Effect of Electron-donating Group on NO Photolysis of {RuNO}6 Ruthenium Nitrosyl Complexes with N2 O2 Lgands Bearing π-Extended Rings.

In this study, we introduced the electron-donating group (-OH) to the aromatic rings of Ru(salophen)(NO)Cl (0) (salophenH2 =N,N'-(1,2-phenylene)bis(salicylideneimine)) to investigate the influence of the substitution on NO photolysis and NO-releasing dynamics. Three derivative complexes, Ru((o-OH)2 -salophen)(NO)Cl (1), Ru((m-OH)2 -salophen)(NO)Cl (2), and Ru((p-OH)2 -salophen)(NO)Cl (3) were developed and their NO photolysis was monitored by using UV/Vis, EPR, NMR, and IR spectroscopies under white room light. Spectroscopic results indicated that the complexes were diamagnetic Ru(II)-NO+ species which were converted to low-spin Ru(III) species (d5 , S=1/2) and released NO radicals by photons. The conversion was also confirmed by determining the single-crystal structure of the photoproduct of 1. The photochemical quantum yields (ΦNO s) of the photolysis were determined to be 0>1, 2, 3 at both the visible and UV excitations. Femtosecond (fs) time-resolved mid-IR spectroscopy was employed for studying NO-releasing dynamics. The geminate rebinding (GR) rates of the photoreleased NO to the photolyzed complexes were estimated to be 0≃1, 2, 3. DFT and TDDFT computations found that the introduction of the hydroxyl groups elevated the ligand π-bonding orbitals (π (salophen)), resulting in decrease of the HOMO-LUMO gaps in 1-3. The theoretical calculations suggested that the Ru-NNO bond dissociations of the complexes were mostly initiated by the ligand-to-ligand charge transfer (LLCT) of π(salophen)→π*(Ru-NO) with both the visible and UV excitations and the decreasing ΦNO s could be explained by the changes of the electronic structures in which the photoactivable bands of 1-3 have relatively less contribution of transitions related with Ru-NO bond than those of 0.

Investigating the Photodissociation Dynamics of CF2BrCF2I in CCl4 through Femtosecond Time-Resolved Infrared Spectroscopy.

The photodissociation dynamics of CF2BrCF2I in CCl4 at 280 ± 2 K were investigated by probing the C-F stretching mode from 300 fs to 10 µs after excitation at 267 nm using time-resolved infrared spectroscopy. The excitation led to the dissociation of I or Br atoms within 300 fs, producing the CF2BrCF2 or CF2ICF2 radicals, respectively. All nascent CF2ICF2 underwent further dissociation of I, producing CF2CF2 with a time constant of 56 ± 5 ns. All nascent g-CF2BrCF2 isomerized into the more stable a-CF2BrCF2 with a time constant of 47 ± 5 ps. Furthermore, a-CF2BrCF2 underwent a bimolecular reaction with either itself (producing CF2BrCF2Br and CF2CF2) or Br in the CCl4 solution (producing CF2BrCF2Br) at a diffusion-limited rate. The secondary dissociation of Br from a-CF2BrCF2 was significantly slow to compete with the bimolecular reactions. Overall, approximately half of the excited CF2BrCF2I at 267 nm produced CF2BrCF2Br, whereas the other half produced CF2CF2. The excess energies in the nascent radicals were thermalized much faster than the secondary dissociation of I from CF2ICF2 and the observed bimolecular reactions, implying that the secondary reactions proceeded under thermal conditions. This study further demonstrates that structure-sensitive time-resolved infrared spectroscopy can be used to study various reaction dynamics in solution in real time.

Dynamics of Irreversible NO Release from Photoexcited Molsidomine.

Molsidomine (SIN-10), an orally administered NO-delivery drug for vasodilation, cannot be used to alleviate hypertensive crisis because it releases NO at a slow rate. SIN-10 may be used to treat sudden cardiac abnormalities if the rapid and immediate release of NO is achieved via photoactivation. The photodissociation dynamics associated with the NO release process from SIN-10 in CHCl3 was investigated using time-resolved infrared spectroscopy. Approximately 41% of photoexcited SIN-10 at 360 nm decomposed into CO2, CH2CH3 radical, and the remaining radical fragment [SIN-1A(-H)] with a time constant of 43 ps. All SIN-1A(-H) released NO spontaneously with a time constant of 68 ns, becoming N-morpholino-aminoacetonitrile, resulting in 41% for the quantum yield of immediate NO release from SIN-10. The results obtained can be used to realize the quantitative control of the NO administration at a specific time, and SIN-10 can be potentially used to address the phenomenon of hypertensive crisis.

Rotational Isomerization of Carbon-Carbon Single Bonds in Ethyl Radical Derivatives in a Room-Temperature Solution.

The rotational isomerization of 1,2-disubstituted ethyl radical derivatives, reaction intermediates often found in the reaction of 1,2-disubstituted ethane derivatives, has never been measured because of their short lifetime and ultrafast rotation. However, the rotational time constant is critical for understanding the detailed reaction mechanism involving these radicals, which determine the stereoisomers of compounds produced via the intermediates. Using time-resolved infrared spectroscopy, we found that the CF2BrCF2 radical in a CCl4 solution rotationally isomerizes with a time constant of 47 ± 5 ps at 280 ± 2 K. From this value and the rotational barrier heights of related compounds, CH3CH2 and CH3CH2CHCH3 radicals in CCl4 were estimated to rotationally isomerize within 1 ps at 298 K, considerably faster than ethane and n-butane, which rotationally isomerize with time constants of 1.8 and 81 ps, respectively. The time constant for the rotational isomerization was similar to that calculated using transition state theory with a transmission coefficient of 0.75.

Visible-light NO photolysis of ruthenium nitrosyl complexes with N2O2 ligands bearing π-extended rings and their photorelease dynamics.

NO photorelease and its dynamics for two {RuNO}6 complexes, Ru(salophen)(NO)Cl (1) and Ru(naphophen)(NO)Cl (2), with salen-type ligands bearing π-extended systems (salophenH2 = N,N'-(1,2-phenylene)-bis(salicylideneimine) and naphophenH2 = N,N'-1,2-phenylene-bis(2-hydroxy-1-naphthylmethyleneimine)) were investigated. NO photolysis was performed under white room light and monitored by UV/Vis, EPR, and NMR spectroscopies. NO photolysis was also performed under 459 and 489 nm irradiation for 1 and 2, respectively. The photochemical quantum yields of the NO photolysis (ΦNO) of both 1 and 2 were determined to be 9% at the irradiation wavelengths. The structural and spectroscopic characteristics of the complexes before and after the photolysis confirmed the conversion of diamagnetic Ru(II)(L)(Cl)-NO+ to paramagnetic S = ½ Ru(III)(L)(Cl)-solvent by photons (L = salophen2- and naphophen2-). The photoreleased NO radicals were detected by spin-trapping EPR. DFT and TDDFT calculations found that the photoactive bands are configured as mostly the ligand-to-ligand charge transfer (LLCT) of π(L) → π*(Ru-NO), suggesting that the NO photorelease was initiated by the LLCT. Dynamics of NO photorelease from the complexes in DMSO under 320 nm excitation were investigated by femtosecond (fs) time-resolved mid-IR spectroscopy. The primary photorelease of NO occurred for less than 0.32 ps after the excitation. The rate constants (k-1) of the geminate rebinding of NO to the photolyzed 1 and 2 were determined to be (15 ps)-1 and (13 ps)-1, respectively. The photochemical quantum yields of NO photolysis (ΦNO, λ = 320 nm) were estimated to be no higher than 14% for 1 and 11% for 2, based on the analysis of the fs time-resolved IR data. The results of fs time-resolved IR spectroscopy and theoretical calculations provided some insight into the overall kinetic reaction pathway, localized electron pathway or resonance pathway, of the NO photolysis of 1 and 2. Overall, our study found that the investigated {RuNO}6 complexes, 1 and 2, with planar N2O2 ligands bearing π-extended rings effectively released NO under visible light.

Photoacid-induced aqueous acid-base reactions probed by femtosecond infrared spectroscopy.

Acid-base reactions involving an excited photoacid have typically been investigated at high base concentrations, but the mechanisms at low base concentrations require clarification. Herein, the dynamics of acid-base reactions induced by an excited photoacid, pyranine (DA), were investigated in the presence of azide ion (N3-) in D2O solution using femtosecond infrared spectroscopy. Specifically, the spectral characteristics of four species (DA, electronically excited DA (DA*), the conjugate base of DA* (A*-), and the conjugate base of DA (A-)) were probed in the spectral region of 1400-1670 cm-1 in the time range of 1 ps-1 µs. This broad timescale encompassed all the acid-base reactions initiated by photoexcitation at 400 nm; thus, reactions related to both DA* and A- could be probed. Furthermore, changes in the populations of N3- and DN3 were monitored using the absorption bands at 2042 and 2133 cm-1, respectively. Following excitation, approximately half of DA* relaxed to DA with a time constant of 0.44 ± 0.04 ns. The remainder underwent an acid-base reaction to produce A*-, which relaxed to A- with a time constant of 3.9 ± 0.3 ns. The acid-base reaction proceeded via two paths, namely, proton exchange with the added base or simple deuteron release to D2O (protolysis). Notably, all the acid-base reactions were well described by the rate constant at the steady-state limit. Thus, although the acid-base reactions at low base concentrations (< 0.1 M) were diffusion controlled, they could be described using a simple rate equation.

Photoexcitation dynamics of bromodiphenyl ethers in acetonitrile-d3 studied by femtosecond time-resolved infrared spectroscopy.

The efficient decomposition of polybrominated diphenyl ethers (PBDEs), onetime prevalent flame retardants, is central to the reduction of their harmful effects on human health. PBDE photodecomposition is a promising method, but its mechanism and products are not well understood. The photoexcitation dynamics of 3- and 4-bromodiphenyl ethers (BDE-2 and BDE-3) in CD3CN were studied from 0.3 ps to 10 µs using time-resolved infrared spectroscopy. An excitation at 267 nm dissociated the Br atom from BDE-2 and BDE-3 within 0.3 ps and 14 ± 3 ps, respectively, producing a radical compound (R) and a Br atom. About 85% of R formed an intermediate (IM) that weakly interacted with the Br atom and the surrounding CD3CN solvent in 7-12 ps. The remaining R separated from the dissociated Br and underwent slow geminate rebinding (GR) with Br within 35 to 54 ns. The IM competitively engaged in GR with the interacting Br in 40-60 ps or formed CD3CN-bound radical compounds (RS) in 100-130 ps. The RS further degraded via either the dissociation of CD3-producing a cyano-bound diphenyl ether (DE) in 150 or 550 ns-or the deuterium abstraction of CD3CN in 180 or 430 ns-producing a deuterated DE. Overall, 33 ± 3 (22 ± 3)% of the photoexcited BDE-2 (BDE-3) decomposed in CD3CN under 267 nm excitation. Efficient binding of the CD3CN solvent to R deterred the yield-diminishing GR and slowed the rate of product formation. The observed photoexcitation dynamics of BDE suggest methods for the efficient decomposition of PBDE.

Midwavelength Infrared Colloidal Nanowire Laser.

Realizing bright colloidal infrared emitters in the midwavelength infrared (or mid-IR), which can be used for low-power IR light-emitting diodes (LEDs), sensors, and deep-tissue imaging, has been a challenge for the last few decades. Here, we present colloidal tellurium nanowires with strong emission intensity at room temperature and even lasing at 3.6 µm (ω) under cryotemperature. Furthermore, the second-harmonic field at 1.8 µm (2ω) and the third-harmonic field at 1.2 µm (3ω) are successfully generated thanks to the intrinsic property of the tellurium nanowire. These unique optical features have never been reported for colloidal tellurium nanocrystals. With the colloidal midwavelength infrared (MWIR) Te nanowire laser, we demonstrate its potential in biomedical applications. MWIR lasing has been clearly observed from nanowires embedded in a human neuroblastoma cell, which could further realize deep-tissue imaging and thermotherapy in the near future.

Modulations of a Metal-Ligand Interaction and Photophysical Behaviors by Hückel-Möbius Aromatic Switching.

In organometallic complexes containing π-conjugated macrocyclic chelate ligands, conformational change significantly affects metal-ligand electronic interactions, hence tuning properties of the complexes. In this regard, we investigated the metal-ligand interactions in hexaphyrin mono-Pd(II) complexes Pd[28]M and Pd[26]H, which exhibit a redox-induced switching of Hückel-Möbius aromaticity and subsequent molecular conformation, and their effect on the electronic structure and photophysical behaviors. In Möbius aromatic Pd[28]M, the weak metal-ligand interaction leads to the π electronic structure of the hexaphyrin ligand remaining almost intact, which undergoes efficient intersystem crossing (ISC) assisted by the heavy-atom effect of the Pd metal. In Hückel aromatic Pd[26]H, the significant metal-ligand interaction results in ligand-to-metal charge-transfer (LMCT) in the excited-state dynamics. These contrasting metal-ligand electronic interactions have been revealed by time-resolved electronic and vibrational spectroscopies and time-dependent DFT calculations. This work indicates that the conspicuous modulation of metal-ligand interaction by Hückel-Möbius aromaticity switching is an appealing approach to manipulate molecular properties of metal complexes, further enabling the fine-tuning of metal-ligand interactions and the novel design of functional organometallic materials.

Photodissociation Dynamics of Nitric Oxide from N-Acetylcysteine- or N-Acetylpenicillamine-bound Roussin's Red Ester.

The photochemical release of nitric oxide (NO) from a NO precursor is advantageous in terms of spatial, temporal, and dosage control of NO delivery to target sites. To realize full control of the quantitative NO administration from photoactivated NO precursors, it is necessary to have detailed dynamical information on the photodissociation of NO from NO precursors. We synthesized two new water-soluble Roussin's red esters (RREs), [Fe2(µ-N-acetylcysteine)2(NO)4] and [Fe2(µ-N-acetylpenicillamine)2(NO)4], which have five times longer lifetime than the well-known [Fe2(µ-cysteine)2(NO)4]. The photodissociation dynamics of NO from these RREs in water were investigated over a broad time range from 0.3 ps to 10 µs after excitation at 310 and 400 nm using femtosecond time-resolved infrared (IR) spectroscopy. When these RREs are excited, they either release one NO, producing a radical species deficient in one NO (R), [Fe2(µ-RS)2(NO)3], or relax into the ground state without photodeligation via an electronically excited intermediate state (M). R appears immediately after photoexcitation, suggesting that one NO is photodissociated faster than 0.3 ps. A certain fraction of R undergoes geminate recombination (GR) with NO with a time constant of 7-9 ps, while the remaining R competitively binds to the solvent. Solvent-bound R eventually bimolecularly recombines with NO with a rate constant of (1.3-1.6) × 108 M-1 s-1. For a given RRE molecule, the fractional yield of M (0.62-0.76) depends on the excitation wavelength (λex); however, the relaxation time of M (6 ± 1 ns) is independent of λex. Although the primary quantum yield of NO photodissociation (Φ1) was found to be 0.24-0.38, the final yield of NO suitable for other reactions (Φ2) was reduced to 0.14-0.29 due to the picosecond GR of the dissociated NO with R. Detailed photoexcitation dynamics of RRE can be utilized in the quantitative control of NO administration at a specific site and time, promoting pin-point usage of NO in chemistry and biology. We demonstrate that femtosecond IR spectroscopy combined with quantum chemical calculations is a powerful method for obtaining detailed dynamic information on photoactivated NO precursors such as Φ1 and Φ2, the GR yield, and secondary reactions of the nascent photoproducts, which are essential information for the design of efficient photoactivated NO precursors and their quantitative utilization.

Dynamics of photodissociation of nitric oxide from S-nitrosylated cysteine and N-acetylated cysteine derivatives in water.

Cysteine and N-acetylated cysteine derivatives are ubiquitous in biological systems; they have thiol groups that bind NO to form S-nitrosothiols (RSNOs) such as S-nitrosocysteine (CySNO), S-nitroso-N-acetylcysteine (NacSNO), and S-nitroso-N-acetylpenicillamine (NapSNO). Although they have been utilised as thermally or catalytically decomposing NO donors, their photochemical applications are yet to be fully explored owing to the lack of photodissociation dynamics. To this end, the photoexcitation dynamics of these RSNOs in water at 330 nm were investigated using femtosecond time-resolved infrared (TRIR) spectroscopy over a broad time range encompassing the entire reaction, which includes the primary reaction, secondary reactions of the reaction intermediates, and product formation. We discovered that the acetate and amide groups in these RSNOs have strong vibrational bands sensitive to the bondage of NO and the electronic state of the compound, which facilitates the identification of reaction intermediates involved in photoexcitation. The simplest thiol available with the acetate group-thioglycolic acid-was nitrosylated; it produced S-nitrosothioglycolic acid (TgSNO) and was comparatively investigated. Transient absorption bands in the TRIR spectra of the RSNOs were assigned using quantum chemical calculations. Photoexcited cysteine-related RSNOs either decompose into RS and NO within 0.3 ps after excitation at 330 nm with a primary quantum yield (Φ1) of 0.46-1 or relax into an electronically excited intermediate state lying at 42 ± 3 kcal mol-1 above the ground state, which relaxes into the ground state with a time constant of 460-520 ps. A majority (62-80%) of the RS radical geminately rebinds with NO at a time constant of 3-7 ps. The remaining RS reacts with the neighbouring RSNO, which produces additional NO and RSSR with a (nearly) diffusion-limited rate constant that doubles the amount of NO produced; further, it remarkably extends the time window for the dissociated NO to react with the target compound. The final fraction of NO produced from these RSNOs at 330 nm was 0.32-0.58, and it depends on the geminate rebinding yield and Φ1. The detailed dynamics of the photoexcited RSNO can be utilised in the quantitative application of these RSNOs in practical use and in the synthesis of more efficient photoactivated NO precursors.

meso-Oxoisocorroles: Tunable Antiaromaticity by Metalation and Coordination of Lewis Acids as Well as Aromaticity Reversal in the Triplet Excited State.

The corrole derivative meso-oxoisocorrole has been theoretically predicted to be antiaromatic, despite its formally cross conjugated electronic system. In this study, this prediction has been experimentally proven by the facile preparation of meso-oxoisocorrole via the oxidation of a meso free corrole with MnO2 and its comprehensive characterization using NMR, UV/vis absorption, FT-IR, and transient-absorption spectroscopy, cyclic voltammetry, and X-ray diffraction analysis. Furthermore, the free base meso-oxoisocorrole was metalated by treatment with Ni(acac)2, PdCl2(PhCN)2, and Zn(OAc)2 to give the corresponding metal complexes. These complexes are more strongly antiaromatic, and their degree of paratropicity depends on their planarity. Thus, fine tuning of their antiaromaticity was achieved with concomitant modulation of their HOMO-LUMO gaps. In the presence of tris(pentafluorophenyl)borane, their antiaromaticity is significantly enhanced due to the elongation of the C═O bond, which promotes the polarized C+-O- resonance state. Furthermore, a distinct frequency shift of the C═O vibrational mode in the triplet state was observed in the time-resolved IR spectra in accordance with the Baird rule, which indicates aromaticity reversal in the excited state.

Conformer-Specific Photodissociation Dynamics of CF2ICF2I in Solution Probed by Time-Resolved Infrared Spectroscopy.

The photodissociation dynamics of CF2ICF2I in solution was investigated from 0.3 ps to 100 µs, after the excitation of CF2ICF2I with a femtosecond UV pulse. Upon excitation, one I atom is eliminated within 0.3 ps, producing a haloethyl radical having a classical structure: anti-CF2ICF2 and gauche-CF2ICF2. All the nascent gauche-CF2ICF2 radicals reacted with the dissociated I atom within the solvent cage to produce a complex, I2··C2F4, in <1 ps. The quasi-stable I2··C2F4 complex in CCl4 (CH3CN or CD3OH) further dissociated into I2 and C2F4 with a time constant of 180 ± 5 (46 ± 3) ps. Some of the anti-CF2ICF2 radicals also formed the I2··C2F4 complex with a time constant of 1.5 ± 0.3 ps, while the remaining radicals underwent secondary elimination of I atom in a few nanoseconds. The time constant for the secondary dissociation of I atom from the anti-CF2ICF2 radical was independent of the excitation wavelength, indicating that the excess energy in the nascent radical is relaxed and that the secondary dissociation proceeds thermally. The formation of the I2··C2F4 complex and the thermal dissociation of the anti-CF2ICF2 radical clearly demonstrate that even a weakly interacting solvent plays a significant role in the modification and creation of reaction.

Photorelease Dynamics of Nitric Oxide from Cysteine-Bound Roussin's Red Ester.

Nitric oxide (NO) can either boost or impede the growth of cancer cells depending on its concentration. Therefore, any anticancer treatment using NO requires precisely controlled NO administration to the target cells in terms of dosage and timing. In this context, photochemically activated NO donors were actively explored, but their detailed NO-releasing dynamics, which is crucial for their use, is not known yet. We determined detailed photoexcitation dynamics of a stable, nontoxic, and water-soluble NO precursor, cysteine-bound Roussin's Red Ester (Cys-RRE), including secondary reactions of the nascent photoproducts. The primary quantum yields of the NO dissociation from the photoexcited Cys-RRE were found to be 24-54% depending on the excitation wavelength; however, the geminate rebinding of NO with the nascent radical reduced the level of biologically available NO to as low as 12%. Such information is useful to achieve efficient NO delivery to practical chemical and biological targets.

Excited-State Aromaticity of Gold(III) Hexaphyrins and Metalation Effect Investigated by Time-Resolved Electronic and Vibrational Spectroscopy.

Expanded porphyrins with appropriate metalation provide an excellent opportunity to study excited-state aromaticity. The coordinated metal allows the excited-state aromaticity in the triplet state to be detected through the heavy-atom effect, but other metalation effects on the excited-state aromaticity were ambiguous. Herein, the excited-state aromaticity of gold(III) hexaphyrins through the relaxation dynamics was revealed via electronic and vibrational spectroscopy. The SQ states of gold [26]- and [28]-hexaphyrins showed interconvertible absorption and IR spectra with those of counterparts in the ground-state, indicating aromaticity reversal. Furthermore, while the T1 states of gold [28]-hexaphyrins also exhibited reversed aromaticity according to Baird's rule, the ligand-to-metal charge-transfer state of gold [26]-hexaphyrins contributed by the gold metal showed non-aromatic features arising from the odd-number of π-electrons.

Two-electron transfer stabilized by excited-state aromatization.

The scientific significance of excited-state aromaticity concerns with the elucidation of processes and properties in the excited states. Here, we focus on TMTQ, an oligomer composed of a central 1,6-methano[10]annulene and 5-dicyanomethyl-thiophene peripheries (acceptor-donor-acceptor system), and investigate a two-electron transfer process dominantly stabilized by an aromatization in the low-energy lying excited state. Our spectroscopic measurements quantitatively observe the shift of two π-electrons between donor and acceptors. It is revealed that this two-electron transfer process accompanies the excited-state aromatization, producing a Baird aromatic 8π core annulene in TMTQ. Biradical character on each terminal dicyanomethylene group of TMTQ allows a pseudo triplet-like configuration on the 8π core annulene with multiexcitonic nature, which stabilizes the energetically unfavorable two-charge separated state by the formation of Baird aromatic core annulene. This finding provides a comprehensive understanding of the role of excited-state aromaticity and insight to designing functional photoactive materials.

Complete photodissociation dynamics of CF2I2 in solution.

Photodissociation dynamics of CF2I2 in cyclohexane were evaluated by probing the C-F stretching mode over a wide time range after ultraviolet excitation using femtosecond infrared spectroscopy. After the ultrafast (<0.2 ps) state-selective photodissociation of CF2I2 as in the gas phase (267 nm excitation led to exclusive three-body dissociation (CF2 + I + I), 350 nm to exclusive two-body dissociation (CF2I + I), and 310 nm to a mixture of three- and two-body dissociations), various secondary reactions were observed. Once produced, some nascent CF2 radicals immediately formed a complex with the departing I atom (ICF2), which produced either CF2I or CF2 radicals. The produced CF2I geminately recombined with the I atom, whereas the CF2 radical reacted bimolecularly to produce C2F4 with a diffusion-limited rate constant of 8.1 × 109 M-1 s-1. Some nascent CF2I radicals were produced with sufficient excess energy to further dissociate into CF2 and I, or immediately reacted with the dissociated I atom to form the I2-CF2 isomer that rapidly dissociated into CF2 and I2. Other nascent CF2I radicals geminately recombined with the I atom with various time constants. Thus, the nascent photoproducts, CF2 and CF2I take various reaction paths: complex formation, secondary dissociation, isomer formation, and fast and slow germinate rebindings. The ensuing reaction path of the nascent photoproduct is dictated by its internal energy as well as solvent environment, which leads to different interactions between the photoproduct and solvent. Measurement over a broad time range with a structure-sensitive probe could reveal the fate of all the reaction intermediates, which allows evaluation of the complete reaction dynamics in solution.

Computational Probing of Watson-Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine.

DNA breathing is a local conformational fluctuation spontaneously occurring in double-stranded DNAs. In particular, the possibility of individual base pairs (bps) in duplex DNA to flip between alternate bp modes, i.e., Watson-Crick (WC)-like and Hoogsteen (HG)-like, at relevant time scales has impacted DNA research fields for many years. In this study, to computationally probe effects of chemical modification on the DNA breathing, we present a free energy landscape of spontaneous thermal transitions between WC and HG bps in a free DNA duplex containing N1-methylated adenine (m1A). For the current free energy computation, a variant of well-tempered metadynamics simulation was extensively performed for a total of 40 µs to produce free energy surfaces. The free energy profile indicated that, upon the chemical modification of adenine, the HG bp (m1A·T) was located in the most favorable conformation (96.7%); however, the canonical WC bp (m1A·T) was distorted into two WC-like bps of WC* (2.8%) and WC** (0.5%). The conformational exchange between these two minor WC-like bps occurs with the first hundred nanoseconds. The transition between WC-like and HG bp features multiple transition pathways displaying various extents of base flipping in combination with glycosidic rotation. Analysis of the simulated ensemble showed that the m1A-induced changes of the backbone and sugar pucker were in a reasonable agreement with previous results inferred from NMR experiments. Also, this study revealed that the formation of the stable HG bp upon the mutation alters the characteristics of dynamic fluctuations of the neighboring WC residues of m1A. We expect this simulation approach to be a robust computational scheme to complement and guide future high-resolution experiments on many outstanding issues of duplex DNA breathing.

Photodissociation of CF2ICF2I in solid para-hydrogen: infrared spectra of anti- and gauche-˙C2F4I radicals.

The photolysis of 1,2-diiodotetrafluoroethane (CF2ICF2I) has served as a prototypical system in ultrafast reaction dynamics. Even though the intermediates, anti- and gauche-iodotetrafluoroethyl (˙C2F4I) radicals, have been characterized with electron diffraction and X-ray diffraction, their infrared spectra are unreported. We report the formation and infrared identification of these radical intermediates upon ultraviolet photodissociation of CF2ICF2I in solid para-hydrogen (p-H2) at 3.3 K. Lines at 1364.9/1358.5, 1283.2, 1177.1, 1162.2, 1126.8, 837.3, 658.0, 574.2, and 555.2 cm-1 are assigned to anti-˙C2F4I, and lines at 1325.9, 1259.7, 1143.4, 1063.4, 921.0, and 765.3 cm-1 to gauche-˙C2F4I. A secondary photodissociation leading to C2F4 was also observed. The assignments were derived according to behavior on secondary photolysis, comparison of the vibrational wavenumbers and the IR intensities of the observed lines with values predicted with the B3PW91/aug-cc-pVTZ-pp method. This spectral identification provides valuable information for future direct spectral probes of these important intermediates.

Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.

The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10-12 µs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15. This study found that the TBA folding occurred via multiple folding pathways with two major free energy barriers of 13 and 15 kcal/mol in the presence of several intermediate states of G-triplex variants. The early formation of these intermediates was associated with a single K+ ion capturing. Interestingly, these intermediate states appear to undergo facile transitions among themselves through relatively small energy barriers.