A Boolean function is a function that produces a Boolean value output by logical calculation of Boolean inputs. It plays key roles in programing algorithms and design of circuits. Minimization of Boolean function is able to optimize the algorithms and circuits. Quine-McCluskey (QM) method is one of the most powerful techniques to simplify Boolean expressions. Compared to other techniques, QM me...

The concept of atomic point charges is well established in theoretical chemistry. Atomic point charges have played an important role in understanding and modeling chemical behavior by allowing to extract and quantify information stored in the molecular electron distribution of chemical compounds. Thus, atomic point charges have been used to estimate reactivity indices, dissociation constants, p...

A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical param...

A hybrid quantum mechanics/molecular mechanics (QM/MM) method for the electronic excited states has been developed. The equation-of-motion coupled cluster with single and double excitations method (EOM-CCSD) is used for the QM region, while the effective fragment potential (EFP) method describes a MM part. The EFP method overcomes the most significant limitation of QM/MM by replacing empirical ...

The hybrid quantum mechanics/molecular mechanics (QM/MM) method IMOMM is applied to the calculation of the reaction of thiophene with Cp*RhPMe3 , which is a good experimental model for homogeneous catalytic hydrodesulfurization (HDS). The validity of the results is checked by comparison with previously reported full QM calculations on the same system. The geometries obtained with IMOMM are in g...

The calculation of binding affinities for flexible ligands has hitherto required the availability of reliable molecular mechanics parameters for the ligands, a restriction that can in principle be lifted by using a mixed quantum mechanics/molecular mechanics (QM/MM) representation in which the ligand is treated quantum mechanically. The feasibility of this approach is evaluated here, combining ...

The approximative density-functional method DFTB3 has been implemented in the Gromacs package version 5, complementing the existing QM/MM interface. The tight integration within the program gives rise to favorable efficiency, and makes it possible to employ a full PME-based treatment of QM/MM electrostatic interaction. Therefore, unnecessary artifacts are avoided in simulations involving polar ...

The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling pack...

For large reactive systems, the calculation of energies can be simplified by treating the active part with a high-level quantum mechanical ~QM! ~ab initio or density functional! approach and the environment with a less sophisticated semiempirical ~SE! approach, as an improvement over the widely used hybrid quantum mechanical/molecular mechanical ~QM/MM! methods. An example is the interaction be...

Partial atomic charges describe the distribution of electron density in a molecule, and therefore they provide clues regarding the chemical behaviour of molecules. Atomic charges are frequently used in molecular modelling applications such as molecular dynamics, docking, conformational searches, binding site prediction, etc. Recently, partial atomic charges have also become popular chemoinforma...