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001-es BibID:	BIBFORM031436
035-os BibID:	WOS:000298552800027
Első szerző:	Bernstein, Noam
Cím:	QM/MM simulation of liquid water with an adaptive quantum region / Noam Bernstein, Csilla Várnai, Iván Solt, Steven A. Winfield, Mike C. Payne, István Simon, Mónika Fuxreiter, Gábor Csányi
Dátum:	2012
ISSN:	1463-9076
Megjegyzések:	The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 angstrom) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	Physical chemistry chemical physics. - 14 : 2 (2012), p. 646-656. -
További szerzők:	Várnai Csilla Solt Iván Winfield, Steven Payne, Mike C. Simon István Fuxreiter Mónika (1969-) (kutató vegyész) Csányi Gábor
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001-es BibID:	BIBFORM069493
Első szerző:	Fekete Attila (vegyész)
Cím:	Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations : the proteolytic reaction of papain / Fekete Attila, Komáromi István
Dátum:	2016
ISSN:	1463-9076
Megjegyzések:	A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine N? atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the N?(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:	Physical Chemistry Chemical Physics. - 18 : 48 (2016), p. 32847-32861. -
További szerzők:	Komáromi István (1957-) (vegyész, molekuláris biológus, biokémikus)
Pályázati támogatás:	OTKA-106294 OTKA OTKA-105459 OTKA TAMOP-4.2.2.C-11/1/KONV-2012-0010.1. TÁMOP NIIF-1057 Egyéb NTP-EFÖ-P-15-0610-A Egyéb
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001-es BibID:	BIBFORM117812
035-os BibID:	(WoS)001137383100001 (Scopus)85181941112
Első szerző:	Shanmuga Sundar, Saravanabhavan
Cím:	In vitro study on the inflammatory response of chitosan nanoparticles as a potential siRNA carrier targeting towards osteosarcoma cells / Shanmuga Sundar S., Natarajan Kannan, Zsolt Sarang, Priya Lakshminarayanan Srimathi, Ayyar Manikandan, Anboo Sasikala, Nissapatorn Veeranoot, Jonna Narendranath, Vasanthapalaniappan Kamalakannan, Packirisamy Rajavelu, Dolma Karma Gyurmey
Dátum:	2024
ISSN:	0942-9352
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	Zeitschrift Fur Physikalische Chemie-International Journal Of Research In Physical Chemistry & Chemical Physics. - [Epub ahead of print] (2024). -
További szerzők:	Kannan, Natarajan Sarang Zsolt (1976-) (mikrobiológus) Lakshminarayanan, Srimathi Priya Manikandan, Ayyar Sasikala, Anboo Veeranoot, Nissapatorn Narendranath, Jonna Kamalakannan, Vasanthapalaniappan Rajavelu, Packirisamy Karma, Gyurmey Dolma
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