1
|
Bregado JL, Secchi AR, Tavares FW. A density functional theory study on interactions in water-bridged dimeric complexes of lignin. Phys Chem Chem Phys 2024; 26:9234-9252. [PMID: 38444363 DOI: 10.1039/d4cp00312h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Lignin is the main plant cell wall component responsible for recalcitrance in the process of lignocellulosic biomass conversion into biofuels. The recalcitrance and insolubility of lignin in different reaction media are due in part to the hydrogen bonds and π interactions that hold syringyl (S) and guaiacyl (G) units together and promote the formation of stable water-bridged dimeric complexes (WBDCs): S⋯G and S⋯S, in native lignin. The current understanding of how each type of interaction influences the stability of these complexes within lignin native cell walls is still limited. Here, we found by DFT calculations that hydrogen bonding is more dominant than π-stacking interaction between aromatic rings of WBDCs. Although there is a stronger interaction of hydrogen bonds between subunits and water and higher π-stacking interaction in the S⋯S complex compared to the S⋯G complex, the former complex is less thermodynamically stable than the latter due to the entropic contribution coming from the methoxy substituents in the S-unit. Our results demonstrate that the methoxylation degree of lignin units does not significantly influence the structural geometries of WBDCs; if anything, an enhanced dispersion interaction between ring aromatics results in quasi-sandwich geometries as found in "coiled" lignin structures in the xylem tissue of wood. In the same way as that with ionic liquids, polar solvents can dissolve S-lignin by favorable interactions with the aliphatic hydroxyl group in the α-position as the key site or the aromatic hydroxyl group as the secondary site.
Collapse
Affiliation(s)
- Jurgen Lange Bregado
- Chemical Engineering Program, COPPE, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-914, Brazil.
| | - Argimiro R Secchi
- Chemical Engineering Program, COPPE, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-914, Brazil.
- Chemical and Biochemical Process Engineering Program, Escola de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-909, Brazil
| | - Frederico W Tavares
- Chemical Engineering Program, COPPE, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-914, Brazil.
- Chemical and Biochemical Process Engineering Program, Escola de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, CP: 21941-909, Brazil
| |
Collapse
|
2
|
Vishwakarma K, Ravi S, Mittal S. Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine. Chemphyschem 2024; 25:e202300552. [PMID: 37983746 DOI: 10.1002/cphc.202300552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/22/2023]
Abstract
Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.
Collapse
Affiliation(s)
- Kamini Vishwakarma
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
| | - Satyam Ravi
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
| | - Sumit Mittal
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
| |
Collapse
|
3
|
Deshmukh PU, Lad SB, Sudarsan A, Sudhakar S, Aggarwal T, Mandal S, Bagale SS, Kondabagil K, Pradeepkumar PI. Human Translesion Synthesis Polymerases polκ and polη Perform Error-Free Replication across N2-dG Methyleugenol and Estragole DNA Adducts. Biochemistry 2023; 62:2391-2406. [PMID: 37486230 DOI: 10.1021/acs.biochem.2c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The secondary metabolites of polypropanoids, methyleugenol (MEG), and estragole (EG), found in many herbs and spices, are commonly used as food flavoring agents and as ingredients in cosmetics. MEG and EG have been reported to cause hepatocarcinogenicity in rodents, human livers, and lung cells. The formation of N2-dG and N6-dA DNA adducts is primarily attributed to the carcinogenicity of these compounds. Therefore, these compounds have been classified as "possible human carcinogens" by the International Agency for Research on Cancer and "reasonably anticipated to be a human carcinogen" by the National Toxicology Program. Herein, we report the synthesis of the N2-MEG-dG and N2-EG-dG modified oligonucleotides to study the mutagenicity of these DNA adducts. Our studies show that N2-MEG-dG and N2-EG-dG could be bypassed by human translesion synthesis (TLS) polymerases hpolκ and hpolη in an error-free manner. The steady-state kinetics of dCTP incorporation by hpolκ across N2-MEG-dG and N2-EG-dG adducts show that the catalytic efficiencies (kcat/Km) were ∼2.5- and ∼4.4-fold higher, respectively, compared to the unmodified dG template. A full-length primer extension assay demonstrates that hpolκ exhibits better catalytic efficiency than hpolη. Molecular modeling and dynamics studies capturing pre-insertion, insertion, and post-insertion steps reveal the structural features associated with the efficient bypass of the N2-MEG-dG adduct by hpolκ and indicate the reorientation of the adduct in the active site allowing the successful insertion of the incoming nucleotide. Together, these results suggest that though hpolκ and hpolη perform error-free TLS across MEG and EG during DNA replication, the observed carcinogenicity of these adducts could be attributed to the involvement of other low fidelity polymerases.
Collapse
Affiliation(s)
- Priyanka U Deshmukh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh B Lad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Akhil Sudarsan
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Tanvi Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Soumyadeep Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
4
|
Presentation of the simple and accurate models for estimating the individual hydrogen bond energies of Watson–Crick base pairs. Struct Chem 2022. [DOI: 10.1007/s11224-022-02071-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
5
|
Quan L, Xin Y, Wu X, Ao Q. Mechanism of Self-Healing Hydrogels and Application in Tissue Engineering. Polymers (Basel) 2022; 14:polym14112184. [PMID: 35683857 PMCID: PMC9183126 DOI: 10.3390/polym14112184] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 12/26/2022] Open
Abstract
Self-healing hydrogels and traditional hydrogels both have three-dimensional polymeric networks that are capable of absorbing and retaining a large amount of water. Self-healing hydrogels can heal and restore damage automatically, and they can avoid premature failure of hydrogels caused by mechanical damage after implantation. The formation mechanism of self-healing hydrogels and the factors that hydrogels can load are various. Researchers can design hydrogels to meet the needs of different tissues through the diversity of hydrogels Therefore, it is necessary to summarize different self-healing mechanisms and different factors to achieve different functions. Here, we briefly reviewed the hydrogels designed by researchers in recent years according to the self-healing mechanism of water coagulation. Then, the factors for different functions of self-healing hydrogels in different tissues were statistically analyzed. We hope our work can provide effective support for researchers in the design process of self-healing hydrogel.
Collapse
|
6
|
Rieger M, Zacharias M. Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations. J Phys Chem B 2022; 126:3640-3647. [PMID: 35549273 DOI: 10.1021/acs.jpcb.2c01138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thermodynamic stability of double-stranded (ds)DNA depends on its sequence. It is influenced by the base pairing and stacking with neighboring bases along DNA molecules. Semiempirical schemes are available that allow us to predict the thermodynamic stability of DNA sequences based on empirically derived nearest-neighbor contributions of base pairs formed in the context of all possible nearest-neighbor base pairs. Current molecular dynamics (MD) simulations allow one to simulate the dynamics of DNA molecules in good agreement with experimentally obtained structures and available data on conformational flexibility. However, the suitability of current force field methods to reproduce dsDNA stability and its sequence dependence has been much less well tested. We have employed alchemical free-energy simulations of whole base pair transversions in dsDNA and in unbound single-stranded partner molecules. Such transversions change the sequence context but not the nucleotide content or base pairing in dsDNA and allow a direct comparison with the empirical nearest-neighbor dsDNA stability model. For the alchemical free-energy changes in the unbound single-stranded (ss)DNA partner molecules, we tested different setups assuming either complete unstacking or unrestrained simulations with partial stacking in the unbound ssDNA. The free-energy simulations predicted nearest-neighbor effects of similar magnitude, as observed experimentally but showed overall limited correlation with experimental data. An inaccurate description of stacking interactions and other possible reasons such as the neglect of electronic polarization effects are discussed. The results indicate the need to improve the realistic description of stacking interactions in current molecular mechanic force fields.
Collapse
Affiliation(s)
- Manuel Rieger
- Physics Department and Center of Protein Assemblies, Technical University of Munich, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, 85748 Garching, Germany
| |
Collapse
|
7
|
How the stability, reactivity and optical response of the protonated base pairs differ with other biologically important adenine–thymine pairs: a DFT and TD-DFT approach. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-020-01474-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
8
|
Zacharias M. Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation. J Phys Chem B 2020; 124:10345-10352. [PMID: 33156627 DOI: 10.1021/acs.jpcb.0c07670] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Double-stranded (ds)DNA formation and dissociation are of fundamental biological importance. The negative DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence-dependent stability of dsDNA. The stability of a dsDNA molecule can be estimated from empirical nearest-neighbor models based on contributions assigned to base-pair steps along the DNA and additional parameters because of DNA termini. In efforts to separate contributions, it has been concluded that base stacking dominates dsDNA stability, whereas base pairing contributes negligibly. Using a different model for dsDNA formation, we reanalyze dsDNA stability contributions and conclude that base stacking contributes already at the level of separate ssDNAs but that pairing contributions drive the dsDNA formation. The theoretical model also predicts that stability contributions of base-pair steps that contain only guanine/cytosine, mixed steps, and steps with only adenine/thymine follow the order 6:5:4, respectively, as expected based on the formed hydrogen bonds. The model is fully consistent with the available stacking data and the nearest-neighbor dsDNA parameters. It allows assigning a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of -0.72 kcal·mol-1 based entirely on the experimental data.
Collapse
Affiliation(s)
- Martin Zacharias
- Physics Department T38, Technical University of Munich, 85748 Garching, Germany
| |
Collapse
|
9
|
Label-Free Oligonucleotide-Based SPR Biosensor for the Detection of the Gene Mutation Causing Prothrombin-Related Thrombophilia. SENSORS 2020; 20:s20216240. [PMID: 33142935 PMCID: PMC7663036 DOI: 10.3390/s20216240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022]
Abstract
Prothrombin-related thrombophilia is a genetic disorder produced by a substitution of a single DNA base pair, replacing guanine with adenine, and is detected mainly by polymerase chain reaction (PCR). A suitable alternative that could detect the single point mutation without requiring sample amplification is the surface plasmon resonance (SPR) technique. SPR biosensors are of great interest: they offer a platform to monitor biomolecular interactions, are highly selective, and enable rapid analysis in real time. Oligonucleotide-based SPR biosensors can be used to differentiate complementary sequences from partially complementary or noncomplementary strands. In this work, a glass chip covered with an ultrathin (50 nm) gold film was modified with oligonucleotide strands complementary to the mutated or normal (nonmutated) DNA responsible for prothrombin-related thrombophilia, forming two detection platforms called mutated thrombophilia (MT) biosensor and normal thrombophilia (NT) biosensor. The results show that the hybridization response is obtained in 30 min, label free and with high reproducibility. The sensitivity obtained in both systems was approximately 4 ΔμRIU/nM. The dissociation constant and limits of detection calculated were 12.2 nM and 20 pM (3 fmol), respectively, for the MT biosensor, and 8.5 nM and 30 pM (4.5 fmol) for the NT biosensor. The two biosensors selectively recognize their complementary strand (mutated or normal) in buffer solution. In addition, each platform can be reused up to 24 times when the surface is regenerated with HCl. This work contributes to the design of the first SPR biosensor for the detection of prothrombin-related thrombophilia based on oligonucleotides with single point mutations, label-free and without the need to apply an amplification method.
Collapse
|
10
|
Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment. Molecules 2019; 24:molecules24183329. [PMID: 31547416 PMCID: PMC6767630 DOI: 10.3390/molecules24183329] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/27/2023] Open
Abstract
Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A-F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X-H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond.
Collapse
|
11
|
Abstract
Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.
Collapse
|
12
|
Talebian S, Mehrali M, Taebnia N, Pennisi CP, Kadumudi FB, Foroughi J, Hasany M, Nikkhah M, Akbari M, Orive G, Dolatshahi‐Pirouz A. Self-Healing Hydrogels: The Next Paradigm Shift in Tissue Engineering? ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801664. [PMID: 31453048 PMCID: PMC6702654 DOI: 10.1002/advs.201801664] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 03/04/2019] [Indexed: 05/18/2023]
Abstract
Given their durability and long-term stability, self-healable hydrogels have, in the past few years, emerged as promising replacements for the many brittle hydrogels currently being used in preclinical or clinical trials. To this end, the incompatibility between hydrogel toughness and rapid self-healing remains unaddressed, and therefore most of the self-healable hydrogels still face serious challenges within the dynamic and mechanically demanding environment of human organs/tissues. Furthermore, depending on the target tissue, the self-healing hydrogels must comply with a wide range of properties including electrical, biological, and mechanical. Notably, the incorporation of nanomaterials into double-network hydrogels is showing great promise as a feasible way to generate self-healable hydrogels with the above-mentioned attributes. Here, the recent progress in the development of multifunctional and self-healable hydrogels for various tissue engineering applications is discussed in detail. Their potential applications within the rapidly expanding areas of bioelectronic hydrogels, cyborganics, and soft robotics are further highlighted.
Collapse
Affiliation(s)
- Sepehr Talebian
- Intelligent Polymer Research InstituteARC Centre of Excellence for Electromaterials ScienceAIIM FacilityUniversity of WollongongNSW2522Australia
- Illawarra Health and Medical Research InstituteUniversity of WollongongWollongongNSW2522Australia
| | - Mehdi Mehrali
- DTU NanotechCenter for Intestinal Absorption and Transport of BiopharmaceuticalsTechnical University of DenmarkLyngby2800KgsDenmark
| | - Nayere Taebnia
- DTU NanotechCenter for Intestinal Absorption and Transport of BiopharmaceuticalsTechnical University of DenmarkLyngby2800KgsDenmark
| | - Cristian Pablo Pennisi
- Laboratory for Stem Cell ResearchDepartment of Health Science and TechnologyAalborg UniversityFredrik Bajers vej 3B9220AalborgDenmark
| | - Firoz Babu Kadumudi
- DTU NanotechCenter for Intestinal Absorption and Transport of BiopharmaceuticalsTechnical University of DenmarkLyngby2800KgsDenmark
| | - Javad Foroughi
- Intelligent Polymer Research InstituteARC Centre of Excellence for Electromaterials ScienceAIIM FacilityUniversity of WollongongNSW2522Australia
- Illawarra Health and Medical Research InstituteUniversity of WollongongWollongongNSW2522Australia
| | - Masoud Hasany
- DTU NanotechCenter for Intestinal Absorption and Transport of BiopharmaceuticalsTechnical University of DenmarkLyngby2800KgsDenmark
| | - Mehdi Nikkhah
- School of Biological Health and Systems Engineering (SBHSE)Arizona State UniversityTempeAZ85287USA
| | - Mohsen Akbari
- Laboratory for Innovations in MicroEngineering (LiME)Department of Mechanical EngineeringUniversity of VictoriaVictoriaBCV8P 5C2Canada
- Center for Biomedical ResearchUniversity of Victoria3800VictoriaCanada
- Center for Advanced Materials and Related TechnologiesUniversity of Victoria3800VictoriaCanada
| | - Gorka Orive
- NanoBioCel GroupLaboratory of PharmaceuticsSchool of PharmacyUniversity of the Basque Country UPV/EHUPaseo de la Universidad 701006Vitoria‐GasteizSpain
- Biomedical Research Networking Centre in BioengineeringBiomaterials, and Nanomedicine (CIBER‐BBN)Vitoria‐Gasteiz28029Spain
- University Institute for Regenerative Medicine and Oral Implantology – UIRMI (UPV/EHU‐Fundación Eduardo Anitua)Vitoria01007Spain
- BTI Biotechnology InstituteVitoria01007Spain
| | - Alireza Dolatshahi‐Pirouz
- DTU NanotechCenter for Intestinal Absorption and Transport of BiopharmaceuticalsTechnical University of DenmarkLyngby2800KgsDenmark
- Department of Dentistry‐Regenerative BiomaterialsRadboud University Medical CenterPhilips van Leydenlaan 25Nijmegen6525EXThe Netherlands
| |
Collapse
|
13
|
Rajpurohit AS, Rajesh R, Muhamed RR, Jaccob M, Adaikala Baskar AJ, Kannappan V. DFT investigation of role of N - H⋯O and N - H⋯π interactions in the stabilization of the hydrogen bonded complexes of anisole with aromatic amines. Heliyon 2019; 5:e02155. [PMID: 31388586 PMCID: PMC6667824 DOI: 10.1016/j.heliyon.2019.e02155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 11/18/2022] Open
Abstract
Theoretical investigations have been performed on hydrogen (H-) bonded complexes of two aromatic amines with anisole to investigate the effect of the methyl substituent on N – H⋯O and N – –H⋯π interactions. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses were done to elucidate the nature of H- bonding. In 1:1 complexes, the total interaction energy of N-methylaniline complex is higher than that of aniline complex. The existence of bond critical point between N–H of amine and oxygen of anisole confirms weak hydrogen bonding. The energy decomposition analysis showed the role of CT in stabilizing complexes.
Collapse
Affiliation(s)
| | - R Rajesh
- Department of Physics, Sri Vijay Vidyalaya College of Arts and Science, Nallampalli, Dharmapuri, 636807, India
| | - R Raj Muhamed
- Department of Physics, Jamal Mohamed College, Tiruchirappalli, 621 004, India
| | - M Jaccob
- Department of Chemistry, Loyola College, Chennai 600 034, India
| | | | - V Kannappan
- Department of Chemistry, Presidency College, Chennai, 600 005, India
| |
Collapse
|
14
|
Shehata MR, Shoukry MM, Mabrouk MA, Kozakiewicz A, van Eldik R. Studies on Pd(1,4-bis(2-hydroxyethyl)piperazine)-dicarboxylic acid complexes as models for carboplatin with structural features enhancing the interaction with DNA. J COORD CHEM 2019. [DOI: 10.1080/00958972.2019.1632441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Mohamed R. Shehata
- Department of Chemistry, Faculty of Science, University of Cairo, Giza, Egypt
| | - Mohamed M. Shoukry
- Department of Chemistry, Faculty of Science, University of Cairo, Giza, Egypt
- Department of Chemistry, Faculty of Science, Islamic University, Madinah, Saudi Arabia
| | - Mahmoud A. Mabrouk
- Egyptian Academy for Engineering & Advanced Technology (EAE & AT) Affiliated to Ministry of Military Production, Cairo, Egypt
| | - Anna Kozakiewicz
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Rudi van Eldik
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| |
Collapse
|
15
|
Komeiji Y, Okiyama Y, Mochizuki Y, Fukuzawa K. Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yuto Komeiji
- Biomedical Research Institute, National Institute of Industrial Science and Technology, AIST Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshio Okiyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kanagawa 210-9501, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| |
Collapse
|
16
|
Brela MZ, Boczar M, Malec LM, Wójcik MJ, Nakajima T. Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 197:194-201. [PMID: 29395929 DOI: 10.1016/j.saa.2018.01.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 06/07/2023]
Abstract
Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.
Collapse
Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Leszek M Malec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan.
| | - Takahito Nakajima
- RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| |
Collapse
|
17
|
Gatti C, Macetti G, Boyd RJ, Matta CF. An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States †. J Comput Chem 2018; 39:1112-1128. [PMID: 29681131 DOI: 10.1002/jcc.25222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/17/2018] [Accepted: 03/19/2018] [Indexed: 01/29/2023]
Abstract
The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, 20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, Via Brera 28, Milano, 20121, Italy
| | - Giovanni Macetti
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, Milano, 20133, Italy
| | - Russell J Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3
| | - Chérif F Matta
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3.,Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada, B3M 2J6.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada, B3H 3C3.,Dép. de chimie, Université Laval, Québec, Québec, Canada, G1V 0A6
| |
Collapse
|
18
|
Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L. Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs. Nucleic Acids Res 2017; 45:11019-11032. [PMID: 28977572 PMCID: PMC5737201 DOI: 10.1093/nar/gkx757] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 08/17/2017] [Indexed: 12/13/2022] Open
Abstract
The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Qingyun Zhang
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy.,King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
19
|
Abstract
The minidumbbell (MDB) is a new type of native DNA structure. At neutral pH, two TTTA or CCTG repeats can fold into the highly compact MDB with a melting temperature of ∼22 °C. Owing to the relatively low thermodynamic stability, MDBs have been proposed to be the structural intermediates that lead to efficient DNA repair escape and thus repeat expansions. In this study, we reveal that two CCTG repeats can also form an extraordinarily stable MDB with a melting temperature of ∼46 °C at pH 5.0. This unusual stability predominantly results from the formation of a three hydrogen bond C+·C mispair between the two minor groove cytosine residues. Due to the drastic stability change, the CCTG MDB, when combined with its complementary sequence, shows instant and complete structural conversions when the pH switches between 5.0 and 7.0, making the system serve as a simple and efficient pH-controlled molecular switch.
Collapse
Affiliation(s)
- Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| |
Collapse
|
20
|
Zheng S, Xu S, Wang G, Tang Q, Jiang X, Li Z, Xu Y, Wang R, Lin F. Proposed Hydrogen-Bonding Index of Donor or Acceptor Reflecting Its Intrinsic Contribution to Hydrogen-Bonding Strength. J Chem Inf Model 2017; 57:1535-1547. [DOI: 10.1021/acs.jcim.7b00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suqing Zheng
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
| | - Shaofang Xu
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
| | - Guitao Wang
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Qing Tang
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
| | - Xiaonan Jiang
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Zhanting Li
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Yong Xu
- Institute
of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science
Park, Guangzhou, Guangdong 510530, P. R. China
| | - Renxiao Wang
- State
Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China
| | - Fu Lin
- School
of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, P. R. China
| |
Collapse
|
21
|
Alswaidan IA, Sooknah K, Rhyman L, Parlak C, Ndinteh DT, Elzagheid MI, Ramasami P. 2,4-Ditellurouracil and its 5-fluoro derivative: Theoretical investigations of structural, energetics and ADME parameters. Comput Biol Chem 2017; 68:56-63. [PMID: 28236747 DOI: 10.1016/j.compbiolchem.2017.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/17/2016] [Accepted: 02/02/2017] [Indexed: 11/29/2022]
Abstract
2,4-Ditellurouracil exhibits keto-enol tautomerism via different pathways resulting in seven tautomers. These pathways were studied in the gas phase using density functional theory method. The functionals used were BLYP, B3LYP and BHLYP and the basis sets were 6-311++G(d,p) for all atoms except that LanL2DZ ECP was used for tellurium atom only. The results indicate that the diketo form is more stable as observed for uracil and its sulfur and selenium analogues. The effect of introducing fluorine at position 5 was also investigated and the energy difference between the diketo and dienol forms is reduced. 2,4-Ditellurouracil and its 5-fluoro analogue are expected to exist exclusively as the diketo form due to the high interconversion energy barrier. We extended the investigation to predict ADME parameters of the most stable diketo and dienol tautomers in view of understanding their biological properties. This research enlightens keto-enol tautomerism of 2,4-ditellurouracil and its 5-fluoro derivative with additional insights to biological functions.
Collapse
Affiliation(s)
- Ibrahim A Alswaidan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kritish Sooknah
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
| | - Lydia Rhyman
- Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg 2028, South Africa; Department of Chemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Cemal Parlak
- Department of Physics, Science Faculty, Ege University, Bornova, Izmir, 35100, Turkey
| | - Derek T Ndinteh
- Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg 2028, South Africa
| | - Mohamed I Elzagheid
- Department of Chemical and Process Engineering, Jubail Industrial College, Jubail Industrial City 31961, Saudi Arabia
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius; Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg 2028, South Africa; Department of Chemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, 2006, South Africa.
| |
Collapse
|
22
|
Shi Y, Jiang W, Zhang Z, Wang Z. Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs. NEW J CHEM 2017. [DOI: 10.1039/c7nj03088f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).
Collapse
Affiliation(s)
- Yulei Shi
- Beijing Key Laboratory for Terahertz Spectroscopy and Imaging
- Key Laboratory of Terahertz Optoelectronics
- Ministry of Education
- Department of Physics
- Capital Normal University
| | - Wanrun Jiang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
| | - Zhiyuan Zhang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
- Institute of Theoretical Chemistry
| |
Collapse
|
23
|
Chakraborty R, Ghosh D. The effect of sequence on the ionization of guanine in DNA. Phys Chem Chem Phys 2016; 18:6526-33. [PMID: 26864778 DOI: 10.1039/c5cp07804k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected ωB97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge-dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge-dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r(3) distance dependence which shows the major role played by charge-dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.
Collapse
Affiliation(s)
- Rahul Chakraborty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| |
Collapse
|
24
|
El-Mellouhi F, Marzouk A, Bentria ET, Rashkeev SN, Kais S, Alharbi FH. Hydrogen Bonding and Stability of Hybrid Organic-Inorganic Perovskites. CHEMSUSCHEM 2016; 9:2648-2655. [PMID: 27604510 DOI: 10.1002/cssc.201600864] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 05/13/2023]
Abstract
In the past few years, the efficiency of solar cells based on hybrid organic-inorganic perovskites has exceeded the level needed for commercialization. However, existing perovskites solar cells (PSCs) suffer from several intrinsic instabilities, which prevent them from reaching industrial maturity, and stabilizing PSCs has become a critically important problem. Here we propose to stabilize PSCs chemically by strengthening the interactions between the organic cation and inorganic anion of the perovskite framework. In particular, we show that replacing the methylammonium cation with alternative protonated cations allows an increase in the stability of the perovskite by forming strong hydrogen bonds with the halide anions. This interaction also provides opportunities for tuning the electronic states near the bandgap. These mechanisms should have a universal character in different hybrid organic-inorganic framework materials that are widely used.
Collapse
Affiliation(s)
- Fedwa El-Mellouhi
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar.
| | - Asma Marzouk
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
| | - El Tayeb Bentria
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
| | - Sergey N Rashkeev
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar.
| | - Sabre Kais
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
- Department of Chemistry, Physics, and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Fahhad H Alharbi
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| |
Collapse
|
25
|
Sponer J, Berger I, Spačková N, Leszczynski J, Hobza P. Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations. J Biomol Struct Dyn 2016; 17 Suppl 1:1-24. [PMID: 22607400 DOI: 10.1080/07391102.2000.10506597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.
Collapse
Affiliation(s)
- J Sponer
- a J. Heyrovský Institute of Physical Chemistiy, Academy of Sciences of the Czech Republic , Dolejškova 3 , 182 23 , Prague , Czech Republic
| | | | | | | | | |
Collapse
|
26
|
Chawla M, Credendino R, Chermak E, Oliva R, Cavallo L. Theoretical Characterization of the H-Bonding and Stacking Potential of Two Nonstandard Nucleobases Expanding the Genetic Alphabet. J Phys Chem B 2016; 120:2216-24. [DOI: 10.1021/acs.jpcb.6b00125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mohit Chawla
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raffaele Credendino
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department
of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
27
|
Ravi Kumar V, Verma C, Umapathy S. Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone. J Chem Phys 2016; 144:064302. [DOI: 10.1063/1.4941058] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
28
|
MP2 study on the hydrogen-bonding interaction between 5-fluorocytosine and DNA bases: A, C, G, T. Struct Chem 2015. [DOI: 10.1007/s11224-015-0624-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
29
|
Matthews RP, Welton T, Hunt PA. Hydrogen bonding and π–π interactions in imidazolium-chloride ionic liquid clusters. Phys Chem Chem Phys 2015; 17:14437-53. [DOI: 10.1039/c5cp00459d] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The importance of 1° and 2° hydrogen-bonding and anion–π+ interactions for ionic liquid structuring.
Collapse
Affiliation(s)
| | - Tom Welton
- Department of Chemistry
- Imperial College London
- London
- UK
| | | |
Collapse
|
30
|
Fukuzawa K, Watanabe C, Kurisaki I, Taguchi N, Mochizuki Y, Nakano T, Tanaka S, Komeiji Y. Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
31
|
Qiu ZM, Wang GL, Wang HL, Xi HP, Hou D. MP2 study on the hydrogen-bonding interaction between 5-fluorouracil and DNA bases: A,C,G,T. Struct Chem 2014. [DOI: 10.1007/s11224-014-0427-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
32
|
Influence of Magnetic Microparticles Isolation on Adenine Homonucleotides Structure. MATERIALS 2014; 7:1455-1472. [PMID: 28788525 PMCID: PMC5453271 DOI: 10.3390/ma7031455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 12/16/2013] [Accepted: 02/17/2014] [Indexed: 02/07/2023]
Abstract
The electroactivity of purine and pyrimidine bases is the most important property of nucleic acids that is very useful for determining oligonucleotides using square wave voltammetry. This study was focused on the electrochemical behavior of adenine-containing oligonucleotides before and after their isolation using paramagnetic particles. Two peaks were detected-peak A related to the reduction of adenine base and another peak B involved in the interactions between individual adenine strands and contributes to the formation of various spatial structures. The influence of the number of adenine bases in the strand in the isolation process using paramagnetic particles was investigated too.
Collapse
|
33
|
Aliakbar Tehrani Z, Jamshidi Z. Watson–Crick versus imidazopyridopyrimidine base pairs: theoretical study on differences in stability and hydrogen bonding strength. Struct Chem 2014. [DOI: 10.1007/s11224-014-0397-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
34
|
MP2 study on the hydrogen-bonding interaction between O 4-methylthymine and DNA bases: A, C, G, and T. Struct Chem 2013. [DOI: 10.1007/s11224-013-0335-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
35
|
Huang X, Dong Y, Huang Q, Cheng Y. Hydrogen bond induced fluorescence recovery of coumarin-based sensor system. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.05.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
36
|
Jissy AK, Konar S, Datta A. Molecular Switching Behavior in Isosteric DNA Base Pairs. Chemphyschem 2013; 14:1219-26. [DOI: 10.1002/cphc.201201083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Indexed: 12/22/2022]
|
37
|
Qiu ZM, Cai HZ, Wang HL, Xia YM, Wang HJ. DFT and MP2 investigations on the hydrogen bonding interaction between 5,6-dihydrothymine and dna bases: A, C, G, T. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476612060042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
38
|
Rees GJ, Day SP, Lari A, Howes AP, Iuga D, Pitak MB, Coles SJ, Threlfall TL, Light ME, Smith ME, Quigley D, Wallis JD, Hanna JV. A multinuclear solid state NMR, density functional theory and X-Ray diffraction study of hydrogen bonding in Group I hydrogen dibenzoates. CrystEngComm 2013. [DOI: 10.1039/c3ce41258j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
39
|
Oliveira BGD. Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H−δ⋯H+δdihydrogen bonds. Phys Chem Chem Phys 2013; 15:37-79. [DOI: 10.1039/c2cp41749a] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
40
|
Synthesis and reactivity of enediyne–nucleobase hybrids: effect of intramolecular π-stacking. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.07.093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
41
|
Seio K, Ukawa H, Shohda KI, Sekine M. Computational Evaluation of Intermolecular Interactions of a Universal Base 3-Nitropyrrole in Stacked Dimers and DNA Duplexes. J Biomol Struct Dyn 2012; 22:735-46. [PMID: 15842178 DOI: 10.1080/07391102.2005.10507040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The stacking interactions between a universal base of 3-nitropyrrole (3NP) and four canonical nucleobases were studied by means of ab initio molecular orbital calculations. The stabilities of the complexes are comparable to those of the stacked dimers of canonical bases reported previously. The detailed analysis of the interaction energies revealed the importance of the dipole-dipole interaction included in the Hartree-Fock terms to determine the geometry dependence of the stacking energies. It was also clarified that the dispersion energies included in the electron-correlation terms were essential to obtain adequate stabilities. The contribution of the nitro group was evaluated by the comparative studies of pyrrole and 3NP. The increased molecular dipole moment and surface are expected to account for the enhancement of the stability of the stacked dimers containing 3NP. The force field parameters required for calculation of the molecular mechanics of 3NP were obtained for 3NP on the basis of these molecular orbital calculations. The energy-minimized structures obtained by the molecular mechanics calculations of 3NP accorded with those obtained by the molecular orbital calculations described above. A DNA duplex structure containing 3NP-A, 3NP-T, or 3NP-C was calculated by use of these force field parameters. In the case of 3NP-A, the computationally calculated structure was in good agreement with that previously determined by use of (1)H-NMR except for the orientation of the nitro group.
Collapse
Affiliation(s)
- Kohji Seio
- Frontier Collaborative Research Center, Tokyo Institute of Technology, Tokyo, Japan
| | | | | | | |
Collapse
|
42
|
Can anion interaction accelerate transformation of cytosine tautomers? Detailed view form QTAIM analysis. Struct Chem 2012. [DOI: 10.1007/s11224-012-9993-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
43
|
MP2 study on the hydrogen bonding interaction between 5-hydroxy-5-methylhydantoin and DNA bases: A, C, G, T. Struct Chem 2011. [DOI: 10.1007/s11224-011-9918-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
44
|
Parthasarathi R, Bellesia G, Chundawat SPS, Dale BE, Langan P, Gnanakaran S. Insights into Hydrogen Bonding and Stacking Interactions in Cellulose. J Phys Chem A 2011; 115:14191-202. [DOI: 10.1021/jp203620x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - S. P. S. Chundawat
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824, United States
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - B. E. Dale
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824, United States
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - P. Langan
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
| | | |
Collapse
|
45
|
Yurenko YP, Zhurakivsky RO, Samijlenko SP, Hovorun DM. Intramolecular CH···O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their Watson-Crick pairs. Quantum chemical and AIM analysis. J Biomol Struct Dyn 2011; 29:51-65. [PMID: 21696225 DOI: 10.1080/07391102.2011.10507374] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The aim of this work is to cast some light on the H-bonds in double-stranded DNA in its AI and BI forms. For this purpose, we have performed the MP2 and DFT quantum chemical calculations of the canonical nucleoside conformers, relative to the AI and BI DNA forms, and their Watson-Crick pairs, which were regarded as the simplest models of the double-stranded DNA. Based on the atoms-in-molecules analysis (AIM), five types of the CH···O hydrogen bonds, involving bases and sugar, were detected numerically from 1 to 3 per a conformer: C2'H···O5', C1'H···O2, C6H···O5', C8H···O5', and C6H···O4'. The energy values of H-bonds occupy the range of 2.3-5.6 kcal/mol, surely exceeding the kT value (0.62 kcal/mol). The nucleoside CH···O hydrogen bonds appeared to "survive" turns of bases against the sugar, sometimes in rather large ranges of the angle values, pertinent to certain conformations, which points out to the source of the DNA lability, necessary for the conformational adaptation in processes of its functioning. The calculation of the interactions in the dA·T nucleoside pair gives evidence, that additionally to the N6H···O4 and N1···N3H canonical H-bonds, between the bases adenine and thymine the third one (C2H···O2) is formed, which, though being rather weak (about 1 kcal/mol), satisfies the AIM criteria of H-bonding and may be classified as a true H-bond. The total energy of all the CH···O nontraditional intramolecular H-bonds in DNA nucleoside pairs appeared to be commensurable with the energy of H-bonds between the bases in Watson-Crick pairs, which implies their possible important role in the DNA shaping.
Collapse
Affiliation(s)
- Yevgen P Yurenko
- Laboratory of Computational Structural Biology, Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Street, Kyiv 03143, Ukraine
| | | | | | | |
Collapse
|
46
|
MP2 study on the hydrogen-bonding interaction between 5-hydroxymethyl-uracil and DNA bases: A, C, G, T. Struct Chem 2010. [DOI: 10.1007/s11224-010-9718-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
47
|
Pyrkov TV, Ozerov IV, Blitskaia ED, Efremov RG. [Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:482-92. [PMID: 20823916 DOI: 10.1134/s1068162010040023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge of 3D-structure of protein-ligand complex is a major prerequisite for understanding the functioning mechanism of cellular proteins and membrane receptors. This is also of a great help in rational drug design projects. In the present paper we briefly review the molecular docking approaches used to predict possible orientation of a ligand in the protein binding site. The recent trends to improve the accuracy and efficiency of docking algorithms are demonstrated with the results obtained in Laboratory of Biomolecular Modeling. Particular attention is paid to protein-ligand hydrophobic and stacking interactions responsible for molecular recognition of ligand fragments. Such type of interactions are not always adequately represented in scoring criteria of docking applications that leads to mismatch in 3D-structure complexes predictions. That is why further inquiry of methods to account for these interactions is now the area of active research.
Collapse
|
48
|
|
49
|
Koller AN, Bozilovic J, Engels JW, Gohlke H. Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs. Nucleic Acids Res 2010; 38:3133-46. [PMID: 20081201 PMCID: PMC2875010 DOI: 10.1093/nar/gkp1237] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The thermodynamics of base pairing is of fundamental importance. Fluorinated base analogs are valuable tools for investigating pairing interactions. To understand the influence of direct base-base interactions in relation to the role of water, pairing free energies between natural nucleobases and fluorinated analogs are estimated by potential of mean force calculations. Compared to pairing of AU and GC, pairing involving fluorinated analogs is unfavorable by 0.5-1.0 kcal mol(-1). Decomposing the pairing free energies into enthalpic and entropic contributions reveals fundamental differences for Watson-Crick pairs compared to pairs involving fluorinated analogs. These differences originate from direct base-base interactions and contributions of water. Pairing free energies of fluorinated base analogs with natural bases are less unfavorable by 0.5-1.0 kcal mol(-1) compared to non-fluorinated analogs. This is attributed to stabilizing C-F(...)H-N dipolar interactions and stronger N(...)H-C hydrogen bonds, demonstrating direct and indirect influences of fluorine. 7-methyl-7H-purine and its 9-deaza analog (Z) have been suggested as members of a new class of non-fluorinated base analogs. Z is found to be the least destabilizing universal base in the context of RNA known to date. This is the first experimental evidence for nitrogen-containing heterocylces as bioisosteres of aromatic rings bearing fluorine atoms.
Collapse
Affiliation(s)
- Alrun N Koller
- Department of Mathematics and Natural Sciences, Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | | | | |
Collapse
|
50
|
Theoretical study of the interaction pattern and the binding affinity between procaine and DNA bases. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.09.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|