We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.

An all atom force field for simulations of proteins and nucleic acids.

Theoretical descriptions of two-dimensional (2D) vibrational and electronic spectroscopy are presented By using a coupled multi-chromophore model, some examples of 2D spectroscopic studies of peptide solution structure determination and excitation transfer process in electronically coupled multi-chromophore system are discussed A few remarks on perspectives of this research area are given

Coherent Two-Dimensional Optical Spectroscopy

This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C—H … O interbase contacts, sugar–base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino–acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation–π interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 3–31, 2002; DOI 10.1002/bip.10048

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.

Injection of electrons into the empty π* molecular orbitals of uracil and the DNA bases creates short-lived anion states whose energies have been determined by electron scattering. A common range of attachment energies into the lowest orbitals is observed in all the bases. Evidence for nuclear motion during the lifetimes of the anions is found in all the compounds except adenine. These properties of the bases as bridge sites along the π-stack of DNA, namely, the effective degeneracy of the anion energies and the strong excitation of vibration, are key parameters for theories of electron-transfer rate, some of which lead to inverse rather than exponentially decreasing bridge-length dependences.

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Electron Attachment Energies of the DNA Bases

Tautomerism and protonation of guanine and cytosine in the gas phase and in aqueous solution have been examined by theoretical methods. High level ab initio calculations with inclusion of correlation effects at the Moller−Plesset level have been used to study these processes in the gas phase. The influence of solvent has been examined using self-consistent reaction field and Monte Carlo free energy perturbation simulations. The results provide a complete and accurate picture of tautomerism and protonation of these nucleic acid bases. Comparison with the available experimental data gives confidence in the quality of the results derived from theoretical computations. Inspection of the most stable tautomeric forms for the neutral and protonated nucleic acid bases allows rationalization of the formation of unusual DNA structures like the triple helix.

Tautomerism and protonation of guanine and cytosine. implications in the formation of hydrogen-bonded complexes

Matrix isolation infrared studies of nucleic acid constituents. 5. Experimental matrix-isolation and theoretical ab initio SCF molecular orbital studies of the infrared spectra of cytosine monomers

Author Institution: Institute of Physics, Polish Academy of Sciences; Department of Chemistry, University of Florida

M. Szczesniak

Papers

Matrix isolation infrared studies of nucleic acid constituents. 5. Experimental matrix-isolation and theoretical ab initio SCF molecular orbital studies of the infrared spectra of cytosine monomers

Matrix isolation studies of nucleic acid constituents. i. infrared spectra of uracil monomers

Matrix isolation infrared studies of nucleic acid constituents: Part 4. Guanine and 9-methylguanine monomers and their keto—enol tautomerism☆

Matrix isolation studies of nucleic acid constituents—III. 1-Methyluracil, 3-methyluracil and 1,3-dimethyluracil monomers

Effect of intermolecular interactions on the infrared spectrum of 1-methyluracil