scholarly journals Revitalizing the concept of bond order through delocalization measures in real space

2018 ◽  
Vol 9 (25) ◽  
pp. 5517-5529 ◽  
Author(s):  
Carlos Outeiral ◽  
Mark A. Vincent ◽  
Ángel Martín Pendás ◽  
Paul L. A. Popelier
Keyword(s):  
Bond Order ◽  
Real Space ◽  
Quantum Mechanical ◽  
Bond Orders ◽  
Exchange Correlation ◽  
Mechanical Bond ◽  
Topological Atoms

Quantum mechanical bond orders are obtained from integration of the exchange–correlation density between topological atoms.

scholarly journals Real space bond orders are energetic descriptors

2018 ◽  
Vol 20 (23) ◽  
pp. 16231-16237 ◽  
Author(s):  
A. Martín Pendás ◽  
E. Francisco
Keyword(s):  
Bond Order ◽  
Real Space ◽  
Bond Orders ◽  
Chemical Interactions ◽  
Position Space

Orbital invariant position space techniques are used to show a theoretical link between the conventional concept of bond order and the energetics of chemical interactions.

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

On the π-Electron Content of Bonds and Rings in Benzenoid Hydrocarbons

2004 ◽  
Vol 59 (4-5) ◽  
pp. 295-298 ◽  
Author(s):  
Ivan Gutman ◽  
Tetsuo Morikawa ◽  
Susumu Narita
Keyword(s):  
Bond Order ◽  
Membered Ring ◽  
Electron Content ◽  
Bond Orders ◽  
Double Bonds ◽  
Benzenoid Hydrocarbons ◽  
Carbon Bond ◽  
Carbon Carbon Bond ◽  
Carbon Carbon Bonds ◽  
Single Bonds

The Pauling bond order can be viewed as a measure of the π-electron content of the respective carbon-carbon bond. In benzenoid hydrocarbons its values lie between 0 (in the case of essential single bonds) and 1 (in the case of essential double bonds). If the benzenoid molecule does not possess essential single and double bonds, then the Pauling bond orders are greater than 0 and less than 1, but may assume values arbitrarily close to 0 and 1. The π-electron content of a ring is equal to the sum of the π-electron contents of the carbon-carbon bonds forming this ring. We show that in benzenoid hydrocarbons the π-electron content of any (six-membered) ring lies between 0 and 5.5. If the molecule does not possess essential single and double bonds, then the π-electron content of any ring is greater than 0 and less than 5.5, but may assume values arbitrarily close to 0 and 5.5.

scholarly journals Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

2020 ◽  
Vol 25 (6) ◽  
pp. 847-861
Author(s):  
Lili Cao ◽  
Octav Caldararu ◽  
Ulf Ryde
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Bound State ◽  
Real Space ◽  
Quantum Mechanical ◽  
Storage Site ◽  
Quantum Mechanical Calculations ◽  
Reaction Intermediate ◽  
Sulphide Ions ◽  
Vanadium Nitrogenase

Abstract Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum–mechanical calculations. This allows us to test various interpretations of the structure, employing quantum–mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH−-bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand. Graphic abstract

Bond order-bond length relationships in conjugated hydrocarbons - the microwave spectrum and structure of 3,4-dimethylenecyclobutene

1983 ◽  
Vol 36 (4) ◽  
pp. 639 ◽  
Author(s):  
RD Brown ◽  
PD Godfry ◽  
BT Hart ◽  
AL Ottrey ◽  
M Onda ◽  
...  
Keyword(s):  
Dipole Moment ◽  
Ab Initio ◽  
Bond Length ◽  
Bond Order ◽  
Microwave Spectrum ◽  
Basis Set ◽  
Molecular Orbital Calculations ◽  
Bond Orders ◽  
Bond Lengths ◽  
Typical Error

The microwave spectrum of the benzene isomer 3,4-dimethylenecyclobutene including spectra of all possible single 13C-substituted and sufficient singly and doubly D-substituted species to give a complete r5 geometry, have been measured and analysed. An estimate of the re geometry has also been derived. The additional precise CC bond lengths obtained for an unsubstituted, conjugated hydrocarbon enable us to examine bond order-bond length relationships more thoroughly than has previously been possible. The CC bond lengths exhibit a noticeably better correlation with SCFMO bond orders than with simple H�ckel bond orders. Further confirmatory measurements of the dipole moment of dimethylenecyclobutene have been made. Ab initio molecular orbital calculations using a 6-31G basis set give an optimized geometry with CC bond lengths within 2 pm of the r5 values. The computed dipole moment agrees almost exactly with experiment but a corresponding calculation on fulvene is discrepant with experiment by 0.16 D, which is probably a more typical error.

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