Anharmonic Vibrational Signatures of DNA Bases and Watson-Crick Base Pairs

Changes of molecular structure and associated charge distributions, and changes of anharmonic vibrational parameters from DNA base monomers to the Watson-Crick base pairs, have been investigated at the density functional theory level. Through examination of the NH2, N H, and C=O stretching vibrational modes that are involved in the multiple H-bonds in the base pairs, sensitivity of their diagonal and off-diagonal anharmonicities, as well as anharmonic vibrational couplings, to the structure change are predicted. Our results reveal the intrinsic connection between the anharmonic vibrational potentials, H-bonding, and electrostatic interactions in DNA bases.

Anharmonic vibrations of nucleobases: Structural basis of one-and two-dimensional infrared spectra for canonical and mismatched base pairs

Canonical Watson-Crick base pairs and four representative mismatched base pairs have been studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal some vibrational signatures characteristic of structural aspects of the base monomers and dimers, which were well manifested in simulated 1D IR and 2D IR spectra. The degree of delocalization of the selected normal modes, represented by the potential energy distribution, was found to vary sig-nificantly from isolated bases to H-bonded dimers, and was accompanied by changes in anharmonicities of these modes. Examples are given for the generally accepted carbonyl stretching mode of base pairs appearing in the 6-m wavelength region of IR spectra.

High-Fidelity Hugoniots of α Phase RDX Solid from High-Quality Force Field with Thermal,Zero-Point Vibration,and Anharmonic Effects

It is shown that the introduction of thermal effect, zero-point vibration, and phonon anharmonicity to a high quality and first-principle-Sased force field （atomic potential） results in a significant improvement in predict- ing the densities for the α phase crystalline hexahydro-1,3,5-trinitro-l,3,5-triazine （RDX）, and derivation of its high-fidelity Hugoniot locus and Mie-Grfineisen equation of state covering a very wide range of pressures and temperatures. This work can be used to efficiently and accurately predict the thermophysical properties of solid explosives over the pressures and temperatures to which they are subjected, which is a long-standing issue in the field of energetic materials.

Advantages and Drawbacks of Quantum Mechanical Static and Dynamic Approaches to Modelling Infrared Spectra

We present quantum mechanical vibrational computations beyond the harmonic approximation from effective second order perturbative and variation perturbation treatments defined as static approaches, as well as vibrational analysis from density functional theory molecular dynamics trajectories at 300 and 600 K. The four schemes are compared in terms of prediction of fundamental transitions, and simulation of the corresponding medium infrared spectrum at the same level of theory using the B3LYP/6-31＋G（d,p） description of the electronic structure. We summarize conclusions about advantages and drawbacks of these two approaches and report the main results obtained for semi-rigid and flexible molecules.