Accurate reaction barrier heights of pericyclic reactions: Surprisingly large deviations for the CBS‐QB3 composite method and their consequences in DFT benchmark studies

Accurate barrier heights are obtained for the 26 pericyclic reactions in the BHPERI dataset by means of the high‐level Wn‐F12 thermochemical protocols. Very often, the complete basis set (CBS)‐type composite methods are used in similar situations, but herein it is shown that they in fact result in surprisingly large errors with root mean square deviations (RMSDs) of about 2.5 kcal mol^?1. In comparison, other composite methods, particularly G4‐type and estimated coupled cluster with singles, doubles, and quasiperturbative triple excitations [CCSD(T)/CBS] approaches, show deviations well below the chemical‐accuracy threshold of 1 kcal mol^?1. With the exception of SCS‐MP2 and the herein newly introduced MP3.5 approach, all other tested Møller‐Plesset perturbative procedures give poor performance with RMSDs of up to 8.0 kcal mol^?1. The finding that CBS‐type methods fail for barrier heights of these reactions is unexpected and it is particularly troublesome given that they are often used to obtain reference values for benchmark studies. Significant differences are identified in the interpretation and final ranking of density functional theory (DFT) methods when using the original CBS‐QB3 rather than the new Wn‐F12 reference values for BHPERI. In particular, it is observed that the more accurate Wn‐F12 benchmark results in lower statistical errors for those methods that are generally considered to be robust and accurate. Two examples are the PW6B95‐D3(BJ) hybrid‐meta‐general‐gradient approximation and the PWPB95‐D3(BJ) double‐hybrid functionals, which result in the lowest RMSDs of the entire DFT study (1.3 and 1.0 kcal mol^?1, respectively). These results indicate that CBS‐QB3 should be applied with caution in computational modeling and benchmark studies involving related systems. © 2015 Wiley Periodicals, Inc.     

One‐carbon unit transfer quantum study of 1,10‐CH+‐tetrahydroquinoxaline analog

Quantum mechanics is used in this article to study one‐carbon unit's transfer from 1,10‐tetrahydroquinoxaline analog to methylamine. The computation result shows this reaction can be completed via two paths. Each path experiences two processes of proton transferring and bond rupturing. The structures and energies of all possible stationary points have been calculated by different methods. By analyzing the result, we can find that along the reaction route the proton transfer reaction has the highest energy barrier, which indicates that a general‐acid catalysis exists in this reaction. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Highly accurate benchmark calculations of the interaction energies in the complexes C6H6···C6X6 (X = F,Cl, Br,and I)

Different from the case of the benzene dimer, the differences between the interaction energies are always less than 0.50 kcal/mol for face‐to‐face eclipsed, face‐to‐face staggered, and parallel‐displaced configurations of all investigated complexes C₆H₆···C₆X₆ (X = F, Cl, Br, and I). Hence, it is a great challenge for quantum chemists to accurately calculate the interaction energies for the three configurations of the complexes C₆H₆···C₆X₆. This work demonstrates that results obtained with the PBE0 density functional combined with the D3 dispersion correction (PBE0‐D3) and the basis set def2‐TZVPP are in excellent agreement with the estimates of the coupled‐cluster singles, doubles, and perturbative triples [CCSD(T)] complete basis set (CBS) limit. The other finding in this study is that, in comparison with the gold‐standard CCSD(T)/CBS benchmark, the spin‐component scaled (SCS) zeroth‐order symmetry‐adapted perturbation theory (SAPT0), when paired with the basis set aug‐cc‐pVDZ, performs also very well, and its performance is even better than that of the PBE0‐D3/def2‐TZVPP method or the conventional SAPT/aug‐cc‐pVQZ method. The findings of this study are very significant because both PBE0‐D3/def2‐TZVPP and SCS‐SAPT0/aug‐cc‐pVDZ can deal with the systems with more than 200 atoms.     

Coupled‐cluster reaction barriers of : An application of the coupled‐cluster//Kohn–Sham density functional theory model chemistry

In this work, we report a theoretical investigation concerning the use of the popular coupled‐cluster//Kohn‐Sham density functional theory (CC//KS‐DFT) model chemistry, here applied to study the entrance channel of the reaction, namely by comparing CC//KS‐DFT calculations with KS‐DFT, MRPT2//CASSCF, and CC//CASSCF results from our previous investigations. This was done by performing single point energy calculations employing several coupled cluster methods and using KS‐DFT geometries optimized with six different functionals, while conducting a detailed analysis of the barrier heights and topological features of the curves and surfaces here obtained. The quality of this model chemistry is critically discussed in the context of the title reaction and also in a wider context. © 2013 Wiley Periodicals, Inc.     

Density functional theory study of a molecular allosteric switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5

A classical model of “molecular machine,” which acts as an ON–OFF switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5 ( L ), has been theoretically studied. It is highly important to understand the mechanism of this switch. The alkali‐metal cations (Na⁺ and K⁺) and W(CO)₄ fragment are introduced to coordinate with the different active sites of L , respectively. The density functional theory (DFT) method is used for understanding the stereochemical structural natures and thermodynamic properties of all the target molecules at B3LYP/6‐31G(d) and SDD (Stuttgart–Dresden) level, together with the corresponding effective core potential (ECP) for tungsten (W). The fully optimized geometries have been performed with real frequencies, which indicate the minima states. The nucleophilicity of L has been investigated by the Fukui functions. The natural bond orbital analysis is used to study the intermolecular charge‐transfer interactions and explore the origin of the internal forces of the molecular switch. In addition, the binding energies, enthalpies, Gibbs free energies, and the cation exchange energies have been studied for L , W(CO)₄ L , and their corresponding complexes. The properties of the complexes displayed by in presence or absence of the W(CO)₄ fragment are also analyzed. The calculated results of allosterism displayed by L are in a good agreement with the experimental results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Computational studies on electron and proton transfer in phenol‐imidazole‐base triads

The electron and proton transfer in phenol‐imidazole‐base systems (base = NH₂^? or OH^?) were investigated by density‐functional theory calculations. In particular, the role of bridge imidazole on the electron and proton transfer was discussed in comparison with the phenol‐base systems (base = imidazole, H₂O, NH₃, OH^?, and NH₂^?). In the gas phase phenol‐imidazole‐base system, the hydrogen bonding between the phenol and the imidazole is classified as short strong hydrogen bonding, whereas that between the imidazole and the base is a conventional hydrogen bonding. The n value in spⁿ hybridization of the oxygen and carbon atoms of the phenolic CO sigma bond was found to be closely related to the CO bond length. From the potential energy surfaces without and with zero point energy correction, it can be concluded that the separated electron and proton transfer mechanism is suitable for the gas‐phase phenol‐imidazole‐base triads, in which the low‐barrier hydrogen bond is found and the delocalized phenolic proton can move freely in the single‐well potential. For the gas‐phase oxidized systems and all of the triads in water solvent, the homogeneous proton‐coupled electron transfer mechanism prevails. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Poly(ε‐caprolactone)–poly(isobutylene): A crystallizing,hydrogen‐bonded pseudo‐block copolymer

The crystallization of block copolymers (BCPs) under homogeneous and heterogeneous nucleation is currently well understood revealing the strong interplay of crystallization in competition to microphase separation. This article reports investigations on synthesis and crystallization processes in weakly interacting supramolecular pseudo‐BCPs, composed of poly(ε‐caprolactone) (PCL) and poly(isobutylene) (PIB) blocks, connected by a specifically interacting hydrogen bond (thymine/2,6‐diaminotriazine). Starting from ring opening polymerization of ε‐caprolactone, the use of “click”‐chemistry enabled the introduction of thymine endgroups onto PCL polymer, thus generating the fully thymine‐substituted pure PCLs ( 1a , 1b ) as judged via NMR and MALDI analysis. Physical mixing of 1a , 1b with a bivalent, bis(2,6‐diaminotriazine)‐containing molecule ( 2 ) generated the bivalent polymers BC1 and BC2 , whereas mixing of 1a or 1b with the 2,6‐diaminotriazine‐substituted PIB ( 3 ) generated the supramolecular pseudo‐BCPs BC3 and BC4 . Thermal investigations (DSC, Avrami analysis) revealed only minor changes in the crystallization behavior of BC1 – BC4 with Avrami exponents close to three, indicative of a confluence of the growing crystals during the crystallization process. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

A Convenient Method for the Preparation of 1,5‐Diaryl‐3‐(arylamino)‐1H‐pyrrol‐2(5H)‐ones

A simple and eco‐friendly method for the preparation of 1,5‐diaryl‐3‐(arylamino)‐1H‐pyrrol‐2(5H)‐ones via the cyclo‐condensation reaction of aldehydes, amines and ethyl pyruvate in the presence of silica supported ferric chloride (SiO₂‐FeCl₃) as reusable heterogeneous catalyst is described. The present methodology offers several advantages such as excellent yields, simple procedure and short reaction times.     

ONIOM study of one‐carbon unit transfer from imidazolidine to dUMP analogue

The ONIOM quantum mechanics method is used in this article to study one‐carbon unit transfer from an imidazolidine to 6‐aminouracil derivates. The computation results show that this reaction can be completed via three paths, owing to the three different proton transfer modes. Each path experiences three processes of nucleophile attacking, proton transferring, and bond rupturing. The focus of discussion falls on the proton transfer process. By analyzing the calculation results, we find that the direct proton transfer is the preferable pathway. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

From Gas‐Phase to Liquid‐Water Chemical Reactions: The Fluorine Atom Plus Water Trimer System

The potential energy profile for the F+(H₂O)₃→HF+(H₂O)₂OH reaction has been investigated using the “gold standard” CCSD(T) method with correlation‐consistent basis sets up to cc‐pVQZ. Four different reaction pathways have been found and these are related, both geometrically and energetically. The entrance complexes F???(H₂O)₃ for all four reaction pathways are found lying ca. 7 kcal mol^?1 below the separated reactants F+(H₂O)₃. The four reaction barriers on their respective reaction coordinates lie ca. 4 kcal mol^?1 below the reactants. There are also corresponding exit complexes HF???(H₂O)₂OH, lying about 13 kcal mol^?1 below the separated products HF+(H₂O)₂OH. Compared with analogous F+(H₂O)₂ and F+H₂O reactions, the F+(H₂O)₃ reaction is somewhat similar to the former but qualitatively different from the latter. It may be reasonable to predict that the reactions between atomic fluorine and water tetramer (or even larger water clusters) may be similar to the F+(H₂O)₃ reaction.     

Theoretical investigation of the structures and spectroscopic properties of (H2O4)n (n = 1–4) clusters

Density functional theory and ab initio calculations were performed to elucidate the hydrogen interactions in (H₂O₄)_n (n = 1–4) clusters. The optimized geometries, binding energies, and harmonic vibrational frequencies were predicted at various levels of theory. The trans conformer of the H₂O₄ monomer was predicted to be the most stable structure at the CCSD(T)/aug‐cc‐pVTZ level of theory. The binding energies per H₂O₄ monomer increased in absolute value by 9.0, 10.1, and 11.8 kcal/mol from n = 2 to n = 4 at the MP2/cc‐pVTZ level of theory (after the zero‐point vibrational energy and basis set superposition error corrections). This result implies that the intermolecular hydrogen bonds were stronger in the long‐chain clusters, that is, the formation of the longer chain in the (H₂O₄)_n clusters was more energetically favorable.     

Exploring the Effect of Bioisosteric Replacement of Carboxamide by a Sulfonamide Moiety on N‐Glycosidic Torsions and Molecular Assembly: Synthesis and X‐ray Crystallographic Investigation of N‐(β‐D‐Glycosyl)sulfonamides as N‐Glycoprotein Linkage Region Analogues

N‐Glycoprotein linkage region constituents, 2‐acetamido‐2‐deoxy‐β‐D ‐glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all the eukaryotes. To gain a better understanding for nature’s choice of GlcNAcβAsn as linkage region constituents and inter‐ and intramolecular carbohydrate–protein interactions, a detailed systemic structural study of the linkage region conformation is essential. Earlier crystallographic studies of several N‐(β‐glycopyranosyl)alkanamides showed that N‐glycosidic torsion, ?_N, is influenced to a larger extent by structural variation in the sugar part than that of the aglycon moiety. To explore the effect of the bioisosteric replacement of a carboxamide group by a sulfonamide moiety on the N‐glycosidic torsions as well as on molecular assembly, several glycosyl methanesulfonamides and glycosyl chloromethanesulfonamides were synthesized as analogues of the N‐glycoprotein linkage region, and crystal structures of seven of these compounds have been solved. A comparative analysis of this series of crystal structures as well as with those of the corresponding alkanamido derivatives revealed that N‐glycosidic torsion, ?_N, does not alter significantly. Methanesulfonamido and chloromethanesulfonamido derivatives of GlcNAc display a different aglycon conformation compared to other sulfonamido analogues. This may be due to the cumulative effect of the direct hydrogen bonding between N1 and O1′ and C? H???O interactions of the aglycon chain, revealing the uniqueness of the GlcNAc as the linkage sugar.     

Assessing the role of Hartree‐Fock exchange,correlation energy and long range corrections in evaluating ionization potential,and electron affinity in density functional theory

Accurate determination of ionization potentials (IPs), electron affinities (EAs), fundamental gaps (FGs), and HOMO, LUMO energy levels of organic molecules play an important role in modeling and predicting the efficiencies of organic photovoltaics, OLEDs etc. In this work, we investigate the effects of Hartree Fock (HF) Exchange, correlation energy, and long range corrections in predicting IP and EA in Hybrid Functionals. We observe increase in percentage of HF exchange results in increase of IPs and decrease in EAs. Contrary to the general expectations inclusion of both HF exchange and correlation energy (from the second order perturbation theory MP2) leads to poor prediction. Range separated Hybrid Functionals are found to be more reliable among various DFT Functionals investigated. DFT Functionals predict accurate IPs whereas post HF methods predict accurate EAs. © 2017 Wiley Periodicals, Inc.     

An Efficient Synthesis of 4‐Arylmethylidene‐3‐substituted‐Isoxazol‐5(4H)‐ones in Aqueous Medium

A series of 4‐arylmethylidene‐3‐substituted‐isoxazol‐5(4H)‐ones were efficiently synthesized by eco‐benign, one pot uncatalyzed reaction of β‐keto‐ester, hydroxylamine hydrochloride, and aromatic aldehyde with electron donating substituent in water.     

Structure determination of three furan‐substituted benzimidazoles and calculation of π–π and C—H...π interaction energies

The synthesis and structural characterization of 2‐(furan‐2‐yl)‐1‐(furan‐2‐ylmethyl)‐1H‐benzimidazole [C₁₆H₁₂N₂O₂, (I)], 2‐(furan‐2‐yl)‐1‐(furan‐2‐ylmethyl)‐1H‐benzimidazol‐3‐ium chloride monohydrate [C₁₆H₁₃N₂O₂⁺·Cl⁻·H₂O, (II)] and the hydrobromide salt 5,6‐dimethyl‐2‐(furan‐2‐yl)‐1‐(furan‐2‐ylmethyl)‐1H‐benzimidazol‐3‐ium bromide [C₁₈H₁₇N₂O₂⁺·Br⁻, (III)] are described. Benzimidazole (I) displays two sets of aromatic interactions, each of which involves pairs of molecules in a head‐to‐tail arrangement. The first, denoted set (Ia), exhibits both intermolecular C—H...π interactions between the 2‐(furan‐2‐yl) (abbreviated as Fn) and 1‐(furan‐2‐ylmethyl) (abbreviated as MeFn) substituents, and π–π interactions involving the Fn substituents between inversion‐center‐related molecules. The second, denoted set (Ib), involves π–π interactions involving both the benzene ring (Bz) and the imidazole ring (Im) of benzimidazole. Hydrated salt (II) exhibits N—H...OH₂...Cl hydrogen bonding that results in chains of molecules parallel to the a axis. There is also a head‐to‐head aromatic stacking of the protonated benzimidazole cations in which the Bz and Im rings of one molecule interact with the Im and Fn rings of adjacent molecules in the chain. Salt (III) displays N—H...Br hydrogen bonding and π–π interactions involving inversion‐center‐related benzimidazole rings in a head‐to‐tail arrangement. In all of the π–π interactions observed, the interacting moieties are shifted with respect to each other along the major molecular axis. Basis set superposition energy‐corrected (counterpoise method) interaction energies were calculated for each interaction [DFT, M06‐2X/6‐31+G(d)] employing atomic coordinates obtained in the crystallographic analyses for heavy atoms and optimized H‐atom coordinates. The calculated interaction energies are −43.0, −39.8, −48.5, and −55.0 kJ mol⁻¹ for (Ia), (Ib), (II), and (III), respectively. For (Ia), the analysis was used to partition the interaction energies into the C—H...π and π–π components, which are 9.4 and 24.1 kJ mol⁻¹, respectively. Energy‐minimized structures were used to determine the optimal interplanar spacing, the slip distance along the major molecular axis, and the slip distance along the minor molecular axis for 2‐(furan‐2‐yl)‐1H‐benzimidazole.     

Study of hydrogen‐bonding strength in poly(ϵ‐caprolactone) blends by DSC and FTIR

The hydrogen‐bonding strength of poly(?‐caprolactone) (PCL) blends with three different well‐known hydrogen‐bonding donor polymers [i.e., phenolic, poly(vinyl‐phenol) (PVPh), and phenoxy] was investigated with differential scanning calorimetry and Fourier transform infrared spectroscopy. All blends exhibited a single glass‐transition temperature with differential scanning calorimetry, which is characteristic of a miscible system. The strength of interassociation depended on the hydrogen‐bonding donor group in the order phenolic/PCL > PVPh/PCL > phenoxy/PCL, which corresponds to the q value of the Kwei equation. In addition, the interaction energy density parameter calculated from the melting depression of PCL with the Nishi–Wang equation resulted in a similar trend in terms of the hydrogen‐bonding strength. Quantitative analyses on the fraction of hydrogen‐bonded carbonyl groups in the molten state were made with Fourier transform infrared spectroscopy for all systems, and good correlations between thermal behaviors and infrared results were observed. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1348–1359, 2001     

Mechanisms of DABCO‐ and DMAP‐catalyzed [2 + 4] cycloaddition reactions of methylallenoate with methyleneindolonone: A DFT study

The mechanisms and stereoselectivities of the [2 + 4] cycloaddition reaction of methylallenoate R1 with methyleneindolonone R2 catalyzed by DABCO (Equation 1) and DMAP (Equation 2) organocatalysts have been examined with density functional theory (M06‐2X) calculations. Several possible reaction pathways (paths 1a, 1b, and 1c for Equation 1 and paths 2a and 2b for Equation 2) were located and compared. The results of our study reveal that for both reactions, three reaction stages have been characterized: nucleophilic addition of the catalyst ( DABCO or DMAP ) to R1 (Stage I ), addition of the other reactant R2 (Stage II ), intramolecular cycloaddition and liberation of the catalyst ( DABCO or DMAP ) afforded the final product (Stage III ). For the DABCO ‐catalyzed cycloaddition, we predict that path 1a leading to P(E) is the most energy favorable pathway among the three possible pathways. The carbon–carbon bond formation step is the rate‐determining step (ΔG ^?=23.6 kcal/mol). With DMAP catalyst, the same reaction gave P(Z) as the major product. The barrier for the rate‐determining step (addition of R1 to DMAP ) is 25.8 kcal/mol. The calculated results are in agreement with the experimental findings. Moreover, for both reactions, the analysis of global reactivity indexes has been carried out to examine the role of catalyst. The present study should provide a general mechanistic framework for the rational design of this kind of reactions.     

One‐Pot Synthesis of (1,2,3‐Triazolyl)methyl 3,4‐Dihydro‐2‐oxo‐1H‐pyrimidine‐5‐carboxylates as Potentially Active Antimicrobial Agents

A simple and efficient one‐pot four‐component procedure has been developed for the synthesis of a wide range of compounds containing the (triazolyl)methyl oxo‐pyrimidine‐carboxylate system from propargyl β‐keto esters, various azides, aldehydes, and urea in the presence of catalytic amounts of (AcO)₂Cu/sodium ascorbate in AcOH. The method worked well with different aryl and heteroaryl aldehydes, and for a variety of substituents in the triazolyl part of the molecule. The antimicrobial activities of the products were evaluated against two Gram‐positive and Gram‐negative bacteria, and one fungus. Compound 5j was active against Staphylococcus aureus and Candida albicans.     

Synthesis of 4‐halo‐2 (5H)‐furanones and their suzuki‐coupling reactions with organoboronic acids. A general route to 4‐aryl‐2 (5 H) ‐furanones

4‐Halo‐2(5H)‐furanones were prepared by the halolactonization of 2,3‐allenoic acids. The subsequent Suzuki coupling reaction of 4‐halo 2(5H)‐furanones with aryl boronic acids was carried out to produce 4‐aryl‐2(5H)‐furanones in excellent yields.     

One‐Pot ‘On‐solvent’ Multicomponent Protocol for the Synthesis of Medicinally Relevant 4H‐Pyrano[3,2‐c]quinoline Scaffold

‘One‐pot’ AcONa‐catalyzed transformation of salicylaldehydes, malononitrile and 4‐hydroxy‐1‐methylquinolin‐2(1H)‐one in the presence of a minimal quantity of EtOH results in fast (3 min) and efficient formation of unknown 2‐amino‐4‐(2‐hydroxyaryl)‐6‐methyl‐5‐oxo‐5,6‐dihydro‐4H‐pyrano[3,2‐c]quinoline‐3‐carbonitriles in 85–98% yields, which are potential pharmaceutical agents for treating disorders responsive to the induction of apoptosis, antiproliferation, or vascular disruption. This efficient ‘on‐solvent’ approach to the 4H‐pyrano[3,2‐c]quinoline scaffold represents a novel synthetic concept for multicomponent reaction (MCR) strategy and allows to combine the synthetic virtues of conventional MCR with ecological benefits and convenience of facile ‘on‐solvent’ procedure.