Density functional calculations on CO attached to PtnRu(10−n) (n = 6–10) clusters

B3LYP and SCF‐Xα calculations have been performed on Pt_nRu_(10−n)CO (n = 6–10) clusters. The work aims to simulate the adsorption of CO on the (111) surface of platinum metal and to examine the electronic effects that arise when some Pt atoms are replaced with Ru. Adsorption energies and Pt C and C O stretching frequencies have been calculated for each cluster. Ru does affect the electronic structure of the clusters, the calculated adsorption energies, and frequencies, the Pt C frequency more than the C O. The donation‐backbonding mechanism that accompanies the shift in CO stretching frequency that occurs when CO adsorbs on platinum does not explain the differences in frequency shift observed in CO on various Pt/Ru surfaces. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 589–598, 2000     

Density functional theory studies of N-protonation of the free base phthalocyanine

The structures and relative energies of twenty-two N-protonated species of the free base phthalocyanine (H₂Pc) have been systematically studied with the density functional theory at the B3LYP/6-31G(d) level of theory. The calculations demonstrated that the N-protonation tends to increase the N–C bonds and the C–N–C angles on the protonation sites. The inner protonation at the isoindole-nitrogen atoms causes significant out-of-plane deformation of the macrocycle, ascribed to the steric hindrance of the central cavity. The relative energies of various protonated species were calculated and compared to deduce the preferred sites for protonation. It was revealed that the outer protonation at the meso-nitrogen atoms is energetically more favorable than the inner protonation at the isoindole-nitrogen atoms. Among the studied twenty-two protonated species, the most stable one is H₆Pc⁴⁺(IS1), for which all the outer meso-nitrogen atoms are protonated. TDDFT calculations have been performed for selected species, and the results were used to analysis the UV–visible spectrum of the concentrated sulfuric acid solution of the free base phthalocyanine.     

Non-empirical SCF MO studies on the protonation of biopolymer constituents

Proton affinities of several of the tautomeric forms of cytosine and thymine have been calculated using theab initio Hartree-Fock-Roothaan SCF method. Several of the most stable protonated forms may be obtained by direct protonation from one of the two most stable neutral forms. The calculated total energies do not exclude the possibility of the coexistence of several protonated forms in acidic solutions.     

Proton‐controlled nitroxide mediated radical polymerization of styrene

The pyridyl alkoxyamine, which is composed of the 1‐phenylethyl radical and a pyridyl nitroxide fragments, displays protonation‐controlled C? ON bond homolysis. Its dissociation rate constant k_d value is approximately halved at 100 °C in tert‐butyl benzene when it is protonated by one equivalent of trifluoroacetic acid. Moreover, the bulk polymerization of styrene at 125 °C is performed with a good control over the molecular weight and the dispersity when initiated with this alkoxyamine under its basic and acidic forms but the protonation has induced a strong decreased polymerization rate. In contrast, in the case of n‐butyl acrylate, the control over the polymerization is lost for the protonated pyridyl alkoxyamine because the pyridyl nitroxide is less thermally stable under its acidic form. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Probing Protonation Sites of Isolated Flavins Using IR Spectroscopy: From Lumichrome to the Cofactor Flavin Mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B₂), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600–1850 cm^?1) by means of IR multiple‐photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low‐energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1‐protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2‐ and N1‐protonated tautomers. The frequencies and relative intensities of the two C?O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.     

Tunable Electronic Properties of a Proton‐Responsive N,N‐Dimethylaminoazobenzene Fullerene (C60) Dyad

A basic N,N‐dimethylaminoazobenzene–fullerene (C₆₀) dyad molecular skeleton is modelled and synthesized. In spite of the myriad use of azobenzene as a photo‐ and electrochromic moiety, the idea presented herein is to adopt a conceptually different path by using it as a bridge in a donor–bridge–acceptor single‐molecular skeleton, connecting the electron acceptor N‐methylfulleropyrrolidine with an electron donor N,N‐dimethylaniline. Addition of trifluoroacetic acid (TFA) results in a drastic colour change of the dyad from yellow to pink in dichloromethane (DCM). The structure of the protonated species are established from electronic spectroscopy and time‐dependent density functional theory (TD‐DFT) calculations. UV/Vis spectroscopic investigations reveal the disappearance of the 409 nm ¹(π→π*) transition with appearance of new features at 520 and 540 nm, attributed to protonated β and α nitrogens, respectively, along with a finite weight of the C₆₀ pyrrolidinic nitrogen. Calculations reveal intermixing of n_(N?N)→π*_(N?N) and charge transfer (CT) transitions in the neutral dyad, whereas, the n_(N?N)→π*_(N?N) transition in the protonated dyad is buried under the dominant ¹(π →π*) feature and is red‐shifted upon Gaussian deconvolution. The experimental binding constants involved in the protonation of N,N‐dimethylanilineazobenzene and the dyad imply an almost equal probability of existence of both α‐ and β‐protonated forms. Larger binding constants for the protonated dyads imply more stable dyad complexes than for the donor counterparts. One of the most significant findings upon protonation resulted in frontier molecular orbital (FMO) switching with the dyad LUMO located on the donor part, evidenced from electrochemical investigations. The appearance of a new peak, prior to the first reduction potential of N‐methylfulleropyrrolidine, clearly indicates location of the first incoming electron on the donor‐centred LUMO of the dyad, corroborated by unrestricted DFT calculations performed on the monoanions of the protonated dyad. The protonation of the basic azo nitrogens thus enables a rational control over the energetics and location of the FMOs, indispensable for electron transport across molecular junctions in realizing futuristic current switching devices.     

Aromatic protonation—part 2 : 1H NMR parameters of the anthracenium ions of some 9-alkyl-, 9-alkyl-α-chloro-, 9,10-dialkyl-anthracenes and 1-chloroanthracene. study on the sit

Seventeen 9-alkylanthracenes (1–17) and 1-chloroanthracene have been protonated with FSO₃H in SO₂CIF as cosolvent at ?78°. For all substrates C(10) protonation was observed, but with some substrates in addition C(9) protonation, if that would lead to relief of steric strain between the substituent at C(9) and the substituent(s) at C(1) [and C(8)]. The C(9) protonated ions exist in the preferred conformation IIa. The ions resulting on ipso-protonation of the 9,10-dialkyl-anthracenes have a similar type of conformation. Based both on this preferred conformation and the peri-chloro effects of the anthracenium ions, it is concluded that these ions are best represented by the equilibirum IIa ? IIb.     

Ionization Energies and Dyson Orbials of Allyl Alcohol and Allyl Mercaptan Conformers

The conformers of allyl alcohol and allyl mercaptan were studied with B3LYP/aug-cc-pVTZ method. Their relative energies were calculated at MP3, MP4(SDQ), and CCSD(T) levels. The most stable conformers for these two molecules are Gauche-gauche' (Gg'). The theo-retical photoelectron spectra simulated with the calculated ionization energies demonstrate that there are at least four conformers in allyl alcohol and four conformers in allyl mercaptan in the gas-phase experiments. The Dyson orbitals of the highest occupied molecular orbital (HOMO) and the next HOMO (HOMO-1) of allyl mercaptan Gg' conformer show strongly mixing n_S and π_C=C characteristics, which may be due to the resonance and inductive effects between π_C=C and n_S in HOMO-1 and HOMO.     

Calculated properties of some possible vinyl chloride metabolites

There is considerable evidence indicating that the carcinogenic action of vinyl chloride involves metabolic conversion to the epoxide (chlorooxirane) as the initial step. In order to learn more about its subsequent behavior, we have computed structures, energies and other properties for two different protonated forms of the epoxide, and also for two possible rearrangement products, chloroacetaldehyde and acetyl chloride. An ab initio SCF -MO procedure (GAUSSIAN 70) was used. Oxygen protonation is found to weaken both C? O bonds, the effect being greater for the bond involving the carbon bearing the chlorine. Chlorine protonation leads to a marked weakening of the C? Cl bond; this suggests a possible loss of HCl, leaving behind a carbonium ion (and possible alkylating agent or rearrangement precursor). Thus, while C? O bond breaking is doubtless an important reaction pathway for chlorooxirane, our results indicate that attention should also be focused upon the C? Cl bond; its rupture may conceivably be a key step in the biological action of vinyl chloride.     

Calculation of the proton affinities of polychlorobenzenes and the activation energies of 1,2-hydrogen shifts in arenonium ions

The proton affinities of benzene, chlorobenzene and polychlorobenzenes with the common formula C₆Cl _n H_6–n (n=0–6) have been calculated by the AM1 method. The proton affinity averaged over the protonated isomers increases monotonically asn growing from 0 to 5, and then decreases when passing from pentato hexachlorobenzene. The energies of proton addition to the different positions in the polychlorobenzene molecules have been estimated. It has been found that unsubstituted carbon atoms are preferred for proton attack. The positions with the highest proton affinity are the carbon atoms with the largest negative charges. The activation energies of 1,2-hydrogen shifts in arenonium ions of the polychlorobenzenes have been calculated.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1213–1217, July, 1993.     

The electronic structure of all-trans-polyenes C2nH2n+2, n = 3–7

The electronic structure of the C_2nH_2n+2 trans-polyenes, n = 3–7, is calculated by the Discrete Variational X_α method (DVM -X_α). The valence ionization potentials (IP ) calculated using the Clementi double zeta basis agree with the known experimental data within several tenths an electron volt. However, the DVM energies of the π → π* optical excitations are systematically underestimated by 0.8–1.0 eV. For polyenes with equal C—C bond lengths, the computed energies of the first optical transitions are smaller than those of polyenes with alternating C—C bond lengths. The charge distribution in polyenes is analyzed in the framework of a Mulliken scheme. The composition of the frontier molecular orbitals (MO ) is analyzed.     

Two competing fragmentation processes in dimethoxybenzenes depending on their positional isomers: Elimination of CH3 and CHnO (n = 1–3) and formation of methoxycyclopentadienyl and protonated phenol ions

All the metastable transitions observed above m/z 39 in the first field-free region were compared for the three positional isomers of dimethoxybenzene. The observed isomer-dependent fragmentation processes, in particular the formation and decomposition of the m/z 95 (C₆H₇O)⁺ ion, are discussed in terms of two competing fragmentations [elimination of CH₃ and CH_nO (n = 1–3) and formation of methoxycyclopentadienyl and protonated phenol ions] and the relative energies of several isomers of the C₆H₇O⁺ ion calculated with molecular orbital theory.     

Theoretical studies of organometallic compounds. III. Structures and bond energies of FeCHn and FeCH (n = 1, 2, 3)

The geometries and dissociation energies for the Fe? C and C? H bonds of FeCH_n and FeCH (n = 1, 2, 3) have been calculated by ab initio quantum mechanical methods using different effective core potential models and Møller–Plesset perturbation theory. The HW3 ECP model, which has a configuration [core] (n?1)s², (n?1)p⁶, (n?1)d¹, (n)s^m for the transition metals, is clearly superior to the larger core LANL1DZ ECP model with the configuration [core] (n?1)d¹, (n)s^m. The Fe? C bond energies calculated at correlated levels using the HW3 ECP are in much better agreement with experiment than the LANL1DZ results. This effect is mainly due to the higher number of correlated electrons rather than the inclusion of the outermost core electrons in the Hartree–Fock calculation. At the PMP4/HW3TZ/6-31G(d)//MP2/HW3TZ/6-31G(d) level, the theoretically predicted Fe? C bond energies for FeCH are in the range of 80% of the experimental values and have nearly the same accuracy as all-electron calculations using large valence basis sets and the MCPF method for the correlation energy. © 1992 by John Wiley & Sons, Inc.     

硼碳团簇BnC2 (n＝1～6)的理论研究

应用密度泛函理论在B3LYP/6-311＋G(d)水平上研究了硼碳团簇B_nC₂ (n＝1～6)的几何结构、生长机制和相对稳定性. 计算结果表明, 对于n＝2～6的簇, 平面多环状构型为最稳定的结构, 其中C原子分布于环的顶点、有尽可能多的三配位硼原子和尽可能多的B—C键. 碳原子作为杂原子倾向掺杂于团簇的顶点位置, 它的掺杂不改变硼团簇的主体结构. 与平面多环状结构相比, 随着簇尺寸的增大, 三维结构和线性链结构更不稳定. 在低能线性结构中, C原子位于链两侧的第二个位置. 计算的碎片分裂能、递增键能以及HOMO-LUMO能隙表明, B₄C₂为幻数簇.     

Conformers and intramolecular hydrogen bonding of the oxalic acid monomer and its anions

Density functional theory, B3LYP/6‐31G** and B3LYP/6‐311+G(2d,p), and ab initio MP2/6‐31G** calculations have been carried out to investigate the conformers, transition states, and energy barriers of the conformational processes of oxalic acid and its anions. QCISD/6‐31G** geometrical optimization is also performed in the stable forms. Its calculated energy differences between the two most stable conformers are very near to the related observed value at 7.0 kJ/mol. It is found that the structures and relative energies of oxalic acid conformers predicted by these methods show similar results, and that the conformer L1 (C_2h) with the double‐interfunctional‐groups hydrogen bonds is the most stable conformer. The magnitude of hydrogen bond energies depends on the energy differences of various optimized structures. The hydrogen bond energies will be about 32 kJ/mol for interfunctional groups, 17 kJ/mol for weak interfunctional groups, 24 kJ/mol for intra‐COOH in (COOH)₂, and 60 kJ/mol for interfunctional groups in (COOH)COO⁻¹ ion if calculated using the B3LYP/6‐311+G(2d,p) method. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 541–551, 2000     

Proton affinities of the N- and C-terminal segments arising upon the dissociation of the amide bond in protonated peptides

Dissociation of the amide bonds in a protonated peptide leads to N-terminal sequence fragments with cyclic structures and C-terminal sequence fragments with linear structures. The ionic fragments containing the N-terminus (b _n ) have been shown to be protonated oxazolones, whereas those containing the C-terminus (y _n ) are protonated linear peptides. The coproduced neutral fragments are cyclic peptides from the N-terminus and linear peptides from the C-terminus. A likely determinant of these structural choices is the proton affinity (PA) of the described peptide segments. This study determines the PA values of such segments (Pep), i.e., cyclic and linear dipeptides and a relevant oxazolone, based on the dissociations of proton-bound dimers [Pep + B _i ]H⁺ in which B _i is a reference base of known PA value (Cooks kinetic method). The dissociations are assessed at different internal energies to thereby obtain both proton affinities as well as entropies of protonation. For species with comparable amino acid composition, the proton affinity (and gas phase basicity) follows the order cyclic peptide ≪ oxazolone ≈ linear peptide. This ranking is consistent with dissociation of the protonated peptide via interconverting proton-bound complexes involving N-terminal oxazolone (O) or cyclopeptide (C) segments and C-terminal linear peptide segments (L), viz. O ⋯ H⁺ ⋯ L ⇄ C ⋯ H⁺ ⋯ L. N-terminal sequence ions (b _n ) are formed with oxazolone structures which can efficiently compete for the proton with the linear segments. On the other hand, N-terminal neutral fragments detach as cyclic peptides, with H⁺ now being retained by the more basic linear segment from the C-terminus to yield y _n .     

Effect of method of ion preparation on low-energy collision-induced dissociation mass spectra

The collision-induced dissociation (CID) mass spectra of protonated cocaine and protonated heroin have been measured using a triple quadrupole mass spectrometer at 50 eV ion/neutral collision energy for protonated molecules prepared by different protonating agents. The CID mass spectra of protonated cocaine using H⁺(H₂O)_n, H⁺(NH₃)_n and H⁺((CH₃)₂NH)_n as protonating agents are essentially identical and it is concluded that, regardless of the initial site of protonation, the fragmentation reactions occurring on collisional activation are identical. By contrast, protonated heorin prepared with H⁺(H₂O)_n and H⁺(NH₃)_n as protonating agents show substantial differences. That formed by reaction of H⁺(H₂O)_n shows a much more abundant peak corresponding to loss of CH₃CO₂H. From a comparison with model compounds, and from a consideration of the three-dimensional structure of heroin, it is concluded that with H⁺(H₂O)_n as protonating agent significant protonation occurs at the acetate group attached to the alicyclic ring, leading to acetic acid loss on collisional activation, but that reaction of H⁺(NH₃)_n leads to protonation at the nitrogen function. The proton attached to nitrogen cannot interact with the acetate group and, consequently, the probability of loss of acetic acid on collislional activation is greatly reduced.     

线性BC2nB (n＝1～12)的结构特征和电子光谱的理论研究

应用密度泛函理论, 在B3LYP/6-31G^*水平上优化得到了线性簇合物BC_2nB (n＝1～12, D_(h)的平衡几何构型, 并计算了它们的谐振动频率. 在优化平衡几何构型下, 通过TD-B3LYP/cc-pvDZ和TD-B3LYP/cc-pvTZ计算, 分别得到了n＝1～12和n＝1～7的电子跃迁的垂直激发能和对应的振子强度. 在B3LYP/6-311＋G^*水平上计算得到了簇合物BC_2nB (n＝1～12, D_(h)的电离能. 基于计算结果, 导出了BC_2nB体系电子跃迁能以及第一电离能与体系大小n的解析表达式.     

Structures and thermochemistry of ions formed by methane chemical ionization of Fe(CO)5. Site of protonation and determination of Fe?H and Fe?CO bond dissociation energies of HFe(CO)n+ ions

High-energy collisional activation mass spectrometry of HFe(CO)₅⁺ ions shows that Fe(CO)₅ is protonated on the iron atom rather than on one of the ligands. This finding is supported by ab initio quantum chemical calculations. The value of the proton affinity of Fe(CO)₅ was measured by high-pressure mass spectrometry to be 857 kJ mol^?1. The Fe? CO bond dissociation energies for HFe(CO)_n⁺ (n = 1–5) were measured by energy-variable low-energy collisional activation mass spectrometry. The Fe? H bond dissociation energies in HFe(CO)_n⁺ ions were also determined. A synergistic effect on the strengths of the Fe? H and Fe? CO bonds in HFe(CO)⁺ is noticed. It is demonstrated that the electronically unsaturated species HFe(CO)_n⁺ (n = 3, 4) formed in exothermic proton-transfer reactions with Fe(CO)₅ form adducts with CH₄. Adducts between C₂H₅⁺ or C₃H₅⁺ and Fe(CO)_n are observed. These adducts are probably formed in direct reactions between the respective carbocations and Fe(CO)₅.     

Geometry,basis set,and correlation energy dependence of computed protonation energies of imino bases

The nitrogen protonation energies of the imino bases HN?CHR, where R is H, CH₃, NH₂, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree–Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree–Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree–Fock nitrogen protonation energies of the imino bases HN?CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O?CHR.