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Wyniki wyszukiwania dla: molecular umbrellas
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling
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The anion [Mg6Cl8Cp*5]-: a final intermediate on the way to the molecular donor-free Grignard compound MgClCp*?
PublikacjaOtrzymano i scharakteryzowano strukturalnie rzadki przypadek związku Grignarda pozbawionego donora. Struktura krystaliczna [Mg6Cl8Cp*5][AlCp*2] C6H6 zawiera zarówno metallocen (Cp*AlCp*) jak i odwrócony metallocen (MgCp*Mg).
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Bacterial SSB-like proteins of family Deinococcaceae - indentification, isolation, obtaining, purification and molecular characteristic
PublikacjaWiększość poznanych białek SSB jest aktywna w formie homotetramerycznej. Od 2002 roku znane są białka organizmów ekstremofilnych. Scharakteryzowano białka mikroorganizmów rodziny Deinococaceae. Uzyskane termostabilne białka stanowią atrakcyjną alternatywę w stosunku do znanych białek SSB w metodach diagnostyki molekularnej, technikach biologii molekularnej i analityce.
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublikacjaDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Selected symmetrically substituted carbazoles: Investigation of anticancer activity and mechanisms of action at the cellular and molecular levels
PublikacjaDNA topoisomerases play a critical role as essential enzymes in controlling alterations in the topology of DNA. They achieve this by orchestrating the coordinated process of breaking and rejoining DNA strands, which is crucial for maintaining the proper structure of DNA during regular cellular development. The search for and development of new potential anticancer drugs is a challenging yet immensely important area of research...
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A DSC and NMR-Relaxation study of the molecular mobility of water protons interacting with chemically modified starches
PublikacjaChanges in the mobility of water protons in the chemically modified starches (CMS)–water system are studied by differential scanning calorimetry and NMR relaxation. The amounts of unfrozen water at negative temperatures and additional (after gelation) unfrozen for CMS are lower than those for native starch. The proton spin–spin relaxation time T2 for CMS samples, conventionally attributed to the water fraction in starch granules,...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublikacjaHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublikacjaThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublikacjaSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublikacjaExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Solubility of dapsone in deep eutectic solvents: Experimental analysis, molecular insights and machine learning predictions
PublikacjaBackground. Dapsone (DAP) is an anti-inflammatory and antimicrobial active pharmaceutical ingredient used to treat, e.g., AIDS-related diseases. However, low solubility is a feature hampering its efficient use. Objectives. First, deep eutectic solvents...
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Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublikacjaIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublikacjaA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublikacjaThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Mangiferin Affects Melanin Synthesis by an Influence on Tyrosinase: Inhibition, Mechanism of Action and Molecular Docking Studies
PublikacjaMangiferin is a strong antioxidant that presents a wide range of biological activities. The aim of this study was to evaluate, for the first time, the influence of mangiferin on tyrosinase, an enzyme responsible for melanin synthesis and the unwanted browning process of food. The research included both the kinetics and molecular interactions between tyrosinase and mangiferin. The research proved that mangiferin inhibits tyrosinase...
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Molecular basis for the DNA damage induction and anticancer activity of asymmetrically substituted anthrapyridazone PDZ-7
Publikacjanthrapyridazones, imino analogues of anthraquinone, constitute a family of compounds with remarkable anti-cancer activity. To date, over 20 derivatives were studied, of which most displayed nanomolar cytotoxicity towards broad spectrum of cancer cells, including breast, prostate and leukemic ones. BS-154, the most potent derivative, had IC50 values close to 1 nM, however, it was toxic in animal studies. Here, we characterize another...
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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublikacjaMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublikacjaShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Selective adsorption of BTEX on calixarene-based molecular coordination network determined by 13C NMR spectroscopy
PublikacjaBenzene, toluene, ethylbenzene, and xylenes (BTEX), a class of volatile organic compounds, are harmful pollutants but also very important precursors in organic industrial chemistry. Among different approaches used for the BTEX treatment, the adsorption technology has been recognized as an efficient approach because it allows to recover and reuse both adsorbent and adsorbate. However, the selective adsorption of the components is...
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Excited state properties of a series of molecular photocatalysts investigated by time dependent density functional theory.
PublikacjaTime dependent density functional theory calculations are applied on a series of molecular photocatalysts of the type [(tbbpy)2M1(tpphz)M2X2]2+ (M1 = Ru, Os; M2 = Pd, Pt; X = Cl, I) in order to provide information concerning the photochemistry occurring upon excitation of the compounds in the visible region. To this aim, the energies, oscillator strengths and orbital characters of the singlet and triplet excited states are investigated....
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublikacjaEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublikacjaReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Multi-state multi-reference Møller-Plesset second-order perturbation theory for molecular calculations
PublikacjaThis work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order...
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublikacjaUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
PublikacjaThe increasing interest in polyurethane materials has raised the question of the environmental impact of these materials. For this reason, the scientists aim to find an extremely difficult balance between new material technologies and sustainable development. This work attempts to validate the possibility of replacing petrochemical polyols with previously synthesized bio-polyols and their impact on the structure and properties...
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The exposure to UV filters: Prevalence, effects, possible molecular mechanisms of action and interactions within mixtures
PublikacjaSubstances that can absorb sunlight and harmful UV radiation such as organic UV filters are widely used in cosmetics and other personal care products. Since humans use a wide variety of chemicals for multiple purposes it is common for UV filters to co-occur with other substances either in human originating specimens or in the environment. There is increasing interest in understanding such co-occurrence in form of potential synergy, antagonist,...
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Theoretical designing of selenium heterocyclic non-fullerene acceptors with enhanced power conversion efficiency for organic solar cells: a DFT/TD-DFT-based prediction and understanding
PublikacjaIn this study, we have designed and explored a new series of non-fullerene acceptors for possible applications in organic solar cells. We have designed four molecules named as APH1 to APH4 after end-capped modification of recently synthesized Y6-Se-4Cl molecule. Density functional theory and time dependent-density functional theory have been employed for computing geometric and photovoltaic parameters of the designed molecules....
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Linear and nonlinear Stark effect in a triangular molecule
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Electron collision with sulfuryl chloride (SO2Cl2) molecule
PublikacjaStosując liniową metodę transmisyjną zmierzono całkowite przekroje czynne (TCS) na zderzenie elektronów z drobinami SO2Cl2 w zakresie energii 0.5-150 eV. Stwierdzono obecność głębokiego minimum przy ok. 1.8 eV i szerokiego maksimum w pobliżu 9.5 eV. Przeprowadzono porównanie z dostępnymi wynikami dla innych związków zawierających grupę sulfonową.
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublikacjaC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Investigation of volatile low molecular weight compounds formed during continuous reclaiming of ground tire rubber
PublikacjaGround tire rubber was thermo-mechanically reclaimed at different temperature conditions (80, 120, 160 °C) using a co-rotating twin screw extruder. The progress of ground tire rubber reclaiming was evaluated with specific mechanical energy, sol fraction and thermogravimetric analysis. Volatile organic compounds (VOCs) including volatile sulfur compounds (VCSs) released from ground tire rubber and ground tire rubber after reclaiming...
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Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging
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Adhesion of the genome-sequenced Lactococcus lactis subsp. cremoris IBB477 strain is mediated by specific molecular determinants
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Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer
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Theoretical Design of the Molecular Structure of Bent-Core Mesogens with Large Second-Order Nonlinear Optical Properties
PublikacjaABSTRACT: The first hyperpolarizability of two series of moleculeswith bent-shaped structures has been calculated at the ab initio level.The two series consist of carboxyl derivatives for which somemolecules are known to exhibit banana phases and of their sulfinatehomologues that have not been synthesized yet. The final purpose isto reveal the relevance or not in synthesizing these latter molecules.The strategy is based on reporting...
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The comparison of semiempirical and ab initio molecular modeling methods in activity and property evaluation of selected antimicrobial sulfonamides
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Differential cross sections for electron impact vibrational excitation of molecular oxygen in the angular range 15° - 180°.
PublikacjaZmierzono absolutne różniczkowe przekroje czynne na wzbudzenie drobin tlenu do poziomów oscylacyjnych v=1-4 stanu podstawowego X3 suma g. Pomiary wykonano dla energii elektronów równej 10eV w zakresie kątów rozproszenia od 15° do 180°.
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
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Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
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Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
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Molecular Characterisation of Uterine Endometrial Proteins during Early Stages of Pregnancy in Pigs by MALDI TOF/TOF
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Gluten-Free Bread with Cricket Powder—Mechanical Properties and Molecular Water Dynamics in Dough and Ready Product
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Biological Activity and Antibiofilm Molecular Profile of Citrus aurantium Essential Oil and Its Application in a Food Model
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TiCoCrFeMn (BCC + C14) High-Entropy Alloy Multiphase Structure Analysis Based on the Theory of Molecular Orbitals
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublikacjaChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Steroidal Molecular Rotors with 1,4-Diethynylphenylene Rotators: Experimental and Theoretical Investigations Toward Seeking Efficient Properties
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