A theoretical study of protonation of triatomic silicon–carbon compounds

Ab initio molecular orbital methods are employed to study the low-lying states of C₃H⁺, SiC₂H⁺, Si₂CH⁺, and Si₃H⁺. Special attention is paid to a comparative study between C₃H⁺ and Si₃H⁺. In both cases a ³B₂ state is found to lie the lowest at the HF level, although inclusion of correlation effects favor a linear structure (¹Σ⁺ state) for C₃H⁺, which lies 25 kcal/mol below the ³B₂ state at the MP 4 level, and a bent structure (¹A′ state) for Si₃H⁺, which lies just 2 kcal/mol below the ³B₂ state. The proton affinities of C₃, SiC₂, Si₂C, and Si₃ are estimated at different levels of theory. Both protonation at carbon and silicon atoms are considered for SiC₂ and Si₂C. It is found that C₃ comparatively has a low proton affinity. On the other hand, Si₃ has a relatively high proton affinity compared with the protonation at silicon atom for both SiC₂ and Si₂C. These results are discussed on the basis of electronic structure arguments.     

Electron‐pair density decomposition for core–valence separable systems

The electron pair density of a core‐valence separable system can be decomposed into three parts: core‐core, core‐valence, and valence‐valence. The core‐core part has a Hartree‐Fock like structure. The core‐valence part can be written as Γ_cv (1,2) = γ_c (1,1)γ_v (2,2) ? γ_c (1,2)γ_v (2,1) + γ_c (2,2)γ_v (1,1) ? γ_c (2,1)γ_v (1,2), where only the 1‐matrices from the core and valence orbitals contribute. The valence‐valence part is left to be determined from the reduced frozen‐core type wave function, which often contains the essential information on the electron correlation and the chemical bond. We demonstrate the analysis to the ground state of negative ion Li^? and 2¹Σ_u⁺ excited state of the Li₂ molecule. © 2012 Wiley Periodicals, Inc.     

Chemical potential of triatomic polar liquids; a computer simulation study

The chemical potential of liquid sulphur dioxide and liquid water is investigated by molecular dynamics simulation. The calculation is based upon the Widom test-particle method. An empirical procedure is applied in order to reduce drastically the computing time needed to sample the computer-generated configurations. The influence of the choice of the effective pair potential is discussed.     

Quantum mechanical calculations of vibrational transition probabilities in collinear atom–triatom collisions

Quantum mechanical calculations have been made of vibrational transition probabilities in the collinear collision of an inert gas atom with either CO₂ or OCS. The dependence of the transition probability on the relative translational energy and the reduced mass is similar to that found for atom–diatom collisions. The transition P_{00 → 10} (excitation of the first stretching mode) is much greater than P_{00 → 01} (the second stretching mode). This is largely due to the difference in frequencies but it has been shown that there is an independent mass factor responsible for this difference.     

Quantum mechanical study of a reaction path bifurcation model

The feasibility of close coupling techniques for bifurcation processes is investigated using a simple model. Density contours and a flux map illustrate the bifurcation process. The relevance of this study to the theory of three-dimensional chemical reactions is discussed.     

Quantum mechanical study of tautomerism of methimazole and the stability of methimazole–I2 complexes

DFT and ab initio theoretical methods were used to calculate the relative stability of tautomers in the methimazole (MMI). The calculations show that the thione form of MMI 1 is more stable than the thiol tautomer in good agreement with the experimental results. The DFT and ab initio calculations were also used to determine the stability of MMI–I₂ complexes. All methods suggest that the methimazole in the MMI–I₂ complex exists almost exclusively as the thione tautomer. The Gibbs free energy difference between planar and perpendicular forms of thione tautomer of MMI–I₂ complex indicates that the planar form is the predominant complex. The counterpoise corrected Gibbs free energy also shows that the MMI–I₂(plan.) complex is more stable than the MMI–I₂(perp.) complex. These predictions are in good agreement with the experimental results. By using the natural bond orbital (NBO) approach, the effects of charge transfer interactions on the stability of MMI–I₂ complexes were investigated. The LP₃(S)→σ*(I–I) and LP₃(I)→σ*(N–H) charge transfer interactions may be very important in the stability of the planar form. The results show that the LP₃(S)→σ*(I–I) charge transfer interaction causes a greater increase in the σ*(I–I) antibond occupation number, and concomitantly, a greater increase in the corresponding I–I bond length in the planar complex with respect to the perpendicular complex. The LP₃(S)→σ*(I–I) charge transfer interaction is assisted by NHI intermolecular hydrogen bonding. The atom in molecule (AIM) analysis shows that the charge density and its Laplacian at the SI bond critical point of the planar complex is greater than the perpendicular complex.     

Intervalence electron transfer through a thiolate bridge ligand: a Fe–S–R–Fe mixed valence complex

The reaction of Cp(dppe)FeI with the ligands 2,2′- and 4,4′-dithiobispyridine (S₂(Py)₂) give the mononuclear or binuclear complexes of the type [Cp(dppe)Fe-S₂(Py)₂]PF₆, [Cp(dppe)Fe---SPy]PF₆ or [{Cp(dppe)Fe}₂-μ-SPy](PF₆)₂ depending on the reaction condition. Reaction of Cp(dppe)FeI with dithiobispyridines in presence of TlPF₆ as halide abstractor and using CH₂Cl₂ as a solvent gives the complexes [Cp(dppe)Fe-4,4′-S₂(Py)₂)₂]PF₆ (1) and [CpFe(dppe)-2,2′-S₂(Py)₂]PF₆ (2) whereas the same reaction using CH₃OH as a solvent and NH₄PF₆ as the halide abstractor leads to the formation of the Fe^III–thiolate complex [Cp(dppe)Fe-2,2′-SPy]PF₆ (3) and the mixed-valence complex [Cp(dppe)Fe^III-μSPy-Fe^II(dppe)Cp](PF₆)₂ (4). Magnetic and ESR measurements are in agreement with one unpaired electron delocalized between them. Mössbauer data indicate clearly the presence of two different iron sites, each one of the N-bonded and S-bonded iron atoms, with intermediate oxidation state Fe^II---Fe^III. An electron transfer intervalence absorption was observed for this complex at 780 nm (in CH₂Cl₂). By applying the Hush theory the intervalence parameters were obtained; =0.028, H_ab=361 cm⁻¹ which indicate Class II Robin–Day. Estimation of the rate electron transfer affords a value k_th=6.5×10⁶ s⁻¹. Solvent effect on the intervalence transition follow the Hush prediction for high dielectric constants solvents which permit the evaluation of the outer and inner-sphere reorganizational parameters, which were analyzed and discussed. The electronic interaction parameters compare well with those found for electron transfer in metalloproteins.     

Alternant and non-alternant systems; valence bond analysis

The properties of the complete CI-matrix in a VB-formalism based on orthogonal (ized) orbitals allow for a direct demonstration of the difference between alternant and non-alternant systems, including the radical ions, carbenions and carbanions derived from them.     

Quantum investigation of linear triatomic exchange reactions. A computational method

The model hamiltonian for a linear triatomic exchange reaction is derived in natural reaction coordinates, and a method is developed to solved the system of wave equations in close coupling approximation. The interaction zone is divided into subintervals, in each of which the coefficients of the system are assumed to be constant; this assumption provides an exact analystical solution over the interval. Special boundary conditions which account for the derivatives of the coefficients are used to match the solutions for adjacent intervals. The method converges to the exact solution with an increasing number of intervals of decreasing length. Results obtained for certain model system illustrate the merits of the method and its convergence.     

Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis

We report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. The assigned role of Tyr728 differs from previous suggestions but is consistent with the established mechanism of other zinc proteases.     

Quantum mechanical study of the nonbonded forces in water-methanol complexes

The water-methanol dimer can adopt two possible configurations (WdM or MdW) depending on whether the water or the methanol acts as the hydrogen bond donor. The relative stability between the two configurations is less than 1 kcal/mol, and as a result, this dimer has been a challenging system to investigate using either theoretical or experimental techniques. In this paper, we present a systematic study of the dependence of the geometries, interaction energies, and harmonic frequencies on basis sets and treatment of electron correlation for the two configurations. At the highest theory level, MP2/aug-cc-pVQZ//MP2/aug-cc-pVTZ, interaction energies of -5.72 and -4.95 kcal/mol were determined for the WdM and MdW configurations, respectively, after correcting for basis set superposition error using the Boys-Bernardi counterpoise scheme. Extrapolating to the complete basis set limit resulted in interaction energies of -5.87 for WdM and -5.16 kcal/mol for MdW. The energy difference between the two configurations is larger than the majority of previously reported values, confirming that the WdM complex is preferred, in agreement with experimental observations. The effects that electron correlation have on the geometry were investigated by performing optimization at the MP2(full), MP4, and CCSD levels of theory. The approach trajectories for the formation of each dimer configuration are presented and the importance of these trajectories in the development of parameters for use in classical force fields is discussed.     

Excited vibrational states near dissociation in weakly bound triatomic systems

The vibrational motion of a weakly bound M₃ complex is investigated using hyperspherical coordinates and an adiabatic separation of the radial and angular motions within the molecule. It is shown that the vibrational energy levels near dissociation correlate to an M atom orbiting about a rotating M₂ core. Application is made to the neon trimer assuming an approximate pairwise additive potential.     

Quantum mechanical effects in acid–base chemistry

Acid–base chemistry has immense importance for explaining and predicting the chemical products formed by an acid and a base when mixed together. However, the traditional chemistry theories used to describe acid–base reactions do not take into account the effect arising from the quantum mechanical nature of the acidic hydrogen shuttling potential and its dependence on the acid base distance. Here, infrared and NMR spectroscopies, in combination with first principles simulations, are performed to demonstrate that quantum mechanical effects, including electronic and nuclear quantum effects, play an essential role in defining the acid–base chemistry when 1-methylimidazole and acetic acid are mixed together. In particular, it is observed that the acid and the base interact to form a complex containing a strong hydrogen bond, in which the acidic hydrogen atom is neither close to the acid nor to the base, but delocalized between them. In addition, the delocalization of the acidic hydrogen atom in the complex leads to characteristic IR and NMR signatures. The presence of a hydrogen delocalized state in this simple system challenges the conventional knowledge of acid–base chemistry and opens up new avenues for designing materials in which specific properties produced by the hydrogen delocalized state can be harvested.

Acid-based theories do not consider the quantum mechanical nature of the acidic hydrogen shuttling potential. Here, it is demonstrated that this particularity is needed to explain the formation acid-base complex with a delocalized acidic hydrogen.     

Influence of core–valence separation of electron localization function

The electron localization function (ELF) shows too-high values when computed from valence densities only (instead of using the total density). This effect is mainly found when d electrons are present in the outermost shell of the core. Although no pronounced qualitative differences could be noticed in the examples studied up to now, it is found that the quantitative differences between the values of ELF obtained from the valence densities only or from the total densities can be large. We also show, for the first time, an example (the Be atom) where ELF is obtained directly from the density. This exemplifies the possibility of computing ELF from highly accurate calculations (or from experimental data). © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1431–1439, 1997     

Quantum mechanical study on plasmon resonances in small ring clusters

The collectivity of the electronic motion in small sodium clusters with ring structure is studied by time‐dependent density functional theory. The formation and development of collective resonances in the absorption spectra were obtained as a function of the ring radius. In small ring clusters, besides the lower‐energy mode and the higher‐energy mode, there is another plasmon resonance mode, that is, the reverse two‐dipole mode. For the reverse two‐dipole mode, the formations of these two dipoles are due to the external field inducement and the shielding effect, although the resonant excitation is mainly due to the coupling effect of the electrons of these two dipoles. © 2012 Wiley Periodicals, Inc.     

Quantum mechanical study of stereoselectivity in the oxazaborolidine-catalyzed reduction of acetophenone

Chiral oxazaborolidines, known as CBS catalysts after the work of Corey, Bakshi and Shibata, are used for the stereoselective reduction of prochiral ketones to secondary chiral alcohols. Due to their relative low cost, ease of use, and high selectivity, their popularity has remarkably grown in the last 15 years. Oxazaborolidine-catalyzed reductions have been much studied, both experimentally and computationally, by means of semiempirical methods. Though, a more accurate high level quantum mechanical study on the complete system, capable of elucidating reliably the origins of stereoselectivity, is still lacking. Therefore, the acetophenone (PhMK) reduction with Corey's oxazaborolidine has been modeled for the first time with ab initio and DFT-B3LYP calculations on the complete system as well as with AM1. Calculations on the complexation of BH(3) to CBS, which can occur only in a cis fashion with respect to the hydrogen on the stereogenic C-4 carbon atom, have allowed us to confirm the great rigidity of Corey's catalyst, possibly determining its excellent enantioselectivity. Acetophenone-CBS-BH(3) complexes were characterized at various levels of theory, and it was found that the picture obtained depends heavily on the method adopted. A computational strategy for identifying the hydride transfer transition states of the competing pathways was developed and tested, using a model system for which the transition state geometry was already known. The application of the TS search method to the reduction of acetophenone allowed the characterization of the TS's for the competing pathways in this reaction, making it possible to predict with good quantitative accuracy the stereochemical outcome of the reaction at all the levels of theory adopted. The characterization of the intermediate oxazadiboretane products confirmed that the highly exothermic hydride transfer provides the thermodynamical drive for the reaction.     

Alcohols as electrophiles in C--C bond-forming reactions: the hydrogen autotransfer process

The hydrogen autotransfer process involves an initial oxidative hydrogen elimination, followed by different types of reactions, and is completed with a reductive hydrogen addition to give the final product. The sequence allows the alkylation of different nucleophilic agents using environmentally benign alcohols as electrophiles, mild conditions, and soft bases, with water produced as the only waste material. Recent examples of modulating the organometallic catalyst have also lent themselves to expansion of the range of available substrates, as described in this Minireview.     

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential with a recently developed semiempirical AM1/d-PhoT model for phosphoryl transfer reactions. Simulations are used to derive one- and two-dimensional potentials of mean force to examine specific reaction paths and assess the feasibility of proposed general acid and base mechanisms. Density-functional calculations of truncated active site models provide complementary insight to the simulation results. Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphorylation are presented, and the roles of A38 and G8 as general acid and base catalysts are discussed. The computational results are consistent with available experimental data, provide support for a general acid/base mechanism played by functional groups on the nucleobases, and offer important insight into the ability of RNA to act as a catalyst without explicit participation by divalent metal ions.     

Phase equilibria in polymer–liquid–liquid systems

The phase equilibria in polymer–liquid 1–liquid 2 ternary systems have been calculated on the basis of the Flory-Huggins theory of polymer solutions. A new approximation method based on the “cluster” concept has been introduced for mixed solvents comprising a solvent and a nonsolvent. This concept has been verified with polystyrene–solvent–methanol systems.