Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition

Liu, Juan; Jian-ping, Zeng; Zhu, Cheng; Miao, Jianwei; Huang, Yu; Heinz, Hendrik

doi:10.1039/d0sc01443e

Cited by 40 publications

(62 citation statements)

References 107 publications

(164 reference statements)

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“…In addition, some random measurement error occurs and these differences explain some deviations. Fully quantitative comparisons of experiments with simulations would benefit from complete stress-strain curves and monitoring all elastic constants (focusing on C 11 , C 12 , and C 44 ) 84,85 .…”

Section: Mechanical Propertiesmentioning

confidence: 99%

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

Kanhaiya

Kim

et al. 2021

npj Comput Mater

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The earlier integration of validated Lennard–Jones (LJ) potentials for 8 fcc metals into materials and biomolecular force fields has advanced multiple research fields, for example, metal–electrolyte interfaces, recognition of biomolecules, colloidal assembly of metal nanostructures, alloys, and catalysis. Here we introduce 12-6 and 9-6 LJ parameters for classical all-atom simulations of 10 further fcc metals (Ac, Ca (α), Ce (γ), Es (β), Fe (γ), Ir, Rh, Sr (α), Th (α), Yb (β)) and stainless steel. The parameters reproduce lattice constants, surface energies, water interfacial energies, and interactions with (bio)organic molecules in 0.1 to 5% agreement with experiment, as well as qualitative mechanical properties under standard conditions. Deviations are reduced up to a factor of one hundred in comparison to earlier Lennard–Jones parameters, embedded atom models, and density functional theory. We also explain a quantitative correlation between atomization energies from experiments and surface energies that supports parameter development. The models are computationally very efficient and applicable to an exponential space of alloys. Compatibility with a wide range of force fields such as the Interface force field (IFF), AMBER, CHARMM, COMPASS, CVFF, DREIDING, OPLS-AA, and PCFF enables reliable simulations of nanostructures up to millions of atoms and microsecond time scales. User-friendly model building and input generation are available in the CHARMM-GUI Nanomaterial Modeler. As a limitation, deviations in mechanical properties vary and are comparable to DFT methods. We discuss the incorporation of reactivity and features of the electronic structure to expand the range of applications and further increase the accuracy.

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Section: Mechanical Propertiesmentioning

confidence: 99%

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

Kanhaiya

Kim

et al. 2021

npj Comput Mater

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“…The force field parameters in eqn (1) include equilibrium bond lengths r 0,ij , harmonic bond stretching constants k r,ij , equilibrium bond angles y 0,ijk , angle bending constants k y,ijk , and atomic charges q i , as well as the equilibrium nonbond diameters s 0,ii and the nonbond well depth e 0,ii . 42 The bonded parameters r 0,ij , k r,ij , y 0,ijk , k y,ijk are used for atoms that are part of predominantly covalent bonds. The nonbonded parameters q i , s 0,ii and e 0,ii apply to all pairs of atoms.…”

Section: Energy Expression and Force Field Parametersmentioning

confidence: 99%

“…Based on our previous work on MoS 2 , 42 the force field parameters of Cr in CVFF and CHARMM were developed according to the procedure described in ESI † Fig. S3.2 and are listed in Table 2.…”

Section: Validation Of Force Field Parametersmentioning

confidence: 99%

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Molecular dynamics study of Cr doping on the crystal structure and surficial/interfacial properties of 2H-MoS₂

XING

Shi

et al. 2022

Phys. Chem. Chem. Phys.

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“…2B), which was also examined as a bio-recognition element (BRE) in the current work. The protein was terminated with histidine, reported to bind to MoS2 [26][27] such that its binding domain was expected to possess an orientation toward the sample.…”

mentioning

confidence: 99%

Biofunctionalized Two-dimensional MoS₂ Receptors for Rapid Response Modular Electronic SARS-CoV-2 and Influenza A Antigen Sensors

Muratore

Austin

et al. 2020

Preprint

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Multiplex electronic antigen sensors for detection of SARS-Cov-2 spike glycoproteins or hemagglutinin from Influenza A in liquid samples with characteristics resembling extracted saliva were fabricated using scalable processes with potential for economical mass-production. The sensors utilize the sensitivity and surface chemistry of a two-dimensional MoS2 transducer for attachment of antibody fragments in a conformation favorable for antigen binding. Ultra-thin layers (3 nm) of amorphous MoS2 were directly sputtered over the entire sensor chip at room temperature and laser annealed to create an array of semiconducting 2H-MoS2 active sensor regions between metal contacts. The semiconducting region was functionalized with monoclonal antibody Fab (fragment antigen binding) fragments derived from whole antibodies complementary to either SARS-CoV-2 S1 spike protein or Influenza A hemagglutinin using a papain digestion to cleave the antibodies at the disulfide hinges. The high affinity for the MoS2 transducer surface with some density of sulfur vacancies for the antibody fragment base promoted chemisorption with antigen binding regions oriented for interaction with the sample. The angiostatin converting enzyme 2 (ACE2) receptor protein for the SARS-CoV-2 spike glycoprotein, was tethered to a hexa-histidine (his6) tag at its c-terminus both for purification purposes, as well as a motif for binding to MoS2. This modified protein was also investigated as a bio-recognition element. Electrical resistance measurements of sensors functionalized with antibody fragments and exposed to antigen concentrations ranging from 2-20,000 picograms per milliliter revealed selective responses in the presence of complementary antigens with sensitivity to SARS-CoV-2 or influenza A on the order of pg/mL and comparable to gold-standard diagnostics such as Polymerase Chain Reaction (PCR) analysis. Lack of antigen sensitivity for the larger ACE2 BRE further demonstrates the utility of the engineered antibody fragment/transducer interface in bringing the target antigen closer to the transducer surface for sensitivity required for early detection viral diagnostics.

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Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition

Abstract: Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by...

Cited by 40 publications

References 107 publications

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

Molecular dynamics study of Cr doping on the crystal structure and surficial/interfacial properties of 2H-MoS₂

Biofunctionalized Two-dimensional MoS₂ Receptors for Rapid Response Modular Electronic SARS-CoV-2 and Influenza A Antigen Sensors

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Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition

Abstract: Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by...

Cited by 40 publications

References 107 publications

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

Molecular dynamics study of Cr doping on the crystal structure and surficial/interfacial properties of 2H-MoS2

Biofunctionalized Two-dimensional MoS2 Receptors for Rapid Response Modular Electronic SARS-CoV-2 and Influenza A Antigen Sensors

Contact Info

Product

Resources

About

Molecular dynamics study of Cr doping on the crystal structure and surficial/interfacial properties of 2H-MoS₂

Biofunctionalized Two-dimensional MoS₂ Receptors for Rapid Response Modular Electronic SARS-CoV-2 and Influenza A Antigen Sensors