Ambident Nucleophilic Substitution: Understanding Non-HSAB Behavior through Activation Strain and Conceptual DFT Analyses

The ability to understand and predict ambident reactivity is key to the rational design of organic syntheses. An approach to understand trends in ambident reactivity is the hard and soft acids and bases (HSAB) principle. The recent controversy over the general validity of this principle prompted us to investigate the competing gas-phase S_N2 reaction channels of archetypal ambident nucleophiles CN⁻, OCN⁻, and SCN⁻ with CH₃Cl (S_N2@C) and SiH₃Cl (S_N2@Si), using DFT calculations. Our combined analyses highlight the inability of the HSAB principle to correctly predict the reactivity trends of these simple, model reactions. Instead, we have successfully traced reactivity trends to the canonical orbital-interaction mechanism and the resulting nucleophile–substrate interaction energy. The HOMO–LUMO orbital interactions set the trend in both S_N2@C and S_N2@Si reactions. We provide simple rules for predicting the ambident reactivity of nucleophiles based on our Kohn–Sham molecular orbital analysis.     

基于概念密度泛函理论磷酸酯类反应性物质毒性预测

磷酸酯类反应性物质是乙酰胆碱酯酶不可逆抑制剂。本文应用概念密度泛函理论(CDFT),采用四组条件(B3LYP/6-311++G(2d, 3p)/gas,B3LYP/6-311++G(2d, 3p)/CPCM/water,MP2/6-311++G(2d, 3p)/gas,MP2/6-311++ G(2d, 3p)/CPCM/water),对20多个磷酸酯反应性物质进行反应性描述指数计算,包括分子的化学势μ,绝对硬度η、亲电性指数ω、分子的前线轨道能量等分子整体描述参数,以及原子福井函数、自然键轨道(NBO)电荷、Wiberg键级、NBO键级等分子局域描述参数。通过对反应性描述指数以及定量构性关系(QSPR)方程预测结果的比较分析,得出结论：大多数化合物亲电进攻的反应中心发生在磷原子上;磷酸酯类化合物侧链乙胺基叔氮的质子化,将显著增强反应中心磷原子的亲电进攻能力;B3LYP/6-311++G(2d, 3p)/gas为最合理的计算条件;应用反应性描述指数建立的QSPR模型明显优于常规的2D-QSPR模型,能够用于乙酰胆碱酯酶不可逆抑制剂的精确毒性预测。     

Berberine alkaloid: Quantum chemical study of different forms by the DFT and MP2 methods

The stable structures and electronic properties for the berberine cation as well as possible ammonium, carbinol and amino-aldehyde forms of protoberberine salts in the presence of hydroxyl ions were investigated by the B3LYP/6-31G(d,p) and MP2/6-31++G(d,p) methods. The geometry optimizations by both methods lead to the nonplanar propeller-twisted and buckled structure for the all forms. The obtained bond lengths and bond angles agree with the experimental values. The comparison of total energies elucidates that the amino-aldehyde form is the most preferable tautomer in gas phase, while the carbinol form is less stable. The least stable tautomer is the ammonium form.     

Quantum chemical DFT calculations of the local structure of the hydrated electron and dielectron

The adiabatic bound state of an excess electron is calculated for a water cluster (H₂O) ₈ ^? in the gas phase using the DFT-B3LYP method with the extended 6-311++G(3df,3pd) basis set. For the liquid phase the calculation is performed in the polarizable continuum model (PCM) with regard to the solvent effect (water, ? = 78.38) in the supermolecule-continuum approximation. The value calculated by DFT-B3LYP for the vertical binding energy (VBE) of an excess electron in the anionic cluster (VBE(H₂O) ₈ ^? = 0.59 eV) agrees well with the experimental value of 0.44 eV obtained from photoelectron spectra in the gas phase. The VBE value of the excess electron calculated by PCM-B3LYP for the (H₂O) ₈ ^? cluster in the liquid phase (VBE = 1.70 eV) corresponds well to the absorption band maximum λ_max = 715 nm (VBE = 1.73 eV) in the optical spectrum of the hydrated electron hydr e _hydr ^? . Estimating the adiabatic binding energy (ABE)e _hydr ^t- in the (H₂O) ₈ ^? cluster (ABE = 1.63 eV), we obtain good agreement with the experimental free energy of electron hydration ΔG ₂₉₈ ⁰ (e _hydr ^? ) = 1.61 eV. The local model (H₂O) ₈ ^2? of the hydrated dielectron is considered in the supermolecule-continuum approximation. It is shown that the hydrated electron and dielectron have the same characteristic local structure: -O-H{↑}H-O- and -O-H{↑↓}H-O-respectively.     

GIAO/DFT evaluation of 13C NMR chemical shifts of selected acetals based on DFT optimized geometries

DFT/B3LYP calculations of the ground-state conformation of eight cyclic and acyclic acetals are presented and compared with experimental data. Results of single-point GIAO/DFT calculations at five different levels of theory show that isotropic shieldings need to be empirically scaled to achieve agreement with experimental chemical shifts. Statistical evaluation of data indicates that the most accurate prediction of 13C chemical shifts is achieved at the MPW1PW91/6-311G** level of theory. An empirical equation describing the relationship between delta values and shielding constants is postulated. This equation has been applied to the non-chair ground-state conformation of the six-membered acetonide and to the conformationally flexible benzodioxonine derivative. The agreement observed between the experimental and predicted chemical shifts shows that calculations at the MPW1PW91/6-311G** level of theory are adequate for addressing questions of conformation.     

Conceptual DFT properties‐based 3D QSAR: Analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme

Structure‐activity relationships of 46 P450 2A6 inhibitors were analyzed using the 3D‐QSAR methodology. The analysis was carried out to confront the use of traditional steric and electrostatic fields with that of a number of fields reflecting conceptual DFT properties: electron density, HOMO, LUMO, and Fukui f⁻ function as 3D fields. The most predictive models were obtained by combining the information of the electron density with the Fukui f⁻ function (r² = 0.82, q² = 0.72), yielding a statistically significant and predictive model. The generated model was able to predict the inhibition potencies of an external test set of five chemicals. The result of the analysis indicates that conceptual DFT‐based molecular fields can be useful as 3D QSAR molecular interaction fields. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

DFT and quantum chemical investigation of molecular properties of substituted pyrrolidinones

The DFT, quantum-chemical calculations and thermodynamics parameters of 1-{2-[(2-hydroxyethyl)thio]ethyl}pyrrolidin-2-one (HTEP); [2-(2-oxo-pyrrolidin-1-yl)-ethyl]-phosphonic acid diethyl ester (EOEP); {[2-(2-oxopyrrolidin-1-yl)ethyl]thio}acetic acid (OETA); (2-pyridin-4-yl-ethyl]thio}acetic acid (PTA) and pyridine (PY) have been calculated with Gaussian 94 and Hybrid B3LYP functional density with 6-31G* basis set. Moreover, the electronic properties such as highest occupied molecular orbital (HOMO), lowest unoccupied orbital (LUMO) energy and molecular densities have been investigated.     

A New View on the Spectrochemical and Nephelauxetic Series on the Basis of Spin‐Polarized Conceptual DFT

In a row: Chemical concepts from the spin‐polarized conceptual DFT field are used to explain the spectrochemical and nephelauxetic series within a group of ruthenium complexes.

     

Tuning the Halogen/Hydrogen Bond Competition: A Spectroscopic and Conceptual DFT Study of Some Model Complexes Involving CHF2I

Insight into the key factors driving the competition of halogen and hydrogen bonds is obtained by studying the affinity of the Lewis bases trimethylamine (TMA), dimethyl ether (DME), and methyl fluoride (MF) towards difluoroiodomethane (CHF₂I). Analysis of the infrared and Raman spectra of solutions in liquid krypton containing mixtures of TMA and CHF₂I and of DME and CHF₂I reveals that for these Lewis bases hydrogen and halogen‐bonded complexes appear simultaneously. In contrast, only a hydrogen‐bonded complex is formed for the mixtures of CHF₂I and MF. The complexation enthalpies for the C?H ??? Y hydrogen‐bonded complexes with TMA, DME, and MF are determined to be ?14.7(2), ?10.5(5) and ?5.1(6) kJ mol^?1, respectively. The values for the C?I ??? Y halogen‐bonded isomers are ?19.0(3) kJ mol^?1 for TMA and ?9.9(8) kJ mol^?1 for DME. Generalization of the observed trends suggests that, at least for the bases studied here, softer Lewis bases such as TMA favor halogen bonding, whereas harder bases such as MF show a substantial preference for hydrogen bonding.     

Understanding the Reactivity of Supported Late Transition Metals on a Bare Anatase (101) Surface: A Periodic Conceptual DFT Investigation

The rapidly growing interest for new heterogeneous catalytic systems providing high atomic efficiency along with high stability and reactivity triggered an impressive progress in the field of single-atom catalysis. Nevertheless, unravelling the factors governing the interaction strength between the support and the adsorbed metal atoms remains a major challenge. Based on periodic density functional theory (DFT) calculations, this paper provides insight into the adsorption of single late transition metals on a defect-free anatase surface. The obtained adsorption energies fluctuate, with the exception of Pd, between −3.11 and −3.80 eV and are indicative of a strong interaction. Depending on the considered transition metal, we could attribute the strength of this interaction with the support to i) an electron transfer towards anatase (Ru, Rh, Ni), ii) s-d orbital hybridisation effects (Pt), or iii) a synergistic effect between both factors (Fe, Co, Os, Ir). The driving forces behind the adsorption were also found to be strongly related to Klechkowsky's rule for orbital filling. In contrast, the deviating behaviour of Pd is most likely associated with the lower dissociation enthalpy of the Pd−O bond. Additionally, the reactivity of these systems was evaluated using the Fermi weighted density of states approach. The resulting softness values can be clearly related to the electron configuration of the catalytic systems as well as with the net charge on the transition metal. Finally, these indices were used to construct a model that predicts the adsorption strength of CO on these anatase-supported d-metal atoms. The values obtained from this regression model show, within a 95 % probability interval, a correlation of 84 % with the explicitly calculated CO adsorption energies.     

Quantum-chemical calculations of NMR chemical shifts of organic molecules: XII. Calculation of the 13C NMR chemical shifts of fluoromethanes at the DFT level

Calculation was carried out of chemical shifts in ¹³C NMR spectra for a series of fluoromethanes CH _n F_4?n (n = 0–4) by the methods of the electron density functional theory GIAO-DFT taking in consideration the solvent effect in the framework of the polarizable continuum model Tomasi IEF-PCM. The best results were obtained at the use of Keal-Tozer KT3 functional combined with Pople standard basis sets 6-311G(d,p) and 6-311++G(d,p), and also with Jensen special set pcS-2 containing tight p-functions. The optimum reference in the calculation of chemical shifts in ¹³C NMR spectra for the fluoromethanes series is TMS.     

On the chemical bonding features in palladium containing compounds: A combined QTAIM/DFT topological analysis

Topological analyses of the electron density on N-benzoyl-L-pheylalanine and its palladium(II) complexes are carried out using the quantum theory of atoms in molecules (QTAIM) at the M06/6-31G(d) theoretical level. The topological parameters derived from the Bader theory are also analyzed; these are characteristics of Pd bond critical points and ring critical points. The calculated structural parameters are the highest occupied molecular orbital energy (E _HOMO), the lowest unoccupied molecular orbital energy (E _LUMO), the hardness (η), the softness (S), the absolute electronegativity (χ), the electrophilicity index (ω), and the fractions of electrons transferred (ΔN) from ethylenediamine, 2,2′-bipyridine and 1,10-phenanthroline complexes to N-benzoyl-L-pheylalanine. The numerous correlations and dependences between the energy terms of the symmetry adapted perturbation theory approach, geometrical, topological, and energy parameters are detected and described.     

Cryptic functions of enzymes in chemical catalysis

Using a number of examples, this article demonstrates how the functional groups responsible for the catalytic activity of an enzyme must be studied within the context of the enzyme-substrate complex. Very often a substrate will actively cooperate with the enzyme to bring about its own transformation. The so-called cryptic functions of enzymes are considered in the case of seryl proteases which, according to the type of substrate or structural modification introduced in the enzyme, may exhibit esterase, amidase, protease, racemase or dehydratase activity. The cryptic functions may possess a physiological significance which reflects the evolutionary history of the protein. Alternatively they may offer a simple way of exploiting the enzymes as catalysts capable of taking part in the chemical reactions of biotechnological interest but little physiological importance.This work is dedicated to Prof.E. Wünsch (München) at the occasion of his 60^th birthday.     

DFT computational schemes for 15N NMR chemical shifts of the condensed nitrogen-containing heterocycles

A systematic density functional theory (DFT) study of the accuracy factors (functionals, basis sets, and solvent effects) for the computation of ¹⁵N NMR chemical shifts has been performed in the series of condensed nitrogen-containing heterocycles. The behavior of the most representative functionals was examined based on the benchmark calculations of ¹⁵N NMR chemical shifts in the reference set of compounds. It was found that the best agreement with experiment was achieved with OLYP functional in combination with aug-pcS-3(N)//pc-2 locally dense basis set scheme providing mean absolute error of 5.2 ppm in the range of about 300 ppm. Taking into account solvent effects was performed within a general Tomasi's polarizable continuum model scheme. It was also found that computationally demanding supermolecular solvation model computations essentially improved some “difficult” cases, as was illustrated with phenanthroline dissolved in methanol. Based on the performed calculations, some 200 unknown ¹⁵N NMR chemical shifts were predicted with a high level of confidence for about 50 real-life condensed nitrogen-containing heterocycles, which could serve as a practical guide in structural elucidation of this class of compounds.     

Co-adsorption NO and organic molecules on Cu sites in zeolites: Quantum chemical DFT calculations

The co-adsorption of organic molecules: acetone, formaldehyde, ethene and acetylene together with NO on the same Cu⁺ site in zeolite CuZSM-5 was investigated by DFT calculations. The aim of this study was to follow the effect of NO on activation of multiple bonds in organic molecules and the effect of organic molecules on the activation of NO bond. The extent of activation of CO, CC, CC as well as of NO bonds was characterized by the result of calculation as the elongation of the multiple bonds, decrease of bond order as the decrease of stretching frequency, while population analysis gave information on the mechanism of activation. It has been found that the presence of NO co-adsorbed on the same Cu⁺ site as organic molecule resulted in more effective activation of CO bond in acetone and formaldehyde, but resulted in a less effective activation of CC and CC bond in ethane and acetylene. On the other hand, the presence of organic molecule resulted in more effective activation of NO bond (more important bond weakening) in NO molecule. The most significant NO bond weakening took place if NO was co-adsorbed with acetone or formaldehyde. Both acetone and formaldehyde transmit the most negative charge to the Cu⁺-zeolite system if adsorbed “solo” in Cu-zeolite. This negative charge may be next transmitted to antibonding NO orbitals resulting in so important NO bond weakening.     

Structure of irradiated polytetrafluoroethylene according to DFT calculations of NMR chemical shifts

Methods of density functional theory were used to calculate ¹H, ¹³C, and ¹⁹F magnetic shielding tensors for C₇F_nH_mO_l model molecules, which can arise as fragments from radiation exposure of polytetrafluoroethylene.     

LOBSTER: A tool to extract chemical bonding from plane‐wave based DFT

The computer program LOBSTER (Local Orbital Basis Suite Towards Electronic‐Structure Reconstruction) enables chemical‐bonding analysis based on periodic plane‐wave (PAW) density‐functional theory (DFT) output and is applicable to a wide range of first‐principles simulations in solid‐state and materials chemistry. LOBSTER incorporates analytic projection routines described previously in this very journal [J. Comput. Chem. 2013 , 34, 2557] and offers improved functionality. It calculates, among others, atom‐projected densities of states (pDOS), projected crystal orbital Hamilton population (pCOHP) curves, and the recently introduced bond‐weighted distribution function (BWDF). The software is offered free‐of‐charge for non‐commercial research. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

One-electron reduction of 8-bromo-2-aminoadenosine in the aqueous phase: radiation chemical and DFT studies of the mechanism

Two tautomeric forms of one-electron oxidized 2-aminoadenosine (2AA) have been produced by reactions of hydrated electrons (e aq-) with 8-bromo-2-aminoadenosine (8-Br-2AA) at natural pH, whereas only one tautomer is formed by oxidation of 2AA. Tailored experiments by pulse radiolysis and time-dependent DFT (TD-B3LYP/6-311G**//B1B95/6-31+G**) calculations allowed the definition of the reaction mechanism in some detail. The electron adducts of 8-Br-2AA protonated at C8 eject Br- and produce the two short-lived tautomers (8 and 9). The first observable species decays by first-order kinetics to produce the second intermediate, which is also obtained by oxidation of 2AA by SO4*-. The rate of tautomerization (k taut = 4.5 x 104 s-1) is strongly accelerated by phosphate and is retarded in D2O (kinetic isotope effect 7). B1B95/6-31+G** calculations showed that the tautomerization is a water-assisted process. In acidic or basic solutions, the "instantaneous" formation of one-electron oxidized 2AA or its deprotonated forms has been produced by reactions of e aq- with 8-Br-2AA. gamma-Radiolysis of 8-Br-2AA in aqueous solutions followed by product studies led to the formation of 2AA as a single product.