A Robust and Cost-Efficient Scheme for Accurate Conformational Energies of Organic Molecules

Several standard semiempirical methods as well as the MMFF94 force field approximation have been tested in reproducing 8 DLPNO-CCSD(T)/cc-pVTZ level conformational energies and spatial structures for 37 organic molecules representing pharmaceuticals, drugs, catalysts, synthetic precursors, industry-related chemicals (37conf8 database). All contemporary semiempirical methods surpass their standard counterparts resulting in more reliable conformational energies and spatial structures, even though at significantly higher computational costs. However, even these methods show unexpected failures in reproducing energy differences between several conformers of the crown ether 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6). Inexpensive force field MMFF94 approximation groups with contemporary semiempirical methods in reproducing the correct order of conformational energies and spatial structures, although the performance in predicting absolute conformational energies compares to standard semiempirical methods. Based on these findings, we suggest a two-step strategy for reliable yet feasible conformational search and sampling in realistic-size flexible organic molecules: i) geometry optimization/preselection of relevant conformers using the MMFF94 force field; ii) single-point energy evaluations using a contemporary semiempirical method. We expect that developed database 37conf8 is going to be useful for development of semiempirical methods.     

含不同质子供体的2-苯基苯并三唑衍生物激发态质子转移的理论研究

用密度泛函理论(DFT)和二级微扰理论(MP2)研究了带不同质子供体的2-苯基苯并三唑衍生物: 2-(2-羟苯基)苯并三唑(H-TIN), 2-(2-氨苯基)苯并三唑(APyBT)和2-(2-巯苯基)苯并三唑(MPyBT)的激发态分子内质子转移(ESIPT)性质以及它们作为紫外光吸收剂的光物理机制. 结果表明, 在基态时三个化合物的最稳定异构体是均存在分子内氢键的正常构型N, 而互变异构体T和其扭曲构型T_twisted都是不稳定的. 激发态势能曲线表明H-TIN和APyBT的ESIPT分别需要克服约7.06和20.7 kJ/mol的能垒, 而MPyBT的ESIPT无需能垒|同时结合分子轨道, 电荷差分密度三维立体图的分析结果表明三个化合物都能发生ESIPT, 并且伴随有扭曲分子内电荷转移, 这些原因均表明它们都具有好的紫外光稳定作用.     

分子形貌所指示的羟基卡宾及其衍生物的质子转移反应

分子形貌(Molecular face, MF)定义分子的内禀电子转折边界面,同时在其上计算并描绘出前沿电子密度(MFED). MF不仅能显示分子的形状和大小,还能够指示分子的化学反应性.应用M06-2X/6-311++G(d,p)理论方法,对单线态和三线态羟基卡宾分子及其衍生物的质子化反应进行研究并计算了这些反应的活化能.结果表明,吸电性和供电性较强的取代基,均使单线态反应活化能增大,只有吸电性较强的─CN才能使三线态反应活化能增大.应用分子形貌理论研究了上述反应,不仅展示出分子的形貌变化、与反应位点的关联,以及有关物理量的变化倾向,而且还定量地显示出,单线态羟基卡宾及其衍生物分子边界面上前沿电子密度极大值与极小值的差值,与其质子转移反应的活化能之间存在线性相关.     

Understanding the Reactivity and Selectivity of Fluxional Chiral DMAP-Catalyzed Kinetic Resolutions of Axially Chiral Biaryls

Fluxional chiral DMAP-catalyzed kinetic resolutions of axially chiral biaryls were examined using density functional theory. Computational analyses lead to a revised understanding of this reaction in which the interplay of numerous non-covalent interactions control the conformation and flexibility of the active catalyst, the preferred mechanism, and the stereoselectivity. Notably, while the DMAP catalyst itself is confirmed to be highly fluxional, electrostatically driven π⋅⋅⋅π⁺ interactions render the active, acylated form of the catalyst highly rigid, explaining its pronounced stereoselectivity.     

Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions

The domain-based local pair natural orbital coupled-cluster with single, double, and perturbative triples excitation (DLPNO-CCSD(T)) method was employed to portray the activation and reaction energies of four ubiquitous enzymatic reactions, and its performance was confronted to CCSD(T)/complete basis set (CBS) to assess its accuracy and robustness in this specific field. The DLPNO-CCSD(T) results were also confronted to those of a set of density functionals (DFs) to understand the benefit of implementing this technique in enzymatic quantum mechanics/molecular mechanics (QM/MM) calculations as a second QM component, which is often treated with DF theory (DFT). On average, the DLPNO-CCSD(T)/aug-cc-pVTZ results were 0.51 kcal·mol⁻¹ apart from the canonic CCSD(T)/CBS, without noticeable biases toward any of the reactions under study. All DFs fell short to the DLPNO-CCSD(T), both in terms of accuracy and robustness, which suggests that this method is advantageous to characterize enzymatic reactions and that its use in QM/MM calculations, either alone or in conjugation with DFT, in a two-region QM layer (DLPNO-CCSD(T):DFT), should enhance the quality and faithfulness of the results.     

Interactions of Molecules with cis and trans Double Bonds: A Theoretical Study of cis‐ and trans‐2‐Butene

Noncovalent interactions of cis‐ and trans‐2‐butene, as the smallest model systems of molecules with cis and trans double bonds, were studied to find potential differences in interactions of these molecules. The study was performed using quantum chemical methods including very accurate CCSD(T)/CBS method. We studied parallel and displaced parallel interactions in 2‐butene dimers, in butane dimers, and between 2‐butene and saturated butane. The results show the trend that interactions of 2‐butene with butane are the strongest, followed by interactions in butane dimers, whereas the interaction in 2‐butene dimers are the weakest. The strongest calculated interaction energy is between trans‐2‐butene and butane, with a CCSD(T)/CBS energy of ?2.80 kcal mol^?1. Interactions in cis‐2‐butene dimers are stronger than interactions in trans‐2‐butene dimers. Interestingly, some of the interactions involving 2‐butene are as strong as interactions in a benzene dimer. These insights into interactions of cis‐ and trans‐2‐butene can improve understanding of the properties and processes that involve molecules with cis and trans double bonds, such as fatty acids and polymers.     

The Experimental Observation of the Intramolecular NO2/CO Interaction in Solution

The weak electrostatic interaction between nitro and carbonyl moieties has been observed by means of variable‐temperature NMR spectroscopy. Its energetic contribution was evaluated to be about 3 kcal mol^?1 by DFT calculations, and confirmed by the measurement of internal energy barriers to the rotation of suitable nitroaryl rings.     

Dual Role of the 1,2,3‐Triazolium Ring as a Hydrogen‐Bond Donor and Anion–π Receptor in Anion‐Recognition Processes

Several bis(triazolium)‐based receptors have been synthesized as chemosensors for anion recognition. The central naphthalene core features two aryltriazolium side‐arms. NMR experiments revealed differences between the binding modes of the two triazolium rings: one triazolium ring acts as a hydrogen‐bond donor, the other as an anion–π receptor. Receptors 9²⁺?2BF₄ ^? (C₆H₅), 11²⁺?2BF₄ ^? (4‐NO₂?C₆H₄), and 13²⁺?2BF^4? (ferrocenyl) bind HP₂O₇^3? anions in a mixed‐binding mode that features a combination of hydrogen‐bonding and anion–π interactions and results in strong binding. On the other hand, receptor 10²⁺?2 BF₄ ^? (4‐CH₃O?C₆H₄) only displays combined Csp₂?H/anion–π interactions between the two arms of the receptors and the bound anion rather than triazolium (CH)⁺???anion hydrogen bonding. All receptors undergo a downfield shift of the triazolium protons, as well as the inner naphthalene protons, in the presence of H₂PO₄^? anions. That suggests that only hydrogen‐bonding interactions exist between the binding site and the bound anion, and involve a combination of cationic (triazolium) and neutral (naphthalene) C?H donor interactions. Theoretical calculations relate the electronic structure of the substituent on the aromatic group with the interaction energies and provide a minimum‐energy conformation for all the complexes that explains their measured properties.     

Influence of Endohedral Confinement on the Electronic Interaction between He atoms: A He2@C20H20 Case Study

The shortest He–He distance! r(He–He)=1.265 Å. The electronic interaction between confined pairs of He atoms in the C₂₀H₂₀ dodecahedrane cage is analyzed (see figure). A key observation about bonding that emerges uniquely from endohedral complexes is that a short internuclear separation does not necessarily imply the existence of a chemical bond.

     

Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell‐Wall Analogue Peptides: Experimental and Theoretical Studies

Charge matters! The charge state significantly influences the conformation and the binding energy between vancomycin antibiotic and bacterial cell‐wall analogue peptides (see figure). Surface‐induced dissociation (SID) studies provide a quantitative comparison between the stabilities of different charge states of the complex.

     

Insights and Activation Energy Surface of the Dehydrogenation of C2HxO Species in Ethanol Oxidation Reaction on Ir(100)

Dehydrogenation of an organic compound is the first and the most fundamental elementary reaction in many organic reactions. In ethanol oxidation reaction (EOR) to form CO₂, there are a total of 46 pathways in C₂H_xO (x=1–6) species leading to the removal of all six hydrogen atoms in five C−H bonds and one O−H bond. To investigate the degree of dehydrogenation in EOR under operando conditions, we performed density function theory (DFT) calculations to study 28 dehydrogenation steps of C₂H_xO on Ir(100). An activation energy surface was then constructed and compared with that of the C−C bond cleavages to understand the importance of the degree of dehydrogenation in EOR. The results show that there are likely 28 dehydrogenations in EOR under fuel cell temperatures and the last two hydrogens in C₂H₂O are less likely cleaved. On the other hand, deep dehydrogenation including 45 dehydrogenations can occur under ethanol steam reforming conditions.     

Insights into N‐Heterocyclic Carbene (NHC)‐Catalyzed Asymmetric Addition of 2H‐Azirine with Aldehyde

The possible mechanisms and origin of the enantioselectivity of the reaction between 2H‐azirine and an aldehyde catalyzed by an N‐heterocyclic carbene (NHC) were theoretically studied and predicted at the M06‐2X/6‐31G(d,p)/IEF‐PCM_MTBE//M06‐2X‐GD3/6‐311++G(2df, 2pd)/IEF‐PCM_MTBE level. The most favorable reaction pathway consists of four steps, i.e., complexation of the NHC and the aldehyde, stepwise [1,2]‐proton transfer, C?C bond formation coupled with another proton transfer, and recycling of the NHC. The computational results indicate that the stereoselectivity‐determining step is also the rate‐determining step, which is the third step (i.e., intermolecular addition). The calculated 99 % ee is very close to the experimentally observed value of 96 % ee, demonstrating that the calculations are reliable. Two important roles of the NHC were identified by global reaction index (GRI) analysis and natural population analysis (NPA), that is, realizing the umpolung reactivity of the aldehyde and facilitating the deprotonation of aldehyde. Moreover, the efficiency of different NHC catalysts can be mainly predicted by computing the nucleophilic index of the corresponding Breslow intermediates. Furthermore, distortion/interaction and noncovalent interaction (NCI) analyses revealed that the π???π interactions between the NHC and substrates were the key factor in the reaction enantioselectivity.     

Gold Behaves as Hydrogen in the Intermolecular Self‐Interaction of Metal Aurides MAu4 (M=Ti,Zr, and Hf)

We performed density functional calculations to examine the intermolecular self‐interaction of metal tetraauride MAu₄ (M=Ti, Zr, and Hf) clusters. We found that the metal auride clusters have strong dimeric interactions (2.8–3.1 eV) and are similar to the metal hydride analogues with respect to structure and bonding nature. Similarly to (MH₄)₂, the (μ‐Au)₃ C_s structures with three three‐center two‐electron (3c–2e) bonds were found to be the most stable. Natural orbital analysis showed that greater than 96 % of the Au 6s orbital contributes to the 3c–2e bonds, and this predominant s orbital is responsible for the similarity between metal aurides and metal hydrides (>99 % H 1s). The favorable orbital interaction between occupied Au 6s and unoccupied metal d orbitals leads to a stronger dimeric interaction for MAu₄‐MAu₄ than the interaction for MH₄‐MH₄. There is a strong relationship between the dimeric interaction energy and the chemical hardness of its monomer for (MAu₄)₂ and (MH₄)₂.     

密度泛函理论处理激发态与多重态结构研究进展

用密度泛函理论处理分子激发态和电子多重态结构是密度泛函理论发展的重要方面, 研究工作一直很活跃。本文对近年来在这一领域取得的重要进展作简要的综述。     

NO双分子和二聚体与Cu2作用的理论计算

采用密度泛函理论(DFT)中的B3LYP方法，在Lanl2DZ基组下，对NO双分子和二聚体与铜原子簇相互作用的结构进行了研究. 结果表明，NO可以在铜表面相邻的两个铜原子上形成稳定的双分子吸附和二聚体吸附，而在双分子吸附形式中NO以氮原子吸附在铜上的构型最稳定，且顶点吸附的稳定性不如非顶点吸附形式.在二聚体吸附形式中， N－N键被加强，而N－O键被削弱的程度大于双分子吸附形式，说明二聚体的形成有利于NO在金属铜表面的直接分解.同时电荷布居分析表明，单重态的二聚体与铜作用时，铜原子上的平均电荷达到0.66 e,说明在这种吸附形式中铜被离子化的倾向较大，而且这种吸附形式最有利于NO的分解.这些结果说明NO经二聚体形式在铜表面直接催化分解是可行的.     

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.     

Revisiting H/Pt(111) by a combined experimental study of the H-D exchange reaction and first-principles calculations

We report a detailed investigation of the behavior of chemisorbed hydrogen atoms (Ha) on Pt(111) by a combination of an ex-perimental study of the Ha + Da reaction and first-principles calculations. The coverage-dependent adsorption and desorption behavior of Ha and Da on Pt(111) have been systematically established and can be well interpreted in terms of repulsive inter-actions between adsorbates. Ha adsorbs exclusively on the face-centered cubic (fcc) sites of Pt(111) at coverages not exceeding 1 monolaye...