Mutual influence between covalent and noncovalent interactions in H3N–MCN–XF (X = H,Li, Cl,Br; M = Ag,Cu, Au)

The interplay between covalent and noncovalent interactions has been investigated in H₃N–MCN–XF (X = H, Li, Cl, Br; M = Ag, Cu, Au) complexes using ab initio calculations at the MP2 level of theory. The coinage metal as a substituent has an irregular enhancing effect (Au < Cu < Ag) on the strength of noncovalent interaction in MCN–XF, while the covalent interaction in H₃N–MCN becomes stronger with the reverse order. Interesting cooperativity effects were observed when covalent and noncovalent interactions coexist in the same complex, and they become more prominent for the stronger covalent and noncovalent interactions. These effects have been characterised in detail with the structural, spectroscopic, energetic, and charge transfer features of the complexes.     

Synthesis and structural study of 2′‐ and 2′,6′‐positioned methyl‐ and nitro‐substituted 3‐(arylhydrazono)pentane‐2,4‐diones

A systematic series of ortho‐methyl‐ and nitro‐substituted arylhydrazones 2–6 formed by Japp–Klingemann reaction between pentane‐2,4‐dione and the respective aryldiazonium salts have been synthesized and studied by X‐ray crystal structure analysis, with added quantum chemical calculations. The optimized molecular geometries based on DFT calculations, enabling determination of relevant rotational barriers, and the calculated bond and ring critical points, using the method of ‘atoms in molecules’, were found to correspond with the experimental data, involving specific molecular conformations and hydrogen‐bonded ring structure dependent on the ortho‐substitution, thus making possible reliable structural prediction of this compound class. Copyright © 2007 John Wiley & Sons, Ltd.     

Interaction of water‐soluble triphenylphosphines with β‐cyclodextrin: a quantum chemistry study

The interaction of β‐cyclodextrin (β‐CD) with meta‐trisulfonated triphenylphosphine derivatives bearing one or two methyl (or methoxy) groups on the aromatic rings has been investigated by PM3 calculations. The results show that phosphine molecules interact with β‐CD having either an unsubstituted sulfophenyl group or a substituted sulfophenyl group at the para and/or meta‐position. The presence of one methyl or methoxy group in the ortho‐position on each aromatic ring prevents the formation of an inclusion complex between meta‐trisulfonated triphenylphosphine derivatives and β‐CD. The deeply included phosphines in the β‐CD cavity show significant van der Waals interactions with β‐CD. These interactions are at the origin of the high association constants between these molecules and β‐CD. Phosphines exhibiting small association constants interact with β‐CD by forming H‐bonds and weak (or null) van der Waals interactions. Copyright © 2011 John Wiley & Sons, Ltd.     

A molecular electron density theory study of the [3 + 2] cycloaddition reaction between an azomethine imine and electron deficient ethylenes

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction of an azomethine imine (AI 12) with p‐nitrobenzylidenemalononitrile (NBMN, 13) have been theoretically studied within the Molecular Electron Density Theory using DFT methods at the MPWB1K/6‐31G(d) computational level. Analysis of the Conceptual DFT reactivity indices indicates that the strong nucleophilic character of AI 12 together with the high electrophilic character of NBMN 13 accounts for the strong polar character of this 32CA reaction, which demands very low activation energy. Analysis of the energy profiles indicates that this polar zw‐type 32CA reaction proceeds completely with a meta/exo selective pathway, in great agreement with the experimental data. Analyses of both molecular electrostatic potential and the non‐covalent interactions at the meta regioisomeric TSs allow explaining the observed exo stereoselectivity. Electron Localisation Function topological analysis indicates that the studied 32CA reaction takes place via a non‐concerted two‐stage one‐step mechanism as a [2n + 2τ] process.     

Interaction of chlorogenic acid with milk proteins analyzed by spectroscopic and modeling methods

Polyphenols are powerful antioxidants implicated in reducing the risk of human cancer and cardiovascular disease. Chlorogenic acid is a principal polyphenol in coffee, a beverage consumed worldwide on an immense scale. In many countries, coffee is consumed with milk, which has been shown to affect the bioavailability of polyphenols. Here we assessed the interactions of chlorogenic acid with five major milk proteins (α-casein, β-casein, κ-casein, α-lactalbumin, and β-lactoglobulin) by spectroscopy and molecular docking calculations. The data showed that the number of binding sites in each chlorogenic acid–milk protein complex was close to 1. Fluorescence quenching of milk proteins by chlorogenic acid occurred through a static mechanism and the binding distance was smaller than 8 nm. Binding constant for chlorogenic acid–β-lactoglobulin was larger than those for chlorogenic acid-α-lactalbumin, chlorogenic acid–α-casein, chlorogenic acid–β-casein, and chlorogenic acid–κ-casein. Thermodynamic parameters revealed that Van der Waals forces and hydrogen bond interactions predominated in chlorogenic acid–α-casein and chlorogenic acid–α-lactalbumin complexes; hydrophobic interactions were predominant in chlorogenic acid–β-casein, chlorogenic acid–κ-casein, and chlorogenic acid–β-lactoglobulin. Molecular docking calculations identified chlorogenic acid was located near Pse66, Ile65, and Pro29 in the chlorogenic acid–α-casein adduct, Leu138, Thr126, Gln123, Ser124, Gln167, Ser166, Ser168 in the chlorogenic acid–β-casein adduct, Glu147, Asn123, Val143, Pse149, Pro120, Leu79, Ala148 in the chlorogenic acid–κ-casein adduct, Glu49, Tyr103, Gln54, His32, Trp104, Leu110 in the chlorogenic acid–α-lactalbumin adduct, and Cys66, Leu22, Lys60, Trp61, Ser21, Lys69, Gln59 in the chlorogenic acid–β-lactoglobulin adduct. Notably, the antioxidant activity of chlorogenic acid decreased significantly on interaction with each of the milk proteins (p < 0.05). This study reveals the binding behaviors of chlorogenic acid with five milk proteins and provides basic data that can help to clarify the binding mechanism.     

A combined experimental and theoretical study on p‐sulfonatocalix[4]arene encapsulated 7‐methoxycoumarin

Host‐guest interactions are essential in chemistry, biology, medicine and environmental science. In this combined experimental and theoretical contribution, the encapsulation of 7‐methoxycoumarin (herniarin, 7MC) with p‐sulfonatocalix[4]arene (p‐SC4) is studied using absorption and fluorescence spectroscopy, cyclic voltammetry and computational approaches. The 1:1 stoichiometry is confirmed using Job's plot. Our results show that the keto group of 7MC is the main source for electrochemical conversion of this complex. The excited state 7MC radiative decay is studied using time‐correlated single photon counting technique. The computed UV‐Vis absorption spectra for this complex at gas phase and solvent are online with the experimental spectra. Moreover, we determined the binding energy and the binding constant of the 7MC‐p‐SC4 complex. Density functional theory computations revealed that stabilization of the complex formed by p‐SC4 and 7MC is due to weak noncovalent and dispersive types of interactions. A comparison with encapsulation of amino acids by p‐SC4 is also conducted. Finally, we show that the flexibility of p‐SC4 and the weak nature of its interaction with 7MC are on the origin of the reversibility of encapsulation, which is mandatory for applications such as drug delivery.     

Intermolecular interactions in organofluorine aggregates probed by laser R2PI spectroscopy

Resonant Two Photon Ionization (R2PI) spectroscopy has been applied to the study of host–guest interactions in molecular clusters formed by supersonic exspansion. Here, the results of R2PI spectroscopy of the fluorinated organic molecules para and ortho-fluoro-sec-butylbenzene and their complexes with water and argon are reported and discussed. In particular, it is shown that the position of the fluorine atom on the aromatic ring influences the formation of different kind of complexes (σ versus π) with argon and water. Ab initio calculations were performed to get insight into the molecular shape and the structure of these clusters.     

Factors affecting the dimerization of persistent nitrogen‐centered 1‐phenyl urazole radicals to tetrazanes

1‐Phenyl urazole radicals are persistent air‐stable nitrogen‐centered radicals that engage in an equilibrium with the corresponding N―N tetrazane dimers in solution. While the equilibrium typically weakly favors the dimer form, for some 1‐phenyl urazole radicals bearing substituents at the ortho position of the benzene ring, the equilibrium instead strongly favors the dimer form. With the recent surge of interest in the properties and potential applications of heterocyclic radicals, the factors that affect this equilibrium are important to determine. We examined the effect of the extent of ortho substitution (none, 1, or 2 substituents) on the equilibrium by experimentally using variable temperature ¹H nuclear magnetic resonance and UV‐visible spectroscopy in addition to supporting computational investigations at the (U)B3LYP/6‐311G(d,p) level of theory. We confirmed that the equilibrium generally favored the dimer in all cases. However, the equilibrium was more favorable towards dimer formation for urazole radicals substituted with 1 and 2 ortho substituents on the aromatic ring. The activation enthalpies for dissociation of singly substituted dimers were greater than that for dimers without ortho substituents, but lower than that for doubly substituted dimers. The greater preference for dimer formation for the ortho‐substituted urazole radicals is attributed to a greater enthalpic advantage for N―N bond formation. This advantage may be traced to a higher concentration of spin density on the urazole unit of the radicals and a lesser deformation energy required for N―N bond formation.     

Molecular structure and vibrational spectra of 3 (or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethiones: FT‐IR,FT‐Raman and DFT quantum chemical calculations

IR and Raman spectra (RS) of polycrystalline 3‐(or 4 or 6)‐methyl‐5‐nitro‐2‐pyridinethione have been measured and analyzed by means of density functional theory (DFT) quantum chemical calculations. The B3LYP/6‐311G(2d,2p) approach has been applied for both the thiol and thione tautomers due to the possibility of the formation of these two thiole forms. Molecular structures of these compounds have been optimized starting from different molecular geometries of the thiol group and thione group. Two conformations of the 2‐mercaptopyridine, trans and cis, have been taken into account. It was shown that the studied compounds appear in the solid state in the thione form. The effect of the hydrogen‐bond formation in the studied compounds has been considered. Copyright © 2008 John Wiley & Sons, Ltd.     

Counterion vibrations in the DNA low-frequency spectra

The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na⁺ , K⁺ , Rb⁺ and Cs⁺ the frequency of ion-phosphate vibrations decreases from 174 to 96cm^-1 as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na⁺ do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs⁺ have effect on the internal vibrations of the DNA structural elements.     

Synthesis and Raman spectroscopic investigation of a new self‐assembly monolayer material 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid for organic light‐emitting devices

We have synthesized 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid (4‐[PBA]) and investigated its molecular vibrations by infrared and Raman spectroscopies as well as by calculations based on the density functional theory (DFT) approach. The Fourier transform (FT) Raman, dispersive Raman and FT‐IR spectra of 4‐[PBA] were recorded in the solid phase. We analyzed the optimized geometric structure and energies of 4‐[PBA] in the ground state. Stability of the molecule arising from hyperconjugative interactions and charge delocalization was studied using natural bond orbital analysis. The results show that change in electron density in the σ* and π* antibonding orbitals and E₂ energies confirm the occurrence of intramolecular charge transfer within the molecule. Theoretical calculations were performed at the DFT level using the Gaussian 09 program. Selected experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumbers by their total energy distribution. The good agreement between the experimental and theoretical spectra allowed positive assignment of the observed vibrational absorption bands. Finally, the calculation results were applied to simulate the Raman and IR spectra of the title compound, which show agreement with the observed spectra. Copyright © 2011 John Wiley & Sons, Ltd.     

Bis‐4,9‐diazapyrenium dications: synthesis of the methylenedibenzyl‐analogue,interactions with nucleotides,DNA, RNA. The antitumour activity of all till now prepared analogues

Novel bis‐4,9‐diazapyrenium dication has shown reversible pH dependent formation of 4,9‐ diazapyrenium pseudobase in water characteristic for most 4,9‐diazapyrenium derivatives. The compound has formed non‐covalent complexes with nucleotides in water, whose stability is controlled dominantly by aromatic stacking interactions. No cooperativity between two 4,9‐diazapyrenium subunits was observed in binding of nucleotides. Novel bis‐4,9‐diazapyrenium dication formed mono‐intercalative complexes with studied double stranded DNA and RNA. Additional interactions of non‐intercalated part were found to depend significantly on the polynucleotide secondary structure, yielding strong DNA over RNA preference. Appearance of ICD band of 3 was found to be specific for DNA polynucleotides and together with observed destabilisation of double stranded RNA is attributed to the aggregation of compound in one of the RNA grooves. All bis‐4,9‐diazapyrenium dications prepared till now have shown considerable antiproliferative activity against five human tumour cell lines, which suggested mechanism of action by interacting with cell DNA. Copyright © 2007 John Wiley & Sons, Ltd.     

Computational (MP2 and DFT) modeling of the substrate/inhibitor interaction with the LDH active pocket in the gas phase and aqueous solution: bimolecular charged (pyruvate/oxamate–guanidinium cation) and neutral adducts (pyruvic/oxamic acids–guanidine)

Two types of bimolecular adducts were studied for the substrate and inhibitor of lactate dehydrogenase (LDH), one type of adducts between ionic species, α‐keto‐carboxylates (pyruvate and oxamate) and the guanidinium cation, and the other type of adducts between neutral species, α‐ketocarboxylic (pyruvic and oxamic) acids and guanidine. Calculations were performed in the gas phase and aqueous solution using the MP2 and PCM methods and the 6‐31++G** basis set. Application of the DFT(B3LYP) and PCM methods led to similar results. A change of the adducts' preference was observed when proceeding from the gas phase to aqueous solution. This change is in good agreement with the acidity–basicity scales in both phases. Formation constant (K_HB) for adduct between neutral species is greater for pyruvic than for oxamic acid in the gas phase, whereas a reverse situation takes place in aqueous solution, where the K_HB value for adduct between ionic species is smaller for pyruvate than for oxamate. The water molecules favor interactions of more polar oxamate with the guanidinium cation. Stronger interaction with this cation, a model of the arginine fragment of the LDH pocket, suggests that oxamate (inhibitor of LDH) has stronger binding properties in aqueous solution than pyruvate (substrate of LDH). Copyright © 2008 John Wiley & Sons, Ltd.     

Intermolecular interactions,ion solvation,and association in mixtures of 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate and γ‐butyrolactone: insights from Raman spectroscopy

By means of Raman spectroscopy coupled with density functional theory (DFT) calculations and perturbation correlation moving window two‐dimensional correlation spectroscopy intermolecular interactions were assessed in mixtures of ionic liquid (IL) 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate (BmimPF₆) with polar aprotic solvent γ‐butyrolactone (γ‐BL) over the entire range of compositions. The symmetrical P―F stretching vibration of the IL anion was found to be insensitive to the changes in mixture concentration in contrast to the CO stretching vibration of the γ‐BL and the imidazolium ring C―H stretching vibrations of the IL cation. Each of these vibrational profiles was decomposed in various spectral contributions, and their number was rationalized by the results of quantum‐chemical calculations and/or previous controversial published data. Progressive redshift of the ring C―H stretching wavenumbers was referred to pronounced solvation of the cation at the imidazolium ring site accompanied with H‐bond formation. This was especially pronounced at IL mole fraction less than 0.18. Complicated variations in the intensities of the individual contributions of the CO profile were treated as a manifestation of the changing with concentration pattern of the intermolecular interactions. The self‐association of γ‐BL molecules and distinct cation solvation as dominant intermolecular interactions at low IL content are replaced with weaker cation solvation and ion association at high concentrations of IL. Possible representative molecular structures were proposed on the basis of DFT calculations. Copyright © 2015 John Wiley & Sons, Ltd.     

Study on the Supramolecular Interactions of p-Sulfonated Calix[4, 6, 8]arenes with Lomefloxacin

The supramolecular interactions between a homologous series of p-sulfonated calix[n]arenes (SCnA, n = 4, 6, 8) as hosts and lomefloxacin (LFLX) were studied by spectrofluorometry. LFLX was found to react with SCnA to produce stable complexes. The fluorescence intensity of the complexes decreased gradually with increasing SCnA concentration. The formation of complexes was further confirmed by ¹H NMR studies and molecular modeling calculations. Data of the stability constants and thermodynamic parameters of the obtained complex showed that the stability of the SC8A-LFLX complex is superior to that of SC6A-LFLX and SC4A-LFLX. A mechanism was proposed to explain the inclusion process.     

Electronic interactions in two-dimensional polymers of the C60 fullerene

The electronic structure of tetragonal and rhombohedral polymers of the C₆₀ fullerene is investigated using x-ray emission spectroscopy. It is found that, compared to the C₆₀ molecular crystals, the formation of intermolecular covalent bonds in two-dimensional layers of the C₆₀ fullerene polymers leads to a broadening of the maxima in the CK _α x-ray emission spectra, a decrease in the density of high-energy states, and an increase in the width of the valence band of the polymer. The experimental data are interpreted by analyzing the results of the calculations performed within the density functional theory for the C₆₀ fullerene cage forming eight and twelve covalent bonds. It is shown that the electronic interactions between C₆₀ molecules in the polymerized layers are provided by two types of molecular orbitals located at energies 0.5–3.0 and ∼5.0 eV below the energy of the Fermi level.     

Extended X‐ray absorption fine structure and multiple‐scattering simulation of nickel dithiolene complexes Ni[S2C2(CF3)2]2n (n = −2, −1, 0) and an olefin adduct Ni[S2C2(CF3)2]2(1‐hexene)

A series of Ni dithiolene complexes Ni[S₂C₂(CF₃)]₂ⁿ (n = ?2, ?1, 0) ( 1 , 2 , 3 ) and a 1‐hexene adduct Ni[S₂C₂(CF₃)₂]₂(C₆H₁₂) ( 4 ) have been examined by Ni K‐edge X‐ray absorption near‐edge structure (XANES) and extended X‐ray absorption fine‐structure (EXAFS) spectroscopies. Ni XANES for 1 – 3 reveals clear pre‐edge features and approximately +0.7 eV shift in the Ni K‐edge position for `one‐electron' oxidation. EXAFS simulation shows that the Ni—S bond distances for 1 , 2 and 3 (2.11–2.16 Å) are within the typical values for square planar complexes and decrease by ～0.022 Å for each `one‐electron' oxidation. The changes in Ni K‐edge energy positions and Ni—S distances are consistent with the `non‐innocent' character of the dithiolene ligand. The Ni—C interactions at ～3.0 Å are analyzed and the multiple‐scattering parameters are also determined, leading to a better simulation for the overall EXAFS spectra. The 1‐hexene adduct 4 presents no pre‐edge feature, and its Ni K‐edge position shifts by ?0.8 eV in comparison with its starting dithiolene complex 3 . Consistently, EXAFS also showed that the Ni—S distances in 4 elongate by ～0.046 Å in comparison with 3 . The evidence confirms that the neutral complex is `reduced' upon addition of olefin, presumably by olefin donating the π‐electron density to the LUMO of 3 as suggested by UV/visible spectroscopy in the literature.     

A DFT study of the mechanism and selectivities of the [3 + 2] cycloaddition reaction between 3‐(benzylideneamino)oxindole and trans‐β‐nitrostyrene

The mechanism and regioselectivities and stereoselectivities of the [3 + 2] cycloaddition (32CA) reaction of 3‐(benzylideneamino) oxindole (AY) and trans‐β‐nitrostyrene have been studied using both B3LYP and ωB97XD density functional theory methods together with the standard 6‐31G(d) basis set. Four reactive pathways associated with the ortho and meta regioselective channels and endo and exo stereoselective approaches modes have been explored and characterized. While the B3LYP functional fails to predict the experimental regioselectivity, the ωB97XD one succeeds to predict the experimentally observed meta regioselectivity favoring the formation of meta/endo cycloadduct as the major isomer. Inclusion of solvent effects increases the regioselectivity and decreases the experimentally observed stereoselectivity. Analysis of the density functional theory global reactivity indices and the Parr functions of the reagents in its ground state allows explaining the reactivity and the meta regioselectivity of this zwitterionic‐type 32CA reaction, which account for the high polar character of this reaction. Non‐covalent interaction analysis of the most favorable meta/endo transition state structure reveals that the formation of a hydrogen‐bond between 1 nitro oxygen and the AY N–H hydrogen is responsible for the selectivity experimentally found in this polar zwitterionic‐type 32CA reaction.     

Binding of regulatory protein omega from Streptococcus pyogenes plasmid pSM19035 to direct and inverted 7‐base pair repeats of operator DNA

pSM19035‐encoded dimeric regulator omega (ω₂) belongs to the MetJ/Arc family of ribbon–helix–helix DNA binding proteins. ω₂ binds to a set of unspaced 7‐base pair repeat units with sequence 5′‐^A/_TATCAC^A/_T‐3′. Protein ω₂ and its variant ω₂ΔN18, lacking the first 18 N‐terminal amino acids, bind poorly to one heptad DNA, but the affinity to DNA markedly increases with two and more heptads organized in direct or inverted orientation. Raman difference spectra indicate that ω₂ and ω₂ΔN18 bind to operator DNA in the major groove and contact thymine, adenine and guanine residues. The mode of ω₂ or ω₂ΔN18 interaction with operator DNA is not affected by the orientation and number of heptads. The Raman data of ω₂T29A, an ω₂ variant with Ala instead of Thr at position 29 of the β‐sheet, show a sequence‐independent binding mode to DNA, which differs from the binding mode of wt ω₂ protein to its cognate site. The Raman data strongly support the notion that the 18 N‐terminal amino acids are not required for ω₂ activity, whereas Thr29 plays an essential role for operator DNA binding. The data suggest the formation of a hydrogen bond between Thr29 of wild‐type ω₂ to one of the bases in the central 5′‐TCA‐3′/5′‐TGA‐3′ stretch of the 7‐bp binding site. Copyright © 2006 John Wiley & Sons, Ltd.     

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

ABSTRACT

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.