Van Der Waals Dispersion Forces Research Articles

Exploring the aqueous solubility and intermolecular interactions of diclofenac Diethylammonium: A molecular modeling study in solid state and solvation processes

Diclofenac, a widely used non-steroidal anti-inflammatory drug with analgesic, anti-inflammatory, and antipyretic properties, presents a challenge in oral administration due to its low aqueous solubility and subsequent low bioavailability. This issue, primarily attributed to the drug's high hydrophobicity, can lead to adverse side effects. To address this, our study delves into the aqueous solvation process of diclofenac through molecular modeling, employing both Carr-Parrinello molecular dynamics and Density Functional Theory. This combined approach enables a comprehensive investigation of the molecular interactions that influence solubility, encompassing non-polar interactions (van der Waals dispersion forces), dipole interactions, and hydrogen bonding. Our results highlight the formation of intermolecular interactions with water molecules through OH⋯Owater and CO⋯Hwater hydrogen bonds. Additionally, we observe intramolecular hydrogen bonds within diclofenac (NH⋯OH and NH⋯Cl) and weaker interactions involving CH⋯Cl. Notably, the protonation of diclofenac contributes to molecular rigidity, hindering hydrogen bonding with adjacent water molecules further. These insights offer a deeper understanding of the solubility challenges associated with diclofenac, paving the way for improved drug formulations that enhance bioavailability. The application of Carr-Parrinello molecular dynamics and density functional theory in this study highlights their valuable role in addressing complex drug solubility and design issues.

Probing chiral discrimination in biological systems using atomic force microscopy: The role of van der Waals and exchange interactions

We analyze from a theoretical perspective recent experiments where chiral discrimination in biological systems was established using Atomic Force Microscopy (AFM). Even though intermolecular forces involved in AFM measurements have different origins, i.e., electrostatic, bonding, exchange, and multipole interactions, the key molecular forces involved in enantiospecific biorecognition are electronic spin exchange and van der Waals (vdW) dispersion forces, which are sensitive to spin–orbit interaction (SOI) and space-inversion symmetry breaking in chiral molecules. The vdW contribution to chiral discrimination emerges from the inclusion of SOI and spin fluctuations due to the chiral-induced selectivity effect, a result we have recently demonstrated theoretically. Considering these two enantiospecific contributions, we show that the AFM results regarding chiral recognition can be understood in terms of a simple physical model that describes the different adhesion forces associated with different electron spin polarization generated in the (DD), (LL), and (DL) enantiomeric pairs, as arising from the spin part of the exchange and vdW contributions. The model can successfully produce physically reasonable parameters accounting for the vdW and exchange interaction strength, accounting for the chiral discrimination effect. This fact has profound implications in biorecognition where the relevant intermolecular interactions in the intermediate-distance regime are clearly connected to vdW forces.

Confining He Atoms in Diverse Ice-Phases: Examining the Stability of He Hydrate Crystals through DFT Approaches

In the realm of solid water hydrostructures, helium atoms have a tendency to occupy the interstitial spaces formed within the crystal lattice of ice structures. The primary objective of this study is to examine the stability of various ice crystals when influenced by the presence of He atoms. Presenting a first attempt at a detailed computational description of the whole energy components (guest–water, water–water, guest–guest) in the complete crystal unit cells contributes to enhancing the knowledge available about these relatively unexplored helium–water systems, which could potentially benefit future experiments. For this purpose, two different ice structures were considered: the previously established He@ice II system, and the predicted (but currently nonexistent) He@ice XVII system. One of the main features of these He-filled structures is the stability conferred by the weak van der Waals dispersion forces that occur between the host lattice and the guest atoms, in addition to the hydrogen bonds established among the water molecules. Hence, it is crucial to accurately describe these interactions. Therefore, the first part of this research is devoted examining the performance and accuracy of various semi-local and non-local DFT/DFT-D functionals, in comparison with previous experimental and/or high-level computational data. Once the best-performing DFT functional has been identified, the stability of these empty and He-filled structures, including different number of He atoms within the lattices, is analysed in terms of their structural (lattice deformation), mechanical (pressure compression effects) and energetic properties (binding and saturation energies). In this manner, the potential formation of these structures under zero temperature and pressure conditions can be evaluated, while their maximum storage capacity is also determined. The obtained results reveal that, despite the weak underlying interactions, the He encapsulation has a rather notable effect on both lattice parameters and energetics, and therefore, the guest–host interactions are far from being negligible. Besides, both ice crystals are predicted to remain stable when filled with He atoms, with ice XVII exhibiting a higher capacity for accommodating a larger number of guest atoms within its interstitial spaces.

Impact of surface roughness, surface charge, and temperature on sandstone wettability alteration by nanoparticles

The wettability of rocks affects the balance between capillary and viscous forces during multiphase flow through porous media, which in turn determines the fluid displacement process governing the recovery of oil from subsurface formations. In this work, the mechanism of wettability reversal of aged synthetic sandstones by metal oxide nanoparticles (SiO2 and Al2O3) was investigated with particular focus on the impact of surface roughness, zeta potential, and temperature. The synthetic surfaces were prepared from powders of Berea sandstone with known grain size ranges and their average roughness and roughness ratio were obtained from the 3D surface reconstruction of their microscope images. Each surface was subsequently aged in Permian crude oil to alter its wettability. For surfaces with larger grain sizes and lower surface roughness ratios, the lower capillary pressure allowed stronger oil/surface interactions, leading to enhanced oil-wetness. The wettability alteration effects of nanoparticles were then examined through real-time top view imaging and dynamic front view contact angle experiments. The negatively charged SiO2 nanoparticles rapidly reversed the sandstone wettability, indicating their potential applicability as wettability alteration agents. By contrast, the positively charged Al2O3 counterpart caused no wettability reversal. The mechanism of wettability alteration was further studied by microscale interaction analyses and nanoscale transmission electron microscopy. Because nanoparticles were only a few nanometers large, the microscale roughness had a negligible effect on the wettability reversal. Instead, the combined effect of van der Waals dispersion forces and surface-charge-induced electrostatic forces were recognized as the two key factors affecting the wettability of sandstone particles. Such interactions may be curbed at elevated temperatures due to a decrease in the zeta potential and colloidal stability of the particles.

Anisotropic van der Waals dispersion forces in polymers: Structural symmetry breaking leads to enhanced conformational search

Both structure and dynamics of (bio)polymers are profoundly affected by van der Waals interactions. Many-body van der Waals forces are shown to depend on the global conformation of polymers, in contrast with the limited distance range of widely used pairwise van der Waals models. This is shown to produce an increased smoothness of the potential energy surface and qualitatively different steady-state geometries.

Different forms of silicon nanotubes and their interactions with DNA nucleotides: A molecular dynamics study

The interaction between different forms of silicon nanotubes (SiNTs) and DNA nucleotides is investigated using molecular dynamics simulations. The optimized geometries of infinite single-walled SiNTs made of hexagonal and tetragonal lattices are assessed at the classical level based on Tersoff and Stillinger-Weber potentials. Properties such as Si–Si bond length, diameters as well as formation energy per Si atom are calculated for different SiNTs. Our results for the armchair and zigzag structures show relatively good agreements with other classical and quantum level studies. Therefore, the same method is applied to the less investigated tetragonal type nanotubes. In the next step, the interaction between different DNA nucleotides and stable SiNTs is investigated. The results indicate that the van der Waals dispersion forces are mainly responsible for the nucleotide-SiNT interaction. A unique interaction feature of each nucleotide with SiNTs provides general guidelines for the design of SiNTs-based biosensors.

Applications of spectroscopic techniques to the study of monomer–dimer equilibria for methylene blue in aqueous solutions containing ionic liquid: Probing the structural interactions involving water and ionic liquids

An understanding of the nature of interaction and bonding in dye aggregation process is important for such diverse problems and applications such as stacking interactions in biomolecules, staining properties, photodynamic therapy for cancer, energy transfer in lasing technology and energy transfer and electron transfer processes. In present communication we report visible absorption spectrums and their analysis for the dye methylene blue (MB) in concentration range of 1∙10–6 – 1∙10–4 M in aqueous solutions containing ionic liquids namely, 1–ethyl–3–methyl–imidazolium bromide, 1–butyl–3–methyl–imidazolium bromide and 1–hexyl–3–methyl–imidazolium bromide at 298 ± 1. In this concentration range of MB only Monomer ⇌ Dimer equilibria for the dye exist and hence the spectral characteristics in the visible range of 550–700 nm have been examined. The spectrums obtained are compared with those obtained in aqueous solutions of NaCl. Using suitable developed method of estimating molar absorption extinction coefficient values, the equilibrium constant values are obtained at various ionic strengths of imidazolium ions. It has been found that monomer and dimer absorption maximum occur at 665 and ≈605/610 nm, respectively, do not get much altered on addition of imidazolium ions. The extent of interaction between the MB and imidazolium cations varies with the concentration of imidazolium cations as well as the nature of imidazolium cations, that is, the chain length of the substituents. The dimer dissociation constant values extrapolated to zero ionic strength of ionic liquids exhibit systematic alteration with respect to alteration of chain length in imidazolium cations. The different interactional phenomena such as the formation of ion–pairs, ion–pair complexes, dimer dissociation, solubilization of monomers and binding of MB with imidazolium cations have been examined. The transfer standard free energy changes have been calculated for the transfer of dimers from aqueous solutions to aqueous solutions containing ionic liquids. The changes in dimer geometry from sandwich type and end–on–end types also have been studied. It is observed that the contribution to the interaction energy is mainly from van der Waals type and dispersion forces, in addition to short range forces involving multipoles. The binding of monomers with imidazolium cations is also examined in terms of formation of micellar type aggregates in solution phase. It is proposed that the water structural interaction and hydrophobic interactions are the major factors in the formation and dissociation of aggregates.

Activated carbon derived from sugarcane and modified with natural zeolite for efficient adsorption of methylene blue dye: experimentally and theoretically approaches

The introduction of activated carbon/natural zeolite (AC/NZ) as an efficient and reliable nanoadsorbent for enhancing methylene blue (MB) dye adsorption. By calcining sugarcane waste at various temperatures between 500 and 900 °C, activated carbons (ACs) are formed. Both XRD and SEM were used for the characterization of the prepared adsorbents. Adsorption measurements for the removal of MB dye were made on the impact of pH, beginning MB concentration, and contact time. The maximum AC500/NZ adsorption capacity for MB dye at 25 °C, pH 7, and an AC500/NZ mass of 50 mg was found to be approximately 51 mg/g at an initial concentration of 30 ppm. The pseudo-second-order kinetics model and the Temkin isotherm model describe the adsorption process. The Temkin model shows that the adsorption energy is 1.0 kcal/mol, indicating that the MB-to-AC500/NZ adsorption process occurs physically. Our Monte Carlo (MC) simulation studies supported our findings and showed that the Van der Waals dispersion force was responsible for the MB molecule's physical adsorption. The AC500/NZ adsorbent is thought to be a strong contender for water remediation.

DMC-ICE13: Ambient and high pressure polymorphs of ice from diffusion Monte Carlo and density functional theory.

Ice is one of the most important and interesting molecular crystals, exhibiting a rich and evolving phase diagram. Recent discoveries mean that there are now 20 distinct polymorphs; a structural diversity that arises from a delicate interplay of hydrogen bonding and van der Waals dispersion forces. This wealth of structures provides a stern test of electronic structure theories, with Density Functional Theory (DFT) often not able to accurately characterize the relative energies of the various ice polymorphs. Thanks to recent advances that enable the accurate and efficient treatment of molecular crystals with Diffusion Monte Carlo (DMC), we present here the DMC-ICE13 dataset; a dataset of lattice energies of 13 ice polymorphs. This dataset encompasses the full structural complexity found in the ambient and high-pressure molecular ice polymorphs, and when experimental reference energies are available, our DMC results deliver sub-chemical accuracy. Using this dataset, we then perform an extensive benchmark of a broad range of DFT functionals. Of the functionals considered, revPBE-D3 and RSCAN reproduce reference absolute lattice energies with the smallest error, while optB86b-vdW and SCAN+rVV10 have the best performance on the relative lattice energies. Our results suggest that a single functional achieving reliable performance for all phases is still missing, and that care is needed in the selection of the most appropriate functional for the desired application. The insights obtained here may also be relevant to liquid water and other hydrogen-bonded and dispersion-bonded molecular crystals.

Density functional theory computation of the binding free energies between various mutations of SARS-CoV-2 RBD and human ACE2: molecular level roots of the contagiousness

The receptor-binding domain (RBD) of SARS-CoV-2 attaches to the human ACE2 to initiate binding of SARS-CoV-2 to human cell and leads to the infection process afterwards. In this study, various mutations of SARS-CoV-2 spike RBD and human ACE2 complexes are investigated via density functional theory (DFT) computations to obtain binding free energies. The DFT computations are performed without fragmenting the interfaces to involve longer-range quantum mechanical interactions for improving accuracy. The vibrational free energies, van der Waals dispersion forces and basis set superposition error corrections are also included in the calculations. The results show that the absolute value of the binding energy of B.1.1.7 mutated spike RBD–ACE2 complex is more than five times higher than that of the original strain. The results of this study are expected to be useful for a deeper understanding of the relation of the binding free energies and the level of contagiousness.

Studies related to changes in ionic strength due to addition of sodium chloride to an aqueous solution of cationic dye methylene blue (MB): Electronic spectra analysis for dimerization equilibria

It is well-known that methylene blue (MB),a cationic dye forms dimer and higher aggregates in aqueous solutions. For specific concentration range (1∙10−6–1∙10−4 M), a D⇌2M equilibria has been postulated and well characterized by visible electronic spectroscopy. The dye molecules can lead to formation of stacking (end on end and sandwich) type structures in solution phase stabilized by weak dispersion van der Waals forces and cation-anion-cation ion pairs and triplet interactions usually referred as hydrophobic interactions. Recent literature reports indicate that excess chemical potential of small hydrophobic particles and the strength of hydrophobic pair interactions appear to be linearly related. Our observations about precipitation of dye (MB) at higher concentrations of salt like sodium chloride (NaCl) made us to study the dimerization equilibria in detail since in the Corona health disaster; use of MB to diagnose the type of Covid variants helped Scientists in a great way. Salting-out of proteins is in general used to explain the specific protein aggregation behaviour observed in Huntington's disease. For model compound like tertiary butyl-alcohol, Geiger et al. reported enhancement of hydrophobic contacts which increase with increase in salt concentration. NaCl is an essential ingredient of biological fluids, of which concentration controls the various biological life governing processes. However, such information is non-existent for aqueous solutions of dyes.We therefore reported measured optical absorbance of aqueous solution containing NaCl (0.1–1.0 M) and dye at different concentrations (1∙10−6–1∙10−4 M) at 298 K spectrophotometrically, in the wavelength range of 550–700 nm. The spectrums are compared to those obtained for binary solutions of MB in water. Analysis of the spectral data yielded the dimer dissociation constant and individual characteristic monomer and dimer spectra. Further information about the geometry and twist angle between the dipoles of the MB molecules in the dimer species has been obtained. The results are analyzed for the monomer-dimer equilibria and salting-out effect as well applications of mass action model and exciton theories are discussed.

Adsorption of a wide variety of antibiotics on graphene-based nanomaterials: A modelling study

The knowledge on the sorption behaviour of antibiotics on nanomaterials is limited, especially regarding the reaction mechanism on the surface of carbon nanomaterials, which may determine both the adsorptive capacity and regeneration efficiency of graphene adsorbers. In this work, we used molecular modelling to generate the most comprehensive (to date) adsorption dataset for pristine and functionalised graphene interacting with 8 β-lactams, 3 macrolide, 12 quinolone, 4 tetracycline, 15 sulphonamide, trimethoprim, 2 lincosamide, 2 phenicole and 4 nitroimidazole antibiotics, and their transformation products in water and n-octanol. Results show that various non-covalent interactions that operate simultaneously, including van der Waals dispersion forces, π-interactions, hydrophobic interaction and hydrogen bonding, facilitate adsorption. The molecular properties of antibiotics and graphene/graphene oxide, as well as the composition of the background solution regulate the magnitude of these interactions. Our findings demonstrate that the most efficient method for the removal of antibiotics from aquatic environments is the use of graphene at environmental pH. The subsequent regeneration of the sorbent is best achieved through washing with slightly basic (pH 8–10) non-polar solvents. The obtained theoretical insights expand and complement experimental observations and provide important information that can contribute to further exploration into the adsorbent properties of graphene-based materials, and towards the development of predictive adsorption models.

2D IR spectra of the intrinsic vibrational probes of ionic liquid from dispersion corrected DFT-MD simulations

We present the vibrational spectral profile of the intrinsic cationic (N-H) and anionic (C-O) probe stretch modes in methylammonium formate (MAF) using first principles molecular dynamics simulations in conjunction with the density functional theory (DFT) approaches. All simulations were performed employing Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE) functionals, using three types of van der Waals (vdW) dispersion-corrected representations (D2, D3, and dispersion-corrected atom-centered one-electron potentials) and two values of plane-wave cut-off (300 and 600 Ry). The long-range electrostatic interactions, directional hydrogen bonds and non-directional van der Waals (vdW) dispersion forces are required to accurately interpret the interionic interactions in the protic ionic liquid, MAF. We compute the 2D IR correlation spectra from the wavelet-derived instantaneous frequencies obtained at each timeframe applying the cumulant expansion truncated at the second order to measure the dynamics of vibrational spectral diffusion. Here, we investigate the effects of electronic structure parameters on the spectral bands of the 2D IR contour plot. The spectral bands for both the N-H and CO stretching vibrations attain a round shape by 1 ps, indicating the loss of frequency correlation irrespective of the type of BLYP or PBE-based functionals. Further, the diagonal linewidth of the 2D IR spectral band agrees with the FWHM (full width at half maxima) of the calculated normalized vibrational stretch frequency distribution. Moreover, this study also finds the reason behind the coalescence of the symmetric and antisymmetric C-O stretches in the computed 2D IR spectra. Besides, these computational results may attract the attention of the experimental spectroscopists as it provides molecular-level interpretation and detailed ultrafast time-resolved spectral information of the intrinsic stretching vibrations and associated dynamics of the protic ionic liquid (PIL). Herein, we inspect the quality of different density functionals along with vdW dispersion corrections. However, even though the experimental data is not available for direct comparison of the results, we finally conclude that the inclusion of the effects of dispersion interactions provides a better estimation of the spectroscopic properties.

Bulk and interfacial nanostructure and properties in deep eutectic solvents: Current perspectives and future directions

Deep eutectic solvents (DESs) are a tailorable class of solvents that are rapidly gaining scientific and industrial interest. This is because they are distinct from conventional molecular solvents, inherently tuneable via careful selection of constituents, and possess many attractive properties for applications, including catalysis, chemical extraction, reaction media, novel lubricants, materials chemistry, and electrochemistry. DESs are a class of solvents composed solely of hydrogen bond donors and acceptors with a melting point lower than the individual components and are often fluidic at room temperature. A unique feature of DESs is that they possess distinct bulk liquid and interfacial nanostructure, which results from intra- and inter-molecular interactions, including coulomb forces, hydrogen bonding, van der Waals interactions, electrostatics, dispersion forces, and apolar-polar segregation. This nanostructure manifests as preferential spatial arrangements of the different species, and exists over several length scales, from molecular- to nano- and meso-scales. The physicochemical properties of DESs are dictated by structure–property relationships; however, there is a significant gap in our understanding of the underlying factors which govern their solvent properties. This is a major limitation of DES-based technologies, as nanostructure can significantly influence physical properties and thus potential applications. This perspective provides an overview of the current state of knowledge of DES nanostructure, both in the bulk liquid and at solid interfaces. We provide definitions which clearly distinguish DESs as a unique solvent class, rather than a subset of ILs. An appraisal of recent work provides hints towards trends in structure–property relationships, while also highlighting inconsistencies within the literature suggesting new research directions for the field. It is hoped that this review will provide insight into DES nanostructure, their potential applications, and development of a robust framework for systematic investigation moving forward.

Modeling the Binding and Conformational Energetics of a Targeted Covalent Inhibitor to Bruton's Tyrosine Kinase.

Targeted covalent inhibitors (TCIs) bind to their targets in both covalent and noncovalent modes, providing exceptionally high affinity and selectivity. These inhibitors have been effectively employed as inhibitors of protein kinases, with Taunton and coworkers (Nat. Chem. Biol. 2015, 11, 525-531) reporting a notable example of a TCI with a cyanoacrylamide warhead that forms a covalent thioether linkage to an active-site cysteine (Cys481) of Bruton's tyrosine kinase (BTK). The specific mechanism of the binding and the relative importance of the covalent and noncovalent interactions is difficult to determine experimentally, and established simulation methods for calculating the absolute binding affinity of an inhibitor cannot describe the covalent bond-forming steps. Here, an integrated approach using alchemical free-energy perturbation and QM/MM molecular dynamics methods was employed to model the complete Gibbs energy profile for the covalent inhibition of BTK by a cyanoacrylamide TCI. These calculations provide a rigorous and complete absolute Gibbs energy profile of the covalent modification binding process. Following a classic thiol-Michael addition mechanism, the target cysteine is deprotonated to form a nucleophilic thiolate, which then undergoes a facile conjugate addition to the electrophilic functional group to form a bond with the noncovalently bound ligand. This model predicts that the formation of the covalent linkage is highly exergonic relative to the noncovalent binding alone. Nevertheless, noncovalent interactions between the ligand and individual amino acid residues in the binding pocket of the enzyme are also essential for ligand binding, particularly van der Waals dispersion forces, which have a larger contribution to the binding energy than the covalent component in absolute terms. This model also shows that the mechanism of covalent modification of a protein occurs through a complex series of steps and that entropy, conformational flexibility, noncovalent interactions, and the formation of covalent linkage are all significant factors in the ultimate binding affinity of a covalent drug to its target.

Isotope effect on the thermal expansion coefficient of atomically thin boron nitride

Atomically thin monoisotopic hexagonal boron nitride (BN) which is electrically insulating and has a high thermal conductivity could be utilized as fillers in electronic packaging materials for thermal dissipation in integrated and miniaturized modern devices. Thermal expansion mismatch in electronic packaging could cause strain and ultimately device failure, so it is valuable to measure and understand the thermal expansion coefficient (TEC) of atomically thin isotopically pure BN. In this work, we studied the TECs of mono-, bi-, and tri-layer isotope-purified BN using Raman spectroscopy and density functional theory calculations including van der Waals dispersion forces. Monolayer (1L) 10BN had a slightly larger experimental TEC than 1L 11BN at close to room temperature: (−5.1 ± 0.8) × 10−6 K−1 and (−4.6 ± 0.8) × 10−6 K−1, respectively. The negative TECs up to 700 K were attributed to the competition between the in-plane stretching vibration modes and out-of-plane bending modes in BN; the lighter isotope leads to a larger absolute TEC due to higher amplitude of its out-of-plane bending modes. The absolute TECs of isotopic BN decreased with increased atomic thickness, which indicates strengthening of the out-of-plane bending rigidity. The deep understanding of the isotope effect on the TEC of two-dimensional (2D) materials also opens a promising pathway to minimize TEC mismatch in 2D van der Waals heterostructures.

Attractive and repulsive residue fragments at the interface of SARS-CoV-2 and hACE2

The initial stages of SARS-CoV-2 coronavirus attachment to human cells are mediated by non-covalent interactions of viral spike (S) protein receptor binding domains (S-RBD) with human ACE2 receptors (hACE2). Structural characterization techniques, such as X-ray crystallography (XRC) and cryoelectron microscopy (cryo-EM), previously identified SARS-CoV-2 spike protein conformations and their surface residues in contact with hACE2. However, recent quantum-biochemical calculations on the structurally related S-RBD of SARS-CoV-1 identified some contact-residue fragments as intrinsically attractive and others as repulsive. This indicates that not all surface residues are equally important for hACE2 attachment. Here, using similar quantum-biochemical methods, we report some four-residue fragments (i.e quartets) of the SARS-CoV-2 S-RBD as intrinsically attractive towards hACE2 and, therefore, directly promoting host–virus non-covalent binding. Other fragments are found to be repulsive although involved in intermolecular recognition. By evaluation of their respective intermolecular interaction energies we found two hACE2 fragments that include contact residues (ASP30, LYS31, HIS34) and (ASP38, TYR41, GLN42), respectively, behaving as important SARS-CoV-2 attractors. LYS353 also promotes viral binding via several mechanisms including dispersion van der Waals forces. Similarly, among others, three SARS-CoV-2 S-RBD fragments that include residues (GLN498, THR500, ASN501), (GLU484, PHE486, ASN487) and (LYS417), respectively, were identified as hACE2 attractors. In addition, key hACE2 quartets identified as weakly-repulsive towards the S-RBD of SARS-CoV-1 were found strongly attractive towards SARS-CoV-2 explaining, in part, the stronger binding affinity of hACE2 towards the latter coronavirus. These findings may guide the development of synthetic antibodies or identify potential viral epitopes.

Experimentally and theoretically approaches for disperse red 60 dye adsorption on novel quaternary nanocomposites

A comprehensive study that combined both experimental and computational experiments was performed to evaluate the usage of organo-metal oxide nanocomposite for the elimination of disperse red 60 dye (DR) from aqueous solutions. Chitosan was modified by Schiff base to form nanoneedles chitosan-4-chloroacetophenone derivative. The derivatives were then impregnated with CeO2–CuO–Fe2O3 or CeO2–CuO–Al2O3 metal oxides to prepare a novel quarternary organo-metal oxide nanocomposite. The novel nanocomposite, chitosan-4-chloroacetophenone/CeO2–CuO–Fe2O3 (CF) and chitosan-4-chloroacetophenone/CeO2–CuO–Al2O3 (CA) are cheap and effective nano adsorbents that can be used for the uptake of DR from aqueous solution. The CF and CA nano-composites were characterized using different techniques. Moreover, the effect of adsorption parameters (initial DR concentration, time of contact, pH, temperature, and adsorbent mass) as well as CA and CF reusability tests were performed. Langmuir adsorption isotherm and pseudo-second-order kinetics models were best fitted with the adsorption process. The maximum amount of DR adsorbed was 100 mg/g on CF and CA at pH 2 and 4, respectively with a physical spontaneous, and exothermic adsorption process. Monte Carlo (MC) simulation studies indicated the adsorption of DR molecule on the CF and CA surfaces following a parallel mode in most of all studied configurations, confirming the strong interactions between the DR and surfaces atoms of CF and CA. The molecular structure analysis of DR dye adsorbed on the surface of CF and CA indicated that the adsorption process related to Van der Waals dispersion force. Consequently, this helps to trap DR dye molecules on the surface of CF and CA (i.e., physical adsorption), which supports our experimental results.

Reactivity of Single Transition Metal Atoms on a Hydroxylated Amorphous Silica Surface: A Periodic Conceptual DFT Investigation.

The drive to develop maximal atom-efficient catalysts coupled to the continuous striving for more sustainable reactions has led to an ever-increasing interest in single-atom catalysis. Based on a periodic conceptual density functional theory (cDFT) approach, fundamental insights into the reactivity and adsorption of single late transition metal atoms supported on a fully hydroxylated amorphous silica surface have been acquired. In particular, this investigation revealed that the influence of van der Waals dispersion forces is especially significant for a silver (98 %) or gold (78 %) atom, whereas the oxophilicity of the Group 8-10 transition metals plays a major role in the interaction strength of these atoms on the irreducible SiO2 support. The adsorption energies for the less-electronegative row 4 elements (Fe, Co, Ni) ranged from -1.40 to -1.92 eV, whereas for the heavier row 5 and 6 metals, with the exception of Pd, these values are between -2.20 and -2.92 eV. The deviating behavior of Pd can be attributed to a fully filled d-shell and, hence, the absence of the hybridization effects. Through a systematic analysis of cDFT descriptors determined by using three different theoretical schemes, the Fermi weighted density of states approach was identified as the most suitable for describing the reactivity of the studied systems. The main advantage of this scheme is the fact that it is not influenced by fictitious Coulomb interactions between successive, charged reciprocal cells. Moreover, the contribution of the energy levels to the reactivity is simultaneously scaled based on their position relative to the Fermi level. Finally, the obtained Fermi weighted density of states reactivity trends show a good agreement with the chemical characteristics of the investigated metal atoms as well as the experimental data.

Contact residue contributions to interaction energies between SARS-CoV-1 spike proteins and human ACE2 receptors

Several viruses of the corona family interact, via their spike (S) proteins, with human cellular receptors. Spike proteins of SARS-CoV-1 and SARS-CoV-2 virions, being structurally related but not identical, mediate attachment to the human angiotensin-converting enzyme 2 (hACE2) receptor in similar but non-identical ways. Molecular-level understanding of interactions between spike proteins and hACE2 can aid strategies for blocking attachment of SARS-CoV-1, a potentially reemerging health threat, to human cells. We have identified dominant molecular-level interactions, some attractive and some repulsive, between the receptor binding domain of SARS-CoV-1 spike proteins (S-RBD) and hACE2. We performed fragment-based quantum-biochemical calculations which directly relate biomolecular structure to the hACE2...S-RBD interaction energy. Consistent with X-ray crystallography and cryo-EM, the interaction energy between hACE2 and S-RBD (approx -26 kcal/mol) corresponds to a net intermolecular attraction which is significantly enhanced by inclusion of dispersion van der Waals forces. Protein fragments at the hACE2...S-RBD interface, that dominate host-virus attraction, have been identified together with their constituent amino acid residues. Two hACE2 fragments which include residues (GLU37, ASP38, TYR41, GLN42) and (GLU329, LYS353, GLY354), respectively, as well as three S-RBD fragments which include residues (TYR436), (ARG426) and (THR487, GLY488, TYR491), respectively, have been identified as primary attractors at the hACE2...S-RBD interface.