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To accurately simulate the inner workings of an enzyme active site with quantum mechanics (QM), not only must the reactive species be included in the model but also important surrounding residues, solvent, or coenzymes involved in crafting the microenvironment. Our lab has been developing the Residue Interaction Network Residue Selector (RINRUS) toolkit to utilize interatomic contact network information for automated, rational residue selection and QM-cluster model generation. Starting from an x-ray crystal structure of catechol-O-methyltransferase, RINRUS was used to construct a series of QM-cluster models. The reactant, product, and transition state of the methyl transfer reaction were computed for a total of 550 models, and the resulting free energies of activation and reaction were used to evaluate model convergence. RINRUS-designed models with only 200–300 atoms are shown to converge. RINRUS will serve as a cornerstone for improved and automated cheminformatics-based enzyme model design.

Formation of Co(III) complexes was achieved via transmetallation with CoCl2 or Co(acac)3 of an isolated CCC–NHC pincer Zr complex. Four new crystal structures are reported, which expand upon the limited scope of first-row transition metal CCC–NHC pincer complexes. DFT computations were utilized to analyze the thermodynamics of cleaving a dimeric cobalt pincer complex with dimethylamine.

Fluxionality of the cyclohexenylmanganese tricarbonyl complex [(C6H9)Mn(CO)3], which has an Mn-H-C 3-center 2-electron agostic interaction, have been analyzed with density functional theory (DFT) computations. The fluxionality of this complex is a classic in organometallic chemistry (as highlighted by its inclusion as a study problem in the textbook by Kegley and Pinhas, Problems and Solutions in Organometallic Chemistry), and we provide new insights into its chemistry. Besides the three previously reported fluxional processes [1,3-endo fast exchange (TS-1), CO ligand equivalence (TS-2), and 1,2-metal migration via Cs η4 diene hydride species (TS-3)], two additional processes were identified: 1,2-agostic isomerization (TS-1-2), and a low-energy hydride transfer process (TS-1-9). This investigation uncovered a previously unidentified agostic interaction in the fluxionality of (C6H9)Mn(CO)3: the 1,2-agostic isomerization leads to a previously uncharacterized “closed” Cs agostomer (structure 2) with a Mn-H distance of 2.04 A, a Mn-H-C bond angle of 104.3°, and the 1H NMR chemical shift of −4.7 ppm. Energetically-similar agostic isomers have previously been defined as “agostomers”. The variable-temperature 1H NMR spectra were also simulated. Excellent agreement is observed (R2 = 0.9949) when comparing the computed and experimental 1H NMR chemical shifts. Reasonable agreements between the computed activation energies (6.1, 12.9, and 13.8 kcal mol−1) and experimental activation energies (8.3 ± 0.3, 13.1 ± 0.1, and 15.4 ± 0.3 kcal mol−1) were found.

The coordination sphere of the reported (1,3-bis(3-butylimidazol-1-yl-2-idene)-2-phenylene)( tert -butylimido) CCC-NHC Ta (V) bis(imido) pincer complex 2 (Helgert et al., 2016, doi: 10.1021/acs.organomet.6b00216 ) has been observed to spontaneously rearrange to yield X-ray quality crystals of a CCC-NHDC/NHC pincer Ta (V) bis(imido) complex ( 3 ). Preliminary computations were consistent with a step-wise mechanism for the formation of the N -heterocyclic dicarbene pincer complex. Over time the CCC-NHC Ta (V) bis(imido) pincer complex 2 reacted with adventitious protons sources to form CCC-NHC Ta(V)( tert -butylamido)( tert -butylimido)iodo complex ( 4 ). The reaction of bis(imido) 2 with excess lithium tert -butylamide at elevated temperatures, in an effort to find a direct synthesis of 3 , yielded methylidyne species 5 .

The metallation/transmetallation strategy has been successfully applied to the preparation of CCC-NHC pincer nickel complexes. Manipulation of the coordination sphere lead to cationic CCC-NHC pincer nickel complexes. These were found to exhibit polymorphism in the solid state with significant differences in the intermolecular distances observed by X-ray crystallography. Three polymorphs were observed for the PF6− salt, and two were observed for the BF4− salt. When BPh4− was the counterion only one morphology was observed, and crystals grown of the triflate salt were too small for analysis. Details of the differences are documented for comparison. Additionally, during crystallization it was found that a rearrangement of the CCC-NHC ligand had occurred, involving coupling of an NHC from two different ligands, which were oxidized.

Many organic corrosion inhibitors are complex and may include complicated chemical structures, mixture of different species, or require numerous and tedious preparation steps. In this study, we demonstrate inhibition by triazole- and imidazole-based compounds, which are synthesized in a one-step method and possess austere chemical structures. The inhibition effect was studied on the corrosion of mild steel in 1.0 M HCl solution at 40 °C by electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, and weight loss. Results from electrochemical measurements showed that the aromatic compounds were effective in inhibiting corrosion in acidic medium, such that the inhibition efficiency increased with increasing inhibitor concentration. The triazole-based compound had the best inhibitive performance (efficiency >90%), followed by the imidazole-based (~85%), at a concentration of 850 μM. These results were supported by analyses obtained from scanning electron and atomic force microscopy, which showed improved mild steel topology and decrease in surface roughness by up to a factor of five, and x-ray diffraction, which revealed the extent of oxide layer formation. In addition, the adsorption of a protective inhibitor layer on the metal surface was confirmed by Raman spectroscopy, while the underlying mode and mechanism were postulated based on a Langmuir adsorption isotherm and computational studies, which showed good correlation between the inhibitive ability and the electron donating and accepting capability of the compounds.

Quantitative β-boration of α,β-unsaturated carbonyl compounds was achieved utilizing the eco-friendly solvent EtOH along with MeOH at room temperature in 1 h, by a CCC-NHC pincer Rh complex mixture. Substrates with β-substituents were successfully converted yielding challenging, quaternary C–B bonds. The air- and water-stable pre-catalyst A , identified as a mixture of iodo and chloro CCC-NHC pincer Rh amine complexes, was evaluated for catalytic activity. This report is the first example of a pincer Rh complex demonstrating catalytic activity in a 1,4-addition at room temperature.

Previously, reactions of the “bow-tie” Ni( η 2 -TEMPO) 2 complex with an assortment of donor ligands have been characterized experimentally and computationally. The X-ray crystal structures afforded Ni( η 2 -TEMPO) 2 with trans -disposed TEMPO ligands, which was validated theoretically. Experimentally, proton transfer from the C–H bond of a variety of alkyne substrates (R) mostly produced cis -disposed ligands of the form Ni( η 2 -TEMPO)( κ 1 -TEMPOH)( κ 1 -R). While computations validated that the experimentally observed cis -disposed products were thermodynamically favored, in all cases, the proposed mechanisms of alkyne addition to cis -Ni( η 2 -TEMPO) 2 were kinetically disfavored. Therefore, a trans – cis isomerization must occur along the addition pathway. In order to better understand this phenomenon, an exhaustive theoretical conformational search of cis-/trans- Ni( η 2 -TEMPO) 2 and Ni( η 2 -TEMPO)( η 1 -TEMPO) structures has been performed. Our results show profound conformational and fluxional complexity for the trans – cis isomerization of the Ni( η 2 -TEMPO) 2 precursor. Surprisingly, the proposed mechanism for trans – cis isomerization indicates that conformational distortion of one of the TEMPO ligands of trans- Ni( η 2 -TEMPO) 2 before ring-opening provides a transition state free energy of activation stabilization of nearly 4.0 kcal mol −1 versus the most “straightforward” isomerization mechanism.

Two new compounds CpFeMn2(CO)7(μ3-S2)2 (2) and Cp3Fe3Mn(CO)4(μ3-S2)2(μ3-S) (3) were obtained by the treatment of [CpFeMn(CO)5(μ3-S2)]2 (1) with CO at room temperature in the presence of room light. Compound 2 contains two triply bridging disulfido ligands on opposite sides of an open FeMn2 triangular cluster. EPR and temperature-dependent magnetic susceptibility measurements show that it is paramagnetic with one unpaired electron per formula equivalent. The electronic structure of 2 was established by DFT and Fenske-Hall (FH) molecular orbital calculations which show that the unpaired electron occupies a low lying antibonding orbital that is located principally on the iron atom. The cyclic voltammogram of 2 exhibits one reversible one-electron oxidation wave at +0.34 V and one irreversible one-electron reduction wave at −0.66 V vs. Ag/AgCl. Compound 3 contains three iron atoms and one manganese atom with two triply bridging disulfido ligands and one triply bridging sulfido ligand and has no unpaired electrons. The molecular structures of compounds 2 and 3 were established by single crystal X-ray diffraction analyses.

Modern density functional theory (DFT) calculations are well suited for designing and testing alternative ligand schemes for transition-metal organometallic complexes. DFT methods have been applied to a variety of ligand systems and substrates (alkanes and silane) for the reaction (ηx-L)L′IrIIIR+R′H⇔(ηx-L)L′IrVRR′H (ηx-L=CpR, Tp, and carborane; L′=PR3, CR3−, SiR3−, and SnR3−; R=CH3, H; R′=Aryl, CR3, and H) with the goal of finding ligand–substrate combinations that will stabilize the Ir(V) species. This species is of particular interest, as it is the putative intermediate in the CH bond activation by Ir(III) complexes. Among the donor ligands examined were various multihapto ligands (ηx-L), alternative phosphines, anionic silanes (SiR3−) and stannanes (SnR3−), and chelating ligands. Cationic Ir(V) intermediates produced by oxidative addition of an alkane are not easily stabilized when compared with their Ir(III) counterparts. Replacing the phosphine donor ligands with more covalent inorganic ligands, specifically silyl and stannyl ligands (AR3), produces neutral Ir(V) complexes that are more stable than the Ir(III) reactants but would be subject to alkane elimination except at very low temperatures. Reacting the unsaturated 16 e− species [CpIrIIIPR3LR3]+ (where R=H, CH3 and L=C, Si) with the appropriate amount of silane (HSiR′3) might also afford Ir(V) complexes [CpIrVPR3LR3SiR′3H]+ that are stable enough to be observed spectroscopically, and in some instances, possibly isolated.

We report extensive density functional theory studies of the structures and vibrational frequencies of Tp 3,5-Me RhH 2 (H 2 ) in its ground and various transition states as well as the first direct comparison of observed and calculated inelastic neutron scattering (INS) vibrational spectra on this type of compound. Geometry optimizations produced canted η 2 -dihydrogen dihydride local minima of C 1 symmetry; with HH distances for the C 1 minimum energy structure of 0.842 and 0.898 A and barriers to rotation of 0.34 and 0.50 kcal mol −1 , respectively for B3LYP/BS1 and BP86/BS1 calculations of Tp 3,5-Me RhH 2 (H 2 ). The latter results from one transition state rotated approximately 60° away (a second lower energy transition state which is a few hundreds of a kcal mol −1 above the C 1 MIN is rotated approximately 30° away). With these calculated d(HH) values for the C 1 MIN the previously reported experimental data on the rotation of the dihydrogen ligand yields an experimental barrier to rotation of ∼1 kcal mol −1 and places the torsional transition at 200 cm −1 in the INS spectrum. Optimization of the Rh structure, that is analogous to the related Ir(V) C s minimum found for TpIrH 4 , generates a high-energy (>4 cal mol −1 ) C s transition state TpRh III H 4 structure with an η 3 -H 3 − ligand. This transition state ( C s TSE) exchanges the hydrogen in the mirror plane between two chiral C 1 MIN structures. Comparisons between observed and computed INS spectra suggests that the experimental INS spectrum be viewed as resulting from a quantum-averaged ground state encompassing at least two of the low energy structures found in our calculations.

Predictions by density functional calculations of the structure and relative energy of various isomers of the hydridotris(pyrazol-1-yl)borate ligand in Tp3R,5R rhodium(I) dicarbonyl complexes (R=H, Me) and their IR and 11B NMR spectra are compared to experimental observations. The lowest energy structure of Tp3,5-Me-, Tp3-Me-, and TpRh(CO)2 is a non-classical square pyramidal (SPy) structure with a long metal apical ligand distance in rapid exchange with an equivalent SPy structure through a low energy trigonal bipyramid (TBP) transition state (a ‘reverse’ Berry pseudorotation). A second higher energy minimum, a pseudo square-planar complex with the third uncoordinated pyrazolyl arm rotated approximately parallel with the metal ligand pseudo-plane (SP1), is accessed through a second low energy transition state. Another pseudo square-planar minimum structure (SP2) is produced by a transition state, which lengthens the rhodium-apical nitrogen (of the third pyrazolyl arm) bond distance. The relative stability of SP2 depends on the degree of tris(pyrazolyl)borate (Tp) substitution, where 5-substituents larger than hydrogen disfavor SP2 because of steric interactions. The previously reported empirical correlation between 11B NMR chemical shifts, νBH stretching frequencies, and the crystallographic Tp ligand denticity is reproduced by our calculations. The variety of structures observed by experiment can be explained by the calculated relative energies of the structures, the bulk dielectric of the solvents when in solution, specific interaction by certain solvents, and conditions of crystallization when in the solid-state.

The previously introduced multiple equilibrium analysis (MEA), which produces equilibrium constants ( K i ), capacities ( n i ), and thermodynamic parameters (enthalpies, Δ H i , and entropies, Δ S i ) of adsorption for each process, has been used to predict adsorption isotherms for N 2 , CO, CH 4 , C 2 H 6 , and SF 6 on one zeolitic (HZSM-5) and five carbonaceous (A-572, A-563, A-600, F-300, and BPL) solids. The adsorption of CO is best reproduced on each of the solids. In general, the adsorption of N 2 has been accurately predicted, while CH 4 and C 2 H 6 are underpredicted and SF 6 is overpredicted. Previously reported high-pressure data for the adsorption of CH 4 on BPL was very accurately predicted. The application of the MEA prediction of adsorption behavior has quite a potential for a variety of applications. Adsorbents can be used for catalyst supports, gas separation, respiratory protection, environmental applications, and even have the potential for fuel storage capabilities. The prediction of adsorption performance will lead to a greater understanding of the fundamental interactions involved in these systems and will help create new and better systems.

A recent article claims that the Cal–Ad method cannot discriminate multiple acid sites in the analysis of the interaction of pyridine (dilute pyridine in n -hexane) with HZSM-5. The Cal–Ad technique measures the enthalpy of a base-displacement reaction, while gas–solid calorimetry is a measure of an adduct formation between pyridine and the solid. A Born–Haber cycle with the appropriate values can demonstrate that the enthalpies derived from gas–solid calorimetry are an average of the two enthalpies of the interaction of pyridine with the two acid sites observed with the Cal–Ad method.

An extension to the Electrostatic-Covalent model is proposed for the prediction of physicochemical properties and enthalpies of interaction for two donor molecules reacting with a single acceptor molecule. The coordination of the first base modifies the acceptor tendencies for binding a second base. Each different base forms a different acceptor for coordinating the second base, so in any model different acceptor parameters are required for the second step for each base. An E and C based model is derived to reflect this behavior and is applied to several 2:1 adducts providing a new interpretation of their reactivity. Literature correlations of 2:1 adducts which use a single average acceptor parameter for the sum of the two steps do not reflect this behavior so the meaning of the fit and the resulting parameters are not clear. Furthermore, since an average does not reflect a different acceptor parameter in the second step for each base the cause of deviations in such a fit is not clear. The model is extended to encompass reactivity of bidentate phosphines. Donor parameters are reported for the first coordination step of bidentate phosphines. The second step of bidentate donor binding is affected by the strength of the acceptor interaction in the first step. Equations are derived to correlate the total enthalpies of reaction of bidentate phosphines. Some generalizations concerning reactivity can be made but limited data precludes a thorough evaluation of the model.