Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study (original) (raw)
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Influence of hydrogen bonding on the geometry of the adenine fragment
Journal of Molecular Structure, 1996
The crystal structures of two adenine derivatives, N(6),9-dimethyl-8-butyladenine (I) and its hydrate (1 : 1) (II), have been determined by single-crystal X-ray diffraction. The geometrical features of both structures are discussed. The influence of protonation, substitution and hydrogen bond formation on the geometry of the adenine fragment was studied, based on data retrieved from the Cambridge Structural Database. Total correlation analysis showed mutual correlation between the structural parameters in the adenine ring system; partial correlation calculations for the adenine nucleoside fragments suggest intercorrelation between the parameters of the hydrogen bonding involved in base pairing and the N(adenine)-C(sugar) bond through the adenine fragment; few such correlations were found for fragments without the sugar substituent.
The Journal of Physical Chemistry B, 2008
The amino group in adenine plays a key role in formation of hydrogen bonds in nucleic acids and in other molecular systems. Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. Ab initio MP2 and density functional B3LYP methods with various basis sets have been used to calculate the optimized structure and the infrared spectrum of adenine (the N9-H tautomer). Calculations at the MP2 level with larger basis sets tend to decrease the degree of pyramidalization of the C-NH 2 group, whereas the B3LYP method consistently yields the planar or nearly planar structure of adenine. MP2 complete basis set (CBS) limit method with the aug-cc-pVTZ f aug-cc-pVQZ (aTZ f aQZ) extrapolation scheme has predicted very small planarization barrier of adenine, 0.015 kcal/mol, which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III, J. Chem. . Similar results were obtained in calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be concluded that the amino group in adenine, in the gas phase, is very flexible with a small degree of nonplanarity. Extremely low planarization barrier implies that adenine requires very little energy to conform the structure of the amino group to formation of the complementary hydrogen bonds with other molecules. This fact is very important for base pairing in nucleic acids or other polymers containing adenine residues. The anharmonic frequencies of adenine have been calculated at the B3LYP/6-311++G(df,pd) level of theory. The theoretical results show excellent agreement with the available experimental data. The revised assignment of the infrared spectrum of adenine in Ar matrix has been made. The predicted anharmonic frequency of the NH 2 inversion, 181 cm -1 , is supported by the experimental data. It is demonstrated that the vibrational frequencies and potential energy distribution (PED) obtained from the B3LYP calculations are more reliable than those obtained at the MP2 level.
Journal of Molecular Structure, 2009
The Raman (3700-100 cm À1 ), infrared (4000-200 cm À1 ), mass spectrum and 1 H NMR temperaturedependent study of adenine have been recorded. Quantum chemical calculations were carried out for N(9)H-amino, N(7)H-amino, N(9)H-imino and N(7)H-imino adenine tautomers using RHF, B3LYP and MP2 with full electron correlation up to 6-311++G(d,p) basis set. The computational results reveal the non-planar N(9)H-amino conformer of adenine to be the most stable structure of adenine. The planar (C s ) form of N(9)H-amino adenine is found to represent a transition state, lying 8 cm À1 above the non-planar conformer and with one imaginary frequency. Comparison between theoretical and experimental 1 H NMR spectra favors the assignment of the signals to N9(H) and N7(H)-amino tautomers over the corresponding imino tautomers. On the other hand, the recorded IR, Raman and 13 C NMR spectra were fully consistent with N9(H)-amino adenine tautomer, therefore it is the only tautomer in both the gas and solid phases and in solution. Moreover, the results of NH 2 potential surface scans utilizing B3LYP and MP2 = full methods at 6-31G(d) basis also support the non-planarity of N(9)H-amino adenine. The mass spectral measurements indicate the presence of 3% adenine dimmer which indicates weak inter-molecular hydrogen bonding interactions in adenine. Additionally, intramolecular hydrogen bonding is also predicted between N 1 and H 15 atoms. The theoretical infrared and Raman spectra have been successfully simulated by means of both DFT and MP2 calculations, allowing the interpretation of the complex bands observed. Aided by normal coordinate analysis, potential energy distributions and the calculated force constants, a revised and accurate vibrational assignment for all fundamentals has been provided for the non-planar N(9)H-adenine tautomer. The results are reported herein and compared with similar molecules whenever appropriate.
The Many Facets of Adenine: Coordination, Crystal Patterns, and Catalysis
Accounts of Chemical Research, 2010
C anonical purine-pyrimidine base pairs, the key to the complementary hydrogen bonding in nucleic acids, are fundamental molecular recognition motifs crucial for the formation and stability of double-helical DNA. Consequently, focused study and modeling of nucleobase hydrogen-bonding schemes have spawned a vast array of chemical and biophysical investigations. The Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen hydrogen-bonding schemes stabilize various nucleic acid structures. As a result, numerous modified bases have been designed to maximize such interactions, addressing specific problems related to base pairing and giving rise to supramolecular ensembles in solution or in the solid state. It is also important to realize that suitably predisposed imino nitrogens and other functional groups present in heterocyclic nucleobases present a versatile molecular framework for the construction of coordination architectures, which may be harnessed to mimic base polyads and higher order nucleic acid structures. Adenine, a purine nucleobase, is an important naturally occurring nitrogen heterocycle present in nucleic acids. It is notable that the adenine unit is also frequently encountered as an inextricable part of enzyme cofactors and second messenger systems, such as NAD + , FADH 2 , and cAMP, which are essential for certain catalytic reactions and biochemical processes. In addition, a crucial catalytic role of the adenine moiety is also observed in group II intron catalysis and at the ribosomal peptidyltransferase center. Such versatile functional roles of the adenine framework serve as an inspiration for addressing research problems, ranging from classical coordination chemistry to the development of new materials. In this Account, we begin by describing the emerging use of adenine nucleobase for the design of metal-nucleobase frameworks. The coordination of metal ions affords a variety of oligomeric and polymeric species; we focus on silver-and copperbased structures and also discuss ferrocenylated adenine tetrads. We then consider the use of supramolecular adenine coordination complexes for transferring molecular properties onto surfaces. This technique is particularly useful for transferring noncovalent interactions, such as van der Waals forces, electrostatic interactions, and hydrogen bonding, to designed architectures in nanoscale applications. Finally, we explore the issue of adenine-based catalytic entities. Here, adenine moieties are first fixed in a polymeric matrix, followed by metalation of the matrix. These metalated adenine-containing polymers are then assayed for catalytic assistance in various chemical and biochemical reactions. Taken together, the versatile coordination abilities and hydrogenbonding capacity of adenine offer a novel entry point for a natural ligand into materials synthesis.
Journal of …, 1990
C A quantum chemical study of 10 substrates of adenosine deaminase is performed. The conformational preference around the glycosidic bond of several 8-substituted derivatives of adenosine is studied using semiempirical modified neglect of diatomic overlap (MNDO) and Austin model 1 (AM1) methods. All the compounds studied show preference for the anti conformation; the synanti energetic differences calculated are small and in excellent agreement with experimental data. A relationship between the ab initio molecular electrostatic potential minimum energy of N 3 and the synanti energetic difference is found. A highly significant relationship is also found between the ab initio net charge over the purine and pyrimidine rings and the logarithm of the maximum rate of deamination (log V, ) of the nucleosides by adenosine deaminase. In contrast, no significant relationship is found between the anti preference of 8-substituted derivatives of adenosine and their log V, of deamination.
Quantum chemical calculation of the (S)-9-(2,3-dihydroxypropyl)adenine molecule a
Nucleic Acids Research, 1980
Quantum chemical calculations of conformational maps of the molecule of a new virostatic agent (S)-9-(2,3-dihydroxypropyl)adenine were performed. The thermodynamically most advantageous conformation I corresponds, for the D-series, to the x-ribo configuration, while the following minima, which are close in energy (II,III), correspond to P-ribo and P-xylo configurations.
Two-dimensional self-assembled structures of adenine molecules: modeling and simulation
Surface Science, 2004
Self-assembly of adenine molecules deposited on a Cu(1 1 1) surface shows some characteristic hydrogen-bonding network patterns, such as hexagonal and 'double-chain'. In order to understand the emergence of energetically less favorable 'double-chain' structure, in which adenine molecules form two rows, possible molecular arrangements in the 'double-chain' structure are investigated by potential energy surface (PES) calculations between two single chains. A series of PES calculations elucidates that there are various stable molecular arrangements for the chain pair models: some of the models have both hexagonal and 'double-chain' (I-type) hydrogen-bonding patterns, while the others have only the latter pattern (II-type). Molecular dynamics simulations starting from the obtained 'double-chain' structures are also performed to assess the thermal stability of the structure. It is revealed that some of the II-type 'double-chain' structures remain even at 300 K, while all I-type ones transform into hexagonal arrays. The former result reminds us that the II-type 'double-chain' structures should be observed at room temperature in the STM experiment.
Differential stabilization of adenine quartets by anions and cations
JBIC Journal of Biological Inorganic Chemistry, 2010
We have investigated the structures and stabilities of four different adenine quartets with alkali and halide ions in the gas phase and in water, using dispersioncorrected density functional theory at the BLYP-D/TZ2P level. First, we examine the empty quartets and how they interact with alkali cations and halide anions with formation of adenine quartet-ion complexes. Second, we examine the interaction in a stack, in which a planar adenine quartet interacts with a cation or anion in the periphery as well as in the center of the quartet. Interestingly, for the latter situation, we find that both cations and anions can stabilize a planar adenine quartet in a stack.
Adenine as a Halogen Bond Acceptor: A Combined Experimental and DFT Study
Crystals
In this work, we report the cocrystallization of N9-ethyladenine with 1,2,4,5-tetrafluoro-3,6-diiodobenzene (TFDIB), a classical XB donor. As far as our knowledge extends, this is the first cocrystal reported to date where an adenine derivative acts as a halogen bond acceptor. In the solid state, each adenine ring forms two centrosymmetric H-bonded dimers: one using N1···HA6–N6 and the other N7···HB6–N6. Therefore, only N3 is available as a halogen bond acceptor that, indeed, establishes an N···I halogen bonding interaction with TFDIB. The H-bonded dimers and halogen bonds have been investigated via DFT (Density Functional Theory) calculations and the Bader’s Quantum Theory of Atoms In Molecules (QTAIM) method at the B3LYP/6-311+G* level of theory. The influence of H-bonding interactions on the lone pair donor ability of N3 has also been analyzed using the molecular electrostatic potential (MEP) surface calculations.