Generation and EPR Spectroscopy of the First Silenyl Radicals,R2C=Si.−R: Experiment and Theory

The first two persistent silenyl radicals (R₂C=Si^.?R), with a half‐life (t_1/2) of about 30 min, were generated and characterized by electron paramagnetic resonance (EPR) spectroscopy. The large hyperfine coupling constants (hfccs) (a(²⁹Si_α)=137.5–148.0 G) indicate that the unpaired electron has substantial s character. DFT calculations, which are in good agreement with the experimentally observed hfccs, predict a strongly bent structure (?C=Si?R=134.7–140.7°). In contrast, the analogous vinyl radical, R₂C=C^.?R (t_1/2≈3 h), exhibits a small hfcc (a(¹³C_α)=26.6 G) and has a nearly linear geometry (?C=C?R=168.7°).     

Generation and EPR Spectroscopy of the First Silenyl Radicals,R2C=Si.−R: Experiment and Theory

The first two persistent silenyl radicals (R₂C=Si^.?R), with a half‐life (t_1/2) of about 30 min, were generated and characterized by electron paramagnetic resonance (EPR) spectroscopy. The large hyperfine coupling constants (hfccs) (a(²⁹Si_α)=137.5–148.0 G) indicate that the unpaired electron has substantial s character. DFT calculations, which are in good agreement with the experimentally observed hfccs, predict a strongly bent structure (?C=Si?R=134.7–140.7°). In contrast, the analogous vinyl radical, R₂C=C^.?R (t_1/2≈3 h), exhibits a small hfcc (a(¹³C_α)=26.6 G) and has a nearly linear geometry (?C=C?R=168.7°).     

Quantum-Chemical Study of the Electronic and Steric Structure of Vinyltetrazoles: II. 2-Vinyltetrazoles

The total Mulliken charges on the C and N atoms, populations of the S-trans-(N¹) conformers, and rotation barriers in the molecules of 2-vinyl-5-R-tetrazoles (R = H, CH₃, CH = CH₂, C₆H₅, CH₂Cl, CF₃) were calculated ab initio (HF/6-31G**, MP2/6-31G**). The results were compared with the ¹H and ¹³C NMR data for these compounds.     

The structure of potassium hydrogentartrate: A combined X-ray,semiempirical, and ab initio study

Single crystals of potassium hydrogentartrate, (2R,2R)-KO₂C(CHOH)₂CO₂H, were taken from a three-year-old wine bottle. The structure was determined by low-temperature single-crystal X-ray diffraction analysis using a Siemens SMART diffractometer. (2R,2R)-KO₂C(CHOH)₂CO₂H crystallizes in the orthorhombic space group P2₁2₁2₁ with Z = 4 and unit cell dimensions a = 7.6065(5), b = 7.7599(5), and c = 10.6054(7) Å. The structure of an isolatedhydrogentartrate anion, (2R,2R)-[O₂C(CHOH)₂-CO₂H]⁻, was calculated at the semiempirical AM1 and PM3 levels of theory with a VSTO-3G* basis set and in addition ab initio at the self-consistent level of theory using a standard 6-31G(d, p) basis set (Non-SI units employed: kcal ≈ 4.184 kJ, Å = 10⁻¹⁰ m).© 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:307–310, 1998     

The Apparent Molal Volume and Compressibility of Seawater Fit to the Pitzer Equations

The density and compressibility of seawater salt solutions for ionic strengths 0to 0.8 m, temperatures 0–40°C, and applied pressure 0 to 1000 barare fitted tothe Pitzer equations. The apparent molal volumes and compressibilities (X) arefitted to equations of the form

Spectroscopic characterization and <Emphasis Type="Italic">Ab initio</Emphasis> calculations of new diazaphosphole and diazaphosphorinane

Phosphoryl chloride is used as a starting material to synthesize new diazaphosphole, (1) and diazaphosphorinane, (2). The products are characterized by ¹H, ¹³C, ³¹P NMR, and IR spectroscopy. A high value ² J(PNH) = 17.0 Hz, 17.2 Hz is measured for two non-equivalent NH protons of endocyclic nitrogen atoms in compound 1, while it greatly decreases to 4.5 Hz in 2. Also, great amounts are obtained for two ² J(P,C) as well as two ³ J(P,C) in the ¹³C NMR spectrum of 1, but they are zero in 2. Here, the effect of ring strain and ring size on the structural and spectroscopic parameters is observed. The ³¹P NMR spectra reveal that δ(³¹P) of compound 1 is far much more downfield (12.63 ppm) relative to that of compound 2 (−10.39 ppm). Furthermore, ab initio quantum chemical calculations are performed to optimize the structures of these molecules by density functional theory (B3LYP) and Hartree-Fock (HF) methods, using the standard 6−31+G** basis set. The stabilization energies are calculated by the equation ΔE _{stabilization} = E _molecule − ΣE _i , where i = atom. To obtain the atomic hybridizations, NBO computations are made at the B3LYP/6−31+G** level. Also, by NMR calculations the ¹H, ¹³C, ³¹P chemical shifts are obtained and compared with the experimental ones.     

Internucleotide J-couplings and chemical shifts of the N-H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs

Internucleotide ^2hJ_NN spin‐spin couplings and chemical shifts (δ(¹H) and Δδ(¹⁵N)) of N? H···N H‐bond units in the natural and radiation‐damaged G‐C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G‐C pairs (viz., dehydrogenated and deprotonated G‐C pairs, GC^?? and GC^?+ radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their ^2hJ_NN spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N? H···N H‐bonds may be taken as an important criterion for prejudging whether the natural G‐C pair is radiation‐damaged or not. Analysis shows that ^2hJ_NN couplings are strongly interrelated with the energy gaps (ΔE_LP→σ*) and the second‐order interaction energies (E(2)) between the donor N lone‐pair (LP_N) and the acceptor σ^*_{N? H} localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N? H) orbital, indicating that ^2hJ_NN couplings across the N? H···N H‐bonds are charge‐transfer‐controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G‐C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

The Detection of tert-Butylthiosulfoxylic Acid,t-BuSSOH,and 1-Oxatrisulfane,HSSOH, in the Gas Phase – Experimental Results and Ab Initio Calculations

Flash vacuum pyrolysis (FVP) of tert-butylthiosulfinic acid S-tert-butylester, t-BuS(O)St-Bu, at a temperature of 500 °C and a pressure of 0.07 hPa leads to the formation of tert-butylthiosulfoxylic acid, t-BuSSOH ( 1 ), and 2-methylpropene as byproduct. 1 has been identified in the gas phase by its IR absorption bands at ν(OH) = 3598 cm^–1, δ(SOH) = 1149 cm^–1 and ν(SO) = 718 cm^–1. At higher temperatures (700 °C) the elimination of a second mole of 2-methylpropene and the shift of ν(SO) to higher wavenumbers (750 cm^–1) indicate the formation of 1-oxatrisulfane, HSSOH. Different sulfenic acids RSOH (R = Me, i-Pr, t-Bu) were synthesized by FVP in order to study the influence of the substituent R on the vibrational wavenumbers ν(OH), ν(SO) and δ(SOH) observed in the gas phase. The strongest effect results for δ(SOH) leading to a decrease by 6 wavenumbers if the methyl group is substituted by a tert-butyl group. The assignment of the experimental wavenumbers has been supported by theoretical values obtained from ab initio calculations at the MP2(fc)/6-311G** level. Furthermore, the theoretical studies show that of all compounds RS₂OR′ (R = R′ = H, Me; R = Me (H), R′ = H (Me)) the unbranched chain isomers RSSOR′ are energetically favored over the branched chain isomers. Relaxed potential energy surface scans at the MP2(fc)/6-311G** level have been carried out to study the rotational isomers of the branched molecules RS(Y)XR′ (R = R′ = H, Me; R = Me (H), R′ = H (Me); X = O (S), Y = S (O)). Of the three conformations (+)syn-clinal, (–)syn-clinal, and anti-periplanar resulting from molecular model considerations only the two latter ones correspond to local minima on the calculated potential curve. The (–)syn-clinal conformation is slightly favored for all other constitutional isomers except for HS(O)SH and MeS(O)SH, which prefer the anti-periplanar conformation.     

Structure‐Based Design of Platinum(II) Complexes as c‐myc Oncogene Down‐Regulators and Luminescent Probes for G‐Quadruplex DNA

A series of platinum(II) complexes with tridentate ligands was synthesized and their interactions with G‐quadruplex DNA within the c‐myc gene promoter were evaluated. Complex 1 , which has a flat planar 2,6‐bis(benzimidazol‐2‐yl)pyridine (bzimpy) scaffold, was found to stabilize the c‐myc G‐quadruplex structure in a cell‐free system. An in silico G‐quadruplex DNA model has been constructed for structure‐based virtual screening to develop new Pt^II‐based complexes with superior inhibitory activities. By using complex 1 as the initial structure for hit‐to‐lead optimization, bzimpy and related 2,6‐bis(pyrazol‐3‐yl)pyridine (dPzPy) scaffolds containing amine side‐chains emerge as the top candidates. Six of the top‐scoring complexes were synthesized and their interactions with c‐myc G‐quadruplex DNA have been investigated. The results revealed that all of the complexes have the ability to stabilize the c‐myc G‐quadruplex. Complex 3 a ([Pt^II L2R ] ⁺ ; L2 =2,6‐bis[1‐(3‐piperidinepropyl)‐1H‐enzo[d]imidazol‐2‐yl]pyridine, R =Cl) displayed the strongest inhibition in a cell‐free system (IC₅₀=2.2 μM ) and was 3.3‐fold more potent than that of 1 . Complexes 3 a and 4 a ([Pt^II L3R ]⁺; L3 =2,6‐bis[1‐(3‐morpholinopropyl)‐1H‐pyrazol‐3‐yl]pyridine, R =Cl) were found to effectively inhibit c‐myc gene expression in human hepatocarcinoma cells with IC₅₀ values of ≈17 μM , whereas initial hit 1 displayed no significant effect on gene expression at concentrations up to 50 μM . Complexes 3 a and 4 a have a strong preference for G‐quadruplex DNA over duplex DNA, as revealed by competition dialysis experiments and absorption titration; 3 a and 4 a bind G‐quadruplex DNA with binding constants (K) of approximately 10⁶–10⁷ dm³ mol^?1, which are at least an order of magnitude higher than the K values for duplex DNA. NMR spectroscopic titration experiments and molecular modeling showed that 4 a binds c‐myc G‐quadruplex DNA through an external end‐stacking mode at the 3′‐terminal face of the G‐quadruplex. Intriguingly, binding of c‐myc G‐quadruplex DNA by 3 b is accompanied by an increase of up to 38‐fold in photoluminescence intensity at λ_max=622 nm.     

Intrinsic Acid–Base Properties of a Hexa‐2′‐deoxynucleoside Pentaphosphate,d(ApGpGpCpCpT): Neighboring Effects and Isomeric Equilibria

The intrinsic acid‐base properties of the hexa‐2′‐deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1?G2?G3?C4?C5?T6)=(HNPP)^5?] have been determined by ¹H NMR shift experiments. The pK_a values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single‐strand conditions (i.e., 10 % D₂O, 47 °C, I=0.1 M , NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G?G), the two (N3)H⁺ (C?C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G?G) and the (N3)H (T) sites. Based on measurements with 2′‐deoxynucleosides at 25 °C and 47 °C, they were transferred to pK_a values valid in water at 25 °C and I=0.1 M . Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pK_a clusters occur, that is those encompassing the pK_a values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five‐fold protonated H₅(HNPP)^±, the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4 %, respectively. Tautomer distributions reveal pathways for proton‐donating as well as for proton‐accepting reactions both being expected to be fast and to occur practically at no “cost”. The eight pK_a values for H₅(HNPP)^± are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1?G2?G3? C4?C5?U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pK_a values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.     

Global genetic analysis of all single nucleotide polymorphisms in exons of the human deoxyribonuclease I-like 3 gene and their effect on its catalytic activity

Deoxyribonucleases (DNases) have been suggested to be implicated in the pathophysiology of autoimmune diseases. In the DNASE1L3 gene encoding human DNase I‐like 3 (DNase 1L3), a member of the DNase I family, only two non‐synonymous (R178 H and R206C) single nucleotide polymorphisms (SNPs) have been examined [Ueki et al., Clin. Chim. Acta 2009, 407, 20–24]. Three other non‐synonymous (G82R, K96N, and I243M) and four synonymous (S17S, T84T, R92R, and A181A) SNPs, in addition to R206C and R178H, have been identified in DNASE1L3. We investigated the distribution of all these SNPs in exons of the gene in eight Asian, three African, and three Caucasian populations worldwide using newly devised genotyping methods. SNP T84T showed polymorphism in all the populations, and R92R was polymorphic in the three African and three Caucasian populations; R206C was distributed only in Caucasian populations. In contrast, no minor allele was found in five SNPs (S17S, G82R, K96N, A181A, and I243M) in DNASE1L3. Generally, the DNase 1L3 gene shows relatively low genetic diversity with regard to exonic SNPs. When the effect of amino acid/nucleotide substitutions resulting from the SNPs on DNase 1L3 activity was examined, none of the synonymous SNPs had any effect on the DNase 1L3 activity, whereas among non‐synonymous SNPs, SNP G82R diminished the activity of the enzyme, being similar to R206C. These findings permit us to assume that, although only R206 exhibits polymorphisms in a Caucasian‐specific manner, at least SNPs G82R and R206C in DNASE1L3 might be potential risk factors for autoimmune disease.     

Exploring the Border between Concerted and Two‐Step Pathways of 1,3‐Dipolar Cycloadditions of Organic Azides to Cyclic Ketene N,X‐Acetals. – Synthesis and 15N‐NMR Spectra of Zwitterions and Spirocyclic Cycloadducts

Cyclic ketene N,X‐acetals 1 are electron‐rich dipolarophiles that undergo 1,3‐dipolar cycloaddition reactions with organic azides 2 ranging from alkyl to strongly electron‐deficient azides, e.g., picryl azide ( 2L ; R¹=2,4,6‐(NO₂)₃C₆H₂) and sulfonyl azides 2M – O (R¹=XSO₂; cf. Scheme 1). Reactions of the latter with the most‐nucleophilic ketene N,N‐acetals 1A provided the first examples for two‐step HOMO(dipolarophile)–LUMO(1,3‐dipole)‐controlled 1,3‐dipolar cycloadditions via intermediate zwitterions 3 . To set the stage for an exploration of the frontier between concerted and two‐step 1,3‐dipolar cycloadditions of this type, we first describe the scope and limitations of concerted cycloadditions of 2 to 1 and delineate a number of zwitterions 3 . Alkyl azides 2A – C add exclusively to ketene N,N‐acetals that are derived from 1H‐tetrazole (see 1A ) and 1H‐imidazole (see 1B , C ), while almost all aryl azides yield cycloadducts 4 with the ketene N,X‐acetals (X=NR, O, S) employed, except for the case of extreme steric hindrance of the 1,3‐dipole (see 2E ; R¹=2,4,6‐(^tBu)₃C₆H₂). The most electron‐deficient paradigm, 2L , affords zwitterions 16D , E in the reactions with 1A , while ketene N,O‐ and N,S‐acetals furnish products of unstable intermediate cycloadducts. By tuning the electronic and steric demands of aryl azides to those of ketene N,N‐acetals 1A , we discovered new borderlines between concerted and two‐step 1,3‐dipolar cycloadditions that involve similar pairs of dipoles and dipolarophiles: 4‐Nitrophenyl azide ( 2G ) and the 2,2‐dimethylpropylidene dipolarophile 1A (R, R=H, ^tBu) gave a cycloadduct 13 H , while 2‐nitrophenyl azide ( 2 H ) and the same dipolarophile afforded a zwitterion 16A . Isopropylidene dipolarophile 1A (R=Me) reacted with both 2G and 2 H to afford cycloadducts 13G , J ) but furnished a zwitterion 16B with 2,4‐dinitrophenyl azide ( 2I) . Likewise, 1A (R=Me) reacted with the isomeric encumbered nitrophenyl azides 2J and 2K to yield a cycloadduct 13L and a zwitterion 16C , respectively. These examples suggest that, in principle, a host of such borderlines exist which can be crossed by means of small structural variations of the reactants. Eventually, we use ¹⁵N‐NMR spectroscopy for the first time to characterize spirocyclic cycloadducts 10 – 14 and 17 (Table 6), and zwitterions 16 (Table 7).     

Are there reliable DFT approaches for 13C NMR chemical shift predictions of fullerene C60 derivatives?

The relationships between experimental and theoretical ¹³C NMR chemical shifts of a pristine fullerene C₆₀, monoadducts from [2 + n] cycloaddition (n = 1–3), and one [2 + 1] bis‐adduct are systematically analyzed for the first time by using diverse quantum‐chemical levels of theory. These levels involved B3LYP, B3PW91, B97‐2, mPW1PW91, PBE1PBE, and X3LYP hybrid functionals combined with 3‐21G, 6‐31G, 6‐31G(d), 6‐31G(d,p), 6‐31G(d,2p), LanL2DZ, and SDDAll basis sets. X3LYP/6‐31G approach is determined to have the lowest deviations from the ¹³C NMR experimental data compared to the other methods for all the fullerene compounds (mean absolute error value is 0.856 ppm and root mean squared error value is 1.197 ppm). The highest deviations are characteristic for α (sp² C2/C5/C8/C10) and β (sp² C6/C7/C11/C12) carbon atoms relative to a functionalization site and for those (sp³ C1/C9) directly attached with a side fragment in the [2 + n] monoadducts (n = 1–3). A probable reason of such deviation is that the approaches do not take into account a contribution of paramagnetic ring currents to ¹³C NMR chemical shifts. The results will be useful in design of novel fullerene derivatives and in performing unambiguous ¹³C NMR chemical shift assignments with modern quantum chemistry calculations.     

An Air- and Water-Stable Hydrogen-Bond-Donor Catalyst for the Enantioselective Generation of Quaternary Carbon Stereocenters by Additions of Substituted Cyanoacetate Esters to Acetylenic Esters

The chiral enantiopure cobalt(III) complex Δ-[Co((S,S)-dpen)₃]³⁺ 2Cl⁻B(C₆F₅)₄⁻ (Δ-(S,S)- 2 ³⁺ 2Cl⁻B(C₆F₅)₄⁻; dpen=1,2-diphenylethylenediamine) is an effective catalyst, together with pyridine (10 mol % each), for enantioselective additions of substituted cyanoacetate esters NCCH(R)CO₂R′ to acetylenic esters R′′C≡CCO₂R′′′. In the resulting adducts NC(R′O₂C)C(R)CR′′C=CHCO₂R′′′, C=C isomers in which the CO₂R′′′ moiety is trans to the new carbon–carbon bond dominate (avg. ratio 98:2). These are obtained in 70–98 % ee (avg. 86 %; data for optimum R′ and R′′′), as determined by ¹H NMR with the chiral solvating agent Λ-(S,S)- 2 ³⁺ 2I⁻B(3,5-C₆H₃(CF₃)₂)₄⁻. NMR experiments show that the cyanoacetate and acetylenic esters and pyridine can hydrogen bond to certain NH groups of the catalyst. Rates are zero order in the cyanoacetate and acetylenic esters as well as the catalyst, and implications are discussed.     

Fragmentation of isomeric intrastrand crosslink lesions of DNA in an ion-trap mass spectrometer

The collision-induced dissociation pathways of isomeric cytosine-guanine and cytosine-adenine intrastrand crosslink-containing dinucleoside monophosphates were investigated with the stable isotope-labeled compounds to gain insights into the effects of chemical structure on the fragmentation pathways of these DNA modifications. A Dimroth-like rearrangement, which was reported for protonated 2′-deoxycytidine and involved the switching of the exocyclic N4 with the ring N3 nitrogen atom, was also observed for the cytosine component in the protonated ions of C[5–8]G, C[5–2]A, and C[5–8]A, but not C[5-N ²]G or C[5-N ⁶]A. In these two sets of crosslinks, the C5 of cytosine is covalently bonded with its neighboring purine base via a carbon atom on the aromatic ring and an exocyclic nitrogen atom, respectively. On the contrary, the rearrangement could occur for the deprotonated ions of C[5-N ²]G, C[5-N ⁶]A, and unmodified cytosine, but not C[5–8]G, C[5–2]A, or C[5–8]A. In addition, ammonia could be lost more readily from C[5-N ²]G and C[5-N ⁶]A than from C[5–8]G, C[5–2]A, and C[5–8]A. The results from the present study afforded important guidance for the application of mass spectrometry for the structure elucidation of other intrastrand/interstrand crosslink lesions.     

Functional carbo‐Butadienes: Nonaromatic Conjugation Effects through a 14‐Carbon, 24‐π‐Electron Backbone

A systematic study of carbo‐butadiene motifs not embedded in an aromatic carbo‐benzene ring is described. Dibutatrienylacetylene (DBA) targets R¹?C(R)?C?C?C(Ph)?C≡C?C(Ph)?C?C?C(R)?R² are devised, in which R is C≡CSiiPr₃ and R¹ and R² are R, H, or 4‐X‐C₆H₄, with the latter including three known representatives (X: H, NMe₂, or NH₂). The synthesis method is based on the SnCl₂‐mediated reduction of pentaynediols prepared by early or late divergent strategies; the latter allows access to a OMe–NO₂ push–pull diaryl‐DBA. If R¹ and R² are H, an over‐reduced dialkynylbutatriene (DAB) with two allenyl caps was isolated instead of the unsubstituted DBA. If R¹=R²=R, the tetraalkynyl‐DBA target was obtained, along with an over‐reduced DBA product with a 12‐membered 1,2‐alkylidene‐1H₂,2H₂‐carbo‐cyclobutadiene ring. X‐ray crystallography shows that all of the acyclic DBAs adopt a planar trans–transoid–trans configuration. The maximum UV/Vis absorption wavelength is found to vary consistently with the overall π‐conjugation extent and, more intriguingly, with the π‐donor character of the aryl X substituents, which varies consistently with the first (reversible) reduction potential and first (irreversible) oxidation peak, as determined by voltammetry.     

Rearrangements in Model Peptide‐Type Radicals via Intramolecular Hydrogen‐Atom Transfer

Intramolecular H‐atom transfer in model peptide‐type radicals was investigated with high‐level quantum‐chemistry calculations. Examination of 1,2‐, 1,3‐, 1,5‐, and 1,6[C ? N]‐H shifts, 1,4‐ and 1,7[C ? C]‐H shifts, and 1,4[N ? N]‐H shifts (Scheme 1), was carried out with a number of theoretical methods. In the first place, the performance of UB3‐LYP (with the 6‐31G(d), 6‐31G(2df,p), and 6‐311+G(d,p) basis sets) and UMP2 (with the 6‐31G(d) basis set) was assessed for the determination of radical geometries. We found that there is only a small basis‐set dependence for the UB3‐LYP structures, and geometries optimized with UB3‐LYP/6‐31G(d) are generally sufficient for use in conjunction with high‐level composite methods in the determination of improved H‐transfer thermochemistry. Methods assessed in this regard include the high‐level composite methods, G3(MP2)‐RAD, CBS‐QB3, and G3//B3‐LYP, as well as the density‐functional methods B3‐LYP, MPWB1K, and BMK in association with the 6‐31+G(d,p) and 6‐311++G(3df,3pd) basis sets. The high‐level methods give results that are close to one another, while the recently developed functionals MPWB1K and BMK provide cost‐effective alternatives. For the systems considered, the transformation of an N‐centered radical to a C‐centered radical is always exothermic (by 25 kJ ? mol^?1 or more), and this can lead to quite modest barrier heights of less than 60 kJ ? mol^?1 (specifically for 1,5[C ? N]‐H and 1,6[C ? N]‐H shifts). H‐Migration barriers appear to decrease as the ring size in the transition structure (TS) increases, with a lowering of the barrier being found, for example when moving from a rearrangement proceeding via a four‐membered‐ring TS (e.g., the 1,3[C ? N]‐H shift, CH₃? C(O)? NH^. → ^.CH₂? C(O)? NH₂) to a rearrangement proceeding via a six‐membered‐ring TS (e.g., the 1,5[C ? N]‐H shift, ^.NH? CH₂? C(O)? NH? CH₃ → NH₂? CH₂? C(O)? NH? CH₂^.).     

Synthesis of 1‐silacyclopent‐2‐ene derivatives using 1,2‐hydroboration, 1,1‐organoboration and protodeborylation

The reaction of di(alkyn‐1‐yl)vinylsilanes R¹(H₂C═CH)Si(C≡C―R)₂ (R¹ = Me ( 1 ), Ph ( 2 ); R = Bu (a), Ph (b), Me₂HSi (c)) at 25°C with 1 equiv. of 9‐borabicyclo[3.3.1]nonane (9‐BBN) affords 1‐silacyclopent‐2‐ene derivatives ( 3a , 3b , 3c , 4a , 4b ), bearing one Si―C≡C―R function readily available for further transformations. These compounds are formed by consecutive 1,2‐hydroboration followed by intramolecular 1,1‐carboboration. Treated with a further equivalent of 9‐BBN in benzene they are converted at relatively high temperature (80–100°C) into 1‐alkenyl‐1‐silacyclopent‐2‐ene derivatives ( 5a , 5b 6a , 6b ) as a result of 1,2‐hydroboration of the Si―C≡C―R function. Protodeborylation of the 9‐BBN‐substituted 1‐silacyclopent‐2‐ene derivatives 3 , 4 , 5 , 6 , using acetic acid in excess, proceeds smoothly to give the novel 1‐silacyclopent‐2‐ene ( 7 , 8 , 9 , 10 ). The solution‐state structural assignment of all new compounds, i.e. di(alkyn‐1‐yl)vinylsilanes and 1‐silacyclopent‐2‐ene derivatives, was carried out using multinuclear magnetic resonance techniques (¹H, ¹³C, ¹¹B, ²⁹Si NMR). The gas phase structures of some examples were calculated and optimized by density functional theory methods (B3LYP/6‐311+G/(d,p) level of theory), and ²⁹Si NMR parameters were calculated (chemical shifts δ²⁹Si and coupling constants ⁿJ(²⁹Si,¹³C)). Copyright © 2014 John Wiley & Sons, Ltd.     

Time‐Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome‐Related Photoreceptors

Time‐resolved photoacoustics (PA) is uniquely able to explore the energy landscape of photoactive proteins and concomitantly detects light‐induced volumetric changes (ΔV) accompanying the formation and decay of transient species in a time window between ca. 20 ns and 5 μs. Here, we report PA measurements on diverse photochromic bilin‐binding photoreceptors of prokaryotic origin: (1) the chromophore‐binding GAF3 domain of the red (R)/green (G) switching cyanobacteriochrome 1393 (Slr1393g3) from Synechocystis; (2) the red/far red (R/FR) Synechocystis Cph1 phytochrome; (3) full‐length and truncated constructs of Xanthomonas campestris bacteriophytochrome (XccBphP), absorbing up to the NIR spectral region. In almost all cases, photoisomerization results in a large fraction of energy dissipated as heat (up to 90%) on the sub‐ns scale, reflecting the low photoisomerization quantum yield (<0.2). This “prompt” step is accompanied by a positive ΔV₁ = 5–12.5 mL mol^?1. Formation of the first intermediate is the sole process accessible to PA, with the notable exception of Slr1393g3‐G for which ΔV₁ = +4.5 mL mol^?1 is followed by a time‐resolved, energy‐conserving contraction ΔV₂ = ?11.4 mL mol^?1, τ₂ = 180 ns at 2.4°C. This peculiarity is possibly due to a larger solvent occupancy of the chromophore cavity for Slr1393g3‐G.     

Contracted helix to stretched helix Rearrangement of an aromatic polyacetylene prepared in n‐hexane with [Rh(norbornadiene)Cl]2‐triethylamine catalyst

p‐n‐Heptylphenylacetylene (pHepPA) was stereoregularly polymerized in n‐hexane at 25 °C using [Rh(nbd)Cl]₂ catalyst (nbd: norbornadiene) and NEt₃, affording the purple‐red Poly( R ) in 97% yield. A 80 °C heat treatment transformed Poly( R ) to the black Poly( B ). The Poly( R ) X‐ray diffraction (XRD) pattern revealed a hexagonal crystal structure comprising contracted cis‐cisoid helices [ ^Hexa Poly( R ) ^CC ]. The 80 °C heat treatment generated two tetragonal crystals: ^Tetra Poly( B ) ^CC containing contracted cis‐cisoid helices and ^Tetra Poly( B ) ^CT containing stretched cis‐transoid helices. The helical diameters before and after heat treatment were estimated using XRD and were consistent with molecular mechanics calculations (MMFF94 force field method). When heated at 80 °C in the solid phase, the λ_max in the diffuse reflective UV–vis spectra of ^Hexa Poly( R ) ^CC shifted from 482 to 560 nm. Additionally, an endothermic transition occurred in the ^Hexa Poly( R ) ^CC differential scanning calorimetric trace at ～80 °C. Therefore, these data corroborated the assertion that ^Hexa Poly( R ) ^CC thermally converted to ^Tetra Poly( B ) ^CC and ^Tetra Poly( B ) ^CT . © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 5177–5183