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Demir Gİ, Tekin A. NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond. J Chem Phys 2023; 159:244117. [PMID: 38153156 DOI: 10.1063/5.0176641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.
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Affiliation(s)
- Gözde İniş Demir
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), Kocaeli, Türkiye
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2
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Demir Gİ, Demir S, Tekin A. 2D‐FFCASP—A New Approach for 2D Structure Prediction Applied to Self‐Assemblies of DNA Bases. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gözde İniş Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
| | - Samet Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
| | - Adem Tekin
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
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3
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Demir S, Tekin A. FFCASP: A Massively Parallel Crystal Structure Prediction Algorithm. J Chem Theory Comput 2021; 17:2586-2598. [PMID: 33798330 DOI: 10.1021/acs.jctc.0c01197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new algorithm called Fast and Flexible CrystAl Structure Predictor (FFCASP) was developed to predict the structure of covalent and molecular crystals. FFCASP is massively parallel and able to handle more than 200 atoms in the unit cell (in other terms, it allows global optimization around 100 individual parameters). It uses a global optimizer specialized for Crystal Structure Prediction (CSP) which combines particle swarm and simulated annealing optimizers. Three different molecular crystals, including diverse intermolecular interactions, namely, cytosine, coumarin, and pyrazinamide, have been selected to evaluate the performance of FFCASP. While cytosine polymorphs have been searched by employing two different force fields (a DFT-SAPT based intermolecular potential and generalized amber force field (GAFF)) up to Z = 16, only GAFF has been used both in coumarin and pyrazinamide polymorph searches up to Z = 4. For these three molecular crystals, FFCASP generated more than 20 000 crystal structures, and the unique ones have been further treated by DFT-D3. A combination of data mining and a machine learning approach was introduced to determine the unique structures and their distribution into different clusters, which ultimately gives an opportunity to retrieve the common features and relations between the resulting structures. There are two known experimental crystal structures of cytosine, and both were successfully located with FFCASP. Two of the reported crystal structures of coumarin have been reproduced. Similarly, in pyrazinamide, three known experimental structures have been rediscovered. In addition to finding the experimentally known structures, FFCASP also located other low-energy structures for each considered molecular crystals. These successes of FFCASP offer the possibility to discover the polymorphic nature of other important molecular crystals (e.g., drugs) as well.
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Affiliation(s)
- Samet Demir
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey.,TÜBİTAK Research Institute for Fundamental Sciences, 41470 Gebze, Kocaeli, Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey.,TÜBİTAK Research Institute for Fundamental Sciences, 41470 Gebze, Kocaeli, Turkey
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Tekin A. Towards the crystal structure of thymine: An intermolecular force field development and parallel global cluster optimizations. J Chem Phys 2019; 151:244302. [DOI: 10.1063/1.5131754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), 41470 Gebze, Kocaeli, Turkey
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Kruse H, Šponer J. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. J Phys Chem A 2019; 123:9209-9222. [PMID: 31560201 DOI: 10.1021/acs.jpca.9b05940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 → 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)δMP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, ωB97M-V, and ωB97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic.,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , 62500 Brno , Czech Republic
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6
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Karatosun A, Çankaya M, Tekin A. Symmetry-adapted perturbation theory potential for the adenine dimer. Phys Chem Chem Phys 2018; 20:26303-26314. [DOI: 10.1039/c8cp03798a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A new ab initio intermolecular interaction potential for the adenine dimer has been developed.
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Affiliation(s)
- Armağan Karatosun
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
| | - Mehmet Çankaya
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
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Manukyan A, Tekin A. The intermolecular dimer potential for guanine. J Chem Phys 2017; 147:154311. [DOI: 10.1063/1.4998792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Artür Manukyan
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
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Venkataramanan NS, Suvitha A. Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches. J Phys Chem B 2017; 121:4733-4744. [DOI: 10.1021/acs.jpcb.7b01808] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Natarajan Sathiyamoorthy Venkataramanan
- Centre
for Computational Chemistry and Materials Science, SASTRA University, Thanjavur 614 001, India
- Department
of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA University, Thanjavur 614 001, India
| | - Ambigapathy Suvitha
- Department
of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA University, Thanjavur 614 001, India
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Nguyen DB, Nguyen TD, Kim S, Joo SW. Raman spectroscopy and quantum-mechanical analysis of tautomeric forms in cytosine and 5-methylcytosine on gold surfaces. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:183-188. [PMID: 27912177 DOI: 10.1016/j.saa.2016.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/16/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm-1 for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms. The relative energetic stabilities of the enol/keto and the amino/imino tautomeric forms of Cyt and 5MC have been estimated using DFT calculations, before and after binding six atom gold clusters. Among the six tautomeric forms, the 7H keto amino and the 4H imino trans forms are expected to be predominant in binding gold atoms, whereas the enol trans/cis conformers would coexist in the free gas phase. Our approach may provide useful theoretical guidelines for identifying 5MC from Cyt by analyzing Raman spectra on gold surfaces on the basis of quantum-mechanical calculations.
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Affiliation(s)
- Dinh Bao Nguyen
- Department of Chemistry, Soongsil University, Seoul 156-743, Republic of Korea; Department of Information Communication, Materials, and Chemistry Convergence Technology, Soongsil University, Seoul 156-743, Republic of Korea
| | - Thanh Danh Nguyen
- Department of Chemistry, Soongsil University, Seoul 156-743, Republic of Korea; Department of Information Communication, Materials, and Chemistry Convergence Technology, Soongsil University, Seoul 156-743, Republic of Korea
| | - Sangsoo Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea
| | - Sang-Woo Joo
- Department of Chemistry, Soongsil University, Seoul 156-743, Republic of Korea; Department of Information Communication, Materials, and Chemistry Convergence Technology, Soongsil University, Seoul 156-743, Republic of Korea.
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González J, Usabiaga I, Arnaiz PF, León I, Martínez R, Millán J, Fernández JA. Competition between stacked and hydrogen bonded structures of cytosine aggregates. Phys Chem Chem Phys 2017; 19:8826-8834. [DOI: 10.1039/c6cp08476a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The four bases of DNA constitute what is known as the “alphabet of life”.
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Affiliation(s)
- Jorge González
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Imanol Usabiaga
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Pedro F. Arnaiz
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Iker León
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
| | - Rodrigo Martínez
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - Judith Millán
- Department of Chemistry
- Faculty of Science and Technology
- University of La Rioja
- Logroño
- Spain
| | - José A. Fernández
- Department of Physical Chemistry
- Faculty of Science and Technology
- University of the Basque Country (UPV/EHU)
- Leioa
- Spain
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12
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Tafipolsky M, Ansorg K. Toward a Physically Motivated Force Field: Hydrogen Bond Directionality from a Symmetry-Adapted Perturbation Theory Perspective. J Chem Theory Comput 2016; 12:1267-79. [DOI: 10.1021/acs.jctc.5b01057] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maxim Tafipolsky
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
| | - Kay Ansorg
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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