Ab Initio Protocol Research Articles

Quantum Chemical Study of the Acrolein (CH2CHCHO) + OH + O2 Reactions

Acrolein, a beta-unsaturated (acrylic) aldehyde, is one of the simplest multifunctional molecules, containing both alkene and aldehyde groups. Acrolein is an atmospheric pollutant formed in the photochemical oxidation of the anthropogenic VOC 1,3-butadiene, and serves as a model compound for methacrolein (MACR) and methyl vinyl ketone (MVK), the major oxidation products of the biogenic VOC isoprene. In addition, acrolein is involved in combustion and biological oxidation processes. This study presents a comprehensive theoretical analysis of the acrolein + OH + O(2) addition reactions, which is a key photochemical oxidation sequence, using the G3SX and CBS-QB3 theoretical methods. Both ab initio protocols provide relatively similar results, although the CBS-QB3 method systematically under-predicts literature heats of formation using atomization enthalpies, and also provides lower transition state barrier heights. Several new low-energy pathways for unimolecular reaction of the acrolein-OH-O(2) radicals are identified, with energy at around or below that of the acrolein-OH isomers + O(2). In each case these novel reactions have the potential to reform the hydroxyl radical (OH) and form coproducts that include glyoxal, glycolaldehyde (HOCH(2)CHO), formaldehyde (HCHO), CO, and substituted epoxides. Analogous reaction schemes are developed for the photochemical oxidation of MACR and MVK, producing a number of observed oxidation products. The reaction MACR + OH + O(2) --> hydroxyacetone + OH + CO is expected to be of particular importance. This study also proposes that O(2) addition to chemically activated acrolein-OH adducts can provide prompt regeneration of OH in the atmospheric oxidation of acrolein, via a double activation mechanism. This mechanism can also be extended to isoprene, MVK, and MACR. The importance of the novel chemistry revealed here in the atmospheric oxidation of acrolein and other structurally related OVOCs and VOCs requires further investigation. Additionally, a critical evaluation of the acrolein heat of formation is presented, and a new value of -16.7 +/- 1.0 kcal mol(-1) is recommended along with other thermochemical properties, from a W1 level calculation.

First‐Principles Prediction of Nucleophilicity Parameters for π Nucleophiles: Implications for Mechanistic Origin of Mayr’s Equation

Quantitative nucleophilicity scales are fundamental to organic chemistry and are usually constructed on the basis of Mayr's equation [log k=s(N+E)] by using benzhydrylium ions as reference electrophiles. Here an ab initio protocol was developed for the first time to predict the nucleophilicity parameters N of various pi nucleophiles in CH(2)Cl(2) through transition-state calculations. The optimized theoretical model (BH&HLYP/6-311++G(3df,2p)//B3LYP/6-311+G(d,p)/PCM/UAHF) could predict the N values of structurally unrelated pi nucleophiles within a precision of ca. 1.14 units and therefore may find applications for the prediction of nucleophilicity of compounds that are not readily amenable to experimental characterization. The success in predicting N parameters from first principles also allowed us to analyze in depth the electrostatic, steric, and solvation energies involved in electrophile-nucleophile reactions. We found that solvation does not play an important role in the validity of Mayr's equation. On the other hand, the correlations of the E, N, and log k values with the energies of the frontier molecular orbitals indicated that electrostatic/charge-transfer interactions play vital roles in Mayr's equation. Surprising correlations observed between the electrophile-nucleophile C-C distances in the transition state, the activation energy barriers, and the E and N parameters indicate the importance of steric interactions in Mayr's equation. A method is then proposed to separate the attraction and repulsion energies in the nucleophile-electrophile interaction. It was found that the attraction energy correlated with N+E, whereas the repulsion energy correlated to the s parameter.

Accurate Simulation of Optical Properties in Dyes

Since Antiquity, humans have produced and commercialized dyes. To this day, extraction of natural dyes often requires lengthy and costly procedures. In the 19th century, global markets and new industrial products drove a significant effort to synthesize artificial dyes, characterized by low production costs, huge quantities, and new optical properties (colors). Dyes that encompass classes of molecules absorbing in the UV-visible part of the electromagnetic spectrum now have a wider range of applications, including coloring (textiles, food, paintings), energy production (photovoltaic cells, OLEDs), or pharmaceuticals (diagnostics, drugs). Parallel to the growth in dye applications, researchers have increased their efforts to design and synthesize new dyes to customize absorption and emission properties. In particular, dyes containing one or more metallic centers allow for the construction of fairly sophisticated systems capable of selectively reacting to light of a given wavelength and behaving as molecular devices (photochemical molecular devices, PMDs).Theoretical tools able to predict and interpret the excited-state properties of organic and inorganic dyes allow for an efficient screening of photochemical centers. In this Account, we report recent developments defining a quantitative ab initio protocol (based on time-dependent density functional theory) for modeling dye spectral properties. In particular, we discuss the importance of several parameters, such as the methods used for electronic structure calculations, solvent effects, and statistical treatments. In addition, we illustrate the performance of such simulation tools through case studies. We also comment on current weak points of these methods and ways to improve them.

Ab Initio Calculations of pKaValues of Transition-Metal Hydrides in Acetonitrile

A well-defined ab initio protocol was developed which could be used to calculate the pKa values of a variety of transition-metal hydrides in acetonitrile with a precision of 1.5 pKa units. The gas-phase energies were calculated using a two-layer ONIOM method where the core layer was handled by the CCSD(T) theory. In addition, the C-PCM solvation model previously developed for small organic molecules was confirmed to be reliable for predicting the solvation energies of bulky organometallic complexes. Using the protocol, we studied the structure−property relationships for the acidities of the Fe-, Co-, and Ni-group metal hydrides. It was found that the pKa values of these hydrides varied considerably with respect to the metal centers. The third-row metal hydrides always appeared to be the least acidic, as compared to the first- and second-row metal hydrides. On the other hand, the relative acidity between the first- and second-row metal hydrides was strongly dependent on the chemical formulas of the metal complexes. Finally, linear correlations were observed between the pKa values of metal hydrides and the NBO (natural bond orbital) charges carried by the chelating phosphorus atoms.

First-principle predictions of basicity of organic amines and phosphines in acetonitrile

Amines and phosphines are widely utilized as bases and basic organocatalysts in organic chemistry. Thus it is highly valuable to develop a coherent theoretical method that can accurately predict the basicity of structurally unrelated amines and phosphines in organic solvents from the first principles. Herein we developed the first ab initio protocol that could predict the p K a value of any protonated amine or phosphine in acetonitrile through systematic benchmarking. By comparing to a variety of available experimental data (total number=98), it was determined that the precision of the optimized method in basicity prediction was as low as 1.1 p K a unit. With the powerful new method in hand, we subsequently conducted some systematic studies about the basicity of organic amines and in particular phosphines, for which very few experimental data were available. It was found that the solvent exerted profound effects on the basicity of amines and phosphines. Accordingly we concluded that it was not valid to use gas-phase data to interpret the solution-phase basicity of amines and phosphines. Next we reported the basicity of a number of synthetically important aliphatic and aromatic amines and phosphines in acetonitrile. We also compared, for the first time, the α-substituent effects on the basicity of aliphatic amines and phosphines and the remote substituent effects on the basicity of aromatic amines and phosphines. Finally, we studied for the first time the basicity of cyclic amines and phosphines. It was found that the ring strain exerted some interesting effects on the basicity of amines and phosphines.

Fomenting proton anisochronicity in the CH2D group.

A novel C-D...N interaction promotes an equilibrium isotope effect that causes a large chemical shift difference (43 ppb, 22 degrees C) for the diastereotopic methyl protons in the (N-CH2D)-(-)-isosparteinium cation. The observed chemical shift difference is in surprising agreement with a prediction of 44 ppb based upon an ab initio protocol. These calculations are also shown to reproduce the experimental shift difference in Anet's alpha-deutero-1,2-dimethylpiperidine (theory, 17 ppb; experiment, 14 ppb). The isosparteine-derived system described herein may provide an improved method for assigning the configuration and enantiomeric purity of stereogenic methyl groups (R-CHDT) by tritium NMR spectroscopy.

Ab initio protein structure prediction: progress and prospects.

Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work.

Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation.

The effects of different non-bonded parameters of force fields for NMR structure calculation on the quality of the resulting NMR solution structures were investigated using Interleukin 4 as a model system. NMR structure ensembles were calculated with an ab initio protocol using torsion angle dynamics. The calculations were repeated with five different non-bonded energy functions and parameters. The resulting ensembles were compared with the available X-ray structures, and their quality was assessed with common structure validation programs. In addition, the impact of torsion angle restraints and dihedral energy terms for the sidechains and the backbone was studied. The further improvement of the quality by refinement in explicit solvent was demonstrated. The optimal parameters, including those necessary for water refinement, are available in the new version of the PARALLHDG force field.