scholarly journals Does Chlorine in CH3Cl Behave as a Genuine Halogen Bond Donor?

Crystals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 146 ◽  
Author(s):  
Pradeep R. Varadwaj ◽  
Arpita Varadwaj ◽  
Helder M. Marques
Keyword(s):  
Halogen Bond ◽  
Theoretical Models ◽  
Lewis Base ◽  
Positive Potential ◽  
Binary Complexes ◽  
Reduced Density Gradient ◽  
Reduced Density ◽  
Cl Atom ◽  
Axial Surface ◽  
Orbital Analysis

The CH3Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base (such as O=CH2). The induced positive potential then has the ability to attract the negative site of the Lewis base, thus explaining the importance of polarization leading to the formation of the H3C–Cl···O=CH2 complex. By examining the nature of the chlorine’s surface in CH3Cl using the molecular electrostatic surface potential (MESP) approach, with MP2/aug-cc-pVTZ, we show that this view is not correct. The results of our calculations demonstrate that the local potential associated with the axial surface of the Cl atom is inherently positive. Therefore, it should be able to inherently act as a halogen bond donor. This is shown to be the case by examining several halogen-bonded complexes of CH3Cl with a series of negative sites. In addition, it is also shown that the lateral portions of Cl in CH3Cl features a belt of negative electrostatic potential that can participate in forming halogen-, chalcogen-, and hydrogen-bonded interactions. The results of the theoretical models used, viz. the quantum theory of atoms in molecules; the reduced density gradient noncovalent index; the natural bond orbital analysis; and the symmetry adapted perturbation theory show that Cl-centered intermolecular bonding interactions revealed in a series of 18 binary complexes do not involve a polarization-induced potential on the Cl atom.

scholarly journals Relativistic Effects on NMR Parameters of Halogen-Bonded Complexes

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4399 ◽  
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Manuel Yáñez ◽  
Otilia Mó ◽  
M. Merced Montero-Campillo
Keyword(s):  
Relativistic Effects ◽  
Lewis Base ◽  
Coupling Constants ◽  
Basic Site ◽  
Lewis Bases ◽  
Nmr Parameters ◽  
Quadrupolar Coupling ◽  
Binary Complexes ◽  
Computational Level ◽  
Bonded Complexes

Relativistic effects are found to be important for the estimation of NMR parameters in halogen-bonded complexes, mainly when they involve the heavier elements, iodine and astatine. A detailed study of 60 binary complexes formed between dihalogen molecules (XY with X, Y = F, Cl, Br, I and At) and four Lewis bases (NH3, H2O, PH3 and SH2) was carried out at the MP2/aug-cc-pVTZ/aug-cc-pVTZ-PP computational level to show the extent of these effects. The NMR parameters (shielding and nuclear quadrupolar coupling constants) were computed using the relativistic Hamiltonian ZORA and compared to the values obtained with a non-relativistic Hamiltonian. The results show a mixture of the importance of the relativistic corrections as both the size of the halogen atom and the proximity of this atom to the basic site of the Lewis base increase.

scholarly journals Crystal Structure and Computational Study on Methyl-3-Aminothiophene-2-Carboxylate

Crystals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 19 ◽  
Author(s):  
Yaping Tao ◽  
Ligang Han ◽  
Andong Sun ◽  
Kexi Sun ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Computational Study ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Dispersion Energy ◽  
Monoclinic Crystal ◽  
Hydrogen Bond Interactions ◽  
Calculation Results ◽  
Reduced Density Gradient ◽  
Reduced Density

Methyl-3-aminothiophene-2-carboxylate (matc) is a key intermediate in organic synthesis, medicine, dyes, and pesticides. Single crystal X-ray diffraction analysis reveals that matc crystallizes in the monoclinic crystal system P21/c space group. Three matc molecules in the symmetric unit are crystallographically different and further linked through the N–H⋯O and N–H⋯N hydrogen bond interactions along with weak C–H⋯S and C–H⋯Cg interactions, which is verified by the three-dimensional Hirshfeld surface, two-dimensional fingerprint plot, and reduced density gradient (RDG) analysis. The interaction energies within crystal packing are visualized through dispersion, electrostatic, and total energies using three-dimensional energy-framework analyses. The dispersion energy dominates in crystal packing. To better understand the properties of matc, electrostatic potential (ESP) and frontier molecular orbitals (FMO) were also calculated and discussed. Experimental and calculation results suggested that amino and carboxyl groups can participate in various inter- and intra-interactions.

scholarly journals Μελέτη της επίδρασης των ligands στη σταθερότητα, διαμόρφωση και διατροπική ανταπόκριση μεταλλικών clusters των μετάλλων νομισμάτων (Cu, Ag, Au) με υπολογιστικές κβαντοχημικές μεθόδους

2013 ◽  
Author(s):  
Ιωάννης Δεπάστας
Keyword(s):  
Density Gradient ◽  
Reduced Density Gradient ◽  
Reduced Density

Σκοπός της διατριβής ήταν η μελέτη των ουδέτερων από άποψη φορτίου ετεροπυρηνικών clusters των μετάλλων των νομισμάτων, με γενικό τύπο Α3Β3 (όπου Α, Β = Cu, Ag ή Αu), καθώς και των επίπεδων και τρισδιάστατων clusters αυτών, που σταθεροποιούνται με την προσθήκη διάφορων ligands. Προσδιορίζονται όλες οι πιθανές δομές αυτών των clusters και μελετάται εκτενώς η σταθερότητα, η διαμόρφωση, η δεσμικότητα, καθώς και τα φάσματα απορρόφησής τους. Αρχικά, στο θεωρητικό μέρος δίνονται οι βασικές αρχές της κβαντικής θεωρίας μαζί με όλες τις απαραίτητες πληροφορίες, καθώς και το απαιτούμενο υπόβαθρο για την κατανόηση των αποτελεσμάτων που παρουσιάζονται στο πειραματικό μέρος της εργασίας. Στη συνέχεια, στο πειραματικό μέρος, γίνεται η επεξεργασία των αποτελεσμάτων, δηλαδή μία μελέτη όλων των γεωμετρικών δομών, όπως αυτές υπολογίστηκαν στο επίπεδο της DFT και συγκρίνεται η σταθερότητα των clusters με βάση την ενέργεια σύνδεσης και την ενέργεια μίξης που παρουσιάζουν. Όλα τα clusters των μετάλλων των νομισμάτων που μελετήθηκαν, αποτελούν ενεργειακά σταθερά μόρια με θετικές ενέργειες μίξης και σύνδεσης και ευνοούνται θερμοδυναμικά απέναντι στα ελεύθερα άτομα Au, Ag και Cu. Υπάρχει επίσης μία σαφής μεταφορά φορτίου, κυρίως στα clusters χρυσού-χαλκού και χρυσού-αργύρου, που ενισχύει την ύπαρξη ηλεκτροστατικού χαρακτήρα στο δεσμό μεταξύ των μετάλλων. Εξετάστηκαν επίσης, τα πιθανά μονοπάτια ανάπτυξης (Growth Format) για όλα τα ουδέτερα clusters που μελετήθηκαν και εξήχθησαν χρήσιμα συμπεράσματα για τους πιθανούς τρόπους παρασκευής τους. Ο αρωματικός χαρακτήρας των εσωτερικών τριμελών δακτυλίων, όλων των υπό μελέτη ενώσεων, διαπιστώθηκε με τη χρήση αρκετών καθιερωμένων δομικών, ενεργειακών και μαγνητικών (NICS-scan-profiles) κριτηρίων. H μελέτη των δισδιάστατων απεικονίσεων της ELF, αποδεικνύει την ύπαρξη ισχυρού απεντοπισμού ηλεκτρονιακής πυκνότητας που με τη σειρά του καταδεικνύει την ύπαρξη αρωματικότητας. Επίσης με την τρισδιάστατη απεικόνιση της ισοεπιφάνειας (isosurface) της RDG (Reduced Density Gradient), υποδεικνύεται η ύπαρξη μη δεσμικής αλληλεπικάλυψης στο εσωτερικό των τριμελών δακτυλίων, η οποία οφείλεται κυρίως στις στερεοχημικές απωθήσεις (steric repulsions). Οι δίσκοι που σχηματίζονται στην απεικόνιση της RDG, στη περιοχή ανάμεσα κυρίως στα περιφερειακά άτομα των μετάλλων των νομισμάτων, καταδεικνύουν τις ασθενείς αλληλεπιδράσεις (metallophilicity) μεταξύ των ατόμων. Τέλος από την φασματοσκοπική μελέτη IR και UV-Vis εξάγονται χρήσιμα στοιχεία για την οιαδήποτε προσπάθεια ταυτοποίησης των εν λόγω ενώσεων.

Interaction and Electron Density Properties of MKr42+ (M=Cu, Ag and Au): ab initio Calculation

2011 ◽  
Vol 64 (3) ◽  
pp. 339 ◽  
Author(s):  
Li Xinying ◽  
Cao Xue
Keyword(s):  
Electron Density ◽  
Quantum Chemical ◽  
Ab Initio Calculation ◽  
Gradient Analysis ◽  
Natural Bond Orbital ◽  
Theoretical Level ◽  
Covalent Contribution ◽  
Reduced Density Gradient ◽  
Reduced Density

Quantum chemical calculations of the structures and stabilities of the MKr42+ series at the CCSD(T) theoretical level have been performed. The role of the interaction was investigated using the natural bond orbital (NBO), Laplacian, electron density deformation, electron localization function and reduced density gradient analysis. The results show that a covalent contribution occurs in the Kr-M2+ bonding.

Using one halogen bond to change the nature of a second bond in ternary complexes with P⋯Cl and F⋯Cl halogen bonds

2017 ◽  
Vol 203 ◽  
pp. 29-45 ◽  
Author(s):  
Janet E. Del Bene ◽  
Ibon Alkorta ◽  
José Elguero
Keyword(s):  
Halogen Bond ◽  
Synergistic Effects ◽  
Ternary Complexes ◽  
Binding Energies ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Halogen Bonds ◽  
Binary Complexes ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to determine the effect of the presence of one halogen bond on the nature of the other in ternary complexes H2XP:ClF:ClH and H2XP:ClF:ClF, for X = F, Cl, H, NC, and CN. The P⋯Cl bonds remain chlorine-shared halogen bonds in the ternary complexes H2XP:ClF:ClH, although the degree of chlorine sharing increases relative to the corresponding binary complexes. The F⋯Cl bonds in the ternary complexes remain traditional halogen bonds. The binding energies of the complexes H2XP:ClF:ClH increase relative to the corresponding binary complexes, and nonadditivities of binding energies are synergistic. In contrast, the presence of two halogen bonds in the ternary complexes H2XP:ClF:ClF has a dramatic effect on the nature of these bonds in the four most strongly bound complexes. In these, chlorine transfer occurs across the P⋯Cl halogen bond to produce complexes represented as (H2XP–Cl)+:−(F:ClF). In the ion-pair, the cation is also halogen bonded to the anion by a Cl⋯F− halogen bond, while the anion is stabilized by an −F⋯Cl halogen bond. The central ClF molecule no longer exists as a molecule. The binding energies of the ternary H2XP:ClF:ClF complexes are significantly greater than the binding energies of the H2XP:ClF:ClH complexes, and nonadditivities exhibit large synergistic effects. The Wiberg bond indexes for the complexes H2XP:ClF, H2XP:ClF:ClH, and H2XP:ClF:ClF, and the cations (H2XP–Cl)+ reflect the changes in the P–Cl and Cl–F bonds. Similarly, EOM-CCSD spin–spin coupling constants are also consistent with the changes in these same bonds. In particular, 1xJ(P–Cl) in H2XP:ClF complexes becomes 1J(P–Cl) in the ternary complexes with chlorine-transferred halogen bonds. A plot of these coupling constants shows a change in the curvature of the trendline as chlorine-shared halogen bonds in H2XP:ClF:ClH become chlorine-transferred halogen bonds in H2XP:ClF:ClF. 1xJ(F–Cl) coupling constants also reflect changes in the nature of F⋯Cl halogen bonds.

Characterizing local metallic bonding variation induced by external perturbation

2020 ◽  
Vol 22 (4) ◽  
pp. 2372-2378 ◽  
Author(s):  
Hongwei Wang ◽  
Jon Fuller ◽  
Peng Chen ◽  
Sergey I. Morozov ◽  
Qi An
Keyword(s):  
Density Gradient ◽  
External Perturbation ◽  
Hole Injection ◽  
Electron Hole ◽  
Fcc Metals ◽  
Reduced Density Gradient ◽  
Metallic Bonding ◽  
Reduced Density

The reduced density gradient analyses on metallic bonding indicate that FCC metals can become more flexible/stronger with the electron/hole injection.

scholarly journals Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5487
Author(s):  
Rodrigo A. Lemos Silva ◽  
Demetrio A. da Silva Filho ◽  
Megan E. Moberg ◽  
Ted M. Pappenfus ◽  
Daron E. Janzen
Keyword(s):  
Interaction Energy ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Basis Set ◽  
Interaction Energies ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Reduced Density Gradient ◽  
Moller Plesset ◽  
Reduced Density

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller–Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (Eint(BSSE)) was determined using a supramolecular approach. The Eint(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.

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