Differential cross-sectional cusps, occurring at the vicinity of newly open channels, are used for enhanced avionic sensing.

Aryl boronate esters, such as 2-phenyl-1,3,2-benzodioxaborole (1), are important components in the formation of a variety of covalent organic frameworks. The addition of substituents on the aromatic rings of aryl boronate esters has the potential to modify the structure, reactivity, and electronic properties of the resulting materials, and so, it is useful to understand at a more fundamental level the properties of these important compounds. Experimental measurements and computational investigations are presented herein that provide insight regarding the structural and electronic properties of parent aryl boronate ester 1 as well as three substituted derivatives: 2-(o-tolyl)-1,3,2-benzodioxaborole (2), 2-(2,6-dimethylphenyl)-1,3,2-benzodioxaborole (3), and 2-(4-(tert-butyl)phenyl)-1,3,2-benzodioxaborole (4). Electronic spectroscopy combined with excited-state calculations reveal two closely spaced electronic states, S1 and S2, which appear to have excitation primarily localized on the aromatic system of the phenyl substituent or the catecholborane moiety, respectively. Interestingly, the ortho-dimethyl derivative (3) shows a significantly red-shifted electronic origin with an extensive vibronic progression of a low-frequency torsional motion about the C-B bond. Franck-Condon calculations on the ab initio determined ground- and excited-state potentials very accurately reproduce this spectrum, confirming the nonplanar ground state of this compound.

New gas phase infrared spectroscopy is reported for an aromatic alpha hydroxy carboxylic acid homo dimer of 9-hydroxy-9-fluorene carboxylic acid (9HFCA)(2), and the hetero dimer of 9HFCA with glycolic acid. In terms of the 9-hydroxy stretching frequency, the 16 cm(-1) blue-shift in the homo dimer and the 17 cm(-1) blue-shift in the hetero dimer, relative to that in 9HFCA monomer, are attributed to collective effects with anti-cooperativity stronger than cooperativity. Furthermore, for the hetero dimer, the two alpha hydroxy groups' stretching frequencies are clearly resolved, and differ by 30cm(-1). This difference represents a modest, quantitative enhancement of the intramolecular H-bond by the fluorene moiety in 9HFCA monomer, as opposed to that in glycolic acid. Accurate vibrational frequencies of the alpha OH, 3568 cm(-1) in the bare glycolic acid, and 3584 cm(-1) in the glycolic acid homo dimer are determined for the first time by comparison to 9HFCA monomer, homo and hetero dimers. The quantitative studies by infrared spectroscopy reveal subtle interactions among intra-and intermolecular H-bonds in the alpha hydroxyl acid dimers, which are also uniquely extended to probe each monomer's subtle intramolecular interactions.

Hydrogen (H) bonds are of fundamental importance in a wide range of molecular sciences. While the study of two-center H-bonding AH is well advanced, much remains to be learned in a quantitative and definitive manner for complexes with multiple H-bonds. Exemplary cases are in the category of alpha hydroxy carboxylic acids, i.e., the complexes of glycolic acid with water and formic acid. In glycolic acid, an intramolecular H-bond forms between the carboxyl group and the alpha OH group. The alpha OH stretching frequency may be affected upon complexing with water or formic acid. Direct study of glycolic acid complexes is unfortunately very difficult. However, an aromatic analogue, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), permits detailed and accurate gas phase spectroscopic studies. Since computational analysis establishes that H-bonding is very similar from glycolic acid complexes to 9HFCA complexes, direct studies on 9HFCA complexes by laser spectroscopy also deduce new and subtle information for glycolic acid complexes in terms of molecular structures, binding strength, and collective effects of multiple H-bonds associated with anti-cooperativity and cooperativity.

The structure and dynamic motions of bases in DNA duplexes and other constructs are important for understanding mechanisms of selectivity and recognition of DNA-binding proteins. The fluorescent guanine analogue, 6-methylisoxanthopterin 6-MI, is well suited to this purpose as it exhibits an unexpected 3- to 4-fold increase in relative quantum yield upon duplex formation when incorporated into the following sequences: ATFAA, AAFTA, or ATFTA (where F represents 6-MI). To better understand some of the factors leading to the 6-MI fluorescence increase upon duplex formation, we characterized the effect of local sequence and structural perturbations on 6-MI photophysics through temperature melts, quantum yield measurements, fluorescence quenching assays, and fluorescence lifetime measurements. By examining 21 sequences we have determined that the duplex-enhanced fluorescence (DEF) depends on the composition of bases adjacent to 6-MI and the presence of adenines at locations n ± 2 from the probe. Investigation of duplex stability and local solvent accessibility measurements support a model in which the DEF arises from a constrained geometry of 6-MI in the duplex, which remains H-bonded to cytosine, stacked with adjacent bases and inaccessible to quenchers. Perturbation of DNA structure through the introduction of an unpaired base 3' to 6-MI or a mismatched basepair increases 6-MI dynamic motion leading to fluorescence quenching and a reduction in quantum yield. Molecular dynamics simulations suggest the enhanced fluorescence results from a greater degree of twist at the X-F step relative to the quenched duplexes examined. These results point to a model where adenine residues located at n ± 2 from 6-MI induce a structural geometry with greater twist in the duplex that hinders local motion reducing dynamic quenching and producing an increase in 6-MI fluorescence.

The ionization potential (IP) of the aromatic alpha hydroxy carboxylic acid, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), is shifted by complexation with hydrogen bonding ligands such as water and formic acid. Generalized Kohn-Sham energy decomposition analysis decomposes the intermolecular binding energies into a frozen energy term, polarization, correlation, and/or dispersion energy terms, as well as terms of geometric relaxation and zero point energy. We observe that in each dimer the attractive polarization always increases upon ionization, enhancing binding in the cation and shifting the IP toward the red. For 9HFCA-H2O, a substantial decrease of the repulsive frozen energy in cation further shifts the IP toward red. For 9HFCA-HCOOH, the increase of the frozen energy actually occurs in the cation and shifts the IP toward blue. Consistent with the experimental measurements, our analysis provides new, non-intuitive perspectives on multiple hydrogen bonds interactions in carboxylic acids and water complexes.

4-propylaniline complexes with one and two argon atoms formed in the molecular beam were studied in the first excited electronic state, S1, using resonance enhanced two-photon ionization spectroscopy and in the cation ground state, D0, using mass analyzed threshold ionization spectroscopy. The combination of electronic and cationic spectra of the clusters allows two conformations to be identified in both aniline-Ar1 and aniline-Ar2, which are assigned to either the gauche configuration or anti-configuration of 4-propylaniline. The gauche isomer exhibits complex bands shifted 29 cm(-1) and 89 cm(-1) from the S1 origin bands and 83 cm(-1) and 148 cm(-1) from the ionization potential assigned to the Ar1 and Ar2 complexes, respectively. For the anti-rotamer, the corresponding shifts actually become nearly additive, 53 cm(-1) and 109 cm(-1) for the S1 origin bands, and 61 cm(-1) and 125 cm(-1) for the ionization potentials. Ab initio calculations provide insights into the influences of the propyl and amino groups on the positions of the argon atoms within the clusters. In addition, the binding energy of one argon with the gauche isomer of 4-propylaniline has been measured to be 550 ± 5 cm(-1) in the D0 state, 496 ± 5 cm(-1) in the S1 state, and 467 ± 5 cm(-1) in the neutral ground state, S0.

Resonance-enhanced multiphoton ionization spectroscopy of supersonically cooled gas-phase 9-hydroxy-9-fluorene carboxylic acid (9HFCA) is reported for its first electronic excited state, S1. The UV-UV hole-burning experiment identifies a single conformer in the molecular beam, stabilized by an intramolecular hydrogen bond. For this Cs symmetric conformer, two low frequencies in the S1 spectrum are assigned: an in-plane rocking mode of the carboxylic acid side chain lies at 58 cm(-1), and an in-plane fluorene bending mode appears at 183 cm(-1). The corresponding mode frequencies in the cation, 58 and 196 cm(-1), are measured by zero electron kinetic energy (ZEKE) spectroscopy upon pumping the S1 vibronic states. The adiabatic ionization potential is measured to be 64 923 ± 5 cm(-1). In addition, a feature established by ZEKE spectroscopy upon pumping the hot band is found at 67 cm(-1). This is assigned as a hot band of the HO-C9-COOH rocking mode in the neutral ground state.

We report mass analyzed threshold ionization spectroscopy of supersonically cooled gas phase carboxylic complexes with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. The vibrationally resolved cation spectrum for the 9HFCA complex with formic acid allows accurate determination of its ionization potential (IP), 64,374 ± 8 cm(-1). This is 545 cm(-1) smaller than the IP of 9HFCA monomer. The IPs of 9HFCA complexes with acetic acid and benzoic acid shift by -1133 cm(-1) and -1438 cm(-1), respectively. Density functional calculations confirm that Cs symmetry is maintained upon ionization of the 9HFCA monomer and its acid complexes, in contrast to the drastic geometric rearrangement attending ionization in complexes of 9-fluorene carboxylic acid. We suggest that the marginal geometry changes and small IP shifts are primarily due to the collective interactions among one intramolecular and two intermolecular hydrogen bonds in the dimer.

Incorporation of fluorescent nucleoside analogues into duplex DNA usually leads to a reduction in quantum yield, which significantly limits their potential use and application. We have identified two pentamer DNA sequences containing 6-methylisoxanthopterin (6-MI) (ATFAA and AAFTA, where F is 6-MI) that exhibit significant enhancement of fluorescence upon formation of duplex DNA with quantum yields close to that of monomeric 6-MI. The enhanced fluorescence dramatically increases the utility and sensitivity of the probe and is used to study protein-DNA interactions of nanomolar specificity in this work. The increased sensitivity of 6-MI allows anisotropy binding measurements to be performed at DNA concentrations of 1 nM and fluorescence intensity measurements at 50 pM DNA. The ATFAA sequence was incorporated into DNA constructs to measure the binding affinity of four different protein-DNA interactions that exhibit sequence-specific and non-sequence-specific recognition. In all cases, the K(d) values obtained were consistent with previously reported values measured by other methods. Time-resolved and steady-state fluorescence measurements demonstrate that 6-MI fluorescence is very sensitive to local distortion and reports on different degrees of protein-induced perturbations with single-base resolution, where the largest changes occur at the site of protein binding.

The structure and dynamics of the bacterial chromosome are maintained by many proteins. One of the most abundant proteins, a member of the DNABII family of DNA-binding proteins, is HU (Heat_Unstable). An architectural protein is a term used to describe proteins that introduce sharp bends (120-160 degrees) into DNA upon binding. DNA bending induced by these proteins is important for transcriptional regulation, initiation of replication, mu transposition, base excision repair, recombination, and negative supercoiling in bacteria. HU exhibits a strong preference for various distortions in DNA; nicks, gaps, cruciform, and sticky ends. The distorted DNA structures seem to share a similar binding motif of a flexible junction. There is little structural or dynamical information related to perturbation of these DNA motifs upon HU binding. A better understanding of HU binding to these motifs would provide insight into HU’s role in the regulation of DNA structure. This information could also give insight into the general mode of recognition and binding for all non-sequence-specific DNA binding proteins found in both prokaryotes and eukaryotes. We have employed various fluorescence spectroscopy techniques to help answer questions related to this problem. Through the use of fluorescence anisotropy we have determined the dissociation constant in solution for HU binding to 3’overhang DNA substrate to be 3.41E-09+/- 1.2E-09 M, which is in good agreement with literature results. The stoichiometry for the specific binding of HU to these substrates is one to one, while non-specific binding may lead to higher order complexes. Fluorescence resonance energy transfer (FRET) results suggest bending of the DNA substrate upon HU binding. We hope to gain further information about the mechanism of HU-induced bending, structural recognition and binding through the use of such techniques as FRET mapping, Time-resolved fluorescence, and stop flow kinetics.

Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

Infrared-ultraviolet two color pump-probe spectroscopy is used to measure the binding energy, D(0,) of a carboxylic acid-water dimer where the acid is 9-hydroxy-9-fluorenecarboxylic acid. The acid-water configuration presents a standard structure for the general acid-water interaction where the water bonds to the carboxylic acid group through two intermolecular hydrogen bonds. Photodissociation studies with product vibrational state resolution have enabled an accurate determination of the binding energy for this acid-water system to be D(0) = 2975 ± 30 cm(-1). Quantum chemical calculations are performed to compare with the experimental observations and a recent measurement on the water dimer (D(0) = 1105 ± 10 cm(-1)).

The relative ionization energies of tryptamine conformations are determined by zero kinetic energy photoelectron spectroscopy and photoionization efficiency measurements. The relative cationic conformational stabilities are compared to the published results for the neutral molecule. In the cation, the interaction strength changes significantly between amino group and either the phenyl or the pyrrole moiety of the indole chromophore where most of the positive charge is located, leading to different conformational structures and relative conformer energies in the cation. In particular, the measured adiabatic ionization potential of isomer B is 60,928 ± 5 cm(-1), at least 400 cm(-1) higher than any of the 6 other tryptamine isomers which all have ionization potentials within 200 cm(-1) of each other. In addition to the monomer, measurements were made on the A conformer of the tryptamine(+)-H(2)O complex including the ionization threshold and cation dissociation energy measured using a threshold photoionization fragmentation method. The water cluster exhibits an unexpectedly high ionization potential of 60,307 ± 100 cm(-1), close to the conformer A monomer of 60 320 ± 100 cm(-1). It also exhibits surprisingly low dissociation energy of 1750 ± 150 cm(-1) compared to other H-bonding involved cation-H(2)O complexes which are typically several thousands of wavenumbers higher. Quantum chemical calculations indicate that upon ionization the structure of the parent molecule in the water complex remains mostly unchanged due to the rigid intermolecular double hydrogen bonded water molecule bridging the monomer backbone and its side chain thus leading to the high ionization potential in the water cluster. The surprisingly low dissociation energy measured in the cationic water complex is attributed to the formation of a much more stable structural isomer H(+) in the exit channel.

The development of fluorescent nucleoside analogs, which hydrogen bond in the same fashion as their counterparts and minimally distort the structure of duplex DNA, has greatly improved the amount of information that can be obtained from both steady-state and time-resolved fluorescence experiments. Reduction in quantum yield observed when probes are incorporated into an oligomer or a duplex limits their potential application. 6-methylisoxanthopterin (6-MI) is a fluorescent guanosine analog which H-bonds with cytosine similar to guanosine. Investigating the photophysical properties of the nucleoside analog; we discovered a pentamer DNA sequence (ATFAA; where F=6-MI) that exhibits an enhancement of fluorescence upon formation of duplex DNA. The enhanced 6-MI fluorescence within a duplex broadens the potential applications by allowing binding and other experiments to occur at nanomolar concentrations. Within, the sequence context of ATFAA, time-resolved measurements reveal that the fluorescent populations shift from 0.4 to 7.2 ns upon formation of duplex and the relative quantum yield increases from 0.2 to 0.8. This implied the pentamer ATFAA fluorescence enhancement is due to 6MI adopting a single conformation that is either "flipped out" from the duplex or sterically constrained. To further investigate the enhancement of fluorescence upon duplex formation, we characterized oligonucleotides local and global structure. Temperature melt and iodide quenching experiments support a model in which enhancement of fluorescence is due to a solvent inaccessible geometry of 6MI remaining H-bonded to cytosine. An increase in solvent accessibility and reduction in the quantum yield were achieved through the introduction of a 3′ bulge or mismatch in the highly fluorescent duplex; suggesting limited dynamics of the 6MI is due to steric hiderance on the 3′ side. This information can now be used to generate other sequence contexts in which 6-MI will exhibit enhanced fluorescence upon duplex formation.

To improve current understanding of the structural recognition mechanism of architectural DNA binding proteins such as HU and IHF, we are investigating the structure and dynamics of different DNA substrates. We are able to make these observations on both global and local levels by incorporating the fluorescent guanosine nucleoside analog 6-methylisoxanthopterin (6-MI), with H-bonds with cytosine similar to guanosine. We have previously shown this probe does not significantly perturb the global structures of duplex DNA molecules. 6-MI was systematically incorporated into a 34 base oligonucleotide. Initial characterization of local DNA environment included time resolved fluorescence and rotational correlation measurements of the duplex oligomers relative to 6-MI monomer and single stranded DNA. Analysis of time-resolved fluorescence decay yields 3 lifetime components of 0.4 ns, 4 ns and 6.5 ns. The largest lived component is similar to that of 6-MI monomer, 7 ns. The position of the probe shifts the fluorescent populations from 0.4 ns to 6.5ns upon formation of duplex, which implies that 6-MI local environment in these positions resembles that of the solvent exposed monomer. However, no direct correlation between adjacent base sequence and the fluorescent properties of 6MI was observed. To further investigate the increase in fluorescence upon duplex formation, we characterized the local and global structure of several oligonucleotides through temperature melts, quantum yield calculations, quenching assays, and Raman spectroscopy. The results suggest that, the position of 6-MI in the duplex sequence, helical turn, and surrounding base sequence determines the dynamics of 6-MI. This potentially leads to the formation of a fixed geometry of 6-MI which stacks poorly with adjacent bases. The lack of stacking interactions causes 6-MI to exhibit fluorescent properties of the monomer.

Using the 4s'[1/2](0) and 4s[3/2](2) metastable states of argon created in a plasma discharge we perform photoionization spectroscopy of even-parity autoionizing Ar(np(')) Rydberg states between the first and second ionization limits. Fitting the data to a sum of Fano-type or Shore-type profiles allows us to extract the widths and energies of the three overlapping resonance states [1/2](1), [3/2](1), and [3/2](2) in the 11p' manifold. We compare the experimental analysis of the 11p' multiplet to theoretical calculations which are based on the configuration interaction Pauli-Fock approach with core polarization. Agreement between the experimental and theoretical resonance parameters is good.

We report the observation of an electric quadrupole transition between the 4s'[1/2](0)(o) and 3d[3/2](2)(o) states in the spectrum of argon and use it in the first step of a scheme to excite Rydberg states. The initial identification of the transition is based on one-color, two-photon photoionization. A different experiment utilizing two-color, two-photon photoexcitation to Rydberg states confirms the identification. Despite the unavoidable background of one-color, two-photon photoionization, the latter experimental technique makes possible two-photon spectroscopy of Rydberg states using a resonant intermediate state populated by an electric quadrupole transition. (C) 2008 Optical Society of America.