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Title: Weak and strong π interactions between two monomers—assessed with local vibrational mode theory
We introduce in this work a unique parameter for the quantitative assessment of the intrinsic strength of the π interaction between two monomers forming a complex. The new parameter is a local intermonomer stretching force constant, based on the local mode theory, originally developed by Konkoli and Cremer, and derived from the set of nine possible intermonomer normal vibrational modes. The new local force constant was applied to a diverse set of more than 70 molecular complexes, which was divided into four groups. Group 1 includes atoms, ions, and small molecules interacting with benzene and substituted benzenes. Group 2 includes transition metal hydrides and oxides interacting with benzene while Group 3 involves ferrocenes, chromocenes, and titanium sandwich compounds. Group 4 presents an extension to oxygen π–hole interactions in comparison with in-plane hydrogen bonding. We found that the strength of the π interactions in these diverse molecular complexes can vary from weak interactions with predominantly electrostatic character, found, e.g., for argon–benzene complexes, to strong interactions with a substantial covalent nature, found, e.g., for ferrocenes; all being seamlessly described and compared with the new intermonomer local mode force constant, which also outperforms other descriptors such as an averaged force constant or a force constant guided by the electron density bond paths. We hope that our findings will inspire the community to apply the new parameter also to other intermonomer π interactions, enriching in this way the broad field of organometallic chemistry with a new efficient assessment tool.  more » « less
Award ID(s):
2102461
NSF-PAR ID:
10430209
Author(s) / Creator(s):
; ; ; ;
Date Published:
Journal Name:
Canadian Journal of Chemistry
ISSN:
0008-4042
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    Version: 2.0

    Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.


    Conventions Used in These Files
    ===============================

    Structure Files
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    - graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)
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    Force Field Parameters
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    CHARMM format parameter files:
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    - par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.
    - toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)

    Template NAMD Configuration Files
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    These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):
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    - template_abf.namd (for adaptive biasing force)

    Minimization
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    - namd/min_*.0.namd

    Equilibration
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    - namd/eq_*.0.namd

    Adaptive biasing force calculations
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    - namd/eabfZRest7_graph_chp1404.0.namd
    - namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)

    Log Files
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    CONTENTS
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    Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.

    Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.

    Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.

    Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.

    Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).

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    Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.

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    This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030. 
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    Abstract

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