A DFT Study on Estrone – TNT Interaction

Trinitrotoluene, known as TNT, is a widely used powerful explosive. It is a poisonous material, which injures almost all cells, especially those of liver, bone marrow, and kidney. Estrone is a sex hormone having an electron rich aromatic (phenolic) ring that is capable of forming a π complex with molecules containing an electron deficient π system. This study has focused on investigating the tendency of the complex formation of TNT with estrone. It has been thought that the formation of estrone‐TNT π complex might take place in a human body exposed to acute or prolong period of this hazardous chemical and consequently estrone activities might be impaired. The complex formation reaction was investigated mainly using DFT method with B3LYP/6‐31G(d, p) basis set in gas phase. The existence of π interaction between estrone and TNT was demonstrated by computational spectroscopic analyses (UV/Vis, IR, and ¹H NMR techniques). The frontier molecular orbital (HOMO and LUMO) analyses have shown that the considered π complex is very resistant to oxidation with respect to its components, estrone and TNT.     

A theoretical exploration of unexpected amine···π interactions

Counterintuitive amine lone pair···π interactions are computationally revealed by MP2 and CCSD(T) methods, attractive lone pair···π interactions are observed when the lone pair of nitrogen points toward the π system. Symmetry adapted perturbation theory (SAPT) calculations and atoms in molecules (AIM) analyses were performed and the origin of the calculated attractive interaction between nitrogen lone pairs and π rings is discussed. Dispersion effects were revealed to play a crucial role in the attractive lone pair···π interaction.     

Intercalation of Epinephrine with Calf-thymus ds-DNA

Interactions of DNA with various molecules are interesting because of its importance in gene expression process of living cells. Several models for the interaction between DNA and some small molecules have been proposed1-4. We are interested in the possibility of the interaction between DNA/RNA and neurotransmitters, such as dopamine and epinephrine, because these species are very important substances for keeping normal physiological functions of brain and neuro system. However, no report…     

Density functional theory study on hydrogen‐bonded complexes of adenine with polyformamide molecules

The structures of hydrogen‐bonded complexes A–F_n (n = 2–7) of adenine with polyformamide molecules have been fully optimized at B3LYP/6‐31G(d) basis set level. All the formamide molecules prefer to be N? H proton donor rather than C? H proton donor and are favorably bound to the five‐numbered moiety of adenine. A displacement of formamide molecules to one side of adenine mean plane has happened with an increasing number of formamide molecules. An obvious effect of hydrogen‐bonding cooperativity can be seen during the complex process. The most interesting geometrical change of adenine upon the complex is the shortening of the bond C4? N6 resulting from the strengthening of the conjugation between the π system of the adenine ring and the lone pair of the nitrogen atom. An existence of weak N? H···π bonding interaction between the π system of adenine and N? H bond of F7 is found and further conformed by an natural bond orbital analysis specially carried out on A–F₇. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The Viologen Cation Radical Pimer: A Case of Dispersion‐Driven Bonding

The π bonds between organic radicals have generated excitement as an orthogonal interaction for designing self‐assembling architectures in water. A systematic investigation of the effect of the viologen cation radical structure on the strength and nature of the pimer bond is provided. A striking and unexpected feature of this π bond is that the bond strength is unchanged by substitution with electron‐donating groups or withdrawing groups or with increased conjugation. Furthermore, the interaction is undiminished by sterically bulky N ‐alkyl groups. Theoretical modeling indicates that strong dispersion forces dominate the interaction between the radicals, rationalizing the insensitivity of the bonding interaction to substituents: The stacking of polarizable π radicals leads to attractive dispersion forces in excess of typical dispersion interactions of small molecules and helps overcome the Coulombic repulsion of bringing two cationic species into contact.     

Inverted Opal Fluorescent Film Chemosensor for the Detection of Explosive Nitroaromatic Vapors through Fluorescence Resonance Energy Transfer

This paper reports an inverted opal fluorescence chemosensor for the ultrasensitive detection of explosive nitroaromatic vapors through resonance‐energy‐transfer‐amplified fluorescence quenching. The inverted opal silica film with amino ligands was first fabricated by the acid–base interaction between 3‐aminopropyltriethoxysilane and surface sulfonic groups on polystyrene microsphere templates. The fluorescent dye was then chemically anchored onto the interconnected porous surface to form a hybrid monolayer of amino ligands and dye molecules. The amino ligands can efficiently capture vapor molecules of nitroaromatics such as 2,4,6‐trinitrotoluene (TNT) through the charge‐transfer complexing interaction between electron‐rich amino ligands and electron‐deficient aromatic rings. Meanwhile, the resultant TNT–amine complexes can strongly suppress the fluorescence emission of the chosen dye by the fluorescent resonance energy transfer (FRET) from the dye donor to the irradiative TNT–amino acceptor through intermolecular polar–polar resonance at spatial proximity. The quenching response of the highly ordered porous films with TNT is greatly amplified by at least 10‐fold that of the amorphous silica films, due to the interconnected porous structure and large surface‐to‐volume ratio. The inverted opal film with a stable fluorescence brightness and strong analyte affinity has lead to an ultrasensitive detection of several ppb of TNT vapor in air.     

A Theoretical Study of NBO,NICS, and 14N NQR Parameters of Adenine Tautomers in the Gas Phase via DFT

The natural bond orbital (NBO) analysis, nucleus independent chemical shift (NICS), and ¹⁴N NQR parameters of the most stable tautomers of adenine in the gas phase were predicted using density functional theory method. The NBO analysis revealed that the resonance interaction between lone pair of the nitrogen atom and empty non‐Lewis NBO increases with increasing the p character of the nitrogen lone pair. The present investigation indicated the π clouds in both the considered heterocyclic rings containing six electrons, and these tautomers has the aromatic character. The NICS study utilizing the gauge‐invariant atomic orbital method showed that there are diatropic currents in the heterocyclic rings of the tautomers, so we determined the order of overall aromaticity of these tautomers. The results of NQR parameter calculations showed three parameters are effective on nuclear quadrupole coupling constant; the p character value of lone pair electrons of nitrogens, and the related occupancies and whenever, the lone pair electrons of nitrogens participate in the formation of chemical bond and/or π system of the ring, the q_zz and consequently its χ decreases.     

Ferrocenyl hetaryl thioketones: A computational study of their conformational stability

In this work, the conformational behavior of ferrocenyl- and hetaryl-functionalized thioketones was studied by means of computational quantum chemical methods. Four hetaryl substituents (furan-2-yl, thiophen-2-yl, selenophen-2-yl, and N-methylpyrrol-2-yl) were taken into account. The conformational space of the four ferrocenyl hetaryl thioketones was explored, and all found conformers were characterized using density functional (B3LYP) and wave function (SCS-MP2) theories. Their stability was explained in terms of intramolecular interactions. Such interactions were described using the methods of natural bond orbitals, “atoms in molecules,” noncovalent interaction index, and localized molecular orbital energy decomposition analysis. The identified conformations essentially differ in the arrangement of hetaryl heteroatom relative to the thiocarbonyl sulfur atom. The furan-2-yl substituent favors an s-trans-like arrangement of its heteroatom, while the remaining hetaryl substituents tend to adopt an s-cis-like arrangement. Such a conformational preference mainly results from the π → π* stabilization between the CS group and the hetaryl ring. Weak intramolecular hydrogen bonding of C H⋯O type was detected in the preferred conformer of ferrocenyl furan-2-yl thioketone. Low-polarity solvents, such as toluene, chloroform, and tetrahydrofuran, have a small effect on the preferred conformers of the four thioketones.     

A Study of Polynuclear Aromatic Hydrocarbons on an Amino Bonded Phase Liquid Chromatographic Column in the Normal and Reversed Phase

Abstract

Experiments were run using an n-propyl amine polar bonded phase (Chromosorb LC-9) liquid chromatographic column in both the normal and reversed phase mode. Results confirm that the mechanism of separation in the normal phase is due mainly to a charge transfer interaction between the lone pair electrons on the stationary phase nitrogen and the π electron cloud of the solute PNAs. Elution order seems to depend upon a combination of π energy, and type of ring condensation of the solute. Plots of log I versus number of aromatic carbons for catacondensed PNAs suggest that while the specific interaction is different than that seen in silica chromatography, the overall adsorption effect is comparable. In the reversed phase there may be two types of separation mechanisms: 1) a pure partitioning effect in highly polar mobile phases (methanol/water), or 2) a mixture of liquid-solid adsorption and liquid-liquid partition in less polar solvent systems (acetonitrile/water).     

Electron transfer in a radical ion pair: quantum calculations of the solvent reorganization energy

Results are presented for an investigation of intermolecular electron transfer (ET) in solution by means of quantum calculations. The two molecules that are involved in the ET reaction form a solvent-separated radical ion pair. The solvent plays an important role in the ET between the two molecules. In particular, it can give rise to specific solute-solvent interactions with the solutes. An example of specific interactions is the formation of a hydrogen bond between a protic solvent and one of the molecules involved in the ET. We address the study of this system by means of quantum calculations on the solutes immersed in a continuum solvent. However, when the solvent can give rise to hydrogen bond formation with the negatively charged ion after ET, we explicitly consider solvent molecules in the solute cavity, determining the hydrogen bond energetic contribution to the overall interaction energy. Solute-solvent pair distribution functions, showing the different arrangement of solvent molecules before and after ET in the first solvation shell, are reported. We provide results of the solvent reorganization energy from quantum calculations for both the two isolated fragments and the ion pair in solution. Results are in agreement with available experimental data.     

Meisenheimer complexes bonded at carbon and at oxygen

The carbon-bonded gas-phase Meisenheimer complex of 2,4,6-trinitrotoluene (TNT) and the nitromethyl carbanion CH(2)NO(2)(-) (m/z 60) is generated for the first time by chemical ionization using nitromethane as the reagent gas. Collision-induced dissociation (CID) of the Meisenheimer complex furnishes deprotonated TNT, a result of the higher gas-phase acidity of TNT than nitromethane. The formation of Meisenheimer complexes with CH(2)NO(2)(-) in the gas phase is selective to highly electron-deficient compounds such as dinitrobenzene and trinitrobenzene and does not occur with organic molecules with lower electron-affinity such as methanol, methylamine, propionaldehyde, acetone, ethyl acetate, chloroform, toluene, m-methoxytoluene, and even nitrobenzene and p-fluoronitrobenzene. As such, the reaction allows selective detection of TNT in mixtures. Meisenheimer complexes between CH(2)NO(2)(-) and the three dinitrobenzene isomers display distinctive fragmentations. The oxygen-bonded sigma-complex of TNT with the deprotonated hemiacetal anion CH(3)OCH(2)O(-) (m/z 61), represents a different type of Meisenheimer complex. It displays characteristic fragmentation involving loss of HNO(2) upon CID. The combination of a selective ion/molecule reaction (Meisenheimer complex formation) followed by a characteristic CID process provides a second novel and highly selective approach to the detection of TNT and closely related compounds in mixtures. The assay is readily implemented using neutral loss scans in a triple quadrupole mass spectrometer. Gas-phase reactions of denitrosylated TNT with benzaldehyde produce the corresponding dihydrofuran in an aldol condensation, a result that parallels the corresponding condensed-phase reaction.     

Complexation, computational, magnetic, and structural studies of the Maillard reaction product isomaltol including investigation of an uncommon π interaction with copper(II)

The metal complexation properties of the naturally occurring Maillard reaction product isomaltol HL(2) are investigated by measurement of its stability constants with copper(II), zinc(II), and iron(III) using potentiometric pH titrations in water, by structural and magnetic characterization of its crystalline complex, [Cu(L(2))(2)]·8H(2)O, and by density functional theory calculations. Strong complexation is observed to form the bis(isomaltolato)copper(II) complex incorporating copper in a typical (pseudo-)square-planar geometry. In the solid state, extensive intra- and intermolecular hydrogen bonding involving all three oxygen functions per ligand assembles the complexes into ribbons that interact to form two-dimensional arrays; further hydrogen bonds and π interactions between the furan moiety of the anionic ligands and adjacent copper(II) centers connect the complexes in the third dimension, leading to a compact polymeric three-dimensional (3D) arrangement. The latter interactions involving copper(II), which represent an underappreciated aspect of copper(II) chemistry, are compared to similar interactions present in other copper(II) 3D structures showing interactions with benzene molecules; the results indicate that dispersion forces dominate in the π system to chelated copper(II) ion interactions.     

Adjacent Lone Pair (ALP) Effect: A Computational Approach for Its Origin

The adjacent lone pair (ALP) effect is an experimental phenomenon in certain nitrogenous heterocyclic systems exhibiting the preference of the products with lone pairs separated over other isomers with lone pairs adjacent. A theoretical elucidation of the ALP effect requires the decomposition of intramolecular energy terms and the isolation of lone pair–lone pair interactions. Here we used the block‐localized wavefunction (BLW) method within the ab initio valence bond (VB) theory to derive the strictly localized orbitals which are used to accommodate one‐atom centered lone pairs and two‐atom centered σ or π bonds. As such, interactions among electron pairs can be directly derived. Two‐electron integrals between adjacent lone pairs do not support the view that the lone pair–lone pair repulsion is responsible for the ALP effect. Instead, the disabling of π conjugation greatly diminishes the ALP effect, indicating that the reduction of π conjugation in deprotonated forms with two σ lone pairs adjacent is one of the major causes for the ALP effect. Further electrostatic potential analysis and intramolecular energy decomposition confirm that the other key factor is the favorable electrostatic attraction within the isomers with lone pairs separated.     

Computational study of the interaction of indole-like molecules with water and hydrogen sulfide

The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H···π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH(2) ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.     

Non-covalent interactions between unsolvated peptides: helical complexes based on acid-base interactions

We have used ion-mobility mass spectrometry to examine the conformations of the protonated complex formed between AcA(7)KA(6)KK and AcEA(7)EA(7), helical alanine-based peptides that incorporate glutamic acid (E) and lysine (K). Designed interactions between the acidic E and basic K residues help to stabilize the complex, which is generated by electrospray and studied in the gas phase. There are two main conformations: (1) a coaxial linear arrangement where the helices are tethered together by an EKK interaction between the pair of lysines at the C-terminus of the AcA(7)KA(6)KK peptide and a glutamic acid at the N-terminus of the AcEA(7)EA(7) peptide and (2) a coiled-coil arrangement with side-by-side antiparallel helices where there is an additional EK interaction between the E and K residues in the middle of the helices. The coiled-coil opens up to the coaxial linear structure as the temperature is raised. Entropy and enthalpy changes for the opening of the coiled-coil were derived from the measurements. The enthalpy change indicates that the interaction between the E and K residues in the middle of the helices is a weak neutral hydrogen bond. The EKK interaction is significantly stronger.     

A Reversible Dual‐Response Fluorescence Switch for the Detection of Multiple Analytes

This paper reports a reversible dual fluorescence switch for the detection of a proton target and 2,4,6‐trinitrotoluene (TNT) with opposite‐response results, based on fluorophore derivatization of silica nanoparticles. Fluorescent silica nanoparticles were synthesized through modification of the surface with a nitrobenzoxadiazole (NBD) fluorophore and an organic amine to form a hybrid monolayer of fluorophores and amino ligands; the resultant nanoparticles showed different fluorescence responses to the proton target and TNT. Protonation of the amino ligands leads to fluorescence enhancement due to inhibition of photoinduced electron transfer (PET) between the amine and fluorophore. By contrast, addition of TNT results in fluorescence quenching because a fluorescence resonance energy transfer (FRET) happens between the NBD fluorophore and the formed TNT–amine complex. The fluorescence signal is reversible through washing with the proper solvents and the nanoparticles can be reused after centrifugal separation. Furthermore, these nanoparticles were assembled into chips on an etched silicon wafer for the detection of TNT and the proton target. The assembled chip can be used as a convenient indicator of herbicide (2,4‐dichlorophenoxyacetic acid) and TNT residues with the use of only 10 μL of sample. The simple NBD‐grafted silica nanoparticles reported here show a reversible signal and good assembly flexibility; thus, they can be applied in multianalyte detection.     

A “double-zeta” type wavefunction for an organometallic: Bis-(π-allyl)nickel

A wavefunction which is of double-zeta quality at the level of the valence orbitals [based on a (11, 7, 5/8, 4/4) gaussian basis set contracted to (4, 3, 2/3, 2/2)] is reported for thebis-(π-allyl)nickel molecule. Independant SCF calculations for two ionized states substantiate the conclusion reached previously for a number of organometallics with a minimal basis set that Koopmans' theorem is not valid for these molecules, namely that the highest occupied orbital from the ground state calculation for the neutral molecule is mostly a ligand π orbital whereas the lowest ionization potential corresponds to the removal of an electron from a molecular orbital which is mostly a metal 3d orbital. The nature of the bonding inbis-(π-allyl)nickel is discussed on the basis of the possible interactions between the metal orbitals and the π orbitals of the allyl group. The interaction between the filled nonbonding π orbital of the allyl group and the empty 3d _xz orbital of the Ni atom appears responsible for most of the bonding, together with some backbonding through an interaction between the 3d x ²?y ²and 3d xyorbitals and the σ and π orbitals of the ligands. The computed value for the rotation barrier about the C-C allyl bond, 90 kcal/mole, rules out this rotation as one of the possible mechanisms which account for the equivalence of the terminal hydrogens in the proton magnetic resonance spectra of π-allyl complexes.     

Infrared spectroscopic and theoretical studies of the OTiF(2), OZrF(2) and OHfF(2) molecules with terminal oxo ligands

The isolated group 4 metal oxydifluoride molecules OMF(2) (M = Ti, Zr, Hf) with terminal oxo groups are produced specifically on the spontaneous reactions of metal atoms with OF(2) through annealing in solid argon. The product structures and vibrational spectra are characterized using matrix isolation infrared spectroscopy as well as B3LYP density functional and CCSD(T) frequency calculations. OTiF(2) is predicted to have a planar structure while both OZrF(2) and OHfF(2) possess pyramidal structures, all with singlet ground states. Three infrared absorptions are observed for each product molecule, one M-O and two M-F stretching modes, and assignments of these molecules are further supported by the corresponding (18)O shifts. The molecular orbitals of the group 4 OMF(2) molecules show triple bond character for the terminal oxo groups, which are also supported by an NBO analysis. These molecular orbitals include a σ bond (O(2p) + Ti(sd hybrid)), a normal electron pair π bond (O(2p) + Ti(d)), and a dative π bond arising from O lone pair donation to the overlapping Ti d orbital. The M-O bond dissociation energies for OMF(2) are comparable to those in the diatomic oxide molecules. The OTiF intermediate is also observed through two slightly lower frequency bond stretching modes, and its yield is increased in complementary TiO + F(2) experiments. Finally, the formation of group 4 OMF(2) molecules is highly exothermic due to the weak O-F bonds in OF(2) as well as the strong new MO and M-F bonds formed.     

Localized emitting state and energy transfer properties of quadrupolar chromophores and (multi)branched derivatives

In order to better understand the nature of intramolecular charge and energy transfer in multibranched molecules, we have synthesized and studied the photophysical properties of a monomer quadrupolar chromophore with donor-acceptor-donor (D-A-D) electronic push-pull structure, together with its V-shaped dimer and star-shaped trimers. The comparison of steady-state absorption spectra and fluorescence excitation anisotropy spectra of these chromophores show evidence of weak interaction (such as charge and energy transfer) among the branches. Moreover, similar fluorescence and solvation behavior of monomer and branched chromophores (dimer and trimer) implies that the interaction among the branches is not strong enough to make a significant distinction between these molecules, due to the weak interaction and intrinsic structural disorder in branched molecules. Furthermore, the interaction between the branches can be enhanced by inserting π bridge spacers (-C═C- or -C≡C-) between the core donor and the acceptor. This improvement leads to a remarkable enhancement of two-photon cross-sections, indicating that the interbranch interaction results in the amplification of transition dipole moments between ground states and excited states. The interpretations of the observed photophysical properties are further supported by theoretical investigation, which reveal that the changes of the transition dipole moments of the branched quadrupolar chromophores play a critical role in observed the two-photon absorption (2PA) cross-section for an intramolecular charge transfer (ICT) state interaction in the multibranched quadrupolar chromophores.     

A supramolecular assembly containing an unusually short n‐h…n hydrogen bond ‐ an x‐ray and neutron diffraction study

A supramolecular assembly formed between phthalimide and 2‐guanidinobenzimidazole, containing a short 2.692(4)AR N‐H…N hydrogen bond, is reported. The crystal structure of this species was determined by both X‐ray and neutron diffraction. The diffraction data reveal that the proton involved in the short hydrogen bond has been transferred from the phthalimide to the guanidinobenzimidazole to form an ion pair. There is also an interesting stacking interaction between the atoms involved in the short hydrogen bond and the π system of a phthalimide molecule that is approximately 3.3 Å away. The structure is compared with the structure of a similar assembly formed between 4‐nitrophthalimide and 2‐guanidinobenzimidazole.