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Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors—molecular dynamics study of the activated receptor–vasopressin–Gα systems
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Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity
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"Car-Parrinello molecular dynamics" jako kluczowe narzędzie informatyczne w badaniach syntezy cienkich warstw diamentowych metodą PA CVD
PublicationPraca omawia zastosowanie metody Car-Parrinello MD w symulacji procesu wzrostu cienkich warstw diamentowych w metodzie PAC VD.
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Human Umbilical Vein Endothelial Cells (HUVECs) Co-Culture with Osteogenic Cells: From Molecular Communication to Engineering Prevascularised Bone Grafts
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Erratum to “Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles” [Biophys. Chem. 105 (2003) 339–359]
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Synergic Effect of Selected Ingredients and Calcium Chloride on the Technological, Molecular and Microbial Usefulness of Eggshells and Their Impact on Sensory Properties in a Food Model System
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A BODIPY‐Based Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐Resolved Emission and Transient Absorption Spectroscopy
PublicationBODIPY and BODIPY-derived systems are widely applied as fluorophores and as probes for viscosity detection in solvents and biological media. Their orientational and rotational dynamics in biological media are thus of vital mechanistic importance and extensively investigated. In this contribution, polarization-resolved confocal microscopy is used to determine the orientation of an amphiphilic BODIPY-cholesterol derivative in homogeneous...
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublicationIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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The effect of sunscreen 4‐methylbenzylidene camphor in different and reproductive models, its bioaccumulation and molecular effects on ligand‐receptor interaction, and protein expression
Publication4-Methylbenzylidene camphor (4-MBC) is a photo-absorbing UV filter prevalently used in cosmetics, which can be absorbed into circulation and cause systemic effects. 4-MBC is continued to be released in the environment despite the growing knowledge about its bioaccumulation and endocrine disrupting effects. Previous reviews have mentioned UV-filter together but this review considers 4-MBC alone, due to its prevalence and concerning...
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Enantiomeric Resolution of N,N'-Dimethyldithiodianthranilide through Diastereomeric silver(I) complex. Chiroptical spectra, racemization barrier and molecular self-assembly
PublicationN,N'-dimetyloditiodiantranilid, związek o chiralności płaszczyznowej, rozdzielono na enancjomery. Optycznie czynne molekuły uzyskano w wyniku tworzenia chiralnego kompleksu N,N'-dimetyloditiodiantranilidu z solą srebrową kwasu (1S)-kamforosulfonowego. W oparciu o badania rentgenostrukturalne monokryształu uzyskanego kompleksu określono absolutną konfigurację przykoordynowanego ligandu jako (R). Enancjomery N,N'-dimetyloditiodiantranilid...
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Water vapor induced self-assembly of islands/honeycomb structure by secondary phase separation in polystyrene solution with bimodal molecular weight distribution
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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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Katarzyna Merkel dr hab.
PeopleOver the past 15 years, my work has mainly been related to the study of liquid crystal compounds with a diverse structure (discotic, dendrimeric, banana, bimedogenic, uniaxial and biaxial nematics and smectics) as well as polymeric materials (biopolymers, nano-composites) and biological materials. My work concerned mainly the issues of organization, observation of orientation effects, studying the dynamics of molecular processes...
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Jan Franz dr hab.
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BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
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COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY
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BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
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BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY
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IEEE Transactions on Molecular, Biological, and Multi-Scale Communications
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JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS
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AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY
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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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Molecular biology GT
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Detection of molecular signatures of oral squamous cell carcinoma and normal epithelium - application of a novel methodology for unsupervised segmentation of imaging mass spectrometry data
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High efficiency protocol of DNA extraction from Micromys minutus mandibles from owl pellets: a tool for molecular research of cryptic mammal species
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Molecular Structures of the Phospha-Wittig Reaction Intermediate: Initial Step in the Synthesis of Compounds with a C═P–P Bond as Products in the Phospha-Wittig Reaction
PublicationThe phospha-Wittig reactivity ofβ-diketiminate titanium(III) complexes with phosphanylphosphido ligands was investigated. The reactions of [MeNacNacTi(Cl){η2-P(SiMe3)-PtBu2}] and [MeNacNacTi(Cl){η2-P(SiMe3)-P(Ph)tBu}] with acetone conducted in toluene solution under mild conditions led to the phospha-Wittig intermediates [{(ArN=C(Me)CHC(Me)=NAr)(C(Me)2O}Ti(Cl){PtBu2-P(SiMe3)C(Me)2O}] (1) and [{(ArN=C(Me)CHC(Me)=NAr) (C-(Me)2O}Ti(Cl){P(Ph)tBu-P(SiMe3)C(Me)2O}]...
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The Ellenbogen’s “Matter as Software” Concept for Quantum Computer Implementation: IV. The X@C60 Molecular Building Blocks (MBBs) and Computing System Lifetime Estimation
PublicationThe problem of approximate lifetimes of individual X@C60 MBBs and tip-based nanofabricated quantum computing device systems is discussed under the conservative assumption of single-point failure. A single chemical transformation of the C60 cage into high-energy opened o-C60 isomer which forms the communication canal for the low energy transfer of an X atom from X@C60 MBB to the outside environment was studied. According to the...
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A. Computational analysis by molecular docking of thirty alkaloid compounds from medicinal plants as potent inhibitors of SARS-CoV-2 main protease(2020).
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Non-Typical Fluorescence Effects and Biological Activity in Selected 1,3,4-thiadiazole Derivatives: Spectroscopic and Theoretical Studies on Substituent, Molecular Aggregation, and pH Effects
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Reversed-Phase TLC and HPLC Retention Data in Correlation Studies with in Silico Molecular Descriptors and Druglikeness Properties of Newly Synthesized Anticonvulsant Succinimide Derivatives
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Prediction of Overall In Vitro Microsomal Stability of Drug Candidates Based on Molecular Modeling and Support Vector Machines. Case Study of Novel Arylpiperazines Derivatives
PublicationOther than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach its therapeutic site of action. Despite many recent excellent achievements in the field of computational methods supporting drug metabolism studies, a well-recognized procedure to model...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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In search of molecular precursors for cadmium sulfide-new complexes with a sulfur-rich kernel: cadmium(II) tri-tert-butoxysilanethiolates with additional diethyldithiocarbamato ligand
PublicationW ramach rozprawy opracowano metodę syntezy związków koordynacyjnych kadmu zawierających mieszane ligandy S-donorowe, które stanowią reszta tri-tert-butoksysilanotiolanowa oraz ditiokarbaminianowa. Zostały one poddane badaniom za pomocą analizy składu pierwiastkowego, metod spektroskopowych (FTIR, FIR, UV-Vis, NMR, MS) oraz termicznych. W celu osadzenia cienkich warstw wybranych związków posłużono się techniką nakładania obrotowego...
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Molecular mechanism of retention in reversed-phase high-performance liquid chromatography and classification of modern stationary phases by using quantitative structure–retention relationships
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Novel 2-alkythio-4-chloro-N-[imino(heteroaryl)methyl]benzenesulfonamide Derivatives: Synthesis, Molecular Structure, Anticancer Activity and Metabolic Stability
PublicationA series of novel 2-alkythio-4-chloro-N-[imino-(heteroaryl)methyl]benzenesulfonamide derivatives, 8–24, were synthesized in the reaction of the N-(benzenesulfonyl)cyanamide potassium salts 1–7 with the appropriate mercaptoheterocycles. All the synthesized compounds were evaluated for their anticancer activity in HeLa, HCT-116 and MCF-7 cell lines. The most promising compounds, 11–13, molecular hybrids containing benzenesulfonamide...
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Molecular basis of essentiality of early critical steps in the lipopolysaccharide biogenesis in Escherichia coli K-12: requirement of MsbA, cardiolipin, LpxL, LpxM and GcvB
PublicationTo identify the physiological factors that limit the growth of Escherichia coli K-12 strains synthesizing minimal lipopolysaccharide (LPS), we describe the first construction of strains devoid of the entire waa locus and concomitantly lacking all three acyltransferases (LpxL/LpxM/LpxP), synthesizing minimal lipid IVA derivatives with a restricted ability to grow at around 21 °C. Suppressors restoring growth up to 37 °C of Δ(gmhD-waaA)...
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Non-volatile molecular composition and discrimination of single grape white of chardonnay, riesling, sauvignon blanc and silvaner using untargeted GC–MS analysis
PublicationThis study developed and applied a GC–MS method aiming at molecular fingerprinting of 120 commercial single grape white wines (Chardonnay, Riesling, Sauvignon Blanc and Silvaner) for possible authentication according to grape variety. The method allowed detection of 372 peaks and tentative identification of 146 metabolites including alcohols, organic acids, esters, amino acids and sugars. The grape variety effect explained 8.3%...
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Deciphering the Molecular Mechanism of Substrate-Induced Assembly of Gold Nanocube Arrays toward an Accelerated Electrocatalytic Effect Employing Heterogeneous Diffusion Field Confinement
PublicationThe complex electrocatalytic performance of gold nanocubes (AuNCs) is the focus of this work. The faceted shapes of AuNCs and the individual assembly processes at the electrode surfaces define the heterogeneous conditions for the purpose of electrocatalytic processes. Topographic and electron imaging demonstrated slightly rounded AuNC (average of 38 nm) assemblies with sizes of ≤1 μm, where the dominating patterns are (111) and...
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Exploring thiophene-2-acetate and thiophene-3-acetate binding modes towards the molecular and supramolecular structures and photoluminescence properties of Pb(ii) polymers
PublicationTo evaluate the impact of the flexible positional isomeric ligands thiophene-2-acetate (2tpacCOO) andthiophene-3-acetate (3tpacCOO) on the construction and self-assembly process of Pb(II) polymers, twonovel compounds, [Pb(2tpacCOO)2(H2O)]n(1) and [Pb(3tpacCOO)2]n(2), were preparedviaanonhydro-thermal method with respect to green chemistry rules. The obtained polymers were fully characterized byelemental analysis, TG/DTG and PXRD,...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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The influence of the type of halogen substituent and its position on the molecular conformation, intermolecular interactions and crystal packing for a series of 1-benzoyl-3-(halogenophenyl)thioureas
PublicationBy the reaction of benzoyl chloride, potassium isothiocyanate and the appropriate halogenoaniline, i.e. 2/3/4-(bromo/iodo)aniline, we have obtained five new 1-benzoyl-3-(halogenophenyl)thioureas, namely, 1-benzoyl-3-(2-bromophenyl)- thiourea and 1-benzoyl-3-(3-bromophenyl)thiourea, C14H11BrN2OS, and 1-benzoyl-3-(2-iodophenyl)thiourea, 1-benzoyl-3-(3-iodophenyl)thiourea and 1-benzoyl-3-(4-iodophenyl)thiourea, C14H11IN2OS. Structural...
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Convenient Syntheses of N-Methylthioamides: A Migration of the H2S Molecule in the Thioamide-nitrile System
PublicationThe reaction of thioamides with the R1R2N-ZnCl ammoniates leads to N-mono-, N,N'-di-, N,N-disubstituted, and unsubstituted amidines with high concns. of amines in abs. ethanol. The efficient direct formation of the N,N'-dimethylamidine can be explained by a greater reactivity of methylamine compared with dimethylamine. Discovery of a new zwitterion (induced by a carbonyl oxygen) suggests that the stabilization in the thymine...
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A dressing of zero-range potentials and electron-molecule scattering problem at low energies
PublicationTechnika ''ubierania'' jest używana do poprawy modelu potencjału zerowego promienia (ZRP). Rozważamy przekształcenia Darboux zaczynające się od ZRP, wynik ''ubierania'' daje potencjał z niezerowym promieniem, który zależy od parametrów rozwiązania.
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Fast dynamics in the optical storage with Langmuira-Blodgett films of a diazocrown ether molecule
PublicationMolekuły z resztą azobenzenu badano z punktu widzenia licznych aplikacji wykorzystujących cykle fotoizomeryzacji trans-cis-trans, wiodących do uporządkowania cząsteczek, a nawet do transportu masy w mikroskali. Ważnym ograniczeniem dla tych materiałów jest powolna dynamika procesu porządkowania, wymagającego molekularnych przekształceń. W tej pracy informujemy o filmach Langmuira-Blodgett (LB) pochodnej eteru azokoronowego (29-membered...
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Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule
PublicationThe ground state geometries and vibrational frequencies as well as the excitation energies and excited state gradients of the S 1(nπ*) and S 2(ππ * ) states of trans - and cis -azobenzene are investigated by several DFT methods, namely B3LYP, PBE, M06-2X, CAM-B3LYP, and ω B97X. Excited state properties and in particular gradients are also assessed using the wave function based methods EOM-CCSD and RASPT2/RASSCF. Comparison with...
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Optimization of the femtosecond laser impulse for excitation and the spin-orbit-mediated dissociation in the NaRb molecule
Open Research DataHigh accuracy ab initio potential energy curves (1tSigma+, 2sSigma+, 1tPi), electronic transition dipole moment function (1tSigma+ - 1tPi), and spin-orbit coupling (2sSigma+ - 1tPi) have been calculated for the NaRb molecule. The time-dependent excitation and dissociation processes in the polar alkali diatomic NaRb molecule and the quantum properties...
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The hydration of selected biologically relevant molecules – the temperature effect on apparent molar volume and compression
PublicationThe densities and sound velocities at T = (288.15, 293.15, 298.15, 303.15 and 308.15) K were measured for aqueous solutions of glycine, trimethylamine-N-oxide, taurine and N-methylacetamide. From these data, the apparent molar volumes, V the apparent molar isentropic compressions, KS,, and the Passynski hydration numbers of solutes were determined. The concentration dependencies of the calculated quantities, their limiting values...
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Computational modeling of molecularly imprinted polymers as a green approach to the development of novel analytical sorbents
PublicationThe development of novel molecularly imprinted polymers (MIP) sorbents for specific chemical compounds require a lot of tedious and time-consuming laboratory work. Significant quantities of solvents and reagents are consumed in the course of the verification of appropriate configurations of polymerization reagents. Implementation of molecular modeling in the MIP sorbent development process appears to provide a solution to this...
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Electron scattering from 2-methyl–1,3-butadiene,C5H8, molecules: Role of methylation
PublicationWe report cross-section results from experimental and theoretical investigations into electron collisions with the 2-methyl–1,3-butadiene [C5H8] molecule. The current results are compared with our previous results for the 1,3-butadiene [C4H6] molecule, a structural homologue of 2-methyl–1,3-butadiene, to investigate how the methylation (the substitution of hydrogen atom by a methyl group) affects the shape and/or magnitude of the...
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PELP1 and SRC kinase as important molecules in the estrogen-mediated pathway in human testis and epididymis
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