Caffeine interactions with nucleic acids. Molecular mechanics calculations of model systems for explanation of mechanisms of biological actions

To understand the molecular mechanisms of the influence of caffeine (CAF) on DNA functioning, molecular mechanics calculations of the interaction energy of CAF with nucleic acid bases and base pairs have been performed. The calculations reveal three types of mutual CAF–base (and CAF–base pair) arrangements corresponding to minima of the interaction energy. Besides well-known stacking mutual positions of the molecules, two other types of arrangements are revealed and studied. One of these arrangements corresponds to the nearly in-plane position of CAF and base (or base pair) and the formation of a single hydrogen bond. Another type of minimum corresponds to nearly perpendicular arrangements of the molecular planes and the formation of intermolecular hydrogen bonds. These two arrangements are possible both for individual nucleic acid monomers and for DNA duplexes. The calculations suggest the molecular mechanisms of the influence of CAF on DNA interactions with other biologically active molecules.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 20002).     

Ab initio force field for simulations of proteins and nucleic acids

We present a new self-consistent set of ab initio analytical pair potential to predict specific nonbonded interactions of protein with nucleic acid, of protein with protein, and of nucleic acid with nucleic acid. The purpose of this study is to represent the interaction between biological molecules with an accuracy equivalent to the ab initio molecular orbital calculations, which are used as reference data to obtain the pair potentials. Atoms in nucleic acids and proteins are classified according to their chemical environments. An “effective charge,” a modification of a charge obtained from the Mulliken population analysis, is introduced and used to represent the electrostatic energy. More than 30,000 SCF interaction energies have been calculated to provide the reference data for the fitting procedure that we have adopted in the parameterization of the potentials. The standard deviation is 1.61 kcal/mol for interaction energies spanning the range from about ?220 kcal/mol to +20 kcal/mol. Molecular dynamics simulations, using the above new set of force field, have been performed successfully for the systems where adequate treatments of specific interactions are required: The stability of α-helix of C-peptide and the interaction of spermine with oligonucleotide are examined as preliminary examples.     

The effect of methylation on the hydrogen-bonding and stacking interaction of nucleic acid bases

Methylated nucleosides play an important role in DNA/RNA function, and may affect republication by interrupting the base-pairing and base-stacking. In order to investigate the effect of methylation on the interaction between nucleic acid bases, this work presents the hydrogen-bonding and stacking interactions between 5-methylcytosine and guanine (G), cytosine (C) and G, 1-methyladenine and thymine (T), as well as adenine and T. Geometry optimization and potential energy surface scan have been performed for the involved complexes by MP2 calculations. The interaction energies, which were corrected for the basis-set superposition error by the full Boys–Bernardi counterpoise correction scheme, were used to evaluate the interaction intensity of these nucleic acid bases. The atoms in molecules theory and natural bond orbital analysis have been performed to study the hydrogen bonds in these complexes. The result shows that the methyl substitute contributes the stability to these complexes because it enhances either the hydrogen bonding or the staking interaction between nucleic acid bases studied.     

Rapid Location of the Preferred Interaction Sites between Small Polar Molecules and Macromolecules. I. Binding of Water to the Component Units of Nucleic Acids

An approximate procedure for the rapid detection of favored sites for the location of bound water on macromolecules has been developed with the aid of accurate electrostatic energy calculations. The method also enables us to picture the lability of the bound water molecules around the substrate. As an application the method has been used to study the interaction surface between nucleic acid components and a water molecule.     

Interaction of p-benzoquinone and mitomycin C with complementary base pairs

Quantum chemical studies on interaction of p-benzoquinone and mitomycin C with complementary base pairs have been performed. The empirical potential function and semitheoretical algorithm were applied for estimation of intermolecular interaction energy. Non-negligible intercalation of the quinone ring into fragments of nucleic acid seems to be justified. Extensive calculations on the specificity of mitomycin C intercalation were performed using AGNAS /IMNAS algorithm based on an empirical potential function. No clear preference for intercalation into any kind of base pairs was found.     

Interaction energy studies of pyrrolopyrimidine nucleoside antibiotics: Sangivamycin

Interaction energy calculations have been employed to study the biological activity of sangivamycin. The interaction energy values and the site of association of the analog have been compared with those for the nucleic acid bases. A comparative estimation of the results with those of other pyrrolopyrimidine nucleosides (Tubercidin and Toyocamycin) has been made. These studies suggest that the activity of pyrrolopyrimidine analogs is of the following order Toyocamycin > Tubercidin > Sangivamycin which is in general agreement with the experimental results.     

Conformational analysis of double-helical polynucleotides

The intramolecular interaction energy of the regular double-helical polynucleotide as a function of variables that determine the mutual position of base pairs and sugar pucker was calculated using atom–atom potentials. The calculations showed the existence of two valley-like regions with minimal values on the energetic surface. One of them corresponds to the A family of nucleic acids, the other to the B family. The points that correspond to the models constructed by means of x-ray data are placed in a conformational space near the lines that describe the position of the bottom of the valleys.     

Ab initio molecular orbital study on the pairing and stacking interactions between nucleic acid bases in relation to the biological activities

Ab initio molecular orbital calculations were performed on the pairing and stacking interaction energies between bases in nucleic acids. Using these values we could explain the biologically important phenomena well. Thus the fact that O⁶-methylguanine (which is formed in small amounts) is more promutagenic than N₇-methylguanine (which is formed in larger amounts) could be explained by the difference in pairing interaction energies for these alkylguanines. To clarify the detailed mechanism of mutation induced by a base analogue (2-aminopurine) the interaction energy for the 2-aminopurine-cytosine pair was calculated by taking into account the tautomeric conversion of base and the base analogue. It was concluded that the base pair formed as an intermediate between the normal form of 2-aminopurine and the imino tautomer of cytosine has an important role in inducing the mutation by 2-aminopurine. The stacking interaction energy was found to be a principal factor in determining the conformation of nucleic acids, and it predicted the preference for the A-form or B-form of the deoxyoligonucleotides well. The stacking interaction energy was resolved into its components, and it was shown that electrostatic energy was base sequence-dependent, whereas the overall stability of the stacked polymers was largely dependent on the dispersion energy.     

Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers

The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.     

Empirical energy functions for energy minimization and dynamics of nucleic acids

An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.     

Polarizable model potential function for nucleic acid bases

A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.     

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

A CSOV study of the difference between HF and DFT intermolecular interaction energy values: the importance of the charge transfer contribution

Intermolecular interaction energy decompositions using the Constrained Space Orbital Variation (CSOV) method are carried out at the Hartree-Fock level on the one hand and using DFT with usual GGA functionals on the other for a number of model complexes to analyze the role of electron correlation in the intermolecular stabilization energy. In addition to the overall stabilization, the results provide information on the variation, with respect to the computational level, of the different contributions to the interaction energy. The complexes studied are the water linear dimer, the N-methylformamide dimer, the nucleic acid base pairs, the benzene-methane and benzene-N2 van der Waals complexes, [Cu+ -(ImH)3]2, where "ImH" stands for the Imidazole ligand, and ImH-Zn++. The variation of the frozen core energy (the sum of the intermolecular electrostatic energy and the Pauli repulsion energy) calculated from the unperturbed orbitals of the interacting entities indicates that the intramolecular correlation contributions can be stabilizing as well as destabilizing, and that general trends can be derived from the results obtained using usual density functionals. The most important difference between the values obtained from HF and DFT computations concerns the charge transfer contribution, which, in most cases, undergoes the largest increase. The physical meaning of these results is discussed. The present work gives reference calculations that might be used to parametrize new correlated molecular mechanics potentials.     

Intermolecular interactions in nitrogen-containing aromatic systems

π–π and CH···N interactions are vital in biological systems. In this study, stacking and hydrogen-bonded interactions in pyrazine and triazine dimers were investigated by density functional theory combined with symmetry-adapted perturbation theory (DFT-SAPT) and counterpoise (CP)-corrected supermolecular MP2, SCS-MP2, B3LYP-D and CCSD(T) calculations. All interaction energies were computed using the optimized structures at the CP-corrected SCS/aug-cc-pVDZ level, which gave 1–2 kJ/mol lower interaction energies than the ones computed at the MP2 level. For both dimers, doubly hydrogen-bonded and cross-(displaced) stacked orientations were found to be the lowest energy ones. The reference CCSD(T) calculations favored the former structure in both dimer systems, whereas MP2 and SCS-MP2 located the latter as the lowest energy isomer. In particular, the former was found to be lower in energy than the latter by 2.28 and 1.01 kJ/mol at the CCSD(T)/aug-cc-pVDZ level for pyrazine and triazine, respectively. B3LYP-D produced interaction energies in agreement with the CCSD(T) at the equilibrium geometries, but it overestimates them at the short range and underestimates at the long intermonomer separations. Furthermore, it tends to give smaller equilibrium distances compared to the CCSD(T). DFT-SAPT method was in a good agreement with the reference CCSD(T) calculations. This suggests that DFT-SAPT can be employed to compute the full potential energy surface of these dimers. Moreover, DFT-SAPT calculations showed that the electrostatic and dispersion contributions are the most important energy components stabilizing these dimers. The present study aims to show which theoretical method is the most promising one for the investigation of intermolecular interactions dominated by π–π and CH···N. Therefore, the findings obtained in this study can be used to unravel the structures of nucleic acid bases and other systems stabilized by π–π and CH···N interactions.     

Full spin-orbit configuration interaction calculations on electronic states of LiBe

Ab initio calculations are reported for the simplest heteronuclear metal cluster, LiBe. Full spin-orbit configuration interaction calculations in the context of relativistic effective core potentials lead to accurate potential energy curves for low-lying states. Results are compared with recent experimental observations and with all electron multi-reference configuration interaction calculations.     

Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids

Calculated indirect NMR spin-spin coupling constants (3)J(P,C) and (2)J(P,H) were correlated with the local structure of the P-O...H-C linkage between the nucleic acid (NA) backbone phosphate and the H-C group(s) of a nucleic acid base. The calculations were carried out for selected nucleotides from the large ribosomal subunit (Ban et al. Science 2000, 289, 905) with the aim of identifying NMR parameters suitable for detection of certain noncanonical RNA structures. As calculations in the model system, dimethyl-phosphate-guanine, suggest, the calculated indirect spin-spin couplings across the linkage are sensitive to the mutual orientation and distance between the phosphate and nucleic acid base. A short distance between the nucleic acid base and phosphate group and the angles C...P-O and P...C-H smaller than 50 degrees are prerequisites for a measurable spin-spin interaction of either coupling (|J| > 1 Hz). A less favorable arrangement of the P-O...H-C motif, e.g., in nucleotides of the canonical A-RNA, results in an effective dumping of both spin-spin interactions and insignificant values of the NMR coupling constants. The present work indicates that quantum chemical calculations of the indirect spin-spin couplings across the P-O...H-C motif can help detect some rare but important backbone topologies, as seen for example in the reverse kink-turn. Measuring of (3)J(P,C) and (2)J(P,H) couplings can therefore provide critical constraints on the NA base and phosphate geometry and help to determine the structure of NAs.     

复合物Ca+-RNA碱基的结构与稳定性

Gas-phase metal ion affinities and optimized structures of RNA nucleic acid bases for the Ca+ were determined at a density functional level employing the hybrid B3LYP exchange correlation potential in connection with the 6-311+G(2df,2p) basis set. All the molecular complexes, obtained by the interaction between several low-lying tautomers of RNA nucleic acid and Ca+ on the different binding sites, were considered. For Cytosine, the most stable complex was obtained starting from the most stable tautomer of the free nucleic acid base tautomers. As to thymine, the bond energy of the ion with the most stable tautomer of the free nucleic acid base is the weakest among the three tautomer’s complexes, and that of the ion with least stable tautomer of the free nucleic acid base is the strongest . Uracil is similar to thymine. The two kinds of relation, bond energy and total energy for the complex, are in disagreement, as the metal affinities of RNA bases for the Ca+ depend on binding sites, and total energy of complex (Ca+-RNA base) relies on all atoms and their relative positions in the complex.     

Computation of large systems with an economic basis set: structures and reactivity indices of nucleic acid base pairs from density functional theory

We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.