scholarly journals Are the program packages for molecular structure calculations really black boxes?

2007 ◽  
Vol 72 (12) ◽  
pp. 1329-1341
Author(s):  
Ana Mrakovic ◽  
Milica Drvendzija ◽  
Aleksandra Samolov ◽  
Milena Petkovic ◽  
Miljenko Peric
Keyword(s):  
Molecular Structure ◽  
Quantum Chemistry ◽  
Periodic Table ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Dissociation Energies ◽  
Black Boxes ◽  
Homonuclear Diatomic Molecules ◽  
Gaussian Program ◽  
Structure Calculations

In this communication it is shown that the widely held opinion that compact program packages for quantum-mechanical calculations of molecular structure can safely be used as black boxes is completely wrong. In order to illustrate this, the results of computations of equilibrium bond lengths, vibrational frequencies and dissociation energies for all homonuclear diatomic molecules involving the atoms from the first two rows of the Periodic Table, performed using the Gaussian program package are presented. It is demonstrated that the sensible use of the program requires a solid knowledge of quantum chemistry.

scholarly journals Report on the Real Structure of Benzene Molecules and the Thickness of Graphene

2021 ◽  
Author(s):  
Ning Wang ◽  
Dulun Wang
Keyword(s):  
Molecular Structure ◽  
Layer Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Quantum Mechanical ◽  
Ultraviolet Spectroscopy ◽  
Quantum Mechanical Calculations ◽  
Covalent Bonds ◽  
Wide Range ◽  
Long Time

Abstract The problem of the benzene molecular structure has not been solved for a long time. This research proposes a new concept of covalent bonds based on the existing theory: each electron shared by the nucleus corresponds to a half-valent bond, and a half-valent bond can be formed between interval carbon atoms of the benzene ring. A new theory was established. Quantum mechanical calculations results can quantitatively explain experimental results, such as the hydrogenation heat and ultraviolet spectroscopy of benzene. It has solved more than one hundred years of difficult problems. The design of the new structural forms of benzene molecules shows half-valent bonds with dotted lines, which have a wide range of adaptability, and shows the structural forms and reaction formulas of more than dozens of benzene homologs and derivatives. Under the guidance of the new theory, the stacked three-dimensional structure of benzene was explored. The thickness of the three-layer benzene tube is calculated to be almost equal to the thickness of the graphene. Therefore, it is speculated that graphene may be a three layer structure.

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Thomas Hamelryck ◽  
Jan H Jensen
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Jan H Jensen ◽  
Thomas Hamelryck
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

Molecular structure of Hf(BH4)4 investigated by quantum mechanical calculations and gas-phase electron diffraction

2004 ◽  
pp. 967 ◽  
Author(s):  
Konstantin B. Borisenko ◽  
Anthony J. Downs ◽  
Heather E. Robertson ◽  
David W. H. Rankin ◽  
Christina Y. Tang
Keyword(s):  
Molecular Structure ◽  
Electron Diffraction ◽  
Gas Phase ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Gas Phase Electron Diffraction

scholarly journals Substituent and structural effects on the kinetics of the reaction of N-(substituted phenylmethylene)-m- and -p-aminobenzoic acids with diazodiphenylmethane

2007 ◽  
Vol 72 (12) ◽  
pp. 1191-1200 ◽  
Author(s):  
Bratislav Jovanovic ◽  
Aleksandar Marinkovic ◽  
Zeljko Vitnik ◽  
Ivan Juranic
Keyword(s):  
Molecular Structure ◽  
Rate Constants ◽  
Experimental Results ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Structural Effects ◽  
Electronic Effects ◽  
Aminobenzoic Acids ◽  
Kinetics Of ◽  
Insight Into

The rate constants for the reaction of twenty-two N-(substituted phenylmethylene)- m- and -p-aminobenzoic acids with diazodiphenylmethane were determined in absolute ethanol at 30 ?C. The effects of substituents on the reactivity of the investigated compounds were interpreted by correlation of the rate constants with LFER equations. The results of quantum mechanical calculations of the molecular structure together with experimental results gave a better insight into the effects of structure on the transmission of electronic effects of the substituents. New ? constants for substituted benzylideneamino group were calculated.

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