Filters
total: 661
filtered: 615
Search results for: physical chemistry
-
Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
-
Electrochemical Stability of Few-Layered Phosphorene Flakes on Boron-Doped Diamond: A Wide Potential Range of Studies in Aqueous Solutions
PublicationTwo-dimensional phosphorene has attracted great interest since its discovery as a result of its extraordinary properties. Two-dimensional single crystals of phosphorene can be useful for electrochemical (EC) sensing applications due to their enhanced surface-to-volume ratio. We proposed to investigate the electrochemical performance of phosphorene deposited directly on boron-doped diamond (BDD) electrodes. Noncovalent interaction...
-
Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
-
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...
-
Enhanced Charge Storage Mechanism And Long-Term Cycling Stability In Diamondized Titania Nanocomposite Supercapacitors Operating In Aqueous Electrolytes
PublicationThe long cycle life stability jointly with high energy density are limiting broader feasible applications of supercapacitors. The novel diamondized titania nanocomposite supercapacitors deliver high power and energy densities along with high capacitance retention rates. Supercapacitor electrodes were fabricated utilizing a combination of Ti anodization followed by chemical vapor deposition resulting in simultaneous growth of complex...
-
Systematic Water Uptake Energetics of Yttrium-Doped Barium Zirconate—A High Resolution Thermochemical Study
PublicationA combination of surface area analyzer and microcalorimetry was employed to investigate the in situ water uptake energetics and the mechanism of proton incorporation in yttrium-doped barium zirconate in the temperature range 200–400 °C. The BaZr1–xYxO3 solid solutions are made with variable yttrium content (x = 10, 20, and 30 mol %) by a controlled oxidant-peroxo synthesis method. The water uptake increases as the partial pressure...
-
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...
-
Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques...
-
On the relationship between the structural and volumetric properties of solvated metal ions in O-donor solvents using new structural data in amide solvents
PublicationThe structures of the N,N-dimethylformamide (dmf), N,N-dimethylacetamide (dma), and N,N-dimethylpropionamide (dmp) solvated strontium and barium ions have been determined in solution using large angle X-ray scattering and EXAFS spectroscopy. The strontium ion has a mean coordination number (CN) between 6.2 and 6.8, and the barium ion has a mean CN between 7.1 and 7.8 in these amide solvents. The non-integer numbers indicates that...
-
Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
-
Ternary Bismuthide SrPtBi2: Computation and Experiment in Synergism to Explore Solid-State Materials
PublicationA combination of theoretical calculation and the experimental synthesis to explore the new ternary compound is demonstrated in the Sr–Pt–Bi system. Because Pt–Bi is considered as a new critical charge-transfer pair for superconductivity, it inspired us to investigate the Sr–Pt–Bi system. With a thorough calculation of all the known stable/metastable compounds in the Sr–Pt–Bi system and crystal structure predictions, the thermodynamic...
-
Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation
PublicationW niniejszej pracy przedstawiono wyniki badań dotyczące hydratacji białka modelowego - lizozymu z jaja kurzego w roztworze wodnym. Wiodącą techniką stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Analiza widma HDO przy pomocy "metody widm zaburzonych" pozwoliła na wyizolowanie widma wody zaburzonej przez lizozym, a tym samym...
-
The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
-
Why the solvation water around proteins is more dense than bulk water
PublicationThe main aim of this work is to propose a rational explanation of commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that geometry of the water-water hydrogen bond network within solvation layer differs from the one in bulk water and it is the effect of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the structure...
-
Hydration of Simple Carboxylic Acids from Infrared Spectra of HDOand Theoretical Calculations
PublicationBadanie hydratacji kwasów karboksylowych w rozcieńczonych roztworach wodnych ma duże znaczenie dla zrozumienia ich funkcji biologicznych. Metodą stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Do analizy danych widmowych wykorzystano ''metodę widm różnicowych''. Widma HDO zaburzonej przez kwasy: mrówkowy, octowy i propionowy...
-
Ionic liquids: predictions of physicochemical properties with experimental and/or DFT-calculated LFER parameters to understand molecular interactions in solution
PublicationPublikacja zawiera modele pozwalające na przewidywanie współczynnika podziału oktanol-woda (log P), rozpuszczalności w wodzie oraz krytycznego stężenia micelizacji (CMC) cieczy jonowych oraz współczynników aktywności anionowej i hydrofobowości w wodzie i w mieszaninie oktanolu z wodą. Modele oparte są na liniowych zależnościach energii swobodnej (LFER) i wykorzystują parametry zmierzone i/lub wyliczone na podstawie funkcjonalnej...
-
Self-assemblies of novel magnesium porphyrins mimicking natural chlorosomal bacteriochlorophylls
PublicationSelf-assembling porphyrins are promising materials to mimic natural bacteriochlorophylls c, d, or e encountered in the chlorosomes of photosynthetic bacteria. We have studied four novel magnesium porphyrins mimicking this chlorosomal antenna system. In contrast to previous articles reporting synthetic Zn-porphyrins, our studies focus on porphyrins with Mg as the central atom, which mimic more closely the natural bacteriochlorophylls....
-
Long-Distance FRET Analysis: A Monte Carlo Simulation Study
PublicationZaproponowano nową metodę na rozszerzenie zakresu stosowalności rezonansowego transferu energii (FRET) przetestowaną przy pomocy metody Monte Carlo. Otrzymane rezultaty dowodzą, że wydajność procesu FRET może być znacząco zwiększona w porównaniu z wydajnością pojedynczego akceptora, gdy dla ustalonej od donora umieścimy układ blisko siebie położonych akceptorów na makromolekule. Z drugiej strony metoda ta umożliwia zwiększenie...
-
An effective method for studying intermolecular interactions in binary liquids with hydrogen bonds: FTIR spectra and ab initio calculations in the N-methylformamide - methanol system
PublicationMolecular complexes in methanol (MeOH)−N-methylformamide (NMF) mixtures were studied based on their FTIR-ATR spectra, to which two methods of analysis were applied: factor analysis and a quantitative version of the difference-spectra method. The mean composition of a complex between NMF and MeOH molecules over the whole range of mixture compositions was determined. Absorbing species differentiated with regard to the interaction...
-
Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing
Publication -
Molecular Origin of Anticooperativity in Hydrophobic Association
Publication -
Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models
Publication -
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
Publication -
Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit
Publication -
Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models
Publication -
Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes
Publication -
Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water
Publication -
Comment on “Molecular Origin of Anticooperativity in Hydrophobic Association”
Publication -
Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
Publication -
Global Optimization-Based Method for Deriving Intermolecular Potential Parameters for Crystals
Publication -
Reply to “Comment on ‘Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions'” by B. P. van Eijck and J. Kroon
Publication -
Chemical Vapor Transport Route toward Black Phosphorus Nanobelts and Nanoribbons
PublicationChemical vapor transport (CVT) method is widely used for bulk black phosphorus (BP) fabrication. In this work, we demonstrate that CVT provides a route for the fabrication of BP nanoribbons and nanobelts. This method consists of a two-step procedure, including initial BP column growth using the CVT technique, followed by ultrasonic treatment and centrifugation. The obtained nanostructures preserve BP column dimensions, forming...
-
Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size
Publication -
Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems
Publication -
Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins
Publication -
Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
Publication -
Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains
Publication -
Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains
Publication -
Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
Publication -
Radiative lifetime of a BODIPY dye as calculated by TDDFT and EOM-CCSD methods: solvent and vibronic effects
Publication -
Programmed metalloporphyrins for self-assembly within light-harvesting stacks: 5,15-dicyano-10,20-bis(3,5-di-tert-butylphenyl)-porphyrinato zinc(II) and its push-pull 15-N,N-dialkylamino-5-cyano congeners obtained by a facile direct amination.
PublicationThe title dicyano compound was synthesized via cyanation and it self-assembles in nonpolar solvents giving red-shifted and broad absorption maxima just as the bacteriochlorophylls which are encountered in the light-harvesting organelles of early photosynthetic bacteria. In the crystal, stacks are formed through a hierarchic combination of π-stacking and a CNZn electrostatic interaction. Push−pull 15-N,N-dialkylamino-5-cyano congeners...
-
Application of the tetraphenylphosphonium tetraphenylborate (TPTB) assumption to the thermodynamic properties of solvated ions in dimethylsulfoxide
PublicationW niniejszej pracy za pomocą spektroskopii ATR FTIR sprawdzano możliwość zastosowania tetrafenyloboranu tetrafenylofosfoniowego w metodzie elektrolitu wzorcowego, służącej do podziału wielkości termodynamicznych elektrolitów w dimetylosulfotlenku na udziały jonowe. Jednoznacznie stwierdzono, że poza termodynamiczne założenie o identycznych oddziaływaniach jonów w elektrolicie wzorcowym z cząsteczkami DMSO jest nieprawdziwe. Uzyskane...
-
Photosensitization of TiO2 and SnO2 by Artificial Self-Assembling Mimics of the Natural Chlorosomal Bacteriochlorophylls
PublicationOf all known photosynthetic organisms, the green sulfur bacteria are able to survive under the lowest illumination conditions due to highly efficient photon management and exciton transport enabled by their special organelles, the chlorosomes, which consist mainly of self-assembled bacteriochlorophyll c, d, or e molecules. A challenging task is to mimic the principle of self-assembling chromophores in artificial light-harvesting...
-
Concentration-Dependent Fluorescence Properties of Rhodamine 6G in Titanium Dioxide and Silicon Dioxide Nanolayers
PublicationWytworzono cienkie warstwy zawierające rodaminę 6G w dwutlenku tytanu (R6G/TiO2) i w dwutlenku krzemu (R6G/SiO2) stosując metodę zol-żel. Badane były dwa rodzaje matryc, w których domieszkowano barwnik rodamina 6G (R6G) o różnych koncentracjach. Został stwierdzony istotny wpływ koncentracji barwnika na widma absorpcji i emisji oraz na czasowo rozdzielone widma fluorescencji. W szczególności stwierdzono znacznie mniejszą zdolność...
-
Local Ordering Changes in Pt-Co Nanocatalyst Induced by Fuel Cell Working Conditions
PublicationPraca poświęcona jest szczegółowej analizie zmian w lokalnej strukturze atomowej i elektronowej nanocząstek Pt-Co pracujących jako katalizatory w polimerowych ogniwach paliwowych wywołanych cyklicznie zmieniającymi się warunkami pracy ogniwa. Do analizy wykorzystano badania XAS realizowane ex-situ i in-situ, XRD i TEM. Analizując widma XAFS wzięto pod uwagę możliwy wpływ nieporządku chemicznego oraz redukcję liczb koordynacyjnych...
-
Limonene: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, electron scattering, He(I) photoelectron spectroscopy and ab initio calculations
PublicationZbadano limonen metodami spektroskopii absorpcyjnej, elektronowej, fotojonizacyjnej. Wyniki porównano z obliczeniami ab initio. Otrzymano strukturę wibracyjną molekuły.
-
A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublicationThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
-
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...
-
Structural Control of Photoinduced Dynamics in 4H-Imidazole- Ruthenium Dyes
PublicationThe photoinduced dynamics of a series ofterpyridine 4H-imidazole-ruthenium complexes, which constitutea new family of panchromatic dyes, is investigated. Thedynamics involves two excited states localized within the 4Himidazolesphere. Upon MLCT excitation, an excited state ispopulated, which is localized on the central part of the 4Himidazoleligand caused by its nonplanar conformation. Thepopulation of the second excited state is...
-
On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...