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Search results for: QUANTUM-CHEMICAL CALCULATIONS
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Evaluation of Chemotherapeutic Activity of the Selected Bases’ Analogues of Nucleic Acids Supported by ab initio Various Quantum Chemical Calculations
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Quantum-classical calculations of the nanomechanical properties of metals
PublicationTradycyjnie symulacje komputerowe układów w skali atomowej prowadzone są przy użyciu klasycznej metody dynamiki molekularnej (MD) bądź kwantowych metod ab initio. Główną wadą ujęcia klasycznego jest jego empiryczna natura, a co za tym idzie - niewielka przenośność, jego prostota natomiast pozwala na przeprowadzanie symulacji układów zawierających miliony atomów. W wyniku zastosowania metod kwantowych otrzymuje się bardziej wiarygodne...
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Quantum chemical modeling of electrochromism of tungsten oxide films
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Polymerization of chloro-p-xylylenes, quantum-chemical study
PublicationThe p-xylylene monomers of parylene N, C and D have similar high polymerization reactivity. For effective copolymerization processes this fact is basically a draw- back and for instance the copolymerization with styrene doesn't go at all (Corley et al. J Pol Sc 13(68):137156, 1954). Substitution of terminal hydrogen atoms by chlorine atoms reduces reactivity dramatically. 7,7,8,8-tetrachloro-p- xylylene and 2,5,7,7,8,8-hexachloro-p-xylylene...
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Chemical Theory of Machines, basic principles of strength with examples of calculations
PublicationThis book encompasses the essential range of information on technical aspects of mechanical design. It was written primarily for the students and staff of chemistry faculties of technical universities, yet it may also be utilized by everyone, who ether would like to try or already enjoys designing, but cannot take advantage of typical stress & machine construction handbooks. These handbooks often require familiarity with the concepts...
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Quantum chemical modelling of the process of lithium insertion into WO3 films
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Spectroscopic and quantum chemical study of phthalocyanines with 1,4,7-trioxanonyl moieties
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TG-FTIR, DSC and quantum chemical studies of the thermal decomposition of quaternary methylammonium halides
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Application of QSAR Analysis and Different Quantum Chemical Calculation Methods in Activity Evaluation of Selected Fluoroquinolones
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Experimental and Quantum Chemical Evaluation of 8-Hydroxyquinoline as a Corrosion Inhibitor for Copper in 0.1 M HCl
PublicationThe corrosion inhibition properties of 8-hydroxyquinoline (8-HQ) in 0.1 M HCl for copper have been investigated by using experimental (electrochemical impedance spectroscopy (EIS), dynamic electrochemical impedance spectroscopy (DEIS), and potentiodynamic polarization) and theoretical methods complemented by surface morphological examination with the aid of scanning electron microscopy (SEM) and electron dispersive X-ray spectroscopy...
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Quantum chemical modeling (DFT) of active species on the VWO catalyst surface in various redox conditions
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The role of tungsten in formation of active sites for no SCR on the V-W-O catalyst surface — quantum chemical modeling (DFT)
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Experimental and quantum chemical evidences for C–H⋯N hydrogen bonds involving quaternary pyridinium salts and pyridinium ylides
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Toward mechanosynthesis of diamondoid sructures: viii. quantum-chemical molecular dynamics simulations of hexagonal silicon-iv structure synthesis with stm
Publicationw tej publikacji badano metodami kwantowo-chemicznymi różne strategie mechanosyntezy heksagonalnego krzemu iv. określono przybliżone warunki mechanosyntezy krzemu w formie lonsdaleitu za pomocą uhv-spm.
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Toward Mechanosynthesis of Diamondoid Structures: VI. Quantum-Chemical Molecular Dynamics Comparison of Conditions for the STM Tip Driven Mechanosynthesis on Hydrogenated Si(111), Si(110) and Si(100) Surfaces.
Publicationmożliwość prototypowania przejściowych generacji nano-urządzeń otrzymanych drogą pozycjonowanej mechanosyntezy za pomocą stm wyposażonego w ostrze typu swcnt są analizowane metodą kwantowo-chemicznej dynamiki molekularnej. proponowana strategia syntezy polega na insercji atomów si oraz cząsteczek sih2 we wiązania si-h na uwodornionej powierzchni si(111), si(110) oraz si(100) kryształu krzemu. rezultaty modelowania sugerują, że...
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Toward Mechanosynthesis of diamondoid structures: III. Quantum-chemical study of silylene molecule and silicon atom transfer mechanism from caped SWCNT tip to the reaction center on a hydrogenated Si(111) surface
PublicationOpublikowana wcześniej (Modelling Simul. Mater. Sci. Eng., Vol. 7, 1999, pp. 43-58) strategia mechanosyntezy struktur krzemu na uwodornionej płaszczyźnie Si(111) została poszerzona poprzez uwzględnienie ostrza w postaci zamkniętej SWCNT jako urządzenia kontrolującego położenie cząsteczki sililenu oraz atomu krzemu.
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Low-energy positron scattering from gas-phase tetrahydrofuran: A quantum treatment of the dynamics and a comparison with experiments
PublicationIn this paper we report new quantum calculations of the dynamics for low-energy 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....
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Rotational state-changing 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 state-changing 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 photo-detachment experiments...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublicationThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublicationWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
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Electrochemical, theoretical and surface physicochemical studies of the alkaline copper corrosion inhibition by newly synthesized molecular complexes of benzenediamine and tetraamine with π acceptor
PublicationTwo charge transfer complexes, namely [(BDAH)+(PA−)] CT1 [(BTAH)2+(PA−)2] and CT2 (BDAH = 1,2-benzenediamine, BTAH = 1,2,4,5-benzenetetramine, and PA− = 2,4,6-trinitrophenolate), were synthesized and fully characterized using various spectroscopic techniques. CT1 and CT2 were tested as inhibitors to effectively control the uniform and anodic corrosion processes of copper in an alkaline electrolyte (1.0 M KOH) using various electrochemical...
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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 non-zero 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...
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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 oxygen-oxygen bond into water and singlet oxygen using multistate multireference second-order 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...
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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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Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
PublicationPartition coefficients define how a solute is distributed between two immiscible phases at equilibrium. The experimental estimation of partition coefficients in a complex system can be an expensive, difficult, and time-consuming process. Here a computational strategy to predict the distributions of a set of solutes in two relevant phase equilibria is presented. The octanol/water and octanol/air partition coefficients are predicted...
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The ONETEP linear-scaling density functional theory program
PublicationWe present an overview of the ONETEP program for linear-scaling 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 Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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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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A general approach to study molecular fragmentation and energy redistribution after an ionizing event
PublicationWe propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron–photoion coincidence experiments and...
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Impact of dyes isomerization effect on the charge transfer phenomenon occurring on the dye/nanosemiconductor interface
PublicationThe present work aimed to find the answer how does the isomerization of the Ru based dyes affect the overall photon-to-current efficiency of the DSSCs and to explain the charge transfer phenomenon occurring on the dye/ nanosemiconductor interface. Therefore, electronic and optical properties of three bipyridine derivatives anchored on the TiO2 electrode were investigated by computational simulations based on quantum chemistry codes...
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Unraveling the role of boron dimers in the electrical anisotropy and superconductivity in boron-doped diamond
PublicationWe use quantum mechanics (QM) to determine the states formed by B dopants in diamond. We find that isolated B sites prefer to form BB dimers and that the dimers pair up to form tetramers (BBCBB) that prefer to aggregate parallel to the (111) surface in the <110> direction, one double layer below the H-terminated surface double layer. These tetramers lead to metallic character (Mott metal Insulator Transition) with holes in the...
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Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment
Publication2-Amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) and ethylenediaminetetraacetic acid (EDTA) are key components of biological buffers and are frequently used as DNA stabilizers in irradiation studies. Such surface or liquid phase studies are done with the aim to understand the fundamental mechanisms of DNA radiation damage and to improve cancer radiotherapy. When ionizing radiation is used, abundant secondary electrons are formed...
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Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
PublicationAb initio quantum chemistry calculations are performed for the mixed alkali triatomic system. Global minima of the ground and first excited doublet states of the trimer are found and Born-Oppenheimer potential energy surfaces of the Li atom interacting with the LiCs molecule were calculated for these states. The lithium atom is placed at various distances and bond angles from the lithium-caesium dimer. Three-body nonadditive forces...
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The importance of anchoring ligands of binuclear sensitizers on electron transfer processes and photovoltaic action in dye-sensitized solar cells
PublicationThe relatively low photon-to-current conversion efficiency of dye-sensitized solar cells is their major drawback limiting widespread application. Light harvesting, followed by a series of electron transfer processes, is the critical step in photocurrent generation. An in-depth understanding and fine optimization of those processes are crucial to enhance cell performance. In this work, we synthesize two new bi-ruthenium sensitizers...
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TINKTEP: A fully self-consistent, 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. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Electron-Induced Decomposition of Uracil-5-yl O-(N,N-dimethylsulfamate): Role of Methylation in Molecular Stability
PublicationThe incorporation of modified uracil derivatives into DNA leads to the formation of radical species that induce DNA damage. Molecules of this class have been suggested as radiosensitizers and are still under investigation. In this study, we present the results of dissociative electron attachment to uracil-5-yl O-(N,N-dimethylsulfamate) in the gas phase. We observed the formation of 10 fragment anions in the studied range of electron...
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Electron-Induced Decomposition of 5-Bromo-4-thiouracil and 5-Bromo-4-thio-2′-deoxyuridine: The Effect of the Deoxyribose Moiety on Dissociative Electron Attachment
PublicationWhen modified uridine derivatives are incorporated into DNA, radical species may form that cause DNA damage. This category of molecules has been proposed as radiosensitizers and is currently being researched. Here, we study electron attachment to 5-bromo-4-thiouracil (BrSU), a uracil derivative, and 5-bromo-4-thio-20 -deoxyuridine (BrSdU), with an attached deoxyribose moiety via the N-glycosidic (N1-C) bond. Quadrupole mass spectrometry...
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Visible light photocatalytic activity of ionic liquid-TiO2 spheres: effect of the ionic liquid's anion structure
PublicationThe effect of the ionic liquid’s (IL) anion type ([BIMIM][X], where X= [Br], [PF6] or [OctSO4]) and content on the morphology, surface properties and photoactivity of TiO2 obtained by solvothermal method has been systematically investigated. Our results revealed that the presence of [Br], [OctSO4] anions favors formation of anatase phase, while presence of [PF6] anion causes formation of mixture of anatase and Ti(OH)PO4 phases....
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Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions
PublicationWe present a method for the calculation of four-centre two-electron repulsion integrals in terms of localised non-orthogonal generalised Wannier functions (NGWFs). Our method has been imple- mented in the ONETEP program and is used to compute the Hartree-Fock exchange energy component of Hartree-Fock and Density Functional Theory (DFT) calculations with hybrid exchange-correlation functionals. As the NGWFs are optimised in situ...
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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Spontaneous electron emission vs dissociation in internally hot silver dimer anions
PublicationReferring to a recent experiment, we theoretically study the process of a two-channel 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 pseudo-potentials and atomic basis sets. We also estimated the non-adiabatic...
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Experimental and theoretical studies on the Sulfamethazine-Urea and Sulfamethizole-Urea solid-liquid equilibria
PublicationThe miscibility of active pharmaceutical ingredients with excipients is an important aspect in pharmaceutical technology protocols. In this study, the differential scanning calorimetry (DSC) was used for Sulfamethazine-Urea (SI–U) and Sulfamethizole-Urea (SO–U) solid-liquid phase diagrams determination. Both sulfonamides form simple binary eutectics with Urea. The lack of new co-crystal phase formation was confirmed by inspection...
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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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Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach
PublicationThe knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular,...
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Noncentrosymmetric Triangular Magnet CaMnTeO6: Strong Quantum Fluctuations and Role of s0 versus s2 Electronic States in Competing Exchange Interactions
PublicationNoncentrosymmetric triangular magnets offer a unique platform for realizing strong quantum fluctuations. However, designing these quantum materials remains an open challenge attributable to a knowledge gap in the tunability of competing exchange interactions at the atomic level. Here, a new noncentrosymmetric triangular S = 3/2 magnet CaMnTeO6 is created based on careful chemical and physical considerations. The model material...
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Redox State Sensitive Spectroscopy of the Model Compound [(H-dcbpy)(2)Ru-II(NCS)(2)](2-) (dcbpy=2,2 '-Bipyridine-4,4 '-dicarboxylato)
PublicationThe charge transfer reaction mechanism in a ruthenium polypyridine model complex with isothiocyanato ligands, i.e., [(H-dcbpy)(2)Ru(NCS)(2)](2-) 2Bu(4)N(+) (Ru2H) (dcbpy = 2,2'-bipyridine-4,4'-dicarboxylato), has been investigated by combining UV-vis absorption, resonance Raman spectroscopy, and electrochemical methods. Understanding the photophysics of light-harvesting complexes of this class is an indispensable prerequisite to...
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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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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/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 linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Quantum Coherence as a Resource
PublicationThe coherent superposition of states, in combination with the quantization of observables, represents one of the most fundamental features that mark the departure of quantum mechanics from the classical realm. Quantum coherence in many-body systems embodies the essence of entanglement and is an essential ingredient for a plethora of physical phenomena in quantum optics, quantum information, solid state physics, and nanoscale thermodynamics....
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Quantum entanglement
PublicationAll our former experience with application of quantum theory seems to say that what is predicted by quantum formalism must occur in the laboratory. But the essence of quantum formalism-entanglement, recognized by Einstein, Podolsky, Rosen, and Schrödinger-waited over 70 years to enter laboratories as a new resource as real as energy. This holistic property of compound quantum systems, which involves nonclassical correlations between...