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Eckstein BJ, Martin HR, Moghadasnia MP, Halder A, Melville MJ, Buzinski TN, Balaich GJ, McGuirk CM. Influence of donor point modifications on the assembly of chalcogen-bonded organic frameworks. Chem Commun (Camb) 2024; 60:758-761. [PMID: 38126447 DOI: 10.1039/d3cc05162e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Incremental, single-atom substitutions of Se-based chalcogen bond (Ch-bond) donors with stronger donating Te centers were implemented in two new triptycene tris(1,2,5-chalcogenadiazole) tectons. The appreciably more favorable Ch-bonding ability of the Te-based donors promotes assembly of low-density networks and more stable Ch-bonded organic frameworks (ChOFs).
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Affiliation(s)
- Brian J Eckstein
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Hannah R Martin
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | | | - Arijit Halder
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Michael J Melville
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Tara N Buzinski
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
| | - Gary J Balaich
- Department of Chemistry & Chemistry Research Center, Laboratories for Advanced Materials, United States Airforce Academy, Colorado Springs, Colorado, 80840, USA
| | - C Michael McGuirk
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, 80401, USA.
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2
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Yang X, Liu R, Xu R, Wang Z. Sequential flipping: the donor-acceptor exchange mechanism in water trimers. Phys Chem Chem Phys 2023; 25:21957-21963. [PMID: 37553960 DOI: 10.1039/d3cp02666c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The donor-acceptor exchange (DAE) is a significant hydrogen bond network rearrangement (HBNR) mechanism because it can lead to the change of the hydrogen bond direction. In this work, we report a new DAE mechanism found in water trimers that is realized by sequential flipping (SF) of all molecules rather than the well-known proton transfer (PT) process. Meanwhile, the SF process has a much smaller potential barrier (0.262 eV) than the previously predicted collective rotation process (about 1.7 eV), implying that the SF process is the main flipping process that can lead to DAE. Importantly, high-precision ab initio calculations show that SF-DAE can make the water ring to show a clear chiral difference from PT-DAE, which brings the prospect of distinguishing the two confusing processes based on circular dichroism spectra. The reaction rate analysis including quantum tunneling indicates an obvious temperature-dependent competitive relationship between the SF and PT processes; specifically, the SF process dominates above 65 K, while the PT process dominates below 65 K. Therefore, in most cases, the contribution for DAE mainly comes from the flipping process, rather than the PT process as previously thought. Our work enriches the understanding of the DAE mechanism in water trimers and provides a piece of the jigsaw that has been sought for the HBNR mechanism.
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Affiliation(s)
- Xinrui Yang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
| | - Rui Liu
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
| | - Ruiqi Xu
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China.
- International Center for Computational Method & Software, College of Physics, Jilin University, Changchun 130012, China
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3
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Othman H, Messaoud HB, Khamessi O, Ben-Mabrouk H, Ghedira K, Bharuthram A, Treurnicht F, Achilonu I, Sayed Y, Srairi-Abid N. SARS-CoV-2 Spike Protein Unlikely to Bind to Integrins via the Arg-Gly-Asp (RGD) Motif of the Receptor Binding Domain: Evidence From Structural Analysis and Microscale Accelerated Molecular Dynamics. Front Mol Biosci 2022; 9:834857. [PMID: 35237662 PMCID: PMC8883519 DOI: 10.3389/fmolb.2022.834857] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
The Receptor Binding Domain (RBD) of SARS-CoV-2 virus harbors a sequence of Arg-Gly-Asp tripeptide named RGD motif, which has also been identified in extracellular matrix proteins that bind integrins as well as other disintegrins and viruses. Accordingly, integrins have been proposed as host receptors for SARS-CoV-2. However, given that the microenvironment of the RGD motif imposes a structural hindrance to the protein-protein association, the validity of this hypothesis is still uncertain. Here, we used normal mode analysis, accelerated molecular dynamics microscale simulation, and protein-protein docking to investigate the putative role of RGD motif of SARS-CoV-2 RBD for interacting with integrins. We found, that neither RGD motif nor its microenvironment showed any significant conformational shift in the RBD structure. Highly populated clusters of RBD showed no capability to interact with the RGD binding site in integrins. The free energy landscape revealed that the RGD conformation within RBD could not acquire an optimal geometry to allow the interaction with integrins. In light of these results, and in the event where integrins are confirmed to be host receptors for SARS-CoV-2, we suggest a possible involvement of other residues to stabilize the interaction.
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Affiliation(s)
- Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Laboratory of Biomolecules, Venoms and Theranostic Applications, LR20IPT01, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- *Correspondence: Houcemeddine Othman, ; Najet Srairi-Abid,
| | - Haifa Ben Messaoud
- National Gene Bank of Tunisia, Boulevard du Leader Yesser Arafet, Tunis, Tunisia
| | - Oussema Khamessi
- Université de Tunis El Manar, Institut Pasteur de Tunis, LR11IPT08 Venins et Biomolecules Therapeutiques, Tunis, Tunisie
| | - Hazem Ben-Mabrouk
- Laboratory of Biomolecules, Venoms and Theranostic Applications, LR20IPT01, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), University of Tunis El Manar, Tunis, Tunisia
| | - Avani Bharuthram
- Department of Virology, National Health Laboratory Services and the School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette Treurnicht
- Department of Virology, National Health Laboratory Services and the School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, South Africa
| | - Najet Srairi-Abid
- Laboratory of Biomolecules, Venoms and Theranostic Applications, LR20IPT01, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- *Correspondence: Houcemeddine Othman, ; Najet Srairi-Abid,
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Arsenie LV, Semsarilar M, Brendel JC, Lacroix-Desmazes P, Ladmiral V, Catrouillet S. Supramolecular co-assembly of water-soluble nucleobase-containing copolymers: bioinspired synthetic platforms towards new biomimetic materials. Polym Chem 2022. [DOI: 10.1039/d2py00872f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study presents the development of new co-assembled copolymers architectures at physiological pH (pH=7.4) formed via H-bonds between complementary nucleobase-containing copolymers. Well-defined hydrophilic copolymers were synthesised by RAFT polymerisation: statistical...
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Slocombe L, Al-Khalili JS, Sacchi M. Quantum and classical effects in DNA point mutations: Watson-Crick tautomerism in AT and GC base pairs. Phys Chem Chem Phys 2021; 23:4141-4150. [PMID: 33533770 DOI: 10.1039/d0cp05781a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Proton transfer along the hydrogen bonds of DNA can lead to the creation of short-lived, but biologically relevant point mutations that can further lead to gene mutation and, potentially, cancer. In this work, the energy landscape of the canonical A-T and G-C base pairs (standard, amino-keto) to tautomeric A*-T* and G*-C* (non-standard, imino-enol) Watson-Crick DNA base pairs is modelled with density functional theory and machine-learning nudge-elastic band methods. We calculate the energy barriers and tunnelling rates of hydrogen transfer between and within each base monomer (A, T, G and C). We show that the role of tunnelling in A-T tautomerisation is statistically unlikely due to the presence of a small reverse reaction barrier. On the contrary, the thermal populations of the G*-C* point mutation could be non-trivial and propagate through the replisome. For the direct intramolecular transfer, the reaction is hindered by a substantial energy barrier. However, our calculations indicate that tautomeric bases in their monomeric form have remarkably long lifetimes.
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Affiliation(s)
- L Slocombe
- Leverhulme Quantum Biology Doctoral Training Centre, UK.
| | - J S Al-Khalili
- Department of Physics, University of Surrey, Guildford, GU2 7XH, UK
| | - M Sacchi
- Department of Chemistry, University of Surrey, Guildford, GU2 7XH, UK.
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Pinacolone-Alcohol Gas-Phase Solvation Balances as Experimental Dispersion Benchmarks. Molecules 2020; 25:molecules25215095. [PMID: 33153022 PMCID: PMC7662480 DOI: 10.3390/molecules25215095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
The influence of distant London dispersion forces on the docking preference of alcohols of different size between the two lone electron pairs of the carbonyl group in pinacolone was explored by infrared spectroscopy of the OH stretching fundamental in supersonic jet expansions of 1:1 solvate complexes. Experimentally, no pronounced tendency of the alcohol to switch from the methyl to the bulkier tert-butyl side with increasing size was found. In all cases, methyl docking dominates by at least a factor of two, whereas DFT-optimized structures suggest a very close balance for the larger alcohols, once corrected by CCSD(T) relative electronic energies. Together with inconsistencies when switching from a C4 to a C5 alcohol, this points at deficiencies of the investigated B3LYP and in particular TPSS functionals even after dispersion correction, which cannot be blamed on zero point energy effects. The search for density functionals which describe the harmonic frequency shift, the structural change and the energy difference between the docking isomers of larger alcohols to unsymmetric ketones in a satisfactory way is open.
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Pohl R, Socha O, Slavíček P, Šála M, Hodgkinson P, Dračínský M. Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations. Faraday Discuss 2018; 212:331-344. [PMID: 30234207 DOI: 10.1039/c8fd00070k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of the nuclei. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of the deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts provide a unique possibility to study NQEs and to evaluate the accuracy of the computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.
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Affiliation(s)
- Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Petr Slavíček
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, DH1 3LE, Durham, UK
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
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Petković M, Ristić M, Etinski M. Stability and Anharmonic N–H Stretching Frequencies of 1-Methylthymine Dimers: Hydrogen Bonding versus π-Stacking. J Phys Chem A 2016; 120:1536-44. [DOI: 10.1021/acs.jpca.5b09946] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Milena Petković
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Miroslav Ristić
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16, 11 158 Belgrade, Serbia
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10
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Lopes S, Domanskaya AV, Räsänen M, Khriachtchev L, Fausto R. Acetic acid dimers in a nitrogen matrix: Observation of structures containing the higher-energy conformer. J Chem Phys 2015; 143:104307. [DOI: 10.1063/1.4929575] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Susy Lopes
- Department of Chemistry, University of Coimbra, Rua Larga, P-3004-535 Coimbra, Portugal
| | - Alexandra V. Domanskaya
- Institute of Physical Chemistry, Georg-August University, Tammannstr 6, D-37077 Göttingen, Germany
| | - Markku Räsänen
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Leonid Khriachtchev
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Rui Fausto
- Department of Chemistry, University of Coimbra, Rua Larga, P-3004-535 Coimbra, Portugal
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Godbeer AD, Al-Khalili JS, Stevenson PD. Modelling proton tunnelling in the adenine–thymine base pair. Phys Chem Chem Phys 2015; 17:13034-44. [DOI: 10.1039/c5cp00472a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Environment-assisted quantum tunnelling is unlikely to play a significant role in adenine–thymine tautomerisation.
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12
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The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine–cytosine base pairs in Watson–Crick and Hoogsteen configurations. J Mol Model 2014; 20:2113. [DOI: 10.1007/s00894-014-2113-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
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13
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EMAMIAN SAEEDREZA, TAYYARI SAYYEDFARAMARZ. Theoretical study of intramolecular hydrogen bonding in the halo derivatives of 1-amino-3-imino-prop-1-ene. J CHEM SCI 2013. [DOI: 10.1007/s12039-013-0466-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Boeckx B, Maes G. Simulating the Interaction between Amino Acids and DNA: A Combined Matrix-Isolation FT-IR and Theoretical Study of the 1-Methyluracil·Glycine H-Bond Complexes Using a Dual Sublimation Furnace. J Phys Chem B 2012; 116:11890-8. [DOI: 10.1021/jp307388e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bram Boeckx
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
| | - Guido Maes
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
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Houjou H. Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond? J Chem Phys 2012; 135:154111. [PMID: 22029301 DOI: 10.1063/1.3652102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.
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Affiliation(s)
- Hirohiko Houjou
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Tokyo 153-8505, Japan.
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Cerón-Carrasco JP, Jacquemin D, Cauët E. Cisplatin cytotoxicity: a theoretical study of induced mutations. Phys Chem Chem Phys 2012; 14:12457-64. [DOI: 10.1039/c2cp40515f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Cerón-Carrasco JP, Jacquemin D. Influence of Mg2+ on the Guanine-Cytosine Tautomeric Equilibrium: Simulations of the Induced Intermolecular Proton Transfer. Chemphyschem 2011; 12:2615-23. [DOI: 10.1002/cphc.201100264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/28/2011] [Indexed: 01/01/2023]
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Bende A, Bogdan D, Muntean CM, Morari C. Localization and anharmonicity of the vibrational modes for GC Watson-Crick and Hoogsteen base pairs. J Mol Model 2011; 17:3265-74. [PMID: 21369937 DOI: 10.1007/s00894-011-1002-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/28/2011] [Indexed: 10/18/2022]
Abstract
We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson-Crick and Hoogsteen base pair configurations. The results are obtained by using two different implementations of the DFT method. We assign the vibrational frequencies to cytosine or to guanine using the vibrational density of states. Next, we investigate the importance of anharmonic corrections for the vibrational modes. In particular, the unusual anharmonic effect of the H(+) vibration in the case of the Hoogsteen base pair configuration is discussed.
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Affiliation(s)
- Attila Bende
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donath Street, No. 65-103, 400293 Cluj-Napoca, Romania
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Tachikawa H, Fukuzumi T. Ionization dynamics of aminopyridine dimer: a direct ab initio molecular dynamics (MD) study. Phys Chem Chem Phys 2011; 13:5881-7. [DOI: 10.1039/c0cp01542c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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