Quantum Mechanics and Molecular Mechanics Studies of the Low-Energy Conformations of 9-Crown-3

1997 ◽  
Vol 101 (10) ◽  
pp. 1920-1926 ◽  
Author(s):  
Wayne P. Anderson ◽  
Philip Behm ◽  
Timothy M. Glennon ◽  
Michael C. Zerner
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Low Energy ◽  
Low Energy Conformations

A/C-Ring Colchicine Analogues: a Comparison of Molecular Conformations of the Minimized and Crystal Structures

1997 ◽  
Vol 50 (2) ◽  
pp. 115
Author(s):  
Kiah H. Ang ◽  
Richard J. Greenwood ◽  
Maureen F. Mackay ◽  
Margaret G. Wong
Keyword(s):  
Solid State ◽  
Molecular Mechanics ◽  
Crystal Structures ◽  
Molecular Orbital ◽  
Low Energy ◽  
Molecular Orbital Calculations ◽  
Tubulin Polymerization ◽  
Ring Systems ◽  
Molecular Conformations ◽  
Low Energy Conformations

Molecular mechanics and molecular orbital calculations have been used to determine the low-energy conformations of six biaryl analogues of colchicine lacking the seven-membered B-ring. A comparison of the conformations resulting from the different minimizations has been made, and these conformations were also compared with those found in the solid state for the respective biaryl analogues and the A/C-ring systems of colchicine and isocolchicine. The barriers to rotation about the A/C-linkage of the analogues were estimated from rotational plots. The MM+ calculations were not satisfactory for estimating the barriers, whilst the MMX, MAXIMIN2 and AM1 values, although agreeing on average only to within 16 kJ mol-1 , exhibited the expected trend in magnitude. This trend, however, did not correlate with the inhibition of tubulin polymerization to microtubules.

Crystallographic and Molecular Mechanics Study of Imidooxy Anticonvulsants

1997 ◽  
Vol 53 (6) ◽  
pp. 945-952
Author(s):  
M. Ciechanowicz-Rutkowska ◽  
H. F. Lieberman ◽  
M. B. Hursthouse ◽  
K. R. Scott
Keyword(s):  
Solid State ◽  
Molecular Mechanics ◽  
Crystal Structures ◽  
Low Energy ◽  
Conformational Space ◽  
Energy Limit ◽  
Substitution Pattern ◽  
X Ray ◽  
New Compounds ◽  
Low Energy Conformations

X-ray crystal structures have been determined of five compounds closely related to N-benzyl-2-azaspiro[4.4]-nonane-l,3-dione (1), which is inactive as an anticonvulsant, and N-(benzyloxy)-2-azaspiro[4.4]nonane-1,3-dione (2), which is active. Conformational analyses have been carried out with (1), (2) and the new compounds N-(2′,4′-dichlorobenzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (3), N-(2′-bromobenzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (4), N-(4′-(trifluoromethyl)benzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (5), which are all active anticonvulsants, and N-(4′-chlorobenzyloxy)-2-azaspiro[4.4]nonane-l,3-dione (6) and N-(4′-bromobenzyloxy)-2-azaspiro[4.4]nonane-1,3-dione (7), which are inactive. Regardless of the substitution pattern, the conformations of compounds (2)–(7) in the crystals are very similar. Among the low-energy conformations, which are well distributed in the conformational space, that present in its solid state is dominant. Ortho-substitution considerably cuts down the number of conformations accessible within the set energy limit. The results of these studies alone do not explain the differences in activity.

On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Quantum Mechanics ◽  
Active Region ◽  
Molecular Mechanics ◽  
Active Regions ◽  
Available Energy ◽  
Adaptive Partitioning ◽  
Different Levels

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching

2007 ◽  
Vol 3 (2) ◽  
pp. 628-639 ◽  
Author(s):  
Patrick Maurer ◽  
Alessandro Laio ◽  
Håkan W. Hugosson ◽  
Maria Carola Colombo ◽  
Ursula Rothlisberger
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Force Fields ◽  
Force Matching
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