Superiority of a new gradient system utilizing a critical threshold for the adsorption capacity of polypeptides to column packing when compared with a standard gradient system for the simultaneous and quantitative analysis of polypeptides

Compared with a standard gradient system, the new gradient system which we developed has a major advantage because it permits a wide range of acetonitrile content, e.g. more than the critical threshold, in the polypeptide solution and allows the quantitative analysis of the polypeptide with satisfactory analytical precision. Additionally, this new gradient system allows the enhancement of the sensitivity of the polypeptide analysis proportionate to the increased volume of solution loaded with the same levels of precision. In contrast, when using a standard gradient system it is difficult to analyze a polypeptide quantitatively with good precision due to either adsorption to various materials or to irregular change in the ratio between a retained and a passed peak of the polypeptide. Additionally, the appearance of a passed peak results in a loss in the sensitivity of the polypeptide analysis, although no adsorption of a polypeptide to various materials occurs in a solution with acetonitrile content more than the critical threshold. Consequently, the new gradient system is effective for the simultaneous and quantitative analysis of different polypeptides with good precision and without any loss of sensitivity due to either adsorption to various materials or the appearance of a passed peak.     

A quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution based on the framework of mixed quantum-classical molecular dynamics

We present a quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution in the framework of mixed quantum-classical molecular dynamics, where the reactant and product states are explicitly defined by dividing the double-well potential into the reactant and product wells. The equation can describe quantum reaction processes such as tunneling and thermal excitation and relaxation assisted by the solvent. Fluctuations of the zero-point energy level, the height of the barrier, and the curvature of the well are all included in the equation. Here, the equation was combined with the surface hopping technique in order to describe the motion of the classical solvent. Applying the present method to model systems, we show two numerical examples in order to demonstrate the potential power of the present method. The first example is a proton transfer by tunneling where the high-energy product state was stabilized very rapidly by solvation. The second example shows a thermal activation mechanism, i.e., the initial vibrational excitation in the reactant well followed by the reacting transition above the barrier and the final vibrational relaxation in the product well.     

Photoelectron spectroscopy of cluster anions of naphthalene and related aromatic hydrocarbons

The electronic structures and structural morphologies of naphthalene cluster anions, (naphthalene)(n)(-) (n=3-150), and its related aromatic cluster anions, (acenaphthene)(n)(-) (n=4-100) and (azulene)(n)(-) (n=1-100), are studied using anion photoelectron spectroscopy. For (naphthalene)(n) (-) clusters, two isomers coexist over a wide size range: isomers I and II-1 (28 < or = n < or =60) or isomers I and II-2 (n > or = ~60). Their contributions to the photoelectron spectra can be separated using an anion beam hole-burning technique. In contrast, such an isomer coexistence is not observed for (acenaphthene)(n) (-) and (azulene)(n) (-) clusters, where isomer I is exclusively formed throughout the whole size range. The vertical detachment energies (VDEs) of isomer I (7 < or = n < or = 100) in all the anionic clusters depend linearly on n(-13) and their size-dependent energetics are quite similar to one another. On the other hand, the VDEs of isomers II-1 and II-2 produced in (naphthalene)(n)(-) clusters with n > or = approximately 30 remain constant at 0.84 and 0.99 eV, respectively, 0.4-0.6 eV lower than those of isomer I. Based upon the ion source condition dependence and the hole-burning photoelectron spectra experiments for each isomer, the energetics and characteristics of isomers I, II-1, and II-2 are discussed: isomer I is an internalized anion state accompanied by a large change in its cluster geometry after electron attachment, while isomers II-1 and II-2 are crystal-like states with little structural relaxation. The nonappearance of isomers II-1 and II-2 for (acenaphthene)(n)(-) and (azulene)(n)(-) and a comparison with other aromatic cluster anions indicate that a highly anisotropic and symmetric pi-conjugated molecular framework, such as found in the linear oligoacenes, is an essential factor for the formation of the crystal-like ordered forms (isomers II-1 and II-2). On the other hand, lowering the molecular symmetry makes their production unfavorable.     

Stable ion NMR and GIAO-DFT study of novel cations from 8,16-dicyano[2.2]metacyclophanedienes and from strategically substituted/benzannelated dihydropyrenes: charge-induced tropicity modulation and pi-switching

The dicyanometacyclophanediene 1 is diprotonated at the cyano groups (1H2 2+) in various superacid media. Upon quenching, intact 1 and the ring-closed CPD 2 were obtained in a 3:2 or 3:1 ratio, depending on the superacid system. Compound 2 undergoes ring opening in the superacid to give the ipso-monoprotonated 2H+, which on quenching furnishes 1-cyanopyrene as a major product together with 2 and 1. The dication 3 2+, with strongly deshielded internal methyls, was generated from the epoxyannulene 3. Ketones 4-6 and ester 7 are O/C diprotonated to give paratropic carboxonium-annulenium dications (4H2 2+, 5H2 2+, 6H2 2+, and 7H2 2+, respectively). Ester 8 gives a trication by two-electron oxidation and O-protonation. Conjugated carboxylic acid 9 gives a mixture of two dications by CO and ring protonation. The dibromo derivatives 10 and 11 form carboxonium ions, whereas the monobromo derivative 12 is O/C diprotonated to give an oxonium-annulenium dication. Charge delocalization modes and tropicity in the resulting species are evaluated by NMR and GIAO-DFT. Facile formation of 2 from 1 in quenching experiments indicates that thermal closing can be achieved with the diprotonated dinitrile, without imposing skeletal rearrangement.     

The Chemistry of Stable Silabenzenes

Stable silabenzenes ( 1a; R = Tbt, 1b; R = Bbt) were synthesized by taking advantage of extremely bulky and efficient steric protection groups, 2,4,6‐tris[bis(trimethylsilyl)methyl]phenyl (Tbt) and 2,6‐bis‐[bis(trimethylsilyl)methyl]‐4‐[tris(trimethylsilyl)methyl]phenyl (Bbt). The structure of Tbt‐substituted 1a was determined by X‐ray crystallographic analysis, which demonstrated the complete delocalization of the π‐electrons of the silabenzene ring. It was found that silabenzene 1a reacted with C–C and C–O multiple bond compounds to give the corresponding [4+2]‐cycloadducts via 1,4‐addition, while 1a underwent both 1,2‐ and 1,4‐additions by the reaction with methanol. Silabenzene 1a dimerized very gradually to afford its [4+2]‐dimer, although 1b showed no change under the same conditions. Photochemical reaction of 1a gave the corresponding silabenzvalene isomer instead of the Dewar silabenzene isomer.     

Column chromatographic boron isotope separation at 5 and 17 MPa with diluted boric acid solution

Boron isotopic fractionation factor (S) between boron taken up in strongly basic anion exchange resin and boron in aqueous solution was determined by breakthrough column chromatography at 5 and 17 MPa at 25 degrees C, using 0.1 mM boric acid solution as feed solution. The S values obtained were 1.018 and 1.012, respectively, which were smaller than the value reported by using the same chromatographic method at the atmospheric pressure at 25 degrees C with the boron concentration of 10mM, but were larger than the values under the same condition with much higher concentration of 100 and 501 mM. Calculations based on the theory of isotope distribution between two phases estimated that 21% (5 MPa) and 47% (17 MPa) of boron taken up in the resin phase was in the three-coordinated B(OH)(3)-form, instead of in the four-coordinated B(OH)(4)-form, at high pressures even with a very diluted boric acid solution. We discussed the present results by introducing (1) hydration and (2) a partial molar volume difference between isotopic molecules. Borate may have been partially dehydrated upon transfer from the solution phase to the resin phase at high pressures, which resulted in smaller S values compared with those at the atmospheric pressure. Instead, it may be possible that the difference in the isotopic partial molar volume difference between B(OH)(3) and B(OH)(4)(-) caused the S value to decrease with increasing pressure.     

Mass spectrometry and photoelectron spectroscopy of o-, m-, and p-terphenyl cluster anions: the effect of molecular shape on molecular assembly and ion core character

Mass spectrometry and photoelectron spectroscopy of o-, m-, and p-terphenyl cluster anions, (o-TP)n(-) (n = 2-100), (m-TP)n(-) (n = 2-100), and (p-TP)n(-) (n = 1-100), respectively, are conducted to investigate the effect of molecular shape on the molecular aggregation form and the resultant ion core character of the clusters. For (o-TP)n(-) and (m-TP)n(-), neither magic numbers nor discernible isomers are observed throughout the size range. Furthermore, their vertical detachment energies (VDEs) increase up to large n and depend linearly on n(-1/3), implying that they possess a three-dimensional (3D), highly reorganized structure encompassing a monomeric anion core. For (p-TP)n(-), in contrast, prominent magic numbers of n = 5, 7, 10, 12, and 14 are observed, and the VDEs show pronounced irregular shifts below n = 10, while they remain constant above n = 14 (isomer A). These results can be rationalized with two-dimensional (2D) orderings of p-TP molecules and different types of 2D shell closure at n = 7 and 14, the monomeric and multimeric anion core, respectively. Above n = 16, the new feature (isomer B) starts to appear at the higher binding side of isomer A, and it becomes dominant with n, while isomer A gradually disappears for larger sizes. In contrast to isomer A, the VDEs of isomer B continuously increase with the cluster size. This characteristic size evolution suggests that the transition to modified 2D aggregation forms from 2D ones occurs at around n = 20.     

Conformation-specific Raman bands and electronic conjugation in substituted thioanisoles

Nonresonant Raman spectra and conformational stability are studied for thioanisole (TA) and substituted analogues [4-XTA, X = NO(2) (1), CN (2), H (3), CH(3) (4), and NH(2) (5)] at the 4-position. The ring-substituent (SCH(3)) vibrational modes of out-of-plane bending and torsional types are calculated to have strong Raman scattering activities only for the vertical conformers. Agreement between observed and calculated Raman spectra is analyzed numerically. The conformational stability of the SCH(3) rotation changes systematically to the electron-withdrawing character of the substituents. The rotational barrier is calculated satisfactorily by B3LYP/6-31++G(d,p) calculations, whereas the second- to fourth-order M?ller-Presset perturbation theory and coupled-cluster with single- and double-excitation calculations tend to overestimate conformational energy barriers with respect to coplanar forms. The coplanar form is obtained for 1 and 2, whereas the vertical conformer is favorable for 4 and 5. The origin of the conformational energy difference, DeltaE, is demonstrated on the basis of canonical molecular orbitals and natural bond orbitals (NBOs) of the ground state. The natural bond orbital interaction between a nonbonding n(S) orbital of the S atom and a pi orbital of the benzene ring is shown to stabilize the coplanar form predominantly. A linear relationship is obtained between the energy of the highest occupied molecular orbitals and DeltaE. The n(S)-pi interaction energy, E(2), based on the NBO representation and the Hammet constants also change linearly with respect to DeltaE.     

Side-chain chiral centers of amino acid and helical-screw handedness of its peptides

Both diastereomeric right-handed (P) and left-handed (M) 310-helices exist in homopeptides having twelve chiral centers at the side-chain bicyclic skeletons.