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Search results for: AB INITIO CALCULATIONS,ASTROCHEMISTRY,POTENTIAL ENERGY SURFACES
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Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods
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Low-energy positron scattering from gas-phase pyrimidine: A quantum treatment of the dynamics and a comparison with experiments
PublicationWe are reporting detailed quantum scattering calculations that describe the diffusion of a beam of low-energy positrons interacting with the pyrimidine target as a gas-phase partner. The calculations have employed an essentially ab initio model for the short-range correlation interaction and for the electrostatic interaction of an impinging positron and the electron+nuclear structure of the target molecule at its equilibrium geometry.
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Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals
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Possible schemes of photoassociation processes in the KLi molecule with newly calculated potential energy curves
PublicationWe present four promising schemes for photoassociative formation of KLi molecule in its ground electronic state. Analysis is based on newly calculated adiabatic potentials supported by transition dipole moments and Franck-Condon factors.
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Investigation of rotational state-changing collisions of C2N− ions with helium
PublicationThe cross sections for rotational inelastic collisions between atoms and a molecular anion can be very large, if the anion has a dipole moment. This makes molecular anions very efficient in cooling atomic gases. We address rotational inelastic collisions of Helium atoms with the molecular anion C2N–. Here we present preliminary calculations of the potential energy surface.
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Facile synthesis of porous iron oxide/graphene hybrid nanocomposites and potential application in electrochemical energy storage
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
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Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins
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Construction of Optimized Energy Potential
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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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Low-energy positron scattering from DNA nucleobases: the effects from permanent dipoles
PublicationAb initio quantum calculations for low-energy positron scattering from gas-phase isolated molecular nucleobases which are part of the DNA structure are presented and discussed over the range of 1 eV to 25 eV. The calculations report the integral cross sections (ICSs) and the momentum-transfer cross sections (MTCSs) for Adenine, Guanine, Thymine and Cytosine. The calculations show very clearly the important role of the dominant...
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins
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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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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models
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On the rising extra storage capacity of ultra-small Fe3O4particles functionalized with HCS and their potential as high-performance anode material for electrochemical energy storage
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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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Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
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Determining the optimal filling of the surface with a linker with Universal Force Field and Reax Force Field
Open Research DataThe DataSet contains the atomic slabs of diamond surfaces with ATP molecules in water. The calculated data includes different sized surfaces from 90 Angstrom^2 to 691 Angstrom^2. Structures were relaxed using the Reax Force Field method with the Limited Memory Broyden–Fletcher–Goldfarb–Shanno algorithm. Structures were calculated with a convergence...
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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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Proton transfer reactions for ionized water clusters
PublicationCalculations of formation energies of the ionized water clusters and energies of reactions between small (including less than eight water molecules) neutral and positively ionized water clusters are presented. Moreover, we discuss some reaction paths between neutral and positively charged dimers, trimers and tetramers and proton transfer reactions (PTR) between cyclic clusters and H3O+ ions which can appear in beam experiments...
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Superconductivity in Bismuth Pyrochlore Lattice Compounds RbBi2 and CsBi2: The Role of Relativistic Effects
PublicationSuperconducting properties of two bismuthide intermetallic compounds, RbBi2 and CsBi2, were studied by means of experimental measurements and ab initio calculations. We show that in both compounds, the superconductivity emerges from the pyrochlore Bi lattice and its formation is heavily influenced by relativistic effects. Based on our analysis of the effect of spin–orbit coupling on the electron–phonon coupling, we suggest a possible...
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On the electronic structure of methyl butyrate and methyl valerate
PublicationWe present novel results of the analysis of the electronic structure of two aliphatic esters: methyl butyrate and methyl valerate. High-resolution photoabsorption spectra were collected and analyzed over the energy range 4.0–10.8 eV and showed for both the molecules not only a clear band of the HOMO to LUMO transition, but also vibronic structure associated with the first Rydberg-valence transition. Photoelectron spectra recorded...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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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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Imidazolium silanethiolates relevant to the active site of cysteineproteases. A cooperative effect in a chain of NH(+)...S(-) hydrogenbonds
PublicationThree imidazolium silanethiolates relevant to the active site of cysteine proteases have been synthesized and investigated by X-ray diffraction, IR spectroscopy and computational methods. As indicated by crystallographic and FT-IR data in the solid state, the transfer of proton from thiol to imidazole takes place and a thiolato-imidazolium ion pair is formed. The FT-IR spectra of crystalline imidazolium silanethiolates exhibit...
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Configurations of H 3 + (H2)n clusters and their energies
PublicationThe H-3(+) ion plays an important role in low temperature astrophysical and laboratory plasmas. It is considered as the initiator of many ion-molecule chemistries. Also its clusters with H-2 are quite interesting. We study configurations of the H-3(+)(H-2)(n) clusters for n = 1 up to n = 12 as a simple test system. Total energies for these structures, with zero point vibration corrections have been calculated. Stabilization energies...
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Multi-state vibronic interactions in the fluorobenzene radical cation: The importance of quadratic coupling terms
PublicationThe multi-mode multi-state vibronic interactions in the set of X^2B_1 - D^2A_1 electronic states of the monofluoro benzene radical cation are investigated theoretically, based on a quadratic vibronic coupling approach. The underlying ionization potentials and coupling constants are obtained from ab initio coupled-cluster calculations. Previous investigations (relying on the linear coupling approach) are extended by including all...
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Polarisation effects in low-energy positron–molecule scattering
PublicationThe UK molecular R-matrix method has been adapted to treat positron collisions from polyatomic targets. A simple empirical enhancement factor which corrects for the underestimation of electron–positron polarisation and correlation effects in the calculations performed with the static-plus-polarization model at low scattering energies is presented. Application of this model to positron scattering from carbon dioxide at energies...
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A first-principles study of electron attachment to the fully hydrated bromonucleobases
PublicationDegradation mechanism of four brominated nucleobases (BrX), potential DNA radiosensitizers, is studied in explicit water solution, using ab initio molecular dynamics. Several fs long dynamics is needed to localize an electron on the nucleobase. Produced by electron attachment BrX anion radical degrades through the bromide anion abstraction, barrier-free (purines) or with low barrier (pyrimidines), to a reactive nucleobase radical....
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Molecular geometry and optical activity of helically chiral N-nitrosamines derived from 1,2,3,4-tetrahydro- and 1,2,3,4,7,8,9,10-octahydro-1,10-phenanthroline
PublicationX-ray crystallographic analysis of the title N-nitrosamines revealed that they assume helical conformations in the solid state. Nitrosamines 1b and 2b were resolved by inclusion crystallization with optically active diols (TADDOLs). The absolute configuration of the guest molecules in the complexes 1b·3b and 2b·3b was assigned as M. The optical activity of the resolved compounds is manifested by their solid state CD spectra, which...
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The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry
Open Research DataThe developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic...
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The role of low-energy electrons in the charging process of LISA test masses
PublicationThe estimate of the total electron yield is fundamental for our understanding of the test-mass charging associated with cosmic rays in the Laser Interferometer Space Antenna (LISA) Pathfinder mission and in the forthcoming gravitational wave observatory LISA. To unveil the role of low energy electrons in this process owing to galactic and solar energetic particle events, in this work we study the interaction of keV and sub-keV...
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Photoelectron spectroscopy of a series of acetate and propionate esters
PublicationThe electronic state and photoionization spectroscopy of a series of acetate esters: methyl acetate, isopropyl acetate, butyl acetate and pentyl acetate as well as two propionates: methyl propionate and ethyl propionate, have been determined using vacuum-ultraviolet photoelectron spectroscopy. These experimental investigations are complemented by ab initio calculations. The measured first adiabatic and vertical ionization energies...
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Beyond the helium buffer: 12C−2 rotational cooling in cold traps with H2 as a partner gas: interaction forces and quantum dynamics
Publicationabstract = { The scattering cross-sections and corresponding rate coefficients for rotationally inelastic collisions of $^{12}$C$_2$^-$ ($^2 \Sigma_g^+$) with H$_2$ ($^1 \Sigma_g^+$) are presented over a broad range of cold-trap temperatures. They have been calculated using quantum scattering theory that employs a new ab initio potential energy surface. The rate coefficients for the inelastic processes in the anionic partner are...
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Tuning the work function of graphite nanoparticles via edge termination
PublicationGraphite nanoparticles are important in energy materials applications such as lithium-ion batteries (LIBs), supercapacitors and as catalyst supports. Tuning the work function of the nanoparticles allows local control of lithiation behaviour in LIBs, and the potential of zero charge of electrocatalysts and supercapacitors. Using large scale density functional theory (DFT) calculations, we find that the surface termination of multilayer...
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Charge Transfer, Complexes Formation and Furan Fragmentation Induced by Collisions with Low-Energy Helium Cations
PublicationThe present work focuses on unraveling the collisional processes leading to the fragmentation of the gas-phase furan molecules under the He+ and He2+ cations impact in the energy range 5–2000 eV. The presence of different mechanisms was identified by the analysis of the optical fragmentation spectra measured using the collision-induced emission spectroscopy (CIES) in conjunction with the ab initio calculations. The measurements of...
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1,3-alternate calix[4]arene-bonded silica stationary phases. Effect of calixarene skeleton substituents on the retention mechanism and column selectivity
PublicationFour novel 1,3-alternate calix[4]arene-bonded silica gel stationary phases possessing different aromatic and aliphatic substituents at the upper rim (CalixNph, CalixBph, CalixHex and CalixDdc) were prepared and structurally characterized. The comparison and selectivity of these phases was done by using alkylbenzenes, fatty acid p-bromophenacyl esters, aromatic positional isomers and polynuclear aromatic hydrocarbons as analytes....
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
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A facile method for Tauc exponent and corresponding electronic transitions determination in semiconductors directly from UV–Vis spectroscopy data
PublicationIn this work, a facile method allowing for estimation of the exponent in the Tauc equation directly from the UV–vis spectra is presented. It is based on the Taylor expansion of the logarithmic version of the Tauc equation. The Tauc exponent is calculated from the tangent slope of the absorption data. Knowledge of this coefficient provides information about the optical transition types and is used as an input for the calculations...
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Zero-range potentials in multi-channel diatomic molecule scattering
PublicationZagadnienie o rozpraszaniu elektronów na molekułach rozwiązuje się w sposób jawny w modelu potencjałów o zerowym promieniu. Uwzględniając stany wzbudzone wprowadzamy potencjał macierzowy. Dla przykładu e+H_2 porównujemy wyniki obliczeń przekrojów czynnych z innymi (ab initio) oraz z doświadczeniem.
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Generalized Zero Range Potentials and Multichannel Electron Molecule Scattering.
PublicationZagadnienie o rozpraszaniu elektronów na molekułach rozwiązuje się w sposób jawny w modelu potencjałów o zerowym promieniu. Uwzględniając stany wzbudzone wprowadzamy potencjał macierzowy. Dla przykładu stanów wibracyjnych e+H_2 porównujemy wyniki obliczeń przekrojów czynnych z innymi (ab initio) oraz z doświadczeniem.
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Thermal and hydraulic phenomena in boundary layer of minijets impingement on curved surfaces
PublicationPresented work considers flow and thermal phenomena occurring during the single minijet impingement on curved surfaces, heated with a constant heat flux, as well as the array of minijets. Numerical analyses, based on the mass, momentum and energy conservation laws, were conducted, regarding single phase and two-phase simulations. Focus was placed on the proper model construction, in which turbulence and boundary layer modeling...
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Studies on the solid-liquid equilibria and intermolecular interactions Urea binary mixtures with Sulfanilamide and Sulfacetamide
PublicationThe binary phase diagrams of Sulfanilamide-Urea (SN-U) and Sulfacetamide-Urea (SC-U) were measured using differential scanning calorimetry technique (DSC). Both examined mixtures were found to form simple binary eutectics. The limited miscibility in the solid state observed by DSC, proving inability of co-crystallization in new multi-molecular form, was also confirmed using PXRD and FTIR-ATR measurements of solid dispersions...
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Modelling charge transfer processes in C2+ -tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks
PublicationInvestigations of collision-induced processes involving carbon ions and molecules of biological interest in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest...
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The Role of Electron Transfer in the Fragmentation of Phenyl and Cyclohexyl Boronic Acids
PublicationIn this study, novel measurements of negative ion formation in neutral potassium-neutral boronic acid collisions are reported in electron transfer experiments. The fragmentation pattern of phenylboronic acid is comprehensively investigated for a wide range of collision energies, i.e., from 10 to 1000 eV in the laboratory frame, allowing some of the most relevant dissociation channels to be probed. These studies were performed in...
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Hydropower potential of the lower Vistula
PublicationThis paper presents an estimate analysis of the hydropower potential of the lower Vistula River from Warsaw to Gdańsk Bay. The calculations were made for a hydraulic model of the lower Vistula which takes into account potential development of barrages in a cascade system. Results obtained from the model simulations and from hydrological calculations were used to estimate the power of hydropower plants and the average annual energy...
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Electron attachment to representative cations composing ionic liquids
PublicationUsing ab initio electronic structure methods with flexible atomic orbital basis sets, we investigated the electronic structure and stability of reduction products of selected representative cations (C+) constituting ionic liquids. We found that an electron attachment to such cations leads to the neutral radicals, whereas a subsequent attachment of another (i.e., excess) electron leads to adiabatically stable anions only in two...
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Linking optical and electronic properties to photoresponse of heterojunctions based on titania nanotubes and chromium, molybdenum, and tungsten oxides
PublicationThe development of photosensitization strategies for titanium dioxide is necessary for the enhancement of its optical and electronic properties towards its application potential in solar photoelectrochemistry. In this work, significant differences in the photosensitizing capability of the 6th group transition metal oxides applied on the surface of titania nanotubes are reported. For the first time, correlations between the experimentally...
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Theoretical Design of the Molecular Structure of Bent-Core Mesogens with Large Second-Order Nonlinear Optical Properties
PublicationABSTRACT: The first hyperpolarizability of two series of moleculeswith bent-shaped structures has been calculated at the ab initio level.The two series consist of carboxyl derivatives for which somemolecules are known to exhibit banana phases and of their sulfinatehomologues that have not been synthesized yet. The final purpose isto reveal the relevance or not in synthesizing these latter molecules.The strategy is based on reporting...