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Year  Points  List 

Year 2022  100  Ministry Scored Journals List 2019 
Year  Points  List 

2022  100  Ministry Scored Journals List 2019 
2021  100  Ministry Scored Journals List 2019 
2020  100  Ministry Scored Journals List 2019 
2019  100  Ministry Scored Journals List 2019 
2018  35  A 
2017  35  A 
2016  35  A 
2015  35  A 
2014  35  A 
2013  35  A 
2012  35  A 
2011  35  A 
2010  32  A 
2009  32  A 
2008  32  A 
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Year  Points 

Year 2020  5.5 
Year  Points 

2020  5.5 
2019  5.2 
2018  5.3 
2017  5.4 
2016  5.4 
2015  5.2 
2014  5.1 
2013  5.6 
2012  5.3 
2011  5.4 
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total: 56
Catalog Journals
Year 2021

Electrochemistry from firstprinciples in the grand canonical ensemble
PublicationProgress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by firstprinciples quantum mechanical simulations with Density Functional Theory (DFT). However, such simulations are...

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...

Massively parallel linearscaling Hartree–Fock exchange and hybrid exchange–correlation functionals with plane wave basis set accuracy
PublicationWe extend our linearscaling approach for the calculation of Hartree–Fock exchange energy using localized in situ optimized orbitals [Dziedzic et al., J. Chem. Phys. 139, 214103 (2013)] to leverage massive parallelism. Our approach has been implemented in the ONETEP (OrderN Electronic Total Energy Package) density functional theory framework, which employs a basis of nonorthogonal generalized Wannier functions (NGWFs) to achieve...

Spontaneous electron emission vs dissociation in internally hot silver dimer anions
PublicationReferring to a recent experiment, we theoretically study the process of a twochannel decay of the diatomic silver anion (Ag2), namely the spontaneous electron ejection giving Ag2 + e and the dissociation leading to Ag + Ag. The ground state potential energy curves of the silver molecules of diatomic neutral and negative ion were calculated using proper pseudopotentials and atomic basis sets. We also estimated the nonadiabatic...

Sumoverstate expressions including secondorder Herzberg–Teller effects for the calculation of absorption and resonance Raman intensities
PublicationThe sumoverstate expressions are derived to calculate the secondorder Herzberg–Teller (HT) effects in absorption and resonance Raman spectroscopies. These effects depend on the second derivatives of the transition dipole moment with respect to the vibrational coordinates. The method is applied to the molecule of 1,3butadiene using density functional theory calculations. It is found that the secondorder HT effects are significant...
Year 2020

Dissociative electron attachment to benzoic acid (C7H6O2)
PublicationThe dissociative electron attachment (DEA) to benzoic acid (C6H5COOH) has been studied using an experimental crossed beam setup of a quadrupole mass spectrometer and a trochoidal electron monochromator. Relative partial cross sections for the DEA to produce negative ion fragments show the main channels for dissociation. The comparison of the present results with the ultraviolet photoelectron spectrum of benzoic acid [J. Meeks,...

Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces
PublicationDensity functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has nonzero charge, electrical neutrality has to be imposed, and this is often done via a uniform background charge of opposite sign (“jellium”). This artificial neutralization does not occur in reality, where a different...

Extension of the forcematching method to coarsegrained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins
Publication 
Interaction of 4nitrothiophenol with low energy electrons: Implications for plasmon mediated reactions
PublicationThe reduction of 4nitrothiophenol (NTP) to 44′dimercaptoazobenzene (DMAB) on laser illuminated noble metal nanoparticles is one of the most widely studied plasmon mediated reactions. The reaction is most likely triggered by a transfer of low energy electrons from the nanoparticle to the adsorbed molecules. Besides the formation of DMAB, dissociative side reactions of NTP have also been observed. Here, we present a crossed electronmolecular...

Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5Bromouracil case study
Publication 
Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5Bromouracil case study
PublicationABSTRACT Laser illuminated gold nanoparticles (AuNPs) efficiently absorb light and heat up the surrounding medium, leading to versatile applications ranging from plasmonic catalysis to cancer photothermal therapy. Therefore, an indepth understanding of the thermal, optical, and electron induced reaction pathways is required. Here, the electrophilic DNA nucleobase analog 5Bromouracil (BrU) has been used as a model compound to...

Rotational statechanging collisions of C2H− and C2N− anions with He under interstellar and cold ion trap conditions: A computational comparison
PublicationWe present an extensive range of quantum calculations for the statechanging rotational dynamics involving two simple molecular anions that are expected to play some role in the evolutionary analysis of chemical networks in the interstellar environments, C2H− (X1Σ+) and C2N− (X3Σ−), but for which inelastic rates are only known for C2H−. The same systems are also of direct interest in modeling selective photodetachment experiments...

The ONETEP linearscaling density functional theory program
PublicationWe present an overview of the ONETEP program for linearscaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Nonorthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
Year 2019

A general method for the derivation of the functional forms of the effective energy terms in coarsegrained energy functions of polymers. III. Determination of scaleconsistent backbonelocal and correlation potentials in the UNRES force field and forcefield calibration and validation
Publication 
Electron collisions with X(CH3)4 molecules (X = C, Si, Ge)
PublicationAbsolute grandtotal cross sections (TCSs) for electron scattering from tetramethylmethane [C(CH3)4], tetramethylsilane [Si(CH3)4], and tetramethylgermane [Ge(CH3)4] molecules have been measured at electronimpact energies extending from around 0.5 to 300 eV in the linear electrontransmission experiment. The measured TCS energy dependences show very pronounced broad enhancement, peaking near 5.5 eV for Si(CH3)4 and Ge(CH3)4 molecules...

Electron scattering from tin tetrachloride (SnCl4) molecules
PublicationAbsolute grandtotal cross section (TCS) for electron scattering from a tin tetrachloride, SnCl4, molecule was measured at electronimpact energies ranging from 0.6 to 300 eV, in the linear electrontransmission experiment. The measured TCS energy dependence shows two very pronounced enhancements peaking near 1.2 eV and around 9.5 eV, separated with a deep minimum centered close to 3 eV. The low energy structure is attributed to...

Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantummechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linearscaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
Year 2018

Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublicationTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into singleion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...

Electron attachment to hexafluoropropylene oxide (HFPO)
PublicationWe probe the electron attachment in hexafluoropropylene oxide (HFPO), C3F6O, a gas widely used in plasma technologies. We determine the absolute electron attachment cross section using two completely different experimental approaches: (i) a crossedbeam experiment at single collision conditions (local pressures of 5 × 10−4 mbar) and (ii) a pulsed Townsend experiment at pressures of 20–100 mbar. In the latter method, the cross sections...

Low energy differential elastic electron scattering from acetonitrile (CH3CN)
PublicationMeasurements of elastic differential cross sections for electron scattering from acetonitrile (CH3CN) have been performed utilizing a crossed electronmolecular beam experiment and with the relative flow method, for the incident electron energy range of 0.7 eV–30 eV and the scattering angle range of 10◦–130◦. These differential cross sections have been used to calculate the elastic integral and momentum transfer cross sections,...

The role of HerzbergTeller effects on the resonance Raman spectrum of transporphycene investigated by time dependent density functional theory.
PublicationThe S1 excited state properties as well as the associated absorption and resonance Raman (RR) spectra of transporphycene are investigated by means of time dependent density functional theory calculations. The relative magnitude of the FranckCondon (FC) contribution and of the HerzbergTeller (HT) effects is evaluated for both the absorption and RR intensities. The accuracy of the calculated spectra is assessed by employing different...

The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
Year 2017

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving selfconsistency is a common feature of BornOppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the selfconsistency procedure can be reduced by reusing...

The accretion of the new ice layer on the surface of hexagonal ice crystal and the influence of the local electric field on this process
PublicationThe process of creation of a new layer of ice on the basal plane and on the prism plane of a hexagonal ice crystal is analyzed. It is demonstrated that the ordering of water molecules in the already existing crystal affects the freezing. On the basal plane, when the orientations of water molecules in the ice block are random, the arrangement of the new layer in a cubic manner is observed more frequently — approximately 1.7 times...
Year 2016

Comparison of simplified sumoverstate expressions to calculate resonance Raman intensities including FranckCondon and HerzbergTeller effects
PublicationSumoverstate (SOS) expressions to simulate absorption spectroscopy and resonance Raman (RR) scattering including FranckCondon (FC) and HerzbergTeller (HT) effects are described. Starting from the general SOS method, several simplified SOS formulae are derived. In particular, within the socalled independent mode displaced harmonic oscillator model, it is shown that including the vibronic structure in the absorption and RR spectra...

Dissociative electron attachment to the radiosensitizing chemotherapeutic agent hydroxyurea
PublicationDissociative electron attachment to hydroxyurea was studied in the gas phase for electron energies ranging from zero to 9 eV in order to probe its radiosensitizing capabilities. The experiments were carried out using a hemispherical electron monochromator coupled with a quadrupole mass spectrometer. Diversified fragmentation of hydroxyurea was observed upon low energy electron attachment and here we highlight the major dissociation...

Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the icebinding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...

TINKTEP: A fully selfconsistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Selfconsistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...

Valence and lowest Rydberg electronic states of phenol investigated by synchrotron radiation and theoretical methods
PublicationWe present the experimental highresolution vacuum ultraviolet (VUV) photoabsorption spectra of phenol covering for the first time the full 4.3–10.8 eV energyrange, with absolute cross sections determined. Theoretical calculations on the vertical excitation energies and oscillator strengths were performed using timedependent density functional theory and the equationofmotion coupled cluster method restricted to single and double...
Year 2015

Electron collisions with methylsubstituted ethylenes: Cross section measurements and calculations for 2methyl–2butene and 2,3dimethyl–2butene
PublicationWe report electronscattering cross sections determined for 2methyl–2butene [(H3C)HC==C(CH3)2] and 2,3dimethyl–2butene [(H3C)2C=C(CH3)2] molecules. Absolute grandtotal cross sections (TCSs) were measured for incident electron energies in the 0.5–300 eV range, using a linear electrontransmission technique. The experimental TCS energy dependences for the both targets appear to be very similar with respect to the shape. In each...

Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that firstshell water molecules accommodate the...

Unusual dynamic properties of water near the icebinding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three welldefined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
Year 2014

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 1422 eV energy range using photoninduced fluorescence spectroscopy. The NH(A 3Π) is produced through excitation of the isoxazole molecules into higherlying superexcited states. Observation of the NH radical, which is not a structural unit of the isoxazole molecule, corroborates the hydrogen atom...

Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublicationMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...

Valence and ionic lowestlying electronic states of ethyl formate as studied by highresolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy, and ab initio calculations
PublicationThe highest resolution vacuum ultraviolet photoabsorption spectrum of ethyl formate, C2H5OCHO, yet reported is presented over the wavelength range 115.0–275.5 nm (10.75–4.5 eV) revealing several new spectral features. Valence and Rydberg transitions and their associated vibronic series, observed in the photoabsorption spectrum, have been assigned in accordance with new ab initio calculations of the vertical excitation energies...
Year 2013

Linearscaling calculation of HartreeFock exchange energy with Nonorthogonal Generalised Wannier Functions
PublicationWe present a method for the calculation of fourcentre twoelectron repulsion integrals in terms of localised nonorthogonal generalised Wannier functions (NGWFs). Our method has been imple mented in the ONETEP program and is used to compute the HartreeFock exchange energy component of HartreeFock and Density Functional Theory (DFT) calculations with hybrid exchangecorrelation functionals. As the NGWFs are optimised in situ...

Lowenergy positron scattering from gasphase tetrahydrofuran: A quantum treatment of the dynamics and a comparison with experiments
PublicationIn this paper we report new quantum calculations of the dynamics for lowenergy positrons interacting with gaseous molecules of tetrahydrofuran. The new quantum scattering cross sections are differential and integral cross sections at collision energies between 1.0 and 25.0 eV and include a careful treatment of the additional effects on the scattering process brought about by the permanent dipole moment of the target molecule....
Year 2012

Refined theoretical study of radiative association: Cross sections and rate constants for the formation of SiN
PublicationRadiative association of silicon mononitride (SiN) in its two lowest molecular electronic states is studied through quantum and classical dynamics. Special attention is paid to the behavior of the cross section at high collision energies. A modified expression for the semiclassical cross section is presented which excludes transitions to continuum states. This gives improved agreement with quantum mechanical perturbation theory...
Year 2011

Electronic states of tetrahydrofuran molecules studied by electron collisions
PublicationElectronic states of tetrahydrofuran molecules were studied in the excitation energy range 5.510 eV using the technique of electron energy loss spectroscopy in the gas phase. Excitation from the two conformations, C2 and Cs, of the ground state of the molecule are observed in the measured energy loss spectra. The vertical excitation energies of the 3(no3s) triplet state from the C2 and Cs conformations of the ground state of the...

Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linearscaling density functional theory
PublicationWe present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linearscaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and the efficacy of using Fourier transforms to compute the Hartree potential. In such...

Fourier transform infrared spectroscopic and theoretical study of water interactions with glycine and its Nmethylated derivatives
PublicationZbadano hydratację glicyny i jej metylowych pochodnych: Nmetyloglicyny (NMG), N,Ndimetyloglicyny (DMG) i N,N,Ntrimetyloglicyny (TMG) przy wykorzystaniu spektroskopii FTIR, z zastosowaniem cząsteczki HDO jako sondy molekularnej. Ilościowa wersja metody widm różnicowych pozwoliła na wyizolowanie widma wody zaburzonej przez substancję rozpuszczoną. Wyniki widmowe zostały skonfrontowane z obliczeniami teoretycznymi w ramach teorii...
Year 2010

The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamineNoxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...

The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamineNoxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
Year 2009

Electron scattering by trimethylene oxide, c(CH2)3O, molecules
PublicationZmierzono całkowity przekrój czynny na rozproszenie elektronów na drobinach c(CH2)3O w zakresie energii 1  400 eV. Wyniki porównano z elastycznymi i jonizacyjnymi przekrojami czynnymi obliczonymi dla tej drobiny. Przedyskutowano energetyczną zależność całkowitego przekroju czynnego na rozproszenie dla rodziny eterów cyklicznych (CH2)nO, n=24.

Production of singlet oxygen atoms by photodissociation of oxywater
PublicationQuantum chemical calculations are reported for the energies of the few lowest electronic singlet states of oxywater along dissociation of the oxygenoxygen bond into water and singlet oxygen using multistate multireference secondorder Møller–Plesset perturbation theory. We compute an energy of 21 kcal/mol to remove one oxygen atom in the lowest singlet state. The two lowest excited singlet states have vertical excitation energies...
Year 2008

Entropy of water calculated from harmonic approximation: estimation of the accuracy of method
PublicationSome molecular dynamics simulations were performed for liquid TIP4P and SPC water at a constant density (1.00 g/cm(3)) and within the temperature range of 590 degrees C. By using harmonic approximation, both the entropy of water SH and the specific heat c(v) were calculated, and the results were compared to literature data. It was found that harmonic approximation overestimates absolute entropy of TIP4P water by 5.6 J/mol K (similar...

Exciton quenching in emitter blends for organic light emitting devices probed by electric fielddependent timeresolved luminescence
PublicationW pracy badano mechanizm wygaszania ekscytonów w układzie dwuamina TPD:organiczny kompleks Eu:matryca TPD przez pomiar zaniku fotoluminescencji w zewnętrznym polu elektrycznym.

Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the unitedresidue model of a polypeptide chain
Publication
Year 2007

Ttotal dissociative electron attachment cross sections of selected amin acids
PublicationZaprezentowano całkowite przekroje czynne na dysocjacyjny wychwyt elektronów przez aminokwasy: glicynę, alaninę, prolinę, tryptofan oraz fenyloalaninę. Wartości przekrojów czynnych wyznaczono z pomiarów wydajności w produkcji jonów dodatnich oraz normalizację do całkowitych przekrojów czynnych na jonizację, obliczonych metodą BEB.
Year 2006

Dissociative electron attachment of furan, tetrahydrofuran, and fructose
PublicationPrzeprowadzono badania wychwytu dysocjacyjnego elektronów w cząsteczkach furanu, tetrahydrofuranu i fruktozy w przedziale energii 014eV. Stwierdzono, że w przypadku wychwytu elektronów o energiach poniżej progu wzbudzenia (< 3eV), jedynie fruktoza jest podatna na rozerwanie pierścienia cukrowego. W cząsteczkach furanu i tetrahydrofuranu struktury rezonansowe odpowiadające fragmentom pierścienia pojawiają się dla energii elektronów...
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