules, detailed experimental and theoretical approaches have provided excellent fundamental data for incorporation into astrochemical models. In other cases, there is an astrochemical requirement for much more laboratory and computational study, and we highlight these needs in our description. Nevertheless, in spite of the limitations of the data, it is possible to infer from astrochemical modelling that surface and solid-state processes play a crucial role in astronomical chemistry from early epochs of the Universe up to the present day.
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Lichołai, Sabina, Dorota Studzińska, Hanna Plutecka, Tomasz Gubała, and Marek Sanak. "Comprehensive Analysis of Circular RNAs in Endothelial Cells." International Journal of Molecular Sciences 24, no. 12 (June 12, 2023): 10025. http://dx.doi.org/10.3390/ijms241210025.
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Non-coding RNAs constitute a heterogeneous group of molecules that lack the ability to encode proteins but retain the potential ability to influence cellular processes through a regulatory mechanism. Of these proteins, microRNAs, long non-coding RNAs, and more recently, circular RNAs have been the most extensively described. However, it is not entirely clear how these molecules interact with each other. For circular RNAs, the basics of their biogenesis and properties are also lacking. Therefore, in this study we performed a comprehensive analysis of circular RNAs in relation to endothelial cells. We identified the pool of circular RNAs present in the endothelium and showed their spectrum and expression across the genome. Using different computational strategies, we proposed approaches to search for potentially functional molecules. In addition, using data from an in vitro model that mimics conditions in the endothelium of an aortic aneurysm, we demonstrated altered expression levels of circRNAs mediated by microRNAs.
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Kumari, Archana, Medha Jyoti, Maneesh Kumar, and Ratnesh Kumar. "Streptomyces tetracycline’s computational behavior against polyketide synthase of aflatoxigenic fungi." IP International Journal of Medical Microbiology and Tropical Diseases 9, no. 2 (July 15, 2023): 85–91. http://dx.doi.org/10.18231/j.ijmmtd.2023.017.
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produces a variety of bioactive compounds that prevent fungal growth, including aflatoxins. Aflatoxigenic fungi ( and ) are being researched concerning spp. and can prevent the spread of aflatoxins-producing fungi. Aflatoxin-degrading enzymes, which can convert poisonous aflatoxins into less dangerous compounds, are also produced by spp. The processes through which these microorganisms can be used to reduce aflatoxins in food and agricultural systems are still the subject of active research. To evaluate the novelty of tetracycline against the biosynthesis of aflatoxin in aflatoxigenic fungi via computational approach. In this study, we performed molecular docking of polyketide synthase (Pks-A), an enzyme that initiates aflatoxin biosynthesis using tetracycline, using the online SeamDock server. Our results showed that tetracycline had a strong affinity for Pks-A in the binding pocket. The binding energy of tetracycline was -12.7 kcal/mol, indicating a strong binding affinity between the two molecules. Furthermore, the binding site was located in the active site, which is a conserved region in Pks-A and is essential for catalysing the formation of aflatoxin. The results of our docking study suggest that tetracycline may be an effective inhibitor of aflatoxin biosynthesis.
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MEI, YE, and JOHN Z. H. ZHANG. "NUMERICAL STABILITIES IN FITTING ATOMIC CHARGES TO ELECTRIC FIELD AND ELECTROSTATIC POTENTIAL." Journal of Theoretical and Computational Chemistry 08, no. 05 (October 2009): 925–42. http://dx.doi.org/10.1142/s0219633609005295.
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It is known that electrostatic potential (ESP) derived atomic charges for molecular systems suffer from rank deficiency in least-square fitting. In this paper, we studied numerical properties of atomic charges by fitting to ESP and electric field (EF) for a series of molecular systems, ranging from small molecules to peptides. Our study shows that although atomic charges of certain atoms in a molecule may differ a lot resulting from different fitting schemes, the effect on some observed physical properties of the molecules, such as solvation free energy and radial distributions of the solvent, are negligible. For all the molecules studied in this paper, it is shown that by incorporating EF terms in the least-square fitting, the rank of the least-squares matrix is increased, and the full rank is achieved when only EF terms are included. The current study demonstrates that by using EF, instead of the widely used ESP, in least-square fitting of atomic charges, one can obtain numerically more stable and better defined atomic charges in molecules. Such derived atomic charges may have more desirable properties and better numerical stabilities in studying detailed molecular processes such as in molecular dynamics simulation of macromolecules.
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van der Hooft, Justin Johan Jozias, Joe Wandy, Michael P. Barrett, Karl E. V. Burgess, and Simon Rogers. "Topic modeling for untargeted substructure exploration in metabolomics." Proceedings of the National Academy of Sciences 113, no. 48 (November 16, 2016): 13738–43. http://dx.doi.org/10.1073/pnas.1608041113.
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The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that enable extraction of key biochemically relevant information. Available tools focus on using mass spectrometry fragmentation spectra to identify molecules whose behavior suggests they are relevant to the system under study. Unfortunately, fragmentation spectra cannot identify molecules in isolation but require authentic standards or databases of known fragmented molecules. Fragmentation spectra are, however, replete with information pertaining to the biochemical processes present, much of which is currently neglected. Here, we present an analytical workflow that exploits all fragmentation data from a given experiment to extract biochemically relevant features in an unsupervised manner. We demonstrate that an algorithm originally used for text mining, latent Dirichlet allocation, can be adapted to handle metabolomics datasets. Our approach extracts biochemically relevant molecular substructures (“Mass2Motifs”) from spectra as sets of co-occurring molecular fragments and neutral losses. The analysis allows us to isolate molecular substructures, whose presence allows molecules to be grouped based on shared substructures regardless of classical spectral similarity. These substructures, in turn, support putative de novo structural annotation of molecules. Combining this spectral connectivity to orthogonal correlations (e.g., common abundance changes under system perturbation) significantly enhances our ability to provide mechanistic explanations for biological behavior.
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LI, XIN, and ZHONG-ZHI YANG. "AN AB INITIO STUDY OF PROTON-TRANSFER REACTION IN Be2+(H2O)n AND THE SPATIAL CHANGING FEATURE IN THE FORMATION PROCESS OF HYDROXIDE." Journal of Theoretical and Computational Chemistry 05, no. 01 (March 2006): 75–85. http://dx.doi.org/10.1142/s0219633606002064.
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The proton-transfer reaction in Be 2+( H 2 O )n is investigated by an ab initio calculation. With an increasing number of water molecules, there are different formation processes of hydroxide, and the reaction barrier is dependent on the cluster size n. By MELD ab initio program and own-coding programs, we have calculated the potential acting on an electron within a molecule, and have investigated the changing of spatial appearance for the formation process of hydroxide, by the molecular intrinsic characteristic contour defined in terms of the classical turning point of electron movement.
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Kosyanchuk, Vasily, and Artem Yakunchikov. "A detailed multiscale study of rotational–translational relaxation process of diatomic molecules." Physics of Fluids 33, no. 2 (February 1, 2021): 022003. http://dx.doi.org/10.1063/5.0037335.
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Kim, Hongdeok, Byeonghwa Goh, Sol Lee, Kyujo Lee, and Joonmyung Choi. "Computational Study on Interfacial Interactions between Polymethyl Methacrylate-Based Bone Cement and Hydroxyapatite in Nanoscale." Applied Sciences 11, no. 7 (March 25, 2021): 2937. http://dx.doi.org/10.3390/app11072937.
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Polymethyl methacrylate (PMMA)-based bone cement (BC) is a key material in joint replacement surgery that transfers external forces from the implant to the bone while allowing their robust binding. To quantitatively evaluate the effect of polymerization on the thermomechanical properties of the BC and on the interaction characteristics with the bone ceramic hydroxyapatite (HAp), molecular dynamics simulations were performed. The mechanical stiffness of the BC material under external loading increased gradually with the crosslinking reaction occurrence, indicating increasing load transfer between the constituent molecules. In addition, as the individual Methyl Methacrylate (MMA) segments were interconnected in the system, the freedom of the molecular network was largely suppressed, resulting in more thermally stable structures. Furthermore, the pull-out tests using HAp/BC bilayer models under different constraints (BC at 40% and 85%) revealed the cohesive characteristics of the BC with the bone scaffold in molecular detail. The stiffness and the fracture energy increased by 32% and 98%, respectively, with the crosslink density increasing.
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Karmakar, Rajesh. "Noise in gene expression may be a choice of cellular system." International Journal of Modern Physics C 30, no. 02n03 (February 2019): 1950014. http://dx.doi.org/10.1142/s0129183119500141.
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Gene expression and its regulation is a nonequilibrium stochastic process. Different molecules are involved in several biochemical steps in this process with low copies. It is observed that the stochasticity in biochemical processes is mainly due to the low copy number of the molecules present in the system. Several studies also show that the nonequilibrium biochemical processes require energy cost. But cellular system has developed itself through natural evolution by minimizing energy cost for optimum output. Here, we study the role of stochasticity qualitatively in a network of two genes using stochastic simulation method and approximately measure the energy consumption for the gene expression process. We find that the noise in gene expression process reduces the energy cost of protein synthesis. Therefore, we argued that the stochasticity in gene expression may be a choice of cellular system for protein synthesis with minimum energy cost.
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Yatskou, M. M., and V. V. Apanasovich. "Data analysis in complex biomolecular systems." Informatics 18, no. 1 (March 29, 2021): 105–22. http://dx.doi.org/10.37661/1816-0301-2021-18-1-105-122.
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The biomolecular technology progress is directly related to the development of effective methods and algorithms for processing a large amount of information obtained by modern high-throughput experimental equipment. The priority task is the development of promising computational tools for the analysis and interpretation of biophysical information using the methods of big data and computer models. An integrated approach to processing large datasets, which is based on the methods of data analysis and simulation modelling, is proposed. This approach allows to determine the parameters of biophysical and optical processes occurring in complex biomolecular systems. The idea of an integrated approach is to use simulation modelling of biophysical processes occurring in the object of study, comparing simulated and most relevant experimental data selected by dimension reduction methods, determining the characteristics of the investigated processes using data analysis algorithms. The application of the developed approach to the study of bimolecular systems in fluorescence spectroscopy experiments is considered. The effectiveness of the algorithms of the approach was verified by analyzing of simulated and experimental data representing the systems of molecules and proteins. The use of complex analysis increases the efficiency of the study of biophysical systems during the analysis of big data.
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Quast, Helmut, Georg Gescheidt, and Martin Spichty. "Topological Dynamics of a Radical Ion Pair: Experimental and Computational Assessment at the Relevant Nanosecond Timescale." Chemistry 2, no. 2 (March 31, 2020): 219–30. http://dx.doi.org/10.3390/chemistry2020014.
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Chemical processes mostly happen in fluid environments where reaction partners encounter via diffusion. The bimolecular encounters take place at a nanosecond time scale. The chemical environment (e.g., solvent molecules, (counter)ions) has a decisive influence on the reactivity as it determines the contact time between two molecules and affects the energetics. For understanding reactivity at an atomic level and at the appropriate dynamic time scale, it is crucial to combine matching experimental and theoretical data. Here, we have utilized all-atom molecular-dynamics simulations for accessing the key time scale (nanoseconds) using a QM/MM-Hamiltonian. Ion pairs consisting of a radical ion and its counterion are ideal systems to assess the theoretical predictions because they reflect dynamics at an appropriate time scale when studied by temperature-dependent EPR spectroscopy. We have investigated a diketone radical anion with its tetra-ethylammonium counterion. We have established a funnel-like transition path connecting two (equivalent) complexation sites. The agreement between the molecular-dynamics simulation and the experimental data presents a new paradigm for ion–ion interactions. This study exemplarily demonstrates the impact of the molecular environment on the topological states of reaction intermediates and how these states can be consistently elucidated through the combination of theory and experiment. We anticipate that our findings will contribute to the prediction of bimolecular transformations in the condensed phase with relevance to chemical synthesis, polymers, and biological activity.
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Ončák, Milan, Rebecca Meißner, Eugene Arthur-Baidoo, Stephan Denifl, Thomas F. M. Luxford, Andriy Pysanenko, Michal Fárník, Jiří Pinkas, and Jaroslav Kočišek. "Ring Formation and Hydration Effects in Electron Attachment to Misonidazole." International Journal of Molecular Sciences 20, no. 18 (September 6, 2019): 4383. http://dx.doi.org/10.3390/ijms20184383.
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We study the reactivity of misonidazole with low-energy electrons in a water environment combining experiment and theoretical modelling. The environment is modelled by sequential hydration of misonidazole clusters in vacuum. The well-defined experimental conditions enable computational modeling of the observed reactions. While the NO 2 − dissociative electron attachment channel is suppressed, as also observed previously for other molecules, the OH − channel remains open. Such behavior is enabled by the high hydration energy of OH − and ring formation in the neutral radical co-fragment. These observations help to understand the mechanism of bio-reductive drug action. Electron-induced formation of covalent bonds is then important not only for biological processes but may find applications also in technology.
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Pellegrino, Roberto Maria, Matteo Giulietti, Husam B. R. Alabed, Sandra Buratta, Lorena Urbanelli, Francesco Piva, and Carla Emiliani. "LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario." Bioinformatics 38, no. 6 (December 31, 2021): 1767–69. http://dx.doi.org/10.1093/bioinformatics/btab867.
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Abstract Summary LC/MS-based analysis techniques combined with specialized lipid tool allow for the qualitative and quantitative determination of thousands of lipid molecules. Some recent bioinformatics tools have been developed to study changes in the lipid profile in case–control experiments and correlate these changes to different enzyme activity or gene expression. However, the existing tools have the limitation to treat only the assembled lipid molecules. In reality, each individual molecule can be considered as an assembly of smaller parts, often called building blocks. These are the result of a myriad of biochemical synthesis and transformation processes that, from a systems biology perspective, should not be ignored. Here, we present LipidOne, a new lipidomic tool which highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and among experimental groups. Thanks to LipidOne, even differences in lipid building blocks can now be linked to the activity of specific classes of enzymes, transcripts and genes. Availability and implementation LipidOne software is freely available at www.dcbb.unipg.it/LipidOne and https://github.com/matteogiulietti/LipidOne. Contact roberto.pellegrino@unipg.it Supplementary information Supplementary data are available at Bioinformatics online.
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RAMALHO, TEODORICO C., ELAINE F. F. DA CUNHA, and RICARDO BICCA DE ALENCASTRO. "THEORETICAL STUDY OF ADIABATIC AND VERTICAL ELECTRON AFFINITY OF RADIOSENSITIZERS IN SOLUTION PART 2: ANALOGUES OF TIRAPAZAMINE." Journal of Theoretical and Computational Chemistry 03, no. 01 (March 2004): 1–13. http://dx.doi.org/10.1142/s0219633604000866.
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Tirapazamine is a radiosensitizer, whose biological activity is associated to its electron affinity (EA). The electron affinity can be divided in two main processes: Vertical and Adiabatic. In this work, we calculated the EAs of nitroimidazoles (Fig. 2) using HF and DFT methods and evaluated solvent effects (water and carbon tetrachloride) on EAs. For water, we combined the Polarized Continuum Model (PCM) and free energy perturbation (Finite Difference Thermodynamic Integration, FDTI) methods. For carbon tetrachloride, we used the FDTI method. The values of adiabatic EA obtained are in agreement with experimental data (deviations of 13.25 meV). The vertical EA were calculated according to Cederbaum's Outer Valence Green Function (OVGF) method. This study, which relays on theoretical aspects of free energy calculations on charged molecules in solution, could be helpful in the rational design of new and more selective bioreductive anticancer drugs.
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Bukowski, Brandon C., Frerich J. Keil, Peter I. Ravikovitch, German Sastre, Randall Q. Snurr, and Marc-Olivier Coppens. "Connecting theory and simulation with experiment for the study of diffusion in nanoporous solids." Adsorption 27, no. 5 (April 22, 2021): 683–760. http://dx.doi.org/10.1007/s10450-021-00314-y.
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AbstractNanoporous solids are ubiquitous in chemical, energy, and environmental processes, where controlled transport of molecules through the pores plays a crucial role. They are used as sorbents, chromatographic or membrane materials for separations, and as catalysts and catalyst supports. Defined as materials where confinement effects lead to substantial deviations from bulk diffusion, nanoporous materials include crystalline microporous zeotypes and metal–organic frameworks (MOFs), and a number of semi-crystalline and amorphous mesoporous solids, as well as hierarchically structured materials, containing both nanopores and wider meso- or macropores to facilitate transport over macroscopic distances. The ranges of pore sizes, shapes, and topologies spanned by these materials represent a considerable challenge for predicting molecular diffusivities, but fundamental understanding also provides an opportunity to guide the design of new nanoporous materials to increase the performance of transport limited processes. Remarkable progress in synthesis increasingly allows these designs to be put into practice. Molecular simulation techniques have been used in conjunction with experimental measurements to examine in detail the fundamental diffusion processes within nanoporous solids, to provide insight into the free energy landscape navigated by adsorbates, and to better understand nano-confinement effects. Pore network models, discrete particle models and synthesis-mimicking atomistic models allow to tackle diffusion in mesoporous and hierarchically structured porous materials, where multiscale approaches benefit from ever cheaper parallel computing and higher resolution imaging. Here, we discuss synergistic combinations of simulation and experiment to showcase theoretical progress and computational techniques that have been successful in predicting guest diffusion and providing insights. We also outline where new fundamental developments and experimental techniques are needed to enable more accurate predictions for complex systems.
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Kumar, Rupesh, Maged Mostafa Mahmoud, Hanaa M. Tashkandi, Shafiul Haque, Steve Harakeh, Kalaiarasan Ponnusamy, and Shazia Haider. "Combinatorial Network of Transcriptional and miRNA Regulation in Colorectal Cancer." International Journal of Molecular Sciences 24, no. 6 (March 10, 2023): 5356. http://dx.doi.org/10.3390/ijms24065356.
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Colorectal cancer is one of the leading causes of cancer-associated mortality across the worldwide. One of the major challenges in colorectal cancer is the understanding of the regulatory mechanisms of biological molecules. In this study, we aimed to identify novel key molecules in colorectal cancer by using a computational systems biology approach. We constructed the colorectal protein–protein interaction network which followed hierarchical scale-free nature. We identified TP53, CTNBB1, AKT1, EGFR, HRAS, JUN, RHOA, and EGF as bottleneck-hubs. The HRAS showed the largest interacting strength with functional subnetworks, having strong correlation with protein phosphorylation, kinase activity, signal transduction, and apoptotic processes. Furthermore, we constructed the bottleneck-hubs’ regulatory networks with their transcriptional (transcription factor) and post-transcriptional (miRNAs) regulators, which exhibited the important key regulators. We observed miR-429, miR-622, and miR-133b and transcription factors (EZH2, HDAC1, HDAC4, AR, NFKB1, and KLF4) regulates four bottleneck-hubs (TP53, JUN, AKT1 and EGFR) at the motif level. In future, biochemical investigation of the observed key regulators could provide further understanding about their role in the pathophysiology of colorectal cancer.
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Raval, Keval, and Tejas Ganatra. "Basics, types and applications of molecular docking: A review." IP International Journal of Comprehensive and Advanced Pharmacology 7, no. 1 (March 15, 2022): 12–16. http://dx.doi.org/10.18231/j.ijcaap.2022.003.
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From hit discovery through lead optimization and beyond, computational methods have become an essential part of many drugs development processes. There are typically several steps in the docking process, and each one provides a new level of complexity. Docking methods are used to place small molecules in the active region of the enzyme. In addition to these methods, scoring functions are used to estimate a compound's biological activity by looking at how it interacts with prospective targets. Molecular docking is considered to be the most widely utilized computational phenomenon in the field of computer-aided drug design (CADD). It is being utilized at the academic level as well as in pharmaceutical companies for the lead discovery process. Molecular docking is mainly associated with two terms: ligand and protein. Protein is the target site where ligand may bind to give specific activity. Molecular docking provides information on the ability of the ligand to bind with protein which is known as binding affinity. Applications of molecular docking in drug development have evolved significantly since it was first created to aid in the study of molecular recognition processes between small and large compounds. This review emphasizes the basic features of molecular docking along with the types, approaches and applications.
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LEE, CHANYOUNG, JOAN T. RICHTSMEIER, and REUBEN H. KRAFT. "A COMPUTATIONAL ANALYSIS OF BONE FORMATION IN THE CRANIAL VAULT USING A COUPLED REACTION–DIFFUSION-STRAIN MODEL." Journal of Mechanics in Medicine and Biology 17, no. 04 (May 28, 2017): 1750073. http://dx.doi.org/10.1142/s0219519417500737.
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Bones of the murine cranial vault are formed by differentiation of mesenchymal cells into osteoblasts, a process that is primarily understood to be controlled by a cascade of reactions between extracellular molecules and cells. We assume that the process can be modeled using Turing's reaction–diffusion equations, a mathematical model describing the pattern formation controlled by two interacting molecules (activator and inhibitor). In addition to the processes modeled by reaction–diffusion equations, we hypothesize that mechanical stimuli of the cells due to growth of the underlying brain contribute significantly to the process of cell differentiation in cranial vault development. Structural analysis of the surface of the brain was conducted to explore the effects of the mechanical strain on bone formation. We propose a mechanobiological model for the formation of cranial vault bones by coupling the reaction-–diffusion model with structural mechanics. The mathematical formulation was solved using the finite volume method. The computational domain and model parameters are determined using a large collection of experimental data that provide precise three-dimensional (3D) measures of murine cranial geometry and cranial vault bone formation for specific embryonic time points. The results of this study suggest that mechanical strain contributes information to specific aspects of bone formation. Our mechanobiological model predicts some key features of cranial vault bone formation that were verified by experimental observations including the relative location of ossification centers of individual vault bones, the pattern of cranial vault bone growth over time, and the position of cranial vault sutures.
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Ivan, Jeremias, Rizky Nurdiansyah, and Arli Aditya Parikesit. "Computational modeling of AGO-mediated molecular inhibition of ARF6 by miR-145." Indonesian Journal of Biotechnology 25, no. 2 (December 2, 2020): 102. http://dx.doi.org/10.22146/ijbiotech.55631.
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Inhibition of ADP-ribosylation factor 6 messenger RNA (ARF6 mRNA) by microRNA-145 (miR-145), mediated by Argonaute (AGO) protein, has been found to play essential roles in several types of cancer and cellular processes. This study aimed to model the molecular interaction between miR-145 and ARF6 mRNA with AGO protein. The sequences of miR-145 and the 3’ untranslated region (UTR) of ARF6 mRNA were retrieved from miRTarBase, followed by miRNA target-site and structure predictions were done using RNAhybrid, RNAfold, and simRNAweb, respectively. The interaction between the miRNA-mRNA duplex and AGO was further assessed via molecular docking, interaction analysis, and dynamics, using PatchDock Server, PLIP, and VMD/NAMD, respectively. The models between miR-145, predicted target site of ARF6 mRNA, and AGO protein returned stable thermodynamic variables with negative free energy. Specifically, the RNA duplex had an energy of -19.80 kcal/mol, while the docking had -84.58 atomic contact energy supported by 70 hydrogen bonds and 14 hydrophobic interactions. However, the stability of the RMSD plot was still unclear due to limited computational resources. Nevertheless, these results computationally confirm favorable interaction of the three molecules, which can be utilized for further transcriptomics-based drugs or treatments.
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Ayyadurai, V. A. Shiva, and Prabhakar Deonikar. "Attenuation of Aging-Related Oxidative Stress Pathways by Phytonutrients: A Computational Systems Biology Analysis." Nutrients 15, no. 17 (August 28, 2023): 3762. http://dx.doi.org/10.3390/nu15173762.
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Aging results from gradual accumulation of damage to the cellular functions caused by biochemical processes such as oxidative stress, inflammation-driven prolonged cellular senescence state, immune system malfunction, psychological stress, and epigenetic changes due to exposure to environmental toxins. Plant-derived bioactive molecules have been shown to ameliorate the damage from oxidative stress. This research seeks to uncover the mechanisms of action of how phytochemicals from fruit/berry/vegetable (FBV) juice powder mitigate oxidative stress. The study uses a computational systems biology approach to (1) identify biomolecular pathways of oxidative stress; (2) identify phytochemicals from FBV juice powder and their specific action on oxidative stress mechanisms; and (3) quantitatively estimate the effects of FBV juice powder bioactive compounds on oxidative stress. The compounds in FBV affected two oxidative stress molecular pathways: (1) reactive oxygen species (ROS) production and (2) antioxidant enzyme production. Six bioactive compounds including cyanidin, delphinidin, ellagic acid, kaempherol, malvidin, and rutin in FBV significantly lowered production of ROS and increased the production of antioxidant enzymes such as catalase, heme oxygenase-1, superoxide dismutase, and glutathione peroxidase. FBV juice powder provides a combination of bioactive compounds that attenuate aging by affecting multiple pathways of oxidative stress.
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Stefaniu, Amalia, and Lucia Camelia Pirvu. "In Silico Study Approach on a Series of 50 Polyphenolic Compounds in Plants; A Comparison on the Bioavailability and Bioactivity Data." Molecules 27, no. 4 (February 19, 2022): 1413. http://dx.doi.org/10.3390/molecules27041413.
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Fifty (50) phytocompounds from several subclasses of polyphenols, chosen based on their abundance in the plant world, were analyzed through density functional methods, using computational tools to evaluate their oral availability and particular bioactivity on several cell modulators; key descriptors and molecular features related to the electron density and electrostatic potential for the lowest energy conformers of the investigated molecules were computed. An analysis of the bioactivity scores towards six cell modulators (GPCR ligand, ion channel modulator, kinase inhibitor, nuclear receptor ligand, protease inhibitor and enzyme inhibitor) was also achieved, in the context of investigating their potential side effects on the human digestive processes. Summarizing, computational results confirmed in vivo and in vitro data regarding the high bioavailability of soy isoflavones and better bioavailability of free aglycones in comparison with their esterified and glycosylated forms. However, by a computational approach analyzing Lipinski’s rule, apigenin and apigenin-7-O-rhamnoside, naringenin, hesperetin, genistein, daidzin, biochanin A and formonetin in the flavonoid series and all hydroxycinnamic acids and all hydroxybenzoic acids excepting ellagic acid were proved to have the best bioavailability data; rhamnoside derivatives, the predominant glycosides in green plants, which were reported to have the lowest bioavailability values by in vivo studies, were revealed to have the best bioavailability data among the studied flavonoids in the computational approach. Results of in silico screening on the phenolic derivatives series also revealed their real inhibitory potency on the six parameters studied, showing a remarkable similitude between the flavonoid series, while flavonoids were more powerful natural cell modulators than the phenyl carboxylic acids tested. Thus, it can be concluded that there is a need for supplementation with digestive enzymes, mainly in the case of individuals with low digestive efficiency, to obtain the best health benefits of polyphenols in humans.
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Ahmed, Aftab, Sajid-ur Rehman, Syeda Abida Ejaz, Aamer Saeed, Rabail Ujan, Pervaiz Ali Channar, Khalida Mahar, et al. "Exploring 2-Tetradecanoylimino-3-aryl-4-methyl-1,3-thiazolines Derivatives as Alkaline Phosphatase Inhibitors: Biochemical Evaluation and Computational Analysis." Molecules 27, no. 19 (October 10, 2022): 6766. http://dx.doi.org/10.3390/molecules27196766.
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The current study focused on the laboratory approach in conjunction with computational methods for the synthesis and bioactivity assessment of unique 2-tetradecanoylimino-3-aryl-4-methyl-1,3-thiazolines (2a–2k). Processes included cyclizing 1-aroyl-3-arylthioureas with propan-2-one in the presence of trimethylamine and bromine. By using spectroscopic techniques and elemental analyses, structures were elucidated. To assess the electronic properties, density functional theory (DFT) calculations were made, while binding interactions of synthesized derivatives were studied by the molecular docking tool. Promising results were found during the evaluation of bioactivity of synthesized compounds against alkaline phosphatase. The drug likeliness score, an indicator used for any chemical entity posing as a drug, was within acceptable limits. The data suggested that most of the derivatives were potent inhibitors of alkaline phosphatase, which in turn may act as lead molecules to synthesize derivatives having desired pharmacological profiles for the treatment of specific diseases associated with abnormal levels of ALPs.
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Asiedu, Seth O., Samuel K. Kwofie, Emmanuel Broni, and Michael D. Wilson. "Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm." Biomolecules 11, no. 5 (April 29, 2021): 653. http://dx.doi.org/10.3390/biom11050653.
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Severely ill coronavirus disease 2019 (COVID-19) patients show elevated concentrations of pro-inflammatory cytokines, a situation commonly known as a cytokine storm. The p38 MAPK receptor is considered a plausible therapeutic target because of its involvement in the platelet activation processes leading to inflammation. This study aimed to identify potential natural product-derived inhibitory molecules against the p38α MAPK receptor to mitigate the eliciting of pro-inflammatory cytokines using computational techniques. The 3D X-ray structure of the receptor with PDB ID 3ZS5 was energy minimized using GROMACS and used for molecular docking via AutoDock Vina. The molecular docking was validated with an acceptable area under the curve (AUC) of 0.704, which was computed from the receiver operating characteristic (ROC) curve. A compendium of 38,271 natural products originating from Africa and China together with eleven known p38 MAPK inhibitors were screened against the receptor. Four potential lead compounds ZINC1691180, ZINC5519433, ZINC4520996 and ZINC5733756 were identified. The compounds formed strong intermolecular bonds with critical residues Val38, Ala51, Lys53, Thr106, Leu108, Met109 and Phe169. Additionally, they exhibited appreciably low binding energies which were corroborated via molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) calculations. The compounds were also predicted to have plausible pharmacological profiles with insignificant toxicity. The molecules were also predicted to be anti-inflammatory, kinase inhibitors, antiviral, platelet aggregation inhibitors, and immunosuppressive, with probable activity (Pa) greater than probable inactivity (Pi). ZINC5733756 is structurally similar to estradiol with a Tanimoto coefficient value of 0.73, which exhibits anti-inflammatory activity by targeting the activation of Nrf2. Similarly, ZINC1691180 has been reported to elicit anti-inflammatory activity in vitro. The compounds may serve as scaffolds for the design of potential biotherapeutic molecules against the cytokine storm associated with COVID-19.
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Sharma, Ashutosh, Paola Isabel Angulo Bejerano, Irais Castillo Maldonado, Marcos de Donato Capote, Alfredo Madariaga-Navarrete, and Sujay Paul. "Genome-wide computational prediction and experimental validation of quinoa (Chenopodium quinoa) microRNAs." Canadian Journal of Plant Science 99, no. 5 (October 1, 2019): 666–75. http://dx.doi.org/10.1139/cjps-2018-0296.
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MicroRNAs (miRNAs) are highly conserved, endogenous, short (21–24 nucleotides), non-coding RNA molecules that play significant roles in post-transcriptional gene silencing by directing target mRNA cleavage or translational inhibition. Nonetheless, highly nutritious “super grain” quinoa (Chenopodium quinoa) is an extreme abiotic stress tolerant Andean seed crop of many potential uses, with outstanding protein quality and a load of vitamins, minerals, as well as flavonoid antioxidants. In this study, applying genome-wide in silico approaches (referring to the recently published quinoa genome) and following a set of stringent filtering measures, a total of 22 potentially conserved microRNAs belonging to 18 families were characterized from quinoa and 11 randomly selected putative microRNAs (cqu-miR160a, cqu-miR162a, cqu-miR164a, cqu-miR166b, cqu-miR167a, cqu-miR172a, cqu-miR319a, cqu-miR390a, cqu-miR393a, cqu-miR394a, and cqu-miR398b) were validated successfully by RT-PCR. Using the psRNATarget tool, a sum of 59 potential miRNA targets, mostly transcription factors, were identified that are involved in biosynthesis, metabolic processes, and signal transduction. Among the detected targets, six target transcripts (F-Box proteins, TCP, MYB, WD protein, NAC, and CSD) were reported to have specific roles in both flavonoids biosynthesis and stress response signaling in some plants. To the best of our knowledge, this is the first report of quinoa microRNAs and their targets.
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Ferrero, Stefano, Stefano Pantaleone, Cecilia Ceccarelli, Piero Ugliengo, Mariona Sodupe, and Albert Rimola. "Where Does the Energy Go during the Interstellar NH3 Formation on Water Ice? A Computational Study." Astrophysical Journal 944, no. 2 (February 1, 2023): 142. http://dx.doi.org/10.3847/1538-4357/acae8e.
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Abstract In the coldest (10–20 K) regions of the interstellar medium, the icy surfaces of interstellar grains serve as solid-state supports for chemical reactions. Among their plausible roles, that of third body is advocated, in which the reaction energies of surface reactions dissipate throughout the grain, stabilizing the product. This energy dissipation process is poorly understood at the atomic scale, although it can have a high impact on astrochemistry. Here we study, by means of quantum mechanical simulations, the formation of NH3 via successive H-additions to atomic N on water ice surfaces, paying special attention to the third-body role. We first characterize the hydrogenation reactions and the possible competitive processes (i.e., H-abstractions), in which the H-additions are more favorable than the H-abstractions. Subsequently, we study the fate of the hydrogenation reaction energies by means of ab initio molecular dynamics simulations. Results show that around 58%–90% of the released energy is quickly absorbed by the ice surface, inducing a temporary increase of the ice temperature. Different energy dissipation mechanisms are distinguished. One mechanism, more general, is based on the coupling of the highly excited vibrational modes of the newly formed species and the libration modes of the icy water molecules. A second mechanism, exclusive during the NH3 formation, is based on the formation of a transient H3O+/NH2 − ion pair, which significantly accelerates the energy transfer to the surface. Finally, the astrophysical implications of our findings relative to the interstellar synthesis of NH3 and its chemical desorption into the gas are discussed.
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Kappel, Kalli, Yinglong Miao, and J. Andrew McCammon. "Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor." Quarterly Reviews of Biophysics 48, no. 4 (July 16, 2015): 479–87. http://dx.doi.org/10.1017/s0033583515000153.
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AbstractElucidating the detailed process of ligand binding to a receptor is pharmaceutically important for identifying druggable binding sites. With the ability to provide atomistic detail, computational methods are well poised to study these processes. Here, accelerated molecular dynamics (aMD) is proposed to simulate processes of ligand binding to a G-protein-coupled receptor (GPCR), in this case the M3 muscarinic receptor, which is a target for treating many human diseases, including cancer, diabetes and obesity. Long-timescale aMD simulations were performed to observe the binding of three chemically diverse ligand molecules: antagonist tiotropium (TTP), partial agonist arecoline (ARc) and full agonist acetylcholine (ACh). In comparison with earlier microsecond-timescale conventional MD simulations, aMD greatly accelerated the binding of ACh to the receptor orthosteric ligand-binding site and the binding of TTP to an extracellular vestibule. Further aMD simulations also captured binding of ARc to the receptor orthosteric site. Additionally, all three ligands were observed to bind in the extracellular vestibule during their binding pathways, suggesting that it is a metastable binding site. This study demonstrates the applicability of aMD to protein–ligand binding, especially the drug recognition of GPCRs.
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Ciesielski, Wojciech, Henryk Kołoczek, Zdzisław Oszczęda, Jacek A. Soroka, and Piotr Tomasik. "Potential risk resulting from the influence of static magnetic field upon living organisms. Numerically simulated effects of the static magnetic field upon fatty acids and their glycerides." BioRisk 19 (March 6, 2023): 1–24. http://dx.doi.org/10.3897/biorisk.19.96250.
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Background: We attempt to recognise the effects of static magnetic field (SMF) of varying flux density on flora and fauna. For this purpose, the influence of static magnetic field is studied for molecules of octadecanoic (stearic), cis-octadec-9-enoic (oleic), cis,cis-octadec-9,12-dienoic (linoleic), all cis-octadec-6,9.12-trienoic (linolenic), trans-octadec-9-enoic – (elaidic), cis-octadec-11-enoic (vaccenic) and all trans-octadec-6,9,12-trienoic (trans-linolenic) acids as well as 1- and 2-caproyl monoglycerides, 1,2- and 1,3-caproyl diglycerides and 1,2,3-caproyl triglyceride. In such a manner we attempt to develop an understanding of the interactions of living cells with SMF on a molecular level. Methods: Computations of the effect of real SMF 0.0, 0.1, 1, 10 and 100 AMFU (Arbitrary Magnetic Field Unit; here 1AMFU > 1000 T) flux density were performed in silico (computer vacuum), involving advanced computational methods. Results: SMF polarises molecules depending on applied flux density It neither ionises nor breaks valence bonds at 0.1 and 1 AMFU. In some molecules under consideration flux density of 10 and 100AMFU some C-H and C-C bonds were broken. Some irregularities were observed in the changes of positive and negative charge densities and bond lengths against increasing flux density. They provide evidence that molecules slightly change their initially fixed positions with respect to the force lines of the magnetic field. The length of some bonds and bond angles change with an increase in the applied flux density providing, in some cases, polar interactions between atoms through space. Conclusions: SMF destabilizes lipid acids and caproyl glycerides irregularly against increasing flux density. That irregularity results from the ability of those molecules to twist out of the initially established SMF plain and squeeze molecules around some bonds. In some molecules SMF flux density of 10 AMFU and above breaks some valence bonds and only in case of elaidic acid the trans-cis conversion is observed. Depending on the structure and applied flux density SMF either stimulates or inhibits metabolic processes of the lipids under study.
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Zellinger, Barbara, Ulrich Bodenhofer, Immanuela A. Engländer, Cornelia Kronberger, Brane Grambozov, Elvis Ruznic, Markus Stana, et al. "Hsa-miR-3651 could serve as a novel predictor for in-breast recurrence via FRMD3." Breast Cancer 29, no. 2 (December 5, 2021): 274–86. http://dx.doi.org/10.1007/s12282-021-01308-y.
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Abstract Background MicroRNAs are small non-coding RNAs with pivotal regulatory functions in multiple cellular processes. Their significance as molecular predictors for breast cancer was demonstrated in the past 15 years. The aim of this study was to elucidate the role of hsa-miR-3651 for predicting of local control (LC) in early breast cancer. Results By means of high-throughput technology, hsa-miR-3651 was found to be differentially expressed between patients who experienced local relapse compared to those without (N = 23; p = 0.0035). This result could be validated in an independent cohort of 87 patients using RT-qPCR (p < 0.0005). In a second analysis step with a chip-based microarray containing 70,523 probes of potential target molecules, FERM domain protein 3 (FRMD3) was found to be the most down-regulated protein (N = 21; p = 0.0016). Computational analysis employing different prediction algorithms revealed FRMD3 as a likely downstream target of hsa-miR-3651 with an 8mer binding site between the two molecules. This could be validated in an independent patient set (N = 20, p = 0.134). Conclusion The current study revealed that hsa-miR-3651 is a predictor of LC in early breast cancer via its putative target protein FRMD3. Since microRNAs interfere in multiple pathways, the results of this hypothesis generating study may contribute to the development of tailored therapies for breast cancer in the future.