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Search results for: FREE ENERGY CALCULATIONS
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LattE- first-principles lattice energy calculations
PublicationCrystal engineering is currently attracting much interest. Its aim is to create materials of predefined properties fulfilling the requirements imposed by the applications. There are several parameters describing crystal structures, but the most important one is probably the energy of a crystal lattice. It is the energy released by the system when crystalline solid is formed out of molecules or ions in gaseous phase. Approximate...
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The laws of thermodynamics: entropy, free energy, information and complexity
PublicationW rozdziale przedstawiono podstawowe Zasady Termodynamiki. Omówiono zagadnienia związane z pojęciem entropii, energii Gibbsa, egzergii oraz systemami złożonymi.
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Model research and numerical calculations of the buoy for capturing of the sea-waves energy
Publicationw pracy przedstawiono konstrukcję i zasadę działania modelu 1:5 boi do pozyskiwania energii fal morskich oraz wyniki badań eksperymentalnych prowadzonych w dużym basenie w Centrum techniki Okrętowej w Gdańsku.Ponadto przedstawiono numeryczny model obliczeniowy i wybrane wyniki symulacji zachowania się boi na fali regularnej.
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublicationAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublicationPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Computed vibrational excitation ofCF4by low-energy electrons and positrons: Comparing calculations and experiments
PublicationQuantum calculations for the excitation of the asymmetric modes of the CF4 target gas, ν3 and ν4, by impact of low-energy electrons and positrons are carried out in the energy range around 1 eV and are compared with recent experimental findings. The similarities and differences between the two types of projectiles, and the two different modes, are analyzed and discussed vis à vis the present accord with the experimental results.
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ENERGY EFFICIENT SMALL INLAND PASSENGER SHUTTLE FERRY WITH HYBRID PROPULSION - CONCEPT DESIGN, CALCULATIONS AND MODEL TESTS
PublicationIn recent years, there has been a significant development in “green” and energy efficient propulsion systems, which fits into the general trend of environmentally friendly “green shipping”. The pursued goal is to construct a safe passenger ship that is low in energy demand and equipped with a highly energy efficient, emission-free propulsion system. The paper presents main problems encountered by designers of a small, hybrid-powered...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Evaluation the environmental fate of pharmaceuticals using a level III model based on poly-parameter linear free energy relationships
PublicationOpisano możliwości zastosowania modelu ''Level III Model'' do opisu losu środowiskowego pozostałości farmaceutyków w środowisku. Zastosowany model umożliwia oszacowanie trwałości, stężeń oraz transportu poszczególnych zanieczyszczeń pomiędzy poszczególnymi elementami składowymi środowiska (powietrze, woda, gleba i osady denne).
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How do sterols determine the antufungal activitiy of amphotericin B? Free energy of binding between the drug and its membrane targets.
PublicationAmphotericin B (AmB) is a well-known polyene antibiotic used to treat systemic fungal infections. It is commonly accepted that the presence of sterols in the membrane is essential for the AmB biological activity, that is, for the formation of transmembrane ion channels. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against...
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Cooperativity of Halogen- and Chalcogen-Bonding Interactions in the Self-Assembly of 4‑Iodoethynyl- and 4,7-Bis(iodoethynyl)benzo-2,1,3-chalcogenadiazoles: Crystal Structures, Hirshfeld Surface Analyses, and Crystal Lattice Energy Calculations
PublicationSeveral new 4-iodoethynyl- and 4,7-bis- (iodoethynyl)benzo-2,1,3-chalcogenadiazoles were prepared, and a comprehensive analysis of the most prominent secondary bonding interactions responsible for the crystal self-assembly was performed using X-ray diffraction. The presence of both the iodoethynyl and chalcogenadiazole moieties allows an evaluation of the preference of these molecules to aggregate through either chalcogen- or halogen-bonding...
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Paweł Możejko dr hab.
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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublicationThis work presents extensive theoretical studies focused on the mixed ion-electron transport in cubic strontium titanate (STO). A new approach to the description of this difficult system was developed within the framework of linear-scaling Kohn–Sham density functional theory, as realized in the ONETEP program. The description we present is free of any empirical parameters and relies on the Hubbard U and Hund’s J corrections applied...
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Ewa Klugmann-Radziemska prof. dr hab.
PeopleEwa Klugmann-Radziemska graduated from the University of Gdansk with a degree in physics, and since 1996 has been associated with the Gdansk University of Technology, when she began PhD studies. Currently, he is a professor at the Faculty of Chemistry at the Gdansk University of Technology, since 2006 head of the Department of Chemical Apparatus and Machinery. In the years 2008–2016 she was the Vice-Dean for cooperation and development,...
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Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution
PublicationFo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay...
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Application of cyanated asphaltenes in gas-phase adsorption processes for removal of volatile organic compounds
PublicationThe paper presents an innovative, chemically modified (methylcyanated) asphaltene-based adsorbent that can be an inter-esting low-cost alternative for traditional adsorbents. Adsorption properties of adsorbents were examined by inverse gas chromatography technique, adsorption isotherms, and breakthrough curves. A significant increase in retention volume for pyridine, 2-pentanone, nitropropane, toluene, and 1-butanol was observed....