Molecular mechanics (MM2) calculations on peptides and on the protein Crambin using the CYBER 205

Lii, Jenn‐Huei; Gallion, Steven L.; Bender, Charles F.; Wikström, Håkan; Allinger, Norman L.; Flurchick, K. M.; Teeter, Martha M.

doi:10.1002/jcc.540100408

Cited by 76 publications

(26 citation statements)

References 10 publications

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“…The isomers of the [16]annulenes were generated by using a Monte Carlo algorithm, through breaking the ring, varying the dihedral angles in steps of 308, and rejoining both ends. [37] The structures were submitted to an optimization using the MM + [38,39] force field and then checked for redundancy. The generation procedure was stopped when no new isomers were found by doubling the number of generated structures.…”

Section: Methodsmentioning

confidence: 99%

Synthesis and Properties of the First Möbius Annulenes

Ajami

Heß

Köhler

et al. 2006

Chemistry A European J

128

126

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Heilbronner in 1964 predicted that annulenes with ".. a planar perimeter of N=4r AO's, which would yield an open shell configuration when occupied by 4r electrons, can be twisted into a closed shell Möbius strip perimeter without loss in pi electron energy". We have been able to synthesize the first [4n]annulene with such a Möbius topology and now present further Möbius isomers and the details of their preparation as stable compounds. To address the question whether the twist in the pi system has an effect on the properties we systematically investigate energy, geometry and magnetic parameters of a large number isomers of [16]annulenes. The Möbius twisted annulenes are consistently more aromatic than the non-twisted isomers. This is true for the parent as well as our benzoannelated systems. Our results are in contrast to those published recently by C. Castro, W. L. Karney, P. von R. Schleyer et al.

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Section: Methodsmentioning

confidence: 99%

Synthesis and Properties of the First Möbius Annulenes

Ajami

Heß

Köhler

et al. 2006

Chemistry A European J

128

126

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show abstract

“…The conformational analysis was performed via the Monte Carlo/multiple minimum (MC/MM) approach, to identify the lowest energy conformation in solution . The solute was described using the all‐atom MM2 potential . The effect of the solvent was incorporated into the MC/MM calculations using the generalised Born/surface area (GB/SA) continuum solvent model for water .…”

Section: Methodsmentioning

confidence: 99%

Conformational study of tylosin A in water and full assignments of ¹H and ¹³C spectra of tylosin A in D₂O and tylosin B in CDCl₃

Arsić

Aguilar

Bryce

et al. 2016

Magnetic Reson in Chemistry

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“…Addition of a few more parameters (e.g., hydrogen bonding [25]) was suggested to provide a reasonable fit of all the data. The MM2 was also parameterized for applicability to proteins and peptide [26].…”

Section: Molecular Mechanics Force Fields Mm2 Mm3 and Mm4mentioning

confidence: 99%

Molecular Mechanics Force Fields and their Applications in Drug Design

Pissurlenkar¹,

Shaikh²,

Iyer³

et al. 2009

AIAMC

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The molecular structures, properties and energies of a molecule are better understood through the use of the "mechanical" molecular model. This model involves the development of a simple molecular mechanics energy equation representing the sum of various energy interaction terms comprised of bonds, angles, torsions of bonded, as well as, nonbonded atoms. Referred to as "force fields", the model serves as a simple "descriptor" for vibrations in molecules. The concept of force fields is now widely employed as one of the simplest tools in molecular modeling.Force fields are fundamentally important in de novo drug design programs, in pharmacophore mapping, and represent the "scoring functions" in many docking programs. As scoring functions, force fields are used to rank "ligand poses" obtained by a docking algorithm, or in de novo ligand design programs to suggest placement of fragments in sites in the enzyme with the highest binding affinity. In all these applications, force fields are mainly used to compute the interaction energy between the protein and the ligand as pair-wise interaction potentials consisting of van der Waals and electrostatic interactions, in addition to H-bond energy between the ligand and the enzyme. Some examples of drug design software where force fields have been implemented as scoring functions are AMBER, GOLD AutoDock and DOCK. Force fields also play an important role in Free Energy perturbations (FEP) calculations that allow the design of newer analogs or inhibitors with an accurate prediction of their activity. This review will provide a historical overview including a discussion of the valence force field, the Urey-Bradley force field (UBFF), and the more recent Class II force fields such as Allinger's MM2-MM4, Accelrys CFF91 and others that apply to a large class of molecules. The GROMOS force field will also be discussed since it takes into consideration the free energies of hydration and the non-polar solvation for a range of compounds. This approach takes into account the relative free enthalpy of solvation between polar and non-polar environments, which is a key property in many biomolecular processes of interest including protein folding, biomolecular association, membrane formation and transport. The review will also focus on the current status of force fields in the study of ligand-protein interactions with particular emphasis on applicability in structure-based drug design.

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Molecular mechanics (MM2) calculations on peptides and on the protein Crambin using the CYBER 205

Cited by 76 publications

References 10 publications

Synthesis and Properties of the First Möbius Annulenes

Synthesis and Properties of the First Möbius Annulenes

Conformational study of tylosin A in water and full assignments of ¹H and ¹³C spectra of tylosin A in D₂O and tylosin B in CDCl₃

Molecular Mechanics Force Fields and their Applications in Drug Design

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Molecular mechanics (MM2) calculations on peptides and on the protein Crambin using the CYBER 205

Cited by 76 publications

References 10 publications

Synthesis and Properties of the First Möbius Annulenes

Synthesis and Properties of the First Möbius Annulenes

Conformational study of tylosin A in water and full assignments of 1H and 13C spectra of tylosin A in D2O and tylosin B in CDCl3

Molecular Mechanics Force Fields and their Applications in Drug Design

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Conformational study of tylosin A in water and full assignments of ¹H and ¹³C spectra of tylosin A in D₂O and tylosin B in CDCl₃