Final Binding Energy Research Articles

Evaluation of quercetin as a potential β-lactamase CTX-M-15 inhibitor via the molecular docking, dynamics simulations, and MMGBSA.

Antimicrobial resistance (AMR) threatens millions of people around the world and has been declared a global risk by the World Economic Forum. One of the important AMR mechanisms in Enterobacteriaceae is the production of extended-spectrum β-lactamases. The most common ESBL, CTX-M β-lactamases, is spread to the world by CTX-M-15 and CTX-M-14. Sulbactam, clavulanic acid, and tazobactam are first-generation β-lactamase inhibitors and avibactam is a new non-β-lactam β-lactamase inhibitor. We studied that avibactam, sulbactam, clavulanic acid, tazobactam, and quercetin natural flavonoids were docked to target protein CTXM-15. Subsequently, the complexes were simulated using the molecular dynamics simulations method during 100 ns for determining the final binding positions of ligands. Clavulanic acid left CTX-M-15 and other ligands remained in the binding site after the simulation. The estimated binding energies were calculated during 100 ns simulation by the MMGBSA-MMPBSA method. The estimated free binding energies of avibactam, sulbactam, quercetin, tazobactam, and clavulanic acid were sorted as –33.61 kcal/mol, –16.04 kcal/mol, –14 kcal/mol, –12.68 kcal/mol, and –2.95 kcal/mol. As a result of both final binding positions and free binding energy calculations, Quercetin may be evaluated an alternative candidate and a more potent β-lactamases inhibitor for new antimicrobial combinations to CTX-M-15. The results obtained in silico studies are predicted to be a preliminary study for in vitro studies for quercetin and similar bioactive natural compounds. These studies are notable for the discovery of natural compounds that can be used in the treatment of infections caused by β-lactamase-producing pathogens.

Quantum study of inelastic processes in low-energy calcium–hydrogen collisions

ABSTRACT Cross-sections and rate coefficients for the partial inelastic processes in calcium–hydrogen collisions are calculated by means of the quantum reprojection method for nuclear dynamics based on the accurate ab initio electronic structure data. That is, the atomic data for the 110 inelastic processes of excitation, de-excitation, ion-pair formation, and mutual neutralization in Ca + H and Ca+ + H− collisions are computed for all transitions between the 11 low-lying CaH(2Σ+) molecular states including ionic one. The quantum chemical data are used in a hybrid diabatic representation, which is derived from the adiabatic representation. It is found that the largest rate coefficients correspond to the mutual neutralization processes. At the temperature 6000 K, the maximal rate is equal to $4.37 \times 10^{-8}\, \mathrm{cm}^{3}\,\mathrm{s}^{-1}$. It is shown that the large-valued rates are determined by long-range ionic–covalent interactions with final binding energies from the optimal window, while moderate- and low-valued rates by both long- and short-range non-adiabatic regions with final energies outside of the optimal window.

Insights into the structure–function relationship of brown plant hopper resistance protein, Bph14 of rice plant: a computational structural biology approach

Brown plant hopper (BPH) is one of the major destructive insect pests of rice, causing severe yield loss. Thirty-two BPH resistance genes have been identified in cultivated and wild species of rice Although, molecular mechanism of rice plant resistance against BPH studied through map-based cloning, due to non-existence of NMR/crystal structures of Bph14 protein, recognition of leucine-rich repeat (LRR) domain and its interaction with different ligands are poorly understood. Thus, in the present study, in silico approach was adopted to predict three-dimensional structure of LRR domain of Bph14 using comparative modelling approach followed by interaction study with jasmonic and salicylic acids. LRR domain along with LRR-jasmonic and salicylic acid complexes were subjected to dynamic simulation using GROMACS, individually, for energy minimisation and refinement of the structure. Final binding energy of jasmonic and salicylic acid with LRR domain was calculated using MM/PBSA. Free-energy landscape analysis revealed that overall stability of LRR domain of Bph14 is not much affected after forming complex with jasmonic and salicylic acid. MM/PBSA analysis revealed that binding affinities of LRR domain towards salicylic acid is higher as compared to jasmonic acid. Interaction study of LRR domain with salicylic acid and jasmonic acid reveals that THR987 of LRR form hydrogen bond with both complexes. Thus, THR987 plays active role in the Bph14 and phytochemical interaction for inducing resistance in rice plant against BPH. In future, Bph14 gene and phytochemicals could be used in BPH management and development of novel resistant varieties for increasing rice yield.

Structural, electronic and vibrational properties of GexCy (x+y=2–5) nanoclusters: A B3LYP-DFT study

An ab-initio study of the stability, structural and electronic properties has been made for 84 germanium carbide nanoclusters, GexCy (x+y=2–5). The configuration possessing the maximum value of final binding energy (FBE), among the various configurations corresponding to a fixed x+y=n value, is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize fully the geometries of the nanoclusters. The binding energies (BE), highest-occupied and lowest-unoccupied molecular orbital (HOMO–LUMO) gaps have been obtained for all the clusters and the bond lengths have been reported for the most stable clusters. We have considered the zero point energy (ZPE) corrections. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have also been investigated for the most stable structures. The configurations containing the carbon atoms in majority are seen to be the most stable structures. The strong C–C bond has important role in stabilizing the clusters. For the clusters containing one germanium atom and all the other as carbon atoms, the BE increases monotonically with the number of the carbon atoms. The HOMO–LUMO gap, IPs and EAs fluctuates with increase in the number of atoms. The nanoclusters containing even number of carbon atoms have large HOMO–LUMO gaps and IPs, whereas the nanoclusters containing even number of carbon atoms have small EAs. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA). The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in the experiments.

Theory and Computer Simulation of Quantum NEMS Energy Storage in Materials

The theory of quantum relaxation of the nanoelectromechanical system (NEMS) energy storage in materials is taken under consideration. By using the method of quantum NEMS kinetics (NK) the relaxation NEMS energy storage in the form of limited planes (100) Fe 172 cube in fcc iron crystal was studied. For comparison, the calculation a similar structure atomic cluster Fe 172 was carried out by the molecular dynamics method (MD) for temperature T = 293 K. Analysis of computer-related experiments have shown that the relaxation of the NEMS energy storage Fe 172 and the MD atomic cluster Fe 172 from an initial nonequilibrium state has significant differences both in the kinetics, and in a variety of structural transformations. It is shown that the iron MD cluster relaxation is insignificant and its final total binding energy per atom is 2 eV/at lower than the crystal one. The NK-method revealed that after relaxation there is a significant change in the shape and the pair radial distribution function of nuclei the NEMS energy storage. It significantly increases the binding energy up to 3.34 eV/at, which is only about 1 eV/at less than the binding energy of the crystalline iron. It is shown an opportunity to undergo a process of self-organization the NEMS energy storage through several intermediate metastable states. It is manifested that fluctuation rebuild the cube into a cuboid with a strong bending of the cube surfaces occurs at 20 ps of relaxation, and there is the second transformation being with trapezoid change of faces at 40 ps of relaxation process. This effect cardinally differentiates NK relaxation of the NEMS energy storage cube Fe 172 from MD relaxation of the atomic cluster Fe 172 in the crystalline iron.

Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

PRE-SUPERNOVA EVOLUTION OF ROTATING SOLAR METALLICITY STARS IN THE MASS RANGE 13-120M☉AND THEIR EXPLOSIVE YIELDS

We present the first set of a new generation of models of massive stars with a solar composition extending between 13 and 120 M ?, computed with and without the effects of rotation. We included two instabilities induced by rotation: the meridional circulation and the shear instability. We implemented two alternative schemes to treat the transport of the angular momentum: the advection-diffusion formalism and the simpler purely diffusive one. The full evolution from the pre-main sequence up to the pre-supernova stage is followed in detail with a very extended nuclear network. The explosive yields are provided for a variety of possible mass cuts and are available at the Web site http://www.iasf-roma.inaf.it/orfeo/public_html. We find that both the He and the CO core masses are larger than those of their non-rotating counterparts. Also the C abundance left by the He burning is lower than in the non-rotating case, especially for stars with an initial mass of 13-25 M ?, and this affects the final mass-radius relation, basically the final binding energy, at the pre-supernova stage. The elemental yields produced by a generation of stars rotating initially at 300?km?s?1 do not change substantially with respect to those produced by a generation of non-rotating massive stars, the main differences being a slight overproduction of the weak s-component and a larger production of F. Since rotation also affects the mass-loss rate, either directly or indirectly, we find substantial differences in the lifetimes as O-type and Wolf-Rayet subtypes between the rotating and non-rotating models. The maximum mass exploding as Type IIP supernova ranges between 15 and 20?M ? in both sets of models (this value depends basically on the larger mass-loss rates in the red supergiant phase due to the inclusion of the dust-driven wind). This limiting value is in remarkably good agreement with current estimates.

A DFT study for the structural and electronic properties of Zn m Se n nanoclusters

An ab initio study has been performed for the stability, structural and electronic properties of 19 small zinc selenide ZnmSen (m + n = 2–4) nanoclusters. Out of these nanoclusters, one nanocluster is found to be unstable due to its imaginary vibrational frequency. A B3LYP-DFT/6-311G(3df) method is used in the optimization of the geometries of the nanoclusters. We have calculated the zero point energy (ZPE), which is ignored by the other workers. The binding energies (BE), HOMO–LUMO gaps and bond lengths have been obtained for all the optimized nanoclusters. For the same value of ‘m’ and ‘n’, we designate the most stable structure the one, which has maximum final binding energy (FBE) per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), dipole moments and charge on atoms have been investigated for the most stable nanoclusters. For the same value of ‘m’ and ‘n’, the nanocluster containing maximum number of Se atoms is found to be most stable.

Energetics and Lateral Effects of CH2ClF Adsorbed on Anatase TiO2 (101) Surface

The adsorbate–substrate interaction between chlorofluoromethane and anatase TiO2 (101) surface has been simulated at DFT/B3LYP level, according to a previous obtained structure involving an acid–base interaction between the Cl atom and one 5-fold coordinated Ti ion and an H-bond between one H atom and one 2-fold coordinated O ion. The adsorption has been investigated considering different periodicities and surface coverages, and the energetics have been analyzed according to a recent procedure taking into account the binding, interaction, and distortion energies. The procedure allows both to quantify the direct and surface-mediated lateral effects due to the interactions between the adsorbed molecules and to determine the energies in the limit of an isolated adsorbed molecule. The obtained results suggest variations in the influence of the surface-mediated and direct lateral effects and a different behavior of the direct ones along the two directions defining the slab. The direct attraction of adsorbed molecules along the b direction leads to binding energies stronger than that referring to the limit of low surface coverage while the direct repulsion along the a direction results in a weaker adsorption. This work, allowing insights about the adsorption of CH2ClF on TiO2, shows clearly how the final binding energy of a generic compound can be affected by the interactions between neighboring molecules.

STRUCTURAL, ELECTRONIC, AND OPTICAL PROPERTIES OF ZnxSy (x + y = 2 TO 4) NANOCLUSTERS: A B3LYP-DFT STUDY

The stability, structural, electronic, and optical properties have been studied for most stable zinc sulfide nanoclusters Zn x S y (x + y = n = 2 to 4). A B3LYP-DFT/6-311G(3df) method is employed to optimize the geometries, and a TDDFT method is used for the study of the optical properties. The binding energies (BE), HOMO–LUMO gaps and the bond lengths have been obtained for all the clusters. We have considered also the zero point energy (ZPE) corrections ignored by the earlier workers. For a fixed value of n, we designate the most stable structure the one, which has maximum final binding energy per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), charge on atoms, dipole moment, and optical properties have been investigated for the most stable structures. The nanoclusters containing large number of S atoms for each "n" are found to be most stable. Except for ZnS nanocluster, the HOMO–LUMO gap increases with the number of S atoms. Similarly, except for ZnS , IP and EA fluctuate with the cluster size but reveal downward trend. The optical absorption is quite weak in visible region but is strong in the ultraviolet region in most of the nanoclusters except a few. The growth of most stable nanoclusters may be possible in the experiments.

Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in CytochromecPeroxidase

We investigate the effect of systematically applying molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) to docked poses in an attempt to improve the correspondence between theoretical prediction and experimental observation. The proposed scheme involves running a short time scale MD simulation on a docked ligand pose (and any known structurally important crystal structure waters in the active site), followed by QM/MM minimization. Both of these steps are relatively fast for moderately sized ligands; longer time scale MD involving the protein is not found to improve the results. The final binding energy is given in terms of the QM/MM total energy, a van der Waals correction, and a term to account for desolvation effects. This methodology is first tested with a trypsin inhibitor, for which we establish the importance of running MD before reoptimizing with QM/MM. The method is then applied to cytochrome c peroxidase using a set of binders and decoys. In this example, the proposed methodology affords much better discrimination between binders and decoys than the traditional docking approach used. For both systems presented, application of this protocol results in a significantly better energetic ranking and a smaller root mean squared deviation from known crystallographic ligand poses. This work highlights the importance of including polarization effects through QM/MM and of sampling with MD to refine a set of initial docked poses.

ChemInform Abstract: Floppy Structure of the Benzene Dimer: Ab initio Calculation on the Structure and Dipole Moment

The structure of the benzene dimer has aroused considerable interest due to recent experimental measurements and hence extensive theoretical calculation is topical. Nine structures of the benzene dimer were investigated using the second‐order Mo/ller–Plesset theory. The calculations were performed with smaller (MIDI‐1+s+p) and larger (6‐31+G*) basis sets. The T‐shape structure was found to be the most stable but with a very shallow minimum; the wagging motion around the lowest hydrogen in the range of ±10° is practically nonhindered. These results together are consistent with the structure found experimentally. The final binding energy for the T structure (distance of molecular centers equal to 5.0 A) is −2.7±0.4 kcal/mol, which is more than the value derived from experiments. The calculated dipole moment is in excellent agreement with experiment.

Ab initio study of structural, electronic, optical, and vibrational properties of Zn x S y (x + y = 2 to 5) nanoclusters

An ab initio study of the stability, structural, electronic. and optical properties has been performed for 46 zinc sulfide nanoclusters ZnxSy (x + y = n = 2 to 5). Five out of them are seen to be unstable as their vibrational frequencies are found to be imaginary. A B3LYP-DFT/6-311G(3df) method is employed to optimize the geometries and a TDDFT method is used for the study of the optical properties. The binding energies (BE), HOMO-LUMO gaps and the bond lengths have been obtained for all the clusters. For the ZnS2, ZnS3, and ZnS4 nanoclusters, our stable structures are seen to be different from those obtained earlier by using the effective core potentials. We have also considered the zero point energy (ZPE) corrections ignored by the earlier workers. For a fixed value of n, we designate the most stable structure the one, which has maximum final binding energy per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), charges on the atoms, dipole moments, optical properties, vibrational frequencies, infrared intensities, relative infrared intensities, and Raman scattering activities have been investigated for the most stable structures. The nanoclusters containing large number of S atoms for each n is found to be most stable. The HOMO-LUMO gap decreases from n = 2–3 and then increases above n = 3. The IP and EA both fluctuate with the cluster size n. The optical absorption is quite weak in visible region but strong in the ultraviolet region in most of the nanoclusters except a few. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every nanocluster and may be used to characterize a specific nanocluster. The growth of most stable nanoclusters may be possible in the experiments.

Benchmark Data for Noncovalent Interactions in HCOOH···Benzene Complexes and Their Use for Validation of Density Functionals.

We present benchmark energetic data for the HCOOH···benzene complexes. The benchmark data were determined by a composite approach based on CCSD(T) calculations. Final binding energies (kcal/mol) are in the range of 1.6-4.8 kcal/mol, and they were used as reference data to test density functionals in the literature. Among the tested local density functionals without empirical dispersion corrections, M06-L is the best performing functional, and M06-L/6-31+G(d,p) gives a mean unsigned error (MUE) of only 0.15 kcal/mol. PBEsol and SOGGA also show promising performance. The best local DFT-D methods are BLYP-D and PBEsol-D, and they give an MUE of 0.15 kcal/mol after removing basis set superposition errors by the counterpoise approach. Empirical dispersion corrections greatly improve the descriptions of noncovalent interactions in HCOOH···benzene dimers. The calculated benchmark data and intermolecular potential are useful for the parametrizations of new force fields and coarse-grained models for chemical species such as the acrylic polymers.

Benchmark Data for Interactions in Zeolite Model Complexes and Their Use for Assessment and Validation of Electronic Structure Methods

We present benchmark binding energies for five zeolite model complexes, with four of the adsorbates bound noncovalently and one covalently. The binding energies were determined as the sum of the infinite-basis-set limit of Moller−Plesset second-order perturbation theory (MP2) energies and a CCSD(T) correction term evaluated with the aug-cc-pVDZ basis set. The basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and separate extrapolation of the Hartree−Fock and correlation energies. We found that correlation contributions beyond MP2 to the final binding energies are small; their magnitude is in the range of 0.02−1.0 kcal/mol. For the MP2 method to describe the interactions in these zeolite model systems accurately, one needs to use a basis set at least the size of aug-cc-pVTZ in conjunction with counterpoise corrections. Final binding energies (kcal/mol) of the model complexes are in the range of 3.5−19.5 kcal/mol, and they were used as...

Modeling the Interaction of the Phosphate Group in Nucleotides with Copper(I) in the Gas Phase: Reactivity of Cu+with Orthophosphoric Acid and Its Monomethyl Ester

The gas-phase reactivity of orthophosphoric acid (HO)3PO with the cation Cu+ has been investigated through the use of mass spectrometry experiments and DFT calculations. Its monomethylated ester (CH3O)(HO)2PO has been also theoretically studied at the same level in order to take into account the possible effects of methylation. Computational results, including structural features, vibrational frequencies, and binding energies, obtained with the hybrid three-parameter B3LYP density functional combined with relativistic ECPs and associated valence basis set, were reported. Final binding energies have been evaluated using extended basis sets. Additional calculations performed with several “all electron” basis sets are also included for comparison. For some of the minima of the [Cu,H3PO4]+ hypersurface, the nature of the different CuO bonds as well as the character of the orbitals involved were analyzed by means of the Bader topological analysis and NBO method.

Hydrogen bonding between aromatics and cationic amino groups

The proximity of cationic amino groups to aromatic rings in proteins as a motif has been used to interpret specificity, structural and conformational stability, and even catalytic activity in biological systems. To quantify these interactions, ammonium cation-aromatic ring complexes have been geometry-optimized using the 3-21G basis set at the Hartree-Fock level. Final binding energies are obtained from single-point RHF and MP2/6-31G * level calculations at the 3-21G optimized geometries. The cation species include NH 4 +, CH 3NH 3 +, and (CH 3) 4N +, and the aromatic systems (models for amino acid side-chains) consist of benzene, toluene (phenylalanine), paramethylphenol (tyrosine) and 4-methylindole (tryptophan). Twenty-five distinct complex geometries are obtained which can be represented by ten generic structures. The MP2 binding energies at the 3-21G optimized geometries compare very well with experiment. Special binding sites at the electronegative atoms (oxygen in paramethylphenol and nitrogen in 4-methylindole) are also found. The effect of basis set and theoretical level on the calculated results is tested and discussed. A reduced variational space binding energy component analysis of the ammonium-benzene complex shows the binding energy to have similar contributions from electrostatic (including exchange repulsion), polarization, and charge transfer terms. Comparison with potassium ion/ benzene shows similar binding energy but significantly different binding energy components.

Chemical hole diving

The non-adiabatic reaction leading to the emission of exoelectrons during the adsorption of oxygen on lithium is exploited to estimate the time that elapses during the dissociation of the molecule. With a three-step model the exoemission probability is calculated. A comparison with experimentally observed probabilities predicts the reaction time to be 75±25 O2p hole lifetimes at the final O2p binding energy. The width of the exoelectron energy distribution reflects this hole lifetime. The absence of visible light emission ( < 10 −10 photons/O 2) is shown to be compatible with the model.

Approximate ways to treat the nucleon-nucleon tensor force in the four-nucleon bound state.

Several approximation methods are tested in the four-nucleon bound-state problem as a means to understand how the two-nucleon tensor force propagates through the underlying (2)+(2) and (3)+1 subsystem amplitudes to yield a final four-nucleon binding energy. The aim is to show how to include as much of the nucleon-nucleon tensor force as possible in the dominant S-state component of the four-nucleon wave function for the purpose of optimizing the starting point in the iterative solution of the full problem.

Relativistic corrections to the triton binding energy.

The influence of relativity on the triton binding energy is investigated. The relativistic three-dimensional version of the Bethe-Salpeter equation proposed by Blankenbecler and Sugar (BbS) is used. Relativistic (nonseparable) one-boson-exchange potentials (constructed in the BbS framework) are employed for the two-nucleon interaction. In a 34-channel Faddeev calculation, it is found that relativistic effects increase the triton binding energy by about 0.2 MeV. Including charge dependence (besides relativity), the final triton binding energy predictions are 8.33 and 8.16 MeV for the Bonn A and B potentials, respectively.