Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.

Theoretical treatment of IO-X (X = N2, CO, CO2, H2O) complexes

Iodine monoxide (IO) is an important component of the biogeochemical cycle of iodine. For instance, it is present in the troposphere, where it plays a crucial role in the physical chemical processes involving iodine containing compounds. Here, we present a theoretical study on a series of atmospherically relevant complexes of IO with N₂, CO, CO₂ and H₂O, where their structural and spectroscopic properties and their interaction energies are computed. Calculations are carried out by means of ab initio post Hartree-Fock (RCCSD(T) and RMP2) methods and density functional theory DFT (PBE0 and M05-2X) based approaches with and without the inclusion of dispersion correction. After comparison to RCCSD(T), we highlight the good performance of M05-2X(+D3) DFT in describing the bonding between IO and X (X = N₂, CO, CO₂, H₂O). Moreover, we found that the IO-X (X = N₂, CO, CO₂, H₂O) complexes are formed by non-covalent interactions between the two monomers. In sum, we characterized two types of complexes: I-bonded and O-bonded, where the former is more stable. The atmospheric implications of the present findings are also discussed such as in the formation of the iodine oxide particles (IOPs).

Generalized gradient approximation adjusted to transition metals properties: Key roles of exchange and local spin density

Perdew-Burke-Ernzerhof (PBE) and PBE adapted for solids (PBEsol) are exchange-correlation (xc) functionals widely used in density functional theory simulations. Their differences are the exchange, μ, and correlation, β, coefficients, causing PBEsol to lose the Local Spin Density (LSD) response. Here, the μ/β two-dimensional (2D) accuracy landscape is analyzed between PBE and PBEsol xc functional limits for 27 transition metal (TM) bulks, as well as for 81 TM surfaces. Several properties are analyzed, including the shortest interatomic distances, cohesive energies, and bulk moduli for TM bulks, and surface relaxation degree, surface energies, and work functions for TM surfaces. The exploration, comparing the accuracy degree with respect experimental values, reveals that the found xc minimum, called VV, being a PBE variant, represents an improvement of 5% in mean absolute percentage error terms, whereas this improvement reaches ~11% for VVsol, a xc resulting from the restoration of LSD response in PBEsol, and so regarded as its variant.

Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids

The hydrated clusters of protonated imidazole (ImH⁺) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.

Multicomponent solid forms of the uric acid reabsorption inhibitor lesinurad and cocrystal polymorphs with urea: DFT simulation and solubility study

Lesinurad (systematic name: 2-{[5-bromo-4-(4-cyclopropylnaphthalen-1-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid, C₁₇H₁₄BrN₃O₂S) is a selective uric acid reabsorption inhibitor related to gout, which exhibits poor aqueous solubility. High-throughput solid-form screening was performed to screen for new solid forms with improved pharmaceutically relevant properties. During polymorph screening, we obtained two solvates with methanol (CH₃OH) and ethanol (C₂H₅OH). Binary systems with caffeine (systematic name: 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione, C₈H₁₀N₄O₂) and nicotinamide (C₆H₆N₂O), polymorphs with urea (CH₄N₂O) and eutectics with similar drugs, like allopurinol and febuxostat, were prepared using the crystal engineering approach. All these novel solid forms were confirmed by XRD, DSC and FT-IR. The crystal structures were solved by single-crystal and powder X-ray diffraction. The crystal structures indicate that the lesinurad molecule is highly flexible and the triazole moiety, along with the rotatable thioacetic acid (side chain) and cyclopropane ring, is almost perpendicular to the planar naphthalene moiety. The carboxylic acid-triazole heterosynthon in the drug is interrupted by the presence of methanol and ethanol molecules in their crystal structures and forms intermolecular macrocyclic rings. The caffeine cocrystal maintains the consistency of the acid-triazole heterosynthons as in the drug and, in addition, they are bound by several auxiliary interactions. In the binary system of nicotinamide and urea, the acid-triazole heterosynthon is replaced by an acid-amide synthon. Among the urea cocrystal polymorphs, Form I (P-1, 1:1) consists of an acid-amide (urea) heterodimer, whereas in Form II (P2₁/c, 2:2), both acid-amide heterosynthons and urea-urea dimers co-exist. Density functional theory (DFT) calculations further support the experimentally observed synthon hierarchies in the cocrystals. Aqueous solubility experiments of lesinurad and its binary solids in pH 5 acetate buffer medium indicate the apparent solubility order lesinurad-urea Form I (43-fold) > lesinurad-caffeine (20-fold) > lesinurad-allopurinol (12-fold) ≃ lesinurad-nicotinamide (11-fold) > lesinurad, and this order is correlated with the crystal structures.

Complexes of Zn(II)-Triazoles with CO2 and H2O: Structures, Energetics, and Applications

Using a first-principle methodology, we investigate the stable structures of the nonreactive and reactive clusters formed between Zn²⁺-triazoles ([Zn²⁺-Tz]) clusters and CO₂ and/or H₂O. In sum, we characterized two modes of bonding of [Zn²⁺-Tz] with CO₂/H₂O: the interaction is established through (i) a covalent bond between Zn²⁺ of [Zn²⁺-Tz] and oxygen atoms of CO₂ or H₂O and (ii) hydrogen bonds through N-H or C-H of [Zn²⁺-Tz] and oxygen atoms of H₂O or CO₂, N-H···O. We also identified intramolecular proton transfer processes induced by complexation. Indeed, water drastically changes the shape of the energy profiles of the tautomeric phenomena through strong lowering of the potential barriers to tautomerism. The comparison to [Zn²⁺-Im] subunits formed with Zn²⁺ and imidazole shows that the efficiency of Tz-based compounds for CO₂ capture and uptake is due to the incorporation of more accessible nitrogen donor sites in Tzs compared to imidazoles. Since [Zn²⁺-Tz] clusters are subunits of an organometallic nanoporous materials and Zn-proteins, our data are useful for deriving force fields for macromolecular simulations of these materials. Our work also suggests the consideration of traces of water to better model the CO₂ sequestration and reactivity on macromolecular entities such as pores or active sites.

Theoretical Insights into the Role of Water Molecules in the Guanidinium-Based Protein Denaturation Process in Specific to Aromatic Amino Acids

Noncovalent interactions between the guanidinium cation (Gdm⁺) and aromatic amino acids (AAs) in the water molecules have been studied using quantum chemical calculation and molecular dynamics (MD) simulations. Our studies show that there are two different modes of interactions between Gdm⁺ and AAs with and without water molecules. It is observed that nonhydrated Gdm⁺ interacts with AAs through N-H···π interactions, whereas hydrated clusters of Gdm⁺ are stabilized by stacking interactions with the help of the water-mediated hydrogen bond. Thus, different hydration patterns have significant effects on the predominant cation···π interactions in AAs-Gdm⁺ complexes. Findings from MD simulation elicit that the interaction pattern of Gdm⁺ with AAs varies as Phe < Tyr < Trp. Both the QM and MD calculations show a similar trend in the interaction of AAs with Gdm⁺. Moreover, the interaction of AAs with Gdm⁺ depends on the spatial orientation of AAs in the protein and the concomitant local structure, that is, the AAs present in the unstructured region of protein such as coils and bends exhibit higher binding for Gdm⁺ when compared to the AAs present in the structured region of the protein such as the α-helix and the β-sheet. Our study clearly reveals that H-bonded water molecules and the hydration pattern of Gdm⁺ as well as the positional presence of these AAs in the protein structure context play determining roles in the denaturation of protein by the Gdm⁺ cation.

Insights on the interaction of Zn2+ cation with triazoles: Structures, bonding, electronic excitation and applications

At present, we investigate the structures, the stability, the bonding and the spectroscopy of the Zn²⁺-triazole complexes (Zn²⁺-Tz), which are subunits of triazolate based porous materials and Zn-enzymes. This theoretical work is performed using ab initio methods and density functional theory (DFT) where dispersion correction is included. Through these benchmarks, we establish the ability and reliability of M05-2X+D3 and PBE0+D3 functionals for the correct description of Zn²⁺-Tz bond since these DFTs lead to close agreement with post Hartree-Fock methods. Therefore, M05-2X+D3 and PBE0+D3 functionals are recommended for the characterization of larger organometallic complexes formed by Zn and N-rich linkers. For Zn²⁺-Tz, we found two stable σ-type complexes: (i) a planar structure where Zn²⁺ links to unprotonated nitrogen and (ii) an out-of-plane cluster where carbon interacts with Zn²⁺. The most stable isomers consist on a coordinated covalent bond between the lone pair of unprotonated nitrogen and the vacant 4s orbital of Zn²⁺. The roles of covalent interactions within these complexes are discussed after vibrational, NBO, NPA charges and orbital analyses. The bonding is dominated by charge transfer from Zn²⁺ to Tz and intramolecular charge transfer, which plays a vital role for the catalytic activity of these complexes. These findings are important to understand, at the microscopic level, the structure and the bonding within triazolate based macromolecular porous materials and Zn-enzymes.

Periodic Dispersion-Corrected Approach for Isolation Spectroscopy of N2 in an Argon Environment: Clusters, Surfaces, and Matrices

Ab initio and Perdew, Burke, and Ernzerhof (PBE) density functional theory with dispersion correction (PBE-D3) calculations are performed to study N₂-Ar_n (n ≤ 3) complexes and N₂ trapped in Ar matrix (i.e., N₂@Ar). For cluster computations, we used both Møller-Plesset (MP2) and PBE-D3 methods. For N₂@Ar, we used a periodic-dispersion corrected model for Ar matrix, which consists on a slab of four layers of Ar atoms. We determined the equilibrium structures and binding energies of N₂ interacting with these entities. We also deduced the N₂ vibrational frequency shifts caused by clustering or embedding compared to an isolated N₂ molecule. Upon complexation or embedding, the vibrational frequency of N₂ is slightly shifted, while its equilibrium distance remains unchanged. This is due to the weak interactions between N₂ and Ar within these compounds. Our calculations show the importance of inclusion of dispersion effects for the accurate description of geometrical and spectroscopic parameters of N₂ isolated, in interaction with Ar surfaces, or trapped in Ar matrices.

Ab initio and density functional theory (DFT) studies on triflic acid with water and protonated water clusters

The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (W_n) and protonated water clusters (TAH⁺W_n, n = 1 - 6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n = 1 and 2) and linear (n = 1 - 6) types of water clusters. Further, the geometries of TAW_n clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H₃O⁺ also called Eigen cation) formation in both TAW_n and protonated TAW_n clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAW_n and TAH⁺W_n clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.

Microscopic investigations of site and functional selectivity of triazole for CO2 capture and catalytic applications

Ab initio and DFT studies on CO₂ interacting with different tautomers and isomers of triazole (TZ) are carried out to understand the adsorption mechanism, site selectivity and their mutual preferential attracting sites.

Structure, Spectroscopy, and Bonding within the Zn(q+)-Imidazole(n) (q = 0, 1, 2; n = 1-4) Clusters and Implications for Zeolitic Imidazolate Frameworks and Zn-Enzymes

Using density functional theory (DFT) with dispersion correction and ab initio post Hartree-Fock methods, we treat the bonding, the structure, the stability, and the spectroscopy of the complexes between Zn(q+) and imidazole (Im), Zn(q+)Imn (where q = 0, 1 and 2; n = 1-4). These entities are subunits of zeolitic imidazolate frameworks (ZIFs) and Zn-enzymes, which possess relevant roles in industrial and biological domains, respectively. We also investigate the Imn (n = 2-4) clusters for comparison. For each species, we determine several new structures that were not found previously. Our calculations show a competition between atomic metal solvation, by either σ-type interactions or π-stacking type interaction, and proton transfer through hydrogen bonding (H-bonding) in charged species. This results in several geometrical environments around the metal. These are connected with structural properties and the functional role of Zn cation within ZIFs and Zn-enzymes. Moreover, we show that the Zn(2+)Imn subunits do not absorb in the visible domain, which may be related to the photostability of ZIFs. Our findings are important for the development of new applications of ZIFs and metalloenzymes.