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Search results for: CHEMICAL STRUCTURE
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Molecular Modelling of the Neurophysin II/Vasopressin Complex
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Role of the sulfur to α-carbon thioether bridges in thurincin H
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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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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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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Excited electronic states of the anion of 7,7,8,8-tetracyanoquinodimethane (TCNQ)
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Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment
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Relationship between electronic structure and geometry of silanethiols and their derivatives. Elucidation of copper group silanethiolates
PublicationWyznaczono strukturę elektronową wybranych silanotioli X3SiSH (dla X=H, C2H5, OCH3, F, Cl i Br) oraz powstalych z nich anionów. Geometrię i funkcje falowe wyznaczono przy użyciu teorii funcjonałów gęstości elektronowej DFT. Przeanalizowano wpływ efektów anomerycznych oraz wielkości calki nakładania sigma(Si-S) na obserwowane skrócenie wiązania Si-S przy deprotonowaniu silanotioli. Podano nowe wyjaśnienie wyjątkowo niskiej kwasowości...
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublicationImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
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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...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
PublicationThe genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublicationWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Influence of stabilizing osmolytes on hen egg white lysozyme fibrillation
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Core–shell excitation of isoxazole at the C, N, and O K-edges – an experimental NEXAFS and theoretical TD-DFT study
PublicationThe near-edge X-ray absorption fine structure (NEXAFS) spectra of the gas-phase isoxazole molecule have been measured by collecting total ion yields at the C, N, and O K-edges. The spectral structures have been interpreted using time-dependent density functional theory (TD-DFT) with the short-range corrected SRC2-BLYP exchange–correlation functional. Experimental and calculated energies of core excitations are generally in good...
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The effects of gas exposure on the graphene/AlGaN/GaN heterostructure under UV irradiation
PublicationThis work demonstrates a graphene/AlGaN/GaN sensing device with two-dimensional electron gas (2DEG) toward nitrogen dioxide (NO2), tetrahydrofuran, and acetone detection under UV light irradiation. We propose combining measurements of the DC characteristics with a fluctuation-enhanced sensing method to provide insight into the gas detection mechanisms in the synergistic structure of highly stable GaN and gas-sensitive graphene....
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Tailoring properties of indium tin oxide thin films for their work in both electrochemical and optical label-free sensing systems
PublicationThis work is devoted to the identification properties of indium tin oxide (ITO) thin films responsible for their possible application in combined optical and electrochemical label-free sensing systems offering enhanced functionalities. Since any post-processing would make it difficult to identify direct relation between deposition parameters and properties of the ITO films, especially when deposition on temperature-sensitive substrates...
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Anionic states of C6Cl6 probed in electron transfer experiments
PublicationThis is the first comprehensive investigation on the anionic species formed in collisions of fast neutral potassium (K) atoms with neutral hexachlorobenzene (C6Cl6) molecules in the laboratory frame range from 10 up to 100 eV. In such ion-pair formation experiments, we also report a novel K+ energy loss spectrum obtained in the forward scattering giving evidence of the most accessible electronic states. The vertical electron affinity...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Noble metal modified TiO2 microspheres: Surface properties and photocatalytic activity under UV-vis and visible light
PublicationComposite photocatalysts that consist of TiO2and noble metal nanostructures have been considered tobe the promising and pivotal material for accessible enhancement of the efficiency in the photocatalyticprocess carried out in the aqueous and gas phases. In this work we fabricated porous TiO2microspheresthrough a hydrothermal process followed by photochemical reduction of noble metal nanoparticles atthe TiO2surface. The morphology...
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Preparation, characterization and photocatalytic activity of TiO2 microspheres decorated by bimetallic nanoparticles
PublicationComposite photocatalysts that consist of TiO2and noble metal nanostructures have been considered tobe the promising and pivotal material for accessible enhancement of the efficiency in the photocatalyticprocess carried out in the aqueous and gas phases. In this work we fabricated porous TiO2microspheresthrough a hydrothermal process followed by photochemical reduction of noble metal nanoparticles atthe TiO2surface. The morphology...
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Magnetically recyclable TiO2/MXene/MnFe2O4 photocatalyst for enhanced peroxymonosulphate-assisted photocatalytic degradation of carbamazepine and ibuprofen under simulated solar light
PublicationIn this study, a novel TiO2/Ti3C2/MnFe2O4 magnetic photocatalyst with dual properties, enabling (i) improved photocatalytic degradation with PMS activation under simulated solar light and (ii) magnetic separation after the degradation process in an external magnetic field was developed and applied for the efficient photodegradation pharmaceutically active compounds (PhACs) frequently present in wastewater and surface waters worldwide. MXene...
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n-butyl 2-(3-chloro-1,2-dihydropyrazin-2-ylidene)-2-cyanoacetate
PublicationStrukturę C11H12ClN3O2 wyznaczono metodą rentgenowskiej analizy strukturalnej. Geometria i długości wiązań w pierścieniu pirazynowym są typowe dla tej klasy związków. Cała cząsteczka, poza ogonem n-butylowym, jest płaska (r.m.s. 0.0131(1)Å). Występujące intramolekularne wiązanie wodorowe N2-H2BO1 tworzy S(6) pierścień stabilizując całą cząsteczkę. W sieci krystalicznej obserwuje się nieuporządkowanie statyczne dla reszty...
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N-Benzoyl-N'-phenylurea
PublicationPublikacja zawiera opis struktury krystalicznej i cząsteczkowej N-benzoilo-N'-fenylomocznika wyznaczonej metodą rentgenowskiej analizy strukturalnej. W krysztale dwie cząsteczki łączą się poprzez wiązania wodorowe typu N-H...O tworząc centrosymetryczne dimery.
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3-[(E)-2-(5,7-dichloro-8-hydroxyquinolin-2-yl)vinyl]-4-hydroxyphenyl acetate
PublicationTytułowy związek otrzymano w reakcji 2,5 dihydroksybenzaldehydu z równomolową ilością 5,7-dichloro-2-metylochinolin-8-olu. Strukturę C19H13Cl2NO4 wyznaczono metodą rentgenowskiej analizy strukturalnej. Zawarte w komórce elementarnej cząsteczki posiadają konfiguracje E a długości wiązań C=C wynoszą w tym przypadku C10-C11 1.328(3) Å oraz C29-C30 1.330(3) Å. Cząsteczki otrzymanego związku stabilizowane są przez układ...
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2,2,6,6-Tetramethylpiperidinium triisopropoxysilanethiolate
PublicationTytułowy związek został otrzymany poprzez reakcję tri-izo-propoksysilanotiolu z 2,2,6,6-tetrametylopiperydyną. Oba fragmenty jonowe powiązane są wiązaniami wodorowymi N-H...S. Strukturę cząsteczkową i krystaliczną wyznaczono posługując się rentgenowską analizą strukturalną.
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Crystal and molecular structure of bis(O,O'-diethyldithiophosphato-S,S')nickel(II): A redetermination
PublicationDoniesienie przedstawia ponownie wyznaczoną strukturę tytułowego, centrosymetrycznego kompleksu, [Ni{S2P(OC2H5)2}2]. Centralny rdzeń (S2P)2 jest płaski, co potwierdza wcześniejsze wyniki uzyskane przez McConnell'a i Kastalsky'ego, przy czym odchylenia standardowe są około siedmiokrotnie mniejsze oraz wyznaczono wszystkie pozycje atomów wodoru. W strukturze krystalicznej zaobserwowano róznież parę krótkich kontaktów HH (2.33 Å).
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5,5-Dimethyl-2-methylseleno-1,3,2-dioxaphosphorinan-2-one
PublicationTytułowy związek otrzymano w reakcji soli potasowej kwasu O,O-neopentylidenomonoselenofosforowego z jodkiem metylu. Analiza krystalograficzna tego estru wykazała, że grupa selenometylowa zajmuje pozycję aksjalną względem sześcioczłonowego pierścienia dioksafosforinanu.
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Dispiro[cyclopropane-1,50-endo-tricyclo-[5.2.1.02,6]deca-3,8-diene-100,100-cyclopropane]
PublicationThe title compound, C14H16, is built up from three fivememberedrings. Two of the five-membered rings display anenvelope conformation and the third one is almost planar(r.m.s. deviation = 0.014 A ° ).
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Trichloridobis(ethyldiphenylphosphine)-(tetrahydrofuran)molybdenum(III)
PublicationIn the mononuclear title compound, [MoCl3(C4H8O)(C14H15P)2], obtained by the reaction of trichlorotris(tetrahydrofuran)molybdenum(III) and ethyldiphenylphosphine in tetrahydrofuran (THF) solution, the MoIII atom is six-coordinated by one O atom of a THF molecule, two P atoms from two ethyldiphenylphosphine ligands and three Cl atoms in a distorted octahedral geometry. The C atoms of the THF molecule are disordered over two positions...
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<i>N,N</i>'-diphenylthiourea acetone monosolvate
PublicationIn the title compound, C13H12N2S·C3H6O, the phenyl rings of the thiourea molecule are in syn and anti positions in relation to the C=S bond. Two molecules are connected by N-HS=C hydrogen bonds into a centrosymmetric dimer. An additional N-HO=C hydrogen bond to the acetone solvent molecule and some weak C-H interactions reinforce the crystal structure.
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Catena-Poly[[(tetrahydrofuran-[kappa]O)lithium(I)]-bis([mu]-trimethylsilanolato-[kappa]2O:O)-gallium(III)-bis([mu]-trimethylsilanolato-[kappa]2O:O)-[(tetrahydrofuran-[kappa]O)lithium(I)]-[mu]-bromido]
PublicationThe title chain polymer compound, [GaLi2Br(C3H9OSi)4(C4H8O)2]n, was obtained in the reaction of GaBr3 with Me3SiOLi in toluene/tetrahydrofuran. The GaIII atom, located on a twofold rotation axis, is coordinated by four trimethylsilanolate ligands and has a distorted tetrahedral geometry. The LiI atom is four coordinated by one bridging Br atom located on an inversion centre, two trimethylsilanolate ligands and one tetrahydrofurane...
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[N,N'-Bis(2,6-diisopropylphenyl)pentane-2,4-diamine(1-)-2[kappa]2N,N']-[mu]2-chlorido-1:2[kappa]2Cl:Cl-chlorido-2[kappa]Cl-bis(1,2-dimethoxyethane-1[kappa]2O,O')iron(II)lithium
PublicationIn the title compound, [FeLi(C29H41N2)Cl2(C4H10O2)2], theFeII atom is coordinated by two N and two Cl atoms,generating a distorted FeN2Cl2 tetrahedral geometry. Additionally,one of the chloride atoms bridges to a lithium ion,which is solvated by two dimethoxyethane molecules and iscoordinated in a distorted trigonal-bipyramidal environment.The central Fe, Cl (*2) and Li atoms are coplanar with amaximum deviation of 0.034 A ° .
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Catena-Poly[{[mu]-[eta]5:[eta]5-1-[2-(dimethylamino)ethyl-[kappa]N]cyclopentadienyl}-lithium(I)-([mu]-1,1,3,3-tetra-tert-butyltriphosphane-[kappa]3P2:P1,P3)lithium(I)]
PublicationThe title compound, [Li2(C9H14N)(C16H36P3)]n, is a by-product of the reaction of [Cp(C5H4CH2CH2NMe2)ZrCl2]n with tBu2P-P(SiMe3)Li in toluene. It is a coordination polymer composed of infinite chains running along [010]. One Li(I) atom is chelated by the cyclopentadienyl ring and and the N atom of the scorpionate ligand and a P atom, whereas the other Li(I) atom is coordinated by the backside of the cyclopentadienyl ring and two...
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Chlorido(ethyldiphenylphosphine-P)(1-pyrrolidinecarbodithioato-S,S)nickel(II)
PublicationPrzedmiotem publikacji jest struktura krystaliczna tytułowego [NiCl{S2CN(CH2)4}Cl(C14H15P)]. Atom niklu jest w tym przypadku skoordynowany przez S,S-chelatującą resztę ditiokarbaminianową, cząsteczkę fosfiny, zaś geometrię koordynacyjną dopełnia atom chloru.
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Tetra-n-butylammonium iodido(pyrrolidine-1-carbodithioato-κ2S,S')(tris-tert-butoxysilane-thiolato-κS)cadmate(II)
PublicationTytułowy (N,N tetrametylenoditiokarbaminiano)(tri-tert-butoksysilanotiolano)jodokadmian tetra-n-butyloamoniowy krystalizuje w układzie jednoskośnym, w grupie P21/c. W anionie [Cd{SSi(OtBu)3}(S2CNC4H9)I]() wyróżnić można centralny rdzeń o składzie CdS3I. Ułożenie atomów donorowych może być, w pierwszym przybliżeniu, opisane jako zniekształcony (ze względu na obecność S,S'-chelatującego liganda) tetraedr z największym kątem S1-Cd1-S2...
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O-4-Chlorobenzoyl diphenylselenophosphinate
PublicationTytułowy związek difenyloselenofosfinian O-4-chlorobenzoilu krystalizuje w układzie jednoskośnym, w grupie P21/c. Upakowanie molekuł w krysztale wskazuje na oddziaływania van der Waalsa pomiędzy pierścieniami aromatycznymi reszt acylowych. Z kolei kąt dwuścienny pomiędzy pierścieniami fenylowymi reszty fosforowej wynosi 72.64 (14) stopni. Geometrię cząsteczki badanego związku porównano z opisanymi w litaraturze chemicznej estrami...
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1,1,2,2-Tetrakis(diisopropylamino)diphosphane
PublicationTytułowy związek otrzymano w trakcie badań raktywności (i-Pr2N)2P-P(SiMe3)Li z Cp2ZrCl2 (Cp-cyklopentadienyl). Strukturę C24H56N4P2 wyznaczono metodą rentgenowskiej analizy strukturalnej. Wiązanie P-P należy do najdłuższych wśród tego typu wiązań wyznaczonych dla niekoordynowanych difosfanów. W sieci krystalicznej obserwuje się nieuporządkowanie...
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(Di-tert-butylmethylphosphane)(η2-di-tert-butylphosphanylphosphinidene)(triphenylphosphane)platinum(0)
PublicationStruktura krystaliczna tytułowego związku, [(Ph3P)(tBu2PMe)Pt(η2-tBu2PP)], zawiera cztery cząsteczki w części niezależnej nieznacznie różniące się konformacjami. Odległości P-P w ligandzie tBu2PP są zbliżone dla wszystkich czterech cząsteczek [2.0661(13)-2.0678(13)A˚]. Odległości te, wskazują na wielokrotny charakter wiązania P-P w ligandzie tBu2PP. Atom platyny w kompleksie wykazuje koordynację płaską kwadratową. Prezentowana...
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Bis(3,5-dimethylpyridine-kN)bis(tri-tert-butoxysilanethiolato-kS)chromium(II)toluene solvate
PublicationW tytułowym związku atom chromu jest czterokrotnie koordynowany: przez dwa atomy siarki grup tri-tert-butoksysilanotiolanowych oraz dwa atomy azotu z dwóch cząsteczek 3,5-dimetylopirydyny. Geometria ligandów wokół centrum metalicznego jest płaska kwadratowa. Cząsteczka leży na dwukrotnej osi symetrii przechodzącej przez atom N 3,5-dimetylopirydyny. Dodatkowo w krysztale na jedną cząsteczkę kompleksu przypada jedna cząsteczka toluenu.
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Chlorido(η5-cyclopentadienyl)[(4a,4b,8a,9,9a-η)-fluorenyl](fluorenyl-κC9)zirconium(IV) toluene solvate
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