Treating the motion of nuclei and electrons in atomic and molecular quantum mechanical calculations on an equal footing: Non-Born–Oppenheimer quantum chemistry

2020 ◽  
pp. 143-166
Author(s):  
Saeed Nasiri ◽  
Sergiy Bubin ◽  
Ludwik Adamowicz
Keyword(s):  
Quantum Chemistry ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Equal Footing

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.

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.

Crystal Forms of Semisynthetic Ergot Alkaloid Terguride

2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ergot Alkaloid ◽  
Simplified Model ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
Torsion Angles ◽  
Crystal Forms ◽  
X Ray ◽  
Independent Molecules

Two new structures of semisynthetic ergot alkaloid terguride created by unusual number of symmetry-independent molecules were determined by X-ray diffraction methods at 150 K. Form A (monoclinic, P212121, Z = 12) contains three symmetry-independent terguride molecules and two molecules of water in the asymmetric part of the unit cell. The form CA (monoclinic, P21, Z = 8) is an anhydrate remarkable by the presence of four symmetry-independent molecules in the crystal structure. Conformations of twelve symmetry-independent molecules that were found in four already described terguride structures are compared with torsion angles obtained by ab initio quantum-mechanical calculations for the simplified model of N-cyclohexyl-N'-diethylurea.

Chemical accuracy from ‘Coulomb hole’ extrapolated molecular quantum-mechanical calculations

2001 ◽  
Vol 567-568 ◽  
pp. 375-384 ◽  
Author(s):  
K.L Bak ◽  
A Halkier ◽  
P Jørgensen ◽  
J Olsen ◽  
T Helgaker ◽  
...  
Keyword(s):  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Coulomb Hole
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