1
|
Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs. Molecules 2022; 27:molecules27020427. [PMID: 35056743 PMCID: PMC8779963 DOI: 10.3390/molecules27020427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 01/27/2023] Open
Abstract
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.
Collapse
|
2
|
Davydova IB, Senyavin VM, Zefirova ON, Kuramshina GM. Vibrational Spectra and Stable Conformations of Methyl 6-Methoxy-2,3,4,9-Tetrahydro-1H-1,4-Ethanocarbazole-3-Carboxylate. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420110047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
Ab initio molecular force fields fitted in Cartesian coordinates to experimental frequencies of isotopic species using symmetry constraints: application to indole and pyrrole molecules. Struct Chem 2019. [DOI: 10.1007/s11224-018-1262-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
4
|
The molecular structure of 4-piperidinemethanol in gas, solutions, and solid state: spectral and theoretical investigations. Struct Chem 2019. [DOI: 10.1007/s11224-019-01296-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
5
|
Srivastava M, Freed JH. Singular Value Decomposition Method To Determine Distance Distributions in Pulsed Dipolar Electron Spin Resonance: II. Estimating Uncertainty. J Phys Chem A 2018; 123:359-370. [PMID: 30525624 DOI: 10.1021/acs.jpca.8b07673] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper is a continuation of the method introduced by Srivastava and Freed (2017) that is a new method based on truncated singular value decomposition (TSVD) for obtaining physical results from experimental signals without any need for Tikhonov regularization or other similar methods that require a regularization parameter. We show here how to estimate the uncertainty in the SVD-generated solutions. The uncertainty in the solution may be obtained by finding the minimum and maximum values over which the solution remains converged. These are obtained from the optimum range of singular value contributions, where the width of this region depends on the solution point location (e.g., distance) and the signal-to-noise ratio (SNR) of the signal. The uncertainty levels typically found are very small with substantial SNR of the (denoised) signal, emphasizing the reliability of the method. With poorer SNR, the method is still satisfactory but with greater uncertainty, as expected. Pulsed dipolar electron spin resonance spectroscopy experiments are used as an example, but this TSVD approach is general and thus applicable to any similar experimental method wherein singular matrix inversion is needed to obtain the physically relevant result. We show that the Srivastava-Freed TSVD method along with the estimate of uncertainty can be effectively applied to pulsed dipolar electron spin resonance signals with SNR > 30, and even for a weak signal (e.g., SNR ≈ 3) reliable results are obtained by this method, provided the signal is first denoised using wavelet transforms (WavPDS).
Collapse
|
6
|
Srivastava M, Freed JH. Singular Value Decomposition Method to Determine Distance Distributions in Pulsed Dipolar Electron Spin Resonance. J Phys Chem Lett 2017; 8:5648-5655. [PMID: 29099190 PMCID: PMC5708871 DOI: 10.1021/acs.jpclett.7b02379] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Regularization is often utilized to elicit the desired physical results from experimental data. The recent development of a denoising procedure yielding about 2 orders of magnitude in improvement in SNR obviates the need for regularization, which achieves a compromise between canceling effects of noise and obtaining an estimate of the desired physical results. We show how singular value decomposition (SVD) can be employed directly on the denoised data, using pulse dipolar electron spin resonance experiments as an example. Such experiments are useful in measuring distances and their distributions, P(r) between spin labels on proteins. In noise-free model cases exact results are obtained, but even a small amount of noise (e.g., SNR = 850 after denoising) corrupts the solution. We develop criteria that precisely determine an optimum approximate solution, which can readily be automated. This method is applicable to any signal that is currently processed with regularization of its SVD analysis.
Collapse
Affiliation(s)
- Madhur Srivastava
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jack H. Freed
- National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Corresponding Author:
| |
Collapse
|
7
|
Kuramshina GM, Vakula OA, Vakula NI, Majouga AG, Senyavin VM, Gorb LG, Leszczynski J. Conformations, vibrational spectra and force field of 1-methyl-2-(2′-pyridyl)benzimidazole: experimental data and density functional theory investigation in comparison with 2-(2′-pyridyl)benzimidazole. Struct Chem 2015. [DOI: 10.1007/s11224-015-0693-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
8
|
Davydova IB, Sharapova SA, Kuramshina GM, Pentin YA. Quantum chemical modeling of the structure and vibrational spectra of two melatonin catabolites: N-γ-acetyl-N-formyl-5-methoxykynuramine and N-γ-acetyl-5-methoxykynuramine. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2015. [DOI: 10.1134/s0036024415100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
Davydova IB, Senyavin VM, Zefirova ON, Kuramshina GM, Pentin YA. Vibrational spectra and stable conformations of N-methylacetamide and (1S,5S,6R)-6-acetylamino-(5′-methoxyindolo[2,3-b])bicyclo[3.2.1]oct-2-ene. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414040050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
10
|
Vakula OA, Vakula NI, Kuramshina GM, Pentin YA. Quantum-chemical modeling of the effect of microhydration and media on the vibrational spectra of 2-(2′-pyridyl)-benzimidazole and its 1-methylsubstituted analogue. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413090288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Vakula NI, Kuramshina GM, Makhmutova SF, Pentin YA. DFT theoretical studies of anions of aniline and its several derivatives. Struct Chem 2010. [DOI: 10.1007/s11224-010-9724-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
Kosenkov D, Kholod YA, Gorb L, Shishkin OV, Kuramshina GM, Dovbeshko GI, Leszczynski J. Effect of a pH change on the conformational stability of the modified nucleotide queuosine monophosphate. J Phys Chem A 2009; 113:9386-95. [PMID: 19630370 DOI: 10.1021/jp903993s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The naturally occurring modified nucleotide queuosine 5'-monophosphate (QMP) related to biochemical regulatory pathways in the cell was investigated using quantum chemical approaches. The relative stability of biologically relevant conformations of QMP in solvent under a pH change was predicted at the BVP86/TZVP and MP2/TZVP levels of theory. Hydrogen bonding in QMP was studied using Bader's approach. The acidity constants of QMP were estimated using the COSMO-RS theory. It has been found that the neutral and anionic forms of QMP are the most stable in the physiological pH range. These forms correspond to the anti/north conformation and exist as zwitterionic tautomers having a negatively charged phosphate group (-1 for neutral and -2 for anionic) and a positively charged secondary amine group in the side chain. It was also found that QMP possesses the syn conformation in the cationic state at pH < 5.0 and undergoes syn to anti conformation transition when the pH increases, remaining in the anti conformation at the higher pH values. The marker IR bands specific for the anionic and neutral QMP forms in the 2300-2700 cm(-1) region were assigned to H-bonded NH groups of the QMP side chain. The bands between 800 and 1300 cm(-1) of the "fingerprint" (400-1500 cm(-1)) region were assigned to the vibrations of the ribose ring, the phosphate group and the side chain of QMP. The predicted IR spectra can be useful for the assignment of vibration bands in the experiential spectra of QMP or identification of the QMP forms. The revealed peculiarities of the QMP conformation sensitivity to a pH change as well as additional formed H-bonds could be responsible for specific nucleotide interactions with enzymes.
Collapse
Affiliation(s)
- Dmytro Kosenkov
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Shukla M, Kuramshina G, Leszczynski J. Evidence of structural non-planarity in excited state: New findings provided by vibrational analysis of the guanine–cytosine base pair. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
14
|
Kholod Y, Okovytyy S, Kuramshina G, Qasim M, Gorb L, Leszczynski J. An analysis of stable forms of CL-20: A DFT study of conformational transitions, infrared and Raman spectra. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.12.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
15
|
Are 1,5- and 1,7-dihydrodiimidazo[4,5-b:4′,5′-e]pyrazine the main products of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) alkaline hydrolysis? A DFT study of vibrational spectra. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.02.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
16
|
Ab initio and DFT theoretical studies of pyridoxal-5′-phosphate methylamine Schiff base isomers. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.11.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
17
|
Kuramshina G, Mogi T, Takahashi H. Structures and vibrational spectra of 5H-dibenz[b,f]azepine and 5H-dibenzo[a,d]cycloheptene-5-ol on the basis of quantum mechanical calculations. J Mol Struct 2003. [DOI: 10.1016/j.molstruc.2003.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
18
|
Vázquez J, López González JJ, Márquez F, Martínez Torres E, Boggs JE. Transferability and Physicochemical Interpretation of Canonical Force Fields in Redundant Internal Coordinates: Pyridazine and 3,6-Dichloropyridazine. J Phys Chem A 2001. [DOI: 10.1021/jp010456i] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Vázquez
- Department of Physical and Analytical Chemistry, University of Jaén, Campus Las Lagunillas s/n, Jaén E-23071, Spain
| | - Juan J. López González
- Department of Physical and Analytical Chemistry, University of Jaén, Campus Las Lagunillas s/n, Jaén E-23071, Spain
| | - Fernando Márquez
- Department of Physical and Analytical Chemistry, University of Jaén, Campus Las Lagunillas s/n, Jaén E-23071, Spain
| | - Emilio Martínez Torres
- Department of Physical Chemistry, University of Castilla-La Mancha, Ciudad Real E-13071, Spain
| | - James E. Boggs
- Institute for Theoretical Chemistry, Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712-1167
| |
Collapse
|
19
|
|
20
|
Kochikov I, Tarasov Y, Spiridonov V, Kuramshina G, Saakjan A, Yagola A. The use of ab initio anharmonic force fields in experimental studies of equilibrium molecular geometry. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(00)00504-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
21
|
Rotational isomerism in 1,2-difluoro-1,1,2-trichloro-ethane as studied by vibrational spectroscopy and ab initio calculations. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(00)00394-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
22
|
Kuramshina G, Pentin Y, Yagola A. New approaches for molecular conformer force field analysis in combination with ab initio results. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(99)00225-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
23
|
Extension of a regularizing algorithm for the determination of equilibrium geometry and force field of free molecules from joint use of electron diffraction, molecular spectroscopy and ab initio data on systems with large-amplitude oscillatory motion. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(99)00185-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
24
|
DFT force fields, vibrational spectra and potential functions for hindered internal rotation of CF3CH2CH2Cl and CCl3CH2CH2Cl. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(98)00629-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
25
|
Kuramshina GM, Weinhold F, Pentin YA. Ab initioand regularized force fields of haloethanes: CH3CH2Cl, CH3CHCl2, CH3CF2Cl, and CH3CFCl2. J Chem Phys 1998. [DOI: 10.1063/1.477404] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
26
|
Kochikov I, Tarasov Y, Kuramshina G, Spiridonov V, Yagola A, Strand T. Regularizing algorithm for determination of equilibrium geometry and harmonic force field of free molecules from joint use of electron diffraction, vibrational spectroscopy and ab initio data with application to benzene. J Mol Struct 1998. [DOI: 10.1016/s0022-2860(97)00428-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
27
|
Kuramshina G, Weinhold F. Constraints on the values of force constants for molecular force field models based on ab initio calculations. J Mol Struct 1997. [DOI: 10.1016/s0022-2860(96)09506-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
28
|
Panchenko YN. Methods of scaling quantum mechanical molecular force fields. J Mol Struct 1997. [DOI: 10.1016/s0022-2860(96)09472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
29
|
Kuramshina GM, Yagola AG. A priori constraints in the force field calculations of polyatomic molecules. J STRUCT CHEM+ 1997. [DOI: 10.1007/bf02762644] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
30
|
Uesugi Y, Mizuno M, Shimojima A, Takahashi H. Transient Resonance Raman and ab Initio MO Calculation Studies of the Structures and Vibrational Assignments of the T1 State and the Anion Radical of Coumarin and Its Isotopically Substituted Analogues. J Phys Chem A 1997. [DOI: 10.1021/jp9626881] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuki Uesugi
- Department of Chemistry, School of Science and Engineering, Waseda University, Tokyo 169, Japan
| | - Misao Mizuno
- Department of Chemistry, School of Science and Engineering, Waseda University, Tokyo 169, Japan
| | - Atsuhiko Shimojima
- Department of Chemistry, School of Science and Engineering, Waseda University, Tokyo 169, Japan
| | - Hiroaki Takahashi
- Department of Chemistry, School of Science and Engineering, Waseda University, Tokyo 169, Japan
| |
Collapse
|
31
|
Abstract
When energy is a critical quantity, accurate biomolecular simulations rest in substantial part on accurate potential energy functions (force fields). Improvements in methodology for determining parameters--particularly, in the systematic use of computational data obtained from quantum chemical calculations--and enhancements in functional form are leading to better potential energy functions. New calculations have been developed for water (including calculations that incorporate electronic polarizability to take account of the degree to which a molecule can be polarized), proteins, nucleic acids, carbohydrates, lipids, and general organic molecules. Most notably, two new biomolecular force fields have recently been derived and significant redeterminations of the parameters of two existing biomolecular force fields have been carried out. Some progress has also been made in incorporating polarizability into potential energy functions for molecules in general and in improving the treatment of metal-ligand interactions in systems of biomolecular interest.
Collapse
|
32
|
Panchenko Y, De Maré G, Stepanov N. Advantages of scaled quantum mechanical molecular force fields. J Mol Struct 1995. [DOI: 10.1016/0022-2860(95)08676-m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
33
|
Molecular force fields obtained using the nonempirical stabilizer of the regularizing functional. J STRUCT CHEM+ 1995. [DOI: 10.1007/bf02578057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
34
|
|
35
|
Leforestier C. Grid method for the Wigner functions. Application to the van der Waals system Ar–H2O. J Chem Phys 1994. [DOI: 10.1063/1.468455] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|