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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....
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Michał Ryms dr inż.
PeopleMichał Ryms, PhD, Eng. is the physicist, graduate of the Gdańsk University of Technology. PhD thesis defended at the Chemical Faculty. Since 2011 an employee at the Department of Chemical Apparatus and Theory of Machines, Chemical Faculty, Gdansk University of Technology, POLAND – now as an assistant professor. His research interests includes: improvement of energy efficiency and possibilities of new application of phase change...
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Hydrogen migration in formation of NH(A3Π) radicals via superexcited states in photodissociation of isoxazole molecules
PublicationFormation of the excited NH(A 3Π) free radicals in the photodissociation of isoxazole (C3H3NO) molecules has been studied over the 14-22 eV energy range using photon-induced fluorescence spectroscopy. The NH(A 3Π) is produced through excitation of the isoxazole molecules into higher-lying superexcited states. Observation of the NH radical, which is not a structural unit of the isoxazole molecule, corroborates the hydrogen atom...
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Elimination and migration of hydrogen in the vacuum-ultraviolet photodissociation of pyridine molecules
PublicationElimination of the excited hydrogen atoms H(n), n = 4–7, and hydrogen migration in formation of the excited NH(A 3Π) free radicals in the photodissociation of pyridine, C5H5N, molecules have been studied over the 17.5–70 eV photon energy range. In the measurements the photon-induced fluorescence spectroscopy technique has been applied. Both fragments are produced through excitation of pyridine molecules into higher-lying superexcited...
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Stability and phase transition investigation of olanzapine polymorphs
PublicationWe use electrical embedded-fragment QM method with both DFT/ωB97XD/6-31G* and MP2/6-31G* to investigate the phase transformations of olanzapine. Gibbs free energy calculations predict that form I is always the most stable structure and form II is the least stable one, while form IV is more stable than form III below about 200 K but less stable above this temperature, implying a polymorphic phase transformation. This may account...
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Comparative study of a combined heat and power plant retrofitted by CO2 capture during the combustion of syngas from sewage sludge gasification versus zero-emission combustion of hydrogen produced using renewables
PublicationWith ecological requirements aimed at limiting the production of CO2, it is necessary to produce all, or most of the energy from RES. During the transformation process, ecological and highly efficient combustion power plants will be needed. The classic cycle of combined heat and power (CCGT) with green improvements will continue to be one of the most suitable technologies for this task. This article presents the modernization of...
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Collagen type II–hyaluronan interactions – the effect of proline hydroxylation: a molecular dynamics study
PublicationHyaluronan–collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents...
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Physical Chemistry_GTM_20_21_winter
e-Learning CoursesThe aim of the subject is to familarize the student with fundamental physico-chemical laws in chemical thermodynamics, phase equilibria and chemical equilibria together with ability of solving relevant text problems involving calculations, as well as teachnig him/her effective and safe carrying out simple experiments/measurements of physico-chemical quantities and proper presentation and interpretation of their results. LECTURES Chemical...
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Quantitative study of free convective heat losses from thermodynamic partitions using Thermal Imaging
PublicationThe following paper presents a simple method of determining the presence, distribution and values of heat losses from external building walls as thermodynamic partitions using a Thermal Imaging Camera (TIC). According to Fourier's equation, the value of heat loss is proportional to the temperature gradient ∂t/∂y|y=0 in air in the y direction perpendicular to the heated surface. Unfortunately, air temperature cannot be measured...
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Thermodynamic Cycle Concepts for High-Efficiency Power Plants. Part B: Prosumer and Distributed Power Industry
PublicationAn analysis was carried out for different thermodynamic cycles of power plants with air turbines. A new modification of a gas turbine cycle with the combustion chamber at the turbine outlet has been described in the paper. A special air by-pass system of the combustor was applied, and in this way, the efficiency of the turbine cycle was increased by a few points. The proposed cycle equipped with an effective heat exchanger could...
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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublicationIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function
PublicationAmphotericin B (AmB), one of the most powerful but also toxic drugs used to treat systemic mycoses, is believed to selectively permeabilize fungal cell membranes to ions in a sterol-dependent manner. Unfortunately, the structure of the biologically active AmB channels has long eluded researchers, obstructing the design of safer alternatives. Here, we investigate the structural and thermodynamic aspects of channel formation, stability,...
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Biochemical, Structural Analysis, and Docking Studies of Spiropyrazoline Derivatives
PublicationIn this study, we evaluated the antiproliferative potential, DNA damage, crystal struc‐ tures, and docking calculation of two spiropyrazoline derivatives. The main focus of the research was to evaluate the antiproliferative potential of synthesized compounds towards eight cancer cell lines. Compound I demonstrated promising antiproliferative properties, especially toward the HL60 cell line, for which IC50 was equal to 9.4 μM/L....
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Equilibrium constants (Keq) of reforming reactions
Open Research DataThe equilibrium constants (K) of reforming reactions in SOFC were supplied with this dataset
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Adiabatic potential energy curves of the triplet Pi gerade states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Pi gerade states have been calculated for the Lithium dimer. The results of the two excited states of the symmetry triplet Pi gerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction of valence electrons...
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Adiabatic potential energy curves of the singlet Pi ungerade states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the singlet Pi ungerade states have been calculated for the Lithium dimer. The results of the two excited states of the symmetry singlet Pi ungerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction of valence electrons...
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Adiabatic potential energy curves of the singlet Pi and Delta gerade states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the singlet Pi and Delta gerade states have been calculated for the Lithium dimer. The results of the three excited states of the symmetries singlet Pi and Delta gerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the triplet Sigma ungerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Sigma ungerade plus states have been calculated for the Lithium dimer. The results of the five excited states of the symmetry triplet Sigma ungerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the singlet Sigma gerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the singlet Sigma gerade plus states have been calculated for the Lithium dimer. The results of the ground state and three excited states of the symmetry singlet Sigma gerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing...
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Adiabatic potential energy curves of the singlet Sigma ungerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the singlet Sigma ungerade plus states have been calculated for the Lithium dimer. The results of the three excited states of the symmetry singlet Sigma ungerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the triplet Sigma gerade plus states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Sigma gerade plus states have been calculated for the Lithium dimer. The results of the three excited states of the symmetry triplet Sigma gerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Adiabatic potential energy curves of the triplet Pi and Delta ungerade states of the Lithium dimer
Open Research DataAdiabatic potential energy curves of the triplet Pi and Delta ungerade states have been calculated for the Lithium dimer. The results of the three excited states of the symmetries triplet Pi and Delta ungerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Euilibrium composition of CH4-CO2-CO-H2-H2O-C system under biogas reforming conditions
Open Research DataThe equilibrium compositions of CH4, CO2, CO, H2, H2O and C under the biogas mixture reforming were supplied with this dataset
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Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
PublicationCoarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...
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Potential energy curves of the doublet Sigma gerade plus states of the Lithium dimer cation
Open Research DataAdiabatic potential energy curves of the doublet Sigma gerade plus (dSg+) states have been calculated for the Lithium dimer cation (Li2+). The results of the ground state and four excited states of the symmetry doublet Sigma gerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials...
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Potential energy curves of the doublet Sigma ungerade plus states of the Lithium dimer cation
Open Research DataAdiabatic potential energy curves of the doublet Sigma ungerade plus (dSu+) states have been calculated for the Lithium dimer cation (Li2+). The results of the five excited states of the symmetry doublet Sigma ungerade plus have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing...
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Potential energy curves of the doublet Pi and Delta gerade states of the Lithium dimer cation
Open Research DataAdiabatic potential energy curves of the doublet Pi and Delta gerade (dPg and dDg) states have been calculated for the Lithium dimer cation (Li2+). The results of the four excited states of the symmetries doublet Pi and Delta gerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials...
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Potential energy curves of the doublet Pi and Delta ungerade states of the Lithium dimer cation
Open Research DataAdiabatic potential energy curves of the doublet Pi and Delta ungerade (dPu and dDu) states have been calculated for the Lithium dimer cation (Li2+). The results of the four excited states of the symmetries doublet Pi and Delta ungerade have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials...
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Euilibrium composition of CH4-CO2-CO-H2-H2O-C system for CO2/H2/H2O methanation
Open Research DataThe equilibrium compositions of CH4, CO2, CO, H2, H2O and C under the methanation reaction of 1:2 CO:H2 syngas mixtures were supplied with this dataset
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Born-Oppenheimer potential energy curves of the NaK molecule
Open Research DataAdiabatic potential energy curves (APEC) of the singlet (s) and triplet (t) Sigma+, Pi, and Delta electronic states have been calculated for the NaK molecule. All results of the presented molecular states have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Euilibrium composition of CH4-CO2-CO-H2-H2O-C system under various compositions syngas methanation
Open Research DataThe equilibrium compositions of CH4, CO2, CO, H2, H2O and C under the methanation reaction of various syngas mixtures (different CO/H2 ratio) were supplied with this dataset