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

2014 ◽  
Vol 16 (42) ◽  
pp. 22935-22952 ◽  
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.

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

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

<p></p><p><b>ABSTRACT</b>. <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></p><br><p></p>

scholarly journals Halogen and Hydrogen Bonding in Halogenabenzene/NH3 Complexes Compared Using Next-Generation QTAIM

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2875 ◽  
Author(s):  
Shuman Li ◽  
Tianlv Xu ◽  
Tanja van Mourik ◽  
Herbert Früchtl ◽  
Steven R. Kirk ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Quantum Theory ◽  
Relativistic Effects ◽  
Halogen Bonding ◽  
Atomic Mass ◽  
Atoms In Molecules ◽  
Next Generation ◽  
Bond Path ◽  
Chemical Character ◽  
Effective Core Potentials

Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.

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

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

<p><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></p>

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

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

<p></p><p><b>ABSTRACT</b>. <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></p><br><p></p>

scholarly journals π-Hole Tetrel Bonds—Lewis Acid Properties of Metallylenes

Crystals ◽  
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.

scholarly journals Halogen bonding in iron(II) and cobalt(II) tris(dichloroglyoximates)

2014 ◽  
Vol 70 (a1) ◽  
pp. C679-C679
Author(s):  
Anna Vologzhanina ◽  
Konstantin Lyssenko
Keyword(s):  
Intermolecular Interactions ◽  
Chlorine Atom ◽  
Russian Federation ◽  
Weak Interactions ◽  
Visual Representation ◽  
Voronoi Tessellation ◽  
Halogen Bonding ◽  
Intermolecular Contacts ◽  
The Russian Federation ◽  
Intermolecular Bonding

The understanding of the interplay between intermolecular strong and weak interactions requires approaches that are able to identify and quantify all of them, and are applicable to as large number of objects as possible. The QTAIM approach [1] nicely meets the first criteria. Less rigorous approaches, such as the Stockholder [2] and the Voronoi [3] partitioning have the second advantage. The latter can also give qualitative, quantitative and visual representation of intermolecular interactions. We compared how all these approaches would perform for two polymorphs of Fe(Cl2Gm)3(BCH3)2 (monoclinic C (1a), and less stable monoclinic P (1b)) and Co(Cl2Gm)3(BCH3)2 (2) isostructural with 1b (Cl2Gm = dichloroglyoximate). The Voronoi and Stockholder partitionings showed that three fourths of molecular surfaces were attributed to Cl...X (X = Cl, O, N) and C-H...Cl bonds. According to the QTAIM theory, each chlorine atom takes part in at least four intermolecular contacts. The Voronoi tessellation was found to be valid for determinating of the graph of intermolecular bonding. Indeed, in the isostructural 1b and 2 the sets of weak interactions do not coincide due to various conformations of iron- and cobalt-containing clathrochelate cages. Nevertheless, the resulting graph of intermolecular bonding (the gpu-x net) is the same. Qualitative (for all three approaches) and quantitative (for two partitionings) correlation for various methods was demonstrated. This study was supported by the Council of the President of the Russian Federation (MK-5181.2013.3 and MD- 3589.2014.3).

Synergic Interplay Between Halogen Bonding and Hydrogen Bonding in the Activation of a Neutral Substrate in a Nanoconfined Space

2020 ◽  
Vol 59 (2) ◽  
pp. 811-818 ◽  
Author(s):  
Pellegrino La Manna ◽  
Margherita De Rosa ◽  
Carmen Talotta ◽  
Antonio Rescifina ◽  
Giuseppe Floresta ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Halogen Bonding

Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) Analyses of Iron-Substituted Borirene and Boryl Isomers

2019 ◽  
Vol 64 (4) ◽  
pp. 472-477 ◽  
Author(s):  
Mina Iranpour ◽  
Reza Fazaeli ◽  
Mirabdolah Seyed Sadjadi ◽  
Mohammad Yousefi
Keyword(s):  
Quantum Theory ◽  
Natural Bond Orbital ◽  
Atoms In Molecules
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