The multiple conformational charge states of zinc(II) coordination by 2His‐2Cys oligopeptide investigated by ion mobility‐mass spectrometry,density functional theory and theoretical collision cross sections

Whether traveling wave ion mobility‐mass spectrometry (IM‐MS), B3LYP/LanL2DZ density functional theory, and ion size scaled Lennard‐Jones (LJ) collision cross sections (CCS) from the B3LYP optimized structures could be used to determine the type of Zn(II) coordination by the oligopeptide acetyl‐His₁‐Cys₂‐Gly₃‐Pro₄‐Tyr₅‐His₆‐Cys₇ (amb₅) was investigated. The IM‐MS analyses of a pH titration of molar equivalents of Zn(II):amb₅ showed that both negatively and positively charged complexes formed and coordination of Zn(II) increased as the His and Cys deprotonated near their pKa values. The B3LYP method was used to generate a series of alternative coordination structures to compare with the experimental results. The method predicted that the single negatively charged complex coordinated Zn(II) in a distorted tetrahedral geometry via the 2His‐2Cys substituent groups, whereas, the double negatively charged and positively charged complexes coordinated Zn(II) via His, carbonyl oxygens and the C‐terminus. The CCS of the B3LYP complexes were calculated using the LJ method and compared with those measured by IM‐MS for the various charge state complexes. The LJ method provided CCS that agreed with five of the alternative distorted tetrahedral and trigonal bipyramidal coordinations for the doubly charged complexes, but provided CCS that were 15 to 31 Ų larger than those measured by IM‐MS for the singly charged complexes. Collision‐induced dissociation of the Zn(II) complexes and a further pH titration study of amb_5B, which included amidation of the C‐terminus, suggested that the 2His‐2Cys coordination was more significant than coordinations that included the C‐terminus. Copyright © 2016 John Wiley & Sons, Ltd.     

Entrapment of amino acids in gas phase surfactant assemblies: The case of tryptophan confined in positively charged (1R,2S)‐dodecyl (2‐hydroxy‐1‐methyl‐2‐phenylethyl) dimethylammonium bromide aggregates

The ability of positively charged aggregates of the surfactant (1R ,2S )‐dodecyl(2‐hydroxy‐1‐methyl‐2‐phenylethyl)dimethylammonium bromide (DMEB) to incorporate D‐tryptophan or L‐tryptophan in the gas phase has been investigated by electrospray ion mobility mass spectrometry (ESI‐IM‐MS). Strongly impacted by the pH of the electrosprayed solutions, both protonated (T⁺) and deprotonated (T⁻) tryptophan are effectively included into the aggregates, whereas, tryptophan in zwitterionic (T⁰) form is practically absent in singly charged DMEB aggregates but can be found in multiply charged ones. The ability to incorporate tryptophan increases with the aggregation number and charge state of aggregates. More than 1 tryptophan species can be entrapped (aggregates including up to 5 tryptophan are observed). Collision induced dissociation experiments performed on the positively singly charged DMEB hexamer containing 1 T⁻ show that at low collision energies the loss of a DMEB molecule is preferred with respect to the loss of the DMEB cation plus T⁻ species which, in turn, is preferred with respect to the loss of mere tryptophan, suggesting that the deprotonated amino acid is preferentially located in proximity of a DMEB head group and with the ionic moiety pointing towards the core of the aggregate. The analysis of the collision cross sections (CCS) of bare and tryptophan containing aggregates allowed evaluating the contributions of tryptophan and bromide ions to the total aggregate CCS. No significant discrimination between D‐tryptophan and L‐tryptophan by the chiral DMEB aggregates has been evidenced by mass spectra data, CID experiments, and CCS values.     

Synthesis,Characterization, and DNA‐Binding Properties of the Chiral Ruthenium(II) Complexes Δ‐ and Λ‐[Ru(bpy)2(dmppd)]2+ (dmppd = 10,12‐Dimethylpteridino[6,7‐f] [1,10]phenanthroline‐11,13(10H,12H)‐dione; bpy = 2,2′‐Bipyridine)

Two novel chiral ruthenium(II) complexes, Δ‐[Ru(bpy)₂(dmppd)]²⁺ and Λ‐[Ru(bpy)₂(dmppd)]²⁺ (dmppd = 10,12‐dimethylpteridino[6,7‐f] [1,10]phenanthroline‐11,13(10H,12H)‐dione, bpy = 2,2′‐bipyridine), were synthesized and characterized by elemental analysis, ¹H‐NMR and ES‐MS. The DNA‐binding behaviors of both complexes were studied by UV/VIS absorption titration, competitive binding experiments, viscosity measurements, thermal DNA denaturation, and circular‐dichroism spectra. The results indicate that both chiral complexes bind to calf‐thymus DNA in an intercalative mode, and the Δ enantiomer shows larger DNA affinity than the Λ enantiomer does. Theoretical‐calculation studies for the DNA‐binding behaviors of these complexes were carried out by the density‐functional‐theory method. The mechanism involved in the regulating and controlling of the DNA‐binding abilities of the complexes was further explored by the comparative studies of [Ru(bpy)₂(dmppd)]²⁺ and of its parent complex [Ru(bpy)₂(ppd)]²⁺ (ppd = pteridino[6,7‐f] [1,10]phenanthroline‐11,13 (10H,12H)‐dione).     

Studies on the Mass Spectra of Monocyclic N‐Aryl‐δ‐Valerolactams

The fragmental behavior of some monocyclic N‐aryl‐δ‐valerolactams in EI‐MS was studied. Their molecular ion peak, together with some characteristic fragments such as [M‐29]⁺, [M‐56]^+?, [M‐69]⁺, and [M‐98]⁺, were always found in a series of N‐aryl‐δ‐valerolactams in EI‐MS spectra. Furthermore, the mechanism for the interpretation of each fragment is described.     

Direct Self‐Assembly of a 2D and 3D Star of David

Two‐ and three‐dimensional metallosupramolecules shaped like a Star of David were synthesized by the self‐assembly of a tetratopic pyridyl ligand with a 180° diplatinum(II) motif and Pd^II ions, respectively. In contrast to other strategies, such as template‐directed synthesis and stepwise self‐assembly, this design enables the formation of 2D and 3D structures in one step and high yield. The structures were characterized by both one‐dimensional (¹H, ¹³C, ³¹P) and two‐dimensional (COSY, NOESY, DOSY) NMR spectroscopy, ESI‐MS, ion‐mobility mass spectrometry (IM–MS), AFM, and TEM. The stabilities of the 2D and 3D structures were measured and compared by gradient tandem mass spectrometry (gMS²). The high stability of the 3D Star of David was correlated to its high density of coordination sites (DOCS).     

High performance collision cross section calculation—HPCCS

Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM‐MS) devices in 2003, a large number of research laboratories have embraced the technique. IM‐MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM‐MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS ) is presented, which performs CCS calculations using high perfomance computing techniques. Based on the trajectory method, HPCCS can accurately calculate CCS for a great variety of molecules, ranging from small organic molecules to large protein complexes, using helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the same level of theory. HPCCS is available as free software under the Academic Use License at https://github.com/cepid-cces/hpccs . © 2018 Wiley Periodicals, Inc.     

Uncovering the Stoichiometry of Pyrococcus furiosus RNase P,a Multi‐Subunit Catalytic Ribonucleoprotein Complex,by Surface‐Induced Dissociation and Ion Mobility Mass Spectrometry

We demonstrate that surface‐induced dissociation (SID) coupled with ion mobility mass spectrometry (IM‐MS) is a powerful tool for determining the stoichiometry of a multi‐subunit ribonucleoprotein (RNP) complex assembled in a solution containing Mg²⁺. We investigated Pyrococcus furiosus (Pfu) RNase P, an archaeal RNP that catalyzes tRNA 5′ maturation. Previous step‐wise, Mg²⁺‐dependent reconstitutions of Pfu RNase P with its catalytic RNA subunit and two interacting protein cofactor pairs (RPP21⋅RPP29 and POP5⋅RPP30) revealed functional RNP intermediates en route to the RNase P enzyme, but provided no information on subunit stoichiometry. Our native MS studies with the proteins showed RPP21⋅RPP29 and (POP5⋅RPP30)₂ complexes, but indicated a 1:1 composition for all subunits when either one or both protein complexes bind the cognate RNA. These results highlight the utility of SID and IM‐MS in resolving conformational heterogeneity and yielding insights on RNP assembly.     

Uncovering the Stoichiometry of Pyrococcus furiosus RNase P,a Multi‐Subunit Catalytic Ribonucleoprotein Complex,by Surface‐Induced Dissociation and Ion Mobility Mass Spectrometry

We demonstrate that surface‐induced dissociation (SID) coupled with ion mobility mass spectrometry (IM‐MS) is a powerful tool for determining the stoichiometry of a multi‐subunit ribonucleoprotein (RNP) complex assembled in a solution containing Mg²⁺. We investigated Pyrococcus furiosus (Pfu) RNase P, an archaeal RNP that catalyzes tRNA 5′ maturation. Previous step‐wise, Mg²⁺‐dependent reconstitutions of Pfu RNase P with its catalytic RNA subunit and two interacting protein cofactor pairs (RPP21?RPP29 and POP5?RPP30) revealed functional RNP intermediates en route to the RNase P enzyme, but provided no information on subunit stoichiometry. Our native MS studies with the proteins showed RPP21?RPP29 and (POP5?RPP30)₂ complexes, but indicated a 1:1 composition for all subunits when either one or both protein complexes bind the cognate RNA. These results highlight the utility of SID and IM‐MS in resolving conformational heterogeneity and yielding insights on RNP assembly.     

Synthesis and antifungal activity of novel 5‐substituted 4‐(1,3,4‐thiadiazol‐2‐yl)benzene‐1,3‐diols

5‐Substituted (amine, alkyl, aryl, heterocyclic) 4‐(1,3,4‐thiadiazol‐2‐yl)benzene‐1,3‐ diols were synthesized, and their antifungal properties were examined. The compounds were obtained by the one‐pot reaction of sulfinylbis((2,4‐dihydroxyphenyl)methanethione) with hydrazides or thiosemicarbazides. Their structures were identified from elemental, IR, ¹H NMR, and MS spectra analyses. The activities of the derivatives against five phytopathogenic fungi in vitro were measured. Moderate fungicidal effect of the compounds under consideration was found. © 2010 Wiley Periodicals, Inc. Heteroatom Chem 21:533–540, 2010; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20645     

Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution

Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting “pure” IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810–1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) “shift factors” to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.₈ Å², 295.₁ Å², 296.₈ Å², and 300.₁ Å²; all four of these CCS values were within 1.5% of independently measured DTIM-MS values.     

Synthesis,DNA‐Binding and Photocleavage Studies of the Ruthenium(II) Complexes [Ru(phen)2(ppd)]2+ and [Ru(phen)(ppd)2]2+ (ppd=Pteridino[6,7‐f] [1,10]phenanthroline‐11,13(10H,12H)‐dione,phen=1,10‐Phenanthroline)

Two new complexes, [Ru(phen)₂(ppd)]²⁺ ( 1 ) and [Ru(phen)(ppd)₂]²⁺ ( 2 ) (ppd=pteridino[6,7‐f] [1,10]phenanthroline‐11,13(10H,12H)‐dione, phen=1,10‐phenanthroline) were synthesized and characterized by ES‐MS, ¹H‐NMR spectroscopy, and elemental analysis. The intercalative DNA‐binding properties of 1 and 2 were investigated by absorption‐spectroscopy titration, luminescence‐spectroscopy studies, thermal denaturation, and viscosity measurements. The theoretical aspects were further discussed by comparative studies of 1 and 2 by means of DFT calculations and molecular‐orbital theory. Photoactivated cleavage of pBR322 DNA by the two complexes were also studied, and 2 was found to be a much better photocleavage reagent than 1 . The mechanism studies revealed that singlet oxygen and the excited‐states redox potentials of the complex may play an important role in the DNA photocleavage.     

Identification and separation of saxitoxins using hydrophilic interaction liquid chromatography coupled to traveling wave ion mobility‐mass spectrometry

The aim of this work was to develop a reliable and efficient analytical method to characterise and differentiate saxitoxin analogues (STX), including sulphated (gonyautoxins, GTX) and non‐sulphated analogues. For this purpose, hydrophilic interaction liquid chromatography (HILIC) was used to separate sulphated analogues. We also resorted to ion mobility spectrometry to differentiate the STX analogues because this technique adds a new dimension of separation based on ion gas phase conformation. Positive and negative ionisation modes were used for gonyautoxins while positive ionisation mode was used for non‐sulphated analogues. Subsequently, the coupling of these three complementary techniques, HILIC‐IM‐MS, permitted the separation and identification of STX analogues; isomer differentiation was achieved in HILIC dimension while non‐sulphated analogues were separated in the IM‐MS dimension. Additional structural characteristics concerning the conformation of STXs could be obtained using IM‐MS measurements. Thus, the collision cross sections (CCS) of STXs are reported for the first time in the positive ionisation mode. These experimental CCSs correlated well with the calculated CCS values using the trajectory method. Copyright © 2015 John Wiley & Sons, Ltd.     

Synthesis and Base Pairing Properties of 1′,5′‐Anhydro‐L‐Hexitol Nucleic Acids (L‐HNA)

Oligonucleotides composed of 1′,5′‐anhydro‐arabino‐hexitol nucleosides belonging to the L series (L ‐HNA) were prepared and preliminarily studied as a novel potential base‐pairing system. Synthesis of enantiopure L ‐hexitol nucleotide monomers equipped with a 2′‐(N⁶‐benzoyladenin‐9‐yl) or a 2′‐(thymin‐1‐yl) moiety was carried out by a de novo approach based on a domino reaction as key step. The L oligonucleotide analogues were evaluated in duplex formation with natural complements as well as with unnatural sugar‐modified oligonucleotides. In many cases stable homo‐ and heterochiral associations were found. Besides T_m measurements, detection of heterochiral complexes was unambiguously confirmed by LC‐MS studies. Interestingly, circular dichroism measurements of the most stable duplexes suggested that L ‐HNA form left‐handed helices with both D and L oligonucleotides.     

Bis(4,4′‐dimethyl‐2,2′‐bipyridine) ruthenium (II) Complexes Containing 2‐Arylimidazo‐ [4,5‐f] [1,10] phenanthroline: Syntheses,Characterization and Third‐order Nonlinear Optical Properties

Four novel mononuclear ruthenium(II) complexes [Ru(dmb)₂L]²⁺ [dmb = 4,4′‐dimethyl‐2,2′‐bipyridine, L = imidazo‐[4,5‐f][1,10]phenanthroline (IP), 2‐phenylimidazo‐[4,5‐f][1,10]phenanthroline (PIP), 2‐(4′‐hydroxyphenyl)imidazo‐[4,5‐f] [1,10] phenanthroline (HOP), 2‐(4′‐dimethylaminophenyl) imidazo‐[4, 5‐f] [1,10] phenanthroline (DMNP)] were synthesized and characterized by ES‐MS, ¹H NMR, UV‐vis and electrochemistry. The nonlinear optical properties of the ruthenium(II) complexes were investigated by Z‐scan techniques with 12 ns laser pulse at 540 nm, and all of them exhibit both nonlinear optical (NLO) absorption and self‐defocusing effect. The corresponding effective NLO susceptibility |x³| of the complexes is in the range of 2.68 × 10^?12‐4.57 × 10^?12 esu.     

Gas phase isomeric differentiation of oleanolic and ursolic acids associated with heptakis‐(2,6‐di‐O‐methyl)‐β‐cyclodextrin by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Oleanolic acid (OA) and ursolic acid (UA) are isomeric triterpenoid compounds with similar pharmaceutical properties. Usually, modern chromatographic and electrophoretic methods are widely utilized to differentiate these two compounds. Compared with mass spectrometric (MS) methods, these modern separation methods are both time‐ and sample‐consuming. Herein, we present a new method for structural differentiation of OA and UA by Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) with the association of heptakis‐(2,6‐di‐O‐methyl)‐β‐cyclodextrin (DM‐β‐CD). Exact MS and tandem MS (MS/MS) data showed that there is no perceptible difference between OA and UA, as well as their β‐cyclodextrin and γ‐cyclodextrin complexes. However, there is a remarkable difference in MS/MS spectra of DM‐β‐CD complexes of OA and UA. The peak corresponding to the neutral loss of a formic acid and a water molecule could only be observed in the MS/MS spectrum of the complex of DM‐β‐CD : OA. Molecular modeling calculations were also employed to further investigate the structural differences of DM‐β‐CD : OA and DM‐β‐CD : UA complexes. Therefore, by employing DM‐β‐CD as a reference reagent, OA and UA could be differentiated with purely MS method. Copyright © 2010 John Wiley & Sons, Ltd.     

Combined 1H, 13C and 11B NMR and mass spectral assignments of boronate complexes of D‐(+)‐glucose,D‐(+)‐mannose,methyl‐α‐D‐glucopyranoside,methyl‐β‐D‐galactopyranoside and methyl‐α‐D‐mannopyranoside

Complex formation between N‐butylboronic acid and D ‐(+)‐glucose, D ‐(+)‐mannose, methyl‐α‐D ‐glucopyranoside, methyl‐β‐D ‐galactopyranoside and methyl α‐D ‐mannopyranoside under neutral conditions was investigated by ¹H, ¹³C and ¹¹B NMR spectroscopy and gas chromatography–mass spectrometry (GC–MS) D ‐(+)‐Glucose and D ‐(+)‐mannose formed complexes where the boronates are attached to the 1,2:4,6‐ and 2,3:5,6‐positions of the furanose forms, respectively. On the other hand, the boronic acid binds to the 4,6‐positions of the two methyl derivatives of glucose and galactose. Methyl α‐D ‐mannopyranoside binds two boronates at the 2,3:4,6‐positions. ¹¹B NMR was used to show the ring size of the complexed sugars and the boronate. GC–MS confirmed the assignments. Copyright © 2003 John Wiley & Sons, Ltd.     

Syntheses,Crystal Structures,and Magnetic Properties of Three Metal‐Nitroxide Complexes with the V‐shaped 4, 4′‐Oxybis(benzoate)

Three new metal–nitroxide complexes {[Ni(NIT4Py)₂(obb)(H₂O)₂] · 1.5H₂O}_n ( 1 ), {[Co(NIT4Py)₂(obb)(H₂O)₂] · 2H₂O}_n ( 2 ), and [Co(IM4Py)₂(obb)₂(H₂O)₂][Co(IM4Py)₂(H₂O)₄] · 10H₂O ( 3 ) with the V‐shaped 4,4′‐oxybis(benzoate) [NIT4Py = 2‐(4′‐pyridyl)‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide, IM4Py = 2‐(4′‐pyridyl)‐4,4,5,5‐tetramethylimidazoline‐1‐oxide, and obb = 4, 4′‐oxybis(benzoate) anion] were synthesized and structurally characterized. Single‐crystal X‐ray analyses indicate that complexes 1 and 2 crystallize in neutral one‐dimensional (1D) zigzag chains, in which the nitroxide–metal–nitroxide units are linked by the V‐shaped 4,4′‐oxybis(benzoate) anions, whereas complex 3 consists of isolated mononuclear [Co(IM4Py)₂(obb)₂(H₂O)₂]^2– anions and [Co(IM4Py)₂(H₂O)₄]²⁺ ions. Magnetic measurements show that complexes 1 and 2 both exhibit weak antiferromagnetic interactions between the metal ions and the nitroxides.     

Polyester from dimethylketene and acetaldehyde: Direct copolymerization and β‐lactone ring‐opening polymerization

Two ways to obtain aliphatic polyesters (PEs) from dimethylketene and acetaldehyde were investigated. On the one hand, a direct anionic copolymerization was carried out in toluene at ?60 °C. The resulting polymer was mainly composed of PE units. On the other hand, a two‐step process involving the synthesis of 3,3,4‐trimethyl‐2‐oxetanone by [2+2] cycloaddition, followed by its ring‐opening polymerization, with various initiators and solvents, led to the expected PE. Molecular weights up to 9000 g mol^?1 (measured by nuclear magnetic resonance (NMR)), with narrow polydispersity around 1.2, were obtained. These polymers were found stable up to 274 °C under nitrogen and a broad and complex endothermic peak attributed to crystallinity was observed near 139 °C by differential scanning calorimetry (DSC). The crystallinity, measured by X‐ray diffraction, was close to 0.45. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

7Li NMR chemical shift titration and theoretical DFT calculation studies: solvent and anion effects on second‐order complexation of 12‐crown‐4 and 1‐aza‐12‐crown‐4 with Lithium cation in several aprotic solvents

⁷Li NMR titration was used to determine stepwise complexation constants for the second‐order complexation of lithium cation with 12‐crown‐4 in acetonitrile, propylene carbonate and a binary mixture of propylene carbonate and dimethyl carbonate. The anions used were perchlorate, hexaflurophosphate and trifluromethanesulfonate. A second ligand 1‐aza‐12‐crown‐4 was similarly investigated. The exchange between the free and complexed cation in these reactions is fast on an NMR timescale resulting in a single lithium peak which is a concentration‐weighted average of the free and bound species. Solvent effects show that the 1:1 complex is much more stable in acetonitrile than in propylene carbonate or in the propylene carbonate dimethyl carbonate mixture. Anion effects for a given solvent were small. Optimized geometries of the free ligands and the 1:1 and 1:2 (sandwich) metal–ligand complexes were predicted by hybrid‐density functional theory using the Gaussian 03 software package. Results were compared to literature values for 1:1 stability constants found by microcalorimetry for several of these systems and are found to be in good agreement. Although microcalorimetry only considered the formation of 1:1 complexes, ⁷Li NMR shows evidence that both 1:1 and 1:2 complexes should be considered. Copyright © 2009 John Wiley & Sons, Ltd.     

Transition Metal Complexes of N‐(4,6‐Dimethoxypyrimidin‐2‐Ylcarbamothioyl)Benzamide: Design,Synthesis and Herbicidal Activity

Transition metal (Cu(II), Zn(II), Co(II)) complexes of N‐(4,6‐dimethoxypyrimidin‐2‐ylcarbamothioyl)benzamide were prepared. The structures of all the newly synthesized complexes were identified by elemental analyses, IR, ¹H NMR, XPS, MS and TG. Their herbicidal activities were evaluated against a variety of weeds. The preliminary results showed that the target complexes had moderate biological activities against both broad leaf weeds and monocotyledon plants. More importantly, the complexes exhibited some improved herbicidal activities over their non‐complexed counterparts. The present work provides a novel class of transition metal‐based derivatives with potent herbicidal activities for further optimization.