Aug 2026· Scientific Data· Vol 13· 0 citations· 123 references
Medicine
Abstract
Polyoxometalates (POMs) are an important class of anionic inorganic compounds because of their rich structural chemistry and properties. POMsDB is a freely accessible database for POMs that collects molecular properties (optimized atomic coordinates, energies, IR spectrum, atomic charges) and force-field (FF) parameters to run molecular dynamic (MD) simulations in common MD programs. FF parameters in this database consist of nonbonded (atomic point charges, Lennard-Jones (LJ)) and bonded parameters. Three distinct types of DFT derived atomic charges and two sets of LJ parameters could be selected. In addition, two definitions of bonding intramolecular parameters are available: one where the POM behaves as a rigid object, and the other where bonds are flexible. By providing open access to the database via ioChem-BD, we seek to accelerate progress in this field enabling systematic molecular dynamics studies for a broad range of POMs in solution accelerating the understanding of assembly, crystal growth, nanomaterials formation of metal-oxo clusters.
A comprehensive quantum chemical study is presented to derive energetic predictors for pnictogen (Pn) bonding interactions. We analyzed the interaction energies of the Lewis acids PnF3 and F2PnX, where Pn represents nitrogen through bismuth and X represents chlorine, bromine, or iodine, acting as σ-hole donors with a diverse set of up to twenty-one different nitrogen- and oxygen-based Lewis bases. All complexes were investigated at the PBE0-D3/def2-TZVP level of theory. For every complex, a topological analysis according to Bader's quantum theory of atoms in molecules (QTAIM) was performed to correlate the interaction energies with the potential energy density values at the bond critical points. We established a linear correlation with reasonable R-squared values for the coordination behavior of each pnictogen atom. Furthermore, the results demonstrate that, as the size, polarizability, and σ-hole intensity of the pnictogen atom increase, the likelihood of forming additional secondary noncovalent interactions also rises. Consequently, a clear differentiation must be made between pure pnictogen bonding and a combination of pnictogen bonding with secondary interactions. This distinction is supported by the analysis of several published crystal structures. We propose general energy predictors for the determination of pure pnictogen bond energies.
Jan Langwald, Antonio Frontera· Chemistry· 0 citations
Weak interactions are ubiquitous and critically modulate the conformational flexibility of polymers. Here, we investigate polyborosiloxane (PBS), a supramolecular polymer renowned for its shear-stiffening behavior. A series of PBS samples with varying molecular weights were synthesized via a condensation reaction and characterized by GPC and FTIR spectroscopy. The nearly identical molecular weights of PBS and its PDMS precursor confirm the absence of significant side reactions. The trends observed in Si-O-B infrared band intensities correlate with the hydroxyl group content in PDMS, verifying the successful formation of PBS. These experimental results guided the construction of initial structural models. Low-energy conformers were identified through a multi-level computational approach combining high-temperature molecular dynamics sampling, semi-empirical pre-screening, and high-level DFT single-point energy calculations. Frequency calculations confirmed all optimized structures as true minima. Weak interactions were comprehensively characterized via advanced wavefunction analyses, including IRI based on AIM theory, energy decomposition analysis, atomic charge calculations, and ESP mapping. These analyses reveal that intramolecular hydrogen bonds are crucial for PBS conformational flexibility. Thermodynamic calculations further confirmed the stability of energetically favorable conformers. A key innovation lies in the integrated, multi-perspective visualization of weak interactions. Our findings provide fundamental insights into the physicochemical properties of PBS isomers and establish a robust protocol for studying complex polymer systems.
Yang Song, Zhiming Zhao, Feng Li et al.· Physical Chemistry, Chemical...· 0 citations
Compounds with the general formula AB2X4 crystallize with the atomic structure of the mineral spinel, MgAl2O4, described by three degrees of freedom: lattice parameter a, anion parameter u, and cation inversion parameter λ. Here, bond valence sum validation of 1244 ambient structures (338 compositions, 1915–2025) from the Inorganic Crystal Structure Database provides the first quantitative assessment. Cubic Fd 3̲$\underline{3} $m accounts for 86% of structures, tetragonal I41/amd for 8%, and B‐site cation‐ordered P4332 for 5%. Normal‐type ordering (A cation tetrahedral) is the majority arrangement (51%). The anion parameter is nearly invariant with cation disorder, shifting by only 0.002 across the full λ range, consistent with thermodynamic equilibrium rather than being a structural defect. The polyhedral volume ratio Voct/Vtet (median 2.9) is 27% below the ideal value, narrowing the tetrahedral–octahedral distinction and lowering the enthalpic cost of cation redistribution. A generalized anion parameter framework (ueff, Δu) is proposed to extend the single cubic anion coordinate to tetragonal and ordered structures for the first time. Oxides (88.9%) are well characterized; sulfides (10.0%) access nonclassical valence combinations at nearly double the oxide rate but remain undercharacterized. Prediction rules, benchmark data for 20 compositions, and refinement guidance are provided.
Nik Reeves-McLaren· Journal of The American Cera...· 0 citations
We redetermine the structure of the disordered metal-organic framework Zn(hba) (hba$^{2-}$ = the dianion of 4-hydroxybenzoic acid). Using single-crystal X-ray diffraction measurements, we characterise the structured diffuse scattering that is experimentally observed for this material and which is characteristic of strongly correlated disorder. We use geometric and crystal chemical arguments to propose a general model for correlated disorder in Zn(hba), and then relate this model to a specific realisation of so-called Truchet tilings. Using Monte Carlo simulations, we proceed to show that the model so developed is simultaneously consistent with both the average crystal structure solution described previously, and the structured diffuse scattering reported here. The existence of ordered analogues with different, but related, chemistry suggests scope for control over correlated disorder in this family of metal-organic frameworks. Our study illustrates the potential for a Truchet-tile formalism to help describe and understand more generally the correlated disorder that occurs in framework materials - even amongst those that are chemically and crystallographically dissimilar.
Hunter J. Windsor, Guy Greenbaum, T. Dolling et al.· 0 citations
Stimulated by the renewed interest and recent developments in semiempirical quantum chemical (SQC) methods for noncovalent interactions, we examine the properties of liquid water under ambient conditions by means of molecular dynamics (MD) simulations, both with the conventional neglect of diatomic differential overlap-type methods, e.g., AM1 and PM6, and with DFTB-type (density-functional tight-binding) methods, e.g., DFTB2 and GFN-xTB (Geometry-Frequency-Noncovalent eXtended Tight-Binding). Besides the original parameter sets, some specifically reparameterized SQC methods (denoted as AM1-W, PM6-fm, and DFTB2-iBi) targeting various smaller water systems ranging from molecular clusters to bulk are considered as well. The quality of these different SQC methods for describing liquid water properties under ambient conditions is assessed by comparison with well-established experimental data and also with BLYP-D3 density functional theory-based ab initio MD simulations. Our analyses reveal that static and dynamic properties of bulk water are poorly described by all considered SQC methods with the original parameters, regardless of the underlying theoretical models, with most of the methods suffering from too weak hydrogen bonds and hence predicting a far too fluid water with highly distorted hydrogen bond kinetics. Meanwhile, the reparameterized force-matched PM6-fm method is shown to be able to quantitatively reproduce the static and dynamic features of liquid water and thus can be used as a computationally efficient alternative to electronic structure-based MD simulations for liquid water that requires extended length and time scales. DFTB2-iBi predicts a slightly overstructured water with reduced fluidity, whereas AM1-W gives an amorphous ice-like structure for water under ambient conditions.
Xin Wu, Hossam Elgabarty, Vahideh Alizadeh et al.· Journal of Chemical Physics· 1 citation
Thermodynamic properties of molecular crystals are the cornerstone of a broad range of applications, spanning pharmaceutics, organic semiconductors, and many more. The reliable modeling of these properties is usually hindered by collective influences of delicate dispersion interactions and insufficient prior knowledge. Providing reasonable accuracy and minimal reliance on experimental data, lattice dynamics (LD) based on the quasi-harmonic approximation (QHA) and density functional theory (DFT) has been widely and successfully adopted for crystal structure prediction (CSP). However, for polymorphic molecular crystals, it remains challenging to accurately establish the relative stability among multiple polymorphs that are distinguished by subtle energy differences. Despite recent intense efforts to achieve calculations that can reproduce observations in well-characterized systems, a comprehensive study elucidating how predictions are governed by errors within the theoretical framework and details of implementation is lacking. This undermines confidence in the transferability and efficiency of QHA LD workflows proposed in the literature. The need for reliable and predictive calculations necessitates systematic investigation and disentangling of the influences from key parameters such as the choice of basis set and Hamiltonian, so the cost and precision of DFT-based QHA LD calculations can be rationally balanced in practical workflows. In this study, paracetamol polymorphs are adopted as the prototype system, as they are well-characterized and display representative chemical interactions, where covalent bonds, hydrogen bonds, and London dispersions are present with sufficient complexity. The intermixed sources of error underlying free-energy predictions are resolved by comparing the structural, vibrational, and thermochemical properties of paracetamol polymorphs with high-quality references. A hierarchy of atomic and plane-wave basis sets are adopted to highlight the significance of basis set completeness, and results with and without the inclusion of Fock exchange identify the particular importance of Hamiltonian for thermochemical properties. Furthermore, an optimal QHA LD workflow is proposed and tested utilizing these insights, which combines results from plane-wave basis set with semilocal functional and local, well-converged def2-TZVP basis set with hybrid functional to efficiently converge the numerical precision for QHA LD. While demonstrated in detail for paracetamol, conclusions of this study are also expected to be of relevance to a wide range of molecular crystals. These findings rigorously set the stage for affordable and reliable QHA LD workflow for molecular crystals, where fortuitous error cancellations are clearly distinguished from converged levels of theory, thereby clarifying the numerical precision attainable before explicit anharmonic and configurational effects are considered for complex organic systems.
Unknown authors· Journal of Chemical Theory a...· 0 citations
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