UV-spectroscopy,electronic structure and ozonolytic reactivity of sesquiterpenes: a theoretical study

Sesquiterpenes, one of the most important classes of biogenic volatile organic compounds, are potentially significant precursors to secondary organic aerosols (SOAs) in nature. The electronic structure of sesquiterpenes and their reactivity in the ozonolysis reaction were investigated by density functional theory. Results from the CIS calculations combined with an analysis of transition intensities show that the first peaks in the ultraviolet (UV) spectra for saturated and unsaturated isomers are σ–σ* and π–π* transitions, respectively. The UV absorption wavelength and absorbency are dictated by the electronic structures of these compounds. An increase in the number of double bonds and formation of a conjugated system expand the range of absorption in the UV region. An isomer with an endocyclic C = C bond presents weaker UV transition intensity than its corresponding exocyclic isomer. Results from conceptual DFT chemical reactivity indices of isomers suggest that no quantitative linear relationships between the structural changes and their reactivity, such as different degrees of unsaturated C = C double bonds, or the number of substituents attached to the C = C bond were discovered. In the ozonolysis reaction of sesquiterpenes, isomers with larger steric hindrance of substituents or endocyclic C = C bond possess higher chemical reactivity compared to isomers with smaller steric hindrandce or with an exocyclic C = C bond. These results are imperative to a better understanding of SOAs production mechanisms in the troposphere.     

Quantum-mechanical treatment of the electronic structure and geometry of hydrogen cyanide dimer

Experiments used to develop theories of chemical evolution seem to indicate that hydrogen cyanide, HCN, was an important molecule in prebiotic synthesis. In particular, polymerization products of hydrogen cyanide have been found to yield polypeptides upon hydrolysis. The proposed key intermediate in prebiotic synthesis is the aminocyanocarbene isomer of the dimer, either as a 1,3 biradical or as a dipolar singlet structure. Since this molecule has never been successfully isolated and characterized, a quantum mechanical study of various structures of the dieter is carried out using the INDO method. The results indicate that the lowest energy isomer is the iminoacetonitrile, with the aminocyanocarbene being next lowest. The triplet and singlet energy surfaces of the aminocyanocarbene intersect, so that for some geometries the singlet is lower in energy than the triplet, for others the reverse is true. The minima of both surfaces correspond to the linear configuration, with slightly different bond lengths. The triplet state minimum is 8·8 kcal/mol lower in energy than the singlet minimum. The calculated spin density distribution for the ground state of the carbene can be qualitatively described as a 1,3 biradical, in agreement with the early proposal of Kliss &; Matthews. The charge distribution of the singlet at its minimum energy geometry was also calculated. We found the charge separation to be less than that proposed for the dipolar structure of Moser et al. These calculations indicate that while the lowest energy isomer is the iminoacetonitrile, the aminocyanocarbene, the lowest-energy triplet, does have the appropriate spin distribution in its ground state for the biradical polymerization proposed in the theory of chemical evolution of Kliss &; Matthews. Experiments are suggested to determine the nature of the HCN polymerization mechanism, especially in the gas phase. By application of standard techniques used in polymer science, the nature of the gas phase polymerization of HCN can be determined, and the role of such reactions in chemical evolution can be better understood.     

Spermine-nucleic acid interactions: a theoretical study

The interaction of spermine with nucleic acids is simulated theoretically using refined semi-empirical energy formulae and an advanced minimization procedure. Various nucleic acids are considered: model homopolymeric DNA's, a dodecamer (CGCGAATTCGCG) of type B-DNA, as well as a transfer RNA, tRNA^Phe. The dominant role of electrostatic potential in determining the preferential binding sites of spermine is demonstrated in each of these cases and the role of counterions, nucleic acid structure, and base-pair sequence is analyzed.     

Experimental and theoretical study on the structure and electronic spectra of imiquimod and its synthetic intermediates

Crystal structure of the imiquimod has been determined by single crystal X-ray analysis, imiquimod crystallizes in orthorhombic space group P2(1)2(1)2(1) and the molecules are linked along the c axis by the strong N-H ... N hydrogen bonds. A density functional theory (DFT) study on the electronic properties of imiquimod and its synthetic intermediates has been performed at B3LYP/6-31G* level, while taking solvent effects into account. Both the single configuration interaction (CIS) method and the time-dependent DFT (TDDFT) approaches have been used to calculate the electronic absorption spectra, and there is a good agreement between the calculated and experimental UV-visible absorption spectra. The fluorescence emission spectra of these three compounds in solution have also been measured, the relatively low fluorescence intensity is attributed to a chlorine-modulated heavy atom effect that enhances intersystem crossing between excited singlet and triplet states, and the relatively high fluorescence intensity of imiquimod results from an extended pi-conjugated system which enhances S(1)-->S(0) radiant transition.     

Wobble base-pairing in codon-anticodon interactions: a theoretical modelling study

The Crick wobble hypothesis attributes the phenomenon of codon degeneracy to a certain impreciseness of pairing between the third base of the codon and the first base of the anticodon. This theoretical study investigates the pairing properties of some wobble bases, including both, observed and unobserved pairs. Some wobble base-pairs are predicted to follow the Watson-Crick pairs in configuration and pairing facility, while others deviate from this norm. The observed U:V pair is unique in that a pairing configuration may be suggested for it wherein the hydrogen-bonding involves the exocyclic 5-carboxymethoxy group of V. By comparing the theoretical data on the configurations of these pairs with the evidence for their existence/non-existence in nature, some guidelines emerge for differentiating between observed and unobserved base pairs on the basis of the pairing configuration.     

Antitumor activity of bent metallocenes: electronic structure analysis using DFT computations

The antitumor activities of bent metallocenes [Cp–M–Cp]²⁺ (M = Ti, V, Nb, Mo) and complexes of them with guanine, adenine, thymine and cytosine nucleotides have been probed using electronic structure calculations. DFT/BP86 calculations have revealed that the bent metallocene–nucleotide interaction strongly depends on the stability of the hydrolyzed form of the bent metallocene dichloride [Cp₂M]²⁺ species, and in turn the stability of the [Cp₂M]²⁺ species strongly depends on the electronic structure of [Cp₂M]²⁺. Detailed electronic structure and Walsh energy analyses have been carried out for the hydrolyzed forms of four [Cp–M–Cp]²⁺ (M = Ti, V, Nb, Mo) species to find out why the bent structure is unusually stable. Energy changes that occur during the bending process in frontier molecular orbitals as well as the p(π)–d(π) overlap have been invoked to account for the anticipated antitumor activities of these species. The bonding situation and the interactions in bent metallocene–nucleotide adducts were elucidated by fragment analysis. Of the four nucleotides complexed with the four bent metallocenes, adenine and guanine show better binding abilities than the other two nucleotides. Metallocenes of second-row transition metals exhibit better binding with pyrimidine-base nucleotides. In particular, the Lewis acidic bent metallocenes interact strongly with nucleotides. The antitumor activity is directly related to the binding strength of the bent metallocene with nucleotide adducts, and the computed interaction energy values correlate very well with the experimentally observed antitumor activities.     

Intramolecular hydrogen bonding, π-π stacking interactions,and substituent effects of 8-hydroxyquinoline derivative supermolecular structures: a theoretical study

Journal of Molecular Modeling - Syn and anti dihydropyrene (DHP) are excellent thermochromes, and therefore extensively studied for their thermochromic and photochromic properties, respectively....     

Revealing substitution effects on the strength and nature of halogen-hydride interactions: a theoretical study

A quantum chemistry study was carried out to investigate the strength and nature of halogen bond interactions in HXeH···XCCY complexes, where X = Cl, Br and Y = H, F, Cl, Br, CN, NC, C₂H, CH₃, OH, SH, NH₂. Examination of the electrostatic potentials V(r) of the XCCY molecules reveals that the addition of substituents has a significant effect upon the most positive electrostatic potential on the surface of the interacting halogen atom. We found that the magnitude of atomic charges and multipole moments depends upon the halogen atom X and is rather sensitive to the electron-withdrawing/donating power of the remainder of the molecule. An excellent correlation was found between the most positive electrostatic potentials on the halogen atom and the interaction energies. For either HXeH···ClCCY or HXeH···BrCCY complexes, an approximate linear correlation between the interaction energies and halogens multipole moments are established, indicating that the electrostatic and polarization interactions are responsible for the stability of the complexes. According to energy decomposition analysis, it is revealed that the electrostatic interactions are the major source of the attraction in the HXeH···XCCY complexes. Furthermore, the changes in the electrostatic term are mainly responsible for the dependence of interaction energy on the halogen atom.

Optical properties of cyclic dimers of amino acids: An experimental and theoretical study

CD spectra have been measured in the vacuum-uv region to about 135 nm for cyclo(L alanyl-glycine), cyclo(L alanyl-L -alanine), and cyclo(L -prolyl-L -proline). In addition to the amide CD bands usually observed at wavelengths longer than 180 nm, a Independent systems calculations show that these intense short-wavelenght bands can be attributed to σσ* transitions of the backbone. Transitions of the amide chromophore expected at wavelenghts shorter than 180 nm cannot account for the observed CD.     

Interactions between nucleotide bases in coplanar and stacking dimers under vacuum. Mass spectrometric study

New temperature-dependent field--ionization mass-spectrometric method is described. It allows to measure enthalpies of associates in vacuum. An analysis of all the experimental results led to a conclusion that interactions in coplanar dimers of nucleic acid bases are stronger than in the stacking ones. A comparison between the vacuum measurements and theoretical data is made.     

Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations

This study of lipid-mediated interactions between proteins is based on a theory recently developed by the authors for describing the structure of the hydrocarbon chains in the neighborhood of a protein inclusion embedded in a lipid membrane [Lagüe et al., Farad. Discuss. 111:165-172, 1998]. The theory involves the hypernetted chain integral equation formalism for liquids. The exact lateral density-density response function of the hydrocarbon core, extracted from molecular dynamics simulations of a pure dipalmitoylphosphatidylcholine bilayer based on an atomic model, is used as input. For the sake of simplicity, protein inclusions are modeled as hard repulsive cylinders. Numerical calculations were performed with three cylinder sizes: a small cylinder of 2.5-A radius, corresponding roughly to an aliphatic chain; a medium cylinder of 5-A radius, corresponding to a alpha-helical polyalanine protein; and a large cylinder of 9-A radius, representing a small protein, such as the gramicidin channel. The calculations show that the average hydrocarbon density is perturbed over a distance of 20-25 A from the edge of the cylinder for every cylinder size. The lipid-mediated protein-protein effective interaction is calculated and is shown to be nonmonotonic. In the case of the small and the medium cylinders, the lipid-mediated effective interaction of two identical cylinders is repulsive at an intermediate range but attractive at short range. At contact, there is a free energy of -2k(B)T for the 2.5-A-radius cylinder and -9k(B)T for the 5-A-radius cylinder, indicating that the association of two alpha-helices of both sizes is favored by the lipid matrix. In contrast, the effective interaction is repulsive at all distances in the case of the large cylinder. Results were obtained with two integral equations theories: hypernetted chain and Percus-Yevick. For the two theories, all results are qualitatively identical.     

Co-operativity in non-covalent interactions in ternary complexes: a comprehensive electronic structure theory based investigation

The structure and stability of various ternary complexes in which an extended aromatic system such as coronene interacts with ions/atoms/molecules on opposite faces of the π-electron cloud were investigated using ab initio calculations. By characterizing the nature of the intermolecular interactions using an energy decomposition analysis, it was shown that there is an interplay between various types of interactions and that there are co-operativity effects, particularly when different types of interactions coexist in the same system.

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Graphical abstract Weak OH-π, π-π and van der Waals-π ternary systems are stabilized through dispersion interactions. Cation-π ternary systems are stabilized by through-space electrostatic interactions.

     

The structural, electronic, and optical properties of ladder-type polyheterofluorenes: a theoretical study

The ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene backbone can influence and modify the optoelectronic properties significantly. The functionalization on the heteroatoms allows for facile derivation and incorporation of substitutes to further tune the properties. Small geometry variations between the ground, anionic/cationic, the first excited singlet and triplet states were observed due to the very rigid ladder-type coplanar backbone. Ladder-type polycarbazole was predicted to have the highest HOMO and LUMO energy levels, polyphosphafluorene oxide have the lowest HOMO energy level, polyborafluorene have the lowest LUMO energy level and bandgap, and polysulfafluorene has the highest bandgap and triplet energy. The ladder-type carbazole and borafluorene show the highest hole and electron injection abilities respectively; while sulfafluorene has the highest electron transfer rate. Most ladder-type heterofluorenes show bipolar charge transport character suggested by the reorganization energy. All of them have significantly short effective conjugation length in comparison with linear conjugated polymers. Their absorption and emission spectra were also simulated and discussed. The diversified electronic and optical properties of the ladder-type polyheterofluorenes with the different incorporated heteroatom and the substituent on it indicate their broad potential applications in organoelectronics.     

Protonation and electronic structure of 2,6-dichlorophenolindophenolate during reduction. A theoretical study including explicit solvent

Protonation in the two-electron/two-proton reduction processes of 2,6-dichlorophenolindophenolate (DCIP) is investigated combining density functional theory (DFT) and molecular dynamics (MD) methods. DCIP (anion), DCIP^?– (radical anion), and DCIP^2? (dianion) are considered, including the electronic structure analysis from the prospective of quantum theory of atoms and molecules (QTAIM). It is shown that oxygen on the indophenolate moiety and nitrogen are the first and/or the second proton acceptor sites and their energetic order depends on the total charge of the system. MD simulations of differently charged species interacting with the solvent molecules have been performed for methanol, water, and oxonium cation (H₃O⁺). Methanol and water molecules are found to form only hydrogen bonds with the solute irrespective of its charge. The calculated pK_a values show that the imino group of DCIPH^? is a weaker acid than water. While in the case of DCIP (and DCIP^?–) plus oxonium cation, proton transfer from the solvent to the solute was evidenced for both aforementioned acceptor sites. In addition, MD simulations of bulks containing 15 and 43 molecules of water around the DCIP molecule have been performed, revealing the formation of 2–4 hydrogen bonds.

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Graphical Abstract 2,6-Dichlorophenolindophenolate interacts with solvent molecules (water, oxonium cation and methanol). Hydrogen transfer and electronic structure are studied by DFT and molecular dynamics methods

     

A theoretical study of lipid-protein interactions in bilayers.

We present a theoretical study of the effect of different types of lipid-protein interactions on the thermodynamic properties of protein-containing lipid bilayers. The basis of this work is a theoretical model for pure lipid bilayer phase transitions developed earlier by Scott. Simple assumptions on the nature of the lipid conformations near a protein strongly affect the predicted properties of the model. Here we consider (a) random protein-lipid contacts, (b) enhanced contact between protein and lipid with a number of gauche bonds, and (c) enhanced contact between protein and all-trans but tilted lipid chains. Comparison of predicted results with experimental data seems to favor point c above but, by itself point c does not work well at larger protein concentrations. The results are discussed in the light of spectroscopic data, lipid-protein (plus annular lipid) miscibility, and interprotein forces.     

Theoretical study of the excited states of the photosynthetic reaction center in photosystem II: electronic structure, interactions, and their origin

The excited states of the chlorophyll 6-mer in the photosystem II (PSII) reaction center (RC) were investigated theoretically using ab initio quantum chemical calculations, and the results are compared with those of the bacterial reaction center (bRC). A significant difference in the peak at the lowest energy in the absorption spectra arises from the structural asymmetry of the special pair (SP). The origin can be traced back to the structural difference in the CD helix. The low-lying excited states are characterized as a linear combination of the excited states of the chlorophyll monomers, which verifies the applicability of exciton theory. Analysis of the molecular interactions clearly explains the cause of the constructive/destructive interferences in the state transition moment. The protein electrostatic potential (ESP) decreases the energy of the charge-transfer (Chl(D1)→Pheo(D1)) state. The ESP also localizes the HOMO distribution to the P(D1) moiety and increases the ionization potential.     

Molecular structure and intra- and intermolecular magnetic interactions in chloro-bridged copper(II) dimers

Magnetic interactions in binuclear copper(II) complexes, [Cu₂(apyhist)₂Cl₂](ClO₄)₂ (1) and [Cu₂(2-pyhist)₂Cl₂](ClO₄)₂ (2) with tridentate diimine ligands and chloro-bridged groups (where apyhist=(4-imidazolyl)ethylene-2-amino-1-ethylpyridine and 2-pyhist=(4-imidazolyl)ethylene-2-aminomethylpyridine) were studied with the aim of better elucidating magneto-structural correlations in such species, both in solution and in solid state. X-ray analyses revealed that chloro-bridged ligands keep the copper(II) ion coordinated to adjacent unit, at Cu-Cl distances of 2.271 and 2.737 Å, and a Cu-Cl-Cu angle of 87.46° in compound 1. Each Cu^II atom is also coordinated to three N atoms from the imine ligand, in a distorted tetragonal pyramidal environment. Magnetic measurements carried out in temperatures from 0.8 to 290 K and in magnetic field up to 170 kOe indicated that besides the intramolecular magnetic coupling between the copper centers [J/k=−(1.93±0.05) K] further interactions between adjacent dimers [J^′z/k=−(1.3±0.1) K] should be taken into account. Similar results were observed for compound 2, for which [J/k=−(4.27±0.05) K] and [J^′z/k=−(3.7±0.1) K]. In solution, the interconversion of the dimer 1 and the related monomer species [Cu(apyhist)(H₂O)₂] (ClO₄)₂ (3) monitored by EPR spectra, was verified to be very dependent on the solvent.     

Exchange interactions in a Fe5 complex: A theoretical study using density functional theory

Theoretical methods based on density functional theory have been employed to analyze the exchange interactions in an Fe₅ complex. The calculated exchange coupling constants are consistent with an S = 15/2 ground state and agree well with those reported previously for other Fe^III polynuclear complexes. The strongest antiferromagnetic interactions are those through a double oxo-benzotriazole bridging ligand, where the benzotriazole ligand seems to play a minor role and the exchange coupling constants present values typical of single oxo bridging systems.