This article addresses a fundamental problem faced by the ab initio community: the lack of an effective formalism for the rapid exploration and exchange of new methods. To rectify this, we introduce a novel, basis-set independent, matrix-based formulation of generalized density functional theories which reduces the development, implementation, and dissemination of new ab initio techniques to th...

RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovere...

In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The bioc...

We report a highly correlated multireference configuration interaction calculation of the near-equilibrium potential energy surface of ozone using a large correlation consistent basis set. Three-dimensional analytical expressions are obtained for the potential energy and dipole moment functions using least-squares fits to ab initio points near the C2v equilibrium geometry. Low-lying vibrational...

This article addresses a fundamental problem faced by the ab initio community: the lack of an effective formalism for the rapid exploration and exchange of new methods. To rectify this, we introduce a novel, basis-set independent, matrix-based formulation of generalized density functional theories which reduces the development, implementation, and dissemination of new ab initio techniques to th...

We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental ...

A systematic method for approximating the ab initio electronic energy of molecules from the energies of molecular fragments has been adapted to estimate the total electronic energy of crystal lattices. The fragmentation method can be employed with any ab initio electronic structure method and allows optimization of the crystal structure based on ab initio gradients. The method is demonstrated o...

The ground-state geometry of the NiC3 and NiC4 clusters is investigated using accurate ab initio methods and compared with predictions using the tight-binding molecular-dynamics ~TBMD! method as well as the density functional theory ~DFT! based SIESTA method. The ab initio methods predict the ground-state geometry of the NiC3 cluster to have a rhomboidal geometry, in agreement with the TBMD met...

The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite ...

For I-(H 2 O) 4 cluster, it has long believed that the C 4 symmetry structure is most stable isomer at low temperature. However, calculated vibrational spectra values using ab initio disagree with experimental values. Therefore, we calculated the structure of I-(H 2 O) 4 using extensive ab initio calculation. Hence, we found most stable isomer for I-(H 2 O) 4 at low temperature. The isomer has ...