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Search results for: 2D molecular descriptors
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
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Screening of potential inhibitors for COVID-19 main protease from phytoconstituents of Tectona grandis Linn: application of molecular modeling studies
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KRAS mutation testing in borderline ovarian tumors and low-grade ovarian carcinomas with a rapid, fully integrated molecular diagnostic system
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The extended version of restriction analysis approach for the examination of the ability of low-molecular-weight compounds to modify DNA in a cell-free system
PublicationOne of the primary requirements in toxicology is the assessment of ability of chemicals to induce DNA covalent modification. There are several well-established methods used for this purpose such as 32P-Postlabeling or HPLC-MS. However, all of these approaches have difficult to overcome limitations, which prevents their use in genotoxin screening. Here, we describe the simple protocol exploiting specificity of restriction enzymes...
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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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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...
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublicationCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
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Molecular geometry and optical activity of helically chiral N-nitrosamines derived from 1,2,3,4-tetrahydro- and 1,2,3,4,7,8,9,10-octahydro-1,10-phenanthroline
PublicationX-ray crystallographic analysis of the title N-nitrosamines revealed that they assume helical conformations in the solid state. Nitrosamines 1b and 2b were resolved by inclusion crystallization with optically active diols (TADDOLs). The absolute configuration of the guest molecules in the complexes 1b·3b and 2b·3b was assigned as M. The optical activity of the resolved compounds is manifested by their solid state CD spectra, which...
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Optical investigation of molecular structure of sophisticated materials forphotonics. Photonics Applications in Astronomy, Communications, Industry and High Energy Physics Experiments.
PublicationZastosowano komplementarne metody optyczne: spektroskopię ramanowską oraz spektroskopię w podczerwieni do badania reakcji zachodzących w czasie wytwarzania polimerów hybrydowych metodą zol-żel. Otrzymane rezultaty umożliwiły uszczegółowienie opisu reakcji hydrolizy monomerów w trakcie żelowania.
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The chaperone-usher pathway of bacterial adhesin biogenesis - from molecular mechanism to strategies of anti-bacterial prevention and modern vaccine design
PublicationSystem chaperone-usher (białko opiekuńcze-białko kanałotwórcze) warunkuje biogenezę powierzchniowych struktur adhezyjnych, odpowiedzialnych za wirulencję wielu bakterii gram-ujemnych. Powyższy mechanizm został zbadany na poziomie strukturalnym w przypadku różnych gatunków bakterii patogennych. Celem powyższej pracy było przedstawienie molekularnego mechanizmu biogenezy struktur adhezyjnych na bazie systemu chaperone-usher. Otrzymane...
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Intermolecular Interactions as a Measure of Dapsone Solubility in Neat Solvents and Binary Solvent Mixtures
PublicationDapsone is an effective antibacterial drug used to treat a variety of conditions. However, the aqueous solubility of this drug is limited, as is its permeability. This study expands the available solubility data pool for dapsone by measuring its solubility in several pure organic solvents: N-methyl-2-pyrrolidone (CAS: 872-50-4), dimethyl sulfoxide (CAS: 67-68-5), 4-formylmorpholine (CAS: 4394-85-8), tetraethylene pentamine (CAS:...
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CD99 correlates with low cyclin D1, high topoisomerase 2 status and triple negative molecular phenotype but is prognostically irrelevant in breast carcinoma
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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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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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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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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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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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Biotransformation of Modified Benzylisoquinoline Alkaloids: Boldine and Berberine and In Silico Molecular Docking Studies of Metabolites on Telomerase and Human Protein Tyrosine Phosphatase 1B
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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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"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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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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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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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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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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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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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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Cobalt(II) tri-tert-butoxysialanethiolates.Synthesis, properties, crystal and molecular structures of [Co{SSi(OtBu)3}2(L)] and[Co{SSi(OtBu)3}2(L)2] type complexes with monodentate nitrogen ligands.
PublicationThe title heteroleptic neutral cobalt(II) tri-tert-butoxysilanethiolate complexes with monodentate nitrogen bases (L) as additional ligands have been prepared by the reactions of [Co{μ-SSi(OtBu)3}{SSi(OtBu)3}(NH3)]2 (1) with respective bases. For pyridine both types have been prepared...
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Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents
PublicationSolubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and...
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Pendant Proton-Relays Systematically Tune the Rate and Selectivity of Electrocatalytic Ammonia Generation in a Fe-Porphyrin Based Metal-Organic Framework
PublicationElectrocatalytic nitrite reduction (eNO2RR) is a promising alternative route to produce ammonia (NH3). Until now, several molecular catalysts have shown capability to homogeneously reduce nitrite to NH3, while taking advantage of added secondary-sphere functionalities to direct catalytic performance. Yet, realizing such control over heterogeneous electrocatalytic surfaces remains a challenge. Herein, we demonstrate that heterogenization...
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Design, synthesis, and molecular docking of new 5-HT reuptake inhibitors based on modified 1,2-dihydrocyclopenta[b] indol-3(4H)-one scaffold
PublicationA new group of serotonin reuptake inhibitors containing 1,2-dihydrocyclopenta[b]indol-3(4H)-one scaffoldwas synthesized, starting from indole 5-((1H-indol-3-yl)(1,3-dioxane-4,6-diones as a key intermediates. Following three transformations including intramolecular cyclization and formation of imines, a series of new ligand for human serotonin transporter was obtained. The ability of these ligands to inhibit human TS3 serotonin transporter...
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Front Cover: Chiral Molecular Cages Based on Cyclotriveratrylene and Sucrose Units Connected with p ‐Phenylene Linkers (Eur. J. Org. Chem. 6/2021)
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Antitumor potential of new low molecular weight antioxidative preparations from the white rot fungus Cerrena unicolor against human colon cancer cells
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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
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Molecular modeling study of tectoquinone and acteoside from Tectona grandis linn: a new SARS-CoV-2 main protease inhibitor against COVID-19
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Anthrapyridones, a novel group of antitumour non-cross resistant anthraqui-none analogues. Synthesis and molecular basis of the cytotoxic activity towards K562/DOX cells
PublicationOpracowano syntezę nowej grupy związków z grupy antrapirydonów z odpowiednimi hydrofobowymi lub hydrofilowymi podstawnikami. Badano działanie tych związków na komórkach K562/S i K562/DOX (nadekspresja P-glikoproteiny). Stwierdzono, że zwiększenie lipofilowości zwiększa szybkość P-gp zależnego efluksu z komórki.
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An influence of molecular weight, deacetylation degree of chitosan xerogels on their antimicrobial activity and cytotoxicity. Comparison of chitosan materials obtained using lactic acid and CO2 saturation.
PublicationThis paper presents a comparison of the antimicrobial activity and cytotoxicity against L929 cells of chitosan xerogels prepared by dissolving the polymer in a solution of lactic acid (LA) or carbonic acid (CO2) and then freeze-drying. There was no simple relationship between the antimicrobial activity and cytotoxicity of the samples obtained using both techniques (LA and CO2). Chitosan materials obtained by the LA method in a...
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Versatile method employing basic techniques of genetic engineering to study the ability of low molecular weight compounds to bind covalently with DNA in cell free systems.
PublicationMechanizm działania większości leków przeciwnowotworowych oraz związków rakotwórczych polega na ich kowalencyjnym wiązaniu z DNA. Poziom tego wiązania jest zazwyczaj bardzo niski, co powoduje, że potrzebne są niezwykle czułe metody aby kowalencyjna modyfikacja mogła być w ogóle wykryta. My podjęliśmy próbę zastosowania w tym celu prostych, szybkich i sprawdzonych technik inżynierii genetycznej: metody PCR do uzyskania fragmentu...
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Cobalt(II) and Cobalt(III) Tri‐tert‐butoxysilanethiolates. Synthesis, Properties, Crystal and Molecular Structures of [Co{μ‐SSi(OBut)3}{SSi(OBut)3}(NH3)]2 and [Co{SSi(OBut)3}2(NH3)4][SSi(OBut)3] Complexes
PublicationThe heteroleptic neutral tri‐tert‐butoxysilanethiolate of cobalt(II) incorporating ammonia as additional ligand (1) has been prepared by the reaction of a cobalt(II) ammine complex with tri‐tert‐butoxysilanethiol in water. Complex 1, dissolved in hexane, undergoes oxidation in an ammonia saturated atmosphere to the ionic cobalt(III) compound 2. Molecular and...
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Optimizing of MALDI-ToF-based low-molecular-weight serum proteome pattern analysis in detection of breast cancer patients; the effect of albumin removal on classification performance.
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Molecular cloning and initial characterization of African green monkey (Cercopithecus aethiops) corticotropin releasing factor receptor type 1 (CRF1) from COS-7 cells
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Exploiting the S4–S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis
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Molecular Docking-Based Study of Vasopressin Analogues Modified at Positions 2 and 3 with N-Methylphenylalanine: Influence on Receptor-Bound Conformations and Interactions with Vasopressin and Oxytocin Receptors
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Preferential solvation in (amide+alcohol) binary mixtures. Part 2. The N-methylpyrrolidinone+methanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez metanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Preferential solvation in (amide+alcohol) binary mixtures. Part 1. The N- methylpyrrolidinone+ethanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez etanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Ranking Speech Features for Their Usage in Singing Emotion Classification
PublicationThis paper aims to retrieve speech descriptors that may be useful for the classification of emotions in singing. For this purpose, Mel Frequency Cepstral Coefficients (MFCC) and selected Low-Level MPEG 7 descriptors were calculated based on the RAVDESS dataset. The database contains recordings of emotional speech and singing of professional actors presenting six different emotions. Employing the algorithm of Feature Selection based...
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Effect of in vitro gastro‐pancreatic digestion on antioxidant activity of low‐molecular‐weight (<3.5 kDa) peptides from dry‐cured pork loins with probiotic strains of LAB
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Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: Molecular dynamics simulation of the agonist-bound state in the membrane–aqueous system
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