Hoogsteen and Stacked Structures of the 9-Methyladenine···1-Methylthymine Pair Are Populated Equally at Experimental Conditions:  Ab Initio and Molecular Dynamics Study

Ryjáček, Filip; Engkvist, Ola; Vacek, Jaroslav; Kratochvíl, Martin; Hobza, Pavel

doi:10.1021/jp003078a

Cited by 31 publications

(26 citation statements)

References 22 publications

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“…The energies and coordinates of the resulting minima are stored and subsequently the MD simulation continues from the point at which it was stopped. A more detailed description of the procedure can be found in reference 22.…”

Section: Methodsmentioning

confidence: 99%

Structure and IR Spectrum of Phenylalanyl–Glycyl–Glycine Tripetide in the Gas‐Phase: IR/UV Experiments, Ab Initio Quantum Chemical Calculations, and Molecular Dynamic Simulations

Rooney

Valdés

Vondrášek

et al. 2005

Chemistry A European J

172

144

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We investigated the potential-energy surface (PES) of the phenylalanyl-glycyl-glycine tripeptide in the gas phase by means of IR/UV double-resonance spectroscopy, and quantum chemical and statistical thermodynamic calculations. Experimentally, we observed four conformational structures and we recorded their IR spectra in the spectral region of 3000-4000 cm(-1). Computationally, we investigated the PES by a combination of molecular dynamics/quenching procedures with high-level correlated ab initio calculations. We found that neither empirical potentials nor various DFT functionals provide satisfactory results. On the other hand, the approximative DFT method covering the dispersion energy yields a reliable set of the most stable structures, which we subsequently investigated with an accurate, correlated ab initio treatment. The global minimum contains three moderately strong intramolecular hydrogen bonds and is mainly stabilized by London dispersion forces between the phenyl ring, the carboxylic acid group, and various peptide bonds. A proper description of the last type of interaction requires accurate correlated ab initio calculations, including the complete basis set limit of the MP2 method and CCSD(T) correction terms. Since in our beam experiments the conformations are frozen by cooling from a higher temperature, it is necessary to localize the most stable structures on the free-energy surface rather than on the PES. We used two different procedures (rigid rotor/harmonic oscillator/ideal gas approximation based on ab initio characteristics and evaluation of relative populations from the molecular dynamic simulations using the AMBER potential) and both yield four structures, the global minimum and three local minima. These four structures were among the 15 most energetically stable structures obtained from accurate ab initio optimization. The calculated IR spectra for these four structures agree well with the experimental frequencies, which validates the localization procedure.

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Section: Methodsmentioning

confidence: 99%

Structure and IR Spectrum of Phenylalanyl–Glycyl–Glycine Tripetide in the Gas‐Phase: IR/UV Experiments, Ab Initio Quantum Chemical Calculations, and Molecular Dynamic Simulations

Rooney

Valdés

Vondrášek

et al. 2005

Chemistry A European J

172

144

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“…First, individual base pairs were studied (uracil dimer 143 , the adenine...2,4-difluorotoluene pair 144 , methyluracil dimers 145 , the adenine...thymine pair 146 and the methyladenine...methylthymine pair 147 ), and, later, all the DNA base pairs and methylated DNA base pairs were also considered 148 .…”

Section: Nucleic Acid Base Pairsmentioning

confidence: 99%

The World of Non-Covalent Interactions: 2006

Hobza¹,

Zahradník²,

Müller‐Dethlefs³

2006

Collect. Czech. Chem. Commun.

Self Cite

247

235

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The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.

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“…The energy of interaction between bases in AT pairs of the AT-TA dimer is the same for both base pairs and its value is intermediate between relevant interaction energies in AT-AT. It should be noted that the values of the interaction energy in hydrogen bonded AT pairs of both dimers is about 1-3 kcal/mol higher as compared to values obtained for Watson-Crick pairs of unsubstituted [6] and methylated [23,24] adenine and thymine.…”

Section: Resultsmentioning

confidence: 60%

Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

Шишкин

Elstner

Frauenheim

et al. 2003

IJMS

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Abstract:The structure of two isomeric stacked dimers of Watson-Crick 9-methyladenine-1-methylthymine pairs was fully optimized using an approximate density functional theory (DFT) method augmented with an empirical dispersion interaction. The results of the calculations reveal that head-to-tail (AT-TA) and head-to-head (AT-AT) dimers possess a significantly different geometry. The structure of both complexes is stabilized by vertical C-H…O and C-H…N hydrogen bonds with the participation of the hydrogen atoms of the methyl groups. The energy of hydrogen bonding and stacking interactions was additionally calculated using the MP2/6-31G*(0.25) method. Differences in the mutual arrangement of the base pairs in two isomeric dimers lead to significant changes of intra and interstrand stacking interaction energies.

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Hoogsteen and Stacked Structures of the 9-Methyladenine···1-Methylthymine Pair Are Populated Equally at Experimental Conditions: Ab Initio and Molecular Dynamics Study

Abstract: The potential energy surface (PES) of the 9-methyladenine‚‚‚1-methylthymine (mA‚‚‚mT) nucleic acid base pair was investigated using molecular dynamics/quenching method utilizing the Cornell et al. (Cornell, W.

Cited by 31 publications

References 22 publications

Structure and IR Spectrum of Phenylalanyl–Glycyl–Glycine Tripetide in the Gas‐Phase: IR/UV Experiments, Ab Initio Quantum Chemical Calculations, and Molecular Dynamic Simulations

Structure and IR Spectrum of Phenylalanyl–Glycyl–Glycine Tripetide in the Gas‐Phase: IR/UV Experiments, Ab Initio Quantum Chemical Calculations, and Molecular Dynamic Simulations

The World of Non-Covalent Interactions: 2006

Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

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