Projector-based embedding has recently emerged as a robust multiscale method for the calculation of various electronic molecular properties. We present the coupling of projector embedding with quantum mechanics/molecular mechanics modeling and apply it for the first time to an enzyme-catalyzed reaction. Using projector-based embedding, we combine coupled-cluster theory, density-functional theor...

Abatrac-A procedure is given by which parameters of nonbonded interactions in a molecular mechanics energy function can be optimized for maximum compatibility with eb inif& force fields and structures. The method is based on a previously derived transformation of ob initio valence parameters to the molecular mechanics formalism. Explicit analytical expressions for the derivatives of the molecul...

There is growing interest in bio(logy)-inspired approaches that are inspired by the principles of biology and that can solve difficult problems. In this paper, we propose a new computational algorithm that is inspired by molecular mechanics for the solution of complex problems. There is a deep and useful connection between mechanics mechanics and combinatorial optimization. This connection expo...

In this study, geometrical optimizations of Clonidine Drug were carried out with the HF/6-31g basissets .Then, drug was put covalently to carbon nanocone with (5, 1) structure and a length of 150A. Weuse chem Office software and hyper chem at the end data will be presented as tables and Figs.Simulation was done in MM+, AMBER and OPLS force fields by Monte Carlo method. Threeimportant energy par...

Abstract Embedding techniques are nowadays considered the go-to-methods to have an optimal trade-off between chemical accuracy and computational cost in modeling large molecular systems. Several efficient strategies of this kind been developed over years, from QM/MM (quantum mechanics/molecular mechanics) more recent promising density functional theory embedding approaches. Along line, we recen...

the combination of quantum mechanics (qm) and molecular mechanics (mm) methods hasbecome alternative tool for many applications that pure qm and mm could not be suitable.the qm/mm method has been used for different type of problems, for example: structuralbiology, surface phenomena, and liquid phase. in this paper we have performed these methods forsome antibiotics and vitamins and then we comp...

A promising approach to developing improved potential functions for modeling macromolecular interactions consists of combining protein structural analysis, quantum mechanical calculations on small molecule models, and molecular mechanics potential decomposition. Here we apply this approach to the interactions of pairs of ring-containing amino acids in proteins. We find reasonable qualitative ag...

Interaction of molecular oxygen 3O2 with the flavin-dependent protein miniSOG after light illumination results in creation singlet 1O2 and superoxide O2●−. Despite recently resolved crystal structures variants, oxygen-binding sites near flavin chromophore are poorly characterized. We report computational studies protein−oxygen systems using dynamics (MD) simulations force-field interaction pote...