Computational study of the fluorination effect on nitrogen–boron bond

The Lewis acid‐base H_3?nF_nN–BF_mH_3?m (n = 0–3; m = 0–3) system was examined using the density functional theory calculations. The N? B bond strength can be adjusted stepwise by increasing the number of substituted fluorine atoms. The main finding of this work is the bond distances of the complexes do not correlate directly with the bond strengths. Some rationalization of this interesting observation was provided by the fluorine substitution effect on the HOMO‐LUMO gap, hybridization of bonding orbitals and electrostatic interaction. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

An AAA–DDD Triply Hydrogen‐Bonded Complex Easily Accessible for Supramolecular Polymers

For a complementary hydrogen‐bonded complex, when every hydrogen‐bond acceptor is on one side and every hydrogen‐bond donor is on the other, all secondary interactions are attractive and the complex is highly stable. AAA–DDD (A=acceptor, D=donor) is considered to be the most stable among triply hydrogen‐bonded sequences. The easily synthesized and further derivatized AAA–DDD system is very desirable for hydrogen‐bonded functional materials. In this case, AAA and DDD, starting from 4‐methoxybenzaldehyde, were synthesized with the Hantzsch pyridine synthesis and Friedländer annulation reaction. The association constant determined by fluorescence titration in chloroform at room temperature is 2.09×10⁷ M ^?1. The AAA and DDD components are not coplanar, but form a V shape in the solid state. Supramolecular polymers based on AAA–DDD triply hydrogen bonded have also been developed. This work may make AAA–DDD triply hydrogen‐bonded sequences easily accessible for stimuli‐responsive materials.     

Identification of the Most Stable Sc2C80 Isomers: Structure,Electronic Property,and Molecular Spectra Investigations

A systematic density functional theory investigation has been carried out to explore the possible structures of Sc₂C₈₀ at the BMK/6‐31G(d) level. The results clearly show that Sc₂@C₈₀‐I_h, Sc₂@C₈₀‐D_5h, and Sc₂C₂@C₇₈‐C_2v can be identified as three isomers of Sc₂C₈₀ metallofullerene with the lowest energy. Frontier molecular orbital analysis indicates that the two Sc₂@C₈₀ isomers have a charge state as (Sc³⁺)₂@C₈₀^6?and the Sc₂C₂@C₇₈ has a charge state of (Sc³⁺)₂C₂^2?@C₇₈^4?. Moreover, the metal‐cage covalent interactions have been studied to reveal the dynamics of endohedral moiety. The vertical electron affinity, vertical ionization potential, infrared spectra and ¹³C nuclear magnetic resonance spectra have been also computed to further disclose the molecular structures and properties.     

A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

Intermolecular H···O═C bonds induced 2D self‐assembly of thiophene based diketopyrrolopyrrole derivative

Compounds with diketopyrrolopyrrole (DPP) and thiophene moieties have attracted considerable attention because of their promising charge transport properties. The molecular conformation and self‐assembly of 2,5‐dihexadecyl‐3,6‐di(thiophen‐2‐yl)‐2,5‐dihydropyrrolo[3,4‐c]pyrrole‐1,4‐dione (TDPP‐C16) molecule have been investigated by scanning tunneling microscopy and density functional theory alculation. The TDPP‐C16 molecules adsorb with their optimized S‐shaped conformation and form a zipper‐like pattern on highly oriented pyrolytic graphite surface. R and S rotated structures are observed. The nanostructure is dominated by intermolecular double hydrogen bonds between C═O of the DPP units and hydrogen atom of thiophene rings in the neighboring molecules in each row. Atomic force microscopy and density functional theory calculation also display the existence of strong intermolecular hydrogen bonding. The results provide molecular evidence for the intermolecular interactions of the surface structure, which could benefit to the design of the organic semiconducting materials and understanding of underlying principle of charge transfer process. Copyright © 2017 John Wiley & Sons, Ltd.     

Photoinduced Triplet–Triplet Energy Transfer in a 2‐Ureido‐4(1H)‐Pyrimidinone‐Bridged,Quadruply Hydrogen‐Bonded Ferrocene–Fullerene Assembly

2‐Ureido‐4(1H)‐pyrimidinone‐bridged ferrocene–fullerene assembly I is designed and synthesized for elaborating the photoinduced electron‐transfer processes in self‐complementary quadruply hydrogen‐bonded modules. Unexpectedly, steady‐state and time‐resolved spectroscopy reveal an inefficient electron‐transfer process from the ferrocene to the singlet or triplet excited state of the fullerene, although the electron‐transfer reactions are thermodynamically feasible. Instead, an effective intra‐assembly triplet–triplet energy‐transfer process is found to be operative in assembly I with a rate constant of 9.2×10⁵ s^?1 and an efficiency of 73 % in CH₂Cl₂ at room temperature.     

Theoretical Studies on the Hydrogen‐bonding and π‐Stacking Interactions in the m‐Nisoldipine Polymorphism Dimers

The intermolecular interactions in the dimers of m‐nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a‐dimer, O···H? N), dimer II (b‐dimer, O···H? N), dimer III (b‐dimer, π‐stacking‐c), and dimer IV (b‐dimer, π‐stacking‐p). The interaction energies of the four dimers are along the sequence of II>I>III>IV. The intermolecular distance of the interactions follows the order: I (O···H? N)II>III>IV, and the electrostatic character decreases along the sequence: I>II>III>IV.     

Experimental Evidence of Intramolecular CAr–H···O=C Hydrogen Bonds in the Structure of (Diaryl)tetrahydrofuranones Using Spectroscopic Tools

The occurrence of bifurcate H‐bonds C_Ar–H···O=C in the structure of (diaryl)‐tetrahydrofuranones was experimentally demonstrated using different methods and techniques. The consistent increasing spin–spin coupling constants ¹J(C,H) of the ortho‐H‐atoms and low‐field shift of v_C=O in IR spectra of 2,2‐(diaryl)tetrahydrofuran‐3(2H)‐ones relative to their 5,5‐diaryl counterparts, as well as pronounced dependence of the ortho‐C–H H‐atoms chemical shifts on the temperature and solvent polarity along with X‐ray diffraction analysis data unambiguously point to the existence of weak C_Ar–H···O=C H‐bonds in these molecules.     

Isolation of a Hydrogen‐Bonded Complex Based on the Anthranol/Anthroxyl Pair: Formation of a Hydrogen‐Atom Self‐Exchange System

A hydrogen‐bonded complex was successfully isolated as crystals from the anthranol/anthroxyl pair in the self‐exchange proton‐coupled electron transfer (PCET) reaction. The anthroxyl radical was stabilized by the introduction of a 9‐anthryl group at the carbon atom at the 10‐position. The hydrogen‐bonded complex with anthranol self‐assembled by π–π stacking to form a one‐dimensional chain in the crystal. The conformation around the hydrogen bond was similar to that of the theoretically predicted PCET activated complex of the phenol/phenoxyl pair. X‐ray crystal analyses revealed the self‐exchange of a hydrogen atom via the hydrogen bond, indicating the activation of the self‐exchange PCET reaction between anthranol and anthroxyl. Magnetic measurements revealed that magnetic ordering inside the one‐dimensional chain caused the inactivation of the self‐exchange reaction.     

Investigating Alanine–Silica Interaction by Means of First‐Principles Molecular‐Dynamics Simulations

In our attempts to achieve a detailed understanding of protein–silica interactions at an atomic level we have, as a first step, simulated a small system consisting of one alanine in different protonation states, and a hydroxylated silica surface, using a first‐principles molecular‐dynamics technique. The simulations are carried out in vacuo as well as in the presence of water molecules. In the case of a negatively charged surface and an alanine cation, an indirect proton transfer from the alanine carboxylic group to the surface takes place. The transfer involves several water molecules revealing an alanine in its zwitterionic state interacting with the neutral surface through indirect hydrogen bonds mediated by water molecules. During the simulation of the zwitterionic state the ammonium group eventually establishes a direct ? N? H???O? Si interaction, suggesting that the surface–amino group interaction is stronger than the interaction between the surface and the carboxylic group. In vacuum simulations, the amino group exhibits clearly stronger interactions with the surface than the carboxylic group.     

Reactions of Diazomethanes with 5‐Benzylidene‐3‐phenylrhodanine – A Computational Study

It has been shown previously that the reaction of diazomethane with 5‐benzylidene‐3‐phenylrhodanine ( 1 ) in THF at ?20° occurs at the exocyclic C?C bond via cyclopropanation to give 3a and methylation to yield 4 , respectively, whereas the corresponding reaction with phenyldiazomethane in toluene at 0° leads to the cyclopropane derivative 3b exclusively. Surprisingly, under similar conditions, no reaction was observed between 1 and diphenyldiazomethane, but the 2‐diphenylmethylidene derivative 5 was formed in boiling toluene. In the present study, these results have been rationalized by calculations at the DFT B3LYP/6‐31G(d) level using PCM solvent model. In the case of diazomethane, the formation of 3a occurs via initial Michael addition, whereas 4 is formed via [3+2] cycloaddition followed by N₂ elimination and H‐migration. The preferred pathway of the reaction of 1 with phenyldiazomethane is a [3+2] cycloaddition, subsequent N₂ elimination and ring closure of an intermediate zwitterion to give 3b . Finally, the calculations show that the energetically most favorable reaction of 1 with diphenyldiazomethane is the initial formation of diphenylcarbene, which adds to the S‐atom to give a thiocarbonyl ylide, followed by 1,3‐dipolar electrocyclization and S‐elimination.     

A theoretical study of the dependence of the ASxSi6−x cluster structures and properties on composition

The effect of the composition ratio between arsenic and silicon atoms on the structures and properties of As_xSi_6?x (x = 0–6) have been systematically investigated using the density functional theory at the B3LYP/6‐311+G* level. The As_xSi_6?x clusters prefer substitutional rather than attaching structures; the Si‐rich clusters favor Si₆‐like structures, whereas the As‐rich clusters prefer As₆‐like structures. The As atoms locating at the framework may explain the difficulty of removal of arsenic impurities from polycrystalline silicon. In general, the average binding energies gradually decrease, implying the As_xSi_6?x clusters become increasingly unstable as x increases. Both the HOMO‐LUMO gaps and the As‐dissociation energies present a strong even–odd alternation, implying alternating chemical stability, with the even x members being more stable than the odd ones. The dissociation energies of an As atom from As_xSi_6?x are: 3.07, 2.84, 1.84, 2.52, 1.86, and 2.85 eV, for x = 1–6, respectively, and 3.80, 3.08, 2.64, 3.01, 2.93, 3.16 eV for Si (x = 0–5). These dissociation energy results should provide a useful reference for further experimental investigations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Experimental and theoretical study of the intramolecular C–H···N and C–H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2‐(alkylsulfanyl)‐5‐amino‐1‐vinylpyrroles: a particular state of amine nitrogen

In the ¹H NMR spectra of the 1‐vinylpyrroles with amino‐ and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the H_A and H_B terminal methylene protons of the vinyl group is discovered. Also, the one‐bond ¹J(C_β,H_B) coupling constant is surprisingly greater than the ¹J(C_β,H_A) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π‐system of the pyrrole ring so that it is directed toward the H_B hydrogen. These factors are favorable to the emergence of the intramolecular C–H_B???N hydrogen bonding in the s‐cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the H_B hydrogen provides an opportunity of the intramolecular C–H_B???S hydrogen bonding in the s‐cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C–H???N and C–H???S hydrogen bonding. Therefore, an unusual high‐frequency shift of the H_B signal and the increase in the ¹J(C_β,H_B) coupling constant can be explained by the effects of hydrogen bonding. Copyright © 2013 John Wiley & Sons, Ltd.     

Van Der Waals heterogeneous layer‐layer carbon nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on graphene and graphane sheets

Noncovalent interactions involving aromatic rings, such as π···π stacking, CH···π are very essential for supramolecular carbon nanostructures. Graphite is a typical homogenous carbon matter based on π···π stacking of graphene sheets. Even in systems not involving aromatic groups, the stability of diamondoid dimer and layer‐layer graphane dimer originates from C − H···H − C noncovalent interaction. In this article, the structures and properties of novel heterogeneous layer‐layer carbon‐nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on [n ]‐graphane and [n ]‐graphene and their derivatives are theoretically investigated for n = 16–54 using dispersion corrected density functional theory B3LYP‐D3 method. Energy decomposition analysis shows that dispersion interaction is the most important for the stabilization of both double‐ and multi‐layer‐layer [n ]‐graphane@graphene. Binding energy between graphane and graphene sheets shows that there is a distinct additive nature of CH···π interaction. For comparison and simplicity, the concept of H‐H bond energy equivalent number of carbon atoms (noted as NHEQ), is used to describe the strength of these noncovalent interactions. The NHEQ of the graphene dimers, graphane dimers, and double‐layered graphane@graphene are 103, 143, and 110, indicating that the strength of C‐H···π interaction is close to that of π···π and much stronger than that of C‐H···H‐C in large size systems. Additionally, frontier molecular orbital, electron density difference and visualized noncovalent interaction regions are discussed for deeply understanding the nature of the C‐H···π stacking interaction in construction of heterogeneous layer‐layer graphane@graphene structures. We hope that the present study would be helpful for creations of new functional supramolecular materials based on graphane and graphene carbon nano‐structures. © 2017 Wiley Periodicals, Inc.     

DFT studies on hydrogen‐bonding,Stacking, and XH···π‐Bonded systems in presence of external electric field

Effect of external electric field on interaction energy as well as stability of the hydrogen‐bonding, stacking, and O? H π‐bonded systems are analyzed in the light of density functional theory (DFT) and conceptual DFT. Interaction energy and stability measured in terms of global hardness and highest occupied molecular orbital energy of the considered systems are observed to be sensitive toward the strength and direction of the applied external electric field. The curvature of the potential energy surfaces gets changed in presence of an external electric field. © 2015 Wiley Periodicals, Inc.     

Spectroscopic and Ab Initio Investigation of C−H⋅⋅⋅N Hydrogen‐Bonded Complexes of Fluorophenylacetylenes: Frequency Shifts and Correlations

The C?H???N hydrogen‐bonded complexes of several fluorophenyacetylenes with ammonia and methylamine were characterized by a redshift in the acetylenic C?H stretching vibration of the phenylacetylene moiety. These redshifts were linearly correlated with the stabilization energies calculated at the CCSD(T)/CBS//MP2‐aug‐cc‐pVDZ level. Analysis of various components of the interaction energy indicated that the observed redshifts were weakly correlated with the electrostatic component. The weaker linear correlation between the frequency shifts and the electrostatic component between two data sets can perhaps be attributed to the marginal differences in the Stark tuning rate and zero‐field shifts. The induction and exchange‐repulsion components were linearly correlated. However, the dispersion component depends on the nature of the hydrogen‐bond acceptor and shows a quantum jump when the hydrogen‐bond acceptor is changed from ammonia to methylamine. The observed linear correlation between the redshifts in the C?H stretching frequencies and the total stabilization energies is due to mutual cancellation of deviations from linearity between various components.     

N‐Triazolylpropanamide – an Acrylamide‐Derived Multifunctional Ligand for the Construction of Supramolecular Hydrogen‐Bonded Networks

The synthesis and single crystal X‐ray structure of the multifunctional acrylamide‐derived ligand N‐triazolylpropanamide ( 1 , = NTPA) are reported. The title compound was prepared in 72 % yield by Michael addition of 1, 2, 4‐triazole and acrylamide in the presence of Triton B (= trimethylbenzylammonium hydroxide) as catalyst. Treatment of 1 with FeCl₃(H₂O)₆ in MeOH/MeCN led to reduction and formation of the iron(II) complex (NTPA)₂FeCl₂(MeOH)₂ ( 2 , yellow prisms, 52 % yield). Both 1 and 2 were structurally characterized by X‐ray diffraction. Surprisingly, the NTPA ligands in 2 are coordinated to iron in a monodentate fashion through a triazole ring nitrogen atom. In the crystal, both compounds form supramolecular hydrogen‐bonded networks.