Chromatographic and spectroscopic properties of regioisomers of some 1H-1,5-benzodiazepines

The separation of the two regioisomeric derivatives of 1H-1,5-benzodiazepine yielded from the reaction of 1,2-diamino-4-methylbenzene with 4-substituted acetophenones was performed by reversed phase high performance liquid chromatography, and the absorption spectra of the separated isomers have been determined for three isomer pairs which have been obtained starting from acetophenones with substituents of different electronegativity. The isomer ratio then could be estimated as well from the ratio of the peak areas as from the absorption spectra. They agree well with the known ratio determined from nmr intensities.     

Unravelling Structural Dynamics within a Photoswitchable Single Peptide: A Step Towards Multimodal Bioinspired Nanodevices

The majority of the protein structures have been elucidated under equilibrium conditions. The aim herein is to provide a better understanding of the dynamic behavior inherent to proteins by fabricating a label-free nanodevice comprising a single-peptide junction to measure real-time conductance, from which their structural dynamic behavior can be inferred. This device contains an azobenzene photoswitch for interconversion between a well-defined cis, and disordered trans isomer. Real-time conductance measurements revealed three distinct states for each isomer, with molecular dynamics simulations showing each state corresponds to a specific range of hydrogen bond lengths within the cis isomer, and specific dihedral angles in the trans isomer. These insights into the structural dynamic behavior of peptides may rationally extend to proteins. Also demonstrated is the capacity to modulate conductance which advances the design and development of bioinspired electronic nanodevices.     

Synthesis, spectroscopic, and electrochemical studies of 1,2-naphthalene-ring-fused tetraazachlorins, -bacteriochlorins, and -isobacteriochlorins: the separation and characterization of structural isomers

1,2-Naphthalene-ring-expanded tetraazachlorins (TACs), tetraazabacteriochlorins (TABCs), and tetraazaisobacteriochlorins (TAiBCs) have been synthesized. Procedures for the synthesis of the starting materials, that is, derivatives of 1,2-naphthalenedicarboxylic acid, have been reinvestigated and improved. Nine possible derivatives, including four, two, and three structural isomers of TACs, TABCs, and TAiBCs, respectively, were separated by using thin-layer chromatography (TLC) or high-performance liquid chromatography (HPLC), and the structure of each isomer was determined by (1)H NMR spectroscopy combined with the NOE technique. The formation ratio of each isomer was rationalized in terms of the intramolecular steric repulsion effect, which was predicted by geometry optimizations at the DFT level. The derived compounds were characterized by using IR, electronic, and magnetic circular dichroism (MCD) spectroscopy, and by electrochemical methods. Frequency calculations at the DFT level correctly reproduced the experimental IR spectra and, in particular, distinguished between the three isomers of the TAiBCs. In the electronic absorption and MCD spectra of the TAC and TABC species, the Q-band splits into two intense components similarly to the 2,3-naphthalene-fused derivatives described in our preceding paper, although no significant spectral differences were observed from species to species. On the other hand, the spectra of the TAiBCs showed moderate differences depending on the structure of the isomer. The spectroscopic properties as well as the electrochemical behavior of these chlorins resemble those of the corresponding benzene-fused derivatives rather than the 2,3-naphthalene-fused derivatives. Molecular-orbital and configuration-interaction calculations within the framework of the ZINDO/S method were helpful in the discussions of the above observations.     

Isomers of C36 and free energy criteria for cluster growth

A molecular dynamics procedure is developed to search for cluster isomers and is used to study the isomer spectrum of C36 with the Brenner potential. Beginning with isolated carbon atom, the procedure quickly arrives at the D6h cage with the lowest potential and produces other 410 isomers. Among these isomers, we selected ones of typical cage, bowl, and sheet structures to calculate their free energies at 2300 K and performed molecular dynamics simulations starting either from 36 free carbon atoms diluted in He buffer gas kept at 2300 K or from the D6h cage under the same conditions, which show that the microsystem reaches a kinetic equilibrium within about 100 ns and that the isomer of the lowest free energy rather than the D6h cage of the lowest potential energy dominates in the resultant cluster.     

Microwave spectroscopy measurements of rotational spectra and DFT calculations for two distinct structural isomers of 1,1'-dimethylferrocene

Microwave spectra were obtained for two distinct structural isomers of 1,1'-dimethylferrocene, an eclipsed synperiplanar isomer (phi = 0 degrees, the E0 isomer), with A = 1176.9003(2) MHz, B = 898.3343(2) MHz, C = 668.7469(2) MHz, and an eclipsed synclinal isomer (phi = 72 degrees, the E72 isomer) with A = 1208.7117(14) MHz, B = 806.4101(12) MHz, and C = 718.7179(8) MHz. The b-dipole, asymmetric-top spectra of both structural isomers were measured in the frequency range of 5-12 GHz using a Flygare-Balle type of spectrometer. A very good fit to observed transitions, with small distortion constants, was obtained for the E0 conformer, indicating that this conformer is nearly rigid. The deviations obtained in a similar least-squares fit for the E72 confomer are significantly larger, indicating possible fluxional behavior for this conformer. In addition, 7 out of the 26 transitions observed for the E72 isomer conformer clearly exhibit very small splittings, giving further evidence for internal motion. DFT calculations for the different possible conformations of 1,1'- dimethylferrocene arising from rotation of one methyl cyclopentadienyl ligand relative to the other about the nominal C5 axis by an angle phi (dihedral angle) were performed using the B3PW91 functional. The calculations converged and were optimized for five structures on this torsional potential energy surface corresponding to different dihedral angles phi; three yielded energy minima, and two gave energy maxima, corresponding to transition states. The experimental results are in very good agreement with the results of the DFT calculations.     

Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics

The NMR spectra of n-pentane as solute in the liquid crystal 5CB are measured at several temperatures in the nematic phase. Atomistic molecular dynamics simulations of this system are carried out to predict the dipolar couplings of the orientationally ordered pentane, and the spectra predicted from these simulations are compared with the NMR experimental ones. The simulation predictions provide an excellent starting point for analysis of the experimental NMR spectra using the covariance matrix adaptation evolutionary strategy. This shows both the power of atomistic simulations for aiding spectral analysis and the success of atomistic molecular dynamics in modeling these anisotropic systems.     

Structures and dynamics of protonated ammonia clusters

The structures and infrared spectra of protonated ammonia clusters NH(4+)(NH3)n, for n < or = 8, are investigated using density functional-theory (DFT) calculations and semiempirical DFT/molecular dynamics simulations. For n < 5 the clusters are found to be mostly stable up to 100 K, while the larger clusters (n > or = 5) isomerize. Temperature effects are taken into account by performing ab initio molecular dynamics simulations with the computationally tractable self-consistent charges density functional tight-binding method. The infrared spectra at 10 K for the most stable isomers for n = 3-8 compare qualitatively with predissociation experiments, and using a common scaling factor almost quantitative agreement is found. For n > or = 6 the notion of multiple isomers present under the experimental conditions is supported. Of the 13 stable structures for n = 8 only three are found to survive at 100 K. All other clusters isomerize. Cluster structures are inferred from the analysis of the cumulative radial distribution function of the ammonia molecules surrounding the NH(4+) core. The infrared spectra are found to be typical for the structure of the clusters, which should help to relate the experimentally measured infrared spectra to the number and identity of the contributing isomers. For clusters that reorganize to a more stable isomer during the dynamics, the infrared spectrum is generally similar to that of the stable isomer itself. The clusters are found to preferably form globular structures, although chain-like arrangements are also among the low-energy configurations.     

Phototransposition reactions of arylboronate esters in acetonitrile and 2,2,2-trifluoroethanol

The phototransposition (para, meta, ortho) reactions of the arylboronate esters 4-, 3-, and 2-(4',4',5',5'-tetramethyl-1',3',2'-dioxaborolanyl)toluenes (1, 2, and 3, respectively) in both acetonitrile and 2,2,2-trifluoroethanol (TFE) using 254 nm irradiation have been examined. The irradiations resulted in steady-state compositions of para (5%), meta (19%), and ortho (76%) isomers in acetonitrile starting from the ortho isomer and para (12%), meta (54%), and ortho (35%) isomers in TFE starting from the para isomer. Analysis of the (13)C NMR spectrum of the product mixture obtained from the photochemistry of the para isomer selectively deuterated at C3 and C5 (1d(2)()) revealed that the boron-substituted carbon is the active one in the phototransposition reactions in both acetonitrile and TFE. Similar results were observed for irradiations of 1 in cyclohexane. Fluorescence spectra, singlet-state lifetimes, and Stern-Volmer quenching of fluorescence with 2,3-dimethyl-1,3-butadiene indicated that the excited singlet states of these three isomers were spectroscopic minima and that the excited singlet state was the reactive one for 3 in acetonitrile.     

The electronic spectrometry of two similar tetrabenzoperylene isomers

The u.v. absorbance and fluorescence excitation spectra of two large polycyclic aromatic hydrocarbons (PAHS) are compared. Tetrabenzo[a,cd,j, lm]perylene, the previously known isomer, behaves as expected, while the new isomer, tetrabenzo[a,cd,f,lm]perylene, has a u.v. absorbance spectrum which is very different from its fluorescence excitation spectrum. This is the only known PAH in which this behavior has been found.     

Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach

Both symmetric and asymmetric forms of the iodide acetonitrile dimer complex are known to exist with a higher stability shown by the symmetric isomer. Dynamics of this isomerization has been investigated on reduced dimensional surface in absence/presence of external electromagnetic field using Gaussian wave packet as the starting wave function. When the symmetric isomer has been taken as the initial structure, isomerization does not takes place without the external field due to high energy barrier, whereas with the asymmetric isomer as the starting one, isomerization takes place spontaneously with an equal population of both isomers. Our target in this study has been to get a dominant population of asymmetric isomer which is not possible without the application of electromagnetic field. However, it has also been seen that a simple monochromatic field cannot achieve this goal. Only by application of optimally designed polychromatic field the dominating population of asymmetric isomer can be obtained.     

Impact on lipid membrane organization by free branched-chain fatty acids

Here, we exploit the non-invasive techniques of solid-state NMR (nuclear magnetic resonance) and differential scanning calorimetry (DSC) to study the effect of free iso and ante-iso branched chain fatty acids (BCFAs) on the physicochemical properties of lipid membranes. Free fatty acids are present in biological membranes at low abundance, but can influence the cellular function by modulating the membrane organization. Solid state NMR spectra of dimyristoylphosphatidylcholine (DMPC) lipid membranes containing either free 12-methyltetradecanoic acid (a15:0) or free 13-methyltetradecanoic acid (i15:0), show significant differences in their impact on the lipid bilayer. Chain order profiles obtained by deuterium NMR on fully deuterated DMPC-d(67) bilayers revealed an ordering effect induced by both fatty acids on the hydrophobic membrane core. This behavior was also visible in the corresponding DSC thermograms where the main phase transition of DMPC bilayers-indicative of the hydrophobic membrane region-was shifted to higher temperatures, with the iso isomer triggering more pronounced changes as compared to the ante-iso isomer. This is probably due to a higher packing density in the core of the lipid bilayer, which causes reduced diffusion across membranes. By utilizing the naturally occurring spin reporters nitrogen-14 and phosphorus-31 present in the hydrophilic DMPC headgroup region, even fatty acid induced changes at the membrane interface could be detected, an observation reflecting changes in the lipid headgroup dynamics.     

Theoretical characterization of four distinct isomer types in hydrated-electron clusters, and proposed assignments for photoelectron spectra of water cluster anions

Water cluster anions, (H(2)O)(N)(-), are examined using mixed quantum/classical molecular dynamics based on a one-electron pseudopotential model that incorporates many-body polarization and predicts vertical electron detachment energies (VDEs) with an accuracy of ~0.1 eV. By varying the initial conditions under which the clusters are formed, we are able to identify four distinct isomer types that exhibit different size-dependent VDEs. On the basis of a strong correlation between the electron's radius of gyration and its optical absorption maximum, and extrapolating to the bulk limit (N → ∞), our analysis supports the assignment of the "isomer Ib" data series, observed in photoelectron spectra of very cold clusters, as arising from cavity-bound (H(2)O)(N)(-) cluster isomers. The "isomer I" data reported in warmer experiments are assigned to surface-bound isomers in smaller clusters, transitioning to partially embedded isomers in larger clusters. The partially embedded isomers are characterized by a partially formed solvent cavity at the cluster surface, and they are spectroscopically quite similar to internalized cavity isomers. These assignments are consistent with various experimental data, and our theoretical characterization of these isomers sheds new light on a long-standing assignment problem.     

Stochastic modeling of CW-ESR spectroscopy of [60]fulleropyrrolidine bisadducts with nitroxide probes

In this work, we address the interpretation of continuous wave electron spin resonance (CW-ESR) spectra of fulleropyrrolidine bisadducts with nitroxide addends. Our approach is based on a definition of the spin Hamiltonian which includes exchange and dipolar interactions and on a complete numerical solution of the resulting stochastic Liouville equation, with inclusion of diffusive rotational dynamics. CW-ESR spectra are simulated for a series of C60 bisadducts made up of four trans isomers and the equatorial isomer. A nonlinear least-squares fitting procedure allows extraction directly from the available experimental spectra of a wide range of parameters, namely interprobe relative distances, diffusion tensors, and values of the exchange parameter J. Results are in good agreement with previous, more phenomenological estimates, proving that the combination of sensitive ESR spectroscopy based on multiple spin labeling with nitroxide radicals and sophisticated modeling can be highly helpful in providing structural and dynamic information on molecular systems.     

Size resolved infrared spectroscopy of Na(CH3OH)n (n = 4-7) clusters in the OH stretching region: unravelling the interaction of methanol clusters with a sodium atom and the emergence of the solvated electron

Size resolved IR action spectra of neutral sodium doped methanol clusters have been measured using IR excitation modulated photoionisation mass spectroscopy. The Na(CH(3)OH)(n) clusters were generated in a supersonic He seeded expansion of methanol by subsequent Na doping in a pick-up cell. A combined analysis of IR action spectra, IP evolutions and harmonic predictions of IR spectra (using density functional theory) of the most stable structures revealed that for n = 4, 5 structures with an exterior Na atom showing high ionisation potentials (IPs) of ~4 eV dominate, while for n = 6, 7 clusters with lower IPs (~3.2 eV) featuring fully solvated Na atoms and solvated electrons emerge and dominate the IR action spectra. For n = 4 simulations of photoionisation spectra using an ab initio MD approach confirm the dominance of exterior structures and explain the previously reported appearance IP of 3.48 eV by small fractions of clusters with partly solvated Na atoms. Only for this cluster size a shift in the isomer composition with cluster temperature has been observed, which may be related to kinetic stabilisation of less Na solvated clusters at low temperatures. Features of slow fragmentation dynamics of cationic Na(+)(CH(3)OH)(6) clusters have been observed for the photoionisation near the adiabatic limit. This finding points to the relevance of previously proposed non-vertical photoionisation dynamics of this system.     

Size-dependent metamorphosis of electron binding motif in cluster anions of primary amide molecules

Electron binding motifs in cluster anions of primary amides, (acetamide)(n)(-) and (propionamide)(n)(-), were studied with photoelectron spectroscopy. For both the amides, two band series due to distinct isomeric species in the multipole-bound states were found in the low electron binding energy region (<~0.4 eV) of the photoelectron spectra at the excitation wavelength of 1064 nm. In the case of acetamide, the isomer of higher band peak energies is predominant for 6≤ n ≤ 8, but it vanishes completely for n ≥ 9 to be replaced with the lower energy isomer. The same spectral behavior was seen for propionamide exhibiting an exception at n = 7. The isomers appearing in the lower and higher energy sides were attributed to the straight and folded forms of ladder-like hydrogen bond network structures, respectively, on the basis of density functional calculations. In the folded forms, the excess electron is held in the space between two terminal amide molecules of the ladder-like networks. Referring to calculations of potential energy curves with respect to the folding coordinate of the ladder-like networks, it is inferred that the major isomer alternation between n = 8 and 9 originates from an increase of stiffness of the molecular ladders depending on the cluster sizes. In photoelectron spectra at the 355 nm excitation, the valence anion state having a band peak around 2.5 eV was observed to emerge with threshold sizes of n = 13 and 9 for acetamide and propionamide, respectively. Static and dynamical effects of alkyl groups on the electron binding motifs are discussed in comparison with the previous study on formamide cluster anions.     

Hydration dynamics and time scales of coupled water-protein fluctuations

We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior. Further constrained MD simulations with either frozen protein or frozen water revealed the molecular mechanism of slow hydration processes and elucidated the role of protein fluctuations. Observation of slow water dynamics in MD simulations requires protein flexibility, regardless of whether the slow Stokes shift component results from the water or protein contribution. The initial dynamics in a few picoseconds represents fast local motions such as reorientations and translations of hydrating water molecules, followed by slow relaxation involving strongly coupled water-protein motions. We observed a transition from one isomeric protein configuration to another after 10 ns during our 30 ns ground-state simulation. For one isomer, the surface hydration energy dominates the slow component of the total relaxation energy. For the other isomer, the slow component is dominated by protein interactions with the chromophore. In both cases, coupled water-protein motion is shown to be necessary for observation of the slow dynamics. Such biologically important water-protein motions occur on tens of picoseconds. One significant discrepancy exists between theory and experiment, the large inertial relaxation predicted by simulations but clearly absent in experiment. Further improvements required in the theoretical model are discussed.     

Spectroscopy and femtosecond dynamics of the ring opening reaction of 1,3-cyclohexadiene

The early stages of the ring opening reaction of 1,3-cyclohexadiene to form its isomer 1,3,5-hexatriene, upon excitation to the ultrashort-lived 1 1B2 state, were explored. A series of one-color two-photon ionization/photoelectron spectra reveal a prominent vibrational progression with a frequency of 1350 cm(-1), which is interpreted in a dynamical picture as resulting from the ultrafast wave packet dynamics associated with the ring opening reaction. Photoionization in two-color three-photon and one-color four-photon ionization schemes show an ionization pathway via the same ultrashort-lived 1 1B2 state, and in addition, a series of Rydberg states with quantum defects of 0.93, 0.76, and 0.15, respectively. Using those Rydberg states as probes for the reaction dynamics in a time-resolved pump-probe experiment provides a direct observation of the elusive 2 1A1 state that has been implicated as an intermediate step between the initially excited 1 1B2 state and the ground electronic state. The rise and decay times for the 2 1A1 state were found to be 55 and 84 fs, respectively.     

Ionization-induced π→ H site switching dynamics in phenol-Ar3

Electronic excitation spectra of the S(1)← S(0) transition obtained by resonance-enhanced two-photon ionization (REMPI) are analysed for phenol-Ar(n) (PhOH-Ar(n)) clusters with n≤ 4. An additivity rule has been established for the S(1) origin shifts upon sequential complexation at various π binding sites, which has allowed for the identification of two less stable isomers not recognized previously, namely the (2/0) isomer for n = 2 and the (2/1) isomer for n = 3. Infrared (IR) spectra of neutral PhOH-Ar(n) and cationic PhOH(+)-Ar(n) clusters are recorded in the vicinity of the OH and CH stretch fundamentals (ν(OH), ν(CH)) in their S(0) and D(0) ground electronic states using IR ion dip spectroscopy. The small monotonic spectral redshifts Δν(OH) of about -1 cm(-1) per Ar atom observed for neutral PhOH-Ar(n) are consistent with π-bonded ligands. In contrast, the IR spectra of the PhOH(+)-Ar(n) cations generated by resonant photoionization of the neutral precursor display the signature of H-bonded isomers, suggesting that ionization triggers an isomerization reaction, in which one of the π-bonded Ar ligands moves to the more attractive OH site. The dynamics of this isomerization reaction is probed for PhOH(+)-Ar(3) by picosecond time-resolved IR spectroscopy. Ionization of the (3/0) isomer of PhOH(+)-Ar(3)(3π) with three π-bonded Ar ligands on the same side of the aromatic ring induces a π→ H switching reaction toward the PhOH(+)-Ar(3)(H/2π) isomer with a time constant faster than 3 ps. Fast intracluster vibrational energy redistribution prevents any H →π back reaction.     

Cationic copolymerization of anethole: Reactivity of geometric isomers of α,β-disubstituted ethylenes

Cationic copolymerizations of anethole were carried out under various conditions in order to confirm the relative reactivities of its geometric isomers. trans-Anethole was more reactive than cis-anethole in copolymerizations with p-methoxystyrene or styrene, but less reactive in the mutual copolymerization of cis- and trans-anethole; i.e., the trans isomer was more reactive to a growing chain end with little steric hindrance. Thus the intrinsic reactivity of an olefinic double bond to carbonium ion is greater for the trans isomer than for the cis isomer. This idea is supported by ¹³C NMR spectra, since the signal of the olefinic β-carbon of the trans isomer is at higher field than that of the cis isomer. The behavior of anethole was compared with the results observed in vinyl ethers, where the cis isomer was always more reactive irrrspective of the structure of the growing chain end. In addition, the dependence of monomer reactivity ratios on polymerization conditions is discussed.     

Tuning of the internal energy and isomer distribution in small protonated water clusters H(+)(H2O)(4-8): an application of the inert gas messenger technique

Infrared spectroscopy of gas-phase hydrated clusters provides us much information on structures and dynamics of water networks. However, interpretation of spectra is often difficult because of high internal energy (vibrational temperature) of clusters and coexistence of many isomers. Here we report an approach to vary these factors by using the inert gas (so-called "messenger")-mediated cooling technique. Protonated water clusters with a messenger (M), H(+)(H(2)O)(4-8)·M (M = Ne, Ar, (H(2))(2)), are formed in a molecular beam and probed with infrared photodissociation spectroscopy in the OH stretch region. Observed spectra are compared with each other and with bare H(+)(H(2)O)(n). They show clear messenger dependence in their bandwidths and relative band intensities, reflecting different internal energy and isomer distribution, respectively. It is shown that the internal energy follows the order H(+)(H(2)O)(n) > H(+)(H(2)O)(n)·(H(2))(2) > H(+)(H(2)O)(n)·Ar > H(+)(H(2)O)(n)·Ne, while the isomer-selectivity, which changes the isomer distribution in the bare system, follows the order H(+)(H(2)O)(n)·Ar > H(+)(H(2)O)(n)·(H(2))(2) > H(+)(H(2)O)(n)·Ne ~ (H(+)(H(2)O)(n)). Although the origin of the isomer-selectivity is unclear, comparison among spectra measured with different messengers is very powerful in spectral analyses and makes it possible to easily assign spectral features of each isomer.