Optimizing Protein–Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field

2013 ◽  
Vol 10 (1) ◽  
pp. 273-281 ◽  
Author(s):  
Dail E. Chapman ◽  
Jonathan K. Steck ◽  
Paul S. Nerenberg
Keyword(s):  
Force Field ◽  
Van Der Waals ◽  
Van Der Waals Interactions

MMPEP: Development and evaluation of peptide parameters for Allinger's MMP2(85) programme, including calculations on crambin and insulin

1988 ◽  
Vol 66 (11) ◽  
pp. 2687-2702 ◽  
Author(s):  
Saul Wolfe ◽  
Donald Fredric Weaver ◽  
Kiyull Yang
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Van Der Waals ◽  
Heavy Atom ◽  
Van Der Waals Interactions ◽  
Heavy Atoms ◽  
Minimization Procedure ◽  
Natural Result ◽  
Experimental Crystal ◽  
Initial Starting

Allinger's MMP2(85) program has been converted to an IBM environment, and the dimensions expanded to a current maximum of 999 atoms. Substantial additional expansion will be possible. An all-atom set of parameters, which permit Allinger's comprehensive force field to be applied to the molecular mechanics treatment of peptides, has been determined. These parameters, termed MMPEP, contain 21 atom types: 5 for carbon, 6 for hydrogen, 5 for nitrogen, 4 for oxygen, and 1 for sulfur, and are based on crystallographic heavy atom bond lengths and bond angles, vibrational and microwave spectra, and ab initio calculations. To minimize the conformational energy of a peptide from an initial starting geometry, all internally stored parameters are released, and replaced by PEPCON, a 360-line external file containing the MMPEP parameters.The ability of the MMPEP parameterization of MM85 to reproduce experimental crystal structures has been tested on several peptides and polypeptides, and the use of a dielectric constant ε = 78.5 D leads to the following results: Ala-Ala-Gly (rms = 0.261); Gly-Gly-Val (rms = 0.349); glutathione (rms = 0.417); crambin (327 heavy atoms; rms = 0.310 for all heavy atoms); insulin (389 heavy atoms; rms = 0.646 for all heavy atoms); the origins of deviations can be interpreted. No problems have been encountered in the application of the Newton–Raphson minimization procedure to such large molecules as crambin and insulin, even though all possible nonbonded interactions have been retained. On the IBM 3081 computer, real time minimization of trip)eptides requires 1–2 min, crambin requires 250 min, and insulin 200 min. Since hydrogen bonding in Allinger's force field is a natural result of electrostatic and van der Waals interactions, in MMPEP hydrogen bonding is taken into account through the large number of hydrogen atom types and their different bond moments and van der Waals radii.

scholarly journals 2019-nCoV vs. SARS-CoV: Which Truly Has a Higher ACE2 Affinity? A Quantum Chemical Perspective on Virus-Receptor Noncovalent Interactions

2020 ◽  
Author(s):  
Nitai Sylvetsky
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Force Field ◽  
Quantum Chemical ◽  
Noncovalent Interactions ◽  
Van Der Waals ◽  
Noncovalent Interaction ◽  
Van Der Waals Interactions ◽  
Virus Receptor ◽  
Electronic Structure Methods

Noncovalent interaction energetics associated with ACE2 affinity differences are investigated using electronic structure methods; Our results were found to challenge previous predictions – claiming a higher affinity for 2019-nCoV compared to SARS-CoV based merely on "chemical intuition". In addition, we demonstrate that a broadly-used classical molecular dynamics force field – MMFF94 – is clearly incapable of reproducing DFT-based noncovalent interaction energetics for the systems at hand (despite being specifically parameterized for van der Waals interactions).

scholarly journals 2019-nCoV vs. SARS-CoV: Which Truly Has a Higher ACE2 Affinity? A Quantum Chemical Perspective on Virus-Receptor Noncovalent Interactions

2020 ◽  
Author(s):  
Nitai Sylvetsky
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Force Field ◽  
Quantum Chemical ◽  
Noncovalent Interactions ◽  
Van Der Waals ◽  
Noncovalent Interaction ◽  
Van Der Waals Interactions ◽  
Virus Receptor ◽  
Electronic Structure Methods

Noncovalent interaction energetics associated with ACE2 affinity differences are investigated using electronic structure methods; Our results were found to challenge previous predictions – claiming a higher affinity for 2019-nCoV compared to SARS-CoV based merely on "chemical intuition". In addition, we demonstrate that a broadly-used classical molecular dynamics force field – MMFF94 – is clearly incapable of reproducing DFT-based noncovalent interaction energetics for the systems at hand (despite being specifically parameterized for van der Waals interactions).

A Transferable, Polarisable Force Field for Ionic Liquids

2019 ◽  
Author(s):  
Kateryna Goloviznina ◽  
José N. Canongia Lopes ◽  
Margarida Costa Gomes ◽  
Agilio Padua
Keyword(s):  
Ionic Liquids ◽  
Force Field ◽  
Force Fields ◽  
Dipole Moments ◽  
Van Der Waals Interactions ◽  
First Principles Calculations ◽  
Ion Diffusion ◽  
Fixed Integer ◽  
Molecular Compounds ◽  
Induced Dipoles

A general, transferable polarisable force field for molecular simulation of ionic liquids and their mixtures with molecular compounds is developed. This polarisable model is derived from the widely used CL\&P fixed-charge force field that describes most families of ionic liquids, in a form compatible with OPLS-AA, one of the major force fields for organic compounds. Models for ionic liquids with fixed, integer ionic charges lead to pathologically slow dynamics, a problem that is corrected when polarisation effects are included explicitly. In the model proposed here, Drude induced dipoles are used with parameters determined from atomic polarisabilities. The CL\&P force field is modified upon inclusion of the Drude dipoles, to avoid double-counting of polarisation effects. This modification is based on first-principles calculations of the dispersion and induction contributions to the van der Waals interactions, using symmetry-adapted perturbation theory (SAPT) for a set of dimers composed of positive, negative and neutral fragments representative of a wide variety of ionic liquids. The fragment approach provides transferability, allowing the representation of a multitude of cation and anion families, including different functional groups, without need to re-parametrise. Because SAPT calculations are expensive an alternative predictive scheme was devised, requiring only molecular properties with a clear physical meaning, namely dipole moments and atomic polarisabilities. The new polarisable force field, CL\&Pol, describes a broad set set of ionic liquids and their mixtures with molecular compounds, and is validated by comparisons with experimental data on density, ion diffusion coefficients and viscosity. The approaches proposed here can also be applied to the conversion of other fixed-charged force fields into polarisable versions.<br>

Crystal Structures of Two New Cyclosporin Clathrates

2000 ◽  
Vol 65 (12) ◽  
pp. 1950-1958 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Alexandr Jegorov
Keyword(s):  
Crystal Structures ◽  
Methyl Ether ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Solvent Molecules ◽  
Butyl Methyl Ether

Two isomorphous clathrates formed by dihydrocyclosporin A or cyclosporin V with tert-butyl methyl ether are reported and compared with the structures of related P21-symmetry cyclosporin clathrates. The cyclosporin molecules in both structures are associated via van der Waals interactions forming cavities occupied by solvent molecules (cyclosporin : tert-butyl methyl ether is 1 : 2).

Van der Waals interactions of the disulfide bond revealed: A microwave spectroscopic study of the diethyl disulfide–argon complex

2021 ◽  
Vol 154 (12) ◽  
pp. 124306
Author(s):  
Tao Lu ◽  
Daniel A. Obenchain ◽  
Jiaqi Zhang ◽  
Jens-Uwe Grabow ◽  
Gang Feng
Keyword(s):  
Spectroscopic Study ◽  
Disulfide Bond ◽  
Van Der Waals ◽  
Van Der Waals Interactions

scholarly journals Microscopic evidence of strong interactions between chemical vapor deposited 2D MoS2 film and SiO2 growth template

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Woonbae Sohn ◽  
Ki Chang Kwon ◽  
Jun Min Suh ◽  
Tae Hyung Lee ◽  
Kwang Chul Roh ◽  
...  
Keyword(s):  
Chemical Vapor Deposition ◽  
Vapor Deposition ◽  
Spherical Aberration ◽  
Van Der Waals ◽  
Chemical Vapor ◽  
Interface Layer ◽  
Van Der Waals Interactions ◽  
Strong Interactions ◽  
Transition Electron Microscopy ◽  
Oxide Substrates

AbstractTwo-dimensional MoS2 film can grow on oxide substrates including Al2O3 and SiO2. However, it cannot grow usually on non-oxide substrates such as a bare Si wafer using chemical vapor deposition. To address this issue, we prepared as-synthesized and transferred MoS2 (AS-MoS2 and TR-MoS2) films on SiO2/Si substrates and studied the effect of the SiO2 layer on the atomic and electronic structure of the MoS2 films using spherical aberration-corrected scanning transition electron microscopy (STEM) and electron energy loss spectroscopy (EELS). The interlayer distance between MoS2 layers film showed a change at the AS-MoS2/SiO2 interface, which is attributed to the formation of S–O chemical bonding at the interface, whereas the TR-MoS2/SiO2 interface showed only van der Waals interactions. Through STEM and EELS studies, we confirmed that there exists a bonding state in addition to the van der Waals force, which is the dominant interaction between MoS2 and SiO2. The formation of S–O bonding at the AS-MoS2/SiO2 interface layer suggests that the sulfur atoms at the termination layer in the MoS2 films are bonded to the oxygen atoms of the SiO2 layer during chemical vapor deposition. Our results indicate that the S–O bonding feature promotes the growth of MoS2 thin films on oxide growth templates.

Concisely modularized assembling of graphene-based thin films with promising electrode performance

2019 ◽  
Vol 3 (7) ◽  
pp. 1462-1470 ◽  
Author(s):  
Weiwei Wei ◽  
Rohit L. Vekariy ◽  
Chuanting You ◽  
Yafei He ◽  
Ping Liu ◽  
...  
Keyword(s):  
Thin Films ◽  
Graphene Oxide ◽  
Reduced Graphene Oxide ◽  
Double Layer ◽  
Van Der Waals ◽  
Cellulose Nanofibers ◽  
Van Der Waals Interactions ◽  
Electrode Performance ◽  
Reduced Graphene

Highly dense thin films assembled from cellulose nanofibers and reduced graphene oxide via van der Waals interactions to realize ultrahigh volumetric double-layer capacitances.

A comparison between approaches for the calculation of van der Waals interactions in flotation systems

2021 ◽  
Vol 167 ◽  
pp. 106804
Author(s):  
C. Weber ◽  
P. Knüpfer ◽  
M. Buchmann ◽  
M. Rudolph ◽  
U.A. Peuker
Keyword(s):  
Van Der Waals ◽  
Van Der Waals Interactions
Sign in / Sign up

Export Citation Format

Share Document