Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field

2014 ◽  
Vol 47 ◽  
pp. 62-76 ◽  
Author(s):  
Cui Liu ◽  
Yang Wang ◽  
Dongxia Zhao ◽  
Lidong Gong ◽  
Zhongzhi Yang
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Ab Initio Method ◽  
Base Pairs ◽  
Polarizable Force Field ◽  
Oxidized Guanine

Search of the conformations of Val-dipeptide and Val-tripeptide by ab initio method and ABEEMσπ polarizable force field

2015 ◽  
Vol 618 ◽  
pp. 147-152 ◽  
Author(s):  
Shuang Xu ◽  
Dong-xia Zhao ◽  
Li-dong Gong ◽  
Cui Liu ◽  
Zhong-Zhi Yang
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Ab Initio Method ◽  
Polarizable Force Field

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

1999 ◽  
Vol 110 (2) ◽  
pp. 741-754 ◽  
Author(s):  
Jay L. Banks ◽  
George A. Kaminski ◽  
Ruhong Zhou ◽  
Daniel T. Mainz ◽  
B. J. Berne ◽  
...  
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Point Charge ◽  
Point Charge Model ◽  
Polarizable Force Field ◽  
Charge Model

Ab initio parametrized polarizable force field for rutile-type SnO2

2012 ◽  
Vol 131 (5) ◽  
Author(s):  
Wojciech Miiller ◽  
Gordon J. Kearley ◽  
Chris D. Ling
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Polarizable Force Field

scholarly journals Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field

2017 ◽  
Vol 19 (7) ◽  
pp. 5579-5590 ◽  
Author(s):  
Alexander Esser ◽  
Saurabh Belsare ◽  
Dominik Marx ◽  
Teresa Head-Gordon
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Amino Acids ◽  
Force Field ◽  
Ab Initio ◽  
Polarizable Force Field

We have used the AMOEBA model to simulate the THz spectra of two zwitterionic amino acids in aqueous solution, which is compared to the results on these same systems using ab initio molecular dynamics (AIMD) simulations.

Ab Initio Extension of the AMOEBA Polarizable Force Field to Fe2+

2013 ◽  
Vol 9 (7) ◽  
pp. 3062-3071 ◽  
Author(s):  
David Semrouni ◽  
William C. Isley ◽  
Carine Clavaguéra ◽  
Jean-Pierre Dognon ◽  
Christopher J. Cramer ◽  
...  
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Polarizable Force Field

Structure and Energetics of Li+–(BF4–)n, Li+–(FSI–)n, and Li+–(TFSI–)n: Ab Initio and Polarizable Force Field Approaches

2014 ◽  
Vol 118 (36) ◽  
pp. 10785-10794 ◽  
Author(s):  
Charles W. Bauschlicher ◽  
Justin B. Haskins ◽  
Eric W. Bucholz ◽  
John W. Lawson ◽  
Oleg Borodin
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Polarizable Force Field ◽  
Field Approaches

scholarly journals Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 427
Author(s):  
Igor Kochikov ◽  
Anna Stepanova ◽  
Gulnara Kuramshina
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Complex Structure ◽  
Local Symmetry ◽  
Nbo Analysis ◽  
Base Pairs ◽  
Scaling Factors ◽  
Cartesian Coordinates ◽  
The Matrix ◽  
Scaling Matrix

The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the joint treatment of ab initio and experimental vibrational data of the four primary nucleobases using a new algorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factors in Cartesian coordinates for the considered molecules includes diagonal elements for all atoms of the molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1–3 and some 1–4 interactions). The choice of the model is based on the results of the second-order perturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital (NBO) analysis. The scaling factors obtained within this model as a result of solving the inverse problem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine molecules were used to correct the Hessians of the canonical base pairs: adenine–thymine and cytosine–guanine. The proposed procedure is based on the block structure of the scaling matrix for molecular entities with non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducing internal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field of a compound of a complex structure with non-covalent H-bonds.

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