亚烷基卡宾及取代亚烷基卡宾与环硫乙烷反应的量子化学研究

用量子化学的密度泛函理论(DFT)在6-311G(d, p)水平上对亚烷基卡宾及取代亚烷基卡宾与环硫乙烷的硫转移反应机理进行了系统的研究. 用IRC对过渡态进行了确认. 并用组态混合模型讨论了反应势垒(ΔE^≠)与XYC＝C的单-三态能量差ΔE_ST之间的关系. 结果表明, 取代基的电负性是控制反应的主要因素, 取代基的电负性越大, 取代基越多, π电子给予体越多, 单-三态能量差ΔE_ST就越小, 该反应的活化能就越小, 反应越容易发生. 同时还讨论了该反应中环硫乙烷的C—S键的解离过程. 并与标题化合物和环氧乙烷的氧转移反应进行了比较.     

A reliable and efficient first principles‐based method for predicting pKa values. 4. organic bases

The ionization (dissociation) constant (pK_a) is one of the most important properties of a drug molecule. It is reported that almost 68% of ionized drugs are weak bases. To be able to predict accurately the pK_a value(s) for a drug candidate is very important, especially in the early stages of drug discovery, as calculations are much cheaper than determining pK_a values experimentally. In this study, we derive two linear fitting equations (pK_a = a × ΔE + b; where a and b are constants and ΔE is the energy difference between the cationic and neutral forms, i.e., ΔE = E_neutral?E_cationic) for predicting pK_as for organic bases in aqueous solution based on a training/test set of almost 500 compounds using our previously developed protocol (OLYP/6‐311+G**//3‐21G(d) with the the conductor‐like screening model solvation model, water as solvent; see Zhang, Baker, Pulay, J. Phys. Chem. A 2010 , 114, 432). One equation is for saturated bases such as aliphatic and cyclic amines, anilines, guanidines, imines, and amidines; the other is for unsaturated bases such as heterocyclic aromatic bases and their derivatives. The mean absolute deviations for saturated and unsaturated bases were 0.45 and 0.52 pK_a units, respectively. Over 60% and 86% of the computed pK_a values lie within ±0.5 and ±1.0 pK_a units, respectively, of the corresponding experimental values. The results further demonstrate that our protocol is reliable and can accurately predict pK_a values for organic bases. © 2012 Wiley Periodicals, Inc.     

Novel Bonding Character of the Cyclic AlS2 and GaS2 Systems

The geometries, the harmonic vibrational frequencies and the bonding properties have been predicted for cyclic AlS2 and GaS₂ species at the density functional theory (DFT), MPn (n = 2, 3, 4), QCISD(T) and CCSD(T) levels with 6‐311 + G (2df) basis set. The novel bonding character was discussed.     

Accurate prediction of proton chemical shifts. II. Peptide analogues

Proton chemical shifts of eight cyclic amide molecules were measured in DMSO and D2O solutions. The magnetic shieldings of the corresponding aliphatic, aromatic, and amide protons were calculated by Hartree-Fock and DFT, using the 6-311G**, 6-311++G**, and TZVP basis sets. For aliphatic protons, all of these methods reproduce the experimental values in DMSO solutions excellently after linear regression. The Hartree-Fock method tends to give slightly better agreement than DFT. The best performance is given by the HF/6-311G** method, with an rms deviation of 0.068 ppm. The deviations from experimental chemical shifts in D2O solutions are only slightly larger than those in DMSO solutions. This suggests that we can use the calculated gas phase proton chemical shifts directly to predict experimental data in various solvents, including water. For amide protons, which exchange with water and form hydrogen bonds with DMSO, only modest agreement is obtained, as expected. The present studies confirm that the GIAO approach can reach high accuracy for the relative chemical shifts of aliphatic and aromatic protons at a low cost. Such calculations may provide constraints for the conformational analysis of proteins and other macromolecules.     

Quantum chemical study on the abstraction reaction of alkylidenegermylene with oxirane and thiirane

The mechanisms of theion reaction of alkylidenegermylene with oxirane and thiirane have been characterized detail in using density functional theory, as well as ab initio method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies were calculated by CCSD(T)/6-311G(d)//B3LYP/6-311G(d,p) method for the involved conformations. The results show that the reaction pathways for both reactions consist of two ways: (1) the reactants can yield bent products (P1; P4) by syn-isomers; (2) the reactants can also yield three-membered products (P2; P5) by anti-isomers, which then further react with oxirane and thiirane to form the ultimate products (P3-1, P3-2; P6). Furthermore, a comparison with alkylidenecarbene, oxirane, and thiirane was done.     

Excited-state properties and environmental effects for protonated schiff bases: a theoretical study.

Complete active space self-consistent field (CASSCF), multireference configuration interaction (MRCI), density functional theory (DFT), time dependent DFT (TDDFT) and the singles and doubles coupled-cluster (CC2) methodologies have been used to study the ground state and excited states of protonated and neutral Schiff bases (PSB and SB) as models for the retinal chromophore. Systems with two to four conjugated double bonds are investigated. Geometry relaxation effects are studied in the excited pipi* state using the aforementioned methods. Taking the MRCI results as reference we find that CASSCF results are quite reliable even though overshooting of geometry changes is observed. TDDFT does not reproduce bond alternation well in the pipi* state. CC2 takes an intermediate position. Environmental effects due to solvent or protein surroundings have been studied in the excited states of the PSBs and SBs using a water molecule and solvated formate as model cases. Particular emphasis is given to the proton transfer process from the PSB to its solvent partner in the excited state. It is found that its feasibility is significantly enhanced in the excited state as compared to the ground state, which means that a proton transfer could be initiated already at an early step in the photodynamics of PSBs.     

A theoretical study of the structure and bonding of UOX4 (X = F, Cl, Br, I) molecules: the importance of inverse trans influence.

During nitroxide-mediated polymerization (NMP) in the presence of a nitroxide R2(R1)NO*, the reversible formation of N-alkoxyamines [P-ON(R1)R2] reduces significantly the concentration of polymer radicals (P*) and their involvement in termination reactions. The control of the livingness and polydispersity of the resulting polymer depends strongly on the magnitude of the bond dissociation energy (BDE) of the C-ON(R1)R2 bond. In this study, theoretical BDEs of a large series of model N-alkoxyamines are calculated with the PM3 method. In order to provide a predictive tool, correlations between the calculated BDEs and the cleavage temperature (T(c)), and the dissociation rate constant (k(d)), of the N-alkoxyamines are established. The homolytic cleavage of the N-OC bond is also investigated at the B3P86/6-311++G(d,p)//B3LYP/6-31G(d), level. Furthermore, a natural bond orbital analysis is carried out for some N-alkoxyamines with a O-C-ON(R1)R2 fragment, and the strengthening of their C-ON(R1)R2 bond is interpreted in terms of stabilizing anomeric interactions.     

Interaction Modes and Absolute Affinities of α‐Amino Acids for Mn2+: A Comprehensive Picture

Manganese is involved as a cofactor in the activation of numerous enzymes as well as the oxygen‐evolving complex of photosystem II. Full understanding of the role played by the Mn²⁺ ion requires detailed knowledge of the interaction modes and energies of manganese with its various environments, a knowledge that is far from complete. To bring detailed insight into the local interactions of Mn in metallopeptides and proteins, theoretical studies employing first‐principles quantum mechanical calculations are carried out on [Mn‐amino acid]²⁺ complexes involving all 20 natural α‐amino acids (AAs). Detailed investigation of [Mn‐serine]²⁺_, [Mn‐cysteine]²⁺, [Mn‐phenylalanine]²⁺, [Mn‐tyrosine]²⁺, and [Mn‐tryptophan]²⁺ indicates that with an electron‐rich side chain, the most stable species involves interaction of Mn²⁺ with carbonyl oxygen, amino nitrogen, and an electron‐rich section of the side chain of the AA in its canonical form. This is in sharp contrast with aliphatic side chains for which a salt bridge is formed. For aromatic AAs, complexation to manganese leads to partial oxidation as well as aromaticity reduction. Despite multisite binding, AAs do not generate strong enough ligand fields to switch the metal to a low‐ or even intermediate‐spin ground state. The affinities of Mn²⁺ for all AAs are reported at the B3LYP and CCSD(T) levels of theory, thereby providing the first complete series of affinities for a divalent metal ion. The trends are compared with those of other cations for which affinities of all AAs have been previously obtained.     

Computational Prediction of 1H and 13C NMR Chemical Shifts for Protonated Alkylpyrroles: Electron Correlation and Not Solvation is the Salvation

Prediction of chemical shifts in organic cations is known to be a challenge. In this article we meet this challenge for α-protonated alkylpyrroles, a class of compounds not yet studied in this context, and present a combined experimental and theoretical study of the ¹³C and ¹H chemical shifts in three selected pyrroles. We have investigated the importance of the solvation model, basis set, and quantum chemical method with the goal of developing a simple computational protocol, which allows prediction of ¹³C and ¹H chemical shifts with sufficient accuracy for identifying such compounds in mixtures. We find that density functional theory with the B3LYP functional is not sufficient for reproducing all ¹³C chemical shifts, whereas already the simplest correlated wave function model, Møller–Plesset perturbation theory (MP2), leads to almost perfect agreement with the experimental data. Treatment of solvent effects generally improves the agreement with experiment to some extent and can in most cases be accomplished by a simple polarizable continuum model. The only exception is the NH proton, which requires inclusion of explicit solvent molecules in the calculation.     

Planarized Intramolecular Charge Transfer: A Concept for Fluorophores with both Large Stokes Shifts and High Fluorescence Quantum Yields

Fluorophores were successfully used in several areas of chemistry and biochemistry. For many purposes, however, it is necessary that the fluorescence compound features a high fluorescence quantum yield as well as a large Stokes shift. The latter is, for example, achieved by the use of a twisted intramolecular charge‐transfer (TICT) compound, which shows a twisted geometry in the excited state. However, the higher the twisting is, the lower becomes in general the fluorescence quantum yield as the resulting emission from the twisted state is forbidden. In order to escape this dilemma, we propose the model of planarized intramolecular charge‐transfer (PLICT) states. These compounds are completely twisted in the ground states and planar in the excited states. By means of quantum chemical calculations (time‐dependent (TD)‐B3LYP and CC2) and experimental studies, we could demonstrate that 1‐aminoindole and its derivatives form photoinduced PLICT states. They show both very large Stokes shifts ( =9000–13 500 cm^?1, i.e., λ=100–150 nm) and high fluorescence quantum yields. These characteristics and their easy availability starting from the corresponding indoles, make them very attractive for the use as optical switches in various fields of chemistry as well as biological probes.     

亚烷基卡宾及取代亚烷基卡宾与环氧乙烷反应的量子化学研究

用量子化学的密度泛函理论(DFT)在6-311G(d,p)水平上对亚烷基卡宾及取代亚烷基卡宾与环氧乙烷的氧转移反应机理进行了系统的研究. 用IRC对过渡态进行了确认. 并用组态混合模型讨论了反应势垒(ΔE^≠)与XYC＝C:的单-三态能量差ΔE_ST之间的关系, 结果表明, 取代基的电负性是控制反应的主要因素, 取代基的电负性越大, 取代基越多, π电子给予体越多, 单-三态能量差ΔE_ST就越小, 该反应的活化能就越小, 反应越容易发生. 同时还研究了该反应中环氧乙烷中C—O键的解离过程. 发现两个C—O键解离是一个不同步的协同过程.     

Chiral Transformation in Protonated and Deprotonated Adipic Acids through Multistep Internal Proton Transfer

Protonated and deprotonated adipic acids (PAA: HOOC? (CH₂)₄? COOH₂⁺ and DAA: HOOC? (CH₂)₄? COO^?) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H₂O???H???OH₂)⁺ Zundel‐like symmetric hydrogen bonding, whereas that of DAA has H₃O⁺ Eigen‐like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel‐like ions for PAA and Eigen‐like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH???O short hydrogen‐bond stretching peaks are predicted in the range of 1000–1700 cm^?1 in the Car–Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen‐bond peaks. The O? H? O stretching peaks in the range of 1800–2700 cm^?1 become insignificant above around 150 K and are almost washed out at about 300 K.     

On the Mechanism of Hydrogen Activation by Frustrated Lewis Pairs

We report herein a comprehensive theoretical study of the thermodynamics and kinetics of molecular hydrogen activation by frustrated Lewis pairs (FLPs). A series of intermolecularly combined boranes (Lewis acids) and phosphines (Lewis bases), with experimentally established different reactivities towards H₂, have been subjected to DFT and (SCS‐)MP2 calculations, and analyzed in terms of their structural properties, the energetics of association of the FLPs, and the kinetics of their interactions with H₂ and hydrogenation to the ion‐pair products. The analysis included the following steps: 1) assessment of the ability/inability of the Lewis species to preorganize into FLPs with an optimum arrangement of the acid and base sites for preconditioning the reaction with H₂, 2) comprehension of the different thermodynamics of hydrogenation of the selected FLPs by comparing the Gibbs energies of the overall reactions, and 3) estimation of the mechanism of the activation of H₂ by identifying the reaction steps and the associated kinetic barriers. The results of our studies correlate well with experimental findings and have clarified the reasons for the observed different reactivities of the investigated systems, ranging from reversible or nonreversible activation to no reaction with H₂. The derived predictions could assist the future design of Lewis acid–base systems with desired properties and applicability as metal‐free hydrogenation catalysts.     

Structural Characteristics of Graphane‐Type C and BN Nanostructures by Periodic Local MP2 Approach

The structural characteristics of fully‐hydrogenated carbon and boron nitride mono‐ and multilayer slabs, together with nanotubes derived from the slabs, are investigated mainly by means of periodic local second‐order Møller–Plesset perturbation (LMP2) calculations and the results are compared with Hartree–Fock (HF), density functional theory (DFT), and dispersion function‐augmented DFT (DFT‐D) obtained ones. The investigated systems are structurally analogous to (111) and (110) slabs of diamond, where the hydrogenated (111) slab of diamond corresponds to the experimentally known graphane. Multilayering of monolayers and nanotubes is energetically favorable at the LMP2 level for both C and BN, while HF and DFT are not able to reproduce this behavior for CH systems. The work highlights the importance of utilizing methods capable of properly describing weak interactions in the investigation of dispersively‐bound systems such as the multilayered graphanes and the corresponding nanotubes.     

Accurate binding energies of hydrogen,halogen, and dihydrogen bonded complexes and cation enhanced binding strengths

Interaction energy (E_int) values of a variety of hydrogen, halogen, and dihydrogen bonded complexes in the weak, medium, and strong regimes have been computed using W1BD, MP2, M06L density functional theory, and hybrid methods MP4//MP2, MP4//M06L, and CCSD(T)//MP2. W1BD level E_int and CCSD(T) results reported in the literature show very good agreement (mean absolute deviation = 0.19 kcal/mol). MP2 underestimates E_int while M06L shows accurate behavior for all except halogen and charge‐assisted hydrogen bonds. MP4//MP2, MP4//M06L, and CCSD(T)//MP2 yield E_int very close to those obtained from W1BD. The high accuracy energy data at MP4/MP2 is used to study the effect of a cation (Li⁺, NH₄⁺) on the E_int. The cation enhances electron donation from the donor to noncovalent bonding region leading to substantial enhancement in E_int (～141–566% for Li⁺ and ～105–539% for NH₄⁺) and promotes a noncovalent bond in the weak regime to medium regime and that in the medium regime to strong regime. © 2014 Wiley Periodicals, Inc.