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Abstract Previous studies on bimetallic paddlewheel compounds have established a direct correlation between metal–metal distance and ligand torsion angles, leading to the rule that higher torsion results in longer metal‐metal bond distances. Here, the new discovery based on diarylformamidinate Ru₂⁵⁺ paddlewheel compounds [Ru2Cl(DArF)4] that show an opposite behavior is reported: higher torsions lead to shorter metal–metal distances. This discovery challenges the assumption that internal rotation solely impacts the δ bond. By combining experimental and theoretical techniques, it is demostrated that this trend is associated with previously overlooked π metal‐ligand interactions. These π metal‐ligand interactions are a direct consequence of the paddlewheel structure and the conjugated nature of the bidentate ligands. This findings offer far‐reaching insights into the influence of equatorial ligands and their π‐conjugation characteristics on the electronic properties of paddlewheel complexes. That this effect is not exclusive of diruthenium compounds but also occurs in other bimetallic cores such as ditungsten or dirhodium is demonstrated, and with other ligands showing allyl type conjugation. These results provide a novel approach for fine‐tuning the properties of these compounds with significant implications for materials design.

We report here a benchmark study on the bimolecular nucleophilic substitution (SN2) reaction between hydride and methane, for which we have obtained reference energies at the coupled cluster toward full configuration-interaction limit (CC-cf/CBS). Several wavefunction (HF, MP2, coupled cluster) and density functional methods are compared for their reliability regarding these reference data.

Recently, we reported that the basis set has a profound influence on the computed values for spin-state splittings [J. Phys. Chem. A2008, 112, 6384]. In particular, small Gaussian-type orbital (GTO) basis sets were shown to be unreliable for the prediction of them. Here, we report simple modifications of the small Pople-type Gaussian-type orbital basis sets (3-21G, 3-21G*, 6-31G, 6-31G*), which correct their faulty behavior for the spin-state energies. We have investigated the basis sets for a set of 13 first-row transition-metal complexes for which reliable reference data have been obtained at the OPBE/TZ2P(STO) level. For several systems, we have used single and double spin-contamination corrections to avoid ambiguity of the results because of spin contamination, that is, the energies and geometries were obtained for the pure spin states. The spin ground states as predicted by the spin-state-corrected GTO basis sets (s6-31G, s6-31G*) are in complete agreement with the reference Slater-type orbital (STO) data, while those of the original basis sets and a recent modification by Baker and Pulay (m6-31G*) are not for all cases. The spin-state-corrected GTO basis sets also improve upon the original and modified basis sets for the accuracy of geometry optimization, while the accuracy of the vibrational frequencies is as good or better. At a limited additional cost, one therefore obtains very reliable results for these important spin-state energies. [ABSTRACT FROM AUTHOR]

We have studied the mechanism of SN2@P reactions in the model systems X−+ PMe2Y and X−+ POR2Y (with R = Me, OH, OMe; and X, Y = Cl, OH, MeO) using density functional theory at OLYP/TZ2P. Our main purpose is to analyze the nature of the Walden inversion in our model nucleophilic substitution reactions. Walden inversion is well-known to proceed, in general, as a concerted umbrella motion of the substituents at the central atom. Interestingly, we find here that, in certain model reactions, Walden inversion can also proceed in a stepwise fashion in which the individual substituents of the umbrella flip, consecutively, from the educt to the product conformation viaseparate barriers on the reaction profile. We also examine how variation in nucleophile and leaving group may tune the pentavalent transition structure between labile transition state (TS) and stable transition complex (TC). Furthermore, we explore the various competing multistep pathways in the symmetric (X = Y) and asymmetric (X ≠ Y) substitution reactions in our model reaction systems. [ABSTRACT FROM AUTHOR]

Thioredoxins (Trx) are enzymes with a characteristic CXYC active-site motif that catalyze the reduction of disulfide bonds in other proteins. We have theoretically explored this reaction mechanism, both in the gas phase and in water, using density functional theory. The mechanism of disulfide reduction involves two consecutive thiol−disulfide exchange reactions, that is, nucleophilic substitutions at sulfur (SN2S):  first, by one Trx cysteine−thiolate group (Cys-32) at a sulfur atom of the disulfide substrate and, second, by the other Trx cysteine−thiolate group (the buried thiol of Cys-35) at the sulfur atom of the first Trx cysteine. We have investigated the intrinsic nature of such SN2S substitution using the simple CH3S-CH3SSCH3model and how it is affected by solvation in aqueous solution. Next, we have examined how the behavior of the elementary SN2S steps changes in the more realistic enzyme−substrate model CGPC CH3SSCH3, which contains the active-site of Trx. In all model reactions, solvation turns the hypervalent trisulfide anion (i.e., the SN2S transition species) from a stable complex into a transition state. Importantly, our analyses suggest that the deprotonation of the buried thiol (which is required before the latter can enter into the second SN2S step) is done by the leaving group evolving from the first SN2S step. Finally, molecular dynamics (MD) simulations, in the gas phase and in water, of CGPC, CGGC, and the corresponding wild-type Trx and P34G Trx show that the activity of the thioredoxin active-site motif (CXYC) is determined not only by the structural rigidity associated with the particular variable residues (XY) but also by the number of amide N−H groups. The latter are involved in the stabilization of the Cys-32 thiolate and thus affect the acidity and nucleophilicity of this residue. [ABSTRACT FROM AUTHOR]

Our work reports in detail the results of systematic large-scale theoretical investigations of the glycosaminoglycan building units 1-OMe IdoA-2SNa2(1; 2H1and 1H2forms), 1-OMe GlcN-S6SNa2(2), 1,4-DiOMe GlcNa (3), 1,4-DiOMe GlcN-S3S6SNa3(4), 1,4-DiOMe IdoA-2SNa2(5; 4C1, 1C4, and 2Soconformations), and 1,4-DiOMe GlcN-S6SNa2(6) at the BP86/TZ2P level of the density functional theory. The optimized geometries indicate that the most stable structure of these monomeric units in the neutral state is stabilized via “multifurcated” sodium bonds. The equilibrium structure of the biologically active anionic forms of the glycosaminoglycans studied changed considerably in a water solution. The computed interaction energies, E, of sodium coordinated systems 1−6are negative and span a rather broad energy interval (from −130 to −590 kcal mol-1). Computations that include the effect of solvation indicated that in water the relative stability of Na···ligand ionic bonds is considerably diminished. The computed interaction energy in water is small (from −20 to −53 kcal mol-1) and negative, that is, stabilizing. [ABSTRACT FROM AUTHOR]

Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the polypeptide chain, using for the ligand residues a set of charges that is modified with respect to the apo form of the protein by the presence of the copper ion. The results show that the different charge values do not lead to relevant effects on the geometry of the active site of the protein, as long as bond distance constraints are used for all the five ligand atoms. The distance constraint on the O atom of Gly45 can be removed without altering the active site geometry. The coordination between Cu and the other axial ligand Met121 is outlined as being flexible. Differences are found between the bonds of the copper ion with the two apparently equivalent N d1 atoms of His46 and His117. The overall findings are discussed in connection with the issue of determining a model for the active site of azurin suitable to be used in molecular dynamics simulations under unfolding conditions. Figure Model of azurin active site. Copper ligand residues are cut off at C a position except Gly45, for which the portion of backbone connecting it to His46 is shown. Only polar H atoms are shown. All atoms are in standard colors (Cu in violet), and the five ligands are labeled [ABSTRACT FROM AUTHOR]