π-Hydrogen bonding wins over conventional hydrogen bonding interaction: a jet-cooled study of indole···furan heterodimer

In this study, we have explored the conformational landscape of the indole···furan dimer in a supersonic jet by using resonant two-photon ionization (R2PI) and IR-UV double-resonance spectroscopic techniques combined with dispersion-corrected density functional theory (DFT) calculations. Only one conformer of the dimer has been observed in the experiment. DFT/B97-D level calculation shows that N-H···π hydrogen-bonded conformer (T') is energetically more stable than the N-H···O hydrogen-bonded conformer (HB). Natural bond orbital (NBO) calculation also shows that the hydrogen-bonding interaction in the HB conformer is very weak. Finally, the structure of the observed dimer has been determined to be tilted T-shaped N-H···π hydrogen-bonded (T') from very excellent agreement between experimental and theoretical N-H stretch frequency. The most significant finding of this study is the first-time observation of a N-H···π bound conformer of a dimer, which wins over a conventional hydrogen-bonded conformer of the dimer.     

Competition between hydrogen bonding and dispersion interactions in the indole···pyridine dimer and (indole)2···pyridine trimer studied in a supersonic jet

Structures of the indole···pyridine dimer and (indole)2···pyridine trimer have been investigated in a supersonic jet using resonant two-photon ionization (R2PI) and IR-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. R2PI spectra of the dimer and the trimer recorded by electronic excitation of the indole moiety show that the red-shift in the band origin of the dimer with respect to the 0(0)(0) band of the monomer is larger compared to that of the trimer. The presence of only one conformer in the case of both the dimer and the trimer has been confirmed from IR-UV hole-burning spectroscopy. The structures of the dimer and the trimer have been determined from resonant ion dip infrared (RIDIR) spectra combined with ab initio as well as DFT/M05-2X and DFT/M06-2X calculations. It has been found that the dimer, observed in the experiment, has a V-shaped geometry stabilized by N–H···N and C–H···N hydrogen bonding interactions, as well as C–H···π and π···π dispersion interactions. The geometry of the trimer has been found to be a cyclic one stabilized by N–H···N, N–H···π, C–H···π, and C–H···N interactions. The most important finding of this current study is the observation of the mixed dimer and trimer, which are stabilized by hydrogen bonding as well as dispersion interactions.     

Revisiting the effects of sequence and structure on the hydrogen bonding and π-stacking interactions in nucleic acids

Calculated electron densities from PBE0/6-31+G(d,p) were analyzed with respect to the hydrogen bonding within a nucleic acid base pair and the π-stacking between sets of base pairs. From published X-ray crystallographic data, base pairs were isolated from a total of 11 DNA and RNA duplexes, and their experimental geometry was maintained throughout the analyses. Focusing solely on Watson-Crick base pairs, from the values of the electron density between interacting nuclei (at the bond critical points), we provide quantitative data on individual weak interactions. For hydrogen bonding, in addition to quantifying the scissoring effect in GC base pairs, the origin of the controversy around the relative stability of AT and AU base pairs is identified and resolved. Thus, it is illustrated how the conclusion as to their relative stability rests on the specific choice of oligonucleotides compared. For π-stacking, sequence effects for tandem AT base pairs are captured, quantified, and explained, and the greater sensitivity of GC, over AT, sequences to the rise parameter is established. The results presented here show that, from experimental geometries and their electron densities, previously determined effects of the sequence and structure of a duplex on the stabilizing interactions can be captured, quantified, and traced back to the geometry of the base pairs.     

Interchromophoric interactions in chiral X-type π-conjugated oligomers: a linear and nonlinear optical study

A concept of chiral, X-type organized π-conjugated oligomers, linked by means of a binaphthalene pincer, is presented. NMR spectroscopy and cyclic and differential pulse voltammetry indicate that these oligomers are in close proximity and influence each other in a through-space manner in their neutral as well as in their oxidized states. The interaction between the oligomers was also confirmed by UV-vis, CD, and emission spectroscopy. The synthetic versatility of this design also enables the development of heterocoupled binaphthalene derivatives BN1-2 and BN1-3, consisting of an electron-neutral oligothiophene or electron-rich oligomer and an electron-poor oligothiazole. Hyper-Rayleigh scattering data show a significant enhancement of the second-order nonlinear hyperpolarizability β for BN1-3 and BN1-2, in contrast with the homocoupled binaphthalene derivatives (BN1-1, BN2-2, and BN3-3). This enhancement provides direct proof for the through-space charge-transfer interaction between the p-type and the n-type oligomers within BN1-3 and BN1-2.     

Field-induced π-polarization in barrelene derivatives: a computational study based on structural variation

Barrelene, H–C(CH=CH)₃C–H, is an unsaturated polycyclic hydrocarbon containing three isolated double bonds in a non-planar arrangement. We have studied the transmission of field effects through the barrelene framework by analyzing the small structural changes occurring in the phenyl group of many Ph–C(CH=CH)₃C–X molecules, where X is a variable substituent. Molecular geometries have been determined by quantum chemical calculations at the HF/6-31G* and B3LYP/6-311++G** levels of theory. Comparison with the results obtained for the corresponding saturated molecules, the bicyclo[2.2.2]octane derivatives Ph–C(CH₂–CH₂)₃C–X, reveals a small, but significant, field-induced π-polarization of the barrelene cage, especially when the remote substituent is a charged group. Additional evidence of π-polarization is obtained by comparing the electric dipole moments of the two sets of uncharged molecules. The structural variation of the barrelene cage caused by the variable substituent in Ph–C(CH=CH)₃C–X molecules has also been investigated. It is much larger than that of the phenyl group and depends primarily on the electronegativity of the substituent. Particularly pronounced is the concerted variation of the non-bonded distance between the bridgehead carbons of the cage, r(C···C) ₁ ^BARR , and the average of the three C–C–C angles at the cage carbon bonded to the variable substituent, α ₁ ^BARR . A scattergram of r(C···C) ₁ ^BARR versus the corresponding parameter for bicyclo[2.2.2]octane derivatives, r(C···C) ₁ ^BCO , shows that the variation of r(C···C) ₁ ^BARR becomes gradually less pronounced than that of r(C···C) ₁ ^BCO as the electronegativity of the substituent increases.     

Constructing a novel nonlinear optical materials: substituents and heteroatoms in π-π systems effect on the first hyperpolarizability

By doping π-π systems with Li atom, a series of Li@sandwich configuration and Li@T-shaped configuration compounds have been theoretically designed and investigated using density functional theory. It is revealed that energy gaps (E _gap) between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of all compounds are in a range of 0.4–0.9 ev. When Li atom is introduced into different sandwich configuration π-π systems (C₆₀-toluene, C₆₀-fluorobenzene, C₆₀-phenol, C₆₀-benzonitrile), Li@C₆₀-benzonitrile exhibits considerable first hyperpolarizability as large as 19,759 au, which is larger by about 18,372–18,664 au than those of other compounds. When Li atom is introduced into different T-shaped configuration π-π systems (C₆₀-pyridine, C₆₀-pyrazine, C₆₀-1, 3, 5-triazine, C₆₀-pyridazine), Li@C₆₀-pyridazine is found to present largest first hyperpolarizability up to 67,945 au in all compounds. All compounds are transparency in the deep ultraviolet spectrum range. We hope that this study could provide a new idea for designing nonlinear optical materials using π-π systems as building blocks.     

A DFT study on the effect of hydrogen bonding on the reaction of a μ-benzoquinone diruthenium complex with acetylene

A DFT study was carried out to investigate the reaction mechanisms of a model μ-benzoquinone diruthenium complex {CpRu(μ-H)}₂(μ-η²:η²-C₆H₄O₂), derived from the experimental compound {Cp*Ru(μ-H)}₂(μ-η²:η²-C₆H₃RO₂) (R = H or R = Me, Cp* = η⁵-C₅Me₅), with acetylene both in aprotic and protic solvents. Results of calculations show that the influence of the solvent methanol on the reaction is mainly on the step of acetylene coordination. Enhanced hydrogen bonding is the reason for acceleration of the reaction in protic solvent, which is supported by NBO charge analysis.     

Tunable far-infrared laser spectroscopy in a planar supersonic jet: The Σ bending vibration of ArH35Cl

The lowest Σ bending vibration (02⁰0) of ArH³⁵Cl has been observed near 23.6 cm⁻¹ from P(23) to R(17), in a continuous planar jet expansion using a tunable far-infrared laser. A least-squares analysis has been performed to determine the centrifugal distortion constants for the ground and excited states, which will greatly facilitate the determination of an accurate intermolecular potential surface.     

Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state

Intramolecular charge transfer (ICT) of gaseous π-conjugated oligo-phenyleneethynylenes (OPE) induced by a homogeneous applied electric field has been theoretically investigated using a combined approach integrating molecular dynamics (MD) simulations and Perturbed Matrix Method calculations. In line with recent investigations, our results indicate the peculiar role of conformational transitions on OPE electronic properties which reflects on a strong temperature effect on ICT. Electron transfer reactions inducing chemical alteration on OPE, also taken into account in this study, revealed extremely important for explaining non-linear ICT effects and probably plays a central role in the mechanisms underlying molecular transport junctions. Our study further points out the necessity of using MD-based approach for modelling molecular electronics, even when relatively rigid molecular systems are concerned.     

Effect of temperature on O⊘ reactions and equilibria: A pulse radiolysis study

The pK_a of the hydroxyl radical was measured over the 20–80°C temperature range. At 20°C, the pK_a was 11.84 and fell to 10.81 at 80°C. The dissociation constant for the ozonide anion (O⊘₃⇌O₂+O⊘) was found to be 5.5 × 10^-7 mol dm^-3 at 20°C and 46.2 × 10^-7 mol dm^-3 at 70°C. The rate constants and activation energies for the reaction of O⊘ and OH with 2-propanol, methanol and 3-hexene-1,6-dicarboxylate ions have also been measured.     

Structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet: competition between N-H···N and N-H···F interactions

In the present work, we have investigated the structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet by employing resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. The R2PI spectrum of the dimer is recorded by electronic excitation of the 7-azaindole moiety, and a few low frequency intermolecular vibrations of the dimer are clearly observed in the spectrum. The electronic origin band of the dimer is red-shifted by 1278 cm(-1) from the S(1) ← S(0) origin band of 7-azaindole monomer. The presence of a single conformer of the dimer is confirmed by IR-UV and UV-UV hole-burning spectroscopic techniques. RIDIR (Resonant ion dip infrared) spectrum of the dimer shows a red-shift of 265 cm(-1) in the N-H stretching frequency with respect to that of the 7-azaindole monomer. Two planar double hydrogen bonded cyclic structures of the dimer have been predicted from DFT calculations. Comparison of experimental and theoretical N-H stretching frequencies confirms that the observed dimer is stabilized by N-H···N and C-H···N hydrogen bonding interactions. The less stable conformer with N-H···F and C-H···N interactions are not observed in the experiment. The competition between N-H···N and N-H···F interactions in the two dimeric structures are discussed from natural bond orbital (NBO) analysis. The current results demonstrate that fluorine makes a hydrogen bond of intermediate strength through cooperative interaction of another hydrogen bond (C-H···N) present in the dimer, although fluorine is believed to be very weak hydrogen bond acceptor.     

Electronic coupling through intramolecular π-π interactions in biscobaltocenes: a structural, spectroscopic, and magnetic study

The paramagnetic dinuclear complexes 1,8-bis(cobaltocenyl)naphthalene (2) and 1,8-bis[(pentamethyl-η(5)-cyclopentadienyl)(η(5)-cyclopentadiendiyl)cobalt(II)]naphthalene (4) were synthesized. The molecular structures were characterized by X-ray structure analysis and consisted of two cobaltocenes linked through a distorted naphthalene clamp. Electronic interactions between the two cobalt atoms were observed by cyclic voltammetric studies. Superconducting quantum interference device (SQUID) measurements of the pure compounds and diluted in their diamagnetic iron derivatives, as well as variable-temperature NMR spectroscopy experiments in solution are presented. Magnetic measurements revealed an antiferromagnetic coupling of the electrons in complexes 2 and 4. From NMR spectroscopy experiments, Curie behavior in the temperature range from -60 to +60 °C can be deduced. The electronic structure and magnetic behavior is supported by results of broken-symmetry DFT and multireference calculations along with UV/Vis spectroscopic data, which revealed an intramolecular through space π-π interaction between the cobaltocene units.     

Effect of inclusion complexation on the photophysical behavior of diphenylamine in β-cyclodextrin medium: a study by electronic spectra

Spectral characteristics of diphenylamine (DPA) have been investigated in β-cyclodextrin (β-CDx) solution. The formation of the complex was revealed by UV, steady state and time-resolved fluorescence spectroscopy. The stoichiometry of DPA:β-CDx complex, determined using Benesi-Hildebrand equation and Job's continuous variation method is 1:1. The binding constants calculated from various methods are reported. This inclusion complex formation from DPA and β-CDx was also confirmed by the FT-IR spectral study and SEM image analysis of solid complex prepared by co-precipitation method.     

Effect of intermolecular O-H ⋯ O hydrogen bonding on the molecular structure of phenol: An ab initio molecular orbital study

The effect of intermolecular O-H O hydrogen bonding on the molecular structure of phenol has been studied by SCF ab initio MO calculations at the HF/6-31G * level. The systems investigated are eight phenol-water complexes and the dimer and trimer of phenol. Optimized geometries show that hydrogen bond formation causes a consistent pattern of changes in the structure of the molecule. When phenol acts as a proton donor, the expected increase ofr (O-H) is accompanied by a slight decrease ofr(C-O) and of the internal ring angles at theipso andpara positions, and by an increase ofr(C _ipso © _ortho ). These changes suggest that the relative contribution of polar canonical forms to the electronic structure of the molecule increases upon hydrogen bond formation, since this enhances the strength of the interaction. The opposite changes occur when phenol acts as a proton acceptor, except forr(O-H), which is the same as in the free molecule. If phenol acts as a proton donorand as a proton acceptor, the two hydrogen bonds become stronger due to a synergic effect. In this case, however, the structural deformation of the molecule is less pronounced than in the previous cases, due to the opposite effect of the two hydrogen bonds. The available experimental evidence on gas-crystal structural differences for phenol is critically reviewed, also in the light of the present results on gas-phase complexes.     

A quantum chemical study of conformational and tautomeric preferences, intramolecular hydrogen bonding and π-electron delocalization on dinitrosomethane; in gas phase and water solution

HF, B3LYP, and MP2 methods with the standard basis set, 6-311++G(d,p), were employed to study various aspects of dinitrosomethane (DNM). These results are compared with the outcomes of G2, G2MP2, G3, and CBS-QB3 methods. In the present study, we first characterized the equilibrium conformations, especially global minima. In general, the nitroso-oxime (NO) tautomers of DNM are stabler than the dioxime and dinitroso ones. Furthermore, it was found that the stablest form of NO tautomer is global minima among the known local minima. Surprisingly, the chelated form of NO tautomer, with O–H···O intramolecular hydrogen bond (IMHB), is less stable than the global minimum. In spite of this instability, we comprehensively studied various aspects of IMHB to evaluate the effect of heteroatom’s (N). The results of open–close and related rotamer models predict that the heteroatoms weaken the hydrogen bond, whereas, the geometric, topologic, and natural bond orbital parameters emphasize on opposite conclusion. The HOMA of aromaticity aromaticity index clearly predicts that the π-electron delocalization of chelated form of NO tautomer is greater than the malonaldehyde. Finally, the solvent effects on the properties of DNM tautomers have been estimated by continuum (PCM, IPCM, and SCIPCM), discrete, and mixed models. Theoretical results clearly show that the potential energy surface of DNM, especially global minima, is strongly affected by the solvent.     

A computational study of cation-π interactions in polycyclic systems: exploring the dependence on the curvature and electronic factors

Density functional theory (B3LYP) calculations with double and triple-ζ quality basis sets were performed on the Li⁺ and Na⁺ π-complexes of corannulene 2, sumanene 3CH₂, heterosumanenes 3X, triphenylene 4 and heterotrindenes 5X. The metal ions bind to both convex and concave faces of buckybowls, with a consistent preference to bind to the convex surface by about 1-4 kcal/mol. The metal ion complexation with the π-framework of the central six-membered ring span wider range compared to benzene, indicating the control of size, curvature and electronic perturbations over the strength of cation-π interactions. Computations show that the bowl-to-bowl inversion barriers are only slightly altered upon metal complexation, indicating the continuity of bowl-to-bowl inversion despite metal complexation. We have calculated the binding energies of model systems, triphenylene (4) and heterotrindenes (5X), which indicate that the interaction energies are controlled by electronic factors. While the inversion barrier is dependent mainly on the size of the heteroatom, the extent of binding is independent of the size of the atom or the bowl depth.     

Effect of noncovalent complexations on coordination interactions in a tricomponent system ofβ-cyclodextrin,copper chloride and hexamethylene tetramine

This study reveals that the noncovalent complexation betweenβ-CD and Cu（HMTA）²⁺ makes a positive contribution to the coordination interaction between Cu²⁺ and HMTA in a tricomponent system.Besides,mono- and binuclear complexes:[β-CDCu]⁺ and[Cu·β-CDCu]⁺ were observed under the condition of ESI-MS.