Generation and dissociation pathways of singly and doubly protonated bisguanidines in the gas phase

Para-bisguanidinyl benzene 1 and its N-permethylated derivative 2 are both sufficiently strong bases to afford not only the monocations [1+H]+ and [2+H]+, but also the doubly protonated ions, [1+2H]2+ and [2+2H]2+, in the gas phase. The title ions generated via electrospray ionization are probed by collision-induced dissociation experiments which inter alia reveal that the dicationic species [1+2H]2+ and [2+2H]2+ can even undergo fragmentation reactions with maintenance of the 2-fold charge. Complementary results from density functional theory predict PAs above 1000 kJ mol(-1) for the neutral compounds, i.e., PA(1) = 1025 kJ mol(-1) and PA(2) = 1067 kJ mol(-1). Due to the stabilization of the positive charge in the guanidinium ions and the para-phenylene spacer separating the basic sites, even the monocations bear sizable proton affinities, i.e., PA([1+H]+) = 740 kJ mol(-1) and PA([2+H]+) = 816 kJ mol(-1).     

Two ion/ion charge inversion steps to form a doubly protonated peptide from a singly protonated peptide in the gas phase

An approach is described to increase the degree of protonation of a polypeptide ion in the gas phase. Sequential charge inversion reactions involving the reactions of oppositely charged ions are used to yield a net increase in ion charge. The approach is illustrated here with the conversion of singly protonated bradykinin to doubly protonated bradykinin. The first step involves conversion of the singly protonated peptide to the singly deprotonated peptide via reactions with multiply charged anions derived from carboxylate-terminated dendrimers. Some of the singly deprotonated peptide was then converted to doubly protonated peptide via reactions with multiply charged cations derived from amino-terminated dendrimers. The overall approach is illustrative of a general strategy for increasing the absolute charge states of large ions in the gas phase.     

Theoretical and experimental study of the adsorption of neutral glycine on silica from the gas phase.

The adsorption of neutral glycine onto amorphous silica was investigated both theoretically and experimentally. DFT calculations were performed at the BLYP-631++G** level using a cluster approach. Several possible configurations involving the formation of H bonds between glycine and one, two, or three silanol groups (SiOH) were considered. The most favorable bonding of glycine with one silanol group (45 kJ mol(-1)) occurs through the COOH moiety, thus forming a cycle in which the CO group is an H-bond acceptor whereas the acidic OH group is an H-bond donor. With two or three silanol groups, additional H bonds are formed between the amine moiety and the silanol groups, which leads to an increased adsorption energy (70 and 80 kJ mol(-1) for two and three silanol groups, respectively). Calculated nu(CO), delta(HNH), and delta(HCH) values are sensitive to the adsorption mode. A bathochromic shift of nu(CO) as compared to the nu(CO) of free glycine (calculated in the 1755-1790 cm(-1) range) is found for glycine in interaction with silanol(s). The more H bonds are formed between the COOH moiety and silanol groups, the higher the bathochromic shift. For delta(HNH), no shift is found for glycine adsorbed on one and two silanol groups (where the amine is either not bound or an H-bond donor), whereas a bathochromic shift is calculated with three silanols when the amine moiety is an H-bond acceptor. Experimental FTIR spectra performed at room temperature for glycine adsorbed at 160 degrees C on Aerosil amorphous silica exhibit bands at 1371, 1423, 1630, and 1699 cm(-1). The experimental/calculated frequencies have their best correspondence for glycine adsorbed on two silanol groups. It is important to note that the forms giving the best correspondence to experimental frequencies are the most stable ones.     

Chlorobis(pentafluoroethyl)phosphane: improved synthesis and molecular structure in the gas phase

(C₂F₅)₂PCl is now accessible through a significantly improved synthesis protocol starting from the technical product (C₂F₅)₃PF₂. (C₂F₅)₃PF₂ was reduced in the first step with NaBH₄ in a solvent‐free reaction at 120 °C. The product, P(C₂F₅)₃, was treated with an excess of an aqueous sodium hydroxide solution to afford the corresponding phosphinite salt Na⁺(C₂F₅)₂PO^? selectively under liberation of pentafluoroethane. Subsequent chlorination with PhPCl₄ resulted in the selective formation of (C₂F₅)₂PCl, which was isolated by fractional condensation in an overall yield of 66 %. The gas electron diffraction (GED) pattern for (C₂F₅)₂PCl was recorded and found to be described by a two‐conformer model. A quantum chemical investigation of the potential‐energy surface revealed the possible existence of many low‐energy conformers, each with a number of low‐frequency vibrational modes and therefore large‐amplitude motions. The conformer calculated to be most stable was also found to be most abundant by GED and comprised 61(5) % of the total. The molecular structure parameters determined by GED were in good agreement with those calculated at the MP2/TZVPP level of theory; the only significant difference was a discrepancy of about 3° in the C‐P‐C angle, which, for the lowest‐energy conformer, was refined to 98.2(4)° and was calculated to be 94.9°.     

Protonation of metal‐bound α‐hydroxycarboxylate ligand and implication for the role of homocitrate in nitrogenase: Computational study of the oxy‐bidentate chelate ring opening

Protonation of the metal‐bound oxy‐bidentate ligand in the model complexes of [(HS)₃(NH₃)M(OCH₂COO)]^q (M = Mo, Fe, V, Co; q = ?2, ?1) in the gas phase and in solutions of water and acetonitrile has been explored by the density functional approach. Calculations show that protonation of the carboxyl oxygen can open the α‐hydroxycarboxylate chelate ring ligated to a transition‐metal center under specific oxidation and spin states. The feasibility of the chelate ring opening by protonation depends on the electronic nature of the metal site in tune with conversion of a six‐coordinate with a five‐coordinate metal atom. Such selective dissociation of the metal‐bound chelate ligand manipulates the availability of an empty site at the metal center and significantly affects reactivity of the metal‐mediated chemical processes. Protonation changes the stability of species with different spin multiplicities and impels spin transition at the metal center in dissociation of the oxy‐bidentate ligand. Solvent environments of water and acetonitrile play an important role in stabilizing the negatively charged species. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Density functional theory on phase space

Forty‐five years after the point de départ [Hohenberg and Kohn, Phys Rev, 1964, 136, B864] of density functional theory, its applications in chemistry and the study of electronic structures keep steadily growing. However, the precise form of the energy functional in terms of the electron density still eludes us—and possibly will do so forever [Schuch and Verstraete, Nat Phys, 2009, 5, 732]. In what follows we examine a formulation in the same spirit with phase space variables. The validity of Hohenberg–Kohn–Levy‐type theorems on phase space is recalled. We study the representability problem for reduced Wigner functions, and proceed to analyze properties of the new functional. Along the way, new results on states in the phase space formalism of quantum mechanics are established. Natural Wigner orbital theory is developed in depth, with the final aim of constructing accurate correlation‐exchange functionals on phase space. A new proof of the overbinding property of the Müller functional is given. This exact theory supplies its home at long last to that illustrious ancestor, the Thomas–Fermi model. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Location of the hole and acid proton in neutral nonprotonated and protonated mixed (phthalocyaninato)(porphyrinato) yttrium double-decker complexes: density functional theory calculations

The location of the hole and acid proton in neutral nonprotonated and protonated mixed (phthalocyaninato)(porphyrinato) yttrium double-decker complexes, respectively, is studied on the basis of density functional theory (DFT) calculations on the molecular structures, molecular orbitals, atomic charges, and electronic absorption and infrared spectra of the neutral, reduced, and two possible protonated species of a mixed (phthalocyaninato)(porphyrinato) yttrium compound: [(Pc)Y(Por)], [(Pc)Y(Por)]-, [(HPc)Y(Por)], and [(Pc)Y(HPor)], respectively. When the neutral [(Pc)Y(Por)] is reduced to [(Pc)Y(Por)]-, the calculated results on the molecular structure, atomic charge, and electronic absorption and infrared spectra show that the added electron has more influence on the Pc ring than on its Por counterpart, suggesting that the location of the hole is on the Pc ring in neutral [(Pc)Y(Por)]. Nevertheless, comparison of the calculation results on the structure, orbital composition, charge distribution, and electronic absorption and infrared spectra between [(HPc)Y(Por)] and [(Pc)Y(HPor)] leads to the conclusion that the acid proton in the protonated mixed (phthalocyaninato)(porphyrinato) yttrium compound should be localized on the Por ring rather than the Pc ring, despite the localization of the hole on the Pc ring in [(Pc)Y(Por)]. This result is in line with the trend revealed by comparative studies of the X-ray single-crystal molecular structures between [MIII{Pc(alpha-OC5H11)4}(TClPP)] and [M(III)H{Pc(alpha-OC5H11)4}(TClPP)] (H2TClPP=5,10,15,20-tetrakis(4-chlorophenyl)porphyrin; M=Sm, Eu). The present work not only represents the first systemic DFT study on the structures and properties of mixed (phthalocyaninato)(porphyrinato) yttrium double-decker complexes, but more importantly sheds further light on the nature of protonated bis(tetrapyrrole) rare-earth complexes.     

Fragmentation reactions of singly and doubly protonated thiourea- and sugar-substituted cyclams and their transition-metal complexes

Cyclam macrocycles tetrasubstituted with amino-, thiourea-, and sugar-terminated side chains are ionized by electrospray ionization mass spectrometry (ESI-MS) as singly or doubly protonated species or as transition-metal complexes. Their fragmentation behavior is examined in a Fourier-transform ion-cyclotron-resonance (FT-ICR) mass spectrometer by collision-induced dissociation (CID) experiments. Typically, fragmentation occurs within the side chains through a number of different 1,2-elimination reactions irrespective of the absence or presence of a transition metal ion such as Co(2+), Ni(2+), or Zn(2+). A remarkable exception is Cu(2+), which induces ring cleavage reactions. This is traced back to an electron transfer from the cyclam nitrogen atoms to the Cu(2+) ion. The electron transfer creates a cation-radical within the macrocycle, which induces typical fragmentation reactions such as alpha-cleavages that lead to fragmentation within the macrocycle. This interpretation is in line with fragmentation experiments on unsubstituted cyclam and its complexes.     

Unimolecular reactivity of uracil-Cu(2+) complexes in the gas phase.

The gas-phase interaction of copper(II) ions with uracil are studied by means of mass spectrometry and B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) calculations. Positive-ion electrospray spectra show that the reaction of uracil with copper(II) gives rise to singly charged species, whereby the [Cu(uracil--H)](+) complex is the most intense ion in the spectra at low concentration. Mass spectrometry/mass spectrometry (MS/MS) experiments show that the loss of HNCO and NCO are the dominant fragmentation processes, accompanied by a minor loss of CO. A systematic study of the spectra obtained with different labeled species, namely, 2-(13)C- (m/z 175), 2-(13)C,1,3-(15)N(2)- (m/z 177) and 3-(15)N-uracil (m/z 175), concludes unambiguously that both the loss of HNCO and NCO involve exclusively C2 and N3, whereas only C4 is involved in the loss of CO. Suitable mechanisms for these fragmentation processes are proposed through a theoretical survey of the corresponding potential energy surface. In these mechanisms, pi complexes, which lie high in energy with respect to the global minimum, play a significant role in the loss of NCO; this explains why both products, HNCO and NCO involve the same atoms of the ring.     

Protonation of water clusters induced by hydroperoxyl radical surface adsorption

We have investigated the HO(2) adsorption and acid dissociation process on the surface of (H(2)O)(20) and (H(2)O)(21) clusters by using quantum-chemistry calculations. Our results show that the radical forms a stable hydrogen-bond complex on the cluster. The HO(2) acid dissociation is more favorable in the case of the (H(2)O)(21) cluster, for which the inner water molecule plays a crucial role. In fact, acid dissociation of HO(2) is found to occur in two steps. The first step involves H(2) O autoionization in the cluster, and the second one involves the proton transfer from the HO(2) radical to the hydroxide anion. The presence of the HO(2) radicals on the surface of the cluster facilitates water autoionization in the cluster.     

tert-Butylphosphonic acid: from the bulk to the gas phase

The structure of tert-butylphosphonic acid in the solid, in solution, and in the gas phase was studied by single-crystal X-ray diffraction, (1)H and (31)P NMR spectroscopic studies in solution, solid-state (31)P NMR spectroscopy, and electrospray ionization mass spectrometry. In addition, density functional theory (DFT) calculations at the B3LYP/6-31G*, B3LYP/6-31+G*, and B3LYP/6-311+G* level of theory for a large number of H-bonded aggregates of the type (tBuPO(3)H(2))(n) (C(n), P(n); n=1-7) support the experimental work. Crystallization of tBuPO(3)H(2) from polar solvents such as CH(3)CN or THF gives the H-bonded one-dimensional polymer 2, whereas crystallization from the less polar solvent CDCl(3) favors the formation of the H-bonded cluster (tBuPO(3)H(2))(6).CDCl(3) (1). In CDCl(3) the hexamer (tBuPO(3)H(2))(6) (C(6)) is replaced by smaller aggregates down to the monomer with decreasing concentration. DFT calculations and natural bond orbital (NBO) analyses for the clusters C(1)-C(7) and the linear arrays P(1)-P(7) reveal the hexamer C(6) to be the energetically favored structure resulting from cooperative strengthening of the hydrogen bonds in the H-bonded framework. However, the average hydrogen bond strengths calculated for C(6) and P(2) do not differ significantly (42-43 kJ mol(-1)). The average distances r(O.O), r(Obond;H), r(Pdbond;O), and r(Pbond;OH) in C(1)-C(7) and P(1)-P(7) are closely related to the hydrogen bond strength. Electrospray ionization mass spectrometry shows the presence of different anionic species of the type [(tBuPO(3)H(2))(n)-H](-) (A(1)-A(7), n=1-7) depending on the instrumental conditions. DFT calculations at the B3LYP/6-31G* level of theory were carried out for A(1)-A(6). We suggest the dimer [(tBuPO(3)H(2))(2)-H](-) (A(2)) and the trimer [(tBuPO(3)H(2))(3)-H](-) (A(3)) are the energetically favored anionic structures. A hydrogen bond energy of approximately 83 kJ mol(-1) was calculated for A(2). Electrospray ionization mass spectrometry is not suitable to study the assembling process of neutral H-bonded tert-butylphosphonic acid since the removal of a proton from the neutral aggregates has a large influence on the hydrogen bond strength and the cluster structure.     

Intercage Electron Transfer Driven by Electric Field in Robin–Day‐Type Molecules

A new class of isomers, namely, intercage electron‐transfer isomers, is reported for fluorinated double‐cage molecular anion e^?@C₂₀F₁₈(NH)₂C₂₀F₁₈ with C₂₀F₁₈ cages: 1 with the excess electron inside the left cage, 2 with the excess electron inside both cages, and 3 with the excess electron inside the right cage. Interestingly, the C₂₀F₁₈ cages may be considered as two redox sites existing in a rare nonmetal mixed‐valent (0 and ?1) molecular anion. The three isomers with two redox sites may be the founding members of a new class of mixed‐valent compounds, namely, nonmetal Robin–Day Class II with localized redox centers for 1 and 3 , and Class III with delocalized redox centers for 2 . Two intercage electron‐transfers pathways involving transfer of one or half an excess electron from one cage to the other are found: 1) Manipulating the external electric field (?0.001 a.u. for 1 → 3 and ?0.0005 a.u. for 1 → 2 ) and 2) Exciting the transition from ground to first excited state and subsequent radiationless transition from the excited state to another ground state for 1 and 3 . For the exhibited microscopic electron‐transfer process 1 → 3 , 2 may be the transition state, and the electron‐transfer barrier of 6.021 kcal mol^?1 is close to the electric field work of 8.04 kcal mol^?1.