On the role of lysine in the active site Ser-X-X-Lys region of penicillin-recognizing enzymes

2010 ◽  
Vol 88 (1) ◽  
pp. 1-4
Author(s):  
Saul Wolfe ◽  
Kiyull Yang
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Basis Set ◽  
Penicillin G ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
One Step ◽  
Optimized Geometries

Using Autodock, docking of penicillin G to the crystal structures of penicillin-recognizing enzymes leads to an alignment in the active site Ser-X-X-Lys region consisting of the serine hydroxyl group, the terminal amino group of lysine, a second hydroxyl group, and the N–C=O of the β-lactam. This alignment is consistent with the notion that acylation of the serine hydroxyl group proceeds by a one-step cooperative mechanism in which C–O bond formation and proton transfer to the β-lactam nitrogen take place through a heteroatom bridge. For the cooperative ring opening of penam by two molecules of methanol and one molecule of methylamine or one molecule of water, density functional theory with the B3LYP DFT gradient-corrected functional and the 6–31G(d) basis set reproduces the alignment seen in the docked structures. Methylamine lowers the barrier calculated at MP2/6–31G(d) from the DFT-optimized geometries by 3 kcal/mol; water increases the barrier by 4 kcal/mol. The function of the conserved lysine in the active sites of penicillin-recognizing enzymes is therefore to catalyze the formation of an acyl enzyme by a cooperative mechanism.

scholarly journals Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

scholarly journals Stability and magnetic properties of isomorphous substituted Si7-xMnx+

2018 ◽  
Vol 56 (1) ◽  
pp. 64
Author(s):  
Nguyen Thanh Tung ◽  
Nguyen Thi Mai ◽  
Ngo Tuan Cuong
Keyword(s):  
Density Functional Theory ◽  
Magnetic Properties ◽  
Magnetic Moment ◽  
Density Functional ◽  
Basis Set ◽  
Pentagonal Bipyramid ◽  
Functional Theory ◽  
Electronic Configurations ◽  
Method Of Density Functional ◽  
Optimized Geometries

The optimized geometries, stability, and magnetic properties of cationic clusters Si7+, Si6Mn+, and Si5Mn2+ have been determined by the method of density functional theory using the B3P86/6-311+G(d) functional/basis set. Their electronic configurations have been analyzed to understand the influence of substituting Si atoms by Mn atoms on the structural and magnetic aspects of Si7+. It is shown that the manganese dopant does not alter the structure of the silicon host but significantly changes its stability and magnetism. In particular, while the magnetic moment of Si7+ is 1 mB, Si5Mn2+ exhibits a strong magnetic moment of 9 mB and that of Si6Mn+ takes a relatively high value of 4 mB. Among studied clusters, the pentagonal bipyramid Si5Mn2+ is assigned as the most stable one.

A Density Functional Theory Study of the Isomerization of Substituted 2and#39;-hydroxychalcones to the Corresponding Flavanones

2021 ◽  
Vol 43 (1) ◽  
pp. 25-25
Author(s):  
Said Abdelqadar Said Said Abdelqadar Said ◽  
Omar A Shareef and Abdulkhalik S Alkazzaz Omar A Shareef and Abdulkhalik S Alkazzaz
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Ring Closure ◽  
Basis Set ◽  
Functional Theory ◽  
Rate Determining Step ◽  
The Density Functional Theory ◽  
Electronic And Structural Properties ◽  
Maximum Hardness Principle

The transformation of 2and#39;-hydroxychalcones to their corresponding flavanones was studied theoretically by the use of the density functional theory (DFT) with B3-LYP/ 6-311G basis set to get important information about the role of both of electronic and structural properties in this process. The obtained energies were found to be in agreement with our previous results that obtained from HPLC studies. The estimated hardness, polarizability, and electrophilicity profiles were found to obey the maximum hardness principle (MHP), minimum polarizability principle (MPP), and the minimum electrophilicity principle (MEP) respectively. Flavanone ring closure was found to be the rate-determining step.

scholarly journals Molecular Geometry, NLO, MEP, HOMO-LUMO and Mulliken Charges of Substituted Piperidine Phenyl Hydrazines by Using Density Functional Theory

2019 ◽  
Vol 32 (2) ◽  
pp. 401-407
Author(s):  
M. Dinesh Kumar ◽  
P. Rajesh ◽  
R. Priya Dharsini ◽  
M. Ezhil Inban
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Molecular Geometry ◽  
Basis Set ◽  
Functional Theory ◽  
B3lyp Method ◽  
Reactivity Descriptor ◽  
Homo Lumo ◽  
Optimized Geometries

The quantum chemical calculations of organic compounds viz. (E)-1-(2,6-bis(4-chlorophenyl)-3-ethylpiperidine-4-ylidene)-2-phenyl-hydrazine (3ECl), (E)-1-(2,6-bis(4-chlorophenyl)-3-methylpiperidine-4-ylidene)-2-phenylhydrazine (3MCl) and (E)-1-(2,6-bis(4-chloro-phenyl)-3,5-dimethylpiperidine-4-ylidene)-2-phenylhydrazine (3,5-DMCl) have been performed by density functional theory (DFT) using B3LYP method with 6-311G (d,p) basis set. The electronic properties such as Frontier orbital and band gap energies have been calculated using DFT. Global reactivity descriptor has been computed to predict chemical stability and reactivity of the molecule. The chemical reactivity sites of compounds were predicted by mapping molecular electrostatic potential (MEP) surface over optimized geometries and comparing these with MEP map generated over crystal structures. The charge distribution of molecules predict by using Mulliken atomic charges. The non-linear optical property was predicted and interpreted the dipole moment (μ), polarizability (α) and hyperpolarizability (β) by using density functional theory.

scholarly journals [3 + 2] versus [2 + 2] Addition: A Density Functional Theory Study on the Mechanistic Aspects of Transition Metal-Assisted Formation of 1,2-Dinitrosoalkanes

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Ernest Opoku ◽  
Richard Tia ◽  
Evans Adei
Keyword(s):  
Transition Metal ◽  
Density Functional ◽  
Basis Set ◽  
Functional Theory ◽  
Activation Barriers ◽  
One Step ◽  
The One ◽  
Electron Donating Groups ◽  
Very High ◽  
Addition Pathway

The pathways for the transition metal-assisted formation of 1,2-dinitrosoalkane complexes of cobalt and its congeners, have been studied using DFT/M06 with theLACVP*basis set. The activation barriers for the one-step [3 + 2] addition pathway for the formation of 1,2-dinitrosoalkanes, proposed by Bergman and Becker, are generally low compared to the activation barriers for the [2 + 2] addition to form an intermediate, which is the first of the two-step pathway proposed by Rappé and Upton, which are very high. The barriers of the rearrangement of the Rappé intermediates to the final products by reductive elimination involving the second metal-nitrogenπ-bond are also very high. The reactions of the Co complexes have lower activation barriers than Rh and Ir complexes. The barriers of the reactions involving olefins with electron-donating groups are generally lower compared to the reactions of the parent (unsubstituted) ethylene while the activation barriers for reactions of olefins with electron-withdrawing groups are generally higher compared to the parent (unsubstituted) ethylene. The one-step [3 + 2] pathway remains the most favoured irrespective of the metal centre or the nature of the olefin. The mechanism of the reaction is therefore settled in favour of the [3 + 2] addition pathway.

Resonance Raman and absorption infrared with density functional theory studies of Fe(III)/Fe(II) and Ni(II) complexes of modified 21-oxaporphyrins

2013 ◽  
Vol 17 (04) ◽  
pp. 289-308 ◽  
Author(s):  
Mateusz Fościak ◽  
Edyta Proniewicz ◽  
Krzysztof Zborowski ◽  
Younkyoo Kim ◽  
Leonard M. Proniewicz
Keyword(s):  
Density Functional ◽  
Theoretical Calculations ◽  
Resonance Raman ◽  
Vibrational Analysis ◽  
Basis Set ◽  
Functional Theory ◽  
B3lyp Level ◽  
Ft Ir ◽  
Optimized Geometries ◽  
Good Agreement

This work presents a complete vibrational analysis of iron [ Fe (II) and Fe (III)] and nickel [ Ni (II)] complexes with 5,10,15,20-tetraphenyl-21-oxaporphyrin [OTPPH] and 5,20-bis(p-tolyl)-10,15-diphenyl-21-oxaporphyrin [ODTDPPH]. In these porphyrins, a furan ring replaces one of the pyrrole rings. The six-coordinate (OTPP) FeIIICl2 and (ODTDPP) FeIIICl2 as well as the five-coordinate (OTPP) FeIICl and (OTPP) NiIICl complexes were investigated using experimental and theoretical methods. The experimental part of this work involved Fourier-transform absorption infrared (FT-IR), resonance Raman (RR), and electron absorption (UV-vis) measurements for all of the investigated complexes. In the theoretical section, optimized geometries and vibrational frequencies for model compounds are provided. The theoretical calculations were performed at the B3LYP level with the LANL2DZ basis set. Good agreement was achieved between the experimental and theoretical vibrational spectra. In addition, charge distributions (GAPT) and geometrical aromaticity indices (Bird's I5 and HOMA) were calculated and discussed.

scholarly journals Dynamics and fragmentation mechanism of (C5H4CH3)Pt(CH3)3 on SiO2 surfaces

2018 ◽  
Vol 9 ◽  
pp. 711-720 ◽  
Author(s):  
Kaliappan Muthukumar ◽  
Harald O Jeschke ◽  
Roser Valentí
Keyword(s):  
Electron Beam ◽  
Active Sites ◽  
Density Functional ◽  
Fragmentation Mechanism ◽  
Functional Theory ◽  
Before And After ◽  
Surface Active ◽  
Dynamics Simulations ◽  
Precursor Molecules

The interaction of trimethyl(methylcyclopentadienyl)platinum(IV) ((C5H4CH3)Pt(CH3)3) molecules on fully and partially hydroxylated SiO2 surfaces, as well as the dynamics of this interaction were investigated using density functional theory (DFT) and finite temperature DFT-based molecular dynamics simulations. Fully and partially hydroxylated surfaces represent substrates before and after electron beam treatment and this study examines the role of electron beam pretreatment on the substrates in the initial stages of precursor dissociation and formation of Pt deposits. Our simulations show that on fully hydroxylated surfaces or untreated surfaces, the precursor molecules remain inactivated while we observe fragmentation of (C5H4CH3)Pt(CH3)3 on partially hydroxylated surfaces. The behavior of precursor molecules on the partially hydroxylated surfaces has been found to depend on the initial orientation of the molecule and the distribution of surface active sites. Based on the observations from the simulations and available experiments, we discuss possible dissociation channels of the precursor.

scholarly journals The Role of the Active Site Tyrosine in the Mechanism of Lytic Polysaccharide Monooxygenase

2020 ◽  
Author(s):  
Aina McEvoy ◽  
Joel Creutzberg ◽  
Raushan Kumar Singh ◽  
Morten J. Bjerrum ◽  
Erik Hedegård
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Renewable Resource ◽  
Lytic Polysaccharide Monooxygenase ◽  
Functional Theory ◽  
Polysaccharide Monooxygenases ◽  
Active Site Tyrosine ◽  
The Difference ◽  
First Time

Natural polysaccharides (such as cellulose) comprise a large bio-renewable resource. However, exploitation of this resource requires energy-efficient polysaccharide degradation, which is currently limited by the inherent recalcitrance of many naturally occurring polysaccharides. Catalytic breakdown of polysaccharides can be achieved more efficiently by means of the enzymes lytic polysaccharide monooxygenases (LPMOs). However, the LPMO mechanism has remained controversial, preventing full exploitation of their potential. One of the controversies has centered around an active site tyrosine, present in most LPMOs. Different roles for this tyrosine have been proposed without direct evidence, but two recent investigations have for the first time obtained direct (spectroscopic) evidence for that chemical modification of this tyrosine is possible. Surprisingly, the spectroscopic features obtained in the two investigations are remarkably different. In this paper we use density functional theory (DFT) in a QM/MM formulation to reconcile these (apparently) conflicting results. By modeling the spectroscopy as well as the underlying reaction mechanism we can show how formation of two isomers (both involving deprotonation of tyrosine) explain the difference in the experimental observed spectroscopic features. The link between our structures and the observed spectroscopy provides a firm ground to investigate the role of tyrosine.

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