Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs
The model of <i>Regularized Quantum Mechanical Force Field</i> (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 fa...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-01-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/27/2/427 |
| _version_ | 1797491558141919232 |
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| author | Igor Kochikov Anna Stepanova Gulnara Kuramshina |
| author_facet | Igor Kochikov Anna Stepanova Gulnara Kuramshina |
| author_sort | Igor Kochikov |
| collection | DOAJ |
| description | The model of <i>Regularized Quantum Mechanical Force Field</i> (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 <i>Natural Bond Orbital</i> (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. |
| first_indexed | 2024-03-10T00:51:00Z |
| format | Article |
| id | doaj.art-7b8c12ff018047e29aeb67167ae74ef9 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T00:51:00Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-7b8c12ff018047e29aeb67167ae74ef92023-11-23T14:51:49ZengMDPI AGMolecules1420-30492022-01-0127242710.3390/molecules27020427Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical PairsIgor Kochikov0Anna Stepanova1Gulnara Kuramshina2Research Computing Centre, Moscow State University, 119991 Moscow, RussiaChemistry Department, Moscow State University, 119991 Moscow, RussiaChemistry Department, Moscow State University, 119991 Moscow, RussiaThe model of <i>Regularized Quantum Mechanical Force Field</i> (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 <i>Natural Bond Orbital</i> (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.https://www.mdpi.com/1420-3049/27/2/427molecular force fieldcartesian coordinatesscaling factorsNBO theoryDNA basesDNA canonical base pairs |
| spellingShingle | Igor Kochikov Anna Stepanova Gulnara Kuramshina Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs Molecules molecular force field cartesian coordinates scaling factors NBO theory DNA bases DNA canonical base pairs |
| title | Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs |
| title_full | Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs |
| title_fullStr | Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs |
| title_full_unstemmed | Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs |
| title_short | Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs |
| title_sort | scaled in cartesian coordinates ab initio molecular force fields of dna bases application to canonical pairs |
| topic | molecular force field cartesian coordinates scaling factors NBO theory DNA bases DNA canonical base pairs |
| url | https://www.mdpi.com/1420-3049/27/2/427 |
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