1
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Gao G, Liang PY, Jin N, Zhao ZB, Tian XC, Xie D, Tu CZ, Zhang HR, Zhou PP, Yang Z. Mechanism and origin of enantioselectivity for organocatalyzed asymmetric heteroannulation of alkynes in the construction of axially chiral C2-arylquinoline. Org Biomol Chem 2024. [PMID: 39189805 DOI: 10.1039/d4ob01127a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Axially chiral C2-arylquinoline has been successfully constructed via asymmetric heteroannulation of alkynes catalyzed by chiral phosphoric acid with high yield and high enantioselectivity. Inspired by this intriguing work, theoretical calculations have been carried out, and the detailed reaction mechanism has been elaborated, in which the whole reaction can be divided into steps including hydrogen transfer, C-N bonding, annulation reaction and the final dehydration processes. The initial hydrogen-transfer reaction has two possible pathways, while the subsequent C-N bonding process has eight possible pathways. Then, after the annulation reaction and the final dehydration processes, the major product and byproduct were formed. QTAIM and IGMH analyses were used to illustrate the role of weak intermolecular interactions in the catalytic process, and the distortion/interaction and EDA analyses provided a deeper understanding of the origin of enantioselectivity. The calculated results are consistent with the experimental results. This work would provide valuable insights into asymmetric reactions catalyzed by chiral phosphoric acid.
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Affiliation(s)
- Ge Gao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Peng-Yu Liang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Nengzhi Jin
- Key Laboratory of Advanced Computing of Gansu Province, Gansu Computing Center, 42 Qingyang Road, Lanzhou 730000, P. R. China
| | - Zi-Bo Zhao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Xiao-Cheng Tian
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Dong Xie
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Chi-Zhou Tu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Hai-Rong Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Pan-Pan Zhou
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Advanced Catalysis of Gansu Province, Advanced Catalysis Center, College of Chemistry and Chemical Engineering, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, P. R. China.
| | - Zhaoyong Yang
- Key Laboratory of Biotechnology of Antibiotics, Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100050, P. R. China.
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2
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Budniak U, Karolak NK, Kulik M, Młynarczyk K, Górna MW, Dominiak PM. The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method. J Phys Chem B 2022; 126:9152-9167. [PMID: 36326196 PMCID: PMC9677429 DOI: 10.1021/acs.jpcb.2c04519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Electrostatic energy has a significant contribution to intermolecular interaction energy, especially in biological systems. Unfortunately, precise quantum mechanics calculations are not feasible for large biological systems; hence, simpler calculation methods are required. We propose a method called UBDB+EPMM (University at Buffalo Pseudoatom DataBank + Exact Potential Multipole Moments), which shortens computational time without losing accuracy. Here, we characterize electrostatic interactions in selected complexes of IFIT proteins with RNA. IFIT proteins are effectors of the innate immune system, and by binding foreign RNA, they prevent the synthesis of viral proteins in human host cells; hence, they block the propagation of viruses. We show that by using the UBDB+EPMM method it is possible to describe protein-RNA interactions not only qualitatively but also quantitatively. Looking at the charge penetration contribution to electrostatic interactions, we find all amino acid residues with strong local interactions. Moreover, we confirm that electrostatic interaction of IFIT5 with pppRNA does not depend on the sequence of the RNA.
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Affiliation(s)
- Urszula
Anna Budniak
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Natalia Katarzyna Karolak
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland,Nencki
Institute of Experimental Biology, Polish
Academy of Sciences, ul. Ludwika Pasteura 3, 02-093 Warszawa, Poland
| | - Marta Kulik
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Młynarczyk
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Maria Wiktoria Górna
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland,E-mail:
| | - Paulina Maria Dominiak
- Biological
and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland,E-mail:
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3
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Electron density is not spherical: the many applications of the transferable aspherical atom model. Comput Struct Biotechnol J 2022; 20:6237-6243. [DOI: 10.1016/j.csbj.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/20/2022] Open
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4
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Liang PY, Shi S, Xu XX, Zhang HR, Che Z, Lu K, Yan CX, Jin NZ, Zhou PP. Organocatalytic synthesis of chiral allene catalyzed by chiral phosphoric acid via asymmetric 1,8-addition of indole imine methide: Mechanism and origin of enantioselectivity. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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5
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Beiranvand N, Freindorf M, Kraka E. Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study. Molecules 2021; 26:2268. [PMID: 33919989 PMCID: PMC8071019 DOI: 10.3390/molecules26082268] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.
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Affiliation(s)
| | | | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA; (N.B.); (M.F.)
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6
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Lu K, Liang PY, Yan CX, Yang FL, Yang X, Dou W, Yu Q, Yang J, Zhou PP. Chiral phosphoric acid catalyzed atroposelective C–H amination of arenes: mechanisms, origin and influencing factors of enantioselectivity. Org Chem Front 2021. [DOI: 10.1039/d0qo01160f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The amination reaction between azonaphthalene and carbazole catalyzed by chiral phosphoric acid was theoretically investigated, and the mechanism, origin and influencing factors of enantioselectivity were elaborated.
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Affiliation(s)
- Ka Lu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- College of Chemistry and Chemical Engineering
- Lanzhou University
| | - Peng-Yu Liang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- College of Chemistry and Chemical Engineering
- Lanzhou University
| | - Chao-Xian Yan
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- College of Chemistry and Chemical Engineering
- Lanzhou University
| | - Fang-Ling Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- College of Chemistry and Chemical Engineering
- Lanzhou University
| | - Xing Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- College of Chemistry and Chemical Engineering
- Lanzhou University
| | - Wei Dou
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- College of Chemistry and Chemical Engineering
- Lanzhou University
| | - Qinwei Yu
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi'an Modern Chemistry Research Institute
- Xi'an
- P. R. China
| | - Jianming Yang
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi'an Modern Chemistry Research Institute
- Xi'an
- P. R. China
| | - Pan-Pan Zhou
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- College of Chemistry and Chemical Engineering
- Lanzhou University
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7
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Liu Y, Yu T, Lai W, Ma Y, Ge Z, Yang FL, Liang PY, Long Y, Zhou PP, Yang Z. High-energetic and low-sensitive 1,3,5-triamino 2,4,6-trinitrobenzene (TATB) crystal: first principles investigation and Hirshfeld surface analysis. NEW J CHEM 2021. [DOI: 10.1039/d1nj00170a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The N–H⋯O hydrogen bonding between neighboring TATB molecules within a planar layer cooperates with π⋯π interaction between two adjacent molecules from two adjacent layers in the TATB crystal.
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Affiliation(s)
- Yingzhe Liu
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Tao Yu
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Weipeng Lai
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Yiding Ma
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Zhongxue Ge
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Fang-Ling Yang
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Peng-Yu Liang
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Yu Long
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Pan-Pan Zhou
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Zhaoyong Yang
- Key Laboratory of Biotechnology of Antibiotics
- Ministry of Health, Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College(PUMC)
- Beijing 100050
- China
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8
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Gruza B, Chodkiewicz ML, Krzeszczakowska J, Dominiak PM. Refinement of organic crystal structures with multipolar electron scattering factors. Acta Crystallogr A Found Adv 2020; 76:92-109. [PMID: 31908353 PMCID: PMC8127334 DOI: 10.1107/s2053273319015304] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022] Open
Abstract
A revolution in resolution is occurring now in electron microscopy arising from the development of methods for imaging single particles at cryogenic temperatures and obtaining electron diffraction data from nanocrystals of small organic molecules or macromolecules. Near-atomic or even atomic resolution of molecular structures can be achieved. The basis of these methods is the scattering of an electron beam due to the electrostatic potential of the sample. To analyse these high-quality experimental data, it is necessary to use appropriate atomic scattering factors. The independent atom model (IAM) is commonly used although various more advanced models, already known from X-ray diffraction, can also be applied to enhance the analysis. In this study a comparison is presented of IAM and TAAM (transferable aspherical atom model), the latter with the parameters of the Hansen-Coppens multipole model transferred from the University at Buffalo Databank (UBDB). By this method, TAAM takes into account the fact that atoms in molecules are partially charged and are not spherical. Structure refinements were performed on a carbamazepine crystal using electron structure-factor amplitudes determined experimentally [Jones et al. (2018). ACS Cent. Sci. 4, 1587-1592] or modelled with theoretical quantum-mechanical methods. The results show the possibilities and limitations of the TAAM method when applied to electron diffraction. Among others, the method clearly improves model fitting statistics, when compared with IAM, and allows for reliable refinement of atomic thermal parameters. The improvements are more pronounced with poorer-resolution diffraction data.
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Affiliation(s)
- Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Joanna Krzeszczakowska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
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9
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Lu K, Feng X, Yan CX, Yang FL, Yang X, Zhou PP, Yang Z. Chiral phosphoric acid catalyzed asymmetric arylation of indolesvianucleophilic aromatic substitution: mechanisms and origin of enantioselectivity. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00008f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Asymmetric arylation of indolesvianucleophilic aromatic substitution can be effectively achieved using chiral phosphoric acid as catalyst, where the mechanisms and origin of enantioselectivity were explored theoretically.
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Affiliation(s)
- Ka Lu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Xiao Feng
- Key Laboratory of Biotechnology of Antibiotics
- Ministry of Health
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC)
- Beijing 100050
| | - Chao-Xian Yan
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Fang-Ling Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Xing Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Pan-Pan Zhou
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Zhaoyong Yang
- Key Laboratory of Biotechnology of Antibiotics
- Ministry of Health
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC)
- Beijing 100050
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10
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Yan CX, Wu RZ, Lu K, Yang FL, Yang XS, Wang R, Yang X, Zhou PP, Shao X. Why electrostatically enhanced thiourea is better than Schreiner's thiourea in both catalytic activity and regioselectivity? Org Chem Front 2019. [DOI: 10.1039/c9qo00251k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatically enhanced thiourea is more active and efficient than Schreiner's thiourea in the ring-opening aminolysis of styrene oxide with aniline, and the underlying reasons were explored by DFT calculations.
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Affiliation(s)
- Chao-Xian Yan
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Rui-Zhi Wu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Ka Lu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Fang-Ling Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Xiao-Shan Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Rui Wang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Xing Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Pan-Pan Zhou
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Xiangfeng Shao
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
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11
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Srinivasadesikan V, Chen YC, Lee SL. On the misincorporation of nucleotides opposite mutagenic cyclic 1,N 2-propanoguanine: A computational investigation. J Mol Graph Model 2018; 85:270-280. [PMID: 30253282 DOI: 10.1016/j.jmgm.2018.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/22/2018] [Accepted: 08/30/2018] [Indexed: 11/30/2022]
Abstract
The misincorporation properties of exocyclic DNA adduct, cyclic 1,N2-propanoguanine with nucleobases have been investigated using DFT and DFT-D methods. Number of possible and stable mispairing conformations of cyclic 1,N2-propanoguanine with A,T,G and C have been considered for our investigation. The single point energy calculations have been carried out at the M06/6-311++G**, ωB97XD/6-311++G** and MP2/6-311++G** levels on corresponding optimized geometries. The reaction enthalpy values were employed at the M06/6-31 + G* and ωB97XD/6-31 + G* levels. The energies have been compared among the cyclic 1,N2-propanoguanine adduct with nucleobases to find the most stable conformer. The CPCM model was utilized on account of solvent phase and overall polarizability. The computed binding energies follow the order as CPr-Gua-G(2)(-23.2 kcal/mol) > CPr-Gua-C(1) (-16.1 kcal/mol) > CPr-Gua-A(2)(-10.6 kcal/mol) > CPr-Gua-T(2)(-9.6 kcal/mol) in the gas phase at M06 level, which indicates the guanine and cytosine are favorable for mispairing with the cyclic 1,N2-propanoguanine adduct. The obtained results using computational tools are in good agreement with the experimental observation.
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Affiliation(s)
- V Srinivasadesikan
- Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan; Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, 522 213, Andhra Pradesh, India
| | - Ya-Chi Chen
- Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan
| | - Shyi-Long Lee
- Department of Chemistry and Biochemistry, National Chung-Cheng University, Chia-Yi, 621, Taiwan.
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12
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Kumar P, Cabaj MK, Pazio A, Dominiak PM. Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions. IUCRJ 2018; 5:449-469. [PMID: 30002846 PMCID: PMC6038959 DOI: 10.1107/s2052252518006346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium-cytosinium trans sugar/sugar edge pair and an adeninium-adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation-cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.
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Affiliation(s)
- Prashant Kumar
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Malgorzata Katarzyna Cabaj
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Aleksandra Pazio
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
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13
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Wang W, Sheng X, Zhang S, Huang F, Sun C, Liu J, Chen D. Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet. Phys Chem Chem Phys 2018; 18:28492-28501. [PMID: 27711557 DOI: 10.1039/c6cp05594j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The addition of the unnatural P:Z base pair to the four naturally occurring DNA bases expands the genetic alphabet and yields an artificially expanded genetic information system (AEGIS). Herein, the structural feature of oligonucleotides containing a novel unnatural P:Z base pair is characterized using both molecular dynamics and quantum chemistry. The results show that the incorporation of the novel artificial base pair (P:Z) preserves the global conformational feature of duplex DNA except for some local structures. The Z-nitro group imparts new properties to the groove width, which widens the major groove. The unnatural oligonucleotides containing mismatched base pairs exhibit low stability. This ensures efficient and high-fidelity replication. In general, the incorporation of the P:Z pair strengthens the stability of the corresponding DNA duplex. The calculated results also show that the thermostability originates from both hydrogen interaction and stacking interaction. The Z-nitro group plays an important role in enhancing the stability of the H-bonds and stacking strength of the P:Z pair. Overall, the present results provide theoretical insights in the exploration of artificially expanded genetic information systems.
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Affiliation(s)
- Wenjuan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Xiehuang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Shaolong Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, P. R. China
| | - Fang Huang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Chuanzhi Sun
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Jianbiao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Dezhan Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
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14
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Yan CX, Zhou PP, Yang FL, Wu RZ, Yang X, Yang F, Shao X. Chiral bisoxazoline catalyzed decarboxylative aldol reactions between β-carbonyl acids and trifluoroacetaldehyde hemiacetals as well as trifluoroacetaldehyde: the mechanism, the origin of enantioselectivity and the role of a catalyst. Org Chem Front 2018. [DOI: 10.1039/c8qo00578h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The role of a catalyst in the decarboxylative aldol reactions between β-carbonyl acids and trifluoroacetaldehyde hemiacetals as well as trifluoroacetaldehyde catalyzed by chiral bisoxazoline were unveiled theoretically.
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Affiliation(s)
- Chao-Xian Yan
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Pan-Pan Zhou
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Fang-Ling Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Rui-Zhi Wu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Xing Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Fan Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Xiangfeng Shao
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
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15
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Jarzembska KN, Řlepokura K, Kamiński R, Gutmann MJ, Dominiak PM, Woźniak K. Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:550-564. [PMID: 28762967 DOI: 10.1107/s2052520617005534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH- anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.
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Affiliation(s)
- Katarzyna N Jarzembska
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Katarzyna Řlepokura
- Department of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Radosław Kamiński
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Matthias J Gutmann
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, England
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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16
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Yan CX, Yang F, Yang X, Zhou DG, Zhou PP. Insights into the Diels–Alder Reaction between 3-Vinylindoles and Methyleneindolinone without and with the Assistance of Hydrogen-Bonding Catalyst Bisthiourea: Mechanism, Origin of Stereoselectivity, and Role of Catalyst. J Org Chem 2017; 82:3046-3061. [DOI: 10.1021/acs.joc.7b00026] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Chao-Xian Yan
- State Key Laboratory of Applied
Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and
Resources Utilization of Gansu Province, College of Chemistry and
Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, P. R. China
| | - Fan Yang
- State Key Laboratory of Applied
Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and
Resources Utilization of Gansu Province, College of Chemistry and
Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, P. R. China
| | - Xing Yang
- State Key Laboratory of Applied
Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and
Resources Utilization of Gansu Province, College of Chemistry and
Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, P. R. China
| | - Da-Gang Zhou
- State Key Laboratory of Applied
Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and
Resources Utilization of Gansu Province, College of Chemistry and
Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, P. R. China
| | - Pan-Pan Zhou
- State Key Laboratory of Applied
Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and
Resources Utilization of Gansu Province, College of Chemistry and
Chemical Engineering, Lanzhou University, 222 South Tianshui Road, 730000, Lanzhou, P. R. China
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17
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Abstract
Hydrogen bond directionality in the water dimer is explained on the basis of symmetry-adapted intermolecular perturbation theory which directly separates the intermolecular interaction energy into four physically interpretable components: electrostatics, exchange-repulsion, dispersion, and induction. Analysis of these four main contributions to the binding energy allows a deeper understanding of the dominant factors ruling the mutual arrangement of the two monomers. A preference for the linear configuration is shown to be due to a subtle interplay of all four energy components. While the first-order terms, electrostatic and exchange-repulsion, almost perfectly cancel each other near the equilibrium geometry of the dimer, the importance of the second- and higher-order terms, induction and dispersion, becomes evident.
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Affiliation(s)
- Maxim Tafipolsky
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Campus Hubland Nord , Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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18
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Malinska M, Dauter Z. Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data. Acta Crystallogr D Struct Biol 2016; 72:770-9. [PMID: 27303797 PMCID: PMC4908868 DOI: 10.1107/s2059798316006355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/14/2016] [Indexed: 11/10/2022] Open
Abstract
In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.
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Affiliation(s)
- Maura Malinska
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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19
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Zhou PP, Yang X, Zhou DG, Liu S. T-shaped phenol–benzene complexation driven by π-involved noncovalent interactions. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1863-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Electrostatic interactions in aminoglycoside-RNA complexes. Biophys J 2015; 108:655-65. [PMID: 25650932 DOI: 10.1016/j.bpj.2014.12.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/20/2014] [Accepted: 12/10/2014] [Indexed: 11/21/2022] Open
Abstract
Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity.
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21
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Cysewski P, Oliński R. Structural, electronic and energetic consequences of epigenetic cytosine modifications. Phys Chem Chem Phys 2015; 17:19616-24. [PMID: 26151626 DOI: 10.1039/c5cp02188j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen bonding patterns of cytosine and its seven C5-modifed analogues paired with canonical guanine were studied using the first principle approach. Both global minima and biologically relevant conformations were studied. The former resulted from full gradient geometry optimizations of hydrogen bonded pairs, while the latter were obtained based on 125 d(GpC) dinucleotides found in the PDB database. The obtained energetic, electronic and structural data lead to the conclusion that the epigenetically relevant modification of cytosine may have serious consequences on hydrogen bonding with guanine. First of all, the significant substituent effects were observed for such trends as charges on sites involved in hydrogen bonding, the total intermolecular interaction energy or electron densities at bond critical points. Moreover, the molecular orbital polarization contribution resulting from energy decomposition expressed in terms of absolutely localized molecular orbitals exhibited an inverse linear correlation with frozen density contributions. A substituent effect on the amount of charge transfer from pyrimidine toward guanine was also observed. The increase of intermolecular interactions of guanine with modified cytosine is associated with the increase of the electro-donating character of the C5-substituent. However, only pairs involving 5-methylcytosine are more stable than those formed by canonical cytosine. Furthermore, the energy differences observed for global minima also remain important for a broad range of displacement and angular parameters defining pair conformations in model d(GpC) dinucleotides. Due to the sensitivities of intermolecular interactions to mutual arrangements of monomers the modification of cytosine at the C5 site can significantly alter the actual energy profiles. Consequently, it may be anticipated that the modified dinucleotides will adopt different conformations than a standard G-C pair in a B-DNA double helix.
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Affiliation(s)
- P Cysewski
- Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Physical Chemistry Department, Kurpińskiego 5, Bydgoszcz, Poland.
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22
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Błasiak B, Cho M. Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method. J Chem Phys 2015; 140:164107. [PMID: 24784253 DOI: 10.1063/1.4872040] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibrational solvatochromism is a solvation-induced effect on fundamental vibrational frequencies of molecules in solutions. Here we present a detailed first-principle coarse-grained theory of vibrational solvatochromism, which is an extension of our previous work [B. Błasiak, H. Lee, and M. Cho, J. Chem. Phys. 139(4), 044111 (2013)] by taking into account electrostatic, exchange-repulsion, polarization, and charge-transfer interactions. By applying our theory to the model N-methylacetamide-water clusters, solute-solvent interaction-induced effects on amide I vibrational frequency are fully elucidated at Hartree-Fock level. Although the electrostatic interaction between distributed multipole moments of solute and solvent molecules plays the dominant role, the contributions from exchange repulsion and induced dipole-electric field interactions are found to be of comparable importance in short distance range, whereas the charge-transfer effect is negligible. The overall frequency shifts calculated by taking into account the contributions of electrostatics, exchange-repulsion, and polarization terms are in quantitative agreement with ab initio results obtained at the Hartree-Fock level of theory.
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Affiliation(s)
- Bartosz Błasiak
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
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23
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Misiaszek T, Czyżnikowska Ż. The nature of interactions in nicotinamide crystal. J Mol Graph Model 2014; 51:73-8. [PMID: 24863341 DOI: 10.1016/j.jmgm.2014.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 11/27/2022]
Abstract
In this study, we analyze the nature of intermolecular interactions in nicotinamide complexes appearing in conformations found in the crystal structure, including many-body effects. In doing so, we employ symmetry-adapted perturbation theory based on density functional theory description of monomers, and we perform the many-body variational-perturbational interaction energy decomposition. The principal finding of this study is that the stability of nicotinamide complexes is a complicated interplay of four (large in magnitude) interaction-energy components, i.e. induction, dispersion, electrostatic and exchange repulsion. However, the last two contributions cancel each other out to a large extent. In the case of considered three-body complexes, the nonadditivity effects are found to be not important. Based on the results of topological analysis of charge densities we characterized also the properties of short H ⋯ H contact and identified it as a weak noncovalent closed shell interaction.
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Affiliation(s)
- Tomasz Misiaszek
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Żaneta Czyżnikowska
- Department of Inorganic Chemistry, Wrocław Medical University, Borowska 211, 50-556 Wrocław, Poland.
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24
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Veljković DŽ, Medaković VB, Andrić JM, Zarić SD. C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study. CrystEngComm 2014. [DOI: 10.1039/c4ce00595c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.
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Affiliation(s)
- D. Ž. Veljković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - J. M. Andrić
- Innovation Center
- Department of Chemistry
- 11000 Belgrade, Serbia
| | - S. D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A&M University at Qatar
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25
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Srinivasadesikan V, Sahu PK, Lee SL. Spectroscopic probe on N-H⋯N, N-H⋯O and controversial C-H⋯O contact in A-T base pair: a DFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:542-547. [PMID: 24374481 DOI: 10.1016/j.saa.2013.11.110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 11/01/2013] [Accepted: 11/29/2013] [Indexed: 06/03/2023]
Abstract
DNA base pair A-T has been investigated by IR and NMR spectroscopy using DFT methods. The results have been analyzed in terms of infrared vibrational frequencies and (1)H NMR chemical shifts. Different types of interactions N-H⋯N, N-H⋯O and C-H⋯O types have been investigated in DNA base pairs. Although, previous reports argued about the third C-H⋯O type interaction in A-T base pair, such typical interaction has been analyzed thoroughly by IR and NMR spectroscopy using DFT methods. Our results show that the CH⋯O interaction in the A-T base pair is a weak interaction compared to normal hydrogen bond interactions.
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Affiliation(s)
| | - Prabhat K Sahu
- Department of Chemistry, National Institute of Science and Technology, Berhampur 761008, India
| | - Shyi-Long Lee
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan.
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26
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Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J. Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. J Chem Theory Comput 2013; 10:463-80. [PMID: 26579924 DOI: 10.1021/ct400837p] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.
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Affiliation(s)
- Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC, Central European Institute of Technology , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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27
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Sahu PK, Srinivasadesikan V, Jhong ML, Lee SL. Model calculations for the base-pairing specificity of mutagenic exocyclic DNA adduct 1,N 6-ethenoadenine. Struct Chem 2013. [DOI: 10.1007/s11224-013-0318-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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The effect of intermolecular interactions on the electric dipole polarizabilities of nucleic acid base complexes. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.10.087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Song QX, Ding ZD, Liu JH, Li Y, Wang HJ. Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases. J Mol Model 2012; 19:1089-98. [PMID: 23138643 DOI: 10.1007/s00894-012-1628-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 10/03/2012] [Indexed: 11/30/2022]
Abstract
N6-methyladenine (m(6)A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH(3). Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m(6)A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH(3) changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m(6)A:G and trans-m(6)A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m(6)A to cis-m(6)A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m(6)A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory.
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Affiliation(s)
- Qi-Xia Song
- The Key Laboratory of Food Colloids and Biotechnology, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
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Srinivasadesikan V, Sahu PK, Lee SL. Quantum mechanical calculations for the misincorporation of nucleotides opposite mutagenic 3,N4-ethenocytosine. J Phys Chem B 2012; 116:11173-9. [PMID: 22889303 DOI: 10.1021/jp307239x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The ubiquitous nature and persistence of exocyclic DNA adducts suggest their involvement as initiators of carcinogenesis. We have investigated the misincorporation properties of the exocyclic DNA adduct, 3,N(4)-ethenocytosine, using DFT and DFT-D methods. Computational investigations have been carried out by using the B3LYP, M062X, and wB97XD methods with the 6-31+G* basis set to determine the hydrogen bonding strengths, binding energy, and physical parameters. The single point energy calculations have been carried out at MP2/6-311++G** on corresponding optimized geometries. The energies were compared among the 3,N(4)-ethenocytosine adduct with DNA bases to find the most stable conformer. The solvent phase calculations have also been carried out using the CPCM model. The computed reaction enthalpy values provide computational insights to the earlier experimental observation in in vitro, E.coli, and mammalian cells of a high level of substitution mutation in which C → A transversion results from εC-T pairing [εC-T3 and εC-T4] in the adduct containing DNA sequence.
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Leonis G, Czyżnikowska Ż, Megariotis G, Reis H, Papadopoulos MG. Computational studies of darunavir into HIV-1 protease and DMPC bilayer: necessary conditions for effective binding and the role of the flaps. J Chem Inf Model 2012; 52:1542-58. [PMID: 22587384 DOI: 10.1021/ci300014z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the main targets toward AIDS therapy. We have selected the potent drug darunavir and a weak inhibitor (fullerene analog) as HIV-1 PR substrates to compare protease's conformational features upon binding. Molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and quantum-mechanical (QM) calculations indicated the importance of the stability of HIV-1 PR flaps toward effective binding: a weak inhibitor may induce flexibility to the flaps, which convert between closed and semiopen states. A water molecule in the darunavir-HIV-1 PR complex bridged the two flap tips of the protease through hydrogen bonding (HB) interactions in a stable structure, a feature that was not observed for the fullerene-HIV-1 PR complex. Additionally, despite that van der Waals interactions and nonpolar contribution to solvation favored permanent fullerene entrapment into the cavity, these interactions alone were not sufficient for effective binding; enhanced electrostatic interactions as observed in the darunavir-complex were the crucial component of the binding energy. An alternative pathway to the usual way of a ligand to access the cavity was also observed for both compounds. Each ligand entered the binding cavity through an opening between the one flap of the protease and a neighboring loop. This suggested that access to the cavity is not necessarily regulated by flap opening. Darunavir exerts its biological action inside the cell, after crossing the membrane barrier. Thus, we also initiated a study on the interactions between darunavir and the DMPC bilayer to reveal that the drug was accommodated inside the bilayer in conformations that resembled its structure into HIV-1 PR, being stabilized via HBs with the lipids and water molecules.
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Affiliation(s)
- Georgios Leonis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece.
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Nikolaienko TY, Bulavin LA, Hovorun DM. Structural flexibility of DNA-like conformers of canonical 2′-deoxyribonucleosides. Phys Chem Chem Phys 2012; 14:15554-61. [DOI: 10.1039/c2cp43120c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fonseca Guerra C, Zijlstra H, Paragi G, Bickelhaupt FM. Telomere Structure and Stability: Covalency in Hydrogen Bonds, Not Resonance Assistance, Causes Cooperativity in Guanine Quartets. Chemistry 2011; 17:12612-22. [DOI: 10.1002/chem.201102234] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Indexed: 11/06/2022]
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Zgarbová M, Jurečka P, Banáš P, Otyepka M, Sponer JE, Leontis NB, Zirbel CL, Sponer J. Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. J Phys Chem A 2011; 115:11277-92. [PMID: 21910417 DOI: 10.1021/jp204820b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base-phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin-ricin loop, which may predetermine the S-turn topology and complex BPh patterns from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions.
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Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
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Srinivasadesikan V, Sahu PK, Lee SL. Model calculations for the misincorporation of nucleotides opposite five-membered exocyclic DNA adduct: N(2),3-ethenoguanine. J Phys Chem B 2011; 115:10537-46. [PMID: 21776999 DOI: 10.1021/jp202738v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Five-membered exocyclic DNA adducts are biologically very significant because of their potential to block DNA replication and transcription. N(2),3-Ethenoguanine (N(2,3)-εG) has been identified in the liver DNA of vinyl chloride-exposed rats as a five-membered DNA adduct. Singer et al. ( Carcinogenesis 1987 , 8 , 745 - 747 ) reported that the misincorporation of thymine (T), with two hydrogen bonds to N(2,3)-εG, represents the mutagenic event. Although the base-pairing specificity and mode of misincorporation have been studied experimentally for the N(2),3-ethenoguanine adduct, molecular-level information is not yet clear. In this study, we have considered all four different DNA nucleotides paired with the N(2),3-ethenoguanine adduct for model calculations toward the determination of base-pairing specificity. To provide insight into the mutagenic process of DNA damage based on geometric characteristics and electronic properties, the B3LYP and M06 methods were employed for these model calculations. Single-point energy calculations at the MP2/6-311++G** level on the corresponding optimized geometries were also carried out to better estimate the hydrogen-bonding strengths. The polarizable conductor calculation model (CPCM), which accounts for the overall polarizability of the solvent, was also employed. The computed reaction enthalpy values lie in the order εG-G(2) (10.3 kcal/mol) > εG-G(4) (9.6 kcal/mol) > εG-T(4) (9.2 kcal/mol) > εG-G(1) (9.1 kcal/mol) > εG-A(5) (8.2 kcal/mol) > εG-C(2) (7.9 kcal/mol) at the M06 level, which indicates that guanine and thymine are most favorable for mispairing with the N(2),3-ethenoguanine adduct.
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Bąk JM, Domagała S, Hübschle C, Jelsch C, Dittrich B, Dominiak PM. Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases. Acta Crystallogr A 2011; 67:141-53. [PMID: 21325717 DOI: 10.1107/s0108767310049731] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 11/28/2010] [Indexed: 11/11/2022] Open
Abstract
The existing pseudoatom databases (ELMAM, Invariom, UBDB and ELMAM2) enable structure refinement to be performed with the use of aspherical scattering factors computed from the transferable aspherical atom model (TAAM) as an alternative to independent atom model refinement. In addition, electrostatic properties can be estimated with the help of the databases. The quality of the structural and electrostatic properties obtained from the individual databases was tested. On the basis of a 100 K high-resolution single-crystal X-ray diffraction experiment on L-His-L-Ala dihydrate and 23 K high-resolution data for L-Ala [Destro & Marsh (1988). J. Phys. Chem. 92, 966-973], the structural properties, electron-density distributions and molecular electrostatic potentials obtained from different TAAMs were compared to each other and to reference models. Experimental multipolar models and theoretical models refined against theoretical structure factors computed from periodic density functional theory (DFT) calculations were compared to the TAAMs in order to determine which model best describes the crystal-field effect. Unperturbed wavefunctions based on the MP2 and DFT calculations and properties obtained directly from these were used as a reference to judge how properly the databases reproduce the properties of isolated molecules. For Gly-L-His dihydrate, D,L-His and the above-mentioned two crystal structures, deviations of the molecular dipole moments and Coulombic intermolecular interaction energies from the reference values were examined. Root-mean-square deviations (RMSDs) and correlation coefficients were used as a quantitative measure of the quality of the analysed properties. TAAM refinements reproduce X-H bond lengths optimized in theoretical periodic calculations. Structural properties obtained from different database models are similar to each other. The anisotropic displacement parameters from TAAMs are similar to the results of experimental multipolar refinement; differences are about 0.5 and 2.5% for high-resolution and low-resolution data, respectively. Differences in dipole-moment magnitudes calculated from database models are about 5%, and directions differ by up to 30°. The values of electrostatic interaction energies estimated from the individual TAAMs differ greatly from each other and from the reference values. RMSDs are about 9-15 and 22-33 kJ mol(-1) for UBDB and the other database models, respectively.
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Affiliation(s)
- Joanna Maria Bąk
- Department of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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