Blue-shifted A-H stretching frequencies in complexes with methanol: the decisive role of intramolecular coupling

The presence of a blue shift of A-H stretching frequencies in intermolecular complexes is directly related to the intramolecular coupling between A-H and vicinal A-X bonds in isolated molecules. The intramolecular coupling between vicinal bonds is the decisive parameter that determines whether a general molecule is a candidate for displaying blue-shifted A-H stretching frequencies in intermolecular complexes, with or without hydrogen bonding. The structures and vibrational spectra of dimeric complexes of methanol with H(2)O, HF, HCN, HNC, HOF, HNO, and HSN are investigated at the MP2/6-311++G(2d,2p) approach. Blue- and red-shifts of the methyl C-H stretches of methanol and the various other A-H stretching frequencies in the complexes can be predicted by normal coordinate analyses of methanol and the partner molecules. It is, hence, suggested that conventional normal coordinate analysis is the appropriate predictive tool to decide beforehand whether a given molecule is a promising candidate for the observation of blue shifts in intermolecular complexes.     

Theoretical elucidation of conflicting experimental data on vertical ionization potentials of microhydrated thymine

In a recent article we reported calculations of the ionization energy thresholds (IET) of microhydrated thymine (Close; et al. J. Phys. Chem. A, 2006, 110, 7485). Calculations showed a distinct effect of microhydration on the IET's of thymine. The first water molecule was seen to decrease the IET by about 0.1 eV, and the second and third water molecules caused a further decrease of less than 0.1 eV each. These changes in IET calculated for the canonical form of thymine with 1-3 waters of hydration are smaller than the experimental values determined by Kim et al. (J. Phys. Chem. C 1996, 100, 7933). In the present study it has been shown that there is considerable reorientation of the water molecules in microhydrated thymine upon ionization. This leads to the expectation that the experimental ionization energies may therefore represent an adiabatic process. The results presented here show that the changes in experimental ionization energies determined by Kim et al. for microhydrated thymine are in good agreement with the calculated adiabatic ionization energies.     

The Role of Small Molecule–small Molecule Interactions in Overcoming Biological Barriers for Antibacterial Drug Action

The ineffectiveness of antibiotics against bacteria can be caused by multidrug resistance (MDR) or by an outer membrane, which restricts the penetration of amphipathic compounds into Gram-negative bacteria. Remarkable activities of plant antimicrobials in the presence of MDR modulators have been observed against a series of MDR and Gram-negative bacteria (Tegos et al., Antimicrob Agents Chemother 46:3133, 2002). Assuming that modulators of MDR might form complexes with substrates of efflux pumps Zloh et al., Biogr Med Chem Lett 14:881, 2004), we have evaluated interaction energies between antimicrobials and MDR modulators reported in Tegos et al. (Antimicrob Agents Chemother 46:3133, 2002). In this paper, we can confirm that modulation activity against the efflux pump NorA in Staphylococcus aureus correlates with the interaction energies between MDR modulator INF271 and antibacterials. Additionally, the change of log P of complexes might be responsible for overcoming the membrane impermeability in Gram-negative bacteria and increasing the antibacterial activity in the presence of the modulator MC207110. This suggests that interactions between small molecules may play an important role in overcoming biological barriers in bacteria.     

Bandgap Engineering through Controlled Oxidation of Polythiophenes

The use of Rozen’s reagent (HOF?CH₃CN) to convert polythiophenes to polymers containing thiophene‐1,1‐dioxide (TDO) is described. The oxidation of polythiophenes can be controlled with this potent, yet orthogonal reagent under mild conditions. The oxidation of poly(3‐alkylthiophenes) proceeds at room temperature in a matter of minutes, introducing up to 60 % TDO moieties in the polymer backbone. The resulting polymers have a markedly low‐lying lowest unoccupied molecular orbital (LUMO), consequently exhibiting a small bandgap. This approach demonstrates that modulating the backbone electronic structure of well‐defined polymers, rather than varying the monomers, is an efficient means of tuning the electronic properties of conjugated polymers.     

A dual-level state-specific time-dependent density-functional theory

A highly efficient new algorithm for time-dependent density-functional theory (TDDFT) calculations is presented. In this algorithm, a dual-level approach to speed up DFT calculations (Nakajima and Hirao, J Chem Phys 2006, 124, 184108) is combined with a state-specific (SS) algorithm for TDDFT (Chiba et al., Chem Phys Lett 2006, 420, 391). The dual-level SS-TDDFT algorithm was applied to excitation energy calculations of typical small molecules, the Q bands of the chlorophyll A molecule, the charge-transfer energy of the zincbacteriochlorin-bacteriochlorin model system, and the lowest-lying excitation of the circumcoronene molecule. As a result, it was found that the dual-level SS-TDDFT gave correct excitation energies with errors of 0.2-0.3 eV from the standard TDDFT approach, with much lower CPU times for various types of excitation energies of large-scale molecules.     

Charge transfer complexes of fullerene C60 with N,N-dimethylaniline derivatives

Charge transfer complexes of a series of p-substituted dimethylanilines with C₆₀ fullerenes were studied by electron absorption spectroscopy. Energies of charge transfer bonds depend on three effects of substituents in the donor molecule (the inductive, resonance, and polarization effects) with domineering of the resonance effect. The energies are linearly proportional to the potentials of electrochemical oxidation of aniline derivatives.     

Can one oxidize an atom by reducing the molecule that contains it?

Negative values for the condensed Fukui function are identified as the key to designing molecules in which reduction of the molecule is associated with oxidation of one of the atomic centers, or vice versa. Sufficient conditions for negative condensed Fukui functions are derived, and metal complexes are identified as likely candidates for this exotic redox chemistry. Based on our theoretical understanding of where negative values of the Fukui function occur [P. W. Ayers, R. C. Morrison and R. K. Roy. J. Chem. Phys., 2002, 116, 8731], molecular-orbital diagrams for molecules where molecular oxidation is coupled to atomic reduction (or vice versa) are sketched. Whether one could design a metal complex with these properties is an open question but, if one could, then that compound would have fascinating redox chemistry and interesting magnetic properties. Candidate molecules for this property include metal complexes with small metal-to-ligand and/or ligand-to-metal charge transfer excitation energies.     

New Conjugated Oligothiophenes Containing the Unique Arrangement of Internal Adjacent [All]‐S,S‐Oxygenated Thiophene Fragments

The quest for obtaining conjugated oligothiophene‐containing molecules with narrower HOMO–LUMO gaps and higher oxidation and reduction potentials is the subject of this study. Molecules containing the bithiophene tetraoxide ( 2 ) and the terthiophene hexaoxide ( 3 ) moieties were prepared and studied. They were obtained by transferring oxygen atoms to the corresponding dibromo oligothiophenes with the HOF ? CH₃CN complex and then cross‐coupling them with either thiophene‐ or acetylene tin derivatives. The photophysical and electrochemical studies of the products revealed that this particular class of mixed thiophenes is characterized by significantly smaller frontier orbital gaps and higher oxidation and reduction potentials compared with any other arrangement of oligothiophenes including various [all]‐S,S‐oxygenated thiophene derivatives.     

Effect of the overall rotation on the cis-trans isomerization of HONO induced by an external field

Rovibrational eigenenergies of HONO are computed and compared to experimental energies available in the literature. For their computation, we use a previously developed potential energy surface (PES) and a newly derived exact kinetic energy operator (KEO) including the overall rotation for a tetra-atomic molecule in non-orthogonal coordinates. In addition, we use the Heidelberg Multi-Configuration Time-Dependent Hartree (MCTDH) package. We compare the experimental rovibrational eigenvalues of HONO available in the literature with those obtained with MCTDH and a previously developed potential energy surface (PES) [F. Richter et al., J. Chem. Phys., 2004, 120, 1306.] for the cis geometry. The effect of the overall rotation on the process studied in our previous work on HONO [F. Richter et al., J. Chem. Phys., 2007, 127, 164315.] leading to the cis→trans isomerization of HONO is investigated. This effect on this process is found to be weak.     

Stabilisation energy of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels

Stabilisation energies of stacked structures of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, CN) complexes were determined at the CCSD(T) complete basis set (CBS) limit level. These energies were constructed from MP2/CBS stabilisation energies and a CCSD(T) correction term determined with a medium basis set (6-31G**). The former energies were extrapolated using the two-point formula of Helgaker et al. from aug-cc-pVDZ and aug-cc-pVTZ Hartree-Fock energies and MP2 correlation energies. The CCSD(T) correction term is systematically repulsive. The final CCSD(T)/CBS stabilisation energies are large, considerably larger than previously calculated and increase in the series as follows: hexafluorobenzene (6.3 kcal mol(-1)), hexachlorobenzene (8.8 kcal mol(-1)), hexabromobenzene (8.1 kcal mol(-1)) and hexacyanobenzene (11.0 kcal mol(-1)). MP2/SDD** relativistic calculations performed for all complexes mentioned and also for benzene[dot dot dot]hexaiodobenzene have clearly shown that due to relativistic effects the stabilisation energy of the hexaiodobenzene complex is lower than that of hexabromobenzene complex. The decomposition of the total interaction energy to physically defined energy components was made by using the symmetry adapted perturbation treatment (SAPT). The main stabilisation contribution for all complexes investigated is due to London dispersion energy, with the induction term being smaller. Electrostatic and induction terms which are attractive are compensated by their exchange counterparts. The stacked motif in the complexes studied is very stable and might thus be valuable as a supramolecular synthon.     

1,3-Diamido-calix[4]arene conjugates of amino acids: recognition of -COOH side chain present in amino acids, peptides, and proteins by experimental and computational studies

Lower rim 1,3-diamido conjugates of calix[4]arene have been synthesized and characterized, and the structures of some of these have been established by single crystal XRD. The amido-calix conjugates possessing a terminal -COOH moiety have been shown to exhibit recognition toward guest molecules possessing -COOH moiety, viz., Asp, Glu, and reduced and oxidized glutathione (GSH, GSSG), by switch-on fluorescence in aqueous acetonitrile and methanol solutions when compared to the control molecules via forming a 1:1 complex. The complex formed has been shown by mass spectrometry, and the structural features of the complexes were derived on the basis of DFT computations. The association constants observed for the recognition of Asp/Glu by Phe-calix conjugate, viz., 532/676 M(-1), are higher than that reported for the recognition of Val, Leu, Phe, His, and Trp (16-63 M(-1)) by a water-soluble calixarene (Arena, G., et al. Tetrahedron Lett. 1999, 40, 1597). For this recognition, there should be a free -COOH moiety from the guest molecule. AFM, SEM, and DLS data exhibited spherical particles with a hundred-fold reduction in the size of the complexes when compared to the particles of the precursors. These spherical particles have been computationally modeled to possess hexameric species reminiscent of the hexameric micellar structures shown for a Ag(+) complex of a calix[6]arene reported in the literature (Houmadi, S., et al. Langmuir 2007, 23, 4849). Both AFM and TEM studies demonstrated the formation of nanospheres in the case of GSH-capped Ag nanoparticles in interaction with the amido-calix conjugate that possesses terminal -COOH moiety. The AFM studies demonstrated in this paper have been very well applied to albumin proteins to differentiate the aggregational behavior and nanostructural features exhibited by the complexes of proteins from those of the uncomplexed ones. To our knowledge, this is the first report wherein a amido-calix[4]arene conjugate and its amino acid/peptide/protein complexes have been differentiated on the basis of spectroscopy and microscopy studies followed by species modeling by computations.     

Graphical prediction of quantum interference-induced transmission nodes in functionalized organic molecules

Quantum interference (QI) in molecular transport junctions can lead to dramatic reductions of the electron transmission at certain energies. In a recent work [Markussen et al., Nano Lett., 2010, 10, 4260] we showed how the presence of such transmission nodes near the Fermi energy can be predicted solely from the structure of a conjugated molecule when the energies of the atomic p(z) orbitals do not vary too much. Here we relax the assumption of equal on-site energies and generalize the graphical scheme to molecules containing different atomic species. We use this diagrammatic scheme together with tight-binding and density functional theory calculations to investigate QI in linear molecular chains and aromatic molecules with different side groups. For the molecular chains we find a linear relation between the position of the transmission nodes and the side group π orbital energy. In contrast, the transmission functions of functionalized aromatic molecules generally display a rather complex nodal structure due to the interplay between molecular topology and the energy of the side group orbital.     

Inverse hydrogen bonds between XeH2 and hydride and fluoride derivatives of Li, Be, Na and Mg

A theoretical study of the inverse hydrogen bonds complexes formed by the XeH₂ molecule and hydride and fluoride derivatives of Li, Be, Na and Mg has been carried out by means of DFT (B3LYP/DGDZVP) and ab initio [MP2/DGDZVP and MP2/LJ18/6-311++G(2d,2p)] calculations. The complexes obtained present interaction energies up to ?81 kJ/mol. The analysis of the electron density shows electron transfer from the XeH₂ to the electron acceptor molecules. The calculated absolute chemical shieldings show the high sensitivity of the xenon atom upon complexation.     

Organic–inorganic hybrid materials based on organophosphorus coupling molecules: from metal phosphonates to surface modification of oxides

Organophosphorus acids (phosphoric, phosphonic, and phosphinic) and their derivatives (salts, esters) are highly promising coupling molecules that allow the anchoring of organic groups to inorganic solids. In this article we briefly review our contribution in the preparation of materials based on organophosphorus coupling molecules: new sol–gel routes to microporous zirconium phosphonates and metal oxide/phosphonate or phosphinate hybrids, and surface modification of metal oxide nanoparticles. The potentialities of the sol–gel and surface modification approaches are illustrated by the immobilization of organometallic metal complexes using phosphine-phosphonate molecules. To cite this article: P.-H. Mutin et al., C. R. Chimie 6 (2003).     

Multireference configuration interaction calculations for complexes of positronium and B, C, N, and O atoms

Positronium (Ps) binding energies for complexes of Ps and atoms with open shell electrons, PsX (X=B, C, N, and O), are calculated using the multireference singly and doubly excited configuration interaction (MRSDCI) method. The effectiveness of this method for the complexes is verified. The MRSDCI calculations are carried out with a frozen-core approximation so as to incorporate only the most important valence correlation effects. Many-body correlation effects and contributions from higher angular momentum orbitals are estimated by extrapolation techniques. The resulting Ps binding energies agree well with the results of diffusion Monte Carlo simulations by Bressanini et al. (Phys Rev A 57:1678,1998) and by Jiang and Schrader (J Chem Phys 109:9430,1998). For PsO the Ps binding energy obtained by Jiang and Schrader is about 1.8 times larger than that of Bressanini et al.; the present calculated value is close to that of Jiang and Schrader.     

Polyvalent scaffolds. Counting the number of seats available for eosin guest molecules in viologen-based host dendrimers

We have prepared and investigated two dendrimers based on a 1,3,5-trisubstituted benzenoid-type core, containing 9 and 21 viologen units in their branches, respectively, and terminated with tetraarylmethane derivatives. We have shown that, in dichloromethane solution, such highly charged cationic species give rise to strong host-guest complexes with the dianionic form of the red dye eosin. Upon complexation, the absorption spectrum of eosin becomes broader and is slightly displaced toward lower energies, whereas the strong fluorescence of eosin is completely quenched. Titration experiments based on fluorescence measurements have shown that each viologen unit in the dendrimers becomes associated with an eosin molecule, so that the number of positions ("seats") available for the guest molecules in the hosting dendrimer is clearly established, e.g., 21 for the larger of the two dendrimers. The host-guest interaction can be destroyed by addition of chloride ions, a procedure which permits eosin to escape from the dendrimer's interior in a controlled way and to regain its intense fluorescence. When chloride anions are precipitated out by addition of silver cations, eosin molecules re-enter the dendrimer's interior and their fluorescence again disappears.     

Photo-induced desorption of NO from NiO(100): calculation of the four-dimensional potential energy surfaces and systematic wave packet studies

The velocity distributions of the laser-induced desorption of NO molecules from an epitaxially grown film of NiO(100) on Ni(100) have been studied [Mull et al., J. Chem. Phys., 1992, 96, 7108]. A pronounced bimodality of velocity distributions has been found, where the NO molecules desorbing with higher velocities exhibit a coupling to the rotational quantum states J. In this article we present simulations of state resolved velocity distributions on a full ab initio level. As a basis for this quantum mechanical treatment a 4D potential energy surface (PES) was constructed for the electronic ground and a representative excited state, using a NiO5Mg(18+)13 cluster. The PESs of the electronic ground and an excited state were calculated at the CASPT2 and the configuration interaction (CI) level of theory, respectively. Multi-dimensional quantum wave packet simulations on these two surfaces were performed for different sets of degrees of freedom. Our key finding is that at least a 3D wave packet simulation, in which the desorption coordinate Z, polar angle theta and lateral coordinate X are included, is necessary to allow the simulation of experimental velocity distributions. Analysis of the wave packet dynamics demonstrates that essentially the lateral coordinate, which was neglected in previous studies [Klüner et al., Phys. Rev. Lett. 1998, 80, 5208], is responsible for the experimentally observed bimodality. An extensive analysis shows that the bimodality is due to a bifurcation of the wave packet on the excited state PES, where the motion of the molecule parallel to the surface plays a decisive role.     

A comprehensive and compact n-heptane oxidation model derived using chemical lumping

A detailed reaction mechanism for n-heptane oxidation has been compiled and subsequently simplified. The model is based on a kinetic model for C1-C4 fuel oxidation of Hoyermann et al. [Phys. Chem. Chem. Phys., 2004, 6, 3824] and a detailed mechanism for n-heptane oxidation developed by Curran et al. [Combust. Flame, 1998, 114, 149]. The generated mechanism is kept compact by limiting the application of the low temperature oxidation pathways to the fuel molecule. The first reaction steps and the complex low temperature paths in the oxidation process have been simplified and reorganized by linear chemical lumping. The reported procedure allows a decrease in number of species and reactions with only a minor loss of model accuracy. The simplified model is of very compact size and gives an advantageous starting point for further model reduction. By this chemically lumped general mechanism without further adjustments the large set of experimental data for the high and low temperature oxidation (ignition delay times, species concentration profiles, heat release and engine pressure profiles, flame speeds and flame structure data) for conditions ranging from very low to high temperatures (550-2300 K), very lean to extremely fuel rich (0.22 < phi < 3) mixtures and pressures between 1 and 42 bar is consistently described providing a basis for reliable predictions for future applications, (i) building reaction mechanisms for similar but chemically more complex fuels (e.g. iso-octane, n-decane,...) and (ii) calculating complex flow fields ("fluid dynamics") after further simplification with advanced reduction tools.     

Theoretical study of the double Renner effect for A2Pi MgNC/MgCN: higher excited rovibrational states

The authors report here the implementation of a newly developed, highly efficient matrix diagonalization routine in the DR program [T. E. Odaka et al., J. Mol. Struct. 795, 14 (2006)]. The DR program solves the rovibronic Schrodinger equation for a triatomic molecule with a double Renner effect, i.e., with two accessible linear arrangements of the nuclei at which the electronic energy is doubly degenerate. With the new routines, the authors can extend the DR calculations of rovibronic energies for A 2Pi MgNC/MgCN by considering a much larger set of rovibronic states, in particular, states at higher J values, than the authors were able to access previously.     

Effects of hydrogen bonding on the acidity of adenine, guanine, and their 8-oxo derivatives

Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density-functional theory. The binding strengths of the neutral and (N9) anionic complexes are considered for a variety of purine binding sites. The effects of hydrogen-bonding interactions on the (N9) acidity of the purine derivatives are considered as a function of the molecule bound and the binding site. It is found that hydrogen-bonding interactions with one molecule can increase the acidity of purine derivatives by up to 60 kJ mol(-1). The (calculated) simultaneous effects of up to four molecules on the acidity of the purine derivatives are also considered. Our data suggest that the effects of more than one molecule on the acidity of the purines are generally less than the sum of the individual (additive) effects, where the magnitude of the deviation from additivity increases with the number, as well as the acidity, of molecules bound. Nevertheless, the increase in the acidity due to additional hydrogen-bonding interactions is significant, where the effect of two, three, or four hydrogen-bonding interactions can be as large as approximately 95, 115, and 130 kJ mol(-1), respectively. The present study provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.