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

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.

1988 ◽  
Vol 66 (5) ◽  
pp. 1318-1332 ◽  
Author(s):  
R. Anthony Shaw ◽  
Charles Ursenbach ◽  
Arvi Rauk ◽  
Hal Wieser

Ab initio harmonic force fields were calculated for ethane, propane, dimethyl ether, and cyclobutane at the STO-3G and 3-21G levels. The calculated frequencies, displacement eigenvectors, and calculated infrared absorption intensities were compared as they derive from force constants that were (i) unsealed; (ii) scaled to fit observed vibrational frequencies reported in the literature; (iii) evaluated at the optimized geometries; and (iv) evaluated at structures for which the bond lengths were corrected from the optimized geometries according to published procedures. A total of nine combinations of ab initio force field/reference geometry/G-matrix geometry were investigated for each of the four molecules. The ability of scaling factors as the only variables to predict vibrational parameters from STO-3G and 3-21G force fields was explored. Conditions were examined for which the scaling factors are satisfactorily transferable among different molecules.


1992 ◽  
Vol 47 (4) ◽  
pp. 614-618 ◽  
Author(s):  
Martin Ystenes ◽  
Wolfgang Brockner ◽  
Frank Menzel

AbstractBy ab initio quantum mechanical calculations on P2S2-6 its equilibrium energy, geometry and vibrational frequencies along with their PED values have been obtained. The basis sets STO-5G, 6-31G, STO-5G* and 6-31G* were employed, and force field calculations were carried out at the STO-5G and the STO-5G* levels. The calculations show that the assignment for some bands between 180 and 260 cm -1 should be corrected. Two scaling factors were needed to fit the calculated frequencies with the observed frequencies within a deviation of less then 20 cm -1 for all vibrations, with the exception of v6(B1g). The calculated frequency of this vibration is very dependent on the polarization functions, and use of STO-2G for the 3d-orbitals corrects most of the deviation. STO-5G* and 6-31G* both give a good description of the geometry of the title ion, although STO-5G* yields a 0.04 Å too short terminal P - S distance.


1997 ◽  
Vol 90 (3) ◽  
pp. 495-497
Author(s):  
CLAUDIO ESPOSTI ◽  
FILIPPO TAMASSIA ◽  
CRISTINA PUZZARINI ◽  
RICCARDO TARRONI ◽  
ZDENEK ZELINGER

1988 ◽  
Vol 53 (9) ◽  
pp. 1943-1945
Author(s):  
Pavel Hobza ◽  
Camille Sandorfy

The interaction of the 6-O methylguanine cation with cytosine and thymine was studied using the ab initio SCF method in combination with a London type expression for dispersion energy. The structure of the complex formed with cytosine differs from that found previously with guanine itself.


2021 ◽  
Vol 11 (12) ◽  
pp. 5570
Author(s):  
Binbin Wang ◽  
Jingze Liu ◽  
Zhifu Cao ◽  
Dahai Zhang ◽  
Dong Jiang

Based on the fixed interface component mode synthesis, a multiple and multi-level substructure method for the modeling of complex structures is proposed in this paper. Firstly, the residual structure is selected according to the structural characteristics of the assembled complex structure. Secondly, according to the assembly relationship, the parts assembled with the residual structure are divided into a group of substructures, which are named the first-level substructure, the parts assembled with the first-level substructure are divided into a second-level substructure, and consequently the multi-level substructure model is established. Next, the substructures are dynamically condensed and assembled on the boundary of the residual structure. Finally, the substructure system matrix, which is replicated from the matrix of repeated physical geometry, is obtained by preserving the main modes and the constrained modes and the system matrix of the last level of the substructure is assembled to the upper level of the substructure, one level up, until it is assembled in the residual structure. In this paper, an assembly structure with three panels and a gear box is adopted to verify the method by simulation and a rotor is used to experimentally verify the method. The results show that the proposed multiple and multi-level substructure modeling method is not unique to the selection of residual structures, and different classification methods do not affect the calculation accuracy. The selection of 50% external nodes can further improve the analysis efficiency while ensuring the calculation accuracy.


Author(s):  
Christopher Antony Ramsden ◽  
Wojciech Piotr Oziminski

AbstractBased on structures determined by X-ray crystallography, ab initio MP2 calculations on type A mesoionic rings give geometries in good agreement with observed values. A study of four mesoionic ring systems, each with exocyclic oxygen, nitrogen or carbon groups, shows that the presence and configuration of exocyclic lone pairs significantly influences the geometry and configurational preference. Using a localised bond model and NBO analysis, these effects are rationalised in terms of an anomeric interaction of lone pairs with the antibonding orbitals of adjacent σ bonds. In agreement with experiment, similar effects are calculated for pyran-2-imines.


1989 ◽  
Vol 130 (1-3) ◽  
pp. 451-456 ◽  
Author(s):  
Javier Fernandez Sanz ◽  
Antonio Marquez ◽  
Claude Pouchan

2004 ◽  
Vol 443-444 ◽  
pp. 333-336
Author(s):  
N. Guillou ◽  
C. Livage ◽  
W. van Beek ◽  
G. Férey

Ni7(C4H4O4)4(OH)6(H2O)3. 7H2O, a new layered nickel(II) succinate, was prepared hydrothermally (180°C, 48 h, autogenous pressure) from a 1:1.5:4.1:120 mixture of nickel (II) chloride hexahydrate, succinic acid, potassium hydroxide and water. It crystallizes in the monoclinic system (space group P21/c, Z = 4) with the following parameters a = 7.8597(1) Å, b = 18.8154(3)Å, c = 23.4377(4) Å,ϐ = 92.0288(9)°, and V = 3463.9(2) Å3. Its structure, which contains 55 non-hydrogen atoms, was solved ab initio from synchrotron powder diffraction data. It can be described from hybrid organic-inorganic layers, constructed from nickel oxide corrugated chains. These chains are built up from NiO6hexameric units connected via a seventh octahedron. Half of the succinates decorate the chains, and the others connect them to form the layers. The three dimensional arrangement is ensured by hydrogen bonds directly between two adjacent layers and via free water molecules.


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