Computational studies on ethylene addition to nickel bis(dithiolene)

The density functionals B3LYP, B3PW91, BMK, HSE06, LC-ωPBE, M05, M06, O3LYP, TPSS, ω-B97X, and ω-B97XD are used to optimize key transition states and intermediates for ethylene addition to Ni(edt)(2) (edt = S(2)C(2)H(2)). The efficacy of the basis sets 6-31G**, 6-31++G**, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ is also examined. The geometric parameters optimized with different basis sets and density functionals are similar and agree well with experimental values. The ω-B97XD functional gives relative energies closest to those from CCSD, while M06 and HSE06 yield results close to those from CCSD(T). CASSCF and CASSCF-PT2 calculation results are also given. Variation of the relative energies from different density functionals appears to arise, in part, from the multireference character of this system, as confirmed by the T1 diagnostic and CASSCF calculations.     

Interaction between ions and substituted buckybowls: A comprehensive computational study

Complexes formed by substituted buckybowls derived from corannulene and sumanene with sodium cation or chloride anion have been computationally studied by using a variety of methods. Best results have been obtained with the SCS‐MP2 method extrapolated to basis set limit, which reproduces the highest‐level values obtained with the MP2.X method. All bowls form stable complexes with chloride anion, with stabilities ranging from ?6 kcal/mol in the methylated corannulene derivative to ?45 kcal/mol in the CN‐substituted sumanene. The opposite trend is observed in sodium complexes, going from deeply attractive complexes with the methylated derivatives (?36 kcal/mol with sumanene derivative) to slightly repulsive ones in the CN‐substituted bowls (2 kcal/mol in the corannulene derivative). Anion complexes are stabilized by large electrostatic interactions combined with smaller though significant dispersion and induction contributions. Conversely, cation complexes are stabilized by large induction contributions capable of holding together the bowl and the cation even in cases where the electrostatic interaction is repulsive. The effect of substitution is mainly reflected on changes in the molecular electrostatic potential of the bowl and, thus, in the electrostatic contribution to the interaction. Therefore, the variations in the stability of the complexes on substitution could be roughly predicted just considering the changes in the electrostatic interaction. However, other contributions also register changes mainly as a consequence of displacements on the position of the ion at the minimum, so the accurate prediction of the stability of this kind of complexes requires going further than the electrostatic approach. © 2014 Wiley Periodicals, Inc.     

Assessment of density functionals and force field methods on anion–π interaction in heterocyclic calix complexes

The performance of ten density functionals and four force field methods in describing non-covalent interactions have been assessed by studying the interaction energies and structures of the four anion–π complexes involving tetraoxacalix[2]arene[2]triazine and various anions. Their structures are optimized at MP2/6-311++G(d,p) level, and interaction energies are obtained at DF-MP2-F12/aug-cc-pVDZ level. The result shows that the functional M06-2X predicts the most reliable interaction energy, followed by wB97XD and BHandH. B97D slightly overestimates the interaction energy. Other functionals and force field methods seriously overestimate the interaction energy. For the structures, three functionals M06-2X, wB97XD and BH and H predict the most reliable results, followed by B97D. The force field methods predict the largest deviations. The present work suggests that the functional M06-2X is a reliable method to describe energies and structural properties of the large molecules involving the anion–π interactions.     

Predictive power of long-range corrected functionals on the spectroscopic properties of tetrapyrrole derivatives for photodynamic therapy

Porphyrin and chlorin based compounds possess promising properties to be utilized as photosensitizers in photodynamic therapy (PDT). However, the photosensitizers available on the market today are not ideal for use in PDT, which has emphasized the need for new photosensitizers with improved photodynamic properties to be developed. Computational drug-design can be utilized in the search for improved pharmaceutical compounds, provided that the methods used are able to reproduce experimental data. In the present study we investigated, by the use of time-dependent density functional theory (TD-DFT), the performance of the long-range corrected functionals ωB97, ωB97X and ωB97XD on their ability to predict low-lying singlet excitations (>600 nm) of a set of well-known photosensitizing compounds. It was found that ωB97X reproduced the experimental red-most absorption band most satisfactorily. The use of either B3LYP, ωB97XD or M06 in geometry optimizations has a minor effect on the spectra in most cases. Calculated energy differences between the optimized singlet ground states and optimized first excited triplet states show consistent and overall higher triplet state energies for B3LYP, M06, and PBE0 compared with ωB97, ωB97X, and ωB97XD. The calculated triplet state energies are, however, sufficient to generate singlet oxygen in most cases.     

Interaction between anions and substituted molecular bowls

Complexes formed by anions and substituted molecular bowls were studied by means of computational methods. The bowls consisted of corannulene molecules substituted with five or ten F, Cl, or CN groups, whereas Cl(-), Br(-) and BF(4)(-) were the anions considered. Substitution with F, Cl and CN hardly affects the geometry of the bowl, but produces an inversion of the molecular electrostatic potential of the bowls, which becomes positive over the two faces of the bowl, therefore interacting favorably with anions. In all cases considered, the most stable complex presents the anion interacting with the concave side of the bowl. The strength of the interaction roughly follows the values of molecular electrostatic potential, being more stable as more positive is the potential. The preference of anions to interact with the concave side of the bowls has its origin in stronger electrostatic and dispersion interactions. Though the solvent produces an important decrease in the stability of the complexes, the results suggest the possibility of employing these substituted buckybowls as anion receptors with a preferential concave complexation, especially for large anions.     

Halogen bonds with benzene: An assessment of DFT functionals

The performance of an extensive set of density functional theory functionals has been tested against CCSD(T) and MP2 results, extrapolated to the complete basis set (CBS) limit, for the interaction of either DCl or DBr (D = H, HCC, F, and NC) with the aromatic system of benzene. It was found that double hybrid functionals explicitly including dispersion, that is, B2PLYPD and mPW2PLYPD, provide the better agreement with the CCSD(T)/CBS results on both energies and equilibrium geometry, indicating the importance of dispersive contributions in determining this interaction. Among the less expensive functionals, the better performance is provided by the ωB97X and M062X functionals, while the ωB97XD and B97D functionals are shown to work very well for bromine complexes but not so well for chlorine complexes. © 2013 Wiley Periodicals, Inc.     

Description of noncovalent interactions involving π-system with high precision: An assessment of RPA,MP2, and DFT-D methods

Efficient approaches with high precision are essential for understanding the formation and stability of noncovalent interaction complexes. Here, 21 noncovalent interaction complexes involving π-system are selected and grouped in three subsets according to ETS–NOCV method: dispersion-dominated, electrostatic-dominated, and mixed. We mainly focus on examining the performance of random-phase approximation (RPA) on these π systems. The tested RPA-based method includes standard RPA and its variants including the related single excitations (SEs), renormalized single excitations (rSEs), second-order screened exchange (SOSEX), and the renormalized second-order perturbation theory (rPT2). The routine second-order Møller–Plesset perturbation theory (MP2) and three popular DFT-D functionals (M06-2X-D3, ωB97XD, and PBE-D3(BJ)) are also assessed for comparison. In this work, besides the calculation of interaction energies at Dunning-type aug-cc-pVDZ and aug-cc-pVTZ basis set, we also present a larger database of interaction energies calculated using MP2 and RPA methods with Dunning-type aug-cc-pVQZ basis set. An accurate CCSD(T)/CBS scheme is used to provide benchmark database. In addition to the high-level results, we also provide potential energy surfaces (PES) of different interaction type. Among all the tested methods, MP2 has a satisfactory performance on electrostatic-dominated and mixed-type systems, except for dispersion-dominated systems. DFT-D functionals, especially ωB97XD functional, has a balanced performance across all the tested systems. Importantly, for RPA-based methods, the calculation accuracy can be dramatically improved by taking into account SE or exchange effects, especially in the mixed complexes. We conclude that rPT2 among all the test RPA-based methods gives an overall satisfactory performance across different interaction types. © 2019 Wiley Periodicals, Inc.     

Stable alkanes containing very long carbon-carbon bonds

The metal-induced coupling of tertiary diamondoid bromides gave highly sterically congested hydrocarbon (hetero)dimers with exceptionally long central C-C bonds of up to 1.71 ? in 2-(1-diamantyl)[121]tetramantane. Yet, these dimers are thermally very stable even at temperatures above 200 °C, which is not in line with common C-C bond length versus bond strengths correlations. We suggest that the extraordinary stabilization arises from numerous intramolecular van der Waals attractions between the neighboring H-terminated diamond-like surfaces. The C-C bond rotational dynamics of 1-(1-adamantyl)diamantane, 1-(1-diamantyl)diamantane, 2-(1-adamantyl)triamantane, 2-(1-diamantyl)triamantane, and 2-(1-diamantyl)[121]tetramantane were studied through variable-temperature (1)H- and (13)C NMR spectroscopies. The shapes of the inward (endo) CH surfaces determine the dynamic behavior, changing the central C-C bond rotation barriers from 7 to 33 kcal mol(-1). We probe the ability of popular density functional theory (DFT) approaches (including BLYP, B3LYP, B98, B3LYP-Dn, B97D, B3PW91, BHandHLYP, B3P86, PBE1PBE, wB97XD, and M06-2X) with 6-31G(d,p) and cc-pVDZ basis sets to describe such an unusual bonding situation. Only functionals accounting for dispersion are able to reproduce the experimental geometries, while most DFT functionals are able to reproduce the experimental rotational barriers due to error cancellations. Computations on larger diamondoids reveal that the interplay between the shapes and the sizes of the CH surfaces may even allow the preparation of open-shell alkyl radical dimers (and possibly polymers) that are strongly held together exclusively by dispersion forces.     

Assessment of dispersion‐improved exchange‐correlation functionals for the simulation of CO2 binding by alcoholamines

In this study, 12 bound complexes were selected to construct a database for testing 15 dispersion‐improved exchange‐correlation (XC) functionals, including hybrid generalized gradient approximation (GGA), modified using the Grimme's pairwise strategy, and double hybrid XC functionals, for specifically characterizing the CO₂ binding by alcoholamines. Bound complexes were selected based on the characteristics of their hydrogen bonds, dispersion, and electrostatic (particularly between the positive charge of CO₂ and the lone pair of N of alcoholamines) interactions. The extrapolated binding energy from the aug‐cc‐pVTZ (ATZ) to aug‐cc‐pVQZ (AQZ) basis set at the CCSD(T)/CBS(MP2+DZ) level was used as the reference for the XC functional comparison. M06‐2X produced the optimal agreement if the optimized geometries at MP2/ATZ level were chosen for all the test bound complexes. However, M06‐L, ωB97X, and ωB97, and were preferred if the corresponding density functional theory (DFT) optimized geometries were adapted for the benchmark. Simple bimolecular reaction between CO₂ and monoethanolamine simulated using polarizable continuum solvation model confirmed that ωB97, ωB97X, and ωB97XD qualitatively reproduced the energetics of MP2 level. The inconsistent performance of the tested XC functionals, observed when using MP2 or DFT optimized geometries, raised concerns regarding using the single‐point ab initio correction combined with DFT optimized geometry, particularly for determining the nucleophilic attack by alcoholamines to CO₂. © 2014 Wiley Periodicals, Inc.     

Topological phase transitions in the vibration–rotation dynamics of an isolated molecule

A computational investigation of anomeric effects in piperidine rings bearing fluoro and trifluoromethyl substituents shows for both compounds the most pronounced evidence of the anomeric effect, as expressed as hyperconjugative delocalization of the nitrogen lone pair, in structures with the substituent in the axial position and the N–H bond in the equatorial position. This structure is the lowest-energy structure in the fluoro case but not in the trifluoromethyl case where there is an increased axial penalty associated with the CF₃ group. The anomeric effect is characterized via geometrical evidence, natural bond orbital analysis, electrostatic effects, and energetic criteria. Computational results from a variety of levels of theory are presented including CCSD(T) with complete basis set extrapolation, B2PLYP-D, ωB97XD, B97-D, M06-2X, B3LYP, and MP2 allowing for a comparison of performance. The CCSD(T)/CBS results are very well represented by either B2PLYP-D or ωB97XD with moderate to large basis sets (aug-cc-pVTZ or aug-cc-pVDZ). Hyperconjugation, electrostatic effects, and steric effects play a role in the relative energetic ordering of the isomers considered.     

Ferric complexes of 3-hydroxy-4-pyridinones characterized by density functional theory and Raman and UV-vis spectroscopies

Deferiprone and other 3-hydroxy-4-pyridinones are used in metal chelation therapy of iron overload. To investigate the structure and stability of these compounds in the natural aqueous environment, ferric complexes of deferiprone and amino acid maltol conjugates were synthesized and studied by computational and optical spectroscopic methods. The complexation caused characteristic intensity changes, a 300× overall enhancement of the Raman spectrum, and minor changes in UV-vis absorption. The spectra were interpreted on the basis of density functional theory (DFT) calculations. The CAM-B3LYP and ωB97XD functionals with CPCM solvent model were found to be the most suitable for simulations of the UV-vis spectra, whereas B3LYP, B3LYPD, B3PW91, M05-2X, M06, LC-BLYP, ωB97XD, and CAM-B3LYP functionals were all useful for simulation of the Raman scattering. Characteristic Raman band frequencies for 3-hydroxy-4-pyridinones were assigned to molecular vibrations. The computed conformer energies consistently suggest the presence of another isomer of the deferiprone-ferric complex in solution, in addition to that found previously by X-ray crystallography. However, the UV-vis and Raman spectra of the two species are similar and could not be resolved. In comparison to UV-vis, the Raman spectra and their combination with calculations appear more promising for future studies of iron sequestrating drugs and artificial metalloproteins as they are more sensitive to structural details.     

Accurate density functional theory description of binding constants and NMR chemical shifts of weakly interacting complexes of C60 with corannulene‐based molecular bowls

Density functional calculations on “catch and release” complexes of C₆₀ with corannulene derived molecular bowls show that computationally obtained ¹H nuclear magnetic resonance (NMR) chemical shifts can be used as a reliable predictor of binding constants. A wide range of functionals was benchmarked against accurate ab initio calculations to ensure a credible representation of the weak forces that dominate the interactions in these systems. The most reliable density functional theory (DFT) results were then calibrated using experimentally observed NMR data. Careful analysis and comparison of a wide range of commonly used density functionals shows that the explicit inclusion of dispersion corrections is currently the only reliable way to accurately describe the systems investigated in our study. Moreover, we are able to show that the B97‐D and ωB97X‐D functionals are not only able to reproduce ab initio benchmark calculations, but they do so accurately with a moderately sized basis sets and without the problems of numerical integration we encountered with other functionals in this study. © 2013 Wiley Periodicals, Inc.     

The relative energies of polypeptide conformers predicted by linear scaling second-order Møller-Plesset perturbation theory

We describe an implementation of the cluster-in-molecule(CIM) resolution of the identity(RI) approximation second-order M?ller–Plesset perturbation theory(CIM-RI-MP2), with the purpose of extending RI-MP2 calculations to very large systems. For typical conformers of several large polypeptides, we calculated their conformational energy differences with the CIM-RI-MP2 and the generalized energy-based fragmentation MP2(GEBF-MP2) methods, and compared these results with the density functional theory(DFT) results obtained with several popular functionals. Our calculations show that the conformational energy differences obtained with CIM-RI-MP2 and GEBF-MP2 are very close to each other. In comparison with the GEBF-MP2 and CIM-RI-MP2 relative energies, we found that the DFT functionals(CAM-B3LYP-D3, LC-?PBE-D3, M05-2X, M06-2X and ?B97XD) can give quite accurate conformational energy differences for structurally similar conformers, but provide less-accurate results for structurally very different conformers.     

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O[ellipsis (horizontal)]N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95?? to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).     

DFT calculations on the catalytic oxidation of CO over Si-doped (6,0) boron nitride nanotubes

The oxidation of carbon monoxide (CO) is important for a series of technological and environmental applications. In this work, the catalytic oxidation of CO on Si-doped (6,0) boron nitride nanotubes (BNNTs) is investigated by using density functional theory calculations. Reaction barriers and corresponding thermodynamic parameters were calculated using the M06-2X, B3LYP and wB97XD density functionals with 6-31G* basis set. Our results indicate that a vacancy defect in BNNT strongly stabilizes the Si adatom and makes it more positively charged. This charging enhances the adsorption of reaction gases (O₂ and CO) and results in the change of the electronic structure properties of the tube. The calculated barrier of the reaction CO + O₂ → CO₂ + O_ads on Si-doped BNNTs following the Langmuir–Hinshelwood is lower than that on the traditional noble metal catalysts. The second step of the oxidation would be the Eley–Rideal reaction (CO + O_ads → CO₂) with an energy barrier of about 1.8 and 10.1 kcal/mol at M06-2X/6-31G* level. This suggests that the CO oxidation catalyzed by the Si-doped BNNTs is likely to occur at the room temperature. The results also demonstrate that the activation energies and thermodynamic quantities calculated by M06-2X, B3LYP and wB97XD functionals are consistent with each other.     

Redox‐Active Corannulene Buckybowls in a Crystalline Hybrid Scaffold

A porous crystalline corannulene‐containing scaffold, which combines the periodicity, dimensionality, and structural modularity of hybrid frameworks with the intrinsic properties of redox‐active π‐bowls, has been prepared. Single‐crystal and powder X‐ray diffraction, ab initio density functional theory computations, gas sorption analysis, fluorescence spectroscopy, and cyclic voltammetry were employed to study the properties of the novel corannulene derivatives and the buckybowl‐based hybrid materials. X‐ray diffraction studies revealed the preservation of the corannulene bowl inside the prepared rigid matrix, which offers the unique opportunity to extend the scaffold dimensionality through the buckybowl curvature. Merging the inherent properties of hybrid frameworks with the intrinsic properties of π‐bowls opens a new avenue for preparing redox‐active materials and potentially improving charge transport in the scaffold.     

Assessment of density functionals with long‐range and/or empirical dispersion corrections for conformational energy calculations of peptides

Density functionals with long‐range and/or empirical dispersion corrections, including LC‐ωPBE, B97‐D, ωB97X‐D, M06‐2X, B2PLYP‐D, and mPW2PLYP‐D functionals, are assessed for their ability to describe the conformational preferences of Ac‐Ala‐NHMe (the alanine dipeptide) and Ac‐Pro‐NHMe (the proline dipeptide) in the gas phase and in water, which have been used as prototypes for amino acid residues of peptides. For both dipeptides, the mean absolute deviation (MAD) is estimated to be 0.22–0.40 kcal/mol in conformational energy and 2.0–3.2° in torsion angles ? and ψ using these functionals with the 6‐311++G(d,p) basis set against the reference values calculated at the MP2/aug‐cc‐pVTZ//MP2/aug‐cc‐pVDZ level of theory in the gas phase. The overall performance is obtained in the order B2PLYP‐D ≈ mPW2PLYP‐D > ωB97X‐D ≈ M06‐2X > MP2 > LC‐ωPBE > B3LYP with the 6–311++G(d,p) basis set. The SMD model at the M06‐2X/6‐31+G(d) level of theory well reproduced experimental hydration free energies of the model compounds for backbone and side chains of peptides with MADs of 0.47 and 4.3 kcal/mol for 20 neutral and 5 charged molecules, respectively. The B2PLYP‐D/6‐311++G(d,p)//SMD M06‐2X/6‐31+G(d) level of theory provides the populations of backbone and/or prolyl peptide bond for the alanine and proline dipeptides in water that are consistent with the observed values. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Density-functional approaches to noncovalent interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality evaluations of binding strength compiled for molecular complexes of diverse size and nature. In particular, the efficacy of functionals deliberately crafted to encompass long-range forces, a posteriori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 [revised in J. Chem. Phys. 132, 144104 (2010)] and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogen-bonded (HBC6) dissociation curves and a pairwise decomposition of a protein-ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X, M06-2X, ωB97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double-ζ or robust triple-ζ basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunction with aug-cc-pVDZ, for a mean absolute deviation of 0.41 - 0.49 kcal/mol, and B3LYP-D3, B97-D3, ωB97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, affording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 - 0.38 kcal/mol.