Structural Dynamics of the Bacillus subtilis MntR Transcription Factor Is Locked by Mn2+ Binding.

Manganese (II) ions are essential for a variety of bacterial cellular processes. The transcription factor MntR is a metallosensor that regulates Mn2+ ion homeostasis in the bacterium Bacillus subtilis. Its DNA-binding affinity is increased by Mn2+ ion binding, allowing it to act as a transcriptional repressor of manganese import systems. Although experimentally well-researched, the molecular mechanism that regulates this process is still a puzzle. Computational simulations supported by circular dichroism (CD), differential scanning calorimetry (DSC) and native gel electrophoresis (native-PAGE) experiments were employed to study MntR structural and dynamical properties in the presence and absence of Mn2+ ions. The results of molecular dynamics (MD) simulations revealed that Mn2+ ion binding reduces the structural dynamics of the MntR protein and shifts the dynamic equilibrium towards the conformations adequate for DNA binding. Results of CD and DSC measurements support the computational results showing the change in helical content and stability of the MntR protein upon Mn2+ ion binding. Further, MD simulations show that Mn2+ binding induces polarization of the protein electrostatic potential, increasing the positive electrostatic potential of the DNA-binding helices in particular. In order to provide a deeper understanding of the changes in protein structure and dynamics due to Mn2+ binding, a mutant in which Mn2+ binding is mimicked by a cysteine bridge was constructed and also studied computationally and experimentally.

Coordination Sites for Sodium and Potassium Ions in Nucleophilic Adeninate Contact ion-Pairs: A Molecular-Wide and Electron Density-Based (MOWED) Perspective.

The adeninate anion (Ade-) is a useful nucleophile used in the synthesis of many prodrugs (including those for HIV AIDS treatment). It exists as a contact ion-pair (CIP) with Na+ and K+ (M+) but the site of coordination is not obvious from spectroscopic data. Herein, a molecular-wide and electron density-based (MOWED) computational approach implemented in the implicit solvation model showed a strong preference for bidentate ion coordination at the N3 and N9 atoms. The N3N9-CIP has (i) the strongest inter-ionic interaction, by -30 kcal mol-1, with a significant (10-15%) covalent contribution, (ii) the most stabilized bonding framework for Ade-, and (iii) displays the largest ion-induced polarization of Ade-, rendering the N3 and N9 the most negative and, hence, most nucleophilic atoms. Alkylation of the adeninate anion at these two positions can therefore be readily explained when the metal coordinated complex is considered as the nucleophile. The addition of explicit DMSO solvent molecules did not change the trend in most nucleophilic N-atoms of Ade- for the in-plane M-Ade complexes in M-Ade-(DMSO)4 molecular systems. MOWED-based studies of the strength and nature of interactions between DMSO solvent molecules and counter ions and Ade- revealed an interesting and unexpected chemistry of intermolecular chemical bonding.

A Molecular-Wide and Electron Density-Based Approach in Exploring Chemical Reactivity and Explicit Dimethyl Sulfoxide (DMSO) Solvent Molecule Effects in the Proline Catalyzed Aldol Reaction.

Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays a double role. Through strong interactions with 1 and acetone 2, it leads to a significant increase of energy barriers at transition states (TS) for the lowest energy conformer 1a of proline. Just the opposite holds for the higher energy conformer 1b. Both the 'inhibitor' and 'catalyst' mode of activity of DMSO eliminates 1a as a catalyst at the very beginning of the process and promotes the chemical reactivity, hence catalytic ability of 1b. Modelling using a Molecular-Wide and Electron Density-based concept of Chemical Bonding (MOWED-CB) and the Reaction Energy Profile-Fragment Attributed Molecular System Energy Change (REP-FAMSEC) protocol has shown that, due to strong intermolecular interactions, the HN-C-COOH (of 1), CO (of 2), and SO (of 3) fragments drive a chemical change throughout the catalytic reaction. We strongly advocate exploring the pre-organization of molecules from initially formed complexes, through local minima to the best structures suited for a catalytic process. In this regard, a unique combination of MOWED-CB with REP-FAMSEC provides an invaluable insight on the potential success of a catalytic process, or reaction mechanism in general. The protocol reported herein is suitable for explaining classical reaction energy profiles computed for many synthetic processes.

A REP-FAMSEC Method as a Tool in Explaining Reaction Mechanisms: A Nucleophilic Substitution of 2-Phenylquinoxaline as a DFT Case Study.

In search for the cause leading to low reaction yields, each step along the reaction energy profile computed for the assumed oxidative nucleophilic substitution of hydrogen (ONSH) reaction between 2-phenylquinoxaline and lithium phenylacetylide was modelled computationally. Intermolecular and intramolecular interaction energies and their changes between consecutive steps of ONSH were quantified for molecular fragments playing leading roles in driving the reaction to completion. This revealed that the two reactants have a strong affinity for each other, driven by the strong attractive interactions between Li and two N-atoms, leading to four possible reaction pathways (RP-C2, RP-C3, RP-C5, and RP-C10). Four comparable in energy and stabilizing molecular system adducts were formed, each well prepared for the subsequent formation of a C-C bond at either one of the four identified sites. However, as the reaction proceeded through the TS to form the intermediates (5a-d), very high energy barriers were observed for RP-C5 and RP-C10. The data obtained at the nucleophilic addition stage indicated that RP-C3 was both kinetically and thermodynamically favored over RP-C2. However, the energy barriers observed at this stage were very comparable for both RPs, indicating that they both can progress to form intermediates 5a and 5b. Interestingly, the phenyl substituent (Ph1) on the quinoxaline guided the nucleophile towards both RP-C2 and RP-C3, indicating that the preferred RP cannot be attributed to the steric hindrance caused by Ph1. Upon the introduction of H2O to the system, both RPs were nearly spontaneous towards their respective hydrolysis products (8a and 8b), although only 8b can proceed to the final oxidation stage of the ONSH reaction mechanism. The results suggest that RP-C2 competes with RP-C3, which may lead to a possible mixture of their respective products. Furthermore, an alternative, viable, and irreversible reaction path was discovered for the RP-C2 that might lead to substantial waste. Finally, the modified experimental protocol is suggested to increase the yield of the desired product.

The CH···HC interaction in biphenyl is a delocalized, molecular-wide and entirely non-classical interaction: Results from FALDI analysis.

In this study we aim to determine the origin of the electron density describing a CH···HC interaction in planar and twisted conformers of biphenyl. In order to achieve this, the fragment, atomic, localized, delocalized, intra- and inter-atomic (FALDI) decomposition scheme was utilized to decompose the density in the inter-nuclear region between the ortho-hydrogens in both conformers. Importantly, the structural integrity, hence also topological properties, were fully preserved as no 'artificial' partitioning of molecules was implemented. FALDI-based qualitative and quantitative analysis revealed that the majority of electron density arises from two, non-classical and non-local effects: strong overlap of ortho CH σ-bonds, and long-range electron delocalization between the phenyl rings and ortho carbons and hydrogens. These effects resulted in a delocalized electron channel, that is, a density bridge or a bond path in a QTAIM terminology, linking the H-atoms in the planar conformer. The same effects and phenomena are present in both conformers of biphenyl. We show that the CH···HC interaction is a molecular-wide event due to large and long-range electron delocalization, and caution against approaches that investigate CH···HC interactions without fully taking into account the remainder of the molecule.

Characterization of bonding modes in metal complexes through electron density cross-sections.

Qualitative inspection of molecular orbitals (MOs) remains one of the most popular analysis tools used to describe the electronic structure and bonding properties of transition metal complexes. In symmetric coordination complexes, the use of group theory and the symmetry-adapted linear combination (SALC) of fragment orbitals allows for a very accurate and informative interpretation of MOs, but the same procedure cannot be performed for asymmetric complexes, such as Schrock and Fischer carbenes. In this work, we present a straight-forward approach for classifying and quantifying MO contributions to a particular metal-ligand interaction. Our approach utilizes the topology of MO density contributions to a cross-section of an inter-nuclear region, and is computationally inexpensive and applicable to symmetric and asymmetric complexes alike. We also apply the same approach with similar decompositions using Natural Bond Orbitals (NBO) and the recently developed Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) density decomposition scheme. In particular, FALDI analysis provides additional insights regarding the multi-centric nature of metal-carbene bonds without resorting to expensive multi-reference calculations.

Molecular Orbitals Support Energy-Stabilizing "Bonding" Nature of Bader's Bond Paths.

Our MO-based findings proved a bonding nature of each density bridge (DB, or a bond path with an associated critical point, CP) on a Bader molecular graph. A DB pinpoints universal physical and net energy-lowering processes that might, but do not have to, lead to a chemical bond formation. Physical processes leading to electron density (ED) concentration in internuclear regions of three distinctively different homopolar H,H atom-pairs as well as classical C-C and C-H covalent bonds were found to be exactly the same. Notably, properties of individual MOs are internuclear-region specific as they (i) concentrate, deplete, or do not contribute to ED at a CP and (ii) delocalize electron-pairs through either in- (positive) or out-of-phase (negative) interference. Importantly, dominance of a net ED concentration and positive e--pairs delocalization made by a number of σ-bonding MOs is a common feature at a CP. This feature was found for the covalently bonded atoms as well as homopolar H,H atom-pairs investigated. The latter refer to a DB-free H,H atom-pair of the bay in the twisted biphenyl (Bph) and DB-linked H,H atom-pairs (i) in cubic Li4H4, where each H atom is involved in three highly repulsive interactions (over +80 kcal/mol), and (ii) in a weak attractive interaction when sterically clashing in the planar Bph.

Origin of Hydrocarbons Stability from a Computational Perspective: A Case Study of Ortho-Xylene Isomers.

It is shown herein that intuitive and text-book steric-clash based interpretation of the higher energy "in-in" xylene isomer (as arising solely from the repulsive CH⋅⋅⋅HC contact) with respect to the corresponding global-minimum "out-out" configuration (where the clashing C-H bonds are tilted out) is misleading. It is demonstrated that the two hydrogen atoms engaged in the CH⋅⋅⋅HC contact in "in-in" are involved in attractive interaction so they cannot explain the lower stability of this isomer. We have proven, based on the arsenal of modern bonding descriptors (EDDB, HOMA, NICS, FALDI, ETS-NOCV, DAFH, FAMSEC, IQA), that in order to understand the relative stability of "in-in" versus "out-out" xylenes isomers one must consider the changes in the electronic structure encompassing the entire molecules as arising from the cooperative action of hyperconjugation, aromaticity and unintuitive London dispersion plus charge delocalization based intra-molecular CH⋅⋅⋅HC interactions.

Quantifying individual (anti)bonding molecular orbitals' contributions to chemical bonding.

The shapes of molecular orbitals (MOs) in polyatomic molecules are often difficult for meaningful chemical interpretations. We report protocols to quantify contributions made by individual orbitals (molecular canonical and natural) of classical bonding, non-bonding or anti-bonding nature to (i) electron density into the inter-nuclear region and (ii) diatomic electron delocalization, DI(A,B). In other words, these protocols universally explain orbital's inputs to two fundamental and energy-lowering mechanisms of chemical bonding (interactions) and ease the chemical interpretation of their character in polyatomic molecules. They reveal that the MO and real-space density descriptions of the interactions are equivalent and, importantly, equally apply to all atom-pairs regardless if they are involved in a highly attractive or repulsive interaction. Hence, they not only remove ambiguity in chemical bonding interpretations (based on either MO or electron density approaches) but also demonstrate complementarity between the two such seemingly different techniques. Finally, our approach challenges some classical assumptions about MOs, such as the role of core electrons, the degree of bonding in antibonding MOs and the relative importance of frontier orbitals. Just as an example, we show that orthodox antibonding orbitals can make a significant contribution of a bonding nature to a classical covalent bond or major contribution to DI(A,B) of an intramolecular and highly repulsive HH interaction.

A reaction energy profile and fragment attributed molecular system energy change (FAMSEC)-based protocol designed to uncover reaction mechanisms: a case study of the proline-catalysed aldol reaction.

A REP-FAMSEC (reaction energy profile-fragment attributed molecular system energy change) protocol designed to explain each consecutive energy change along the reaction pathway is reported. It mainly explores interactions between meaningful polyatomic fragments of a molecular system and, by quantifying energetic contributions, pin-points fragments (atoms) leading to or opposing a chemical change. Its usefulness is tested, as a case study, on the proline-catalysed aldol reaction for which a number of mechanisms have been debated for over four decades. The relative stability of S-proline conformers, their catalytic (in)activity and the superior affinity of the higher energy conformer to acetone is fully explained at atomic and molecular fragment levels, but still appealing to general chemist knowledge. We found that (i) contrary to the generally accepted view, CN-bond formation cannot be explained by the Nδ-, Cδ+ atom pair, but rather by the O-atom of acetone and its strongest inter-molecular attractive interactions with the N-atom as well as the C-atom of the COO group of proline (at this initial stage the lower energy conformer of proline is eliminated) and (ii) the following 'first' H-transfer from N to O atoms of the proline moiety is nearly energy-free even though initially the H-atom interacts three times stronger with the N- than O-atom; a full explanation of this phenomenon is provided.

Reliability of HF/IQA, B3LYP/IQA, and MP2/IQA data in interpreting the nature and strength of interactions.

Mainly focusing on the B3LYP level, the reliability of level of theory (LoT)-dependent IQA-defined energy terms (self- and additive atomic energies, interaction energy and its components) in interpreting interactions was investigated at three LoTs using default settings in AIMAll software explicitly implementing the actual B3LYP exchange-correlation functional. Reliability was quantified using relative errors (REs) defined as, for example, RE = B3LYP/IQA(computed) - B3LYP/IQA(expected), using reference CCSD/BBC1/IQA data to obtain the LoT/IQA(expected) terms. On average, B3LYP produced the most accurate IQA energies among the LoTs investigated, affording REs an order of magnitude smaller than those at the HF level. The B3LYP/IQA description of the O4H6 and O3O4 interactions in glycol conformers compared well with the CCSD/BBC1/IQA-generated picture. Exceptionally reliable data were obtained at the B3LYP level for changes in the IQA energies computed for structural changes in glycol. The FAMSEC-based interpretation produced exact qualitative description and perfectly quantitatively comparable values to CCSD/BBC1/IQA data. The ΔEIQA = ΔE criterion (representing changes between the final and any suitably selected initial structure of a molecular system) is reported to 'validate' or predict the usefulness of changes in the LoT/IQA computed energy terms with respect to interaction interpretability. This was supported by (i) the smallest errors in the IQA energy changes being obtained at MP2/Müller, despite EIQA largely overestimating E (by -170 kcal mol-1 due to large REs in self-atomic energies) and (ii) reasonable HF-generated FAMSEC descriptors, regardless of the largest REs in the HF/IQA data. Finally, adding Grimme's D3 empirical dispersion correction had no significant effect on the REs.

FALDI-based criterion for and the origin of an electron density bridge with an associated (3,-1) critical point on Bader's molecular graph.

The total electron density (ED) along the λ2 -eigenvector is decomposed into contributions which either facilitate or hinder the presence of an electron density bridge (DB, often called an atomic interaction line or a bond path). Our FALDI-based approach explains a DB presence as a result of a dominating rate of change of facilitating factors relative to the rate of change of hindering factors; a novel and universal criterion for a DB presence is, thus, proposed. Importantly, facilitating factors show, in absolute terms, a concentration of ED in the internuclear region as commonly observed for most chemical bonds, whereas hindering factors show a depletion of ED in the internuclear region. We test our approach on four intramolecular interactions, namely (i) an attractive classical H-bond, (ii) a repulsive O⋅⋅⋅O interaction, (iii) an attractive Cl⋅⋅⋅Cl interaction, and (iv) an attractive CH⋅⋅⋅HC interaction. (Dis)appearance of a DB is (i) shown to be due to a "small" change in molecular environment and (ii) qualitatively and quantitatively linked with specific atoms and atom-pairs. The protocol described is equally applicable (a) to any internuclear region, (b) regardless of what kind of interaction (attractive/repulsive) atoms are involved in, (c) at any level of theory used to compute the molecular structure and corresponding wavefunction, and (d) equilibrium or nonequilibrium structures. Finally, we argue for a paradigm shift in the description of chemical interactions, from the ED perspective, in favor of a multicenter rather than diatomic approach in interpreting ED distributions in internuclear regions. © 2018 Wiley Periodicals, Inc.

Exact and exclusive electron localization indices within QTAIM atomic basins.

Novel measures of electron (de)localization within the Quantum Theory of Atoms in Molecules (QTAIM) atomic basins are presented which, unlike orthodox localization indices (LIs), are fully exclusive and can be easily visualized. This work shows that QTAIM-defined LIs describe a portion of interatomic delocalized electrons; hence, the chemical/physical interpretation of orthodox LIs is misleading. Using the recently introduced Fragment, Atomic, Localized, Delocalized, and Interatomic (FALDI) density decomposition technique we derive two novel sets of LIs and delocalization indices (DIs), by accounting for the overlap between localized and delocalized density functions. The FALDI-based LIs and DIs perfectly recover chemically expected core and bonded electron count. Usefulness of new (de)localization indices and their 3D representations were demonstrated on a number of examples, including formamide and benzene. We therefore expect that the scheme reported in this work will provide a valuable stepping stone between classical conceptual chemistry and quantum chemical topology. © 2018 Wiley Periodicals, Inc.

FALDI-based decomposition of an atomic interaction line leads to 3D representation of the multicenter nature of interactions.

Atomic interaction lines (AILs) and the QTAIM's molecular graphs provide a predominantly two-center viewpoint of interatomic interactions. While such a bicentric interpretation is sufficient for most covalent bonds, it fails to adequately describe both formal multicenter bonds as well as many non-covalent interactions with some multicenter character. We present an extension to our Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) electron density (ED) decomposition scheme, with which we can measure how any atom-pair's delocalized density concentrates, depletes or reduces the electron density in the vicinity of a bond critical point. We apply our method on five classical bonds/interactions, ranging from formal either two- or three-center bonds, a non-covalent interaction (an intramolecular hydrogen bond) to organometallic bonds with partial multicenter character. By use of 3D representation of specific atom-pairs contributions to the delocalized density we (i) fully recover previous notion of multicenter bonding in diborane and predominant bicentric character of a single covalent CC bond, (ii) reveal a multicenter character of an intramolecular H-bond and (iii) illustrate, relative to a Schrock carbene, a larger degree of multicenter MC interaction in a Fischer carbene (due to a presence of a heteroatom), whilst revealing the holistic nature of AILs from multicenter ED decomposition. © 2018 Wiley Periodicals, Inc.

Reliability of interacting quantum atoms (IQA) data computed from post-HF densities: impact of the approximation used.

The performance of BBC1, BBC2 and Müller approximations, in terms of reliability of IQA data, was investigated at the CCSD, CCSD(T) and MP2 levels using glycol, as a case study, in interpreting the relative stability of its conformers, one with H-bond type intramolecular interaction and the other with a steric clash between two O-atoms. The CCSD/BBC1 level appeared to be perfectly suited as a reference needed to evaluate all possible levels of theory/approximation combinations (LoT/LoA). We found the reliability trend LoT/BBC1 > LoT/BBC2 > LoT/Müller (as well as its origin) and concluded that the Müller approximation should not be used when the accuracy of IQA-defined energy terms is considered. Moreover, we have established that the requirement of reproducing, by IQA calculations, electronic energy is desirable but not a necessary requirement when a comparative approach is used, such as in FAMSEC-based analysis (FAMSEC = fragment attributed molecular system energy change). A new criterion is proposed to assess the quality of IQA data for comparative analyses, ΔE(IQA) ≈ ΔE, where ΔE(IQA) and ΔE are the IQA and electronic energy differences, respectively, between the fin-state and ref-state of a molecular system. The closer ΔE(IQA) approaches ΔE, the closer the FAMSEC data approach values obtained at the exceptionally well performing CCSD/BBC1 level, regardless of the LoT/LoA combination used. Importantly, the MP2/BBC1 level performed nearly as well as the CCSD/BBC1 level in comparative studies. The origin of the MP2/BBC1 approximation's exceptional and the MP2/Müller approximations's acceptable performance in explaining the relative stability of glycol conformers has been uncovered and discussed in detail.

Gold(I) Hydrides as Proton Acceptors in Dihydrogen Bond Formation.

Wavefunction and DFT calculations indicate that anionic dihydride complexes of AuI form strong to moderate directed Au-H⋅⋅⋅H bonds with one or two HF, H2 O and NH3 prototype proton donor molecules. The largely electrostatic interaction is influenced by relativistic effects which, however, do not increase the binding energy. Very weak Au⋅⋅⋅H associations-exhibiting a corresponding bond path-occur between neutral AuH and HF units, although ultimately F becomes the preferred donor atom in the most stable structure. Increasing the hydridicity of AuH by attachment of an electron donating NHC ligand effects Au-H⋅⋅⋅H bonding of moderate strength only with HF, whereas competing Au⋅⋅⋅H interactions dominate for H2 O and NH3 . Rare η2 coordinated and HX (X=F or OH) associated H2 complexes are produced during interaction with a single ion of stronger acidity, H2 F+ or H3 O+ . Theoretically, reaction of excess [AuH2 ]- as proton acceptor with H3 O+ or NH4+ in 3:1 or 4:1 ionic ratios, respectively, affords H⋅⋅⋅H bonded analogues of Eigen-type adducts. Outstanding analytical relationships between selected bonding parameters support the integrity of the results.

Toward deformation densities for intramolecular interactions without radical reference states using the fragment, atom, localized, delocalized, and interatomic (FALDI) charge density decomposition scheme.

A novel approach for calculating deformation densities is presented, which enables to calculate the deformation density resulting from a change between two chemical states, typically conformers, without the need for radical fragments. The Fragment, Atom, Localized, Delocalized, and Interatomic (FALDI) charge density decomposition scheme is introduced, which is applicable to static electron densities (FALDI-ED), conformational deformation densities (FALDI-DD) as well as orthodox fragment-based deformation densities. The formation of an intramolecular NH⋅⋅⋅N interaction in protonated ethylene diamine is used as a case study where the FALDI-based conformational deformation densities (with atomic or fragment resolution) are compared with an orthodox EDA-based approach. Atomic and fragment deformation densities revealed in real-space details that (i) pointed at the origin of density changes associated with the intramolecular H-bond formation and (ii) fully support the IUPAC H-bond representation. The FALDI scheme is equally applicable to intra- and intermolecular interactions. © 2017 Wiley Periodicals, Inc.

Application of Protocols Devised to Study Bi(III) Complex Formation by Voltammetry: The Bi(III)-Picolinic Acid System.

Bi(III) coordination chemistry has been largely neglected due to the difficulties faced when studying these systems even though Bi(III) is used in various medicinal applications. This study of the Bi(III)-picolinic acid system by voltammetry applies the rigorous methodologies already developed to enable the study of Bi(III) systems starting in very acidic solutions to prevent precipitation. This includes calibrating the glass electrode accurately at these low pHs, compensating for the diffusion junction potential below pH 2 and determining the reduction potential of uncomplexed Bi(III) which cannot be directly measured. The importance of including nitrate from the background electrolyte as a competing species is highlighted, especially for data acquired below pH ∼ 2. From analysis of the voltammetric data, it was not clear whether a ML3OH species formed in solution or whether it was a combination of ML4 and ML4OH. Information from crystal structures and electrospray ionization-mass spectrometry measurements was thus used to propose the most probable species model. The log ß values determined were 7.77 ± 0.07 for ML, 13.89 ± 0.07 for ML2, 18.61 ± 0.01 for ML3, 22.7 ± 0.2 for ML4, and 31.4 ± 0.2 for ML4OH. Application of these methodologies thus opens the door to broaden our understanding of Bi(III) complexation.

On the Stability of Cis- and Trans-2-Butene Isomers. An Insight Based on the FAMSEC, IQA, and ETS-NOCV Schemes.

In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H-H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH-HC fragment (loc-FAMSEC = -3.6 kcal/mol) with most favourably changed intrafragment interactions on trans-eq→cis-eq. Moreover, lower stability of cis-eq vs. trans-eq is linked with the entire HCCH (ethylenic) fragment which destabilized cis-eq (mol-FAMSEC, +3.9 kcal/mol) the most. Although the H-H contact can be linked with smaller, relative to trans-, rotational energy barrier in cis-2-butene, we have proven that to rationalize this phenomenon one must account for changes in interactions between various fragments that constitute the entire molecule. Importantly, we discovered a number of comparable trends in fundamental properties of equivalent molecular fragments on a methyl group rotation; for example, interaction between BP-free H-atoms in trans-eq (involving CH bonds of the methyl and ethylenic units) and BP-linked H-atoms in cis-eq. Clearly, rotational energy barrier cannot be entirely (i) rationalized by the properties of or (ii) attributed to the H-H contact in cis-eq. © 2016 Wiley Periodicals, Inc.

Measurements and Modeling To Determine the Reduction Potential of Uncomplexed Bi(III) in Nitrate Solutions for Application in Bi(III)-Ligand Equilibria Studies by Voltammetry.

The free metal ion potential, E(M), is a critical parameter in the calculation of formation constants when using voltammetry. When studying complex formation of Bi(III), however, E(Bi) cannot be directly measured. In this work a nitrate background electrolyte was employed to obtain reversible reduction waves. To determine E(Bi), measurements have to be made below pH ∼ 2 before the bismuth-oxy-nitrate species precipitates and thus corrections for the diffusion junction potential (monitored using Tl(I) as an internal reference ion) must be made. Additionally shifts in potential due to both Bi(III) hydrolysis and Bi(III) nitrate formation must also be compensated for before E(Bi) can be evaluated. The value of E(Bi) was determined relative to E(Tl) so that in an experiments where ligand is added to determine formation constants, E(Bi) can be determined as accurately as possible (since E(Tl) can generally still be measured). The value of E(Bi) - E(Tl) was found to be 495.6 ± 1.4 mV for the conditions employed.