Performance of Density Functional Theory Procedures for the Calculation of Proton-Exchange Barriers: Unusual Behavior of M06-Type Functionals

Theoretical Insights into the Generation Mechanism of the Tyr122 Radical Catalyzed by Intermediate X in Class Ia Ribonucleotide Reductase

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides in all organisms. There is an ∼35 Å long-range electron-hole transfer pathway during the catalytic process of class Ia RNR, which can be described as Tyr122β ↔ [Trp48β]? ↔ Tyr356β ↔ Tyr731α ↔ Tyr730α ↔ Cys439α. The formation of the Y122• radical initiates this long-range radical transfer process. However, the generation mechanism of Y122• is not yet clear due to confusion over the intermediate X structures. Based on the two reported X structures, we examined the possible mechanisms of Y122• generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y122• radical from the two different core structures of X was via a similar two-step reaction, with the first step of proton transfer for the formation of the proton receptor of Y122 and the second step of a proton-coupled long-range electron transfer reaction with the proton transfer from the Y122 hydroxyl group to the terminal hydroxide ligand of Fe1III and simultaneously electron transfer from the side chain of Y122 to Fe2IV. These findings provide an insight into the formation mechanism of Y122• catalyzed by the double-iron center of the β subunit of class Ia RNR.

Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials

Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.

Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials

There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.

Free Energy Profiles of Proton Transfer Reactions: Density Functional Benchmark from Biased Ab Initio Dynamics

By coupling an enhanced sampling algorithm with an orbital-localized variant of Car-Parrinello molecular dynamics, the so-called atomic centered density matrix propagation model, we reconstruct the free energy profiles along reaction pathways using different density functional approximations (DFAs) ranging from locals to hybrids. In particular, we compare the computed free energy barrier height of proton transfer (PT) reactions to those obtained by a more traditional static approach, based on the intrinsic reaction coordinate (IRC), for two case systems, namely malonaldehyde and formic acid dimer. The obtained results show that both the IRC profiles and the potentials of mean force, derived from biased dynamic trajectories, are very sensitive to the density functional approximation applied. More precisely, we observe that, with the notable exception of M06-L, local density functionals always strongly underestimate the reaction barrier heights. More generally, we find that also the shape of the free energy profile is very sensitive to the density functional choice, thus highlighting the effect, often neglected, that the choice of DFA has also in the case of dynamics simulations.

D–π–A-type fluorinated tolanes with a diphenylamino group: crystal polymorphism formation and photophysical behavior

Ph2N-Substituted fluorinated tolanes produced two polymorphisms, which display a distinct photoluminescence behavior; one polymorphism showed green PL and the other exhibited yellow PL.

Effect of Fluoroalkyl-Substituent in Bistolane-Based Photoluminescent Liquid Crystals on Their Physical Behavior

Photoluminescent liquid crystals (PLLCs) have attracted significant attention owing to their broad applicability in thermosensing and PL switching. Extensive efforts have been made to develop bistolane-based PLLCs containing flexible units at both molecular terminals, and it has been revealed that their PL behavior can switch with the phase transition between the crystalline and LC phases. Although slight modulation of the flexible unit structure dramatically alters the LC and PL behaviors, few studies into the modification of the flexible units have been conducted. With the aim of achieving dynamic changes in their physical behaviors, we developed a family of bistolane derivatives containing a simple alkyl or a fluoroalkyl flexible chain and carried out a detailed systematic evaluation of their physical behaviors. Bistolanes containing a simple alkyl chain showed a nematic LC phase, whereas switching the flexible chain in the bistolane to a fluoroalkyl moiety significantly altered the LC phase to generate a smectic phase. The fluoroalkyl-containing bistolanes displayed a stronger deep blue PL than their corresponding non-fluorinated counterparts, even in the crystalline phase, which was attributed to the construction of rigid molecular aggregates through intermolecular F···H and F···F interactions to suppress non-radiative deactivation.

Remote Water-Mediated Proton Transfer Triggers Inter-Cu Electron Transfer: Nitrite Reduction Activation in Copper-Containing Nitrite Reductase

The copper-containing nitrite reductase (CuNiR) catalyzes the biological conversion of nitrite to nitric oxide; key long-range electron/proton transfers are involved in the catalysis. However, the details of the electron-/proton-transfer mechanism are still unknown. In particular, the driving force of the electron transfer from the type-1 copper (T1Cu) site to the type-2 copper (T2Cu) site is ambiguous. Here, we explored the two possible proton-transfer channels, the high-pH proton channel and the primary proton channel, by using two-layered ONIOM calculations. Our calculation results reveal that the driving force for electron transfer from T1Cu to T2Cu comes from a remote water-mediated triple-proton-coupled electron-transfer mechanism. In the high-pH proton channel, the water-mediated triple-proton transfer occurs from Glu113 to an intermediate water molecule, whereas in the primary channel, the transfer is from Lys128 to His260. Subsequently, the two channels employ another two or three distinct proton-transfer steps to deliver the proton to the nitrite substrate at the T2Cu site. These findings explain the detailed proton-/electron-transfer mechanisms of copper-containing nitrite reductase and could extend our understanding of the diverse proton-coupled electron-transfer mechanisms in complicated proteins.

Stereochemistry, Stereodynamics, and Redox and Complexation Behaviors of 2,2'-Diaryl-1,1'-Biazulenes

2,2'-Diaryl-1,1'-biazulenes were synthesized and electronic communication between the azulene subunits was suggested based on redox measurements. The linkage of azulene at the 1-position also appeared to increase the HOMO levels. In addition, cyclic voltammetry measurements of 2-arylazulenes showed a return peak associated with the oxidation, which was not observed for azulene. The stabilization of the single-electron oxidant may be due to the SOMO-HOMO energy inversion phenomenon. X-ray crystallography of the azulene dimers revealed that this species possessed a syn-type structure in which both aryl groups in the 2-positions formed π-stacks. The twisted structure was indicated to be in the (R)- or (S)-configuration for all molecules in the unit cell. Spontaneous resolution was also shown. Furthermore, from the solid circular dichroism (CD) spectral measurements, the relationship between the absolute configuration of the molecules and the CD spectra was determined. A racemization rotational barrier of ca. 27 kcal mol^-1 was calculated. Moreover, the pyridylazulene dimer cyclized upon reaction with PdCl₂ to form a 3 : 3 complex, in which the biazulene units cyclized to give ratios between the (R)- and (S)-forms of either 2 : 1 or 1 : 2.

A DFT mechanistic, thermodynamic and kinetic study on the reaction of 1, 3, 5-trihydroxybenzene and 2, 4, 6-trihydroxyacetophenone with •OOH in different media

A theoretical investigation on the reactions of 1, 3, 5-trihydroxybenzene (PG) and 2, 4, 6-trihydroxyacetophenone (ACPG) with •OOH has been performed with the aim of elucidating the peroxyl radical scavenging properties of PG and its acylated derivative. The study has considered the hydrogen atom transfer (HAT), the single electron transfer-proton transfer and the sequential proton loss-electron transfer mechanisms and determined the geometric, energetic and electronic properties of the reaction species as well as the kinetic parameters for the HAT mechanism. DFT/M06-2X, DFT/MPW1K and DFT/BHHLYP calculation methods have been utilized in combination with the 6-311++G(3df, 2p) basis set. The DFT methods were benchmarked using the CBS-QB3 method. Thermodynamic parameters such as bond dissociation enthalpy (BDE) and ionization energy suggest that the thermodynamically preferred mechanism is the HAT mechanism. The geometric, electronic and energetic parameters suggest that the preferred site for the abstraction of the free phenolic H atom in ACPG is the ortho position. Spin density and branching ratio values indicate that the most stable and preferable product formed is for the reaction of ACPG [Formula: see text] •OOH at the ortho position. The estimated rate constants obtained indicate that the reaction of ACPG [Formula: see text] •OOH is kinetically preferred to the reaction of PG [Formula: see text] •OOH, which is in agreement with experimental findings.

A DFT mechanistic and kinetic study on the reaction of phloroglucinol with •OH in different media: Hydrogen atom transfer versus oxidation

A theoretical study on the reaction of phloroglucinol with •OH has been performed with the aim of elucidating the geometric, energetic and kinetic properties of the reaction as well as identifying the preferred reaction pathway. Three reaction mechanisms have been considered, namely, direct hydrogen atom abstraction, addition–elimination mechanism in the absence and in the presence of a base catalyst and oxidation mechanism in the absence and in the presence of O2. The study has been performed using the DFT/M06[Formula: see text]2X, DFT/BHHLYP and DFT/MPW1K methods in conjunction with either the 6-31++G(d,p) or the 6-311++G(3df,2p) basis set. The energetic parameters are influenced by the type of function utilized and the media in which the calculation is done. The direct hydrogen abstraction mechanism provides the smallest branching ratio with respect to the •OH addition mechanisms. The PG + •OH reaction under atmospheric conditions saturated with O2 would predominantly form tetrahydroxybenzene; the predominant product within the biological system would largely depend on physiological conditions; under pH [Formula: see text] 7 and with oxygen dissolved within the biological system, the preferred product would be tetrahydroxybenzene; however, if the reaction takes place in some part of the biological system where the pH [Formula: see text] 7, the preferred product would be the phenoxyl radical.

A Benchmark of Density Functional Approximations For Thermochemistry and Kinetics of Hydride Reductions of Cyclohexanones

The performance of density functionals and wavefunction methods for describing the thermodynamics and kinetics of hydride reductions of 2-substituted cyclohexanones has been evaluated for the first time. A variety of exchange correlation functionals ranging from generalized gradient approximations to double hybrids have been tested and their performance to describe the facial selectivity of hydride reductions of cyclohexanones has been carefully assessed relative to the CCSD(T) method. Among the tested methods, an approach in which single-point energy calculations using the double hybrid B2PLYP-D3 functional on ωB97X-D optimized geometries provides the most accurate transition state energies for these kinetically-controlled reactions. Moreover, the role of torsional strain, temperature, solvation, noncovalent interactions on the stereoselectivity of these reductions was elucidated. Our results indicate a prominent role of the substituent on the cis/trans ratios driven by the delicate interplay between torsional strain and dispersion interactions.

Survival of the most transferable at the top of Jacob's ladder: Defining and testing the ωB97M(2) double hybrid density functional

A meta-generalized gradient approximation, range-separated double hybrid (DH) density functional with VV10 non-local correlation is presented. The final 14-parameter functional form is determined by screening trillions of candidate fits through a combination of best subset selection, forward stepwise selection, and random sample consensus (RANSAC) outlier detection. The MGCDB84 database of 4986 data points is employed in this work, containing a training set of 870 data points, a validation set of 2964 data points, and a test set of 1152 data points. Following an xDH approach, orbitals from the ωB97M-V density functional are used to compute the second-order perturbation theory correction. The resulting functional, ωB97M(2), is benchmarked against a variety of leading double hybrid density functionals, including B2PLYP-D3(BJ), B2GPPLYP-D3(BJ), ωB97X-2(TQZ), XYG3, PTPSS-D3(0), XYGJ-OS, DSD-PBEP86-D3(BJ), and DSD-PBEPBE-D3(BJ). Encouragingly, the overall performance of ωB97M(2) on nearly 5000 data points clearly surpasses that of all of the tested density functionals. As a Rung 5 density functional, ωB97M(2) completes our family of combinatorially optimized functionals, complementing B97M-V on Rung 3, and ωB97X-V and ωB97M-V on Rung 4. The results suggest that ωB97M(2) has the potential to serve as a powerful predictive tool for accurate and efficient electronic structure calculations of main-group chemistry.

Unification of the W1X and G4(MP2)-6X Composite Protocols

We have devised the composite procedures WG and WGh to unify the W1X and the (computationally more economical) G4(MP2)-6X protocols. The WG procedure employs a combination of MP2, MP2-F12, CCSD-F12b, and CCSD(T) to approximate the all-electron scalar-relativistic CCSD(T)/CBS energy. In addition, it incorporates features such as the scaling of the energy components and an empirical "higher-level-correction" term. The WGh protocol represents a somewhat more economical variant of WG with partial removal of diffuse functions. Our benchmark shows that, in general, both WG and WGh have similar performance to that for W1X-2, with WGh (predictably) performing somewhat less well for electron affinities. In terms of computational efficiency, WG is approximately an order of magnitude less costly than W1X-2, while WGh gives not only a further slight savings in computer time but also a notably reduced disk requirement.

How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses.

Employing Range Separation on the meta-GGA Rung: New Functional Suitable for Both Covalent and Noncovalent Interactions

We devise a scheme for converting an existing exchange functional into its range-separated hybrid variant. The underlying exchange hole of the Becke-Roussel type has the exact second-order expansion in the interelectron distance. The short-range part of the resulting range-separated exchange energy depends on the kinetic energy density and the Laplacian even if the base functional lacks the dependence on these variables. The most successful practical realization of the scheme, named LC-PBETPSS, combines the range-separated Perdew-Burke-Ernzerhof (PBE) exchange lifted to the hybrid meta-generalized gradient approximation rung and the Tao-Perdew-Staroverov-Scuseria (TPSS) correlation. The value of the range-separation parameter is estimated theoretically and confirmed by empirical optimization. The D3 dispersion correction is recommended for all energy computations employing the presented functional. Numerical tests show remarkably robust performance of the method for noncovalent interaction energies, barrier heights, main-group thermochemistry, and excitation energies.

Dominant Decomposition Pathways for Ethereal Solvents in Li-O2 Batteries

The promise of high specific energies for Li-O2 batteries has driven research toward the development of new compatible materials for this emerging technology. Obtained energies, however, fall short of the theoretical values partly due to parasitic chemistries arising from organic solvent decomposition during battery cycling. Electrolyte solvent and salt decomposition have also been identified as limiting factors for rechargeability of the battery. Although lithium trifluorosulfonamide (LiTFSI) dissolved in 1,2-dimethoxyethane (DME) has been shown to be a promising solvent/electrolyte candidate for Li-O2 batteries, significant challenges remain, namely minimizing decomposition of both the solvent and electrolyte salt during battery cycling. Herein, we provide spectroscopic labeling studies to identify the source of H2 at high potentials during charge and propose a decomposition pathway for DME to lithium formate and acetate products at low potentials. NMR studies were preformed to show that DME decomposes to lithium formate and acetate in aqueous Li2O2, products which are also observed after D2O workups on cathodes after discharge. Finally, we use density functional theory (DFT) to elucidate a mechanistic pathway for DME decomposition that is based on known organic oxidation processes.

Spectroscopic signatures and structural motifs in isolated and hydrated serotonin: a computational study

The conformational landscapes of neutral serotonin characterized by MP2, CC2 and DFT methods. The Gph-out/anti conformation is found most stable.