Relevant bibliographies by topics / Weakly Bound Molecules/Complexes - Computational Study

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Academic literature on the topic 'Weakly Bound Molecules/Complexes - Computational Study'

Author: Grafiati
Published: 7 September 2023

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Journal articles on the topic "Weakly Bound Molecules/Complexes - Computational Study"

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Garcia Guerrero, Estefania, Jose Antonio Pérez Simon, Luis Ignacio Sánchez Abarca, Irene Diaz Moreno, Miguel Angel De la rosa, and Antonio Diaz Quintana. "Molecular Dynamics As a Computational Tool to Study the Immune Reactivity: Identification of Conformational Changes in the Major Histocompatibility Complex." Blood 124, no. 21 (December 6, 2014): 2735. http://dx.doi.org/10.1182/blood.v124.21.2735.2735.

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Abstract Introduction: The generation of the immune response requires the recognition of peptides presented by the major histocompatibility complex (MHC) through the T cell receptor (TCR). In the hematopoietic transplantation context, T cells (LT) from the donor recognize foreign MHC or own MHC bound to foreign peptides (pMHC), generating an alloimmune response. Currently, the molecular mechanisms of LT alloimmune activation are unknown. In order to analyze the molecular interactions between peptides, MHC and TCR, we have implemented Molecular Dynamics techniques. We have compared immunologically reactive complexes (HLA-A2/TAX/TCR-A6) to non/weakly reactive complexes (HLA-A2/V7R/TCR-A6; HLA-A2/P6A/TCR-A6; HLA-A2/Y8A/TCR-A6). Methods: Starting structure of a reactive complex was downloaded from the PDB database and used to model mutations known to lead to different degrees of immune reactivity. Dynamics simulations were performed and analyzed using the program AMBER version 9. The simulation time was approximately 10 ns. Further analysis was carried out using the script ARO (Díaz-Moreno et al. 2009) in the VMD Tk console. Results: A total of 10 MD trajectories have been reckoned, to simulate the behavior of isolated components of the different pMHC-TCR complexes. Analysis of the fluctuations show that pMHC binding barely restrains TCR motions, affecting mostly to CDR3 loops. Opposite, pMHC displayed substantial changes in its dynamics upon comparing its free versus ternary form (pMHC-TCR). Moreover, we studied the salt-bridges formed between peptide and MHC and we observed a significant loss of salt-bridges in non reactive complexes as compared to reactive ones. Furthermore, the loss of salt-bridges in non reactive complexes affects the electrostatic potential of pMHC complex. According to these results, we next studied the salt-bridges formed between pMHC and TCR. As observed within the binary complex p-MHC, we confirmed a significant loss of salt-bridges in non reactive as compared to reactive complex. Finally, we also analyzed the electrostatic potential of pMHC-TCR complexes and we observed differences between reactive complex and weakly/non reactive complexes. Conclusions: The MHC shows strong changes in its molecular dynamics upon binding to TCR, decreasing its mobility. The “pattern” of salt-bridges between the peptides and the MHC varies depending on the reactivity of the complex, with a loss of salt-bridges in the non-reactive as compared to the reactive ones, which results in change in the electrostatic pattern. In addition, also the number of salt-bridges between pMHC and TCR increases in reactive complexes as compared to non-reactive ones. Disclosures No relevant conflicts of interest to declare.
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Grabowsky, Simon, Allan H. White, Peter C. Healy, Kim M. Lapere, Seik Weng Ng, Brian W. Skelton, Duncan A. Wild, Graham A. Bowmaker, and John V. Hanna. "Solid-State NMR, X-Ray Diffraction, and Theoretical Studies of Neutral Mononuclear Molecular Bis(triphenylphosphine)silver(I) Mono-Carboxylate and -Nitrate Systems." Australian Journal of Chemistry 73, no. 6 (2020): 556. http://dx.doi.org/10.1071/ch19616.

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Neutral mononuclear molecular silver(i) carboxylate complexes of the form [(Ph3P)2Ag(O2XY)] with O2XY=O2CCH2Ph, O2CCHPh2, O2CC(CH3)3, O2CCH2C(CH3)3, and O2CCF3 (compounds 1–4 and 5β) have been investigated in the solid state using single-crystal X-ray structure determinations, 1D 31P CPMAS NMR and 2D 31P–31P CPCOSY NMR measurements, and ab initio computational modelling. The results show that these complexes contain P2AgO2 molecular cores with four-coordinate silver in which the carboxylate ligands are weakly bound to the silver atoms via the two oxygen atoms giving rise to unsymmetrical chelate units. Crystal structure determinations and solid-state NMR spectra have also been analysed for the mononuclear molecular silver(i) nitrate complex [(Ph3P)2Ag(O2NO)] (9α) and two polymorphs of its toluene monosolvate (11α, β). In 9α, the two PPh3 ligands are of the same chirality, whereas in 11α, β, they are opposed. The crystalline environments in the polymorphs have been explored by way of Hirshfeld surface analyses, after quantum-mechanical isolated-molecule calculations had shown that although the molecular energies of the experimental geometries of 9α, and 11α, β are significantly different from each other and from the energies of the optimized geometries, the latter, in contrast, do not differ significantly from each other despite the conformational isomerism. It has further been shown using 9α as an example that the energy dependence on variation of the P–Ag–P angle over a range of ~15° is only ~5 kJ mol−1. All this indicates that the forces arising from crystal packing result in significant perturbations in the experimental geometries, but do not alter the stereoisomerism caused by the donor atom array around the Ag atom. In the NMR study, a strong inverse correlation has been found between 1J(107/109Ag,31P) and the Ag–P bond length across all carboxylate and nitrate compounds.
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Krupa, Justyna, Maria Wierzejewska, and Jan Lundell. "Matrix Isolation FTIR and Theoretical Study of Weakly Bound Complexes of Isocyanic Acid with Nitrogen." Molecules 27, no. 2 (January 13, 2022): 495. http://dx.doi.org/10.3390/molecules27020495.

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Weak complexes of isocyanic acid (HNCO) with nitrogen were studied computationally employing MP2, B2PLYPD3 and B3LYPD3 methods and experimentally by FTIR matrix isolation technique. The results show that HNCO interacts specifically with N2. For the 1:1 stoichiometry, three stable minima were located on the potential energy surface. The most stable of them involves a weak, almost linear hydrogen bond from the NH group of the acid molecule to nitrogen molecule lone pair. Two other structures are bound by van der Waals interactions of N⋯N and C⋯N types. The 1:2 and 2:1 HNCO complexes with nitrogen were computationally tracked as well. Similar types of interactions as in the 1:1 complexes were found in the case of the higher stoichiometry complexes. Analysis of the HNCO/N2/Ar spectra after deposition indicates that the 1:1 hydrogen-bonded complex is prevalent in argon matrices with a small amount of the van der Waals structures also present. Upon annealing, complexes of the 1:2 and 2:1 stoichiometry were detected as well.
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Keefe, C. Dale, and Zuzana Istvankova. "Computational study of proper and improper hydrogen bonding in methanol complexes." Canadian Journal of Chemistry 89, no. 1 (January 2011): 34–46. http://dx.doi.org/10.1139/v10-155.

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The bulk properties of alcohols, like those of aqueous solutions, are governed mostly by hydrogen bonding; however, in contrast with water molecules, the chemical structure of a simple alcohol such as methanol offers an opportunity to explore the effects of both proper and improper hydrogen bonding on a single hydrogen donor. The presence of the hydroxyl group generally gives rise to a strong proper hydrogen bond, while the methyl group of methanol is likely involved in the weaker improper hydrogen bond, among other weak non-covalent interactions. The effects of the two types of hydrogen bonds on the stability, geometric parameters, and properties of electron density of methanol complexes are examined while considering different geometrical arrangements of the methanol dimer and the binary complexes of methanol with water, acetonitrile, and chloromethane. Subsequently, potential conclusions about the nature of improper hydrogen bonding and the origin of the C–H bond contraction that results upon complex formation are discussed. Quantum theory of atoms in molecules and natural bond orbital methods were used in the analysis; all calculations were performed at the MP2(full)/6-311++G(d,p) level of theory.
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Jimenez-Fabian, Issac, Abraham Jalbout, and Abderahim Boutalib. "Conformational study on the structures and energies of the weakly bound complexes of AlCl3 with diatomic molecules." Open Chemistry 5, no. 4 (December 1, 2007): 1007–18. http://dx.doi.org/10.2478/s11532-007-0046-4.

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AbstractIn this work we present the results of high level ab initio calculations on weakly bound complexes of aluminium trichloride and hydrogen halides, HX, halogens, X2 and diatomic interhalogens, XY (where X, Y = F, Cl, Br). Based upon these calculations we have predicted that all structures in the staggered conformation (except for Cl3AlFH and Cl3AlClH) are stable minima while those in the eclipsed configurations are transition state structures. In the XH complexes the strength of interaction with the Cl3Al group is FH > ClH > BrH. In the case of X2 species it is Br2 > F2 > Cl2, and finally in the XY (YX) group it is: FBr > ClBr > FCl > BrCl > BrF > ClF.
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Jimenez-Fabian, Isaac, Abraham Jalbout, and Abderahim Boutalib. "Conformational study on the structures and energies of the weakly bound complexes of AlCl3 with diatomic molecules." Open Chemistry 6, no. 1 (March 1, 2008): 133. http://dx.doi.org/10.2478/s11532-007-0057-1.

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Ritschel, Thomas, Lutz Zülicke, and Philip J. Kuntz. "Cationic Van-der-Waals Complexes: Theoretical Study of Ar2H+ Structure and Stability." Zeitschrift für Physikalische Chemie 218, no. 4 (April 1, 2004): 377–90. http://dx.doi.org/10.1524/zpch.218.4.377.29196.

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AbstractThe electronic and geometric structure, stability and molecular properties of the cationic van-der-Waals complex Ar2H+ in its ground electronic state are studied by means of two ab-initio quantum-chemical approaches: conventional configuration interaction (multi-reference and coupled-cluster methods) and a diatomics-in-molecules model with ab-initio input data. To ensure consistency between the two approaches, one and the same one-electron atomic basis set (aug-cc-pVTZ by Dunning) is employed in both. The topography of the ground-state potential-energy surface is examined with respect to the nature of the binding and the stability of structures corresponding to stationary points. In accordance with most earlier theoretical work, there are two local minima at linear arrangements: a strongly bound centro-symmetric moiety, (Ar–H–Ar)+, and a weakly bound van-der-Waals complex, Ar···ArH+. These are separated by a low barrier. Only the centro-symmetric molecule is significantly stable (De = 0.68eV) against fragmentation into Ar + ArH+ and should have structural and dynamical relevance. A fairly simple diatomics-in-molecules model taking into account only the few lowest electronic fragment states yields a qualitatively correct description of the ground state but shows quantitative deviations from the more accurate configuration-interaction data in detail. Nevertheless, it should provide a good starting point for the treatment of larger complexes ArnH+ with n > 2.
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Kraevsky, Sergey V., Nikolay A. Barinov, Olga V. Morozova, Vladimir V. Palyulin, Alena V. Kremleva, and Dmitry V. Klinov. "Features of DNA–Montmorillonite Binding Visualized by Atomic Force Microscopy." International Journal of Molecular Sciences 24, no. 12 (June 6, 2023): 9827. http://dx.doi.org/10.3390/ijms24129827.

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In the present work, complexes of DNA with nano-clay montmorillonite (Mt) were investigated by means of atomic force microscopy (AFM) under various conditions. In contrast to the integral methods of analysis of the sorption of DNA on clay, AFM allowed us to study this process at the molecular level in detail. DNA molecules in the deionized water were shown to form a 2D fiber network weakly bound to both Mt and mica. The binding sites are mostly along Mt edges. The addition of Mg2+ cations led to the separation of DNA fibers into separate molecules, which bound mainly to the edge joints of the Mt particles according to our reactivity estimations. After the incubation of DNA with Mg2+, the DNA fibers were capable of wrapping around the Mt particles and were weakly bound to the Mt edge surfaces. The reversible sorption of nucleic acids onto the Mt surface allows it to be used for both RNA and DNA isolation for further reverse transcription and polymerase chain reaction (PCR). Our results show that the strongest binding sites for DNA are the edge joints of Mt particles.
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Martinez, Arturo I. "Computational Study of Organometallic Structures for Hydrogen Storage, Effects of Ligands." Journal of Nano Research 5 (February 2009): 113–19. http://dx.doi.org/10.4028/www.scientific.net/jnanor.5.113.

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Density functional theory calculations of hydrogen storage capacity for different organometallic structures have been carried out. Complexes involving Sc, Ti and V bound to C4H4, C5H5, C5F5 and B3N3H6 molecules have been considered, and all present a hydrogen storage capability limited by the 18-electron rule. In order to stabilize the complexes, which the 18-electron rule is not completed, additional ligands are considered, namely -H, -CH3, -NH2, -OH and -F. These ligands affect the H2-metal bond; particularly the back donation effect from the metal atom to the * antibonding state of H2 and then its H2 storage capacity.
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Voute, Alexandre, Fabien Gatti, Klaus B. Møller, and Niels E. Henriksen. "Femtochemistry of bimolecular reactions from weakly bound complexes: computational study of the H + H′OD → H′OH + D or HOD + H′ exchange reactions." Physical Chemistry Chemical Physics 23, no. 48 (2021): 27207–26. http://dx.doi.org/10.1039/d1cp04391a.

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The femtochemistry of the reaction between H and HOD, initiated by the photodissociation of HCl in the weakly bound complex (HCl)⋯(HOD), is explored in this computational work. Despite non-reactive scattering is the most probable outcome, H-to-H and H-to-D exchange products can be observed in different proportions whereas no products of the abstraction reaction channel are detectable.
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Book chapters on the topic "Weakly Bound Molecules/Complexes - Computational Study"

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Wittig, Curt, and Ahmed H. Zewail. "Dynamics of Ground State Bimolecular Reactions." In Chemical Reactions in Clusters. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195090048.003.0006.

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During the past decade, the study of photoinitiated reactive and inelastic processes within weakly bound gaseous complexes has evolved into an active area of research in the field of chemical physics. Such specialized microscopic environments offer a number of unique opportunities which enable scientists to examine regiospecific interactions at a level of detail and precision that invites rigorous comparisons between experiment and theory. Specifically, many issues that lie at the heart of physical chemistry, such as reaction probabilities, chemical branching ratios, rates and dynamics of elementary chemical processes, curve crossings, caging, recombination, vibrational redistribution and predissociation, etc., can be studied at the state-to-state level and in real time. Inevitably, understanding the photophysics and photochemistry of weakly bound complexes lends insight into corresponding processes in less rarefied surroundings, for example, molecules physisorbed on crystalline insulator and metal surfaces, molecules residing on the surfaces of various ices, and molecules weakly solvated in liquids. However, such ties to the real world are not the main driving force behind studies of photoinitiated reactions in complexed gaseous media. Rather, it is the lure of going a step beyond the more common molecular environments. Theoretical modeling, which in many areas purports to challenge experiment, must rise to the occasion here if it is to offer predictive capability for even the simplest of such microcosms. Subtleties abound. Roughly speaking, two disparate regimes can be identified which are accessible experimentally and which correspond to qualitatively different kinds of chemical transformations. These are distinguished by their reactants: electronically excited versus ground state. For example, it is possible to study the chemical selectivity that derives from the alignment and orientation of excited electronic orbitals, albeit at restricted sets of nuclear coordinates. This is achieved by electronically exciting a complexed moiety, such as a metal atom, which then undergoes chemical transformations that depend on the geometric properties of the electronic orbitals such as their alignments and orientations relative to the other moiety (or moieties) in the complex.
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Conference papers on the topic "Weakly Bound Molecules/Complexes - Computational Study"

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Hockey, Emily, Leah Dodson, Jessica Palko, Thomas Howard, and Korina Vlahos. "WEAKLY-BOUND COMPLEX FORMATION BETWEEN HCN AND CH3Cl: A MATRIX-ISOLATION AND COMPUTATIONAL STUDY." In 2022 International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2022. http://dx.doi.org/10.15278/isms.2022.tg04.

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Zinn, Sabrina, Melanie Schnell, Chris Medcraft, and Thomas Betz. "BROADBAND MICROWAVE SPECTROSCOPY AS A TOOL TO STUDY THE STRUCTURES OF ODORANT MOLECULES AND WEAKLY BOUND COMPLEXES IN THE GAS PHASE." In 70th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2015. http://dx.doi.org/10.15278/isms.2015.mg11.

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