Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of ne...

Density-functional and semiempirical quantum methods and continuum dielectric and explicit solvation models are applied to study the role of solvation on the stabilization of native and thio-substituted transphosphorylation reactions. Extensive comparison is made between results obtained from the different methods. For the semiempirical methods, explicit solvation was treated using a hybrid qua...

There are many claims that quantum mechanics plays a key role in the origin and/or operation of biological organisms. The mechanism of the meiosis, mitosis and gametes life cycle from the view-point of quantum for human has been represented. The quantum gates have been used to simulate these processes for the first time. The reason of several hundred sperms has been explained in the male too

here, the concept of quantum potential that has been illustrated in extended phase space (eps) in previous works is explored for its marginal behavior. unlike in configuration space, different representations of the quantum mechanics can be found in eps when exploiting appropriate canonical transformations. these canonical transformations revealed that there exist several representations in whi...

In molecular simulations with fixed-charge force fields, the choice of partial atomic charges influences numerous computed physical properties, including binding free energies. Many molecular mechanics force fields specify how nonbonded parameters should be determined, but various choices are often available for how these charges are to be determined for arbitrary small molecules. Here, we comp...

Neglect of diatomic differential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models commonly employed in combined quantum mechanical/molecular mechanical simulations fail to adequately describe the deoxyribose and ribose sugar ring puckers. This failure limits the application of these methods to RNA and DNA systems. In this work, we provide bench...

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical qu...

This essay provides a perspective on several issues in valence bond theory: the physical significance of semilocal bonding orbitals, the capability of valence bond concepts to explain systems with multireferences character, the use of valence bond theory to provide analytical representations of potential energy surfaces for chemical dynamics by the method of semiempirical valence bond potential...