Fragment Molecular Orbital (FMO) Calculations of Peptoids

Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations

Biomolecular calculations based on electron-correlated fragment molecular orbital methods

Kitaura et al. [1] have proposed an ab initio FMO method by which large molecules such as proteins and nucleic acids can be easily treated with chemical accuracy. In the ab initio FMO method, a molecule or a molecular cluster is divided into fragments, and the MO calculations on the fragments (monomers) and the fragment pairs (dimers) are performed to obtain the total energy that is expressed a...

Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6-31G* level) is used to opti...

Comparison of the local structural stabilities of mammalian prion protein (PrP) by fragment molecular orbital calculations

Bovine spongiform encephalopathy (BSE), a member of the prion diseases, is a fatal neurodegenerative disorder suspected to be caused by a malfunction of prion protein (PrP). Although BSE prions have been reported to be transmitted to a wide range of animal species, dogs and hamsters are known to be BSE-resistant animals. Analysis of canine and hamster PrP could elucidate the molecular mechanism...

Molecular Orbital Calculations of Cu-Halides

An ab initio HF MO theory is applied to CuX, CuX2 (X = F and Cl) and (CuCl)3. Although the detailed sequence of energy levels depends upon the basis set used, high-lying orbital energy levels have largely halogen p-like character, whereas low-lying orbital energy levels have largely Cu 3 d-like character. This is in agreement with the chemical intuition of a highly ionic character of these comp...