Filters
total: 244
filtered: 231
Search results for: molecular interactions
-
Removal of diphenols using pine biochar. Kinetics, equilibrium, thermodynamics, and mechanism of uptake
PublicationThermal pyrolysis synthesized activated biochar from the Pinus elliottii sawdust (PS) at 600° C. The obtained activated biochar (PB600) was used for the removal of three diphenols, catechol (CAT), resorcinol (RES), and hydroquinone (HYD), which are utilized mainly in different industries. The PB600 was characterized by several analytical techniques. The BET surface area of 1473 m2.g−1 and a total pore volume of 0.707 cm3 g−1 was...
-
A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
Publication -
Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
-
Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid
PublicationOne of the possible applications of ionic liquids is to produce electricity from heat. The iron oxide nanoparticle is a potent electrical particle, which is expected to improve the heat’s efficiency to electricity conversion, however, it is prone to aggregation and sedimentation, which hamper its application. One of the methods to enhance the nanoparticle’s solubility and electrical properties is the use of a stabilizing component...
-
Interactions in Ternary Aqueous Solutions of NMA and Osmolytes—PARAFAC Decomposition of FTIR Spectra Series
PublicationIntermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel...
-
Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations
PublicationCalculations are reported for electron and positron scattering from isolated cytosine and thymine, where the two pyrimidinic single-ring DNA bases, in the gas-phase at energies near the elastic threshold, they reveal the special features of the dipole-driven scattering states. All molecules examined exhibit, in fact, supercritical (>1.67 D) permanent dipoles which can therefore also support, below threshold, excited bound compound...
-
Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
-
Synthesis of green benzamide-decorated UiO-66-NH2 for biomedical applications
PublicationMetal-organic frameworks (MOFs) biocompatible systems can host enzymes/bacteria/viruses. Herein we synthesized a series of fatty acid amide hydrolase (FAAH)-decorated UiO-66-NH2 based on Citrus tangerine leaf extract for drug delivery and biosensor applications. Five chemically manipulated FAAH-like benzamides were localized on the UiO-66-NH2 surface with physical interactions. Comprehensive cellular and molecular analyses were...
-
Structure-property relationships disclosed in the family of acridinium esters – chemiluminogenic molecules of great practical importance
PublicationAcridinium esters (AE), since their introduction to the analytics 30 years ago, make one of the most important groups of chemiluminogenic (CL) systems, that have been employed in medical diagnostics and environmental analysis today. So far, however, no systematic studies on the structureproperty relationships were carried out in this family of compounds. The latter features likely determine their practical utility and facilitate...
-
Torsional elasticity and energetics of F1-ATPase
PublicationFoF1-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded Fo generates the rotary torque that drives the rotation of the asymmetric shaft of F1. Mechanical energy of the rotating shaft is used by the F1 catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant...
-
Superconducting SrSnP with Strong Sn–P Antibonding Interaction: Is the Sn Atom Single or Mixed Valent?
PublicationThe large single crystals of SrSnP were prepared using Sn self-flux method. The superconductivity in the tetragonal SrSnP is observed with the critical temperature of ∼2.3 K. The results of a crystallographic analysis, superconducting characterization, and theoretical assessment of tetragonal SrSnP are presented. The SrSnP crystallizes in the CaGaN structure type with space group P4/nmm (S.G. 129, Pearson symbol tP6) according...
-
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...
-
(4-(Bis(4-Fluorophenyl)Methyl)Piperazin-1-yl)(Cyclohexyl)Methanone Hydrochloride (LDK1229): A New Cannabinoid CB1 Receptor Inverse Agonist from the Class of Benzhydryl Piperazine Analogs
PublicationSome inverse agonists of cannabinoid receptor type 1 (CB1) have been demonstrated to be anorectic antiobesity drug candidates. However, the first generation of CB1 inverse agonists, represented by rimonabant (SR141716A), otenabant, and taranabant, are centrally active, with a high level of psychiatric side effects. Hence, the discovery of CB1 inverse agonists with a chemical scaffold distinct from these holds promise for developing...
-
Assessing the Interactions of Statins with Human Adenylate Kinase Isoenzyme 1: Fluorescence and Enzyme Kinetic Studies
Publication -
Interactions of fish gelatin and chitosan in uncrosslinked and crosslinked with EDC films: FT-IR study
PublicationFilms based on fish gelatin, chitosan and blend of fish gelatin and chitosan before and after cross-linking with EDC have been characterized by FT-IR spectroscopy. The FT-IR spectrum of fish gelatin film showed the characteristic amide I, amide II and amide III bands, and the FT-IR spectrum of chitosan film confirmed that the polymer was only a partially deacetylated product, and included CH3-C=O and NH2 groups, the latter both...
-
Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens
Publication -
Antibiotic-sterol interactions provide insight into the selectivity of natural aromatic analogues of amphotericin B and their photoisomers
PublicationAromatic heptaene macrolides (AHMs) belong to the group of polyene macrolide antifungal antibiotics. Members of this group were the first to be used in the treatment of systemic fungal infections. Amphotericin B (AmB), a non-aromatic representative of heptaene macrolides, is of significant clinical importance in the treatment of internal mycoses. It includes the all-trans heptaene chromophore, whereas the native AHMs contain two...
-
Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
-
Nanofiltration-Assisted Concentration Processes of Phenolic Fractions and Carotenoids from Natural Food Matrices
PublicationIn new food formulations, carotenoids and phenolic compounds are likely to be the most sought after food ingredients according to their bioactivity, nutraceutical, nutritional value, and compatibility properties once incorporated into food formulations. Such solutes are naturally present in many plant-based sources, and some portions are directly consumed when enriching food products and formulations; however, some portions, which...
-
Copper(I) iodide ribbons coordinated with thiourea derivatives
PublicationTwo products of the reactions of CuI with 1-benzoyl-3-(4-bromophenyl)thiourea and with 1-benzoyl-3-(2-iodophenyl)thiourea have been obtained and characterized, namely poly[[[1-benzoyl-3-(4-bromophenyl)thiourea-κS]-µ3-iodidocopper(I)] acetone hemisolvate], {[CuI(C₁₄H₁₁BrN₂OS)]‧0.5C₃H₆O}ₙ, and poly-[µ₄-iodido-µ₃-iodido-[N-(benzo[d]thiazol-2-yl)benzamide-κN]dicopper(I)], [Cu₂I₂(C₁₄H₁₀N₂OS)]ₙ. Their structures, determined by single-crystal...
-
Synthesis and biological evaluation of fluorinated N-benzoyl and N-phenylacetoyl derivatives of 3-(4-aminophenyl)-coumarin-7-O-sulfamate as steroid sulfatase inhibitors
PublicationIn the present work, we report convenient methods for the synthesis of 3-(4-aminophenyl)-coumarin-7-O-sulfamate derivatives N-acylated with fluorinated analogues of benzoic or phenylacetic acid as steroid sulfatase (STS) inhibitors. The design of these potential STS inhibitors was supported by molecular modeling techniques. Additionally, computational docking methods were used to determine the binding modes of the synthesized inhibitors...
-
Engineering boron and nitrogen codoped carbon nanoarchitectures to tailor molecularly imprinted polymers for PFOS determination
PublicationPer- and polyfluoroalkyl substances (PFAS) have gained significant attention as emerging contaminants due to their persistence, abundance, and adverse health effects. Consequently, the urgent need for ubiquitous and effective sensors capable of detecting and quantifying PFAS in complex environmental samples has become a priority. In this study, we present the development of an ultrasensitive molecularly imprinted polymer (MIP)...
-
The interactions of monomeric acridines and unsymmetrical bisacridines (UAs) with DNA duplexes: an insight provided by NMR and MD studies
PublicationMembers of a novel class of anticancer compounds, exhibiting high antitumor activity, i.e. the unsymmetrical bisacridines (UAs), consist of two heteroaromatic ring systems. One of the ring systems is an imidazoacridinone moiety, with the skeleton identical to the structural base of Symadex. The second one is a 1-nitroacridine moiety, hence it may be regarded as Nitracrine’s structural basis. These monoacridine units are connected...
-
Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
-
Thermodynamics and Intermolecular Interactions of Nicotinamide in Neat and Binary Solutions: Experimental Measurements and COSMO-RS Concentration Dependent Reactions Investigations
PublicationIn this study, the temperature-dependent solubility of nicotinamide (niacin) was measured in six neat solvents and five aqueous-organic binary mixtures (methanol, 1,4-dioxane, acetonitrile, DMSO and DMF). It was discovered that the selected set of organic solvents offer all sorts of solvent effects, including co-solvent, synergistic, and anti-solvent features, enabling flexible tuning of niacin solubility. In addition, differential...
-
Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
-
Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
-
Structural, spectral and magnetic properties of Ni(II), Co(II) and Cd(II) compounds with imidazole derivatives and silanethiolate ligands
PublicationA series of new metal heteroleptic complexes have been obtained in simple reactions of 1-(3-aminopropyl)-imidazole (api) and 1,4-bis(imidazol-1-yl)-butane (bbi) ligands with metal silanethiolates or acetylacetonates. The obtained complexes are the coordination polymers [Ni{SSi(tBuO)3}2(μ-api)]n1, [Co{SSi(tBuO)3}2(μ-api)]n2, [Cd{SSi(tBuO)3}2(μ-api)·2CH3OH]n3, [Cd{SSi(tBuO)3}2(μ-bbi)·CHCl3]n4 and the dimer [Co{SSi(tBuO)3}2(μ-bbi)·3CH3OH]25....
-
Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
-
Novel Cell Permeable Polymers of N-Substituted L-2,3-Diaminopropionic Acid (DAPEGs) and Cellular Consequences of Their Interactions with Nucleic Acids
Publication -
Interactions between hydration spheres of two different solutes in solution: The least squares fitting with constraints as a tool to determine water properties in ternary systems
PublicationBiological systems are complex and the problem of their description lies in mutual interactions between their components. This paper is focused on model experiment-based studies which can reduce these difficulties. The ternary aqueous N-methylacetamide (NMA)–Na2HPO4 system has been studied by means of the FTIR spectroscopy. A novel difference spectra method aimed to extract the spectral contribution of water affected simultaneously...
-
Nonlocal Models of Plates and Shells with Applications in Micro- and Nanomechanics
PublicationNowadays, the use of small-scale structures in micro/nanomachines has become more and more widespread. The most important applications of such small-sized parts are in micro-electro-mechanical systems (MEMS) as well as nano-electro-mechanical systems (NEMS) as actuators, sensors, energy harvesters. For example, nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and...
-
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...
-
Molecularly targeted nanoparticles: an emerging tool for evaluation of expression of the receptor for advanced glycation end products in a murine model of peripheral artery disease
PublicationAbstract Background: Molecular imaging with molecularly targeted probes is a powerful tool for studying the spatio-temporal interactions between complex biological processes. The pivotal role of the receptor for advanced glycation end products (RAGE) in numerous pathological processes, aroused the demand for RAGE targeted imaging in various diseases. In the study, we evaluated the use of a diagnostic imaging agent for RAGE quantification...
-
Polarisation effects in low-energy positron–molecule scattering
PublicationThe UK molecular R-matrix method has been adapted to treat positron collisions from polyatomic targets. A simple empirical enhancement factor which corrects for the underestimation of electron–positron polarisation and correlation effects in the calculations performed with the static-plus-polarization model at low scattering energies is presented. Application of this model to positron scattering from carbon dioxide at energies...
-
Electrochemical simulation of enzymatic transformations studied for the selected antitumor acridine derivatives
PublicationThe elucidation of the metabolic pathways and the biotransformation mechanisms of potential drugs is a crucial point in drug development. It allows to know the activation routes of the new biologically active compounds, especially in respect to their possible toxicity. Generally, in vivo or in vitro experiments with liver microsomes or hepatocytes are performed. However, these testing schemes are tedious, time consuming and of...
-
Protective effect of Aronia melanocarpa polyphenols against cadmium-induced disorders in bone metabolism: A study in a rat model of lifetime human exposure to this heavy metal
Publication -
Cellular uptake of biotransformed graphene oxide into lung cells
Publication -
Elucidating of oxidative distress in COVID-19 and methods of its prevention
Publication -
Butyrylcholinesterase signal sequence self-aggregates and enhances amyloid fibril formation in vitro
PublicationAlzheimer’s disease (AD) pathogenesis has been attributed to extracellular aggregates of amyloid β (Aβ) plaques and neurofibrillary tangles in the human brain. It has been reported that butyrylcholinesterase (BChE) also accumulates in the brain Aβ plaques in AD. We have previously found that the BChE substitution in 5′UTR caused an in-frame N-terminal extension of 41 amino acids of the BChE signal peptide. The resultant variant...
-
Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
-
Syntheses, spectroscopic and structural properties of phenoxysilyl compounds: X-ray structures, FT-IR and DFT calculations
PublicationThe reaction of silicon disulfide with alkylphenols leads to tetraphenoxysilane, cyclodisilthiane and silanethiol. The products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---π (X = C, S) whereas the intermolecular interactions are either very weak CH---π/CH---O contacts found in aryloxysilane...
-
Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublicationInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
-
Weak hydrogen bonding interaction S-H···O=C studied by FT-IR spectroscopy and DFT calculations
PublicationInteractions between the thiolate group of tri-tert-butoxysilanethiol (TBST) and carbonyl group of acetone are studied with the use of FT-IR spectroscopy and DFT calculations.
-
Cooperation of mono- and bi-articular muscles: human lower limb
PublicationObjectives: The aim of this study was to create and analyze a Pareto-optimal problem that would describe cooperation between mono- and bi-articulate lower limb muscles in sagittal plane. Methods: Equations describing the problem were derived and analyzed, additional constrains were introduced and experimental verification based on gait video analysis was performed. Results: Uncertainty of Pareto-optimal solution is shown for the...
-
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...
-
Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublicationA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
-
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...
-
Jahn-Teller and related conical intersections in the benzene radical cation and the monofluoro derivate
PublicationThe multi-state multi-mode vibronic interactions in the benzene radical cation and its monofluoro derivative have been investigated theoretically, based on high-level electronic structure calculations for the system parameters and a quantum treatment of the nuclear motion. The available experimental data are well reproduced. The interplay of different vibronic coupling mechanisms is pointed out leading to multiple nonadiabatic...
-
Simplified AutoDock force field for hydrated binding sites
Publicationhas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...