Search results for: MOLECULAR DATA
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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 dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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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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Encapsulation of Amikacin into Microparticles Based on Low-Molecular-Weight Poly(lactic acid) and Poly(lactic acid-co-polyethylene glycol)
PublicationThe aim of this study was to fabricate novel microparticles (MPs) for efficient and long-term delivery of amikacin (AMI). The emulsification method proposed for encapsulating AMI employed low-molecular-weight poly(lactic acid) (PLA) and poly(lactic acid-co-polyethylene glycol) (PLA−PEG), both supplemented with poly(vinyl alcohol) (PVA). The diameters of the particles obtained were determined as less than 30 μm. Based on an in-vitro...
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Novel 1,2,3-Triazole Derivatives as Mimics of Steroidal System—Synthesis, Crystal Structures Determination, Hirshfeld Surfaces Analysis and Molecular Docking
PublicationHerein, we present the synthesis and crystal structures determination of five 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives containing halogen atoms, 6a–e, which may be used as an excellent mimic of steroids in the drug development process. Good quality crystals obtained for all of the synthesized compounds allowed the analysis of their molecular structures. Subsequently, the determined crystal structures were used to calculate...
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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublicationThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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Elastic scattering of electrons by water: An ab initio study
PublicationIn this work we devise a theoretical and computational method to compute the elastic scattering of electrons from a non-spherical potential, such as in the case of molecules and molecular aggregates. Its main feature is represented by the ability of calculating accurate wave functions for continuum states of polycentric systems via the solution of the Lippmann-Schwinger equation, including both the correlation effects and multi-scattering...
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Experimental and Machine-Learning-Assisted Design of Pharmaceutically Acceptable Deep Eutectic Solvents for the Solubility Improvement of Non-Selective COX Inhibitors Ibuprofen and Ketoprofen
PublicationDeep eutectic solvents (DESs) are commonly used in pharmaceutical applications as excellent solubilizers of active substances. This study investigated the tuning of ibuprofen and ketoprofen solubility utilizing DESs containing choline chloride or betaine as hydrogen bond acceptors and various polyols (ethylene glycol, diethylene glycol, triethylene glycol, glycerol, 1,2-propanediol, 1,3-butanediol) as hydrogen bond donors. Experimental...
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Experimental and Machine-Learning-Assisted Design of Pharmaceutically Acceptable Deep Eutectic Solvents for the Solubility Improvement of Non-Selective COX Inhibitors Ibuprofen and Ketoprofen
PublicationDeep eutectic solvents (DESs) are commonly used in pharmaceutical applications as excellent solubilizers of active substances. This study investigated the tuning of ibuprofen and ketoprofen solubility utilizing DESs containing choline chloride or betaine as hydrogen bond acceptors and various polyols (ethylene glycol, diethylene glycol, triethylene glycol, glycerol, 1,2-propanediol, 1,3-butanediol) as hydrogen bond donors. Experimental...
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Amphotericin B and Its New Derivatives - Mode of Action
PublicationAmphotericin B (AmB) is a well known antifungal and antiprotozoal antibiotic used in the clinic for several decades. Clinicalapplications of AmB, however, are limited by its nephrotoxicity and many other acute side effects which are not acceptable by patientswhen their life is not threaten. In order to improve the therapeutic index of this drug, lipid formulations have been introduced and manyefforts have been made to obtain less...
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Experimental and theoretical solubility advantage screening of bi-component solid curcumin formulations
PublicationA comprehensive experimental and theoretical screening was performed for identification of curcumin solubilizers. Experimental data led to formulation of a non-linear QSPR model correlating molecular descriptors with measured solubilities. The majority of synthesized binary systems exhibited a moderate enhancement of curcumin solubility, which was found to be the highest in the case of curcumin cocrystallized with pyrogallol. New...
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Low-energy positron scattering from gas-phase benzene
PublicationIn this paper we are presenting calculations of the elastic cross section of positrons with gas-phase benzene for the energy range from 0.25 eV to 9.0 eV. The calculations are done with the molecular R-matrix method for positron-scattering from poly-atomic molecules using a scaling factor to scale the electron-positron interaction. The scaling factor influences the position of the poles of the R-matrix. We adjust the scaling factor...
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Optimizing Construction Engineering Management Using Metaheuristic Methods and Bayesian Networks
PublicationThe construction of buildings invariably involves time and costs, and disruptions impact ongoing construction projects. Crisis situations in management strategies, structural confusion, and finan-cial miscalculations often arise due to misguided decision-making. This article proposes a method that combines the learning of Bayesian Networks and heuristic techniques to optimize deci-sion-making processes in construction scheduling....
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Polyacrylamide substrate viscosity impact on temozolomide activity in glioblastoma cells by flow cytometry and rheological measurements
Open Research DataDataset includes raw data on cell lines LN-229 and LN-18 treated with temozolomide measured by flow cytometry, rheometry and cell projections. It also includes calculations necessary for creation of figures and conclusions based on those figures in the publication titiled: "Substrate viscosity impairs temozolomide-mediated inhibition of glioblastoma...
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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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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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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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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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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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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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"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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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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Synthesis, Molecular Structure, Anticancer Activity, and QSAR Study of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)Benzenesulfonamide Derivatives
PublicationA series of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)benzenesulfonamides were synthesized from 4-amino-N-(aryl/heteroaryl)benzenesulfonamides and 2,5-dimethoxytetrahydrofuran. All the synthesized compounds were evaluated for their anticancer activity on HeLa, HCT-116, and MCF-7 human tumor cell lines. Compound 28, bearing 8-quinolinyl moiety, exhibited the most potent anticancer activity against the HCT-116, MCF-7, and HeLa cell lines,...
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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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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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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Thermophysical study of the binary mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide – Experimental and theoretical approach
PublicationDensities at (293.15, 298.15, 303.15 and 308.15) K, and viscosities and ultrasonic velocities at 298.15 K of binary liquid mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide have been measured over the entire range of composition at p = 0.1 MPa. From the experimental data, values of excess molar volume, excess isentropic compressibility, viscosity deviation and excess Gibbs energy...
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Optoelectronic system for monitoring of thin diamond layers growth
PublicationDevelopment of the optoelectronic system for monitoring of diamond/DLC (Diamond-Like-Carbon) thin films growth during mu PA ECR CVD (Microwave Plasma Assisted Electron Cyclotron Resonance Chemical Vapour Deposition) process is described. The multi-point Optical Emission Spectroscopy (OES) and Raman spectroscopy were employed as non-invasive optoelectronic tools. Dissociation of H-2 molecules, excitation and ionization of hydrogen...
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Environmental exposure to cadmium in breast cancer – association with the Warburg effect and sensitivity to tamoxifen
PublicationThe association between cadmium and breast cancer remains unexplained due to inconsistent epidemiological data and unknown underlying mechanisms. This study aimed to assess the relationship between environmental exposure to cadmium and the Warburg effect in breast cancer and, thus, its possible interference with breast cancer treatment. The observational study in two groups of breast cancer patients indicated a positive correlation between...
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Ellipsometric investigation of nitrogen doped diamond thin films grown in microwave CH4/H2/N2 plasma enhanced chemical vapor deposition
PublicationThe influence of N2 concentration (1%–8%) in CH4/H2/N2 plasma on structure and optical properties of nitrogen doped diamond (NDD) films was investigated. Thickness, roughness, and optical properties of the NDD films in the VIS–NIR range were investigated on the silicon substrates using spectroscopic ellipsometry. The samples exhibited relatively high refractive index (2.6 6 0.25 at 550 nm) and extinction coefficient (0.05 6 0.02...
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Unveiling the electron-induced ionization cross sections and fragmentation mechanisms of 3,4-dihydro-2H-pyran
PublicationThe interactions of electrons with molecular systems under various conditions are essential to interdisciplinary research fields extending over the fundamental and applied sciences. In particular, investigating electron-induced ionization and dissociation of molecules may shed light on the radiation damage to living cells, the physicochemical processes in interstellar environments, and reaction mechanisms occurring in combustion...
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A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism
PublicationThis work reports detailed characteristics of the antimicrobial peptide Intestinalin (P30), which is derived from the LysC enzyme of Clostridium intestinale strain URNW. The peptide shows a broader antibacterial spectrum than the parental enzyme, showing potent antimicrobial activity against clinical strains of Gram-positive staphylococci and Gram-negative pathogens and causing between 3.04 ± 0.12 log kill for Pseudomonas aeruginosa...
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PLS-Based and Regularization-Based Methods for the Selection of Relevant Variables in Non-targeted Metabolomics 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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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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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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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 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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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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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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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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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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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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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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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...