Hydrogenic Stretch Spectroscopy of Glycine-Water Complexes: Anharmonic Ab Initio Classical Separable Potential Calculations.

The anharmonic frequencies of O-H, C-H, and N-H stretching modes of hydrogen-bonded glycine-H2O complexes are calculated using ab initio classical separable potential approximation. In this approach, ab initio molecular dynamic simulations are used to determine an effective classical potential for each of the normal modes of the system. The frequencies are calculated by solving the time-independent Schrödinger equation for each mode using time-averaged potentials. Three complex structures are studied, which differ in the location of the water molecule on the amino acid. Significant differences are found between the spectra of the three structures, and signatures of individual complexes are established. It is demonstrated that anharmonic effects are essential in the discrimination between different structures, while frequency differences at the harmonic level are much smaller. Intensities are also computed and found to carry information on differences between structures, but the role of anharmonicity in this is small.

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

I-motif nanospheres: unusual self-assembly of long cytosine strands.

The synthesis and characterization of novel DNA structures based on tetraplex cytosine (C) arrangements, known as i-motifs or i-tetraplexes, is reported. Atomic force microscopy (AFM) investigation shows that long C-strands in mild acidic conditions form compact spherically shaped nanostructures. The DNA nanospheres are characterized by a typical uniform shape and narrow height distribution. Electrostatic force microscopy (EFM) measurements performed on the i-motif spheres clearly show their electrical polarizability. Further investigations by scanning tunneling microscopy (STM) at ultrahigh vacuum reveals that the structures exhibit an average voltage gap of 1.9 eV, which is narrower than the voltage gap previously measured for poly(dG)-poly(dC) molecules in similar conditions.

High-resolution STM imaging of novel single G4-DNA molecules.

The molecular morphology of long G4-DNA wires made by a novel synthetic method was, for the first time, characterized by high-resolution scanning tunneling microscopy (STM). The STM images reveal a periodic structure seen as repeating "bulbs" along the molecules. These bulbs reflect the helix morphology of the wires. The STM measurements were supported by a statistical morphology analysis of the DNA pitch length and apparent height relative to the surface. In the absence of X-ray and NMR data for these wires, the STM measurements provide a unique alternative to characterize the helix morphology.