Spin-coupled study of the electronic mechanism of the hetero-Diels-Alder reaction of acrolein and ethene

Modern valence bond theory, in its spin coupled form, is used to elucidate the electronic rearrangements that take place during the course of the gas-phase hetero-Diels-Alder cycloaddition reaction of s-cis-acrolein (cis-1-oxabutadiene or cis-propeneal) and ethene. It is found that the most dramatic changes to the electronic structure occur in a relatively narrow interval of the reaction pathway soon after the transition state and that the system passes through a geometry at which it can be considered to be significantly aromatic. Although concerted, the reaction is markedly asynchronous, with the breaking of the carbon-oxygen pi bond, and the formation of the new carbon-oxygen sigma bond, "lagging behind" somewhat the other bond-making and bond-breaking processes.     

The importance of aromatic-type interactions in serotonin synthesis: protein-ligand interactions in tryptophan hydroxylase and aromatic amino acid decarboxylase

The biosynthesis of serotonin requires aromatic substrates to be bound in the active sites of the enzymes tryptophan hydroxylase and aromatic amino acid decarboxylase. These aromatic substrates are held in place partially by dispersion and induction interactions with the enzymes' aromatic amino acid residues. Mutations that decrease substrate binding can result in a decrease in serotonin production and thus can lead to depression and related disorders. We use optimized crystal structures of these two enzymes to examine pair-wise electronic interaction energies between aromatic residues in the active sites and the aromatic ligands. We also perform in silico mutations on the aromatic residues to determine the change in interaction energies as mutations occur. Our second-order Moller-Plessett perturbation theory calculations show that drastic changes in interaction energy can occur and, in light of our previous work, we are able to use these data to offer predictions on the loss of protein function and on the possibility of disease upon mutation. We also examine local and gradient corrected density functional theory methods to evaluate their ability to predict these induction/dispersion-dominated interaction energies. We find that the hybrid B3LYP cannot model these interactions well, whereas the GGA HCTH407 offers largely qualitatively correct results, and the local functional SVWN quantitatively mimics the MP2 results rather well.     

Substituent effects in synthetic lectins--exploring the role of CH-π interactions in carbohydrate recognition

Contacts between aromatic surfaces and saccharide CH groups are common motifs in natural carbohydrate recognition. These CH-π interactions are modeled in "synthetic lectins" which employ oligophenyl units as apolar surfaces. Here we report the synthesis and study of new synthetic lectins with fluoro- and hydroxy-substituted biphenyl units, designed to explore the role of π-electron density in carbohydrate CH-π interactions. We find evidence that recognition can be moderated through electronic effects but that other factors such as cavity hydration are also important and sometimes predominant in determining binding strengths.     

Photohole screening effects in polythiophenes with pendant groups

We compare two mechanisms that dominate the temperature-dependent changes in electronic structure for poly(3-hexylthiophene-2,5 diyl) (P3HT). Structural changes in the relative orientation and configuration of the aromatic ring backbone are observed to occur over a wide range in temperature and affect the local final state screening in photoemission. There are also changes in conductivity and carrier concentration at lower temperatures leading to altered long-range intramolecular screening of photoholes and final state effects that affect excitation spectroscopies including photoemission. For polyethylenedioxythiophene (PEDOT), temperature-dependent changes in the structure and configuration of the polymer backbone are not as significant, although temperature-dependent final state effects are observed.     

Electronic and molecular structure of some substituted azomethines: A gas-phase u.v. photoelectron spectroscopic investigation

Four azomethinic molecules, three of which present a seven-member ring with two carbon atoms shared with an aromatic system, have been studied by gas-phase u.v. photoelectron spectroscopy with the aim of correlating their electronic and molecular structure. The analysis of the experimental findings, supported by quantum-mechanical calculation (EHT and HAM/3) on model molecules, showed that no appreciable interactions occur between the systems of the aromatic and of the seven-member ring, and that the electronic structure of these molecules depends critically on the geometry. The comparison with smaller parent molecules pointed out that the formation of the seven-member ring induces drastic changes in the electronic structure of the valence levels.     

Femtosecond electron-transfer reactions in mono- and polynucleotides and in DNA

Quenching of redox active, intercalating dyes by guanine bases in DNA can occur on a femtosecond time scale both in DNA and in nucleotide complexes. Notwithstanding the ultrafast rate coefficients, we find that a classical, nonadiabatic Marcus model for electron transfer explains the experimental observations, which allows us to estimate the electronic coupling (330 cm(-1)) and reorganization (8070 cm(-1)) energies involved for thionine-[poly(dG-dC)](2) complexes. Making the simplifying assumption that other charged, pi-stacked DNA intercalators also have approximately these same values, the electron-transfer rate coefficients as a function of the driving force, DeltaG, are derived for similar molecules. The rate of electron transfer is found to be independent of the speed of molecular reorientation. Electron transfer to the thionine singlet excited state from DNA obtained from calf thymus, salmon testes, and the bacterium, micrococcus luteus (lysodeikticus) containing different fractions of G-C pairs, has also been studied. Using a Monte Carlo model for electron transfer in DNA and allowing for reaction of the dye with the nearest 10 bases in the chain, the distance dependence scaling parameter, beta, is found to be 0.8 +/- 0.1 A(-1). The model also predicts the redox potential for guanine dimers, and we find this to be close to the value for isolated guanine bases. Additionally, we find that the pyrimidine bases are barriers to efficient electron transfer within the superexchange limit, and we also infer from this model that the electrons do not cross between strands on the picosecond time scale; that is, the electronic coupling occurs predominantly through the pi-stack and is not increased substantially by the presence of hydrogen bonding within the duplex. We conclude that long-range electron transfer in DNA is not exceptionally fast as would be expected if DNA behaved as a "molecular wire" but nor is it as slow as is seen in proteins, which do not benefit from pi-stacking.     

A spin-coupled study of the Claisen rearrangement of allyl vinyl ether

The spin-coupled (SC) form of modern valence bond (VB) theory is utilised to examine the electronic structure of the transition state (TS) and the electronic reaction mechanism of the Claisen rearrangement of allyl vinyl ether. The differences between the spin-coupling patterns and orbital overlap integrals at the optimised TS geometries obtained using B3LYP/6-31G^*, MP2/6-31G^* and MP4(SDQ)/6-31G^* wavefunctions are minimal, and the SC picture suggests that the TS is non-aromatic. SC calculations along the intrinsic reaction coordinates computed at these three levels of theory also produce near identical results. The SC wavefunctions at different stages of the reaction provide easily interpretable orbital diagrams which, in combination with the changes in the orbital overlap integrals, indicate an electronic reaction mechanism involving concerted, though not entirely synchronous, bond breaking and bond formation processes. The evolution of the active space spin-coupling pattern, which is closely related to the classical VB concept of resonance, combined with the changes in the orbital overlap integrals, show that the reaction path involves a region in which the electronic structure of the reacting system becomes similar to that of benzene. This suggests that during the Claisen rearrangement the reacting system can attain moderately aromatic character but that this does not necessarily happen at the TS. The results of the SC analysis indicate that the most appropriate schematic representation of the Claisen rearrangement is furnished by a homolytic mechanism in which six harpoons describe the changes in the bonding pattern from reactant to product     

Ultrafast irreversible phototautomerization of o-nitrobenzaldehyde

o-Nitrobenzaldehyde is photolabile because of an irreversible phototautomerization, whereas comparable aromatic compounds function as photoprotectors because the tautomerization is reversible. In this experimental and theoretical study we track down the cause of this difference to the electronic changes that occur during the tautomerization.     

Ab Initio simulations of nonstoichiometric Cd(x)Te(1-x) liquids

We present ab initio molecular-dynamics simulations for Cd(x)Te(1-x) liquids where the composition is nonstoichiometric. The simulations are performed following Born-Oppenheimer molecular dynamics. The required forces are obtained from a solution of the Kohn-Sham equation using ab initio pseudopotentials. We consider stoichiometries of the form: Cd(x)Te(1-x), where x=0.2, 0.4, 0.6, and 0.8. For each composition of the melt, we consider a range of temperatures near the experimentally determined liquid temperatures. We examine the microstructural properties of the melt, the viscosity, and self-diffusion properties of the liquid as a function of the stoichiometry and temperature. We also perform an analysis of the distribution of the electronic density of states in these liquids. We find that structural changes in the local order, experimentally predicted to occur when the concentration of Cd is increased, are closely related to changes in the electronic properties of the melt.     

The structural transformations of silicon phthalocyanine in reaction with magnesium and trimethylchlorosilane

The reaction of PcSi(OSiMe₃)₂ with Mg in the presence of Me₃SiCl at 20–100°C was shown to cause the phthalocyamine macrocycle contraction and give the silicon α,β,γ-triazatetrabenzocorrole macrocycle. The reaction proceeds in the polar donor solvents (THF, pyridine), but does not occur in aromatic hydrocarbons. The electronic and EPR spectra indicate that the silicon phthalocyanine mono- and dianions are active intermediate reaction products.     

Matrix EPR and QM study of a model aromatic thioether radical-cation

The electronic structure and EPR properties of the model aromatic benzyl phenyl thioether radical cation [Ph-S-CH₂-Ph]⁺ have been assessed and compared to those of the aliphatic analogues. In the most stable conformation spin and charge are almost equally distributed between the sulfur atom and the adjacent phenyl ring. In correspondence of favourable conformations spin and charge transfer from the aryl to the benzyl ring is predicted to occur thus suggesting the possibility of solvent effects on the reactivity distribution. Contrariwise to the aliphatic analogues, the major reaction mode in the chlorofluorocarbon matrix above 77 K is the C-S bond splitting.     

Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch

In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.     

In situ Raman monitoring triazole formation from self-assembled monolayers of 1,4-diethynylbenzene on Ag and Au surfaces via "click" cyclization

We prepared acetylenyl-terminated aromatic self-assembled monolayers (SAMs) of 1,4-diethynylbenzene on silver and gold. After the fabrication of pendent acetylenyl SAMs, the formation of triazoles was performed via Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition "click" chemistry. A density functional theory (DFT) calculation of Raman frequencies showed good agreement with our experimental data to provide evidence of the formation of the triazole molecule. Our results indicated that "click" chemistry could be successfully applied to simple aromatic SAMs proximate (<1 nm) to roughened gold surfaces. The reaction process could be monitored in real time by measuring intensity changes of the nu(CC)(free) band in surface-enhanced Raman scattering (SERS) spectra.     

Selective response of mesoporous silicon to adsorbants with nitro groups

We demonstrate that the electronic structure of mesoporous silicon is affected by adsorption of nitro-based explosive molecules in a compound-selective manner. This selective response is demonstrated by probing the adsorption of two nitro-based molecular explosives (trinitrotoluene and cyclotrimethylenetrinitramine) and a nonexplosive nitro-based aromatic molecule (nitrotoluene) on mesoporous silicon using soft X-ray spectroscopy. The Si atoms strongly interact with adsorbed molecules to form Si-O and Si-N bonds, as evident from the large shifts in emission energy present in the Si L(2,3) X-ray emission spectroscopy (XES) measurements. Furthermore, we find that the energy gap (band gap) of mesoporous silicon changes depending on the adsorbant, as estimated from the Si L(2,3) XES and 2p X-ray absorption spectroscopy (XAS) measurements. Our ab initio molecular dynamics calculations of model compounds suggest that these changes are due to spontaneous breaking of the nitro groups upon contacting surface Si atoms. This compound-selective change in electronic structure may provide a powerful tool for the detection and identification of trace quantities of airborne explosive molecules.     

Size-expanded DNA bases: an ab initio study of their structural and electronic properties

The size-expanded DNA bases, xA, xC, xG, and xT, are benzo-homologue forms of the natural DNA bases; i.e., their structure can be seen as the fusion of a natural base and a benzene ring. Recently, a variety of DNAs, known as xDNAs, have been synthesized in which size-expanded and natural bases are paired. In this paper we use second-order M?ller-Plesset perturbation theory and density functional theory to investigate the structural and electronic properties of xA, xC, xG, and xT and their natural counterparts. We find that whereas natural and size-expanded bases have both nonplanar amino groups the latter have also nonplanar aromatic rings. When density functional theory is used to investigate the electronic properties of size-expanded and natural bases, it is found that the HOMO-LUMO gap of the size-expanded bases is smaller than that of the natural bases. Also, xG should be easier to oxidize than G.     

Factors controlling the energetics of the oxygen reduction reaction on the Pd-Co electro-catalysts: insight from first principles

We report here results of our density functional theory based computational studies of the electronic structure of the Pd-Co alloy electrocatalysts and energetics of the oxygen reduction reaction (ORR) on their surfaces. The calculations have been performed for the (111) surfaces of pure Pd, Pd(0.75)Co(0.25) and Pd(0.5)Co(0.5) alloys, as well as of the surface segregated Pd/Pd(0.75)Co(0.25) alloy. We find the hybridization of dPd and dCo electronic states to be the main factor controlling the electrocatalytic properties of Pd/Pd(0.75)Co(0.25). Namely the dPd-dCo hybridization causes low energy shift of the surface Pd d-band with respect to that for Pd(111). This shift weakens chemical bonds between the ORR intermediates and the Pd/Pd(0.75)Co(0.25) surface, which is favorable for the reaction. Non-segregated Pd(0.75)Co(0.25) and Pd(0.5)Co(0.5) surfaces are found to be too reactive for ORR due to bonding of the intermediates to the surface Co atoms. Analysis of the ORR free energy diagrams, built for the Pd and Pd/Pd(0.75)Co(0.25), shows that the co-adsorption of the ORR intermediates and water changes the ORR energetics significantly and makes ORR more favorable. We find the onset ORR potential estimated for the configurations with the O-OH and OH-OH co-adsorption to be in very good agreement with experiment. The relevance of this finding to the real reaction environment is discussed.     

Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions

Carbohydrate-protein recognition has been studied by electronic structure calculations of complexes of fucose and glucose with toluene, p-hydroxytoluene and 3-methylindole, the latter aromatic molecules being analogues of phenylalanine, tyrosine and tryptophan, respectively. We use mainly a density functional theory model with empirical corrections for the dispersion interactions (DFT-D), this method being validated by comparison with a limited number of high level ab initio calculations. We have calculated both binding energies of the complexes as well as their harmonic vibrational frequencies and proton NMR chemical shifts. We find a range of minimum energy structures in which the aromatic group can bind to either of the two faces of the carbohydrate, the binding being dominated by a combination of OH-pi and CH-pi dispersive interactions. For the fucose-toluene and alpha-methyl glucose-toluene complexes, the most stable structures involve OH-pi interactions, which are reflected in a red shift of the corresponding O-H stretching frequency, in good quantitative agreement with experimental data. For those structures where CH-pi interactions are found we predict a corresponding blue shift in the C-H frequency, which parallels the predicted proton NMR shift. We find that the interactions involving 3-methylindole are somewhat greater than those for toluene and p-hydroxytoluene.     

The experimental visualisation of molecular structural changes during both photochemical and thermal reactions by real-time vibrational spectroscopy

Have you ever hoped to observe transition states? Chemists have long desired to monitor the deformation of molecular structures via transition states to understand the mechanisms of complicated reactions. Detailed knowledge of transition states helps find strategies to develop novel reaction schemes for introducing new functionalities to chemicals. Molecular structural changes via transition states can be observed by real-time vibrational spectroscopy using sub-5 fs laser pulses. In this paper, I report the direct observation of time-dependent frequency shifts of relevant molecular vibrational modes, which allowed for the clear visualization of ultrafast structural changes in molecules during bond breaking and bond reformation steps. Various mechanisms for photochemical reactions were clarified using sub-5 fs laser pulses. Moreover, a non-thermal vibrational excitation method for efficiently driving chemical reactions in the electronic ground state in solution with the use of broadband visible sub-5 fs laser pulses has been developed. The respective chemical reaction processes were directly observed, including transition states during not only "photochemical" but also "thermal" reactions. Time-resolved spectroscopy with a time resolution of a few femtoseconds enables observation of real-time vibrational amplitudes of complicated molecules and opens up new ways for clarifying reaction mechanisms and developing new chemical transformations.     

Exciton coherence lifetimes from electronic structure

We model the coherent energy transfer of an electronic excitation within covalently linked aromatic homodimers from first-principles. Our results shed light on whether commonly used models of the bath calculated via detailed electronic structure calculations can reproduce the key dynamics. For the systems we model, the time scales of coherent transport are experimentally known from time-dependent polarization anisotropy measurements, and so we can directly assess whether current techniques are predictive for modeling coherent transport. The coupling of the electronic degrees of freedom to the nuclear degrees of freedom is calculated from first-principles rather than assumed, and the fluorescence anisotropy decay is directly reproduced. Surprisingly, we find that although time-dependent density functional theory absolute energies are routinely in error by orders of magnitude more than the coupling energy between monomers, the coherent transport properties of these dimers can be semi-quantitatively reproduced from these calculations. Future directions which must be pursued to yield predictive and reliable models of coherent transport are suggested.     

Calculated electronic transitions of the water ammonia complex

We have calculated vertical excitation energies and oscillator strengths of the low lying electronic transitions in H2O, NH3, and H2ONH3 using a hierarchy of coupled cluster response functions [coupled cluster singles (CCS), second order approximate coupled cluster singles and doubles (CC2), coupled cluster singles and doubles (CCSD), and third order approximate coupled cluster singles, doubles, and triples (CC3)] and correlation consistent basis functions (n-aug-cc-pVXZ, where n=s,d,t and X=D,T,Q). Our calculations indicate that significant changes in the absorption spectra of the photodissociative states of H2O and NH3 monomers occur upon complexation. In particular, we find that the electronic transitions originating from NH3 are blueshifted, whereas the electronic transitions originating from H2O are redshifted.