Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems

Nakamura, Taiji; Yokaichiya, Tomoko; Fedorov, Dmitri G.

doi:10.1021/acs.jpclett.1c02510

Cited by 13 publications

(10 citation statements)

References 52 publications

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“…This motivates us to further explore the applicability of the fast DFTB or semiempirical methods to modeling NA-MD in extended systems. Although the DFTB approach has been successful in modeling many bio and organic structures, − including modeling NA dynamics, ,, its parameterization is limited for inorganic systems, rendering many inorganic materials of interest to solar cell harvesting out of its scope. Recently, Bannwarth et al − proposed the extended tight-binding (xTB) method as a novel TB approach for simulating systems up to few thousands of atoms.…”

Section: Introductionmentioning

confidence: 99%

Nonadiabatic Molecular Dynamics with Extended Density Functional Tight-Binding: Application to Nanocrystals and Periodic Solids

Shakiba

Stippell

et al. 2022

J. Chem. Theory Comput.

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In this work, we report a new methodology for nonadiabatic molecular dynamics calculations within the extended tight-binding (xTB) framework. We demonstrate the applicability of the developed approach to finite and periodic systems with thousands of atoms by modeling “hot” electron relaxation dynamics in silicon nanocrystals and electron–hole recombination in both a graphitic carbon nitride monolayer and a titanium-based metal–organic framework (MOF). This work reports the nonadiabatic dynamic simulations in the largest Si nanocrystals studied so far by the xTB framework, with diameters up to 3.5 nm. For silicon nanocrystals, we find a non-monotonic dependence of “hot” electron relaxation rates on the nanocrystal size, in agreement with available experimental reports. We rationalize this relationship by a combination of decreasing nonadiabatic couplings related to system size and the increase of available coherent transfer pathways in systems with higher densities of states. We emphasize the importance of proper treatment of coherences for obtaining such non-monotonic dependences. We characterize the electron–hole recombination dynamics in the graphitic carbon nitride monolayer and the Ti-containing MOF. We demonstrate the importance of spin-adaptation and proper sampling of surface hopping trajectories in modeling such processes. We also assess several trajectory surface hopping schemes and highlight their distinct qualitative behavior in modeling the excited-state dynamics in superexchange-like models depending on how they handle coherences between nearly parallel states.

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Section: Introductionmentioning

confidence: 99%

Nonadiabatic Molecular Dynamics with Extended Density Functional Tight-Binding: Application to Nanocrystals and Periodic Solids

Shakiba

Stippell

et al. 2022

J. Chem. Theory Comput.

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“…

normalΔ E_{I}^{SP}

depends on the box size: having a larger box increases the separation between image copies and thus decreases the self‐polarization. When boxes are used to describe pure liquids, this dependence is artificial, but in case of crystals, such as protein crystals, 59 where the cell size has a physical significance, it is a useful property. Likewise, for a solution the box size is related to the concentration and has a physical significance.…”

Section: Methodsmentioning

confidence: 99%

“…In FMO‐DFTB/PBC, 58 the equations for the energy and embedding have the same form as without PBC, because the summation over cells, infinite via the use of the Ewald summation, is conveniently contained 58 in the γ and Γ functions (appearing in Equation ), so that in the final expressions one simply uses PBC‐summed γ and Γ functions (usually denoted with tildes,

\overset{γ}{true}

and

\overset{Γ}{true}

) 59 . Therefore, the above formulation without PBC can also be used with PBC, with the replacement of γ and Γ by their periodic equivalents.…”

Section: Methodsmentioning

confidence: 99%

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Polarization energies in the fragment molecular orbital method

Fedorov

2022

J Comput Chem

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Using isolated and polarized states of fragments, a method for computing the polarization energies in density functional theory (DFT) and density‐functional tight‐binding (DFTB) is developed in the framework of the fragment molecular orbital method. For DFTB, the method is extended into the use of periodic boundary conditions (PBC), for which a new component, a periodic self‐polarization energy, is derived. The couplings of the polarization to other components in the pair interaction energy analysis (PIEDA) are derived for DFT and DFTB, and compared to Hartree–Fock and second‐order Møller‐Plesset perturbation theory (MP2). The effect of the self‐consistent (DFT) and perturbative (MP2) treatment of the electron correlation on the polarization is discussed. The difference in the polarization in the bulk (PBC) and micro (cluster) solvation is elucidated.

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“…For a cluster model of finite size, FMO has been applied to nanoparticles of ice, zeolite adsorption, fullerite, and some surfaces of covalent crystals. − FMO has been used to evaluate the lattice energy . FMO has been combined with density-functional tight-binding (DFTB) and PBC, recently applied to the structure optimization of protein crystals …”

Section: Introductionmentioning

confidence: 99%

Analysis of Guest Adsorption on Crystal Surfaces Based on the Fragment Molecular Orbital Method

2022

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For gaining insights into interactions in periodic systems, an analysis is developed based on the fragment molecular orbital method combined with periodic boundary conditions. The adsorption energy is decomposed into guest and surface polarization and deformation energy, guest−surface and guest−guest interactions, and the vibrational free energy. The analysis is applied to the adsorption of guest molecules to Ih (001) ice surface. The cooperativity effects result in a non-linear change in the adsorption energy with coverage due to many-body effects. The role of dispersion is found to be dominant for guests with long hydrophobic tails. A rule is proposed relating the length of the alkyl tail with the formation of the guest layer. The computed binding enthalpies are in good agreement with experimental values. For high coverage, adsorbed molecules can form an ordered layer known as self-assembled monolayer.

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Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems

Cited by 13 publications

References 52 publications

Nonadiabatic Molecular Dynamics with Extended Density Functional Tight-Binding: Application to Nanocrystals and Periodic Solids

Nonadiabatic Molecular Dynamics with Extended Density Functional Tight-Binding: Application to Nanocrystals and Periodic Solids

Polarization energies in the fragment molecular orbital method

Analysis of Guest Adsorption on Crystal Surfaces Based on the Fragment Molecular Orbital Method

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