The ThermoML Archive is a subset of Thermodynamics Research Center (TRC) data holdings corresponding to cooperation between NIST TRC and five journals: Journal of Chemical Engineering and Data (ISSN: 1520-5134), The Journal of Chemical Thermodynamics (ISSN: 1096-3626), Fluid Phase Equilibria (ISSN: 0378-3812), Thermochimica Acta (ISSN: 0040-6031), and International Journal of Thermophysics (ISSN: 1572-9567). Data from initial cooperation (around 2003) through the 2019 calendar year are included. The archive has undergone a major update with the goal of improving the FAIRness and user experience of the data provided by the service. The web application provides comprehensive property browsing and searching capabilities; searching relies on a RESTful API provided by the Cordra software for managing digital objects. JSON files with a schema derived from ThermoML are provided as an additional serialization to lower the barrier to programmatic consumption of the information, for stakeholders who may have a preference of JSON over XML. The ThermoML and JSON files for all available entries can be downloaded from data.nist.gov (https://data.nist.gov/od/id/mds2-2422).

Revised versions of our published pob-TZVP basis sets [Laun, J.; Vilela Oliveira, D. and Bredow, T., J. Comput. Chem., 2018, 39 (19), 1285-1290] have been derived for periodic quantum-chemical solid-state calculations. They complete our pob-TZVP-rev2 series [Vilela Oliveira, D.; Laun, J.; Peintinger, M. F. and Bredow, T., J. Comput. Chem., 2019, 40 (27), 2364-2376 and Laun, J. and Bredow, J. Comput. Chem. 2021; 42 (15), 1064-1072] for the elements of the fifth period and are based on the fully relativistic effective core potentials (ECPs) of the Stuttgart/Cologne group and the def2-TZVP valence basis of the Ahlrichs group. The pob-TZVP-rev2 basis sets are developed to minimize the basis set superposition error (BSSE) in crystalline systems. For the applied PW1PW hybrid functional, the overall performance, transferability, and SCF stability of the resulting pob-TZVP-rev2 basis sets are significantly improved compared to the original pob-TZVP basis sets. After augmentation with single diffuse s- and p-functions, reference plane-wave band structures of metals can be accurately reproduced.

Reactive force fields (ReaxFF) are a classical method to describe material properties based on a bond-order formalism, that allows bond dissociation and consequently investigations of reactive systems. Semiclassical treatment of electrons was introduced within ReaxFF simulations, better known as electron reactive force fields (eReaxFF), to explicitly treat electrons as spherical Gaussian waves. In the original version of eReaxFF, the electrons and electron-holes can lead to changes in both the bond energy and the Coulomb energy of the system. In the present study, the method was modified to allow an electron to modify the valence energy, therefore, permitting that the electron's presence modifies the three-body interactions, affecting the angle among three atoms. When a reaction path involving electron transfer is more sensitive to the geometric configuration of the molecules, corrections in the angular structure in the presence of electrons become more relevant; in this case, bond dissociation may not be enough to describe a reaction path. Consequently, the application of the extended eReaxFF method developed in this work should provide an improved description of a reaction path. As a first demonstration this semiclassical force field was parametrized for hydrogen and oxygen interactions, including water and water's ions. With the modified methodology both the overall accuracy of the force field but also the description of the angles within the molecules in presence of electrons could be improved.

Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the σ -hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the σ -hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the restricted electrostatic potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The σ -hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.

Structure-based pharmacophore models are often developed by selecting a single protein-ligand complex with good resolution and better binding affinity data which prevents the analysis of other structures having a similar potential to act as better templates. PharmRF is a pharmacophore-based scoring function for selecting the best crystal structures with the potential to attain high enrichment rates in pharmacophore-based virtual screening prospectively. The PharmRF scoring function is trained and tested on the PDBbind v2018 protein-ligand complex dataset and employs a random forest regressor to correlate protein pocket descriptors and ligand pharmacophoric elements with binding affinity. PharmRF score represents the calculated binding affinity which identifies high-affinity ligands by thorough pruning of all the PDB entries available for a particular protein of interest with a high PharmRF score. Ligands with high PharmRF scores can provide a better basis for structure-based pharmacophore enumerations with a better enrichment rate. Evaluated on 10 protein-ligand systems of the DUD-E dataset, PharmRF achieved superior performance (average success rate: 77.61%, median success rate: 87.16%) than Vina docking score (75.47%, 79.39%). PharmRF was further evaluated using the CASF-2016 benchmark set yielding a moderate correlation of 0.591 with experimental binding affinity, similar in performance to 25 scoring functions tested on this dataset. Independent assessment of PharmRF on 8 protein-ligand systems of LIT-PCBA dataset exhibited average and median success rates of 57.55% and 74.72% with 4 targets attaining success rate > 90%. The PharmRF scoring model, scripts, and related resources can be accessed at https://github.com/Prasanth-Kumar87/PharmRF.

The geometries, electronic structures, and bonding properties of the title endohedral Zintl clusters have been studied by using ab initio calculations. [Fe@Ge10 ]4- and [Co@Ge10 ]3- have D5h -symmetric pentagonal prismatic structure and [Fe@Sn10 ]4- adopts the C2v -symmetric structure as their ground-state structures, whereas all the other clusters possess D4d bicapped square antiprismatic structures, in consistent with the experimental values when available. Natural bonding orbital and electron localization function disclosed that the negative charges are localized on the central atoms rather than the cages while the TME ionic bonding interactions increase in the order of Ge < Sn < Pb. The energy decomposition analysis revealed that the total bonding energy ∆Eint between central TM and E10 cage is above 150 kcal/mol. The ionic bonding interaction termed as electrostatic interaction ∆Eelstat increases in the order of Ge < Sn < Pb and becomes higher than the covalent bonding interactions termed as total orbital interactions ∆Eorb . Among the total orbital interactions, the π back donations from the TM-d orbitals to the empty cage orbitals consisting of E-p orbitals, the magnitude of which is importantly affected by the cage symmetry, are dominant contributions.

The potential energy functions of the aluminum dimer, Al2 , in its lowest-energy electronic states, X 3Πu and A 3∑g-,  have been determined from ab initio calculations using the multi-reference averaged coupled-pair functional method in conjunction with the correlation-consistent basis sets up to septuple-zeta quality. The core-electron correlation, scalar relativistic, and spin-orbit effects were taken into account. The vibration-rotation energy levels for both the states of Al2 were calculated to near the "spectroscopic" accuracy. The 3Πu state was unequivocally confirmed to be the electronic ground state of Al2 , and the electronic term value T0 of the 3∑g- state was predicted to be 247 cm-1 . The energies and intensities of direct electronic-vibration transitions X 3Πu  ↔ A 3∑g- were predicted.

We investigated the flow of electron density along the cyclocondensation reaction between ethyl acetate 2-oxo-2-(4-oxo-4H-pyrido[1.2-a]pyrimidin-3-yl) polyazaheterocycle (1) and ethylenediamine (2) at the ωB97XD/6-311++G(d,p)computational method within of bond evolution theory (BET). The exploration of potential energy surface shows that this reaction has three channels (1-3) with the formation of product 3 via channel-2 (the most favorable one) as the main product and this is in good agreement with experimental observations. The BET analysis allows identifying unambiguously the main chemical events happening along channel-2. The mechanism along first step (TS2-a) is described by a series of four structural stability domains (SSDs), while five SSDs for the last two steps (TS2-b and TS2-c). The first and third steps can be summarized as follows, the formation of N1-C6 bond (SSD-II), then, the restoration of the nitrogen N1 lone pair (SSD-III), and finally, the formation of the last O1-H1 bond (SSD-IV). For the second step, the formation of hydroxide ion is noted, as a result of the disappearance of V(C6,O7) basin and the transformation of C6-N1 single bond into double one (SSD-IV). Finally, the appearance of V(O7,H2) basin lead to the elimination of water molecule within the last domain is observed.

The mechanistic study of CO2 coupling with propylene oxide (PO) into cyclic carbonate catalyzed by (CH3 )4 PI has been investigated using the B3 LYP/6-311++G (d, p)/B3 LYP/6-31G (d) level of theory for non-iodine atoms and LANL2DZ was used, together with its associated basis set for the iodine atom. Two hypothetical reaction mechanisms were proposed for the studied reaction and thermodynamic and kinetic parameters were computed for each step to determine the more favorable route. The density functional theory (DFT) study reveals that the reaction prefers to proceed through a three-step mechanism (pathway II) than a tri-molecular intermediate (pathway I) where the CO2 and the catalyst act simultaneously on the PO ring. The rate-determining step of the catalytic reaction is found to be the ring-opening step with an energy barrier of 27.1 kcal/mol (pathway II) in the gas phase, which is kinetically more favorable than that of non-catalytic CO2 fixation with a relatively higher barrier of 63.7 kcal/mol. The synergetic effect of MgCl2 is tested as a cocatalyst for the (CH3 )4 PI/MgCl2 catalyzed reaction and it gave a better result and minimized the activation energy for the reaction and the rate-determining step was the ring closure with the free energy of activation 18.8 kcal/mol in the gas phase. The polarizable continuum model was used to account for the solvent effect, obtaining the best results of 23.1 kcal/mol in water for pathway I and 16.5 kcal/mol and 14.9 kcal/mol in dimethyl sulfoxide for pathway II and binary system, respectively.

Peptide T is a synthetic octapeptide fragment, which corresponds to the region 185-192 of the gp120 HIV coat protein and functions as a viral entry inhibitor. In this work, a folding molecular dynamics simulation of peptide T in a membrane-mimicking (DMSO) solution was performed with the aim of characterizing the peptide's structural and dynamical properties. We show that peptide T is highly flexible and dynamic. The main structural characteristics observed were rapidly interconverting short helical stretches and turns, with a notable preference for the formation of β-turns. The simulation also indicated that the C-terminal part appears to be more stable than the rest of the peptide, with the most preferred conformation for residues 5-8 being a β-turn. In order to validate the accuracy of the simulations, we compared our results with the experimental NMR data obtained for the T-peptide in the same solvent. In agreement with the simulation, the NMR data indicated the presence of a preferred structure in solution that was consistent with a β-turn comprising the four C-terminal residues. An additional comparison between the experimental and simulation-derived chemical shifts also showed a reasonable agreement between experiment and simulation, further validating the simulation-derived structural characterization of the T-peptide. We conclude that peptide folding simulations produce physically relevant results even when performed with organic solvents that were not part of the force field parameterization procedure.

Sodium polyanionic compounds with transition metals are of considerable research interest for the search of new cathode materials for sodium-ion batteries. In this work, we employed ab initio calculations to evaluate three key battery properties: phase stability, diffusion barriers and redox voltage of low-symmetry molybdates NaMFe(MoO4 )3 (M = Mg, Ni) with α- and β-NaFe2 (MoO4 )3 structures. First, we showed that the Hubbard Ucorrection within the GGA + Uapproach is necessary to correctly refer these molybdates to semiconductors. The sodium diffusion along various pathways was thoroughly examined, which allowed us to establish the most probable pathways with the lowest migration barriers. These compounds have different directions of sodium diffusion with twice different barriers that was associated to the peculiarities of their crystal structure. The high potentials and structural stability during sodium extraction, along with low-diffusion barriers predicted for NaMFe(MoO4 )3 (M = Mg, Ni) indicate that these molybdates may be promising high-voltage cathode materials for sodium-ion batteries.

Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several anomer types which can be linked in a variety of ways. Here we present a stand-alone tool implemented in the widely-used software CPPTRAJ that can be used to automate building structures and generating a "ready to run" parameter and coordinate file pair. This tool automatically identifies carbohydrate anomer type, configuration, linkage, and functional groups, and performs topology modifications (e.g., renaming residue/atom names) required to build the final system using state of the art GLYCAM force field parameters. It will also generate the necessary commands for bonding carbohydrates and creating any disulfide bonds.

Nanodiamonds (NDs) are modern high-potential materials relevant for applications in biomedicine, photocatalysis, and various other fields. Their electronic surface properties, especially in the liquid phase, are key to their function in the applications, but we show that they are sensitively modified by their interactions with the environment. Two important interaction modes are those with oxidative aqueous adsorbates as well as ND self-aggregation towards the formation of ND clusters. For planar diamond surfaces it is known that the electron density migrates from the diamond towards oxidative adsorbates, which is known as transfer doping. Here, we quantify this effect for highly curved NDs of varying sizes (35-147 C atoms) and surface terminations (H, OH, F), focusing on their interactions with the most abundant aqueous oxidative adsorbates (H3 O+ , O2 , O3 ). We prove that the concept of transfer doping stays valid for the case of the high-curvature NDs and can be tuned via the ND's specific properties. Secondly, we investigate the electronic structures of clusters of NDs which are known to form in particular in aqueous dispersions. Upon cluster formation, we find that the optical gaps of the structures are significantly reduced, which explains why different experimental values were obtained for the optical gap of the same structures, and the cluster's LUMO shapes resemble atom-type orbitals, as in the case of isolated spherical NDs. Our findings have implications for ND applications as photocatalysts or electronic devices, where the specific electronic properties are key to the functionality of the ND material.

Conformation has a key role in the mechanism of interaction between small molecules and biological receptors. However, encoding this type of information in molecular descriptors for the construction of robust quantitative structure-activity relationships (QSAR) models is not an easy task and, so far, the dependence of these models on such feature has not been thoroughly investigated. In the present study, the authors explore the effects of conformational information on a 3D-QSAR technique by comparing models built with descriptors that encode fully described tridimensional aspects (structures docked inside a biological target), with descriptors in which this information is suppressed (flat structures) or not fully described (structures with quantum-chemically optimized geometries). As a result, the validation parameters indicate that the robustness of the models seems to be more related to the alignment aspect of the structures than to how well their tridimensional features are described.

The human Son of Sevenless (SOS) activates the signal-transduction protein Ras by forming the complex SOS·Ras and accelerating the guanosine triphosphate (GTP) exchange in Ras. Inhibition of SOS·Ras could regulate the function of Ras in cells and has emerged as an effective strategy for battling Ras related cancers. A key factor to the success of this approach is to understand the conformational change of Ras during the GTP exchange process. In this study, we perform an extensive molecular dynamics simulation to characterize the specific conformations of Ras without and with guanine nucleotide exchange factors (GEFs) of SOS, especially for the substates of State 1 of HRasGTP∙Mg2+ . The potent binding pockets on the surfaces of the RasGDP∙Mg2+ , the S1.1 and S1.2 substates in State 1 of RasGTP∙Mg2+ and the ternary complexes with SOS are predicted, including the binding sites of other domains of SOS. These findings help to obtain a more thorough understanding of Ras functions in the GTP cycling process and provide a structural foundation for future drug design.

Density functional theory (DFT) is used to explore the structure, stability, and bonding in CSiGaAl2 -/0 and CGeGaAl2 -/0 systems having planar tetracoordinate carbon (ptC). The neutral systems have 17 valence electrons and the mono-anionic systems have 18 valence electrons. The ab initio molecular dynamics simulations for 2000 fs time at two different temperatures (300 and 500 K) supported the kinetic stability of the systems. From the natural bond orbital (NBO) analysis it is shown that there is a strong electron donation from the ligand atoms to the ptC atom. We have used Li+ ion for the neutralization of the mono-anionic systems and more interestingly it does not disrupt the planar structure. The most preferable site for binding of Li+ ion is along the AlAl bond in both of the mono-anionic systems. All the systems in this work have both σ and π aromaticity which is predicted from the computations of nucleus independent chemical shift (NICS). Although the anionic species obey the 18 valence electronic rule, the neutral systems break the rule with 17 valence electrons. However, both sets of systems are stable in the planar form. The bonding analysis of the systems includes molecular orbital, adaptive natural density partitioning (AdNDP), quantum theory of atoms in molecules (QTAIM), electron localization function (ELF) basin, and aromaticity analyses. The energy decomposition analysis (EDA) determines the interaction of Li+ ion with CSiGaAl2 - and CGeGaAl2 - in Li@SiGaAl2 and Li@GeGaAl2 , respectively.