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At least 793 records · Page 44Linked to original sources
PubMed2004

Hydrogen-bonding-induced shifts of the excitation energies in nucleic acid bases: an interplay between electrostatic and electron density overlap effects.

The theoretically calculated dimerization-induced shifts of the lowest excitation energies in two model systems, adenine-thymine and guanine-cytosine base pairs, are analyzed. The applied formalism is based on first principles and allows one to study the influence of the microscopic environment of a given molecule on its ground- [Wesolowski, T. A.; Warshel, A. J. Phys. Chem. 1993, 97, 8050] and excited-state [Casida, M. E.; Wesolowski, T. A. Int. J. Quantum Chem. 2004, 96, 577] properties. The assessment of the relative importance of such effects as (a) Coulomb interactions, (b) orbital interactions, (c) electronic polarization of the environment, and (d) electron density overlap effects is straightforward in this formalism. In the applied formalism, electron density overlap effects can be further decomposed into the exchange-correlation component which provides a small attractive contribution and the repulsive kinetic energy-dependent component. It is shown that the shifts can be attributed to the electrostatic interactions and the repulsive overlap-dependent term in the embedding potential. The electronic polarization of the environment plays a significant role (up to 30% of the total shift) only in transitions involving the orbitals localized on hydrogen bond donor groups. For all analyzed shifts, the contribution of the intermolecular orbital interactions is negligible. The analysis of this work provides strong evidence supporting the use of the widely applied embedding-molecule strategy in computational studies of chromophores in a condensed phase even in such cases where only one end of the hydrogen bond is included in the quantum mechanical part.

Adenine↗
PubMed2005

Experimental study of the interplay between long-range electron transfer and redox probe permeation at self-assembled monolayers: evidence for potential-induced ion gating.

Evidence for the competition between long-range electron transfer across self-assembled monolayers (SAMs) and incorporation of the redox probe into the film is reported for the electroreduction of Ru(NH(3)) at hydroxyl- and carboxylic-acid-terminated SAMs on a mercury electrode, by using electrochemical techniques that operate at distinct time scales. Two limiting voltammetric behaviors are observed, consistent with a diffusion control of the redox process at mercaptophenol-coated electrodes and a kinetically controlled electron transfer reaction in the presence of neutral HS-(CH(2))(10)-COOH and HS-(CH(2))(n)()-CH(2)OH (n = 3, 5, and 10) SAMs. The monolayer thickness dependence of the standard heterogeneous electron transfer rate constant shows that the electron transfer plane for the reduction of Ru(NH(3)) at hydroxyl-terminated SAMs is located outside the film | solution interface at short times. However, long time scale experiments provide evidence for the occurrence of potential-induced gating of the adsorbed structure in some of the monolayers studied, which takes the form of a chronoamperometric spike. Redox probe permeation is shown to be a kinetically slow process, whose activation strongly depends on redox probe concentration, applied potential, and chemical composition of the intervening medium. The obtained results reveal that self-assembled monolayers made of mercaptobutanol and mercaptophenol preserve their electronic barrier properties up to the reductive desorption potential of a fully grown SAM, whereas those of mercaptohexanol, mercaptoundecanol, and mercaptoundecanoic acid undergo an order/disorder transition below a critical potential, which facilitates the approach of the redox probe toward the electrode surface.

Journal Article↗
PubMed2005

Electronic coupling in tetraanisylarylenediamine mixed-valence systems: the interplay between bridge energy and geometric factors.

We have investigated three organic mixed-valence systems that possess nearly identical inter-redox site distances and differ by the nature of the bridging units benzene, naphthalene, and anthracene: the N,N,N',N'-tetra(4-methoxyphenyl)-1,4-phenylenene-diamine radical cation (1+), the 1,4-bis(N,N-di(4-methoxyphenyl)-amino)naphthalene radical cation (2+), and the 9,10-bis(N,N-di(4-methoxyphenyl)amino)anthracene radical cation (3+). The electronic interactions in these systems have been studied by means of gas-phase ultraviolet photoelectron spectroscopy, vis/NIR spectroscopy, and electronic-structure calculations. The experimental and theoretical results concur to indicate that the strength of electronic interaction decreases in the following order of bridging units: benzene > naphthalene > anthracene. This finding contradicts the usual expectation that anthracene is superior to benzene as a driving force for electronic communication. We explain these results in terms of a super-exchange mechanism and its strong dependence on steric interactions.

Journal Article↗
PubMed2006

Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach.

The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.

Journal Article↗
PubMed2006

Interplay of structure and reactivity in a most unusual furan Diels-Alder reaction.

Difluorinated alkenoate ethyl 3,3-difluoro-2-(N,N-diethylcarbamoyloxy)-2-propenoate reacts rapidly and in high yield with furan and a range of substituted furans in the presence of a tin(IV) catalyst. Non-fluorinated congener 2-(N,N-diethylcarbamoyloxy)-2-propenoate fails to react at all under the same conditions. These reactions have been explored using density functional theory (DFT) calculations. They reveal a highly polar transition state, which is stabilized by the Lewis acid catalyst SnCl(4) and by polar solvents. In the presence of both catalyst and solvent, a two-step reaction is predicted, corresponding to the stepwise formation of the two new carbon-carbon bonds via transition states which have similar energies in all cases. Our experimental observations of the lack of reaction of the non-fluorinated dienophile, the stereochemical outcomes, and the rate acceleration accompanying furan methylation are all well predicted by our calculations. The calculated free energy barriers generally correlate well with measured reaction rates, supporting a reaction mechanism in which zwitterionic character is developed strongly. An in situ ring opening reaction of exo-cycloadduct ethyl exo-2-(N,N-diethylcarbamoyloxy)-3,3-difluoro-7-oxabicyclo[2.2.1]hept-5-enyl-2-endo-carboxylate, which results in the formation of cyclic carbonate ethyl 4,4-difluoro-5-hydroxy-2-oxo-5,7a-dihydro-4H-benzo[1,3]dioxole-3a-carboxylate by a Curtin-Hammett mechanism, has also been examined. Substantial steric opposition to Lewis acid binding prevents carbonate formation from 2-substituted furans.

Alkenes↗
PubMed2007

Interplay among folding, sequence, and lipophilicity in the antibacterial and hemolytic activities of alpha/beta-peptides.

Host-defense peptides inhibit bacterial growth but manifest relatively little toxicity toward eukaryotic cells. Many host-defense peptides adopt alpha-helical conformations in which cationic side chains and lipophilic side chains are segregated to distinct regions of the molecular surface ("globally amphiphilic helices"). Several efforts have been made to develop unnatural oligomers that mimic the selective antibacterial activity of host-defense peptides; these efforts have focused on the creation of molecules that are globally amphiphilic in the preferred conformation. One such endeavor, from our laboratories, focused on helix-forming alpha/beta-peptides, i.e., oligomers containing a 1:1 pattern of alpha- and beta-amino acid residues in the backbone [Schmitt, M. A.; Weisblum, B.; Gellman, S. H. J. Am. Chem. Soc. 2004, 126, 6848-6849]. We found, unexpectedly, that the most favorable biological activity profile was displayed by a "scrambled" sequence, which was designed not to be able to form a globally amphiphilic helix. Here we report new data, involving an expanded set of alpha/beta-peptides, from experiments designed to elucidate the origins of this surprising result. In addition, we evaluate the susceptibility of alpha/beta-peptides to proteolytic degradation. Our results support the hypothesis that the ability to adopt a globally amphiphilic helical conformation is not a prerequisite for selective antibacterial activity. This conclusion represents a significant advance in our understanding of the relationship among molecular composition, conformation, and biological activity. Our results should therefore influence the design of other unnatural oligomers intended to function as antibacterial agents.

Anti-Bacterial Agents↗
PubMed1995

1,1-Bisphosphonate squalene synthase inhibitors: interplay between the isoprenoid subunit and the diphosphate surrogate.

Inhibitors of squalene synthase have the potential to be superior cholesterol-lowering agents. We previously disclosed that lipophilic 1,1-bisphosphonates I are potent squalene synthase inhibitors and orally active cholesterol-lowering agents in animal models (Ciosek, C. P., Jr.; et al. J. Biol. Chem. 1993, 268, 24832-24837). In this paper, we describe modifications to the bisphosphonate moiety, in an attempt to reduce the number of acidic functions contained in these inhibitors. Replacing one of the acidic groups with a methyl (II, R2 = CH3) results in potent inhibitors when paired with a close mimic of the naturally occurring farnesyl moiety (R1 = farnesylethyl) but not when paired with the shorter isoprene surrogates (R1 = geranylethyl or 4-biphenylpropyl). In contrast, all three corresponding bisphosphonates I are potent squalene synthase inhibitors. Inhibitory potency is recovered with the shorter isoprene surrogates when R2 is CH2OH or CH2OCH3. It is proposed that these R2 groups serve as hydrogen bond acceptors with the active site of the enzyme. The properties of these compounds as cholesterol biosynthesis inhibitors in rats are described, and synthetic routes to these and related compounds are detailed.

Animals↗
PubMed2004

Synthesis of novel potent dipeptidyl peptidase IV inhibitors with enhanced chemical stability: interplay between the N-terminal amino acid alkyl side chain and the cyclopropyl group of alpha-aminoacyl-l-cis-4,5-methanoprolinenitrile-based inhibitors.

A series of methanoprolinenitrile-containing dipeptide mimetics were synthesized and assayed as inhibitors of the N-terminal sequence-specific serine protease dipeptidyl peptidase IV (DPP-IV). The catalytic action of DPP-IV is the principle means of degradation of glucagon-like peptide-1, a key mediator of glucose-stimulated insulin secretion, and DPP-IV inhibition shows clinical benefit as a novel mechanism for treatment of type 2 diabetes. However, many of the reversible inhibitors to date suffer from chemical instability stemming from an amine to nitrile intramolecular cyclization. Installation of a cyclopropyl moiety at either the 3,4- or 4,5-position of traditional 2-cyanopyrrolidide proline mimetics led to compounds with potent inhibitory activity against the enzyme. Additionally, cis-4,5-methanoprolinenitriles with beta-branching in the N-terminal amino acid provided enhanced chemical stability and high inhibitory potency. This class of inhibitors also exhibited the ability to suppress prandial glucose elevations after an oral glucose challenge in male Zucker rats.

Animals↗
PubMed2000

Aromaticity interplay between quinodimethanes and C(60) in diels-alder reactions: insights from a theoretical study

A theoretical study is performed of the Diels-Alder reactions of various o-quinodimethanes (QDM) with C(60) by the AM1 model and limited ab initio and DFT techniques. All reactions are shown to proceed through a concerted transition state possessing a considerable net aromaticity as evidenced from bond orders and magnetic criteria such as the magnetic susceptibility exhaltations (MSE) and nucleus independent chemical shifts (NICS) and produce different kinds of aromatic stabilized fullerene cycloadducts. Computations show that a strong LUMO-dienophile control of C(60) is realized by the influence of pyramidalization, but its high reactivity over alkene appears to be governed by the global aromaticity on fullerene rather than its strain. The aromatic functionalization occurring in QDM upon cycloaddition drastically increases the reaction rate and exothermicity of all QDM-C(60) reactions as compared to the butadiene-C(60) reaction. In fact, the simultaneously existing aromatic destabilization in fullerene indicates its opposite effect to the resonance stabilization in diene; it is thus fully restricted when the gained aromaticity is transmitted from the nucleophilic QDM to the fullerene electrophile in a push-pull manner. However, the overall aromaticity effect shown by the aromatization as well as the aromaticity of C(60) seems to accelerate these reactions at an increased rate.

Journal Article↗
PubMed2001

Lithium reduction of the bowl-shaped C60 fragment diindeno[1,2,3,4-defg;1',2',3',4'-mnop]chrysene: an interplay between experiment and calculation.

Diindeno[1,2,3,4-defg;1',2',3',4'-mnop]chrysene (DIC) (one of the smallest symmetrical bowl-shaped fragments of C60) and its tetra-tert-butyl derivative are reduced with lithium metal to yield dianions and tetraanions. Due to the high degree of symmetry (C2v) of DIC and its derivative, their NMR spectra cannot be assigned using the standard two-dimensional NMR techniques. A novel carbon-edited NOESY method was used to complete the assignments of the neutral and dianion species, whereas the tetraanions are aided by DFT calculations for their assignment. Experimental charge-distribution patterns were obtained and match those of the calculations. An extension of the empirical approach for estimating the charge distribution from the 13C NMR spectra enables a direct comparison between experimentally derived charge-distribution data and the computed electron density in each of the lowest unoccupied molecular orbitals. The overall picture evolving from the orbital structure of DIC is presented and reflects the surface reactivity of C60.

Journal Article↗
PubMed2003

Enantioselective [6pi]-photocyclization reaction of an acrylanilide mediated by a chiral host. Interplay between enantioselective ring closure and enantioselective protonation.

The [6pi]-photocyclization of the anilides 1a and 5 was studied in the absence and in the presence of the enantiomerically pure chiral lactam 4. The relative configuration of the products was unambiguously established by single-crystal X-ray crystallography and by NMR spectroscopy. A significant enantiomeric excess was observed upon reaction of compound 1a to its photocyclization products at -55 degrees C employing lactam 4 as a chiral complexing agent in toluene as the solvent (66% yield). The trans product ent-3a was obtained in 57% ee, and the minor diastereoisomer (trans/cis = 73/27), cis product ent-2a, was obtained in 30% ee. DFT calculations were conducted modeling the complexation of intermediates 8 and ent-8 to host 4. In agreement with steric arguments concerning the conrotatory ring closure of 1a, the formation of ent-8 is favored leading to the more stable complex 4.ent-8 as compared to 4.8. Whereas the enantioselectivity in the photocyclization to trans compound ent-3a increased upon reduction in the reaction temperature, the enantiomeric excess in the formation of cis compound ent-2a went through a maximum at -15 degrees C (45% ee) and decreased at lower temperatures. Deuteration experiments conducted with the pentadeuterated analogue of 1a, d(5)-1a, revealed that the protonation of the intermediates 8 and ent-8 is influenced by chiral amide 4. In the formation of ent-3a/3a, both the enantioselective ring closure and the enantioselective protonation by amide 4 favor the observed (6aS,10aS)-configuration of the major enantiomer ent-3a. In the formation of ent-2a/2a, the enantioselective ring closure (and the subsequent diastereoselective protonation) favors the (6aR,10aS)-configuration that is found in compound 2a. Contrary to that, the enantioselective protonation by amide 4 shows a preference for ent-2a with the (6aS,10aR)-configuration.

Journal Article↗
PubMed2004

Evidence of substituent-induced electronic interplay. Effect of the remote aromatic ring substituent of phenyl benzoates on the sensitivity of the carbonyl unit to electronic effects of phenyl or benzoyl ring substituents.

Carbonyl carbon (13)C NMR chemical shifts delta(C)(C[double bond]O) measured in this work for a wide set of substituted phenyl benzoates p-Y-C(6)H(4)CO(2)C(6)H(4)-p-X (X = NO(2), CN, Cl, Br, H, Me, or MeO; Y = NO(2), Cl, H, Me, MeO, or NMe(2) ) have been used as a tool to study substituent effects on the carbonyl unit. The goal of the work was to study the cross-interaction between X and Y in that respect. Both the phenyl substituents X and the benzoyl substituents Y have a reverse effect on delta(C)(C[double bond]O). Electron-withdrawing substituents cause shielding while electron-donating ones have an opposite influence, with both inductive and resonance effects being significant. The presence of cross-interaction between X and Y could be clearly verified. Electronic effects of the remote aromatic ring substituents systematically modify the sensitivity of the C[double bond]O group to the electronic effects of the phenyl or benzoyl ring substituents. Electron-withdrawing substituents in one ring decrease the sensitivity of delta(C)(C[double bond]O) to the substitution of another ring, while electron-donating substituents inversely affect the sensitivity. It is suggested that the results can be explained by substituent-sensitive balance of the contributions of different resonance structures (electron delocalization, Scheme 1).

Journal Article↗
PubMed2005

The interplay of thio(seleno)amide/vinylogous thio(seleno)amide "resonance" and the anisotropic effect of thiocarbonyl and selenocarbonyl functional groups.

Amino-substituted thio(seleno)acrylamides 1-4 were synthesized and their 1H and 13C NMR spectra assigned. Both the NMR data and the results of theoretical calculations at the ab initio level of theory were employed to elucidate the adopted structures of the compounds in terms of E/Z isomerism and s-cis/s-trans configuration. In the case of the asymmetrically N(Me)Ph-substituted compounds, ab initio GIAO-calculated ring current effects of the N-phenyl group were applied to successfully determine the preferred conformer bias. The restricted rotations about the two C-N partial double bonds were studied by DNMR and the barriers to rotation (DeltaG(c)++) determined at the coalescence temperatures, and these were discussed with respect to the structural differences between the compounds. The barriers to rotation were also calculated at the ab initio level of theory where the best results (R(2) = 0.8746) were obtained only with inclusion of the solvent at the SCIPCM-HF/6-31G* level of theory. The calculations also provided means of assessing structural influences which were not available due to inaccessible rotation barriers. By means of natural bond orbital (NBO) analysis of 1-4, the occupation numbers of nitrogen lone pairs and bonding/antibonding pi/pi orbitals were shown to quantitatively describe thio(seleno)amide/vinylogous thio(seleno)amide "resonance". Finally, the thio(seleno)carbonyl anisotropic effect was quantitatively calculated by the GIAO method and visualized by isochemical shielding surfaces (ICSS). Only marginal differences between the two anisotropic effects were calculated and are therefore of questionable utility for previous and future applications with respect to stereochemical assignments.

Journal Article↗
PubMed2006

Interplay between intramolecular resonance-assisted hydrogen bonding and aromaticity in o-hydroxyaryl aldehydes.

In this work, we analyze a series of o-hydroxyaryl aldehydes to discuss the interrelation between the resonance-assisted hydrogen bond (RAHB) formation and the aromaticity of the adjacent aromatic rings. As compared to the nonaromatic reference species (malonaldehyde), the studied compounds can be separated into two groups: first, the set of systems that have a stronger RAHB than that of the reference species, for which there is a Kekulé structure with a localized double CC bond linking substituted carbon atoms; and second, the systems having a weaker RAHB than that of the reference species, for which only pi-electrons coming from a localized Clar pi-sextet can be involved in the RAHB. As to aromaticity, there is a clear reduction of aromaticity in the substituted ipso ring for the former group of systems due to the formation of the RAHB, while for the latter group of species only a slight change of local aromaticity is observed in the substituted ipso ring.

Aldehydes↗
PubMed1996

Interplay of Theory and Experiment: Reversal of the Torquoselectivity of the Electrocyclic Ring Opening of 3-Acetylcyclobutene by a Lewis Acid.

Theoretical predictions, accompanied by firm experimental verification, are presented on the "torquoselectivity" of the thermal ring opening of 3-acetylcyclobutene (1). 3-Acetylcyclobutene was synthesized from commercially available 1,1-cyclobutanedicarboxylic acid. Thermolysis of 3-acetylcyclobutene resulted in a mixture of E- and Z-dienes with a slight preference for the E-diene. This preference was reversed by the Lewis acid, ZnI(2), as predicted from theoretical calculations.

Journal Article↗
PubMed2005

Formation of a high coverage (3 x 3) NO phase on Pd(111) at elevated pressures: interplay between kinetic and thermodynamic accessibility.

Using in situ polarization modulation infrared reflection absorption spectroscopy and density functional theory calculations, a new high-coverage monomeric NO adsorption state on Pd(111) was observed and proposed to have a (3 x 3)-7NO structure. Formation of this high coverage NO phase was found to take place only at elevated pressure and temperature conditions showing that some of the accessible thermodynamic equilibrium states at elevated temperatures and pressures are thermodynamically unfavorable or kinetically hindered at lower temperatures and pressures. Our results emphasize the danger of extrapolating results from traditional surface science experiments performed under ultrahigh vacuum to elevated temperature and pressure conditions encountered in heterogeneous catalysis.

Journal Article↗
PubMed2005

Interplay of one- and two-step channels in electrovibrational two-photon absorption.

We present a theory of two-photon absorption that addresses the formation of spectral shapes taking the vibrational degrees of freedom into account. The theory is used to rationalize the observed differences between the spectral shapes of one- and two-photon absorption. We find that the main cause of these differences is that the two-step and coherent two-photon spectral bands are different even considering a single final state. Our formalism is applied to the N101 molecule (p-nitro-p'-diphenylamine stilbene), which was recently studied experimentally. Simulations show that the two-step two-photon electrovibrational absorption results in a blue shift of the absorption spectrum in agreement with the measurements.

Journal Article↗
PubMed2006

Interplay between barrier width and height in electron tunneling: photoinduced electron transfer in porphyrin-based donor-bridge-acceptor systems.

The rate of electron tunneling in molecular donor-bridge-acceptor (D-B-A) systems is determined both by the tunneling barrier width and height, that is, both by the distance between the donor and acceptor as well as by the energy gap between the donor and bridge moieties. These factors are therefore important to control when designing functional electron transfer systems, such as constructs for photovoltaics, artificial photosynthesis, and molecular scale electronics. In this paper we have investigated a set of D-B-A systems in which the distance and the energy difference between the donor and bridge states (DeltaEDB) are systematically varied. Zinc(II) and gold(III) porphyrins were chosen as electron donor and acceptor because of their suitable driving force for photoinduced electron transfer (-0.9 eV in butyronitrile) and well-characterized photophysics. We have previously shown, in accordance with the superexchange mechanism for electron transfer, that the electron transfer rate is proportional to the inverse of DeltaEDB in a series of zinc/gold porphyrin D-B-A systems with bridges of constant edge to edge distance (19.6 A) and varying DeltaEDB (3900-17 600 cm(-1)). Here, we use the same donor and acceptor but the bridge is shortened or extended giving a set of oligo-p-phenyleneethynylene bridges (OPE) with four different edge to edge distances ranging from 12.7 to 33.4 A. These two sets of D-B-A systems-ZnP-RB-AuP+ and ZnP-nB-AuP+-have one bridge in common, and hence, for the first time both the distance and DeltaEDB dependence of electron transfer can be studied simultaneously in a systematic way.

Journal Article↗