New chiral macrocyclic phosphoramidate self‐associated by an intermolecular N–H ··· O = P hydrogen bond

New macrocyclic chiral phosphoramidates containing 2,5‐diaryl‐1,3, 4‐oxadiazole and L‐alanine methyl ester units were synthesized by a convenient one‐pot procedure, X‐ray analysis of one chiral macrocycle shows that the phosphoramidate molecules are self‐associated by intermolecular N–H ··· O = P hydrogen bonds, the layer stacking along the b axis forming channels parallel to the b axis. © 2001 John Wiley & Sons, Inc. Heteroatom Chem 12:480–484, 2001     

Computational study of structure,electronic, and microscopic charge transport properties of small conjugated diketopyrrolopyrrole‐thiophene molecules

π‐Conjugated small molecules containing diketopyrrolopyrrole (DPP) and thiophene moieties represent a modern class of functional materials that exhibit promising charge transport properties and therefore have great potential as building blocks of active elements of electronic devices. As a starting point of this computational study, the molecular structure, electronic characteristics, and reorganization energies associated with electron or hole transfer are considered. Prediction of molecular crystal packing is followed by the calculation of couplings between adjacent molecules and detection of the effective charge transfer pathways. Finally, the rates of charge transfer process are evaluated. The obtained results shed light not only on the properties of materials containing low‐molecular species but also serve as a benchmark for further classical force‐field simulations of DPP‐based polymers.     

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane): single‐crystal X‐ray and theoretical study

Single crystals of (2S,5R)‐2‐isopropyl‐5‐methyl‐7‐(5‐methylisoxazol‐3‐yl)cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane), C₁₆H₂₆N₂O₅, have been studied via X‐ray diffraction. The tetraoxazocane ring adopts a boat–chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6‐31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,?1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O—C—O and N—C—O fragments. There is a two‐cross hyperconjugation in the N—C—O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C—O bond (σ*_C—O) and vice versa between lpO and σ*_C—N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,?1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C—H…N and C—H…O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,?1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C—H…N interactions being electrostatic in origin. The molecules are further stacked due to C—H…O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.     

Molecular Engineering of Conjugated Acetylenic Polymers for Efficient Cocatalyst‐free Photoelectrochemical Water Reduction

Conjugated polymers featuring tunable band gaps/positions and tailored active centers, are attractive photoelectrode materials for water splitting. However, their exploration falls far behind their inorganic counterparts. Herein, we demonstrate a molecular engineering strategy for the tailoring aromatic units of conjugated acetylenic polymers from benzene‐ to thiophene‐based. The polarized thiophene‐based monomers of conjugated acetylenic polymers can largely extend the light absorption and promote charge separation/transport. The C≡C bonds are activated for catalyzing water reduction. Using on‐surface Glaser polycondensation, as‐fabricated poly(2,5‐diethynylthieno[3,2‐b]thiophene) on commercial Cu foam exhibits a record H₂‐evolution photocurrent density of 370 μA cm^?2 at 0.3 V vs. reversible hydrogen electrode among current cocatalyst‐free organic photocathodes (1–100 μA cm^?2). This approach to modulate the optical, charge transfer, and catalytic properties of conjugated polymers paves a critical way toward high‐activity organic photoelectrodes.     

Thioacetanilide at 120 K

The title compound, C₈H₉NS, has four symmetry‐independent molecules in the asymmetric unit. These molecules link into two independent infinite N—H...S hydrogen‐bonded chains in the a‐axis direction with graph‐set notation C₂²(8). The NH—CS group adopts a trans conformation and forms a dihedral angle of about 50° with the phenyl ring. The intermolecular hydrogen‐bond energy calculated by the density functional theory (DFT) method is −14.95 kJ mol⁻¹. The correlation between the IR spectrum of this compound and the hydrogen‐bond energy is also discussed. This molecular system is of interest because of its biological function.     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.     

吡咯并吡咯二酮与低聚噻吩共聚物电荷传输性质的理论研究

利用密度泛函理论对吡咯并吡咯二酮(DPP)与噻吩形成共聚物的低聚物(PDPP-n T)m的电子结构及二体堆积模型的电荷传输性质进行计算.结果表明,随着聚合物单元内DPP浓度增加,噻吩数减少,聚合物分子的HOMO和LUMO能级同时降低,并且HOMO-LUMO带隙变小;链内相邻DPP单元的电子波函数有效重叠增大,显著改善了链内的电子传输能力;同时分子主链的刚性增强,使分子链间LUMO轨道重叠增强,电子转移积分增大;最终体系由p型向双极性材料转化.     

Theoretical characterization and design of small molecule donor material containing naphthodithiophene central unit for efficient organic solar cells

To seek for high‐performance small molecule donor materials used in heterojunction solar cell, six acceptor–donor–acceptor small molecules based on naphtho[2,3‐b:6,7‐b′]dithiophene ( NDT ) units with different acceptor units were designed and characterized using density functional theory and time‐dependent density functional theory. Their geometries, electronic structures, photophysical, and charge transport properties have been scrutinized comparing with the reported donor material NDT(TDPP)₂ ( TDPP = thiophene‐capped diketopyrrolopyrrole). The open circuit voltage (V_oc), energetic driving force(ΔE_L‐L), and exciton binding energy (E_b) were also provided to give an elementary understanding on their cell performance. The results reveal that the frontier molecular orbitals of 3–7 match well with the acceptor material PC₆₁BM , and compounds 3–5 were found to exhibit the comparable performances to 1 and show promising potential in organic solar cells. In particular, comparing with 1 , system 7 with naphthobisthiadiazole acceptor unit displays broader absorption spectrum, higher V_oc, lower E_b, and similar carrier mobility. An in‐depth insight into the nature of the involved excited states based on transition density matrix and charge density difference indicates that all S₁ states are mainly intramolecular charge transfer states with the charge transfer from central NDT unit to bilateral acceptor units, and also imply that the exciton of 7 can be dissociated easily due to its large extent of the charge transfer. In a word, 7 maybe superior to 1 and may act as a promising donor candidate for organic solar cell. © 2013 Wiley Periodicals, Inc.     

N‐Methyl‐N‐phenylaminomethyl 2‐naphthyl ketone: an X‐ray diffraction and density functional theory study

The crystallographically observed molecular structure of the title compound, C₁₉H₁₇NO, and its inverted counterpart are compared with that calculated by density functional theory (DFT) at the B3LYP/6‐311++G(d,p) level. The results from both methods suggest that the observed molecular conformation of the title compound is primarily determined by intermolecular interactions in the crystal structure. The periodic organization of the molecules is stabilized by weak C—H...O and C—H...π hydrogen bonds and thus a two‐dimensional puckered network consisting of R₄⁴(22) and R₄⁴(38) ring motifs is established. The title molecule has a (+)‐antiperiplanar conformation about the C—C bond in the aminoacetone bridge. The pyramidal geometry observed around the vertex N atom is flattened by the presence of bulky phenyl and naphthylethanone fragments.     

N,N′‐Dicyclohexyl‐N‐[4‐(1H‐indol‐3‐yl)butanoyl]urea

The title compound, C₂₅H₃₅N₃O₂, is a novel urea derivative. Pairs of intermolecular N—H...O hydrogen bonds join the molecules into centrosymmetric R₂²(12) and R₂²(18) dimeric rings, which are alternately linked into one‐dimensional polymeric chains along the [010] direction. The parallel chains are connected via C—H...O hydrogen bonds to generate a two‐dimensional framework structure parallel to the (001) plane. The title compound was also modelled by solid‐state density functional theory (DFT) calculations. A comparison of the molecular conformation and hydrogen‐bond geometry obtained from the X‐ray structure analysis and the theoretical study clearly indicates that the DFT calculation agrees closely with the X‐ray structure.     

Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

Gas-phase interaction of thiophene with the Ti(8)C(12)(+) and Ti(8)C(12) met-car clusters

The reactivity of the Ti(8)C(12)(+) met-car cation toward thiophene was investigated using density functional theory (DFT) and mass selective ion chemistry. It is shown that the experimentally observed mass spectrum can be well described by the DFT calculations. In contrast to the weak bonding interactions seen for thiophene on a TiC(001) surface, the Ti(8)C(12)(+) met-car cation is able to interact strongly with up to four thiophene molecules with the cluster staying intact. In the most stable conformation, the thiophene molecules bond to the four low-coordinated Ti(0) sites of Ti(8)C(12)(+) via a eta(5)-C,S coordination. The stability and the activity of the Ti(8)C(12)(+) met-car is observed to increase with an increasing number of attached thiophene molecules at the Ti(0) sites, which is associated with a significant transfer of electron density from thiophene to the cluster. The additional electron density on the Ti(8)C(12)(+) cation cluster, however, is not sufficient to cleave the C-S bonds of thiophene and the dissociation reaction of thiophene is predicted to be a highly activated process. By contrast, DFT calculations for the neutral Ti(8)C(12) met-car predict that the dissociation reaction leading to adsorbed S and C(4)H(4) fragments is energetically favorable for the first thiophene molecule. The binding behavior for subsequent addition of thiophene molecules to the neutral met-car is also presented and compared to that of the cation.     

CB‐TE2A+·Cl−·3H2O: a short intermolecular hydrogen bond between zwitterionic bicyclo[6.6.2]tetraamine macrocycles

1,4,8,11‐Tetraazabicyclo[6.6.2]hexadecane‐4,11‐diacetic acid (CB‐TE2A) is of much interest in nuclear medicine for its ability to form copper complexes that are kinetically inert, which is beneficial in vivo to minimize the loss of radioactive copper. The structural chemistry of the hydrated HCl salt of CB‐TE2A, namely 11‐carboxymethyl‐1,8‐tetraaza‐4,11‐diazoniabicyclo[6.6.2]hexadecane‐4‐acetate chloride trihydrate, C₁₆H₃₁N₄O₄⁺·Cl⁻·3H₂O, is described. The compound crystallized as a positively charged zwitterion with a chloride counter‐ion. Two of the amine groups in the macrocyclic ring are protonated. Formally, a single negative charge is shared between two of the carboxylic acid groups, while one chloride ion balances the charge. Two intramolecular hydrogen bonds are observed between adjacent pairs of N atoms of the macrocycle. Two intramolecular hydrogen bonds are also observed between the protonated amine groups and the pendant carboxylate groups. A short intermolecular hydrogen bond is observed between two partially negatively charged O atoms on adjacent macrocycles. The result is a one‐dimensional polymeric zigzag chain that propagates parallel to the crystallographic a direction. A second intermolecular interaction is a hydrogen‐bonding network in the crystallographic b direction. The carbonyl group of one macrocycle is connected through the three water molecules of hydration to the carbonyl group of another macrocycle.     

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.     

Influence of Backbone Chlorination on the Electronic Properties of Diketopyrrolopyrrole (DPP)‐Based Dimers

Chlorination of π‐conjugated backbones is garnering great interest because of fine‐tuning electronic properties of conjugated materials for organic devices. Herein we report a synthesis of thiophene‐based diketopyrrolopyrrole (DPP) dimers and their chlorinated counterparts by introducing a chlorine atom in the outer thiophene ring to investigate the influence of the chlorination on charge transport. The backbone chlorination lowers both the HOMO and the LUMO of the dimers and leads to a blue‐shift of maximum absorption in compared to unsubstituted counterparts. X‐ray analysis reveals that the chlorine atom prompts the outer thiophene ring out of the planarity of the backbone with a relatively large torsional angle. The chlorinated dimers exhibit slipped one‐dimensional packing decorated with multiple intermolecular interactions, because of a combination of a negative inductive effect and a positive mesomeric effect of the halogen atom, which might facilitate charge transport within the oligomeric backbones. The mobility in the single‐crystal OFET devices of the chlorinated dimers is up to 1.5 cm² V^?1 s^?1, which is two times higher than that of the non‐chlorinated DPP dimers. Our results indicate that the chlorine atom plays a key role in directing non‐covalent interactions to lock the slipped stacks, enabling electronic coupling between adjacent molecules for efficient charge transport. In addition, our results also demonstrate that these DPP dimers with straight n‐octyl chains exhibit higher mobilities than the dimers with branched 2‐ethylhexyl chains.     

Probing the relationships between molecular conformation and intermolecular contacts in N,N‐dibenzyl‐N′‐(furan‐2‐carbonyl)thiourea

In the crystal structure of the title compound, C₂₀H₁₈N₂O₂S, molecules are linked by bifurcated C—H...O hydrogen‐bond interactions, giving rise to chains whose links are composed of alternating centrosymmetrically disposed pairs of molecules and characterized by R₂²(10) and R₂²(20) hydrogen‐bonding motifs. Also, N—H...S hydrogen bonds form infinite zigzag chains along the [010] direction, which exhibit the C(4) motif. Hirshfeld surface and fingerprint plots were used to explore the intermolecular interactions in the crystal structure. This analysis confirms the important role of C—H...O hydrogen bonds in the molecular conformation and in the crystal structure, providing a potentially useful tool for a full understanding of the intermolecular interactions in acylthiourea derivatives.     

Adlayer structures of aza- and/or oxo-bridged calix[2]arene[2]triazines on Au(111) investigated by scanning tunneling microscopy (STM)

The adlayers formed by a series of aza- and/or oxo-bridged calix[2]arene[2]triazines on Au(111) surfaces were investigated by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. 1,3-Alternate configurations of these molecules are preserved on gold surfaces as in their three-dimensional crystals. STM images show that the cavity sizes of these molecules are finely tuned by substituting the bridging nitrogen atom with oxygen atoms, which change the strengths and densities of the intermolecular hydrogen bonds. Hydrogen bond interaction influences the molecular orientation and conformation in the adlayers, and it plays a key role in the formation of these two-dimensional supramolecular architectures. Coadsorption of calix[2]arene[2]triazine with 1,3,5-tris(5-carboxyamyloxy)benzene (TCAB) intervenes with the intermolecular hydrogen bond formations among the calix[2]arene[2]triazine molecules and consequently causes a conformational transition of the calixarene molecules from rhombic to square. These results demonstrate the role of hydrogen bonds in molecular assembly formations.     

Structure‐Independent Conductance of Thiophene‐Based Single‐Stacking Junctions

The experimental investigation of intermolecular charge transport in π‐conjugated materials is challenging. Herein, we describe the investigation of charge transport through intermolecular and intramolecular paths in single‐molecule and single‐stacking thiophene junctions by the mechanically controllable break junction (MCBJ) technique. We found that the ability for intermolecular charge transport through different single‐stacking junctions was approximately independent of the molecular structure, which contrasts with the strong length dependence of conductance in single‐molecule junctions with the same building blocks, and the dominant charge‐transport path of molecules with two anchors transited from an intramolecular to an intermolecular path when the degree of conjugation increased. An increase in conjugation further led to higher binding probability owing to the variation in binding energies, as supported by DFT calculations.     

Theoretical Study on Hydrogen Bonding of Mono‐ and Dihydrated Complexes of 7‐(3′‐Pyridyl)indole in Excited States

The intermolecular hydrogen bonds of mono‐ and dihydrated complexes of 7‐(3′‐Pyridyl)indole (7‐3′PI) have been investigated using the time‐dependent density functional theory (TD‐DFT) method. The electrostatic potential analysis of monomer 7‐3′PI and 7‐(3′‐Pyridyl)indole‐water (7‐3′PI‐W) indicates that an intermolecular hydrogen bond between two waters can be formed for 7‐(3′‐Pyridyl)indole‐2water (7‐3′PI‐2W) complex. The calculated bond lengths of the intermolecular hydrogen bonds of 7‐3′PI‐W and 7‐3′PI‐2W in the S₁ state (the first excited singlet state) are all shortened compared to the ground state. By the analysis of bond length, charge population and infrared spectra, it is demonstrated that the intermolecular hydrogen bonds of 7‐3′PI‐W and 7‐3′PI‐2W are all strengthened upon electronic excitation to the S1 state. Moreover, the fluorescence of 7‐3′PI‐W and 7‐3′PI‐2W are all red‐shifted to larger wavelength compared to monomer 7‐3′PI. The red‐shift of fluorescence peak of 7‐3′PI‐W and 7‐3′PI‐2W should be attributed to the change of hydrogen bond interaction before and after photoexcitation. Therefore, it can be concluded that the intermolecular hydrogen bonding strengthening in the excited S₁ state induces the fluorescence weakening of 7‐3′PI.     

Hyperbranched narrow‐bandgap DPP homopolymers synthesized via direct arylation polycondensation

Narrow bandgap and hyperbranched polymers (h‐PTDPP) are synthesized by directly arylation polymerization (DAP) of 2‐bromo‐thiophene‐flanked diketopyrrolopyrrole (Br‐TDPP) as the monomer. Their optical properties as well as chemical structures are studied. The detailed optimization of DAP conditions from catalyst, temperature, solvent, ligand to additive not only leads to high molecular weight h‐PTDPP, but also provides some insight to minimize structural defects in DAP when brominated TDPP is involved as a monomer. The increase in the degree of branching results in lower charge‐carrier mobilities in organic field‐effect transistors involving h‐PTDPP‐3 as the semiconducting channel. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 1040–1047