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PubMed2006

Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives.

The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.

Models, Molecular↗

PubMed1993

Molecular shape comparison of angiotensin II receptor antagonists.

A new and powerful analytical method for comparing molecular shapes by optimizing the overlap of molecular volumes has been developed. This shape comparison method provides both a quantitative measure of the shape similarity of molecules and a means to align molecules such that shape similarity if maximized. Our MSC method has been enhanced with an option to allow discrimination between groups with different chemical properties. Atoms or groups of atoms may be assigned to different classes based on specific properties such as electrostatic potential, hydrogen bonding ability, or hydrophobicity. This enables matches based on criteria such as alignment of hydrophobic groups or hydrogen bond acceptor groups. In this study, we report shape comparisons of angiotensin II (AII) receptor antagonists from two structural classes, 4-(biphenyl-4-ylmethoxy)-quinoline derivatives such as ICI D8731 and N-(biphenyl-4-ylmethyl)imidazole derivatives, such as DuP753. Starting with a list of low-energy conformations for the two molecules, each conformation of the first molecule is paired with each of the conformations of the second molecule. For each of these conformational pairs, an MSC comparison, which generates multiple MSC maxima, is initiated. Eight high scoring conformational pairings were found with shape matching based on the intersection of the total molecular volume, while nine high-scoring pairs were identified with matching by atom type. MSC identifies conformational pairs with high shape similarity, as measured by the intersection volume, and thus generates and prioritizes several alternative models for the AII antagonist pharmacophore.

Angiotensin Receptor Antagonists↗

PubMed2003

A new class of linear tetrapyrroles: acetylenic 10,10a-didehydro-10a-homobilirubins.

Novel bilirubin analogues with dipyrrinones conjoined to an acetylene rather than a methylene group were synthesized and examined spectroscopically. Despite the increased separation of the dipyrrinones forced by replacing a -CH(2)- by a -C(triple bond)C- unit, molecular dynamics calculations show that, like bilirubin, they may still engage in intramolecular hydrogen bonding to carboxylic acid groups when the propionic acid chains are slightly lengthened, e.g., butanoic acids. Unlike bilirubin, however, which is bent in the middle and has a ridge-tile shape, the acetylene orients the attached dipyrrinones along a linear path, and intramolecular hydrogen bonding preserves a twisted linear molecular shape. The extended planes of the dipyrrinones intersect along the -C(triple bond)C- axis at an angle of 136 degrees for the conformation stabilized by intramolecular hydrogen bonding in the bis-butyric acid rubin (1b). With shorter acid chains (propionic), only one CO(2)H can engage an opposing dipyrrinone in intramolecular hydrogen bonding, and in this energy-minimum conformation of the linear pigment 1a, the intersection of the extended planes of the dipyrrinones has an angle of 171 degrees. Spectroscopic evidence for such linearized and twisted structures was found in the pigments' NMR spectral data and their exciton UV-vis and induced circular dichroism spectra.

Bilirubin↗

PubMed2005

Singlet excited-state dynamics of 5-fluorocytosine and Cytosine: an experimental and computational study.

The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by 2 orders of magnitude from 720 fs to 73 +/- 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethyl sulfoxide. The insensitivity of the S(1) lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited-state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the (1)pi,pi state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.

Absorption↗

PubMed2006

Combined theoretical and FTIR spectroscopic studies on hydrogen adsorption on the zeolites Na-FER and K-FER.

The interaction between molecular hydrogen and the alkali-metal-exchanged zeolites Na-FER and K-FER at a low temperature was investigated by combining variable-temperature infrared spectroscopy and theoretical calculations by using a periodic DFT model. The experimentally determined values of standard adsorption enthalpy, DeltaH degrees , were -6.0 (+/-0.8) and -3.5 (+/-0.8) kJ mol(-1) for Na-FER and K-FER, respectively. These results were found to be in agreement with corresponding DeltaH degrees values obtained from calculations on the periodic model. Two types of alkali-metal cation sites in FER were found: channel intersection sites and channel wall sites. Calculations showed a similar interaction energy for both site types, and similar structures of adsorption complexes. Up to two dihydrogen molecules can be physisorbed on the alkali-metal cation located on the intersection of two channels, while only one H2 molecule is physisorbed on the cation at the channel wall site. The adsorption enthalpies of H2 on alkali-metal-exchanged FER are significantly smaller than those found previously for the MFI-type zeolites Na-ZSM-5 and K-ZSM-5, which is likely due to a difference in the alkali-metal cation coordination in the two zeolite frameworks.

Journal Article↗

PubMed2006

Diffusion of long n-alkanes in silicalite. A comparison between neutron scattering experiments and hierarchical simulation results.

New quasi-elastic neutron scattering (QENS) data are presented for the self-diffusion of normal alkanes up to hexadecane in the zeolite silicalite at low occupancy. Measured diffusivities at 300 K are higher than in Na-ZSM-5 and agree with the predictions of molecular dynamics and a hierarchical transition-state theory/Brownian dynamics conducted on the same systems. Activation energies for diffusion are around 5 kJ/mol for C1-C6 but rise with carbon number for C8-C16 to approximately 15 kJ/mol for C16. An explanation is suggested by the hierarchical simulation, which finds that C1-C6 tend to reside entirely within the interiors of single channel segments and diffuse through jumps across energetically less favorable channel intersections, while longer molecules straddle channel intersections and must undergo conformational rearrangements in order to diffuse. The agreement between QENS and simulations reflects that the two methods probe motion over the same small (nm) length scales. Self-diffusivities measured by pulsed field gradient nuclear magnetic resonance (PFG-NMR) in the same systems are appreciably lower. This is because PFG-NMR probes motion over significantly longer (microm) length scales and is therefore more sensitive to defects in the silicalite crystals.

Journal Article↗

PubMed2006

Role of electron-driven proton-transfer processes in the excited-state deactivation of the adenine-thymine base pair.

Exploratory electronic structure calculations have been performed with the CC2 (simplified singles and doubles coupled-cluster) method for two conformers of the adenine (A)-thymine (T) base pair, with emphasis on excited-state proton-transfer reactions. The Watson-Crick conformer and the most stable (in the gas-phase) conformer of the A-T base pair have been considered. The equilibrium geometries of the ground state and of the lowest excited electronic states have been determined with the MP2 (second-order Møller-Plesset) and CC2 methods, respectively. Vertical and adiabatic excitation energies, oscillator strengths, and dipole moments of the excited states are reported. Of particular relevance for the photochemistry of the A-T base pair are optically dark (1)pipi* states of charge-transfer character. Although rather high in energy at the ground-state equilibrium geometry, these states are substantially lowered in energy by the transfer of a proton, which thus neutralizes the charge separation. A remarkable difference of the energetics of the proton-transfer reaction is predicted for the two tautomers of A-T: in the Watson-Crick conformer, but not in the most stable conformer, a sequence of conical intersections connects the UV-absorbing (1)pipi* state in a barrierless manner with the electronic ground state. These conical intersections allow a very fast deactivation of the potentially reactive excited states in the Watson-Crick conformer. The results provide evidence that the specific hydrogen-bonding pattern of the Watson-Crick conformer endows this structure with a greatly enhanced photostability. This property of the Watson-Crick conformer of A-T may have been essential for the selection of this species as carrier of genetic information in early stages of the biological evolution.

Adenine↗

PubMed2006

Solvent effect on the singlet excited-state dynamics of 5-fluorouracil in acetonitrile as compared with water.

The excited-state dynamics of 5-fluorouracil in acetonitrile has been investigated by femtosecond fluorescence upconversion spectroscopy in combination with quantum chemistry TD-DFT calculations ((PCM/TD-PBE0). Experimentally, it was found that when going from water to acetonitrile solution the fluorescence decay of 5FU becomes much faster. The calculations show that this is related to the opening of an additional decay channel in acetonitrile solution since the dark n/pi* excited state becomes near degenerate with the bright pi/pi* state, forming a conical intersection close to the Franck-Condon region. In both solvents, a S1-S0 conical intersection, governed by the out-of-plane motion of the fluorine atom, is active, allowing an ultrafast internal conversion to the ground state.

Acetonitriles↗

PubMed2006

Unified model for the ultrafast decay of pyrimidine nucleobases.

Ultrafast decay processes detected after absorption of UV radiation in gas-phase pyrimidine nucleobases uracil, thymine, and cytosine are ascribed to the barrierless character of the pathway along the low-lying 1(pipi*) hypersurface connecting the Franck-Condon region with an out-of-plane distorted ethene-like conical intersection with the ground state. Longer lifetime decays and low quantum yield emission are on the other hand related to the presence of a 1(pipi*) state planar minimum on the S1 surface and the barriers to access other conical intersections. A unified model for the three systems is established on the basis of accurate multiconfigurational CASPT2 calculations, whereas the effect of the different levels of theory on the results is carefully analyzed.

Models, Chemical↗

PubMed2005

Concentration dependence of the methane structure in silicalite-1: a molecular dynamics study using the Møller-Plesset-based potential.

Møller-Plesset perturbation-based potentials have been used in molecular dynamics simulations to examine methane diffusion in silicalite-1. The simulation box contains 2 unit cells of silicalite-1 and varying loading numbers (n(ld)) from 1, 2, 3, to 4 methane molecules per intersection, corresponding to 8, 16, 24, and 32 molecules per simulation box, respectively. Consistent with the previous study, a preferential diffusing path for methane is close to the channel axes. The structure of the methane molecules in the silicalite-1 pore was exhibited in terms of the methane-methane radial distribution function (RDF) in which the first peak appears at 6.4 A for n(ld) < or = 2, becomes a broad maximum at n(ld) = 3, and splits into two sharp peaks centered at 6.4 and 8.6 A at n(ld) = 4. This fact can be clearly described by an intensification of the methane density in the straight and zigzag channels but a decrease in the intersection when the loading increases. These features of the observed RDFs are in contrast with the previous report using a molecular dynamics force-field potential in which the RDFs for all concentrations show first maxima at approximately 4 A. The analysis of the relative residence times of methane at different sites inside the silicalite suggests that the zigzag channel is the most favored location. The computed self-diffusion coefficients as well as the heat of adsorptions are in reasonable agreement with the available values.

Journal Article↗

PubMedDate not supplied

Monte Carlo calculation on trans/cis-polysarcosine.

Monte Carolo calculations were made on unperturbed trans-polysarcosine chain, non-self-intersecting trans-polysarcosine chain, and also non-self-intersecting trans/cis-polysarcosine chain by using a hard-sphere model. In the last case, an attempt was first made to introduce cis amide bond into the Monte Carlo calculation of polypeptide chain. Dipeptide energy maps for four different trans/cis dyad sequences were calculated. The allowed regions were consistent with the pairs of dihedral angles observed in cyclo-pentasarcosyl and cyclo-octasarcosyl. The mean-square end-to-end distance and higher even moments were obtained. The distribution function of the end-to-end distance was calculated from the even moments by using Nagai's equation and compared with the direct Monte Carlo data. The best agreement was obtained by cutting off the terms containing much higher order even moments than a critical order. The fractions of cis amide bond and of the four different trans/cis dyad sequences in polysarcosine were calculated. The results of calculation were compared with the 220-MHz NMR spectra of polysarcosine in three different solvents. Qualitative agreement was stained for longer chains.

Amides↗

PubMed2001

Charge separation in photosynthetic reaction centers under femtosecond excitation.

The process of electron transfer from the primary electron donor P* to the primary electron acceptor BA in the reaction center of Rhodobacter sphaeroides R-26 under 30 fsec pulse excitation was studied in this work with the aim of establishing a relationship between the nuclear subsystem motion and charge transfer. For this purpose the fsec and psec oscillations in the bands of stimulated emission of P* and in the band of reaction product BA- at 1020 nm were investigated. It was established that the reversible formation of the P+BA- state is characterized by two vibration modes (130 and 320 cm(-1)) and connected with an arrival of the wavepacket induced by fsec excitation to the intersection of potential surfaces P*BA and P+BA-. The irreversible formation of the P+BA- state with the time constant of 3 psec is followed by oscillations with frequencies of 9 and 33 cm(-1). These results show that the irreversibility of electron transfer is determined by two factors: 1) by a difference between the energy width of the wavepacket and the gap between the named surfaces; 2) by a difference between the duration of wavepacket residence near the intersection of the surfaces and the relaxation time of the P+BA- state.

Electron Transport↗

PubMed2003

The role of Bcl-2 family members in the progression of cutaneous melanoma.

The overwhelming problem of cutaneous melanoma is chemoresistance. Subversion of the biochemical changes that lead to chemoresistance intersects the apoptosis pathways. The mitochondrion has been a focal point of this intersection for the development of therapeutic strategies aimed at reducing the progression of melanoma. The Bcl-2 family of apoptotic regulators is arguably the most pivotal component to this mitochondrial response. The shear number of studies conducted on the relationship between melanoma and Bcl-2 members prompted us to evaluate the literature available and discern some rational utility of the data. We have found that there are striking inconsistencies for the expression of Bcl-2 family proteins with melanoma progression, particularly for Bcl-2. Roughly one-third of the data suggests an increase in Bcl-2 expression with advancing melanoma, while another third suggests a decrease. Furthermore, the remaining third found on the whole, a detectable level of Bcl-2 in all tissues of melanocytic origin. These discrepancies are difficult to rectify in light of the apparent success of recent clinical trials utilizing Bcl-2 antisense strategies. The general consensus in the literature is that pro-apoptotic Bax is decreased with melanoma progression while anti-apoptotic Bcl-xL and Mcl-1 appear to increase with progression. We suggest that the biochemical techniques being used for analysis present too great of a heterogeneity, which could be mitigated with more standard procedures and reagents. Finally the utility of 'multi-specific' antisense tactics could be a more effective way of targeting advanced melanoma disease.

Apoptosis↗

PubMed1994

Perception of rigid motion in depth from the optical deformations of shadows and occlusion boundaries.

Three experiments were designed to examine the abilities of observers to determine an object's 3-dimensional structure and motion from various types of optical deformations. Observers were required to discriminate whether pairs of moving ellipsoids were rotating rigidly about a single axis or nonrigidly about different axes that varied in slant. Discrimination thresholds were significantly influenced by whether the ellipsoids were intersecting or nonintersecting and whether they contained identifiable texture elements. Performance was unaffected by precession movements of the axis of rotation, by increasing the number of intersecting ellipsoids beyond 2, or by replacing the deforming silhouettes with the projected motions of cast shadows presented in isolation against a planar background. These findings indicate that observers can perceive structure from motion based on several different types of optical deformation, including the deformations of shadows and silhouettes that do not contain identifiable features on which most existing theoretical analyses are designed to operate.

Adult↗

PubMed1985

Search asymmetry: a diagnostic for preattentive processing of separable features.

The search rate for a target among distractors may vary dramatically depending on which stimulus plays the role of target and which that of distractors. For example, the time required to find a circle distinguished by an intersecting line is independent of the number of regular circles in the display, whereas the time to find a regular circle among circles with lines increases linearly with the number of distractors. The pattern of performance suggests parallel processing when the target has a unique distinguishing feature and serial self-terminating search when the target is distinguished only by the absence of a feature that is present in all the distractors. The results are consistent with feature-integration theory (Treisman & Gelade, 1980), which predicts that a single feature should be detected by the mere presence of activity in the relevant feature map, whereas tasks that require subjects to locate multiple instances of a feature demand focused attention. Search asymmetries may therefore offer a new diagnostic to identify the primitive features of early vision. Several candidate features are examined in this article: Colors, line ends or terminators, and closure (in the sense of a partly or wholly enclosed area) appear to be functional features; connectedness, intactness (absence of an intersecting line), and acute angles do not.

Adult↗

PubMed1987

Piecemeal organization and cognitive components in object perception: perceptually coupled responses to moving objects.

In three experiments, observers who were instructed to perceive one of two alternative depth arrangements of a three-dimensional wire cube fixated near one of two intersections that differed in the degree to which they specified the cube's veridical depth organization. In order to separate perceptual effects from experimenter effects, we measured indirect reports about variables perceptually coupled to perceived depth rather than direct reports about perceived depth. In all three experiments, reversal durations at the two intersections differed, even though the two were parts of a single object. In addition, reversals varied with viewers' intentions. Thus, the unit of perceptual organization may be smaller than the entire object, and viewers' intentions can influence the perception of real moving objects. In additional analyses, reversal durations were separated into two components: nonelective instability and malleability; the question of whether these two components of ambiguity are functionally distinct could not be decided.

Depth Perception↗

PubMed1994

Combining graded categories: membership and typicality.

Forming a conjoint category (square tables) from constituent categories (squares and tables) has traditionally been modeled by formal set intersection. In this traditional view, in which categories are treated as precisely defined sets, an item is a member of the conjoint category if and only if it is a member of both constituent categories. However, as is now widely believed, many categories should be treated as graded, with members that vary in typicality and boundaries that are inexact. In the present article, it is argued that set intersection is inappropriate for combining graded categories. The authors propose an alternative formal mechanism in which a conjoint category is constructed from constituent categories by forming a joint distribution of values. The proposed model accounts for both membership and typicality of instances in conjoint categories, but only when the constituent categories are independent, or the relation between them is known.

Color Perception↗

PubMed1993

Interaction between the 67 kilodalton metastasis-associated laminin receptor and laminin.

Normal and neoplastic cells interact with laminin via a variety of cell surface proteins. The specific binding sites on laminin for each particular cell surface laminin-binding protein have not yet been identified. In this study, the interaction between laminin and the high affinity metastasis-associated 67 kD laminin receptor (67 LR) was investigated by electron microscopy using the rotary shadowing technique. Laminin receptor that was purified from human colon carcinoma metastases appeared as a globular structure with a diameter of 5.2 +/- 0.8 nm. The 67 LR specifically bound to laminin on its long arm close to the intersection of the long and the short arms. There was no specific interaction of bovine serum albumin with laminin. Biochemical confirmation of the rotary shadowing experiments included slot blot solid phase assays in which [I125]-labeled 67 LR bound in a dose dependent manner to laminin as well as to the chymotrypsin resistant (C1) fragment of laminin that contains a short piece of the long arm. [I125]-labeled 67 LR did not bind to the pepsin resistant (P1) fragment of laminin that did not contain that segment on the long arm. This study therefore identifies the binding site on laminin for the 67 kD metastasis-associated laminin receptor as a region on the long arm of laminin close to the intersection of the four arms.

Amino Acid Sequence↗