Academic literature on the topic 'Hybrid QM / MM methodologies'
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Journal articles on the topic "Hybrid QM / MM methodologies"
Illingworth, Christopher J. R., Stuart R. Gooding, Peter J. Winn, Garth A. Jones, György G. Ferenczy, and Christopher A. Reynolds. "Classical Polarization in Hybrid QM/MM Methods." Journal of Physical Chemistry A 110, no. 20 (May 2006): 6487–97. http://dx.doi.org/10.1021/jp046944i.
Full textPan, Xiaoliang, Edina Rosta, and Yihan Shao. "Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations." Molecules 23, no. 10 (September 29, 2018): 2500. http://dx.doi.org/10.3390/molecules23102500.
Full textApostolov, Rossen, Y. Yonezawa, and H. Nakamura. "Aquaporin1 channel proteins : Hybrid-QM/MM Computer Simulation." Seibutsu Butsuri 43, supplement (2003): S185. http://dx.doi.org/10.2142/biophys.43.s185_2.
Full textTchougréeff, Andrei L., and Andrei M. Tokmachev. "Physical Principles of Constructing Hybrid QM/MM Methods." Journal of Computational Methods in Sciences and Engineering 2, no. 3-4 (August 1, 2002): 309–14. http://dx.doi.org/10.3233/jcm-2002-23-403.
Full textHillier, Ian H. "Chemical reactivity studied by hybrid QM/MM methods." Journal of Molecular Structure: THEOCHEM 463, no. 1-2 (April 1999): 45–52. http://dx.doi.org/10.1016/s0166-1280(98)00391-1.
Full textWang, Yingjie, and Jiali Gao. "Projected Hybrid Orbitals: A General QM/MM Method." Journal of Physical Chemistry B 119, no. 3 (October 15, 2014): 1213–24. http://dx.doi.org/10.1021/jp507983u.
Full textLiang, Dongyue, Jiewei Hong, Dong Fang, Joseph W. Bennett, Sara E. Mason, Robert J. Hamers, and Qiang Cui. "Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations." Physical Chemistry Chemical Physics 20, no. 5 (2018): 3349–62. http://dx.doi.org/10.1039/c7cp06709g.
Full textHORI, TAKUMI, HIDEAKI TAKAHASHI, and TOMOSHIGE NITTA. "HYBRID QUANTUM MECHANICAL/MOLECULAR MECHANICAL APPROACH TO ENZYMATIC REACTIONS BY UTILIZING THE REAL-SPACE GRID TECHNIQUE." Journal of Theoretical and Computational Chemistry 04, no. 03 (September 2005): 867–82. http://dx.doi.org/10.1142/s0219633605001799.
Full textNakata, K., Y. Yonezawa, H. Nakamura, and T. Takada. "2P098 Development of the Method of Hybrid QM/MM Simulation including chemical bond on QM/MM boundary." Seibutsu Butsuri 45, supplement (2005): S144. http://dx.doi.org/10.2142/biophys.45.s144_2.
Full textHagiwara, Yohsuke, Takehiro Ohta, and Masaru Tateno. "QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines." Journal of Physics: Condensed Matter 21, no. 6 (January 20, 2009): 064234. http://dx.doi.org/10.1088/0953-8984/21/6/064234.
Full textDissertations / Theses on the topic "Hybrid QM / MM methodologies"
Sauer, Susanne [Verfasser], and Bernd [Gutachter] Engels. "Implementation and Application of QM/MM Hybrid Methods / Susanne Sauer ; Gutachter: Bernd Engels." Würzburg : Universität Würzburg, 2021. http://d-nb.info/1240614764/34.
Full textWebb, Benjamin M. "Development of polarizable force fields and hybrid QM/MM methods for the study of reaction mechanisms." Thesis, University of Oxford, 2003. http://ora.ox.ac.uk/objects/uuid:5bf68dc6-0d39-464e-b145-16e255b043c4.
Full textWhite, Justin K. "Investigations into the Non-Mevalonate Isoprenoid Biosynthesis Pathway's First Two Enzymes utilizing Hybrid QM/MM Techniques." Thesis, University of South Florida, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10680472.
Full textMolecular drug design begins with the identification of a problem to solve. This work identifies the growing resistance among human pathogens to current treatments. Once the problem is identified and understood, solutions must be proposed. This one is straight forward, we need new antimicrobial drugs. More specifically, we need to identify novel targets to inhibit. A large portion of antibiotics focus on disruption of macromolecular production while only a few target metabolic systems. Finally, you need to propose solutions based on the information gathered. In order to avoid existing resistance, it is important to avoid the macromolecular route and focus on metabolic enzymes. Preferably, the pathway would have little overlap or similarity with pathways found in the treatment organism. With this in mind, the non-mevalonate (NMA) pathway poses as a very good target for drug design. Many pathogens have been found to be strictly dependent on this pathway while it is absent in humans. Additionally, fosmidomycin has already been shown to inhibit this pathway. Initially thought to just inhibit the 1-deoxy-D-xylulose 5-phosphate (DXP) reductoisomerase (DXR), it has been shown to inhibit several enzymes along the path to a lesser extent. Ideally, this could be repeated or improve upon for future drug design.
With this in mind, the initial stages of the first two enzymes of the NMA pathway were examined utilizing quantum mechanical/molecular mechanical (QM/MM) techniques. The first enzyme was DXP synthase (DXS), which catalyzes a transketolase-like condensation of pyruvate and glyceraldehyde-3-phosphate to produce DXP. DXS and other transketolases are dependent on the thiamine diphosphate (TDP) cofactor, which must be deprotonated of the imidazolium C2 atom producing a highly reactive ylide. A tautomerization occurs prior to this deprotonation to prime the pyrimidinium ring N4 atom to perform the C2 abstraction. The question at hand was the identity of a general base to perform the N4 abstraction. The results favored a water-mediate mechanism with a higher than usual ΔEz of 22.7 kcal/mol. An observation pertaining the tautomerization pertained to the aromaticity of the pyrimidine ring. Upon further investigation, aromaticity was found to play a significant role in the ΔE observed. Aromaticity might contribute 14.2 kcal/mol to the barrier height. This high energy would drive the reaction forward producing the ylide.
Investigation of the DXR enzyme followed this work. Initially, the work was going to focus on the 2 mechanisms proposed for activity, alpha-ketol rearrangement and retroaldol/ aldol mechanism. Subsequent publications involving secondary kinetic isotope effects (KIEs) add to the pile of evidence supporting the retro-aldol/aldol mechanism. So the project was retooled to investigate the energetic differences between two metal binding modes. The results of this work support a metal coordination across the C3-C4 bond, which eventually extends coordination to include the C2 oxygen. This conformation was help explain the tight binding effecting observation of the putative intermediates (transition states) and aldehyde intermediate. Additionally, as the C2-C3 mode consistently transfers a proton to the phosphate group of DXP or produces an elongated C-O bond, the C2-C3 mode would not be favorable.
Further investigations of these enzymes (e.g. completing the step begin, continuing through the reaction) could provide further illumination into the mechanism of action and possibly reveal new avenues of drug design. Examining the enzymes downstream in the NMA pathway might provide details of interest. Of particular interest is the radical reaction proposed for HDR/IspH. The final step of the pathway produces IDP and DMADP in a 4:1 proportion, which corresponds to the general system requirements for production of the long chain, branched isoprenoids. It would be interesting to compute the mechanism to see if energetics could provide further insights. Additionally, normal mode analysis coupled with vibrational subsystem analysis could identify allosteric sites for feedback sensitivity.
White, Justin K. "Investigations into the Non-Mevalonate Isoprenoid Biosynthesis Pathway's First Two Enzymes utilizing Hybrid QM/MM Techniques." Scholar Commons, 2017. http://scholarcommons.usf.edu/etd/7107.
Full textPatel, Chandan. "Hybrid molecular simulations of oxidative complex lesions." Thesis, Lyon, École normale supérieure, 2013. http://www.theses.fr/2013ENSL0835.
Full textDNA is continuously exposed to a vast number of damaging events triggered by endogenous and exogenous agents. Numerous experimental studies have provided key information regarding structural properties of some of the DNA lesions and their repair. However, they lack in mechanistic or energetic information pertaining to their formation. Computational Biochemistry has emerged as a powerful tool to understand biochemical reactions and electronic properties of large systems.In this thesis we study the formation of inter- and intra-strand cross-links. These tandem lesions pose a potent threat to genome integrity, because of their high mutagenic frequency. First, we discuss the formation of complex defects which arise from the attack of a pyrimidine radical onto guanine. In comparison with the reactivity of isolated nucleobases, our hybrid Car-Parrinello Molecular Dynamics simulations reveal that the reactivity of hydrogen-abstracted thymine and cytosine is reversed within a B-helix environment. Further, our data also suggest a more severe distortion of the B-helix for G[8-5]C.Second, we rationalize the higher reactivity of cytosine vs. purines toward the multistep formation of inter-strand crosslinks with a C4' oxidized a basic site, which is in qualitative agreement with experiments on isolated nucleobases, using explicit solvent simulations combined to density functional theory
Woiterski, André. "Density functional and hybrid QM-MM calculations of Cu13-clusters with alkylthiolate ligands and their two-dimensional periodic arrangements." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=96891845X.
Full textCrous, Werner. "The evaluation of the ONIOM-EE method for the QM/MM hybrid modeling of HF, CO and CO/HF Clusters." Thesis, Stellenbosch : Stellenbosch University, 2006. http://hdl.handle.net/10019.1/21774.
Full textENGLISH ABSTRACT: Quantum mechanics is the method of choice when it comes to the accurate modeling of single molecules and clusters. The correlation energy is the single most important aspect when studying clusters computationally, and reproducing the correlation energy accurately poses a bigger challenge to the computational chemist than in the modeling of single molecules. Very high levels of theory and large basis sets need to be used. Nevertheless, since the calculation of large systems, such as crystals and biological systems, is generally beyond the capacity of quantum mechanics, molecular mechanics is generally used for these systems. Unfortunately due to its nature, molecular mechanics cannot model important quantum effects, but this problem can be solved by a hybrid system in which one part of the system is treated by quantum mechanics and the remaining part by molecular mechanics. In order to combine quantum mechanics with molecular mechanics one needs to optimize the parameters for the molecular mechanics part to allow it to function with the quantum mechanics. The research described in this work is based on the ONIOM-EE method, which is such a hybrid method. In this work we investigate the applicability of the ONIOM-EE method in modeling hydrogen fluoride, carbon monoxide and CO/HF clusters. Most of the clusters’ geometries in this work are not experimentally or computationally known. We therefore perform a computational analysis of all of the clusters by using various methods including Atoms in Molecules, Natural Bond Orbital analysis, Mulliken population analysis and the analysis of delocalized molecular orbitals to obtain information for the development of hybrid systems. During this process we look at different charge derivation schemes and at two different methods of optimizing force field parameters for these clusters. We develop a method to make force field optimization faster and better for specific hybrid systems. This method showed that in all cases the optimized parameters were an improvement on those of the Universal Force Field. We show the importance of an accurate description of the electrostatic interactions in HF, CO and CO/HF clusters and that this is the Achilles heel when attempting to optimize van der Waals parameters for force fields. We further show that atomic point charges are not a good approximation of a molecules’ charge density in hybrid methods. In addition, we make suggestions on how the present method for ONIOM-EE can be improved to make the modeling of van der Waals clusters feasible.
AFRIKAANSE OPSOMMING: Kwantum meganika is die metode van keuse wanneer enkele molekule en molekulêre sisteme op rekenaar gemodeleer moet word. Dit is egter bekend dat die modelering van molekulêre sisteme ’n groter uitdaging stel aan die molekulêre modeleerder, aangesien baie hoë vlakke van teorie en groot basisstelle gebruik moet word om die korrelasie-energie, rekenkundig te produseer. Die akkurate herprodusering van die korrelasie-energie is seker die heel belangrikste vereiste waaraan voldoen moet word as molekulêre sisteme d.m.v. ’n rekenaar gemodeleer word. Nietemin is dit onprakties om kwantum meganiese metodes te gebruik vir groot sisteme soos kristalle of biologiese molekule en juis om dié rede word molekulêre meganika meestal ingespan vir sulke gevalle. Molekulêre meganika is egter ondoeltreffend om belangrike kwantumeffekte te modeleer. Tog is daar ’n oplossing vir hierdie probleem in die vorm van ’n hibried sisteem waar een deel van die sisteem met kwantum meganika en die oorblywende deel van die sisteem met molekulêre meganika behandel word. Om dit moontlik te maak om molekulêre meganika met kwantum meganika te kombineer, moet parameters vir die molekulêre meganika deel geoptimiseer word sodat dit saam met die kwantum meganiese deel kan funksioneer. Die navorsing wat in hierdie studie beskryf word is gebaseer op so ’n hibriedmetode wat bekend staan as ONIOM-EE. In hierdie studie bestudeer ons die moontlikheid om ONIOM-EE te gebruik vir die modelering van molekulêre sisteme van waterstoffluoried, koolstofmonoksied en CO/HF sisteme. Die meeste van die sisteme, wat in hierdie studie behandel word, se strukture is onbekend, beide in terme van eksperimentele gegewens en molekulêre modelering. Ons voer dus ’n volledige analise van al die sisteme uit deur van verskeie metodes soos “Atoms in Molecules”, “Natural Bond Orbital” analise, Mulliken populasie analise en die analise van gedelokaliseerde molekulêre orbitale, gebruik te maak. Dit stel ons in staat om ’n hibriedsisteem te ontwikkel vir die molekulêre sisteme. Gedurende die proses ondersoek ons ook die gebruik van verskillende ladingsafleidings-sisteme en twee metodes word ondersoek waarop ’n kragveld vir ’n hibriedsisteem geoptimiseer kan word. Ons toon aan dat die geoptimiseerde parameters beter resultate lewer as die van die “Universal Force Field” en lig ook die belangrikheid daarvan uit dat die elektrostatiese interaksies se beskrywing ’n hibriedsisteem se Achilles hiel is indien van der Waals parameters geoptimiseer moet word. Ons toon aan dat die gebruik van puntladings op atome om die ladingsdigtheid in molekulêre sisteme te beskryf, ’n onakkurate benadering is. Sekere aanbevelings hoe om die ONIOM-EE metode sodanig te verbeter, dat dit wel gebruik kan word om van der Waals sisteme suksesvol te modeleer, word ook gemaak.
Amaral, Marcos Serrou do. "Estudo teórico dos espectros de absorção e fluorescência do triptofano e análogos." Universidade de São Paulo, 2001. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-09122013-105102/.
Full textSemi-empirical and ab-initio calculations were performed on 5-hydroxytryptophan (5-OH-trp), 7-aza-tryptophan (7-aza-trp) and tryptophan (trp). The potential energy surface (PES) of the ground state (GS) and the lowest exited state (1ES) was determined as a function X IND. 1 e X IND. 2 angles corresponding to the dihedrals N-C IND.alfa-C IND.beta-C IND.gama e C IND.alfa-C IND.beta-C IND.gama- C IND.delta2, respectively. The compounds were studied in the zwitterionic, neutral and anionic states. The PES of the GS was obtained using the AM1 semi-empirical method and was used as a reference for the ab-initio calculations. The configuration interaction method with single excitations (CIS) was used for the calculations of the 1ES with frozen internal orbitals. After geometry optimization of GS, the transition energies to 1ES were obtained by INDO/S-CIS, giving the theoretical optical absorption spectrum. Similarly, following the geometry optimization of 1ES, the transition energies to GS were determined, giving the fluorescence emission spectrum. Experimental results were obtained for optical absorption and fluorescence spectra of 5-OH-trp and 7-aza-trp in phosphate buffer solution, pH 7.4. The fluorescence decay of the compounds was also examined. Decay profiles fitted to multiexponential function were analyzed in terms of Boltzmann relative populations in the GS and 1ES. The non-radioactive electron transfer rates in the excited state were obtained by computational implementation of the Marcus Theory with renormalized perturbation expansion method (RPE). In this study, optimizations of the transition states in the PES of the ground and lower excited states were performed by the Synchronous Transit-Guided Quasi-Newton method and the Berny algorithm modified. For further comparison with experimental conditions, molecular dynamic simulations for the zwitterionic 5-OH-trp were performed using the hybrid QM/MM method with explicit representation of the aqueous solvent. To start the simulations the results from ab-initio calculations were used. The conformations for the GS, the theoretical absorption spectrum and the solvation layers were compared to the experimental results
David, Rolf. "Chemins de protonation et réactivité des métalloenzymes : application à la superoxide réductase." Thesis, Université Grenoble Alpes (ComUE), 2017. http://www.theses.fr/2017GREAV087/document.
Full textObtaining targeted molecules under gentle, selective and sustainable conditions is still a major challenge. Artificial metalloenzymes are animportant line of enquiry, because by playing, for example, with the second sphere of coordination, it is possible to strongly modify thereactivity of these bio-inspired systems. The development of this chemistry presupposes a thorough knowledge of the different stages of themechanism of the reaction under study. For this reason, theoretical chemistry is essential to rationalize chemical reactivity, but it still suffersfrom many shortcomings for the systems we propose to study.In this work, we study the superoxide reductase, a detoxifying enzyme of the superoxide radical. While many experiments are available detailingsome intermediates, the precise mechanism is not well documented. The aim was to implement a complete methodology ranging from thedevelopment of specific MM parameters to the study of reactivity by QM/MM metadynamics.The development of MM parameters for the iron active site allowed its study by MM dynamics giving informations on the conformation ofthe peptide backbone as well as on the interaction with solvent molecules. Due to the nature of the iron, a QM description of the active sitewas required using hybrid DFT. QM/MM metadynamics have allowed us to explore reaction pathways and to characterize the compoundsformed to obtain the needed activation energies. This methodology made it possible to understand the native reactivity of the wild form ofthe SOR, but also to explore the new reactivity of the mutations of the SOR and thus to define the crucial role of the second coordination sphere
Renison, Carina Alicia. "The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics." Doctoral thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/23054.
Full textBooks on the topic "Hybrid QM / MM methodologies"
Harrison, Martin James. Modelling the enzyme papain: A hybrid QM/MM study. Manchester: University of Manchester, 1997.
Find full textBook chapters on the topic "Hybrid QM / MM methodologies"
Tchougréeff, A. L., and A. M. Tokmachev. "Physical Principles of Constructing Hybrid QM/MM Procedures." In Advanced Topics in Theoretical Chemical Physics, 207–45. Dordrecht: Springer Netherlands, 2003. http://dx.doi.org/10.1007/978-94-017-0635-3_7.
Full textBucher, Denis, Fanny Masson, J. Samuel Arey, and Ursula Röthlisberger. "Hybrid QM/MM Simulations of Enzyme-Catalyzed DNA Repair Reactions." In Quantum Biochemistry, 517–35. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2010. http://dx.doi.org/10.1002/9783527629213.ch17.
Full textYockel, Scott, and George C. Schatz. "Dynamic QM/MM: A Hybrid Approach to Simulating Gas-Liquid Interactions." In Multiscale Molecular Methods in Applied Chemistry, 43–67. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/128_2011_130.
Full textMonari, Antonio, and Xavier Assfeld. "Hybrid QM/MM Methods: Treating Electronic Phenomena in Very Large Molecular Systems." In Challenges and Advances in Computational Chemistry and Physics, 1–20. Dordrecht: Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-017-9257-8_1.
Full textLodola, Alessio, Donatella Callegari, Laura Scalvini, Silvia Rivara, and Marco Mor. "Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations." In Methods in Molecular Biology, 307–37. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0282-9_19.
Full textGeorg, H. C., T. S. Fernandes, S. Canuto, N. Takenaka, Y. Kitamura, and M. Nagaoka. "A Combination of the Sequential QM/MM and the Free Energy Gradient Methodologies with Applications." In Practical Aspects of Computational Chemistry III, 231–47. Boston, MA: Springer US, 2014. http://dx.doi.org/10.1007/978-1-4899-7445-7_8.
Full textVreven, Thom, and Keiji Morokuma. "Chapter 3 Hybrid Methods: ONIOM(QM:MM) and QM/MM." In Annual Reports in Computational Chemistry, 35–51. Elsevier, 2006. http://dx.doi.org/10.1016/s1574-1400(06)02003-2.
Full text"Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods: Challenges, Methods, and Recent Applications." In Molecular Modeling at the Atomic Scale, 54–103. CRC Press, 2014. http://dx.doi.org/10.1201/b17282-7.
Full textConference papers on the topic "Hybrid QM / MM methodologies"
Pereira, Washington A., Érica C. M. Nascimento, and João B. L. Martins. "Estudo QM/MM da proteína tirosina Bcr-Abl mutada T315I." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020148.
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