Relevant bibliographies by topics / Ligand Structure Effects

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Ligand Structure Effects'

Author: Grafiati
Published: 5 June 2025
Last updated: 24 June 2025

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Journal articles on the topic "Ligand Structure Effects"

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Zhao, Yi, Qun Chen, Mingyang He, et al. "Tris(Butadiene) Compounds versus Butadiene Oligomerization in Second-Row Transition Metal Chemistry: Effects of Increased Ligand Fields." Molecules 26, no. 8 (2021): 2220. http://dx.doi.org/10.3390/molecules26082220.

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The geometries, energetics, and preferred spin states of the second-row transition metal tris(butadiene) complexes (C4H6)3M (M = Zr–Pd) and their isomers, including the experimentally known very stable molybdenum derivative (C4H6)3Mo, have been examined by density functional theory. Such low-energy structures are found to have low-spin singlet and doublet spin states in contrast to the corresponding derivatives of the first-row transition metals. The three butadiene ligands in the lowest-energy (C4H6)3M structures of the late second-row transition metals couple to form a C12H18 ligand that binds to the central metal atom as a hexahapto ligand for M = Pd but as an octahapto ligand for M = Rh and Ru. However, the lowest-energy (C4H6)3M structures of the early transition metals have three separate tetrahapto butadiene ligands for M = Zr, Nb, and Mo or two tetrahapto butadiene ligands and one dihapto butadiene ligand for M = Tc. The low energy of the experimentally known singlet (C4H6)3Mo structure contrasts with the very high energy of its experimentally unknown singlet chromium (C4H6)3Cr analog relative to quintet (C12H18)Cr isomers with an open-chain C12H18 ligand.
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Genest, Alexander, Sven Krüger, Alexei B. Gordienko, and Notker Rösch. "Gold-Thiolate Clusters: A Relativistic Density Functional Study of the Model Species Au13(SR)n, R = H, CH3, n = 4, 6, 8." Zeitschrift für Naturforschung B 59, no. 11-12 (2004): 1585–99. http://dx.doi.org/10.1515/znb-2004-11-1232.

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The binding of sulfanyl and alkylsulfanyl model ligands to gold clusters was studied for the case of Au13(SR)n with R = H, CH3 and n = 4, 6, 8. Accurate all-electron electronic structure calculations and geometry optimizations of these gold-thiolate clusters have been performed with a scalar relativistic Kohn-Sham procedure as implemented in the density functional program PARAGAUSS. In all structures obtained, bridge coordination was preferred for both types of ligands; no higher coordinated sites where occupied. While in many cases ligand decoration did not change the overall structure of the Au13 core, also more open structures with Au-Au distances elongated beyond the bulk value have been obtained. The effects due to increasing ligand decoration were small: a small decrease of the binding energy per ligand does not exclude higher ligand coverages. The differences between the model ligands SH and SCH3 were consistent in all cases considered: SCH3 exhibits weaker binding and a slightly smaller charge separation between cluster core and ligand shell, which amounts up to about 1.5 e for 8 ligands. Overall, the Au13 core of the clusters was found to be quite flexible. This can be rationalized by the fact that the calculated binding energy per ligand is comparable or even exceeds the binding energy per atom in Au13.
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Bilodeau, Camille, Edmond Y. Lau, Steve Cramer, and Shekhar Garde. "The Effects of Ligand Structure on Protein-Multimodal Ligand Interactions." Biophysical Journal 116, no. 3 (2019): 477a. http://dx.doi.org/10.1016/j.bpj.2018.11.2579.

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HARRIS, DANNI L., and GILDA H. LOEW. "Proximal ligand effects on electronic structure and spectra of compound I of peroxidases." Journal of Porphyrins and Phthalocyanines 05, no. 03 (2001): 334–44. http://dx.doi.org/10.1002/jpp.316.

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Computational studies exploring the extent to which differences in proximal axial ligands modulate structure, spectra, and function of peroxidases have been performed. To this end, three heme models of compound I were characterized differing only in the axial ligand. The axial ligands considered were L = ImH , Im -, that are alternative protonation models for a typical peroxidase with an imidazole ligand such as horseradish peroxidase (HRP-I), and L = SCH - that is a model for an unsual peroxidase, chloroperoxidase (CPO-I). Density functional calculations (DFTs) were performed to determine the optimized geometries and electronic structure of each of these three species. Their electronic spectra were also calculated at the DFT optimized geometries, using the INDO/S/CI method. The results of these studies led to the following conclusions: (1) the presence of the nearby Asp in a typical peroxidase does indeed decrease the energy required to deprotonate the imidazole making the two forms essentially degenerate, (2) neither the state of protonation of the imidazole ligand nor the change in axial ligand from an imidazole in typical peroxidases such as HRP to a mercaptide in CPO significantly alters the characteristics of the lowest energy spin state or the electronic structure of compound I in a way that can obviously affect function, (3) both the Im - and ImH forms of the peroxidase compound I (HRP-I) lead to the same dramatic reduction in intensity relative to the ferric resting form observed experimentally. However, only in the ImH form of HRP-I does the calculated relative shift of one component of the Soret bands relative to CPO-I agree with that observed in the transient spectra of HRP-I compared to CPO-I. These results taken together strongly indicate that factors other than the nature of the proximal axial ligand are the main determinants of function.
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Langelaan, David N., and Jan K. Rainey. "Membrane catalysis of peptide–receptor bindingThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 2 (2010): 203–10. http://dx.doi.org/10.1139/o09-129.

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The membrane catalysis hypothesis states that a peptide ligand activates its target receptor after an initial interaction with the surrounding membrane. Upon membrane binding and interaction, the ligand is structured such that receptor binding and activation is encouraged. As evidence for this hypothesis, there are numerous studies concerning the conformation that peptides adopt in membrane mimetic environments. This mini-review analyzes the features of ligand peptides with an available high-resolution membrane-induced structure and a characterized membrane-binding region. At the peptide–membrane interface, both amphipathic helices and turn structures are commonly formed in peptide ligands and both hydrophobic and electrostatic interactions can be responsible for membrane binding. Apelin is the ligand to the G-protein coupled receptor (GPCR) named APJ, with various important physiological effects, which we have recently characterized both in solution and bound to anionic micelles. The structural changes that apelin undergoes when binding to micelles provide strong evidence for membrane catalysis of apelin–APJ interactions.
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O'Callaghan, Chris A., Aleksandra A. Watson, Angharad E. Fenton-May, and Charita M. Christou. "Structure and function of the activating receptor CLEC-2. (134.10)." Journal of Immunology 182, no. 1_Supplement (2009): 134.10. http://dx.doi.org/10.4049/jimmunol.182.supp.134.10.

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Abstract We are studying the immune recognition of diseased or damaged cells. In cytotoxic cells, the C-type lectin-like receptor NKG2D plays a key role in this distinction. A number of related receptors are expressed on immune cells and we are studying their function. CLEC-2 is an activating receptor which is also expressed on platelets. We have crystallized CLEC-2 and solved its structure. We have used recombinant CLEC-2 as a probe to identify an endogenous ligand for CLEC-2, which is known as podoplanin. The podoplanin-CLEC-2 interaction triggers an activating signal in the cell expressing CLEC-2. We have also solved the crystal structure of rhodocytin, an exogenous ligand for CLEC-2. The structures of both ligand and receptor allow us to produce molecular models of the interactions and its effects. These suggest that the ligand-receptor interactions will cluster CLEC-2 on the cell surface. We have used surface plasmon resonance to define the binding characteristics of the interactions of CLEC-2 with both its exogenous and endogenous ligands.
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Halbert, Stéphanie, and Hélène Gérard. "A computational study of the effects of ancillary ligands on copper(i)–ethylene interaction." New Journal of Chemistry 39, no. 7 (2015): 5410–19. http://dx.doi.org/10.1039/c5nj00546a.

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Pippal, Jyotsna B., and Peter J. Fuller. "Structure–function relationships in the mineralocorticoid receptor." Journal of Molecular Endocrinology 41, no. 6 (2008): 405–13. http://dx.doi.org/10.1677/jme-08-0093.

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The signature action of aldosterone in the regulation of electrolyte and fluid balance is well established. However, the role of aldosterone as an important contributor to morbidity and mortality in heart failure has gained a heightened interest in recent years, but the mechanisms of this action are not well understood. Aldosterone is the principal physiological ligand for the mineralocorticoid receptor (MR), a ligand-activated transcription factor, that also binds to the physiological glucocorticoid, cortisol. Both classes of hormones bind with similar affinity to the MR, but the molecular basis of selective and tissue-specific effects of MR ligands is not yet fully documented. The structural and functional determinants of MR function are described and their significance is discussed.
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Zhu, Yu, Qiaohong Li, Dongsheng Li, Jian Zhang, and Lei Zhang. "Functional ligand directed assembly and electronic structure of Sn18-oxo wheel nanoclusters." Chemical Communications 57, no. 42 (2021): 5159–62. http://dx.doi.org/10.1039/d1cc00651g.

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The bilayer hexagonal Sn<sub>18</sub>-oxo cluster, as the largest tin-oxo wheel, was constructed by a ligand templating method. Moreover, the ligands also show important effects on electronic structure and third-order nonlinear optical property of the wheel.
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Chiu, Cheng-Chang, Gene-Hsiang Lee, Tien-Sung Lin, and Shie-Ming Peng. "Ligand effects on the structure, mixed-valence sites and magnetic properties of novel pentanickel string complexes." Dalton Transactions 48, no. 23 (2019): 8464–77. http://dx.doi.org/10.1039/c9dt01363f.

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Four redox pairs of pentanickel metal string complexes containing pyridine-, naphthyridine- and the corresponding sulfonyl substituted ligands were synthesized to examine the ligand effects on their electronic structures and magnetic properties.
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Dissertations / Theses on the topic "Ligand Structure Effects"

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McFail-Isom, Lori. "Effects of ligand binding, coordinate error and ion binding on nucleic acid structure and conformation." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/30735.

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Durivage, Jason Curtis. "Ligand Effects on Metal-Metal Bonding: Photoelectron Spectroscopy and Electronic Structure Calculations of Dimetal Paddlewheel Complexes." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/145427.

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Paddlewheel complexes are molecules in which two interacting metal atoms are bridged by four chelating ligands. This class of complexes has a large range of electronic variability while keeping a rigid geometric structure. This variability has led to their use as catalysts, strong reductants, anti-tumor agents, and electron transfer agents. This dissertation examines the effects of changing both the dimetal core and the surrounding ligands on the electronic structure properties of the paddlewheel complexes. Examination of Bi₂(O₂CCF₃)₄, a p-orbital dimetal paddlewheel complex, provided a way to probe the orbitals that are important in metal-ligand σ bonding. The b(1g) and b(2u) ligand orbitals of Bi₂(O₂CCF₃)₄ have no dimetal orbital counterpart, unlike the case of the more familiar d-orbital dimetal paddlewheel complexes such as Mo₂(O₂CCF₃)₄. This had the effect of destabilizing these ligand orbitals compared to d-orbital paddlewheel complexes. The ligand a1g orbital in Bi₂(O₂CCF₃)₄ was also destabilized due to nodal differences in the dimetal σ orbital. The unusual coincidence of Mo-Mo σ and π ionization bands is due to a greater amount of ligand character in the Mo-Mo σ orbital compared to its ditungsten analogue, which has separate ionization bands for the σ and π bonds. A series of p-substituted dimolybdenum tetrabenzoate complexes was synthesized and studied by photoelectron spectroscopy in order to further examine the delocalization of electron density from the metals to the ligands in these complexes. A 0.89 eV shift in the δ ionization band was observed from Mo₂(O₂CPh-p-OMe) ₄ and Mo₂(O₂CPh-p-CF₃)₄. Overlap effects are the major factor causing the shift in the δ bond ionization, as the calculated charges on the molybdenum and oxygen atoms did not vary significantly on change of substituent. Molybdenum and tungsten guanidinate paddlewheel complexes have promise as good reducing agents due to their extremely low ionization energies. The solubility of the complexes poses a problem for their widespread adoption for use as reducing agents. Alkyl substituents were added to the complexes to increase their solubility. W₂(TEhpp)₄ was observed to have the lowest ionization energy at 3.71 eV (vertical ionization) and 3.40 eV (onset ionization) of any molecule yet prepared.
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Pollard, John Randolph 1969. "Ligand effects and periodic trends in metal-metal multiple bonds: Theoretical and experimental studies of electronic structure by gas-phase photoelectron spectroscopy." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/282196.

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Gas-phase photoelectron spectroscopy was utilized to study a series of metal-metal bonded complexes. Molecular mechanics, Fenske-Hall and ab-initio theoretical calculations were performed on many of the systems. The central focus of all the studies was to identify metal-metal ionizations, and observe how ligands effects influence metal-metal interactions. This information was then used to describe various physical and chemical properties of the species. The first group of compounds studied were molybdenum and tungsten D₃(h) triply-bonded hexa-alkoxides of the form M₂(OC(CH₃)n(CF₃)₃₋n)₆ (where M=Mo, W and n = 1, 2, 3). The metal-metal π and σ ionizations were identified. It is observed that sequential fluorination of the ligands shifts all the valence ionizations. Because the shifts are found to be dominated by charge effects, the virtual levels are assumed to be equally shifted. This information was used to describe the similarity of the UV absorption spectra of the compounds. The next group studied are electron-rich single-bonded Rh(II)-Rh(II) complexes. The previously assigned PES data for Mo₂(O₂CCF₃)₄ was used as a reference point when interpreting the data for Rh₂(O₂CCF₃)₄. The electron configuration orbital ordering for the Rh-Rh bond in Rh₂(O₂CCF₃)₄ is determined to be σ²π⁴δ²δ*²π*⁴, with the δ* and π* being nearly degenerate. It is observed that if the acetates are replaced with more electron-donating ligands, as with Rh₂(O₂CCF₃)₂(form)₂, Rh₂(form)₄ (form = N-N’-p-tolylformamidine, C₁₅H₁₅N₂) and Rh₂(dpf)₄ (dpf = diphenylformamidine, C₁₃H₁₁N₂), the δ* ionizations are destabilized relative to the other Rh-Rh ionizations. In addition, ligand-based ionizations overlap into metal-metal ionizations making it more difficult to interpret data. This information is then used to understand the data and electron structures of Rh₂(pfb)₄ (pfb = perfluorobutyrate, CF₃(CF₂)₂CO₂⁻), Rh₂(capy)₄ (capy = caprolactamate, ⁻OC(CH₂)₅N), Rh₂(OCCH₃NC₆H₅)₄ and Rh₂(OCCH₃NC₆F₅)₄. Rh₂(OCCH₃NC₆H₅)₄ and Rh₂(OCCH₃NC₆F₅)₄ provide examples where charge and overlap effects can be utilized to assign Rh-Rh ionizations. Rh₂(pfb)₄ and Rh₂(capy)₄ exhibit very high and different product selectivities when employed as catalysts in reactions involving carbenes derived from diazo-carbonyl complexes. A mechanism for this catalysis is derived which correlates with the observed selectivities.
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Meyer, Marleen J. [Verfasser], Werner [Gutachter] Weitschies, Mladen V. [Gutachter] Tzvetkov, Jörg [Gutachter] König, and Joachim [Gutachter] Geyer. "Effects of ligand structure, amino acid substitutions, and species differences on the function of organic cation transporter OCT1: utilizing polyspecificity for understanding structure-function relationships / Marleen J. Meyer ; Gutachter: Werner Weitschies, Mladen V. Tzvetkov, Jörg König, Joachim Geyer." Greifswald : Universität Greifswald, 2020. http://d-nb.info/1224047362/34.

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Green, Michael Roger. "Ligand and substituent effects on the electronic structures of mononuclear transition metal complexes /." The Ohio State University, 1987. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487331541710079.

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Xu, Rong. "The effects of structural modifications on sigma receptor binding." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4742.

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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.<br>The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on December 18, 2007) Vita. Includes bibliographical references.
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Patirana, Charles Gamini. "Ligand effects on the structures of Rh¦6(CO)¦1¦5L clusters, the novel coordination of a new bisthiophosphorus ligand to a triosmium carbonyl cluster." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/MQ62944.pdf.

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Herbert, Paul. "The heteromeric 5-HT3A/B receptor : the effect of 5-HT3B subunits on receptor structure and ligand recognition." Thesis, Aston University, 2008. http://publications.aston.ac.uk/11070/.

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The 5-HT3 receptors are members of the cys-loop family of ligand-gated ion channels. Two functional subtypes are known, the homomeric 5HT3A and the heteromeric 5HT3A/B receptors, which exhibit distinct biophysical characteristics but are difficult to differentiate pharmacologically. Atomic force microscopy has been used to determine the stoichiometry and architecture of the heteromeric 5HT3A/B receptor. Each subunit was engineered to express a unique C-terminal epitope tag, together with six sequential histidine residues to facilitate nickel affinity purification. The 5-HT3 receptors, ectopically expressed in HEK293 cells, were solubilised, purified and decorated with antibodies to the subunit specific epitope tags. Imaging of individual receptors by atomic force microscopy revealed a pentameric arrangement of subunits in the order BBABA, reading anti-clockwise when viewed from the extracellular face. Homology models for the heteromeric receptor were then constructed using both the electron microscopic structure of the nicotinic acetylcholine receptor, from Torpedo marmorata, and the X-ray crystallographic structure of the soluble acetylcholine binding protein, from Lymnaea stagnalis, as templates. These homology models were used, together with equivalent models constructed for the homomeric receptor, to interpret mutagenesis experiments designed to explore the minimal recognition differences of both the natural agonist, 5-HT, and the competitive antagonist, granisetron, for the two human receptor subtypes. The results of this work revealed that the 5-HT3B subunit residues within the ligand binding site, for both the agonist and antagonist, are accommodating to conservative mutations. They are consistent with the view that the 5-HT3A subunit provides the principal and the 5-HT38 subunit the complementary recognition interactions at the binding interface.
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Huang, Shih-huang. "Synthetic, Mechanistic, and Structural Studies of Polynuclear Metal Clusters and Hydrazido-Substituted Tantalum(V) Compounds." Thesis, University of North Texas, 2010. https://digital.library.unt.edu/ark:/67531/metadc33166/.

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A combined experimental and computational study on the reversible ortho-metalation exhibited by the triosmium cluster Os3(CO)10(dppm) (dppm = 1,1-bis(diphenylphosphino)methane is reported. The conversion of nonacarbonyl cluster HOs3(CO)9[&#61549;-PhP(C6H4)CH2PPh2] to Os3(CO)10(dppm) is independent of added CO and exhibits a significant inverse equilibrium isotope effect (EIE). Reductive coupling of the C-H bond in HOs3(CO)9[&#61549;-PhP(C6H4)CH2PPh2] leads to the formation of agostic C-H and two distinct aryl-&#960; species prior to the rate-limiting formation of the unsaturated cluster Os3(CO)9(dppm). Heating the unsaturated dimer H2Re2(CO)8 with Cp*Rh(CO)2 (Cp* = 1,2,3,4,5-pentamethylcyclopentadiene) at elevated temperature affords the new trimetallic clusters H2RhRe2Cp*(CO)9 and HRh2ReCp*2(CO)6, and the spiked-triangular cluster HRhRe3Cp*(CO)14. H2Re2(CO)8 reacts with Cp*2Rh2(CO)2 under identical conditions to furnish H2RhRe2Cp*(CO)9 and HRh2ReCp*2(CO)6 as the principal products, in addition to the tetrahedral cluster H2Rh2Re2Cp*2(CO)8. H2RhRe2Cp*(CO)9 undergoes facile fragmentation in the presence of halogenated solvents and the thiols RSH (where R = H, C6H4Me-p) to afford the structurally characterized products Cp*Rh(&#61549;-Cl)3Re(CO)3, S2Rh3Cp*(CO)4, Cp*Rh(&#61549;-Cl)(&#61549;-SC6H4Me-p)2Re(CO)3, and Cp*Rh(&#61549;-SC6H4Me-p)3Re(CO)3. The new hydrazido-substituted compounds TaCl(NMe2)3[N(TMS)NMe2] (TMS = tetramethylsilyl) and Ta(NMe2)4[N(TMS)NMe2] have been synthesized and their structures established by X-ray crystallography. The latter product represents the first structurally characterized octahedral tantalum(V) complex containing a single hydrazido(I) ligand in an all-nitrogen coordinated environment about the metal center. The fluxional properties of the amido and hydrazido ligands in these new compounds have been established by VT 1H NMR spectroscopy (VT = variable temperature). Preliminary data using Ta(NMe2)4[N(TMS)NMe2] as an ALD (ALD = atomic layer deposition) precursor for the preparation of tantalum nitride and tantalum oxide thin films are presented.
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Parkes, Roberta Leigh. "Part A. Intrazeolite organometallic kinetics, Part B. Ligand effects on the structures of Rh¦6(CO)¦1¦4LL clusters." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/MQ62943.pdf.

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Books on the topic "Ligand Structure Effects"

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Leijon, Mikael. Structure and dynamics of DNA: Sequence dependent effects and ligand interactions studied by NMR. Stockholm University, Dept. of Biophysics, 1995.

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Knaggs, Roger D. The molecular structure of the μ‎-opioid receptor. Редактори Paul Farquhar-Smith, Pierre Beaulieu та Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0038.

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The landmark paper discussed in this chapter describes the crystal structure of the μ‎-opioid receptor (also known as MOP-1). Opioids are some of the oldest known drugs and have been used for over 4,000 years; however, in addition to having beneficial analgesic effects, they are associated with a myriad of side effects that can minimize their use. Although the gene sequences of the opioid receptors were determined in the 1990s it has taken much longer to translate this into visualizing their three-dimensional structure. The μ‎-opioid receptor consists of seven transmembrane α‎-helices that are connected by three extracellular loops and three intracellular loops, with a wide open binding pocket which offers many potential ligand interaction sites, and evidence of dimerization. Understanding the crystal structure of the μ‎-opioid receptor in much more detail aids explanation of the molecular determinants of ligand recognition and selectivity and will be of use in designing novel opioids with improved efficacy and fewer side effects.
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Patirana, Charles Gamini. Ligand effects on the structures of Rh6(CO)15L clusters. The novel coordination of a new bisthiophosphorus ligand to a triosmium carbonyl cluster. 2001.

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Parkes, Roberta Leigh. Part A: Intrazeolite organometallic kinetics. Part B: Ligand effects on the structures of Rh6(CO)14LL clusters. 2001.

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High-Resolution NMR Techniques in Organic Chemistry. Elsevier Science, 2016.

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Book chapters on the topic "Ligand Structure Effects"

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Chabannon, Christian, and Chiara Bonini. "Structure of and Signalling Through Chimeric Antigen Receptor." In The EBMT/EHA CAR-T Cell Handbook. Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-94353-0_1.

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AbstractChimeric antigen receptor (CAR) is a synthetic transmembrane protein expressed at the surface of immune effector cells (IECs) that are reprogrammed either in vitro or in vivo (June et al. 2018; June and Sadelain 2018). Techniques for genetic engineering of autologous or allogeneic IECs are described in the next chapter. The synthetic CAR incorporates several functional domains. The extracellular domain is composed of a single chain variable fragment (ScFV) of immunoglobulin and recognizes the “tumour” antigen. The clinical relevance of the selected tumour antigen—with a view to minimize “on-target/off-tumour” side effects—is discussed in the third chapter of this section. Bispecific and trispecific CARs are currently being evaluated in preclinical and early clinical trials (Bielamowicz et al. 2018; Shah et al. 2020). The use of an immunoglobulin domain as the ligand of the target antigen means that recognition is not restricted to HLA antigens and that CAR-T cells are universally applicable as opposed to T cell receptor (TCR) transgenic T cells that recognize antigenic peptides presented in the context of a defined major histocompatibility complex (MHC), limiting clinical applications to subsets of patients with defined HLA typing. The intracellular domain is composed of the intracellular domain of the zeta chain of the CD3 component of the TCR, which will trigger signalling when the CAR engages the targeted ligand. The transmembrane region links the two extracellular and intracellular domains through the cell membrane and plays an important role in determining the conformation and flexibility of the CAR and its ability to efficiently bind the targeted antigen/epitope. Association of only these three functional domains characterized first generation CARs, as described in the original publications (Kuwana et al. 1987; Eshhar et al. 1993). However, full activation of T cells requires the addition of one (second generation CARs) or two (third generation CARs) domains from costimulatory molecules, such as CD28, 4-1BB/CD137, or OX40/CD134, that provide the T cell costimulatory signal. Currently approved CAR-T cells are second generation CAR-T cells; as an illustration, the CAR in tisagenlecleucel contains a 4-1BB domain, while the CAR in axicabtagene ciloleucel contains a CD28 domain. The nature of the costimulatory domain influences the ability of CAR-T cells to expand or persist (limit T cell exhaustion) in vivo after infusion into the patient, although it is unclear how this translates clinically and affects disease control, occurrence of adverse events, and overall survival due to the lack of head-to-head comparison between approved products. Finally, fourth generation CAR-T cells have been developed for preclinical projects. These cells, named armoured CAR cells or T cells redirected for universal cytokine-mediated killing (TRUCKS), encode not only a CAR (usually with one costimulatory domain, such as in second generation CARs) but also a cytokine, interleukin, pro-inflammatory ligand, or chemokine that will counteract the immune suppressive microenvironment that prevails in most solid tumours (Eshhar et al. 1993; Chmielewski and Abken 2015).
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Wilson, W. David, Farial A. Tanious, Henryk Buczak, M. K. Venkatramanan, B. P. Das, and David W. Boykin. "The Effects of Ligand Structure on Binding Mode and Specificity in the Interaction of Unfused Aromatic Cations with DNA." In The Jerusalem Symposia on Quantum Chemistry and Biochemistry. Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-011-3728-7_23.

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Arai, Toru, Toshiaki Ohtsu, and Shigeru Suzuki. "The effects of the bridge structure and the ligand system of zirconocene catalysts on the copolymerization of styrene and ethylene." In Metalorganic Catalysts for Synthesis and Polymerization. Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-60178-1_41.

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Mazzobre, M. F., B. E. Elizalde, C. dos Santos, P. A. Ponce Cevallos, and M. P. Buera. "Nanoencapsulation of Food Ingredients in Cyclodextrins: Effect of Water Interactions and Ligand Structure." In Functional Food Product Development. Wiley-Blackwell, 2010. http://dx.doi.org/10.1002/9781444323351.ch2.

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Radić, Zoran, and Palmer Taylor. "The Effect of Peripheral Site Ligands on the Reaction Kinetics of Phosphyl and Carboxyl Esters with Acetylcholinesterase." In Structure and Function of Cholinesterases and Related Proteins. Springer US, 1998. http://dx.doi.org/10.1007/978-1-4899-1540-5_55.

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Cesario, M., J. Guilhem, C. Pascard, et al. "Binuclear Copper(II) Complexes of Cyclo-Bis Intercaland Receptors. Effect of the Ligand on the Crystal Structure and Complexation Properties." In Molecular Recognition and Inclusion. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-5288-4_40.

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Phillips, M. Ian, Keping Qian, and Dagmara Mohuczy. "In vivo gene transfer of antisense to receptors: methods for antisense delivery with adeno-associated virus." In Receptors: Structure and function. Oxford University PressOxford, 2001. http://dx.doi.org/10.1093/oso/9780199638819.003.0012.

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Abstract Ligand receptor binding is a critically important step in the process of many diseases. Over-production of a ligand can be as pathogenic as under-production or lack of a ligand and up-regulation of receptors can produce the same defect as over-production of a ligand. Likewise, down-regulation of receptors can result in the same effects as under-production of the ligand. For example, drugs used to treat hypertension, a chronic disease affecting millions, have included p-adrenergic receptor blockers, ot-adrenergic receptor blockers and, more recently, angiotensin type 1 receptor (ATrR) blockers and Ca2+ channel blockers. All are aimed at reducing the ligand receptor binding interaction by drug receptor antagonism.
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Storz, Jay F. "Hemoglobin structure and allosteric mechanism." In Hemoglobin. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198810681.003.0004.

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Chapter 4 provides an overview of hemoglobin structure and explains the mechanistic basis of ligand-binding dynamics and allosteric effects. The chapter provides an overview of decades of research on structure-function relationships based on X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. This body of work has provided atomic level insights into the structural mechanisms underlying key functional properties. The chapter also reviews experimental data on the ligand-binding behavior of hemoglobin, and discusses how the oxygenation properties of blood reflect a complex and dynamic interplay between the intrinsic O<sub>2</sub>-binding properties of hemoglobin and its operating conditions in the chemical milieu of the red blood cell.
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Sharma, Priyankal, Rupal Mishra, Aparna Patil Kose, et al. "STRUCTURE-BASED DRUG DESIGN: UNDERSTANDING DANCING BIO-MOLECULES." In Futuristic Trends in Biotechnology Volume 3 Book 2. Iterative International Publisher, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3bgbt2p2ch3.

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Structure-based drug design (SBDD) is a powerful approach that leverages the 3D structures of target proteins to guide the rational design of potential drug candidates. By identifying and optimizing ligands that specifically interact with the active sites of target proteins, SBDD aims to develop drugs with enhanced potency, selectivity, and reduced off-target effects. This review provides an overview of the key principles and methodologies involved in SBDD, including target selection, protein structure determination, active site identification, ligand docking, and scoring algorithms. We discuss the advantages and challenges of SBDD, such as addressing target flexibility, modeling membrane proteins, and incorporating water molecules in ligand-protein interactions. Furthermore, we explore emerging trends in SBDD, including the integration of artificial intelligence and machine learning techniques, multi-target drug design, and personalized medicine applications. The potential impact of SBDD on drug discovery for rare diseases and drug resistance is also highlighted. Despite its successes, future issues for SBDD, such as data management, reproducibility, ethical considerations, and regulatory adaptation, need to be addressed to maximize its potential in accelerating drug development. In conclusion, SBDD continues to be a critical component of the drug discovery pipeline, and its continued advancement promises to drive the development of innovative and targeted therapeutics for a wide range of diseases.
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Orchard, A. F. "Paramagnetism – part II Compounds of the transition elements." In Magnetochemistry. Oxford University Press, 2003. http://dx.doi.org/10.1093/hesc/9780198792789.003.0005.

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This chapter deals with transition metals. These form an enormous variety of compounds and display a remarkable diversity of magnetic properties. It looks at paramagnetic phases and subtle aspects of paramagnetic behaviour, which provides a rich source of information about electronic structure. It also recounts the crucial role of the contemplation of paramagnetic properties in the development of ideas concerning the electronic structures of transition metal compounds, which formed the basis of the ligand field theory. The chapter discusses the importance of magnetic measurements of susceptibility and the EPR spectrum in the characterization of a newly synthesized compound. It mentions the 5-fold degeneracy of the d-orbitals characteristic of spherical symmetry. This, it states, is unsustainable in compounds of the transition elements due to the discriminating effects of the ligand environment.
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Conference papers on the topic "Ligand Structure Effects"

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Kuznetsov, Yu I. "The Role of Chemical Structure of Organic Compounds in Corrosion Inhibition." In CORROSION 1989. NACE International, 1989. https://doi.org/10.5006/c1989-89134.

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Abstract Some achievements in corrosion inhibition of metals by organic compounds are considered on the basis of analysing the scientific publications during the last decade. The influence of chemical structure of organic compounds on inhibitor protection of various metals dissolving from the active state or undergoing localized corrosion is given special attention. The great importance of considering both the electronic and solvation effects as well as further development of the complex formation concept for better understanding of the inhibition process is emphasized. Attention is drawn to the fact that corrosion inhibition is frequently the consequence of reactions of nucleophilic substitution of ligands in metal surface complexes. The potentialities of the quantitative approach (using the linear free energy and the HSAB principles) for finding out the relations between the chemical structures of compounds and their effectiveness as corrosion inhibitors are demonstrated. The main features of corrosion inhibition in media of various compositions are outlined.
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"Effects of the original synthetic ligand of benzodiazepine receptors in long-term alcoholized mice." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-415.

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Radovanović, Marko D., Ignjat Filipović, Maja Djukić, Marija Ristić, Matija Zlatar, and Zoran D. Matović. "Relativistic DFT calculation and their effect on the accuracy of results." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.653r.

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This study explores the significance of density functional theory (DFT) calculations with relativistic effects for two ethylenediaminetetraacetate (edta) type complexes: trans(O5)-[M(eddadp)]- (M = Rh3+, Co3+). Relativistic effects affect the electronic structure of a molecule and, thus, its chemical and spectroscopic properties. With the use of scalar relativistic corrections (SR-ZORA), as implemented in the ADF package, with the B3LYP functional, the TZP basis set and the COSMO solvation model, structural analyses show improved predictions for the geometries of both complexes. In the case of the Rh3+ complex, the differences in metal-ligand bond lengths with and without the relativistic effects were small. In the case of the Co3+ complex, the changes in metal-ligand bond lengths due to the relativistic effects were slightly more pronounced. Compared to experimental values, excitation energies are better when including relativistic corrections, especially for the Rh3+ complex. These results indicate the importance of relativistic DFT calculations for heavy element compounds.
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Greve, Daniel R., Tommy Geisler, Thomas Bjørnholm, and Jan C. Petersen. "Third-Order Nonlinear Optical Effects in Organic Nickel Complexes and Triarylmethyl Cations." In Organic Thin Films for Photonic Applications. Optica Publishing Group, 1995. http://dx.doi.org/10.1364/otfa.1995.md.23.

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The second molecular hyperpolarizability, γ, has been determined at 1064 nm by Third- Harmonic Generation (THG) using the Maker fringe technique, for a family of triarylmethyl cations and for a familiy of organic Nickel complexes as guests in PMMA thin films. For the metal complexes it is a well established notion that the low-lying transition with ligand to metal charge transfer character is important for the nonlinear optical properties(1). However, ambiguity arises due to large discrepancies between different measurements(2-5), as well as difficulties in assessing the exact contribution to γ of the ligand to metal charge transfer transition(2,6). To assess the latter question by experimental means, we present here a comparison between a family of Nickel complexes, and triarylmethyl cations. The electronic structure of the triarylmethyl cations resemble that of the metal complexes in the sense that intramolecular charge transfer from the periphery to the central atom takes place upon excitation in the first electronic band. This is shown by semi-empirical PM3 calculations on the three members of the family shown in figure 1. For the amino substituted compound 1 the calculations reveal a significant charge transfer from the amino moiety to the central carbon atom. For the molecules 2 and 3 this effect decreases due to the less efficient donor substituents (2) or forced planarity (3) resulting in more delocalized electronic states both in the HOMO and the LUMO. The observed γ values (table 1) can be correlated with the PM3 calculations in the way that the greater the amount of charge moved and the longer the spatial distance over wich it is moved, the greater is γ. The calculated static γ values, using the semi-empirical PM3/Finite-Field method follow the same trend although much smaller values are obtained.
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Dzichenka, Yaraslau, Michail Shapira, Sergei Usanov, et al. "NOVEL LIGANDS OF HUMAN CYP7 ENZYMES – POSSIBLE MODULATORS OF CHOLESTEROL BLOOD LEVEL: COMPUTER SIMULATION STUDIES." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.435d.

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Our in vitro studies showed that a couple of perspective steroidal derivatives showed previously biomedical potential via enzyme inhibition, receptor binding or antiproliferative effect against the cancer cells of reproductive tissues are able to bind to human CYP7 enzymes – key enzymes taking part in hydroxylation of cholesterol, 25-, 27-hydroxycholesterol and a number of steroidal hormones. In silico screening of binding affinity of the modified steroids toward CYP7 enzymes showed that interaction energy for the new ligands is comparable with consequent values, calculated for the ‘essential’ substrates of the enzymes – cholestenone (CYP7A1) and DHEA (CYP7B1). However, no correlation between binding energy and the affinity of the ligand was found. Novel ligands interact with conserved amino acids taking part in stabilization of natural substrates of CYP7 enzymes. A couple of structural features, governing ligand binding, were identified. Among which are planar structure of A-ring for CYP7A1 ligands, absence of many polar fragments in side-chain and presence of polar group at C3 position. Analysis of the docking results showed that CYP7B1 higher selectivity in comparison with CYP7A1 is connected by the structure of the cavity formed by α-helices I and B`. The data obtained will be used for the explanation of ligand specificity of human sterol- hydroxylases.
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Kralj, Sebastjan, Milan Hodošček, Marko Jukić, and Urban Bren. "A comprehensive in silico protocol for fast automated mutagenesis and binding affinity scoring of protein-ligand complexes." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.674k.

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Protein-protein interactions (PPI) are critical for cellular functions, host-pathogen dynamics and are crucial with drug design efforts. The interaction of proteins is dependent on the amino acid sequence of a protein as it determines its binding affinity to various molecules, including drugs, DNA, RNA, and proteins. Polymorphisms, natural DNA variations, affect PPIs by altering protein structure and stability. Computational chemistry is vital for the prediction of ligand-protein interactions through techniques such as docking and molecular dynamics and can elucidate the changes in energy associated with such mutations. We present a user-friendly protocol that uses the INTE command of CHARMM to predict the effects of mutations on PPIs. This command-line tool automates mutation analysis and interaction energy estimation, is applicable to different ligand types (protein, DNA, RNA, ion, small molecule) and provides various other features. The energy values yield absolute and normalized heat maps that allow rapid identification of stabilizing and destabilizing mutations. Our protocol forms the basis for automated programs that facilitate studies of binding-altering mutations in host-pathogen, protein-protein, and drug-target interactions.
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Kesić, Ana S., Snežana Radisavljević, and Biljana V. Petrović. "SUBSTITUTION REACTIONS OF THE MONOFUNCTIONAL GOLD(III) COMPLEX AND SULPHUR-DONOR BIOLOGICALLY IMPORTANT LIGANDS." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.391k.

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Gold(III) complexes have found application in catalysis, materials science and medical inorganic chemistry. Considering that the right choice of inert ligands in the structure of Au(III) complexes is crucial for their properties and reactivity toward biomolecules, we have studied the substitution reactions between monofunctional Au(III) complex, [Au(Cl-Ph-tpy)Cl]Cl2 (Cl- Ph-tpy = 4′-(4-chlorophenyl)-2,2′:6′, 2″-terpyridine) and sulfur-donor biomolecules, glutathione (GSH) and L-methionine (L-Met), in 25 mM Hepes buffer (pH = 7.2) and 40 mM NaCl. The reactions were followed under the pseudo-first-order conditions as a function of ligand concentration and temperature, using the stopped-flow technique. Calculations were made by Microsoft Excel 2019 and Origin2019b 64Bit. Observed kinetics traces follow a single exponential function, suggesting that the process of the substitution undergoes as one reversible step. Also, L-Met was more reactive than GSH. This order is related to the positive inductive effect of the methyl group, which increases the nucleophilicity of the thioether. According to the values of the activation parameters, the reactions follow an associative model. These results demonstrate the strong connection between the reactivity of Au(III) complexes and the structural and electronic characteristics of the biologically important ligands.
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Xu, Chao, Yu Du, Tingting Liu, and Suliang Yang. "Extraction of Nd(III), Eu(III), Am(III) and Cm(III) With 6-Carboxylic Di(2-Ethylhexyl) Amide Pyridine." In 2022 29th International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2022. http://dx.doi.org/10.1115/icone29-90818.

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Abstract Solvent extraction has been widely used in spent fuel reprocessing because of its advantages such as high mass transfer rate, short production cycle, easy operation and large extraction capacity. The ligands containing soft S and N atoms usually have a good effect on the separation of trivalent lanthanides actinides. Herein, a novel extractant, 6-carboxylic di(2-ethylhexyl) amide pyridine (DEHAPA, HA), containing carboxyl and amide pyridine, was designed. The extraction of Nd(III), Eu(III), Am(III) and Cm(III), representing trivalent lanthanides and actinides, from nitric solution has been carried out by DEHAPA diluted in toluene as the organic phase. According to the slope analysis, the results show that the extraction of Ln(III) and An(III) with DEHAPA was governed by ion-exchange mechanism and the extraction equilibrium constants of Nd(III), Eu(III), Am(III) and Cm(III) have been calculated. The effect of concentration indicated that the structure of extraction complexes are 1:3/LnA3 and 1:3/AnA3. The temperature has a slight influence to distribution ratio of extraction Nd(III) and Eu(III). The infrared spectrum of DEHAPA and extracted complex analysis showed that -N-C = O and -O-C = O group coordinated with Nd(III). According to 1:3/LnA3 extracted complex structure, the Nd(III) ion in complex was coordinated with three -N-C = O, -O-C = O and pyridine group from three tridentate A− ligands by three tridentate A− ligand in organic solvent. This work reveals the unique extraction and coordination structure and provides a value reference to design more effective extraction ligands for Ln(III)/An(III) separation.
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Jovanović Stević, Snežana, Snežana Radisavljević, Aleksandar Mijatović, Biljana Petrović, and Ana Kesić. "The influence of structural modification of Pd(II) pincer-type complexes on the kinetics of substitution reactions." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.411js.

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This mini-review summarizes the kinetic data obtained for the substitution reactions of some palladium(II) complexes containing bis-pyrazolylpyridine derivatives as pincer-type ligands with biologically significant nitrogen- and sulfur-donor biomolecules as nucleophiles. Three structurally different palladium(II) complexes were selected: [Pd(L1)Cl]+(Pd1), [Pd(L2)Cl]+(Pd2) and [Pd(L3)Cl]+(Pd3) (where L1 = bis(2-(1H-pyrazol-1-yl)ethyl)amine, L2 = 2,6-bis(5-(tert-butyl)-1H-pyrazol-3-yl)pyridine, and L3 = 2,6-bis(5-(tert-butyl)-1-methyl-1H-pyrazol-3-yl)pyridine, while for the entering nucleophiles thiourea (Tu), L-methionine (L-met), and guanosine-5’-monophosphate (5’-GMP) were used. Kinetic measurements were carried out for all systems as pseudo-first order reactions (at least 10 times the ligand in excess relative to the complex) under physiological conditions using a stopped-flow UV-Vis spectrophotometer. By comparing the published results for the second-order rate constant, the relationship between the structural properties of the complexes and their reactivity towards selected nucleophiles was established. This overview shows that by tuning the lability of the inert ligands through steric and electronic (σ-donor and π-acceptor) effects, the biological behavior of the complexes can be significantly changed.
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Dimić, Dušan, Dejan Milenković, Edina Avdović, Goran Kaluđerović, and Jasmina Dimitrić Marković. "MOLECULAR DOCKING AND MOLECULAR DYNAMICS STUDIES OF THE INTERACTION BETWEEN COUMARIN-NEUROTRANSMITTER DERIVATIVES AND CARBONIC ANHYDRASE IX." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.056d.

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Novel biologically active compounds can be obtained by the structural modification of coumarins. In this contribution, five new derivatives of 4-hydroxycoumarin with tyramine, octopamine, norepinephrine, 3-methoxytyramine, and dopamine were obtained. Their structures were optimized based on the previously obtained crystal structure of the 4-hydroxycoumarin-dopamine derivative. The special emphasis was put on the effect of various substituents on the structure of obtained compounds and intramolecular interactions governing the stability. To investigate their possible antitumor activity, molecular docking and molecular dynamics simulations were performed with Carbonic anhydrase, a prognostic factor in several cancers, and compared to the native ligand, 5-acetamido-1,3,4-thiadiazole- 2-sulfonamide. The results have shown that all of the coumarin-neurotransmitter derivatives bind to the active pocket of protein with the binding energies higher than for the native ligand. The main contributions to the binding energies were discussed. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of gyration (Rg), as results of MD simulations, were used to predict the activity of compounds towards chosen protein. The highest MD binding energies were obtained for the derivatives with dopamine and 3-methoxytyramine, with the van der Waals interaction and hydrogen bonds being the most important contributors.
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Reports on the topic "Ligand Structure Effects"

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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Gordon, Dalia, Ke Dong, and Michael Gurevitz. Unexpected Specificity of a Sea Anemone Small Toxin for Insect Na-channels and its Synergic Effects with Various Insecticidal Ligands: A New Model to Mimic. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7697114.bard.

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Motivated by the high risks to the environment and human health imposed by the current overuse of chemical insecticides we offer an alternative approach for the design of highly active insect-selective compounds that will be based on the ability of natural toxins to differentiate between insect and mammalian targets. We wish to unravel the interacting surfaces of insect selective toxins with their receptor sites on voltage-gated sodium channels. In this proposal we put forward two recent observations that may expedite the development of a new generation of insect killers that mimic the highly selective insecticidal toxins: (i) A small (27aa) highly insecticidal sea anemone toxin, Av3, whose toxicity to mammals is negligible; (ii) The prominent positive cooperativity between distinct channel ligands, such as the strong enhancement of pyrethroids effects by anti-insect selective scorpion depressant toxins. We possess a repertoire of insecticidal toxins and sodium channel subtypes all available in recombinant form for mutagenesis followed by analysis of various pharmacological, electrophysiological, and structural methods. Our recent success to express Av3 provides for the first time a selective toxin for receptor site-3 on insect sodium channels. In parallel, our recent success to determine the structures and bioactive surfaces of insecticidal site-3 and site-4 toxins establishes a suitable system for elucidation of toxin-receptor interacting faces. This is corroborated by our recent identification of channel residues involved with these two receptor sites. Our specific aims in this proposal are to (i) Determine the bioactive surface of Av3 toward insect Na-channels; (ii) Identify channel residues involved in binding or activity of the insecticidal toxins Av3 and LqhaIT, which differ substantially in their potency on mammals; (iii) Illuminate channel residues involved in recognition by the anti-insect depressant toxins; (iv) Determine the face of interaction of both site-3 (Av3) and site-4 (LqhIT2) toxins with insect sodium channels using thermodynamic mutant cycle analysis; and, (v) Examine whether Av3, LqhIT2, pyrethroids, and indoxacarb (belongs to a new generation of insecticides), enhance allosterically the action of one another on the fruit fly and cockroach paraNa-channels and on their kdr and super-kdr mutants. This research establishes the grounds for rational design of novel anti-insect peptidomimetics with minimal impact on human health, and offers a new approach in insect pest control, whereby a combination of allosterically interacting compounds increases insecticidal action and reduces risks of resistance buildup.
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Yang, Nacy Y. C. Effect of Substrate Configuration on the Grain Structure and Morphology of Electrodeposited Ni for Prototyping LIGA. Office of Scientific and Technical Information (OSTI), 2002. http://dx.doi.org/10.2172/797427.

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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
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