Rotational spectra and computational analysis of two conformers of leucinamide

Rotational spectra were recorded for two isotopic species of two conformers of the amide derivative of leucine in the range of 10.5-21 GHz and fit to a rigid rotor Hamiltonian. Ab initio calculations at the MP2/6-311++G(d,p) level identified the low energy conformations with different side chain configurations; the rotational spectra were assigned to the two lowest energy ab initio structures. We recorded 16 a- and b-type rotational transitions for conformer 1; the rotational constants of the normal species are A = 2275.6(2), B = 1033.37(2) and C = 911.71(5) MHz. We recorded 23 a- and b-type rotational transitions for conformer 2; the rotational constants of the normal species are A = 2752.775(8), B = 843.502(1) and C = 796.721(1) MHz. The rotational spectra of the (15)N(amide) isotopomer of each conformer were recorded and the atomic coordinates of the amide nitrogen were determined by Kraitchman's method of isotopic substitution. The experimentally observed structures are significantly different from the crystal structures of leucinamide and the gas-phase structures of leucine, and a natural bond orbital analysis revealed the donor-acceptor interactions governing side chain configuration.     

Hyperfine splittings in spin-frustrated trinuclear Cu(3) clusters

The hyperfine structures of the EPR spectra of the spin-frustrated and distorted Cu(II) trimers were calculated in the spin-coupling model. The correlations between the hyperfine structures of the EPR spectra and geometry of the Cu(3) clusters (equilateral, isosceles, and scalene triangles) were found. For the EPR spectrum of the spin-frustrated ground state 2(S = 1/2) of an equilateral triangle Cu(3) cluster (J(12) = J(13) = J(23) = J), the calculated hyperfine structure represents the complicated spectrum of the 24 hyperfine lines, of total length 5a, where a is the hyperfine constant of the mononuclear Cu center. For an isosceles Cu(3) cluster (J(12) not equal J(13) = J(23)), the hyperfine splittings of the EPR spectra of the two split S = 1/2 levels with intermediate spins S(12) = 0 and S(12) = 1 are essentially different. The EPR signal of the |(S(12) = 0)S = 1/2> level is characterized by the four equally spaced hyperfine lines (interval A = a) with the same relative spectral amplitudes 16:16:16:16 and total length 3a. For the |(S(12) = 1)S = 1/2> level, the calculated hyperfine structure represents the spectrum of the 16 hyperfine lines with equal spacing (interval A' = a/3), the spectral intensity distribution 1:1:3:3:5:5:7:7:7:7:5:5:3:3:1:1 and total length 5a. These hyperfine spectra differ from the hyperfine structure (10 lines with interval a/3) of the EPR signals of the excited S = 3/2 level of the Cu(3) cluster. The quartet hyperfine structure, characteristic of a single Cu(2+) nucleus, which was observed experimentally for the doublet ground state of the spin-frustrated Cu(3)(II) clusters, corresponds to the hyperfine structure of the EPR signal of the |(S(12) = 0)S = 1/2> level. This hyperfine structure is evidence of the lowering of the Cu(3) cluster symmetry from trigonal to orthorhombic and the small splitting of the spin-frustrated 2(S = 1/2) ground state.     

Synthesis of Biocompatible Glycodendrimer based on Fluorescent Perylene Bisimides and Its Bioimaging

A novel water‐soluble fluorescent glycodendrimer based on perylene bisimides is synthesized, which exhibits high fluorescence quantum yield of 54%. While the binding interactions of PBI‐Man with Concanavalin A (Con A) are studied by fluorescence spectra and CD spectra, which show strong binding affinity for Con A with the binding constant of 3.8 × 10⁷m ⁻¹ for monomeric mannose, nearly four orders of magnitude higher affinity than the monovalent mannose ligand. Furthermore, the fluorescence imaging of macrophage cell with PBI‐Man is investigated, and shows selectively binding interaction with the mannose receptor‐medicated cell entry. Moreover, the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide (MTT) activities of PBI‐Man show that PBI‐Man as a biocompatible agent is noncytotoxic to living cells.

     

Phase-resolved fluorimetric determination of two albumin-bound fluorescein species

A new approach is described for phase-resolved fluorescence spectroscopy, for use in resolving mixtures of two components with very similar fluorescence spectra and life-times. Results are given for application of the technique to solutions containing fluorescein physically bound to albumin and fluorescein isothiocyanate covalently bound to albumin. Because the two fluorescein species have essentially identical fluorescence spectra and a phase-angle difference of only 2°, the conventional phase-resolved method in which measurements are made at the two phase angles at which the fluorescence contribution from one or the other of the components is zero will not resolve the components. Solutions containing 25–50 nM of each component were successfully resolved by making measurements at two other phase angles and solving the pair of simultaneous equations that is generated. Accuracy is best (average relative error, 3%) using detector phase angles corresponding to a 45° shift from the phase angles of the components. Relative standard deviations of ±16% are obtained at these phase angles. Solutions containing 5–50 nM fluorescein and 50–500 nM fluorescein isothiocyanate conjugated to albumin could also be resolved, with an average relative error of 16% and ±2.4 r.s.d. The method could be used for simultaneous determination of a fluorophore in two different microenvironments, as in protein-ligand binding studies and in homogeneous immunoassay.     

NMR Parameters and Vibrational Investigation of 2-Dicyanovinyl-5-（4-ethoxyphenyl） thiophene by ab initio HF and DFT Calculations

Optimized geometry and harmonic vibrational frequency of 2-dicyanovinyl-5-(4- ethoxyphenyl)thiophene (C16H12N2OS) are calculated at the HF/6-31++G(d,p) and B3LYP/6- 311++G(d,p) levels. Mulliken charges in the ground state are also calculated. The research shows the presence of intermolecular interaction in the title compound. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. A detailed interpretation of the infrared spectra of the title compound is reported. The theoretical spectrograms for IR spectra of the title compound have been constructed. The isotropic chemical shift computed by 13C and 1H NMR analyses also shows good agreement with the experimental observations.     

Spectroscopic properties of rare earth borohydrides: Er(BH4)3·3THF in pure and mixed crystals

The optical spectra of Er(BH₄)₃·3THF neat crystals and La, Gd, Y(BH₄)₃·3THF mixed crystals are reported and analyzed. Lanthanum borohydride is found to have a different room temperature crystal structure (triclinic) from Er, Gd, Y(BH₄)₃·3THF (Pbcn). At low temperature the Pbcn crystals undergo a phase transition to a structure with two crystallographically inequivalent sites in a unit cell. The optical spectra of Er(BH₄)₃·3THF in Er, Y, Gd(BH₄)₃·3THF crystals clearly evidence these two sites. Large vibronic intensity is observed at 1.6 K and 77 K and nine “molecular” vibrations are assigned. These modes are quite similar to those found for U(BH₄)₄. Er (BH₄)₃·3THF spectra are very different: no vibronic transitions are observed but many (often upwards of fifty for a given manifold) weak sharp “satellite” lines are found associated with pure electronic transitions. These data are discussed in terms of structural differences and comments on bonding and covalent character in lanthanide borohydrides are made.     

Synthesis and physicochemical properties of new fluorescent derivatives of cytosine

Sixteen new fluorescent N⁴‐(E)‐stilbenyloxyalkylcarbonyl‐cytosines 9–16 and N⁴‐(E)‐stilbenyloxyalkylcarbonyl‐1‐methylcytosines 17–24 have been synthesized. The differences in ¹H and ¹³C NMR spectra in two solvents (DMSO and TFA) have been pointed out and discussed. Assignment of the signals in the spectra of the compounds 9–24 in NMR in DMSO‐d₆ solutions has been made the basis of the homonuclear (COSY) and heteronuclear (HETCOR) spectra. The effect of the substituent (Cl, Br, NO₂) on the stilbene moiety on the fluorescence spectrum of each compound has been discussed.     

A density functional theory study of the structure and vibrational spectra of beta-carotene, capsanthin, and capsorubin

A theoretical study of the structure and the vibrational spectra of the beta-carotene molecule and its derivatives capsanthin and capsorubin is carried out. We first investigate systematically the theoretical method which provides the best results for beta-carotene by performing ab initio calculations at the HF/6-31G(d), SVWN/6-31G(d), PBE0/6-31G(d), BLYP/6-31G(d), B3LYP/6-31G(d), B3LYP/6-31G(d,p), B3LYP/6-311G(d), and B3LYP/6-311G(d,p) levels and by using previous theoretical results available in the literature obtained at the AM1 and BPW91/6-31G(d) levels. The influence of both the level of calculation and the size of the basis set used in the geometry optimization and in the determination of the IR and Raman spectra of this molecule is thus analyzed. It is confirmed that the hybrid functional B3LYP with the basis 6-31G(d) is the method that gives the best results as a whole. By use of this level of calculation, we next optimize the molecular geometries of related molecules of capsanthin and capsorubin, which to the best of our knowledge have only been studied at the semiempirical AM1 level. In addition we calculate the IR and Raman spectra of these molecules at the B3LYP/6-31G(d) level of theory. The results obtained for capsanthin show on the one hand that the double bond of the beta-ionone ring is outside the polyene chain plane, due to the repulsion between the hydrogen atoms of the ring methyl groups and the hydrogen atoms of the polyene chain, and on the other hand that the carbonyl double bond in the other headgroup is very close to planarity with the polyene chain, since in this case such a repulsion does not exist. For the molecule of capsorubin the two carbonyl groups also take the same coplanar orientation relative to the polyene chain. The IR and Raman spectra theoretically computed for these two molecules are finally compared with their experimental spectra and the vibrational normal modes of the main signals are interpreted.     

Conformational and structural studies of ethyl fluorosilane from temperature dependent FT-IR spectra of krypton solutions and ab initio calculations

The infrared spectra (3200–30 cm⁻¹) of gaseous and solid ethyl fluorosilane, CH₃CH₂SiH₂F, have been recorded. Additionally, the Raman spectra (3200–30 cm⁻¹) of the liquid and solid have been recorded and quantitative depolarization values obtained. Both the gauche and trans conformers have been identified in the fluid phases but only the gauche conformer remains in the solid. Variable temperature (−105 to −150°C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data, the enthalpy difference has been determined to be 54±16 cm⁻¹ (646±191 J/mol) with the gauche conformer the more stable form. This is consistent with the predictions from ab initio, MP2/6-311+G(2d,2p), calculation as well as those with smaller basis sets with full electron correlations. A complete vibrational assignment is proposed for both the trans and gauche conformers based on infrared band contours, relative intensities, depolarization values, and group frequencies, which are supported by normal-coordinate calculations utilizing the force constants from MP2/6-31G(d) ab initio calculations. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing a variety of basis sets up to 6-311+G(2d,2p) at levels of restricted Hartree–Fock (RHF) and/or Moller Plesset to the second order (MP2) with full electron correlation. The adjusted r₀ parameters have been obtained for both conformers from a combination of the previously reported rotational constants with ab initio predicted values. All results are compared to similar quantities of some corresponding molecules.     

Recent topics in annulation reaction via double CH bond cleavage and double CC bond formation

Cyclic compounds have been consistently key components in organo functional molecules. To construct cycles, a catalytic two CH bond-cleaving annulation is one of the most ideal and straightforward methods with atom and step economies. Recently, many patterns of such annulation reactions have been developed, which construct a variety of cyclic compounds consisted of from simple to complex frameworks. This Digest focuses a recent progress in two or more than three CH bond-cleaving annulation reactions and is outlined as follows: (1) intramolecular annulation, (2) intermolecular annulation via double CH bond cleavages in one molecule, and (3) intermolecular annulation via double CH bond cleavages in two molecules.     

Synthesis and radical ring-opening polymerization of spiro o-carbonates

Syntheses and radical ring-opening polymerization of spiro o-carbonates(I-IV) were investigated. These polymers were yellow powders and soluble in common organic solvents. The infrared and NMR spectra indicated that the polymers were alternate copolymers of either and carbonate containing double bonds. The polymerization mechanism is discussed.     

NMR spectra of salicylohydroxamic acid in DMSO-d6 solution: a DFT study

The ¹H, ¹³C and ¹H, ¹³C COSY NMR spectra of salicylohydroxamic acid (sha) were measured in DMSO-d₆ solution. The B3LYP GIAO method with the 6-311++G(d,p) basis set was chosen to reproduce the experimental spectra. All possible zusammen and entgegen conformers of monomeric sha were computed. After geometry optimisation (B3LYP/6-311++G(d,p)) only nine independent models of the molecule were shown to be stable. Additionally, the NMR chemical shifts of the Onsager model of the most stable monomer were calculated. The computed chemical shifts for the labile protons for all aforementioned geometries meaningfully underestimated experimental results suggesting the existence of the H-bonded structure of sha in DMSO solution. The most probable two dimeric structures along with two solvent-bounded aggregates were subsequently calculated at the same level of theory. The best agreement was obtained for sha H-bonded with two DMSO molecules (confirmed by the absence of concentration effect). The relative error not exceeding 10 and 4% for chemical shifts in ¹H and ¹³C NMR spectra of sha–(DMSO)₂, respectively, showed that the applied method with the B3LYP/6-311++G(d,p) basis set was efficient to predict the NMR shifts of a compound with strong H-bonds. Thus, this allows to assign properly NMR resonances to specific structure formed in DMSO solution.     

Fingerprint patterns from laser-induced Azido photochemistry of spin-labeled photoaffinity ATP analogs in matrix-assisted laser desorption/ionization mass spectrometry

The photochemical reaction of azide derivatives induced by ultraviolet (UV) laser in matrix-assisted laser desorption/ionization mass spectrometry (MALDI) is reported. A novel synthesized class of azide aromatic derivatives, spin-labeled photoaffinity non-nucleoside adenosine triphosphate (ATP) analogs which are useful probes in study of muscle contraction mechanism, is used in this investigation. In the negative ion MALDI spectra of these ATP analogs, “fingerprint” peaks corresponding to [M − 10 − 1]⁻, [M − 12 − 1]⁻, [M − 16 − 1]⁻, [M − 26 − 1]⁻, [M − 28 − 1]⁻, [M − 41 − 1]⁻, and [M − 42 − 1]⁻ were observed with relative intensities depending on the MALDI matrix. Only the [M − 16 − 1]⁻ is present in the similar mass spectra of the analog in which the azido group is replaced by a hydrogen. A model is suggested for the photochemical reactions of azide derivatives under UV laser irradiation. The photoreaction fingerprint information is diagnostically useful in characterization of azido compounds, especially for spin-labeled photoaffinity non-nucleoside ATP analogs.     

Theoretical investigation into optical and electronic properties of oligothiophene derivatives with phenyl ring as core or end-capped group in linear and V-shape

A series of thiophene-based oligomers has been designed to explore their optical, electronic, and charge transport properties for charge transport materials. These oligomers consist of oligothiophene, oligo(thienylenevinylene), and m- or p-phenyl as the core in two shapes (linear shape and V-shape). Phenyl ring as the end-capped group is also investigated in the linear shape. The DFT-PBE0/6-31G(d,p) and the TD-PBE0/6-31+G(d,p) calculated results reported herein show that the V-shape oligomers have larger HOMO-LUMO gaps because of meta-substitutions on phenyl cores, corresponding to blue shifts of absorption spectra. The linear oligomers with phenyl ring as end-capped group display red shifts of absorption spectra. The V-shape oligomers provide small reorganization energies. Our recommended polymer possessing 1,2,4-phenyl core and longer OTV side fragments is a good candidate for the design of charge transport and/or solar cell materials.     

Structural assignment of regioisomeric 3-[2- or 5-anilino-2-(alkylamino)phenyl]propanoic acids, 2H-1,4-benzothiazin-3(4H)-ones and 2,3-dihydro-1,5-benzothiazepin-4(5H)-ones by 1D NOE and gHMBC NMR techniques

The 1H and 13C NMR spectra of compounds 1-11 and 16-22 in CDCl3 and DMSO-d6 solutions allowed structural assignment to regioisomers 1/5 and 2/6 and their regioselective cyclization products 16-18 utilizing one- and two-dimensional NMR techniques (APT, DEPT, NOE difference, COSY, NOESY, HETCOR and gHMQC, gHMBC). Temperature-dependent 1H NMR spectra of 8-anilino-5-(4-methyl-2-pentyl)-2,3-dihydro-1,5-benzothiazepin-4(5H)-one (18) indicated a free energy of activation (deltaG++) of ca 17 kcal mol(-1) for interconversion between rotamers. The 1H and 13C NMR spectra of 20 and 22 containing two chiral centers exhibit duplication of several signals, indicating the existence of two diastereomeric forms. The structure of 4 was unambiguously confirmed by x-ray crystallography.     

Syntheses, crystal structures and electronic properties of a series of copper(II) complexes with 3,5-halogen-substituted Schiff base ligands and their solutions

We have systematically investigated the structural features, electronic properties, thermally-induced structural phase transitions and absorption spectra depending on the solvent for ten Cu(II) complexes with 3,5-halogen-substituted Schiff base ligands. Structural characterization of two new complexes, bis(N-R-1-phenylethyl- and N-R,S-2-butyl-5-bromosalicydenaminato-κ²N,O)copper(II), reveals that they afford a compressed tetrahedral trans-[CuN₂O₂] coordination geometry with trans-N–Cu–N = 159.4(2)° and trans-O–Cu–O = 151.7(3)° for the 1-phenylethyl complex and trans-N–Cu–N = 157.9(3)° and trans-O–Cu–O = 151.0(3)° for the 2-butyl one. All the complexes exhibit a structural phase transition by heating in the solid state regardless of their structures at room temperature. The absorption spectra of a series of ten complexes exhibit a slight shift of the d–d band at 16 000–20 000 cm⁻¹ and remarkable shift of the π–π* band at 24 000–28 000 cm⁻¹, which suggests that the dipole moment of the solvents presumably affects the conformation of the π-conjugated moieties of the ligands rather than the coordination environment. We have also attempted ‘photochromic solute-induced solvatochromism’ by a system of bis(N-R-1-phenylethyl-3,5-dichlorosalicydenaminato-κ²N,O)copper(II) and photochromic 4-hydroxyazobenzene in chloroform solution. We successfully observed a change of the d–d and π–π* bands of the complex in the absorption spectra caused by cis–trans photoisomerization of 4-hydroxyazobenzene.     

Density functional theory investigations on the conformational stability and vibrational spectra of the model compound of vitamin K

Becke 3-Lee–Yang–Parr density functional theory (DFT/B3LYP) using 6-31G(d) and 6-311G(d) basis sets and the scaled quantum mechanics (SQM) force field method are used to study molecular conformations and vibrational spectra of a model compound of vitamin K (VK). In this molecule, there are six conformers on the torsional potential energy map of the dihedral angles C₈C₁₄C₁₅C₁₆ () and C₇C₈C₁₄C₁₅ (β). It is shown that the VK_1 conformer ( = 237.7° and β = 274.2°) is the most stable form. For this lowest energy conformer, the harmonic force fields calculated by B3LYP/6-311G(d) and B3LYP/6-31G(d) methods are scaled with one scale factor of 0.9623 and a set of different scale factors transferred from the previous studies for the other similar molecules, respectively. The vibrational frequencies, IR intensities, and Raman activities are obtained for the lowest energy conformer. On the basis of B3LYP calculations, the normal mode analysis is performed to assign the vibrational fundamental frequencies according to the potential energy distributions. The computational frequencies are in good agreement with the observed results.     

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

We report electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD) of doubly protonated and protonated/alkali metal ionized oligodeoxynucleotides. Mass spectra following ECD of the homodeoxynucleotides polydC, polydG, and polydA contain w or d "sequence" ions. For polydC and polydA, the observed fragments are even-electron ions, whereas radical w/d ions are observed for polydG. Base loss is seen for polydG and polydA but is a minor fragmentation pathway in ECD of polydC. We also observe fragment ions corresponding to w/d plus water in the spectra of polydC and d(GCATGC). Although the structure of these ions is not clear, they are suggested to proceed through a pentavalent phosphorane intermediate. The major fragment in ECD of d(GCATGC) is a d ion. Radical a- or z-type fragment ions are observed in most cases. IRMPD primarily results in base loss, but backbone fragmentation is also observed. IRMPD provides more sequence information than ECD, but the spectra are more complex due to extensive base and water losses. It is proposed that the smaller degree of sequence coverage in ECD, with fragmentation mostly occurring close to the ends of the molecules, is a consequence of a mechanism in which the electron is captured at a P=O bond, resulting in a negatively charged phosphate group. Consequently, at least two protons (or alkali metal cations) must be present to observe a w or d fragment ion, a requirement that is less likely for small fragments.