Effects of extending the computational model on DNA-protein T-shaped interactions: the case of adenine-histidine dimers

The MP2/6-31G*(0.25) π-π or π(+)-π T-shaped (edge-to-face) interactions between neutral or protonated histidine and adenine were considered using computational models of varying size to determine the effects of the protein and DNA backbones on the preferred dimer structure and binding strength. The overall consequences of the backbones are reasonably subtle for the neutral adenine-histidine T-shaped dimers. Furthermore, the minor changes in the binding strengths of these dimers upon model extension arise from additional (attractive) backbone-π (bb-π) contacts and changes in the preferred π-π orientations, which is verified by the quantum theory of atoms in molecules (QTAIM). Since the binding strength of the extended dimer equals the sum of the individual backbone-π and π-π contributions, the π-π component is not appreciably affected by polarization of the ring upon inclusion of the biological backbone. In contrast, the larger effect of the backbone on the protonated histidine dimers cannot simply be predicted as the sum of changes in the π-π and bb-π components regardless of the dimer type or model. This suggests, and QTAIM qualitatively supports, that the magnitude of the π(+)-π contribution changes, which is likely due to alterations in the electrostatic landscape of the monomer rings upon inclusion of the biological backbone that largely affect T-shaped dimers. These findings differ from those previously reported for (neutral) π-π stacked and (metallic) cation-π interactions, which highlights the distinct properties of each (π-π, π(+)-π, and cation-π) classification of noncovalent interaction. Furthermore, these results emphasize the importance of considering backbone-π interactions when analyzing contacts that appear in experimental crystal structures and cautions the use of truncated models when evaluating the magnitude of the π(+)-π contribution present in large biological complexes.     

Differences in structure, energy, and spectrum between neutral, protonated, and deprotonated phenol dimers: comparison of various density functionals with ab initio theory

We have carried out extensive calculations for neutral, cationic protonated, anionic deprotonated phenol dimers. The structures and energetics of this system are determined by the delicate competition between H-bonding, H-π interaction and π-π interaction. Thus, the structures, binding energies and frequencies of the dimers are studied by using a variety of functionals of density functional theory (DFT) and M?ller-Plesset second order perturbation theory (MP2) with medium and extended basis sets. The binding energies are compared with those of highly reliable coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set (CBS) limit. The neutral phenol dimer is unique in the sense that its experimental rotational constants have been measured. The geometry of the neutral phenol dimer is governed by the hydrogen bond formed by two hydroxyl groups and the H-π interaction between two aromatic rings, while the structure of the protonated/deprotonated phenol dimers is additionally governed by the electrostatic and induction effects due to the short strong hydrogen bond (SSHB) and the charges populated in the aromatic rings in the ionic systems. Our salient finding is the substantial differences in structure between neutral, protonated, and deprotonated phenol dimers. This is because the neutral dimer involves in both H(π)···O and H(π)···π interactions, the protonated dimer involves in H(π)···π interactions, and the deprotonated dimer involves in a strong H(π)···O interaction. It is important to compare the reliability of diverse computational approaches employed in quantum chemistry on the basis of the calculational results of this system. MP2 calculations using a small cc-pVDZ basis set give reasonable structures, but those using extended basis sets predict wrong π-stacked structures due to the overestimation of the dispersion energies of the π-π interactions. A few new DFT functionals with the empirical dispersion give reliable results consistent with the CCSD(T)/CBS results. The binding energies of the neutral, cationic protonated, and anionic deprotonated phenol dimers are estimated to be more than 28.5, 118.2, and 118.3 kJ mol(-1), respectively. The energy components of the intermolecular interactions for the neutral, protonated and deprotonated dimers are analyzed.     

A comparative study of the dimers of selected hydroxybenzenes

Hydroxybenzenes are the parent compounds of large classes of derivatives, many of which exhibit biological activities. This work presents the results of a comparative study of the dimers of selected hydroxybenzenes, considering all the possible mutual geometrical arrangements of the two monomers and comparing their relative stabilities and interaction energies. The OH···OH hydrogen bond between the two monomers is the dominant stabilizing factor, with frequent preference for mutual perpendicularity of the two aromatic rings. C? H···O unconventional H‐bonds, OH···π unconventional H‐bonds, H···π interactions and π··π interactions also may play significant roles. The factors stabilizing individual hydroxybenzenes (presence of intramolecular hydrogen bonds; number, positioning and orientation of the OH groups; symmetry features) have greater influence on the dimers' relative energy than on the interaction energy between monomers. While results from different calculations methods (HF, MP2, and DFT/B3LYP) show consistency for all the features just‐mentioned, they show some relevant differences in the way they take into account different types of interactions between monomers, resulting in some differences in the geometry arrangements of the monomers in the lowest energy dimers and in differences in the relative preferences among higher‐energy dimer geometries. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Etude du Groupe Azomethine par RMN du Carbone-13. Cétimines et Dibenzo[b,f] diazocines[1,4]

Carbon-13 chemical shifts (substituents effects, variations of shielding and deshielding related to the magnitude of n.π or π.π interactions) not only confirm the non-planar conformation of ketimines of the benzalaniline type, but provide torsional angles of the aromatic rings. Carbon-13 chemical shifts of dibenzo[b,f] diazocines[1,4] confirm the tub-like conformations and the presence of n.π and π.π interactions.     

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.     

Enormously extended π-electronic conjugation system of dimeric octaethylporphyrin transmitted with anthracene

Based on the fact that anthracene (Anth) possesses much higher similarity in electron-releasing ability to porphyrin nucleus than the other polyacenes, the dimeric octaethylporphyrin (OEP) derivatives 4 and 5 (OEP–Anth–OEP) were synthesized and their structure–property relationships were examined, as compared with related OEP dimers 1–3. Among them, the derivative 4 showed enormously high electronic communication between two terminal OEP rings, potentially providing a suitable unit of the electronic structure for molecular design of the OEP devices operating with less energy and with higher sensitivity to outside stimuli.     

双卟啉化合物的构象平衡及π-π作用研究

制备并表征了一系列以柔韧烷氧化相连的自由双卟啉及其锌配合物,以＾１Ｈ－ＮＭＲ考察了烷氧链长度及锌离子对双卟啉构象平衡的影响。结果表明,双卟啉存在开放式及闭合式构象平衡,随烷氧链的增长,构象平衡由开放式向闭合式移动,当链上碳原子数为４时最有利于双卟啉形成闭合式构象。     

Effects of carbon-metal-carbon linkages on the optical, photophysical, and electrochemical properties of phosphametallacycle-linked coplanar porphyrin dimers

5-(Diphenylphosphanyl)-10,15,20-triarylporphyrins (meso-phosphanylporphyrins) underwent complexations with palladium(II) and platinum(II) salts to afford phosphapalladacycle- and phosphaplatinacycle-fused coplanar porphyrin dimers, respectively, via regioselective peripheral β-C-H activation of the meso-phosphanylporphyrin ligands. The optical and electrochemical properties of these metal-linked porphyrin dimers as well as their porphyrin monomer/dimer references were investigated by means of steady-state UV-vis absorption/fluorescence spectroscopy, cyclic and differential pulse voltammetry, time-resolved spectroscopy (fluorescence and transient absorption lifetimes and spectra), and magnetic circular dichroism spectroscopy. All the observed data clearly show that the palladium(II) and platinum(II) linkers play crucial roles in the electronic communication between two porphyrin chromophores at the one-electron oxidized state and in the singlet-triplet intersystem-crossing process at the excited state. It has also been revealed that the C-Pt-C linkage makes more significant impacts on these fundamental properties than the C-Pd-C linkage. Furthermore, density functional theory calculations on the metal-linked porphyrin dimers have suggested that the antibonding dπ-pπ orbital interaction between the peripherally attached metal and adjacent pyrrolic β-carbon atoms destabilizes the highest occupied molecular orbitals of the porphyrin π-systems and accounts for the observed unique absorption properties. On the basis of these experimental and theoretical results, it can be concluded that the linear carbon-metal-carbon linkages weakly but definitely perturb the optical, photophysical, and electrochemical properties of the phosphametallacycle-linked coplanar porphyrin dimers.     

The nmr spectra of porphyrins—15: Self-aggregation in zinc(II) protoporphyrin-IX dimethyl ester

Complex formation in Zn(II) protoporphyrin-IX dimethyl ester has been studied by proton and ¹³C NMR spectroscopy. The large concentration dependence of the spectra has been studied by the technique of porphyrin/axial ligand titration, which together with selective decoupling and regiospecific deuterium labelling allows the assignment of all the peripheral proton and ¹³C nuclei in both the monomeric and aggregated species. Titration of the metalloporphyrin with various basic ligands (pyrrolidine, pyridine, lutidine) showed that dissociation of the aggregate was complete for a 1:1 porphyrin/added base ratio. The concentration dependence of the spectra was then analyzed to give the monomer and monomer-dimer shifts for all the assigned nuclei. Analysis of the monomer-dimer shifts in terms of the ring current model gives good agreement with a dimer geometry in which the inter-ring separation is ca. 4.5 Å and there is a smaller lateral displacement of the porphyrin rings. The dimer geometry is such that rings A and B of one porphyrin molecule are situated over rings C and D of the other. These results confirm our earlier suggestions of intermolecular metal-to-porphyrin binding in these metalloporphyrins, and further suggest that charge-transfer interactions may also be present in appropriate cases. The discrepancy between the absolute values of the observed and calculated monomer-dimer shifts, which was formerly attributed to multiple aggregation, is now suggested to be due to ensemble-averaging in the dimer structure.     

Through Bridge Spin Coupling in Homo- and Heterobimetallic Porphyrin Dimers upon Stepwise Oxidations: A Spectroscopic and Theoretical Investigation

We have described copper(II)-iron(III) and copper(II)-manganese(III) heterobimetallic porphyrin dimers and compared them with the corresponding homobimetallic analogs. UV-visible spectra are very distinct in the heterometallic species while electrochemical studies demonstrate that these species, as compared to the homobimetallic analog, are much easier to oxidize. Combined Mössbauer, EPR, NMR, magnetic and UV-visible spectroscopic studies show that upon 2e-oxidation of the heterobimetallic complexes only ring-centered oxidation occurs. The energy differences between HOMO and LUMO are linearly dependent with the low-energy NIR band obtained for the 2e-oxidized complexes. Also, strong electronic communication between two porphyrin rings through the bridge facilitates coupling between various unpaired spins present while the coupling model depends on the nature of metal ions used. While unpaired spins of Fe(III) and the porphyrin π-cation radical are strongly antiferromagnetically coupled, such coupling is rather weak between Mn(III) and a porphyrin π-cation radical. Moreover, the coupling between two π-cation radicals are much stronger in the 2e-oxidized complexes of dimanganese(III) and copper(II)-manganese(III) porphyrin dimers as compared to their diiron(III) and copper(II)-iron(III) analogs. Furthermore, coupling between the unpaired spins of a π-cation radical and copper(II) is much stronger in the 2e-oxidized complex of copper(II)-iron(III) porphyrin dimer as compared to its copper(II)-manganese(III) analog. The Mulliken spin density distributions in 2e-oxidized homo- and heterobimetallic complexes show symmetric and asymmetric spread between the two macrocycles, respectively. In both the 2e-oxidized heterobimetallic complexes, the Cu(II) porphyrin center acts as a charge donor while Fe(III)/Mn(III) porphyrin center act as a charge acceptor. The experimental observations are also strongly supported by DFT calculations.     

Experimental support for the role of dispersion forces in aromatic interactions

Herein a core scaffold of 1-phenylnaphthalenes and 1,8-diphenylnaphthalenes with different substituents on the phenyl rings was used to study substituent effects on parallel-displaced aromatic π???π interactions. The energetics of the interaction was evaluated in gas phase based on the standard molar enthalpies of formation, at T=298.15?K, for the compounds studied; these values were derived from the combination of the results obtained by combustion calorimetry and Knudsen/Quartz crystal effusion. A homodesmotic gas-phase reaction scheme was used to quantify and compare the intramolecular interaction enthalpies in various substituted 1,8-diphenylnaphthalenes. The application of this methodology allowed a direct evaluation of aromatic interactions, and showed that substituent effects on the interaction enthalpy cannot be rationalized solely on classical electrostatic grounds, because no correlation with the σ(meta) or σ(para) Hammett constants was observed. Moreover, the results obtained indicate that aromatic π???π interactions are significantly enhanced by substitution, in a way that correlates with the ability of the interacting aryl rings to establish dispersive interactions. A combined experimental and computational approach for calculation of the true aromatic π???π interaction energies in these systems, free of secondary effects, was employed, and corroborates the rationale derived from the experimental results. These findings clearly emphasize the role of dispersion and dilute the importance of electrostatic forces on this type of interactions.     

Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials

Noncovalent interactions involving aromatic rings, such as π‐stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion‐corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene???methane and cyclohexane???methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel‐displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non‐additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials.     

Meso位直结型稳定双卟啉的合成及性质

利用氧化法成功地合成了同核meso位直结型稳定卟啉二聚体锌络合物,收率接近理论值;无论是碱式还是金属络合物都显示出卟啉环间成平面正交的电子吸收光谱;在循环伏安图谱中都显示出卟啉环间再氧化还原过程中较强烈的库仑作用;每个卟啉环的一电子氧化或还原均为可逆过程。     

Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry

Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.     

Spectra of 3-benzoxazolonylpropanones

The effect of substituents on the vibrational frequencies of oxazolonyl and acetonyl carbonyl groups was studied by means of the IR and PMR spectra of a series of substituted (in the benzene ring) 3-benzoxazolonylpropanones. The experimental data and the results of correlation analysis show that the carbonyl group of the acetonyl grouping is situated along the axis perpendicular to the plane of the benzene and heterocyclic rings and the substituent. The mechanism of transmission of the effect of substituents on the characteristic frequencies and the chemical shifts of the protons of the acetonyl group in the spectra are discussed.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 191–194, February, 1979     

Pyridine-2-thione (pySH) derivatives of silver(I): Synthesis and crystal structures of dinuclear [Ag2Cl2(μ-S-pySH)2(PPh3)2] and [Ag2Br2(μ-S-pySH)2(PPh3)2] complexes

Reaction of silver(I) halides with PPh₃ in acetonitrile and then with pyridine-2-thione (pySH) chloroform (1:1:1 molar ratio) has yielded sulfur bridged dimers of general formula, [Ag₂X₂(μ-S-pySH)₂(PPh₃)₂] (X = Cl, 1, Br, 2). Both these complexes have been characterized using analytical data, NMR spectroscopy and single crystal X-crystallography. The central Ag₂S₂ cores form parallelograms with unequal Ag–S bond distances (2.5832(8), 2.7208(11) Å) in 1 and (2.6306(4), 2.6950(7) Å) in 2, respectively. The Ag?Ag contacts of compounds 1 and 2 are 3.8425(8) and 3.8211(4) Å, respectively. The angles around Ag (in the range 87.19(2)–121.71(2)° in 1 and 87.81(2)–121.53(2)° in 2) reveal highly distorted tetrahedral geometry. There are inter dimer π–π stacking interactions between pyridyl rings (inter ring distances of 3.498 and 3.510 Å in complexes 1 and 2, respectively). The solution state ³¹P NMR spectroscopy has shown the existence of both monomers and dimers. The studies reveal relatively weaker intramolecular –NH?Cl hydrogen bonding in case of AgCl vis-à-vis that in CuCl which favored both a monomer and a dimer with AgCl, and only a monomer with CuCl.     

The NMR spectra of porphyrins-25: Meso-substituent effects in neutral and protonated porphyrins

The meso (methine) substituent chemical shifts (SCS) of a range of common functional groups have been obtained both for the neutral porphyrin molecule, and for the corresponding dications, in substituted octaethylporphyrin (OEP), etioporphyrin-I, and pyrroetioporphyrin-XV derivatives. The SCS are discussed in terms of both ring current variations and specific effects at the neighboring betasubstituents and the meso-proton opposite the perturbing substituent, using a ring current model to quantify the former. In the neutral molecules, meso substitution in OEP (Me, NO₂, CN, CHO) causes a 10% decrease in the macrocyclic ring current, and marked anisotropic shifts at the beta-positions flanking the meso function. The meso-NH₂ group introduces a much larger decrease (ca 35%) in the main ring current, due to conjugation of the amino group with the porphyrin π-system. In the porphyrin dications, SCS are much larger and there is some evidence of a concomitant decrease in the ring current of the adjacent pyrrole subunits. The meso-NMe₂; substituent at the γ-meso-position in pyrroetioporphyrin-XV has only small SCS in the neutral molecule, but a large shift (similar to that of NH₂) in the dication, due to the different orientation of the substituent with respect to the porphyrin plane in each case. The meso-OH substituent in the oxophlorin from etioporphyrin-I behaves as a conjugated OH group in the dication. The anomalous position of the meso-proton opposite to the perturbing substituent is noteworthy, and this could be due to electronic (resonance) effects, or to some protonation at this position.     

Microsheets assembled from pyridinium-tailored anthracenes

A facile strategy to construct microsheets assembled from 9-substituted anthracene-pyridinium compounds (APs) has been developed. With the different length of linkers, APs could form the ‘v’-shaped dimer or ‘face-to-face’ dimer, respectively, driven by CH–π interactions and π-stacking interactions, which consequently lead to the assembly of final microsheets.     

Effect of acceptor heteroatoms on π-hydrogen bonding interactions: A study of indole⋅⋅⋅thiophene heterodimer in a supersonic jet

Resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations have been used to determine the structure of indole???thiophene dimer observed in a supersonic jet. With the help of combined experimental and theoretical IR spectra it has been found that the observed dimer has a N-H???π hydrogen bonded slanted T-shaped structure. The present study demonstrates the effect of heteroatoms present in the acceptors on the strength of the π-hydrogen bonding interactions. It was concluded by Sherrill and co-workers from their theoretical study of benzene???pyridine dimer that aromatic rings containing heteroatoms are poorest π-hydrogen bond acceptors [E. G. Hohenstein and C. D. Sherrill, J. Phys. Chem. A 113, 878 (2009)]. But the current spectroscopic investigation exhibits that five membered aromatic heterocycles are favorable π-hydrogen bond acceptors. In this study, it has also been shown that thiophene is a better π-hydrogen bond acceptor than furan. The present work has immense biological significance as indole is the chromophore of tryptophan residue in the proteins and thiophene derivatives have potential therapeutic applications. Thus, understanding the binding motif between indole and thiophene in the heterodimer studied in this work may help in designing efficient drugs.     

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.