Calculation of Higher Protonation States and of a New Resting State for Vanadium Chloroperoxidase Using QM/MM, with an Atom-in-Molecules Analysis

10.26434/chemrxiv.7357244 ◽

2020 ◽

Author(s):

Gregory Anderson ◽

Raghu Nath Behera ◽

Ravi V. Gomatam

Keyword(s):

Hydrogen Bonding ◽

Electronic Structure ◽

Resting State ◽

Natural Bond Orbital ◽

Atoms In Molecules ◽

Aim Analysis ◽

Neutral Ph

ABSTRACT. <a></a><a></a><a>Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated states of the vanadate cofactor. Herein, we report a new extensive QM/MM study that includes the tri- and quadprotonated states of VCPO at neutral pH. We identify certain di- and triprotonated states as being candidates for the resting state based on a comparison of relative energies. The quadprotonated states as well as some of the triprotonated states are ruled out as the resting state. An Atoms-in-Molecules (AIM) analysis of the complex hydrogen bonding around the vanadate cofactor helps to explain the relative energies of the protonation states considered herein, and it also indicates new hydrogen bonding which has not been recognized previously. A Natural Bond Orbital (NBO) study is presented to give a better understanding of the electronic structure of the vanadate co-factor.</a>

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Higher Protonation States of Vanadium Chloroperoxidase: A QM/MM Study with an Atom-in-Molecules Analysis

10.26434/chemrxiv.7357244.v1 ◽

2018 ◽

Author(s):

Gregory Anderson ◽

Raghu Nath Behera ◽

Ravi V. Gomatam

Keyword(s):

Hydrogen Bonding ◽

Resting State ◽

Natural Bond Orbital ◽

Atoms In Molecules ◽

Large Decrease

<a>Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated forms of the vanadate cofactor. But recent arguments have been made that vanadate is in a quadprotonated form at pH 6.3. In this regard, an extensive QM/MM study on various possible protonation states of VCPO has been carried out. A large decrease in energy (about 200 kcal/mol per additional proton) has been found while going from mono-, di-, tri- to quad- protonated states. Separate QM studies on the isolated cofactor shows a similar trend in energies for different protonation states. A natural bond orbital (NBO) study shows extensive delocalization in quadprotonated states, and an Atoms-in-Molecules (AIM) study predicts some important hydrogen bonding not reported earlier.</a>

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Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

Physical Chemistry Chemical Physics ◽

10.1039/c4cp02585g ◽

2014 ◽

Vol 16 (42) ◽

pp. 22935-22952 ◽

Cited By ~ 105

Author(s):

Abhishek Shahi ◽

Elangannan Arunan

Keyword(s):

Hydrogen Bonding ◽

Bond Order ◽

Natural Bond Orbital ◽

Halogen Bonding ◽

Atoms In Molecules ◽

Lithium Bonding ◽

Intermolecular Bonding ◽

Molecular Bonding

In D–X⋯A bonding (X = H/Cl/Li), there is a conservation of bond order that includes both ionicity and covalency in both D–X and X⋯A bonds. This should be applicable to any atom X involved in intermolecular bonding.

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Molybdenum disulfide monolayer electronic structure information as explored using density functional theory and quantum theory of atoms in molecules

Applied Surface Science ◽

10.1016/j.apsusc.2021.149545 ◽

2021 ◽

pp. 149545

Author(s):

Nicholas Dimakis ◽

Om Vadodaria ◽

Korinna Ruiz ◽

Sanju Gupta

Keyword(s):

Density Functional Theory ◽

Electronic Structure ◽

Quantum Theory ◽

Molybdenum Disulfide ◽

Density Functional ◽

Atoms In Molecules ◽

Functional Theory ◽

Structure Information

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The Electronic Structure of FeV-cofactor in Vanadium-Dependent Nitrogenase

Chemical Science ◽

10.1039/d0sc06561g ◽

2021 ◽

Author(s):

Zhi-yong Yang ◽

Emilio Jimenez-Vicente ◽

Hayden Kallas ◽

Dmitriy A Lukoyanov ◽

Hao Yang ◽

...

Keyword(s):

Electronic Structure ◽

Active Site ◽

Resting State ◽

Metal Cofactor ◽

Open Question

The electronic structure of the active-site metal cofactor (FeV-cofactor) of resting-state V-dependent nitrogenase has been an open question, with earlier studies indicating that it exhibits a broad S = 3/2...

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Intramolecular hydrogen bonding guides a cationic amphiphilic organocatalyst to highly stereoselective aldol reactions in water

RSC Advances ◽

10.1039/c5ra12135c ◽

2015 ◽

Vol 5 (77) ◽

pp. 62331-62335 ◽

Cited By ~ 10

Author(s):

Ángel M. Valdivielso ◽

Alba Catot ◽

Ignacio Alfonso ◽

Ciril Jimeno

Keyword(s):

Hydrogen Bonding ◽

Intramolecular Hydrogen Bonding ◽

Structural Motif ◽

Aldol Reactions ◽

Asymmetric Aldol ◽

Neutral Ph ◽

Intramolecular Hydrogen

A novel amphiphilic acylguanidine organocatalyst using intramolecular hydrogen bonding as a key structural motif is efficient for asymmetric aldol reactions of ketones in water at neutral pH.

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Synthesis, DFT calculations, electronic structure, electronic absorption spectra, natural bond orbital (NBO) and nonlinear optical (NLO) analysis of the novel 5-methyl-8H-benzo[h]chromeno[2,3-b][1,6] naphthyridine-6(5H),8-dione (MBCND)

Journal of Molecular Structure ◽

10.1016/j.molstruc.2016.10.058 ◽

2017 ◽

Vol 1130 ◽

pp. 543-558 ◽

Cited By ~ 21

Author(s):

Shimaa Abdel Halim ◽

Magdy A. Ibrahim

Keyword(s):

Electronic Structure ◽

Dft Calculations ◽

Absorption Spectra ◽

Electronic Absorption ◽

Nonlinear Optical ◽

Natural Bond Orbital ◽

Electronic Absorption Spectra ◽

The Novel

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ELECTRONIC STRUCTURE OF METHYLIDINESULFOXIDALCANES

Вестник Тверского государственного университета. Серия: Химия ◽

10.26456/vtchem2020.4.12 ◽

2020 ◽

pp. 106-113

Author(s):

Наталья Петровна Русакова ◽

Елена Михайловна Чернова ◽

Владимир Владимирович Туровцев ◽

Юрий Димитриевич Орлов

Keyword(s):

Electronic Structure ◽

Quantum Theory ◽

Functional Groups ◽

Atoms In Molecules

В рамках «квантовой теории атомов в молекулах» (QTAIM) определено электронное строение молекул ряда метилидинсульфоксидалканов n-C H-S(О)СН, где 1 ≤ n ≤ 10. Составлена качественная шкала электроотрицательностей функциональных групп. Within the framework of the «quantum theory of atoms in molecules» (QTAIM), the electronic structure of the molecules of a series of methylidinesulfoxidealkanes n-CH-S(О)СН, where 1 ≤ n ≤ 10, was determined. A qualitative scale of electronegativities of functional groups was compiled.

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π-Hole Tetrel Bonds—Lewis Acid Properties of Metallylenes

Crystals ◽

10.3390/cryst12010112 ◽

2022 ◽

Vol 12 (1) ◽

pp. 112

Author(s):

Sławomir J. Grabowski

Keyword(s):

Quantum Theory ◽

Crystal Structures ◽

Lewis Acid ◽

Natural Bond Orbital ◽

Database Search ◽

Lewis Base ◽

Atoms In Molecules ◽

Acid Properties ◽

Structural Database ◽

Tetrel Bonds

The MP2/aug-cc-pVTZ calculations were performed on the dihalometallylenes to indicate their Lewis acid and Lewis base sites. The results of the Cambridge Structural Database search show corresponding and related crystal structures where the tetrel center often possesses the configuration of a trigonal bipyramid or octahedron. The calculations were also carried out on dimers of dichlorogermylene and dibromogermylene and on complexes of these germylenes with one and two 1,4-dioxide molecules. The Ge⋯Cl, Ge⋯Br, and Ge⋯O interactions are analyzed. The Ge⋯O interactions in the above mentioned germylene complexes may be classified as the π-hole tetrel bonds. The MP2 calculations are supported by the results of the Quantum Theory of Atoms in Molecules (QTAIM) and the Natural Bond Orbital (NBO) approaches.

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