XYG3 and XYGJ-OS performances for noncovalent binding energies relevant to biomolecular structures

The enzyme-containing magnetic composites are presented. The magnetic matrix for enzyme immobilization is obtained by sequential application of an amine-containing polysaccharide—chitosan and a synthetic polymer—poly(ethylene-alt-maleic acid) to the magnetite microparticles to form the interpolyelectrolyte complex shell. Then, the enzyme (trypsin) is immobilized by covalent or noncovalent binding. Thus, the suggested composites can be readily obtained in the environmentally friendly manner. The enzyme capacity of the resulting composites reaches 28.0–32.6 mg/g. The maximum hydrolysis rates of the H-Val-Leu-Lys-pNA substrate provided by these composites range within 0.60·10–7–0.77·10–7 M/min.

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Hydrogen in amorphous Ni–Zr: Pressure concentration isotherms, site occupation, and binding energies

Journal of Materials Research ◽

10.1557/jmr.1986.0765 ◽

1986 ◽

Vol 1 (6) ◽

pp. 765-773 ◽

Cited By ~ 36

Author(s):

E. Batalla ◽

J.O. Strom-Olsen ◽

Z. Altounian ◽

D. Boothroyd ◽

R. Harris

Keyword(s):

Binding Energies ◽

Site Occupation ◽

Pressure Concentration

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Multiple Donors in Zinc Oxide Substrates

MRS Proceedings ◽

10.1557/proc-719-f2.4 ◽

2002 ◽

Vol 719 ◽

Cited By ~ 2

Author(s):

K. Thonke ◽

N. Kerwien ◽

A. Wysmolek ◽

M. Potemski ◽

A. Waag ◽

...

Keyword(s):

Zinc Oxide ◽

Chemical Vapor ◽

Binding Energies ◽

Vapor Transport ◽

Chemical Vapor Transport ◽

Oxide Substrates ◽

Multiple Donors ◽

Major Donors ◽

Available Zinc ◽

Transport Technique

AbstractWe investigate by photoluminescence (PL) nominally undoped, commercially available Zinc Oxide substrates (from Eagle Picher) grown by seeded chemical vapor transport technique in order to identify residual donors and acceptors. In low temperature PL spectra the dominant emission comes from the decay of bound exciton lines at around 3.36 eV. Zeeman measurements allow the identification of the two strongest lines and some weaker lines in-between as donorrelated. From the associated two-electron satellite lines binding energies of the major donors of 48 meV and 55 meV, respectively, can be deduced.

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MAGNETIC FIELD, PRESSURE AND TEMPERATURE DEPENDENT OPTICAL PROPERTIES IN A GaAs 9.0 P 1.0 QUANTUM DOT

JOURNAL OF ADVANCES IN PHYSICS ◽

10.24297/jap.v6i2.1791 ◽

2014 ◽

Vol 6 (2) ◽

pp. 1178-1190

Author(s):

A. JOHN PETER ◽

Ada Vinolin

Keyword(s):

Magnetic Field ◽

Optical Properties ◽

Quantum Dot ◽

Field Strength ◽

Magnetic Field Strength ◽

Photon Energy ◽

Nonlinear Optical ◽

Binding Energies ◽

Nonlinear Optical Properties ◽

Optical Rectification

Simultaneous effects of magnetic field, pressure and temperature on the exciton binding energies are found in a 9.0 1.0 6.0 4.0 GaAs P / GaAs P quantum dot. Numerical calculations are carried out taking into consideration of spatial confinement effect. The cylindrical system is taken in the present problem with the strain effects. The electronic properties and the optical properties are found with the combined effects of magnetic field strength, hydrostatic pressure and temperature values. The exciton binding energies and the nonlinear optical properties are carried out taking into consideration of geometrical confinement and the external perturbations.Compact density approach is employed to obtain the nonlinear optical properties. The optical rectification coefficient is obtained with the photon energy in the presence of pressure, temperature and external magnetic field strength. Pressure and temperature dependence on nonlinear opticalÂ susceptibilities of generation of second and third order harmonics as a function of incident photon energy are brought out in the influence of magnetic field strength. The result shows that the electronic and nonlinear optical properties are significantly modified by the applications of external perturbations in a 9.0 1.0 6.0 4.0 GaAs P / GaAs P quantum dot.

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Divergence of Many-Body Perturbation Theory for Noncovalent Interactions of Large Molecules

10.26434/chemrxiv.11124251.v1 ◽

2019 ◽

Author(s):

Brian Nguyen ◽

Guo P Chen ◽

Matthew M. Agee ◽

Asbjörn M. Burow ◽

Matthew Tang ◽

...

Keyword(s):

Perturbation Theory ◽

System Size ◽

State Density ◽

Second Order ◽

Binding Energies ◽

Basis Set ◽

Many Body ◽

Many Body Perturbation Theory ◽

Relative Errors ◽

Ground State Density

Prompted by recent reports of large errors in noncovalent interaction (NI) energies obtained from many-body perturbation theory (MBPT), we compare the performance of second-order Møller–Plesset MBPT (MP2), spin-scaled MP2, dispersion-corrected semilocal density functional approximations (DFA), and the post-Kohn–Sham random phase approximation (RPA) for predicting binding energies of supramolecular complexes contained in the S66, L7, and S30L benchmarks. All binding energies are extrapolated to the basis set limit, corrected for basis set superposition errors, and compared to reference results of the domain-based local pair-natural orbital coupled-cluster (DLPNO-CCSD(T)) or better quality. Our results confirm that MP2 severely overestimates binding energies of large complexes, producing relative errors of over 100% for several benchmark compounds. RPA relative errors consistently range between 5-10%, significantly less than reported previously using smaller basis sets, whereas spin-scaled MP2 methods show limitations similar to MP2, albeit less pronounced, and empirically dispersion-corrected DFAs perform almost as well as RPA. Regression analysis reveals a systematic increase of relative MP2 binding energy errors with the system size at a rate of approximately 1‰ per valence electron, whereas the RPA and dispersion-corrected DFA relative errors are virtually independent of the system size. These observations are corroborated by a comparison of computed rotational constants of organic molecules to gas-phase spectroscopy data contained in the ROT34 benchmark. To analyze these results, an asymptotic adiabatic connection symmetry-adapted perturbation theory (AC-SAPT) is developed which uses monomers at full coupling whose ground-state density is constrained to the ground-state density of the complex. Using the fluctuation–dissipation theorem, we obtain a nonperturbative “screened second-order” expression for the dispersion energy in terms of monomer quantities which is exact for non-overlapping subsystems and free of induction terms; a first-order RPA-like approximation to the Hartree, exchange, and correlation kernel recovers the macroscopic Lifshitz limit. The AC-SAPT expansion of the interaction energy is obtained from Taylor expansion of the coupling strength integrand. Explicit expressions for the convergence radius of the AC-SAPT series are derived within RPA and MBPT and numerically evaluated. Whereas the AC-SAPT expansion is always convergent for nondegenerate monomers when RPA is used, it is found to spuriously diverge for second-order MBPT, except for the smallest and least polarizable monomers. The divergence of the AC-SAPT series within MBPT is numerically confirmed within RPA; prior numerical results on the convergence of the SAPT expansion for MBPT methods are revisited and support this conclusion once sufficiently high orders are included. The cause of the failure of MBPT methods for NIs of large systems is missing or incomplete “electrodynamic” screening of the Coulomb interaction due to induced particle–hole pairs between electrons in different monomers, leaving the effective interaction too strong for AC-SAPT to converge. Hence, MBPT cannot be considered reliable for quantitative predictions of NIs, even in moderately polarizable molecules with a few tens of atoms. The failure to accurately account for electrodynamic polarization makes MBPT qualitatively unsuitable for applications such as NIs of nanostructures, macromolecules, and soft materials; more robust non-perturbative approaches such as RPA or coupled cluster methods should be used instead whenever possible.

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On the Adsorption of Aspartate Derivatives to Calcite Surfaces in Aqueous Environment

10.26434/chemrxiv.11558430.v1 ◽

2020 ◽

Author(s):

Robert Stepic ◽

Lara Jurković ◽

Ksenia Klementyeva ◽

Marko Ukrainczyk ◽

Matija Gredičak ◽

...

Keyword(s):

Active Sites ◽

Realistic Model ◽

Binding Energies ◽

Inhibition Mechanism ◽

Aqueous Environment ◽

Binding Modes ◽

Carboxylate Groups ◽

Dissolved Ions ◽

Living Organisms ◽

Dynamics Simulations

In many living organisms, biomolecules interact favorably with various surfaces of calcium carbonate. In this work, we have considered the interactions of aspartate (Asp) derivatives, as models of complex biomolecules, with calcite. Using kinetic growth experiments, we have investigated the inhibition of calcite growth by Asp, Asp2 and Asp3.This entailed the determination of a step-pinning growth regime as well as the evaluation of the adsorption constants and binding free energies for the three species to calcite crystals. These latter values are compared to free energy profiles obtained from fully atomistic molecular dynamics simulations. When using a flat (104) calcite surface in the models, the measured trend of binding energies is poorly reproduced. However, a more realistic model comprised of a surface with an island containing edges and corners, yields binding energies that compare very well with experiments. Surprisingly, we find that most binding modes involve the positively charged, ammonium group. Moreover, while attachment of the negatively charged carboxylate groups is also frequently observed, it is always balanced by the aqueous solvation of an equal or greater number of carboxylates. These effects are observed on all calcite features including edges and corners, the latter being associated with dominant affinities to Asp derivatives. As these features are also precisely the active sites for crystal growth, the experimental and theoretical results point strongly to a growth inhibition mechanism whereby these sites become blocked, preventing further attachment of dissolved ions and halting further growth.

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In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

10.26434/chemrxiv.12480434.v1 ◽

2020 ◽

Author(s):

Sahar Qazi ◽

Mustafa Alhaji Isa ◽

Adam Mustapha ◽

Khalid Raza ◽

Ibrahim Alkali Allamin ◽

...

Keyword(s):

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

In Silico ◽

Md Simulation ◽

Binding Energies ◽

Anacardium Occidentale ◽

Upper Respiratory Tract ◽

Ligand Complex ◽

In Silico Docking ◽

Main Protease

The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of Zingiber offinale and Anacardium occidentale using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of Zingiber offinale and the leaves of Anacardium occidentale. These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), Pan-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907).

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In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

10.26434/chemrxiv.12480434 ◽

2020 ◽

Author(s):

Sahar Qazi ◽

Mustafa Alhaji Isa ◽

Adam Mustapha ◽

Khalid Raza ◽

Ibrahim Alkali Allamin ◽

...

Keyword(s):

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

In Silico ◽

Md Simulation ◽

Binding Energies ◽

Anacardium Occidentale ◽

Upper Respiratory Tract ◽

Ligand Complex ◽

In Silico Docking ◽

Main Protease

The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of Zingiber offinale and Anacardium occidentale using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of Zingiber offinale and the leaves of Anacardium occidentale. These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), Pan-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907).

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Highly Fluorescent Au25-xAgx Nanoclusters Protected with Poly(ethylene glycol) - and Zwitterion-Modified Thiolate Ligands

10.26434/chemrxiv.6987479 ◽

2018 ◽

Author(s):

Dinesh Mishra ◽

Sisi Wang ◽

Zhicheng Jin ◽

Eric Lochner ◽

Hedi Mattoussi

Keyword(s):

Quantum Yield ◽

Near Infrared ◽

Small Diameter ◽

Binding Energies ◽

Thiolate Ligands ◽

Nir Emission ◽

Thiolate Complexes ◽

Long Lifetime ◽

Poly Ethylene

We describe the growth and characterization of highly fluorescing, near-infrared-emitting nanoclusters made of bimetallic Au25-xAgx cores, prepared using various monothiol-appended hydrophobic and hydrophilic ligands. The reaction uses well-defined triphenylphosphine-protected Au11 clusters (as precursors), which are reacted with Ag(I)-thiolate complexes. The prepared nanoclusters are small (diameter < 2nm, as characterized by TEM) with emission peak at 760 nm and long lifetime (~12 µs). The quantum yield measured for these materials was 0.3 - 0.4 depending on the ligand. XPS measurements show the presence of both metal atoms in the core, with measured binding energies that agree with reported values for nanocluster materials. The NIR emission combined with high quantum yield, small size and ease of surface functionalization afforded by the coating, make these materials suitable to implement investigations that address fundamental questions and potentially useful for biological sensing and imaging applications.

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