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1.
J Chem Theory Comput ; 18(11): 6920-6931, 2022 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-36269878

RESUMO

Protons display a high chemical activity and strongly affect the charge storage capability in confined interlayer spaces of two-dimensional (2D) materials. As such, an accurate representation of proton dynamics under confinement is important for understanding and predicting charge storage dynamics in these materials. While often ignored in atomistic-scale simulations, nuclear quantum effects (NQEs), e.g., tunneling, can be significant under confinement even at room temperature. Using the thermostatted ring polymer molecular dynamics implementation of path integral molecular dynamics (PIMD) in conjunction with the ReaxFF force field, density functional tight binding (DFTB), and NequIP neural network potential simulations, we investigate the role of NQEs on proton and water transport in bulk water and aqueous electrolytes under confinement in Ti3C2 MXenes. Although overall NQEs are relatively small, especially in bulk, we find that they can alter both quantitative values and qualitative trends on both proton transport and water self-diffusion under confinement relative to classical MD predictions. Therefore, our results suggest the need for NQEs to be considered to simulate aqueous systems under confinement for both qualitative and quantitative accuracy.

2.
RSC Adv ; 12(39): 25500-25510, 2022 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-36275866

RESUMO

We report quantum chemical molecular dynamics (MD) simulations based on the density-functional tight-binding (DFTB) method to investigate the effect of K+, Na+, and Mg2+ ions in aqueous solutions on the static and dynamic structure of bulk water at room temperature and with various concentrations. The DFTB/MD simulations were validated for the description of ion solvation in aqueous ionic solutions by comparing static pair distribution functions (PDFs) as well as the cation solvation shell between experimental and available ab initio DFT data. The effect of the cations on the water structure, as well as relative differences between K+, Na+, and Mg2+ cations, were analyzed in terms of atomically resolved PDFs as well as time-dependent Van Hove correlation functions (VHFs). The investigation of the VHFs reveals that salt ions generally slow down the dynamic decay of the pair correlations in the water solvation sphere, irrespective of the cation size or charge. The analysis of partial metal-oxygen VHFs indicates that there are long-lived correlations between water and Na+ over long distances, in contrast to K+ and Mg2+.

3.
Nat Commun ; 13(1): 5285, 2022 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-36075915

RESUMO

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO226-234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.


Assuntos
COVID-19 , SARS-CoV-2 , Antivirais/química , Cisteína Endopeptidases/metabolismo , Humanos , Peptídeo Hidrolases , Proteínas
4.
J Chem Theory Comput ; 18(2): 1213-1226, 2022 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-34978438

RESUMO

Semiempirical methods like density functional tight-binding (DFTB) allow extensive phase space sampling, making it possible to generate free energy surfaces of complex reactions in condensed-phase environments. Such a high efficiency often comes at the cost of reduced accuracy, which may be improved by developing a specific reaction parametrization (SRP) for the particular molecular system. Thiol-disulfide exchange is a nucleophilic substitution reaction that occurs in a large class of proteins. Its proper description requires a high-level ab initio method, while DFT-GAA and hybrid functionals were shown to be inadequate, and so is DFTB due to its DFT-GGA descent. We develop an SRP for thiol-disulfide exchange based on an artificial neural network (ANN) implementation in the DFTB+ software and compare its performance to that of a standard SRP approach applied to DFTB. As an application, we use both new DFTB-SRP as components of a QM/MM scheme to investigate thiol-disulfide exchange in two molecular complexes: a solvated model system and a blood protein. Demonstrating the strengths of the methodology, highly accurate free energy surfaces are generated at a low cost, as the augmentation of DFTB with an ANN only adds a small computational overhead.

5.
bioRxiv ; 2021 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-34816264

RESUMO

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like (3CLpro) protease can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.14 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226-235 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro- NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for in the pathology of COVID-19.

6.
Sci Adv ; 7(42): eabk2451, 2021 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-34652933

RESUMO

Tough adhesives provide resistance against high debonding forces, and these adhesives are difficult to design because of the simultaneous requirement of strength and ductility. Here, we report a design of tough reversible/recyclable adhesive materials enabled by incorporating dynamic covalent bonds of boronic ester into commodity triblock thermoplastic elastomers that reversibly bind with various fillers and substrates. The spectroscopic measurements and density functional theory calculations unveil versatile dynamic covalent binding of boronic ester with various hydroxy-terminated surfaces such as silica nanoparticles, aluminum, steel, and glass. The designed multiphase material exhibits exceptionally high adhesion strength and work of debonding with a rebonding capability, as well as outstanding mechanical, thermal, and chemical resistance properties. Bonding and debonding at the interfaces dictate hybrid material properties, and this revelation of tailored dynamic interactions with multiple interfaces will open up a new design of adhesives and hybrid materials.

7.
ACS Omega ; 6(31): 20530-20548, 2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34395999

RESUMO

In this work, a set of density-functional tight-binding (DFTB) parameters for the Zr-Zr, Zr-O, Y-Y, Y-O, and Zr-Y interactions was developed for bulk and surface simulations of ZrO2 (zirconia), Y2O3 (yttria), and yttria-stabilized zirconia (YSZ) materials. The parameterization lays the ground work for realistic simulations of zirconia-, yttria-, and YSZ-based electrolytes in solid oxide fuel cells and YSZ-based catalysts on long timescales and relevant size scales. The parameterization was validated for the zirconia and yttria polymorphs observed under standard conditions based on density functional theory calculations and experimental data. Additionally, we performed DFTB-based molecular dynamics (MD) simulations to compute structural and vibrational properties of these materials. The results show that the parameters can give a qualitatively correct phase ordering of zirconia, where the tetragonal phase is more stable than the cubic phase at a lower temperature. The lattice parameters are only slightly overestimated by 0.05-0.1 Å (2% error), still within the typical accuracy of first-principles methods. Additionally, the MD results confirm that zirconia and yttria phases are stable against transformations under standard conditions. The parameterization also predicts that vibrational spectra are within the range of 100-1000 cm-1 for zirconia and 100-800 cm-1 for yttria, which is in good agreement with predictions both from full quantum mechanics and a recently developed classical force field. To further demonstrate the advantage of the developed DFTB parameters in terms of computational resources, we conducted DFTB/MD simulations of the YSZ4 and YS12 models containing approximately 750 atoms.

8.
J Org Chem ; 86(15): 10501-10516, 2021 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-34282918

RESUMO

A double-stranded spiroborate helicate bearing a bisporphyrin unit in the middle forms an inclusion complex with electron-deficient aromatic guests that are sandwiched between the porphyrins. In the present study, we systematically investigated the effects of size, electron density, and substituents of a series of aromatic guests on inclusion complex formations within the bisporphyrin. The thermodynamic and kinetic behaviors during the guest-encapsulation process were also investigated in detail. The guest-encapsulation abilities in the helicate increased with the increasing core sizes of the electron-deficient aromatic guests and decreased with the increasing bulkiness and number of substituents of the guests. Among the naphthalenediimide derivatives, those with bulky N-substituents at both ends hardly formed an inclusion complex. Instead, they formed a [2]rotaxane-like inclusion complex through the water-mediated dynamic B-O bond cleavage/reformation of the spiroborate groups of the helicate, which enhanced the conformational flexibility of the helicate to enlarge the bisporphyrin cavity and form an inclusion complex. Based on the X-ray crystal structure of a unique pacman-like 1:1 inclusion complex between the helicate and an ammonium cation as well as the molecular dynamics simulation results, a plausible mechanism for the inclusion of a planar aromatic guest within the helicate is also proposed.


Assuntos
Elétrons , Simulação de Dinâmica Molecular , Estabelecimentos Correcionais , Cinética , Termodinâmica
9.
J Phys Chem A ; 125(28): 6042-6058, 2021 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-34232640

RESUMO

Experimental and theoretical studies disagree on the energetics of methane adsorption on carbon materials. However, this information is critical for the rational design and optimization of the structure and composition of adsorbents for natural gas storage. The delicate nature of dispersion interactions, polarization of both the adsorbent and the adsorbate, interplay between H-bonding and tetrel bonding, and induced dipole/Coulomb interactions inherent to methane physisorption require computational treatment at the highest possible level of theory. In this study, we employed the smallest reasonable computational model, a maquette of porous carbon surfaces with a central site for substitution and methane binding. The most accurate predictions of methane adsorption energetics were achieved by electron-correlated molecular orbital theory CCSD(T) and hybrid density functional theory MN15 calculations employing a saturated, all-electron basis set. The characteristic geometry of methane adsorption on a carbon surface ("lander approach") arises due to bonding interactions of the adsorbent π-system with the proximal H-C bonds of methane, in addition to tetrel bonding between the antibonding orbital of the distal C-H bond and the central atom of the maquette (C, B, or N). The polarization of the electron density, structural deformations, and the comprehensive energetic analysis clearly indicate a ∼3 kJ mol-1 preference for methane binding on the N-substituted maquette. The B-substituted maquette showed a comparable or lower binding energy than the unsubstituted, pure C model, depending on the level of theory employed. The calculated thermodynamic results indicate a strategy for incorporating electron-enriched substitutions (e.g., N) into carbon materials as a way to increase methane storage capacity over electron-deficient (e.g., B) modifications. The thermochemical analysis was revised for establishing a conceptual agreement between the experimental isosteric heat of adsorption and the binding enthalpies from statistical thermodynamics principles.

10.
J Am Chem Soc ; 143(24): 8970-8975, 2021 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-34110806

RESUMO

Hydroxide anion transport is essential for alkaline fuel cells, but hydroxide anion has an inherently low conductivity owing to its small diffusion coefficient and high mass. Ordered open channels found in covalent organic frameworks are promising as pathways to enable hydroxide anion transport, but this remains to be explored. Here we report designed synthesis of anionic covalent organic frameworks that promote hydroxide anion transport across the one-dimensional channels. Engineering cationic chains with imidazolium termini onto the pore walls self-assembles a supramolecular interface of single-file hydroxide anion chains in the channels. The frameworks facilitate hydroxide anion transport to achieve an exceptional conductivity of 1.53 × 10-2 S cm-1 at 80 °C, which is 2-6 orders of magnitude higher than those of linear polymers and other porous frameworks. Impedance spectroscopy at different temperatures and studies on deuterated samples reveal that hydroxide anions transport via a proton-exchange hopping mechanism. These results open a way to design framework materials for energy conversions via engineering an anionic interface.

11.
J Phys Chem A ; 125(10): 2184-2196, 2021 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-33645988

RESUMO

Density-functional tight-binding (DFTB) parameters are presented for the simulation of the bulk phases of zirconium. Electronic parameters were obtained using a band structure fitting strategy, while two-center repulsive potentials were created by particle swarm optimization. As objective functions for the repulsive potential fitting, we employed the Birch-Murnaghan equations of state for hexagonal close-packed (HCP), body-centered cubic (BCC) and ω phases of Zr from density-functional theory (DFT). When fractional atomic coordinates are not allowed to change in the generation of the equation-of-state curves, long-range repulsive DFTB potentials are able to almost perfectly reproduce equilibrium structures, relative DFT energies of the bulk phases, and bulk moduli. However, the same potentials lead to artifacts in the DFTB potential energy surfaces when atom positions in the unit cell are allowed to fully relax during the change of unit cell parameters. Conventional short-range repulsive DFTB potentials, while inferior in their ability to reproduce DFT bulk energetics, are able to correctly reproduce the qualitative shape of the DFT potential energy surfaces, including the location of global minima, and can therefore be considered more transferable.

12.
ACS Nano ; 15(3): 4504-4517, 2021 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-33651582

RESUMO

Tailoring the grain boundaries (GBs) and twist angles between two-dimensional (2D) crystals are two crucial synthetic challenges to deterministically enable envisioned applications such as moiré excitons, emerging magnetism, or single-photon emission. Here, we reveal how twisted 2D bilayers can be synthesized from the collision and coalescence of two growing monolayer MoS2 crystals during chemical vapor deposition. The twisted bilayer (TB) moiré angles are found to preserve the misorientation angle (θ) of the colliding crystals. The shapes of the TB regions are rationalized by a kink propagation model that predicts the GB formed by the coalescing crystals. Optical spectroscopy measurements reveal a θ-dependent long-range strain in crystals with stitched grain boundaries and a sharp (θ > 20°) threshold for the appearance of TBs, which relieves this strain. Reactive molecular dynamics simulations explain this strain from the continued growth of the crystals during coalescence due to the insertion of atoms at unsaturated defects along the GB, a process that self-terminates when the defects become saturated. The simulations also reproduce atomic-resolution electron microscopy observations of faceting along the GB, which is shown to arise from the growth-induced long-range strain. These facets align with the axes of the colliding crystals to provide favorable nucleation sites for second-layer growth of a TB with twist angles that preserve the misorientation angle θ. This interplay between strain generation and aligned nucleation provides a synthetic pathway for the growth of TBs with deterministic angles.

13.
ACS Nano ; 15(2): 2994-3003, 2021 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-33513013

RESUMO

Layered titanium carbide (Ti3C2Tx) MXene is a promising electrode material for use in next-generation electrochemical capacitors. However, the atomic-level information needed to correlate the distribution of intercalated cations with surface redox reactions, has not been investigated in detail. Herein we report on sodium preintercalated MXene with high sodium content (up to 2Na per Ti3C2Tx formula) using a solution of Na-biphenyl radical anion complex (E0 ≈ -2.6 SHE). Multiple sodiation sites and formation of a two-dimensional sodium domain structure at interfaces/surfaces is identified through combined computational simulations with neutron pair distribution function analysis. The induced layer charges and the redox process characterized by the density-functional tight-binding method on a local scale are found to greatly depend on the location of sodium ions. Electrochemical testing of the pre-sodiated MXene as an electrode material in a sodium-ion capacitor shows excellent reversibility and promising performance, indicating the feasibility of chemical preintercalation as an approach to prepare MXene electrodes for ion capacitors.

14.
J Chem Theory Comput ; 17(10): 5992-6005, 2021 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-34516134

RESUMO

We present molecular-simulation-based calculations of the Van Hove correlation function (VHF) of water using multiple modeling approaches: classical molecular dynamics with simple three-site nonpolarizable models, with a polarizable model, and with a reactive force field; density functional tight-binding molecular dynamics; and ab initio molecular dynamics. Due to the many orders of magnitude difference in the computational cost of these approaches, we investigate how small and short the simulations can be while still yielding sufficiently accurate and interpretable results for the VHF. We investigate the accuracy of the different models by comparing them to recently published inelastic X-ray scattering measurements of the VHF. We find that all of the models exhibit qualitative agreement with the experiments, and in some models and for some properties, the agreement is quantitative. This work lays the foundation for future simulation approaches to calculating the VHF for aqueous solutions in bulk and under nanoconfinement.

15.
J Am Chem Soc ; 142(16): 7655-7667, 2020 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-32248688

RESUMO

Recently, there have been renewed interests in exploring new catalysts for ammonia synthesis under mild conditions. Electride-based catalysts are among the emerging ones. Ruthenium particles supported on an electride composed of a mixture of calcium and aluminum oxides (C12A7) have attracted great attention for ammonia synthesis due to their facile ability in activating N2 under ambient pressure. However, the exact nature of the reactive hydrogen species and the role of electride support still remain elusive for this catalytic system. In this work, we report for the first time that the surface-adsorbed hydrogen, rather than the hydride encaged in the C12A7 electride, plays a major role in ammonia synthesis over the Ru/C12A7 electride catalyst with the aid of in situ neutron scattering techniques. Combining in situ neutron diffraction, inelastic neutron spectroscopy, density functional theory (DFT) calculation, and temperature-programmed reactions, the results provide direct evidence for not only the presence of encaged hydrides during ammonia synthesis but also the strong thermal and chemical stability of the hydride species in the Ru/C12A7 electride. Steady state isotopic transient kinetic analysis (SSITKA) of ammonia synthesis showed that the coverage of reactive intermediates increased significantly when the Ru particles were promoted by the electride form (coverage up to 84%) of the C12A7 support rather than the oxide form (coverage up to 15%). Such a drastic change in the intermediate coverage on the Ru surface is attributed to the positive role of electride support where the H2 poisoning effect is absent during ammonia synthesis over Ru. The finding of this work has significant implications for understanding catalysis by electride-based materials for ammonia synthesis and hydrogenation reactions in general.

16.
J Chem Phys ; 152(15): 154102, 2020 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-32321259

RESUMO

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

17.
Angew Chem Int Ed Engl ; 59(29): 12162-12169, 2020 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-32329936

RESUMO

A strategy is presented for the synthesis of crystalline porous covalent organic frameworks via topology-templated polymerization. The template is based on imine-linked frameworks and their (001) facets seed the C=C bond formation reaction to constitute 2D sp2 carbon-conjugated frameworks. This strategy is applicable to templates with different topologies, enables designed synthesis of frameworks that cannot be prepared via direct polymerization, and creates a series of sp2 carbon frameworks with tetragonal, hexagonal, and kagome topologies. The sp2 carbon frameworks are highly luminescent even in the solid state and exhibit topology-dependent π transmission and exciton migration; these key fundamental π functions are unique to sp2 carbon-conjugated frameworks and cannot be accessible by imine-linked frameworks, amorphous analogues, and 1D conjugated polymers. These results demonstrate an unprecedented strategy for structural and functional designs of covalent organic frameworks.

18.
Methods Mol Biol ; 2114: 149-161, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32016892

RESUMO

Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.


Assuntos
Descoberta de Drogas/métodos , Proteínas/química , Simulação de Dinâmica Molecular , Peptídeos/química , Preparações Farmacêuticas/química , Teoria Quântica
19.
Chem Sci ; 11(48): 13113-13128, 2020 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-34094493

RESUMO

We report a parameterization of the second-order density-functional tight-binding (DFTB2) method for the quantum chemical simulation of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces. Our parameterization extends the previously released DFTB2 "auorg" parameter set by connecting it to the electronic parameter of phosphorus in the "mio" parameter set. Although this connection could technically simply be accomplished by creating only the required additional Au-P repulsive potential, we found that the Au 6p and P 3d virtual atomic orbital energy levels exert a strong influence on the overall performance of the combined parameter set. Our optimized parameters are validated against density functional theory (DFT) geometries, ligand binding and cluster isomerization energies, ligand dissociation potential energy curves, and molecular orbital energies for relevant phosphine-ligated Au n clusters (n = 2-70), as well as selected experimental X-ray structures from the Cambridge Structural Database. In addition, we validate DFTB simulated far-IR spectra for several phosphine- and thiolate-ligated gold clusters against experimental and DFT spectra. The transferability of the parameter set is evaluated using DFT and DFTB potential energy surfaces resulting from the chemisorption of a PH3 molecule on the gold (111) surface. To demonstrate the potential of the DFTB method for quantum chemical simulations of metalloid gold clusters that are challenging for traditional DFT calculations, we report the predicted molecular geometry, electronic structure, ligand binding energy, and IR spectrum of Au108S24(PPh3)16.

20.
J Chem Phys ; 151(21): 214304, 2019 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-31822077

RESUMO

The excited-state intramolecular proton transfer process in 3-hydroxyflavone is investigated based on the computed structural parameters and energetics of stationary points of vibronically coupled S1-S2 potential energy surfaces. A conical intersection close to the Franck-Condon point on S1 is identified. The minimum energy of the conical intersection is found to be near-degenerate with the equilibrium minimum of S2. Quantum nuclear wavepacket simulations revealed a small population transfer from the "bright" S1 to "dark" S2 on a time scale shorter than the O-H stretching vibrational period. Such a nonadiabatic transition opens up the possibility of new photophysical and photochemical pathways, including the proton transfer via S2.

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