LICHEM 1.1: Recent Improvements and New Capabilities

Gökcan, Hatice; Vázquez-Montelongo, Erik Antonio; Cisneros, G. Andres

doi:10.26434/chemrxiv.7556744.v1

Cited by 3 publications

(8 citation statements)

References 5 publications

(6 reference statements)

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“…We used the LICHEM [60,61] (Layered Interacting CHEmical Models) code to perform a single point QM/MM analysis of the structures closest to the centroids of each cluster. QM subsystem calculations were carried out with the ωB97-XD functional and the Def2-SVP basis set using Gaus-sian16.…”

Section: Methodsmentioning

confidence: 99%

Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu(II) by Polarizable MD and QM/MM Simulations

Nochebuena

Quintanar

Vela

et al. 2021

Preprint

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Prions have been linked to neurodegenerative diseases that affect various species of mammals including humans. The prion protein, located mainly in neurons, is believed to play the role of metal ion transporter. High levels of copper ions have been related to structural changes. A 32-residue region of the N-terminal domain, known as octarepeat, can bind up to four copper ions. Different coordination modes have been observed and are strongly dependent on Cu 2+ concentration.Many theoretical studies carried out so far have focused on studying the coordination modes of a single copper ion. In this work we investigate the octarepeat region coordinated with four copper ions. Molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations using the polarizable AMOEBA force field have been carried out. The polarizable MD simulations starting from a fully extended conformation indicate that the tetra-Cu 2+ /octarepeat complex forms a globular structure. The globular form is stabilized by interactions between Cu 2+ and tryptophan residues resulting in some coordination sites observed to be in close proximity, in agreement with experimental results. Subsequent QM/MM simulations on several snapshots suggests the system is in a high-spin quintet state, with all Cu 2+ bearing one single electron, and all unpaired electrons are ferromagnetically coupled. NMR simulations on selected structures provides insights on the chemical shifts of the first shell ligands around the metals with respect to inter-metal distances.

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Section: Methodsmentioning

confidence: 99%

Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu(II) by Polarizable MD and QM/MM Simulations

Nochebuena

Quintanar

Vela

et al. 2021

Preprint

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“…AMOEBA is an example of a polarizable force field that employs the induced dipole formalism and has been implemented for QM/MM simulations 66–71 . AMOEBA uses the following functional form:

\begin{matrix} lefttrue \\ E_{int}^{AMOEBA} (r^{N}) = \underset{bonds}{false\sum} k_{i}^{b} {((), l_{i} - l_{i, 0})}^{2} [1 + 2.55 (l_{i} - l_{i, 0}) + 3.793125 {((), l_{i} - l_{i, 0})}^{2}] \\ + \underset{angles}{false\sum} k_{i}^{θ} {((), θ_{i} - θ_{i, 0})}^{2} [1 + 0.014 (θ_{i} - θ_{i, 0}) + 5.6 \times 10^{- 5} {((), θ_{i} - θ_{i, 0})}^{2} \\ + 7.0 \times 10^{- 7} {((), θ_{i} - θ_{i, 0})}^{3} + 2.2 \times 10^{- 8} {((), θ_{i} - θ_{i, 0})}^{4}] \\ + \underset{torsions}{false\sum} \frac{V_{n}}{2} (1 + \cos (nω - γ)) + \underset{oop}{false\sum} 0.02191414 k_{χ} χ^{2} \\ + \underset{str ‐ bend}{false\sum} k_{italicsb} (b_{i} - b_{i, 0}) (θ_{i} - θ_{i, 0}) + \underset{PI ‐ tor}{false\sum} U_{PI ‐ tor, i} + \underset{tor ‐ tor}{false\sum} U_{} \end{matrix}

…”

Section: Classical MM Environments In Qm/mmmentioning

confidence: 99%

“…For the current implementation, the total QM/MM interaction energy between the subsystems, E QM/GEM , involves four terms: Coulomb, Exchange‐repulsion, polarization, and dispersion:

E_{Coul}^{QM / GEM} + E_{exch}^{QM / GEM} + E_{pol}^{QM / GEM} + E_{disp}^{QM / GEM}

. 70 …”

Section: Qm/mm With Advanced Potentialsmentioning

confidence: 99%

“…The QM/GEM implementation in LICHEM was assessed by comparing the total intermolecular interaction Energies, as well as the individual interaction terms for a subset of the water dimer potential reported by Babin et al 123 as described in Ref. 70 The maximum unsigned error (MUE), and root mean squared error (RMSE) for the clustered dimers is shown in Figure 8. In the original comparison, the term‐by‐term comparison was done with respect to SAPT2+3/aug‐cc‐pVTZ, which does not provide a straightforward separation of the induction and polarization components.…”

Section: Qm/mm With Advanced Potentialsmentioning

confidence: 99%

“…Various methods described above including the pseudobond, and QM/MM‐LREC, have been implemented in the LICHEM software (Layered Interacting CHEmical Models) package in the context of both nonpolarizable and polarizable potentials including AMOEBA, GEM, and MB‐Pol 70,131,132 . At its core, LICHEM is an interface that can couple QM codes such as Gaussian, 76 NWChem 133 and Psi4 130 and MM codes such as TINKER, 134 TINKER‐HP, 77 and LAMMPS 135 …”

Section: Lichemmentioning

confidence: 99%

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Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials

Nochebuena

Naseem-Khan

Cisneros

2021

WIREs Comput Mol Sci

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Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed‐phase and biological systems. The combination of QM and MM methods to represent a system gives rise to several challenges that need to be addressed. The increase in computational speed has allowed the expanded use of more complicated and accurate methods for both QM and MM simulations. Here, we review some approaches that address several common challenges encountered in QM/MM simulations with advanced polarizable potentials, from methods to account for boundary across covalent bonds and long‐range effects, to polarization and advanced embedding potentials. This article is categorized under: Electronic Structure Theory > Combined QM/MM Methods Molecular and Statistical Mechanics > Molecular Interactions Software > Simulation Methods

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A Many-Body, Fully Polarizable Approach to QM/MM Simulations

Lambros

Lipparini

Cisneros

et al. 2020

J. Chem. Theory Comput.

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We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible 1 dipoles and uses permutationally invariant polynomials to effectively account for quantummechanical contributions (e.g., exchange-repulsion, and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit 2-body and 3-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 2body and 3-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.

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LICHEM 1.1: Recent Improvements and New Capabilities

Cited by 3 publications

References 5 publications

Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu(II) by Polarizable MD and QM/MM Simulations

Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu(II) by Polarizable MD and QM/MM Simulations

Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials

A Many-Body, Fully Polarizable Approach to QM/MM Simulations

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