Quantum-chemical calculations were used to describe both the acidity of aluminabenzene-based Lewis acids and stability of aluminabenzene-based anions. Aluminabenzene itself was found to exhibit greater acidity than antimony pentaflouride, and thus can be qualified as a Lewis superacid. Substitution of the heterocyclic ring with electron withdrawing groups results in formation of extremely strong Lewis superacids. Two of them, namely AlC5 Cl5 and AlC5 (CN)5 are the strongest Lewis acids described in the literature so far. Whereas, anions formed after the addition of fluoride anion to substituted aluminabenzene-based Lewis acids, while characterized by somewhat lower electronic stability than the least coordinating anions hitherto known, are considerably more stable in terms of thermodynamic stability (measured by the propensity to electrophile attack). On this account they are expected to act as counterions for the most reactive cations. The proposed Lewis acids may be prone to the isomerization and dimerization, whereas studied anions are expected to be stable with regard to such processes.

In designing three-dimensional (3-D) molecular stars, it is very difficult to enhance the molecular rigidity through forming the covalent bonds between the axial and equatorial groups because corresponding axial groups will generally break the delocalized π bond over equatorial frameworks and thus break their star-like arrangement. In this work, exemplified by designing the 3-D stars Be2 ©Be5 E5 + (E = Au, Cl, Br, I) with three delocalized σ bonds and delocalized π bond over the central Be2 ©Be5 moiety, we propose that the desired covalent bonding can be achieved by forming the delocalized σ bond(s) and delocalized π bond(s) simultaneously between the axial groups and equatorial framework. The covalency and rigidity of axial bonding can be demonstrated by the total Wiberg bond indices of 1.46-1.65 for axial Be atoms and ultrashort Be-Be distances of 1.834-1.841 Å, respectively. Beneficial also from the σ and π double aromaticity, these mono-cationic 3-D molecular stars are dynamically viable global energy minima with well-defined electronic structures, as reflected by wide HOMO-LUMO gaps (4.68-5.06 eV) and low electron affinities (4.70-4.82 eV), so they are the promising targets in the gas phase generation, mass-separation, and spectroscopic characterization.

Recently, halogen bonding (XB) has received increased attention as a new type of non-covalent interaction widely present in nature. In this work, quantum chemical calculations at DFT level have been carried out to investigate halogen bonding interactions between COn (n = 1 or 2) and dihalogen molecules XY (X = F, Cl, Br, I and Y = Cl, Br, I). Highly accurate all-electron data, estimated by CCSD(T) calculations, were used to benchmark the different levels of computational methods with the objective of finding the best accuracy/computational cost. Molecular electrostatic potential, interaction energy values, charge transfer, UV spectra, and natural bond orbital (NBO) analysis were determined to better understand the nature of the XB interaction. Density of states (DOS) and projected DOS were also computed. Hence, according to these results, the magnitude of the halogen bonding is affected by the halogen polarizability and electronegativity, where for the more polarizable and less electronegative halogen atoms, the σ-hole is bigger. Furthermore, for the halogen-bonded complexes involving CO and XY, the OC∙∙∙XY interaction is stronger than the CO∙∙∙XY interaction. Thus, the results presented here can establish fundamental characteristics of halogen bonding in media, which would be very helpful for applying this noncovalent interaction for the sustainable capture of carbon oxides.

Consistent basis sets of triple-zeta valence quality for the elements La-Lu were derived for periodic quantum-chemical solid-state calculations. They are an extension of the pob-TZVP-rev2 [D. Vilela Oliveira, et al., J. Comput. Chem. 2019, 40(27), 2364-2376], [J. Laun and T. Bredow, J. Comput. Chem. 2021, 42(15), 1064-1072], [J. Laun and T. Bredow, J. Comput. Chem. 2022, 43(12), 839-846] basis sets and are based on the fully relativistic effective core potentials of the Stuttgart/Cologne group and on the def2-TZVP valence basis of the Ahlrichs group. The basis sets are constructed to minimize the basis set superposition error in crystalline systems. The contraction scheme, orbital exponents, and contraction coefficients were optimized in order to ensure robust and stable self-consistent-field convergence for a set of compounds and metals. For the applied PW1PW hybrid functional, the average deviations of the calculated lattice constants from experimental references are smaller with pob-TZV-rev2 than with standard basis sets available from the CRYSTAL basis set database. After augmentation with single diffuse s- and p-functions, reference plane-wave band structures of metals can be accurately reproduced.

A major difference between amyloid precursor protein (APP) isoforms (APP695 and APP751) is the existence of a Kunitz type protease inhibitor (KPI) domain which has a significant impact on the homo- and hetero-dimerization of APP isoforms. However, the exact molecular mechanisms of dimer formation remain elusive. To characterize the role of the KPI domain in APP dimerization, we performed a single molecule pull down (SiMPull) assay where homo-dimerization between tethered APP molecules and soluble APP molecules was highly preferred regardless of the type of APP isoforms, while hetero-dimerization between tethered APP751 molecules and soluble APP695 molecules was limited. We further investigated the domain level APP-APP interactions using coarse-grained models with the Martini force field. Though the model initial ternary complexes (KPI-E1, KPI-KPI, KPI-E2, E1-E1, E2-E2, and E1-E2) generated using HADDOCK (HD) and AlphaFold2 (AF2), the binding free energy profiles and the binding affinities of the domain combinations were investigated via the umbrella sampling with Martini force field. Additionally, membrane-bound microenvironments at the domain level were modeled. As a result, it was revealed that the KPI domain has a stronger attractive interaction with itself than the E1 and E2 domains, as reported elsewhere. Thus, the KPI domain of APP751 may form additional attractive interactions with E1, E2 and the KPI domain itself, whereas it is absent in APP695. In conclusion, we found that the APP751 homo-dimer formation is predominant than the homodimerization in APP695, which is facilitated by the presence of the KPI domain.

The intrinsic ability of clathrate hydrates to encage gaseous molecules is explored. Encapsulation ability depends on the cavity size and the type of guest gaseous species in addition to the physical parameters, temperature and pressure. Here we have reported the structure, stability and nature of interaction in dissimilar guest occupied sH hydrate cavity. Diatomic gas molecules and small polyatomic hydrocarbons are considered as guests. The irregular icosahedron (512 68 ) cavity of sH hydrate is the host. Different thermodynamic parameters for the guest molecules encapsulation were calculated using three different hybrid DFT functionals, B3LYP, M05-2X, M06, and moreover using dispersion correction (PBE0-D3). With the consideration of large H-bonded systems the 6-31G* and cc-pVTZ basis sets were used for two set of computations. To disclose the nature of interaction between the host-guest systems as well as the interaction between the guest molecules inside the host the non-covalent interaction (NCI) indices and energy decomposition analysis (EDA) were done. Impact of host-guest and guest-guest interactions are discussed.

The diagonal components and the trace of two tensors which account for chiroptical response of the leucoindigo molecule C16H12N2O2 that is, static anapole magnetizability, and dynamic electric dipole-magnetic dipole polarisability depending on the frequency of impinging light, are a function of the ϕ dihedral angle of torsion about the central CC bond, assumed to lie in the y direction of the coordinate system. They vanish for symmetry reasons at ϕ = 0∘ and ϕ = 180∘ , corresponding respectively to C2v and C2h point group symmetries, that is, cis and trans conformers characterized by the presence of molecular symmetry planes. Nonetheless, diagonal components and average value of static anapole polarizability and optical rotation tensors vanish at ϕ = 90∘ , where leucondigo is unquestionably chiral from the geometrical viewpoint. Vanishing values of the average chiroptical properties have been observed also in the proximity of other ϕ angles. Attempts have been made to explain the occurrence of accidental zeros of chiroptical properties in terms of transition frequencies and scalar products appearing in the numerator of their quantum mechanical definitions. Within the electric dipole approximation, the presence of anomalous vanishing values of tensor components of anapole magnetizability and electric-magnetic dipole polarizability is ascribed to physical achirality, arising from the lack of either toroidal or spiral electron flow along the x , y and z directions.

The OCNH unit is one of the most frequently encountered structural motifs in rings in drugs which serves dual role as the proton donor through NH bond and proton acceptor through the CO bond. Here, we predicted the HB strength (Eint ) of OCNH motif with H2 O for commonly observed 37 rings in drugs with DFT method M06L/6-311++G(d,p). The HB strength is rationalized in terms of molecular electrostatic potential (MESP) topology parameters ΔVn(NH) and ΔVn(CO) which describe the relative electron deficient/rich nature of NH and CO, respectively, with respect to the reference formamide. The Eint of formamide is -10.0 kcal/mol whereas the Eint of ring systems is in the range -8.6 to -12.7 kcal/mol-a minor increase/decrease compared to the formamide. The variations in Eint are addressed using the MESP parameters ΔVn(NH) and ΔVn(CO) and proposed the hypothesis that a positive ΔVn(NH) enhances NH…Ow interaction while a negative ΔVn(CO) enhances the CO…Hw interaction. The hypothesis is proved by expressing Eint jointly as ΔVn(NH) and ΔVn(CO) and also verified for twenty FDA approved drugs. The predicted Eint for the drugs using ΔVn(NH) and ΔVn(CO) agreed well with the calculated Eint . The study confirms that even delicate variations in the electronic feature of a molecule can be quantified in terms of MESP parameters and they provide a priori prediction of the HB strength. The MESP topology analysis is recommended to understand the tunability of HB strength in drug motifs.

We report new results on the translational-rotational (T-R) states of the CO2 molecule inside the sI clathrate-hydrate cages. We adopted the multiconfiguration time-dependent Hartree methodology to solve the nuclear molecular Hamiltonian, and to address issues on the T-R couplings. Motivated by experimental X-ray observations on the CO2 orientation in the D and T sI cages, we aim to evaluate the effect of the CO2 -water interaction on quantum dynamics. Thus, we first compared semiempirical and ab initio-based pair interaction model potentials against first-principles DFT-D calculations for ascertaining the importance of nonadditive many-body effects on such guest-host interactions. Our results reveal that the rotational and translational excited states quantum dynamics is remarkably different, with the pattern and density of states clearly affected by the underlying potential model. By analyzing the corresponding the probability density distributions of the calculated T-R eigenstates on both semiempirical and ab initio pair CO2 -water nanocage potentials, we have extracted information on the altered CO2 guest local structure, and we discussed it in connection with experimental data on the orientation of the CO2 molecule in the D and T sI clathrate cages available from neutron diffraction and 13C solid-state NMR studies, as well as in comparison with previous molecular dynamics simulations. Our calculations provide a very sensitive test of the potential quality by predicting the low-lying T-R states and corresponding transitions for the encapsulated CO2 molecule. As such spectroscopic observables have not been measured so far, our results could trigger further detailed experimental and theoretical investigations leading to a quantitative description of the present guest-host interactions.

Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET-based solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self-consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D-RISM calculations compared to AMBER-RISM software. EPISOL consists of both a user-friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force-field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL.

The spike protein of SARS-CoV-2 exists in two major conformational states, namely the 'open' and 'closed' states which are also known as the 'up' and 'down' states, respectively. In its open state, the receptor binding domain (RBD) of the protein is exposed for binding with ACE2, whereas the spike RBD is inaccessible to ACE2 in the closed state of the protein. In the current work, we have performed all-atom microsecond simulations of the full-length trimeric spike protein solvated in explicit aqueous medium with an average system size of ~0.7 million atoms to understand the molecular nature of intra- and inter-chain interactions, water-bridged interactions between different residues that contribute to the stability of the open and closed states of the protein, and also the free energy landscape for transition between the open and closed states of the protein. We have also examined the changes of such interactions that are associated with switching from one state to the other through both unbiased and biased simulations at all-atom level with total run length of 4 μs. Interestingly, after about 0.8 μs of unbiased molecular dynamics run of the spike system in the open state, we observed a gradual transition of the monomeric chain (B) from open to its partially closed or down state. Initially the residues at the interface of chain B RBD in the open state spike protein were at non-hydrogen-bonding distances from the residues of chain C RBD. However, the two RBDs gradually came closer and finally the residue S459 of the RBD of chain B made a hydrogen bond with F374 of chain C in the last 200 ns of the simulation along with formation of a few more hydrogen bonds involving other residues. Since no transition from closed to the open state of the protein is observed in the present 1 μs unbiased simulation of the closed state protein, the current study seems to suggest that the closed conformational state is preferred for the spike protein of SARS-CoV-2 in aqueous medium. Furthermore, calculations of the free energy surface of the conformational transition from open (up) to the closed (down) state using a biased simulation method reveal a free energy barrier of ~3.20 kcal/mol for the transition of RBD from open to the closed state, whereas the barrier for the reverse process is found to be significantly higher.

The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that sits in the VLP shell) and the P2 subdomain (that protrudes outside) of the major VP1 protein, this resulting in a correlated wagging motion of the P2 subdomains with respect to the VLP surface. The fluctuations of the P2 subdomain were found to be more pronounced and the P2 domain made a greater angle with the normal to the VLP surface for the GII.2 strain, which could explain the inability of this strain to bind the histo-blood group antigens (HBGAs).

Some straightforward improvements designed to make grid-based quantum chemical topology more efficient and faster are presented. The strategy focuses on both the evaluation of the scalar function over three-dimensional discrete grids and the algorithms aimed to follow and integrate gradient trajectories over the basin volumes together. Beyond the density analysis, we show that the scheme is quite suitable for the electron localization function and its complex topology. With this speed-up of the parallelized process used to generate 3d-grids, this new scheme is several orders of magnitude faster than the original grid-based method implemented in our laboratory (TopMod09). The efficiency of our implementation (TopChem2) was also compared with well-known grid-based algorithms designed to assign the grid points to basins. The performances, speed versus accuracy have been discussed on the basis of results obtained from selected illustrative examples.

In the computation of molecular dynamic magnetizabilities and magnetic dipole moments, three different reference points are required: (i) origin of coordinate system, (ii) origin of vector potential A , and (iii) origin of multipole expansion. This study shows that methods relying on continuous translation of origin of the current density IB(r,ω,t) induced by optical magnetic fields provide an effective solution to the problem of choices (i) and (ii), in that they yield origin independent IB within the algebraic approximation, for any basis set. Frequency-dependent magnetizabilities are also invariant with respect to (iii), as a consequence of symmetry, for a number of molecular point groups. In molecules of lower symmetries, computed magnetizabilities depend on origin of the multipole expansion. Large basis set computations carried out for water, ammonia, methane, ethane, ethylene, boranylborane, and hydroxilamine, at the DFT level, have been reported to document these statements. A comparison is made for results obtained within the conventional common origin approach for static magnetic field. Sum rules for invariance of computed properties are discussed. Representations of streamlines and stagnation graphs of dynamical current density vector field induced in the water molecule by monochromatic waves of four frequencies are displayed.

The probe rheology simulation technique is a technique for measuring the viscosity of a fluid by measuring the motion of an inserted probe particle. This approach has the benefit of greater potential accuracy at a lower computational cost than other conventional simulation techniques used for the calculation of mechanical properties, such as the Green-Kubo approach and nonequilibrium molecular dynamics simulations, and the potential to allow for sampling local variations of properties. This approach is implemented and demonstrated for atomistically detailed models. The viscosity of four different simple Newtonian liquids is calculated from both the Brownian motion (passive mode) and the forced motion (active mode) of an embedded probe particle. The probe particle is loosely modeled as a nano-sized diamond particle: a rough sphere cut out of an FCC lattice made of carbon atoms. The viscosities obtained from the motion of the probe particle are compared with those obtained from the periodic perturbation method, and good agreement between the two sets of values is observed once the probe-fluid interaction strength (i.e., εij in the pair-wise Lennard-Jones interaction) is two times higher than their original values, and the artificial hydrodynamic interactions between the probe particle and its periodic images are accounted for. The success of the proposed model opens new opportunities for applying such a technique in the rheological characterization of local mechanical properties in atomistically detailed molecular dynamics simulations, which can be directly compared with or help guide experiments of similar nature.

Janus kinase 2 (JAK2) is emerging as a potential therapeutic target for many inflammatory diseases such as myeloproliferative disorders (MPD), cancer and rheumatoid arthritis (RA). In this study, we have collected experimental data of JAK2 protein containing 6021 unique inhibitors. We then characterized them based on Morgan (ECFP6) fingerprints followed by clustering into training and test set based on their molecular scaffolds. These data were used to build the classification models with various supervised machine learning (ML) algorithms that could prioritize novel inhibitors for future drug development against JAK2 protein. The best model built by Random Forest (RF) and Morgan fingerprints achieved the G-mean value of 0.84 on the external test set. As an application of our classification model, virtual screening was performed against Drugbank molecules in order to identify the potential inhibitors based on the confidence score by RF model. Nine potential molecules were identified, which were further subject to molecular docking studies to evaluate the virtual screening results of the best RF model. This proposed method can prove useful for developing novel target-specific JAK2 inhibitors.