Absolute thermodynamic measurements of alkali metal cation interactions with a simple dipeptide and tripeptide

Absolute bond dissociation energies (BDEs) of glycylglycine (GG) and glycylglycylglycine (GGG) to sodium and potassium cations and sequential bond energies of glycine (G) in Na+G2 were determined experimentally by threshold collision-induced dissociation (TCID) in a guided ion beam tandem mass spectrometer. Experimental results showed that the binding energies follow the order of Na+ > K+ and M+GGG > M+GG > M+G. Theoretical calculations at the B3LYP/6-311+G(d) level show that all complexes had charge-solvated structures (nonzwitterionic) with either [CO,CO] bidentate or [N,CO,CO] tridentate coordination for M+GG complexes, [CO,CO,CO] tridentate or [N,CO,CO,CO] tetradentate coordination for M+GGG complexes, and [N,CO,N,CO] tetradentate coordination for Na+G2. Ab initio calculations at three different levels of theory (B3LYP, B3P86, and MP2(full) using the 6-311+G(2d,2p) basis set with geometries and zero-point energies calculated at the B3LYP/6-311+G(d) level) show good agreement with the experimental bond energies. This study demonstrates for the first time that TCID measurements of absolute BDEs can be successfully extended to biological molecules as complex as a tripeptide.     

CO2 insertion into metal-carbon bonds: a computational study of Rh(I) pincer complexes

Catalytic carboxylation reactions that use CO(2) as a C1 building block are still among the 'dream reactions' of molecular catalysis. To obtain a deeper insight into the factors that control the fundamental steps of potential catalytic cycles, we performed a detailed computational study of the insertion reaction of CO(2) into rhodium-alkyl bonds. The minima and transition-state geometries for 38 pincer-type complexes were characterized and the according energies for the C-C bond-forming step were determined. The electronic properties of the Rh-alkyl bond were found to be more important for the magnitude of the activation barrier than the interaction between rhodium and CO(2). The charge of the alkyl-chain carbon atom, as well as agostic and orbital interactions with the rhodium, exhibit the most pronounced influence on the energy of the transition states for the CO(2) insertion reaction. By varying the backbone and the donor groups of the pincer ligand those properties can be tuned over a very broad range. Thus, it is possible to match the electronic and steric properties with the fundamental requirements of the CO(2) insertion into rhodium-alkyl bonds of the ligand framework.     

Ethanol electrooxidation onto stepped surfaces modified by Ru deposition: electrochemical and spectroscopic studies

Oxidation of ethanol on ruthenium-modified Pt(775) and Pt(332) stepped electrodes has been studied using electrochemical and FTIR techniques. It has been found that the oxidation of ethanol on these electrodes takes place preferentially on the step sites yielding CO(2) as the major final product. The cleavage of the C-C bond, which is the required step to yield CO(2), occurs only on this type of site. The presence of low ruthenium coverages on the step sites promotes the complete oxidation of ethanol since it facilitates the oxidation of CO formed on the step from the cleavage of the C-C bond. However, high ruthenium coverages have an important inhibiting effect since the adatoms block the step sites, which are required for the cleavage of the C-C bond. Under these conditions, the oxidation current diminishes and the major product in the oxidation process is acetic acid, which is the product formed preferentially on the (111) terrace sites.     

The catalytic mechanism of mouse renin studied with QM/MM calculations

Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.     

Progressive systematic underestimation of reaction energies by the B3LYP model as the number of C-C bonds increases: why organic chemists should use multiple DFT models for calculations involving polycarbon hydrocarbons

[reaction: see text] Computational studies of three different reaction types involving hydrocarbons (homolytic C-C bond breaking of alkanes, progressive insertions of triplet methylene into C-H bonds of ethane, and [2+2] cyclizations of methyl-substituted alkenes to form polymethylcyclobutanes) show that the B3LYP model consistently underestimates the reaction energy, even when extremely large basis sets are employed. The error is systematic and cumulative, such that the reaction energies of reactions involving hydrocarbons with more than 4-6 C-C bonds are predicted quite poorly. Energies are underestimated for slightly and highly methyl-substituted cyclic and acyclic hydrocarbons, so the errors do not arise from structural issues such as steric repulsion or ring strain energy. We trace the error associated with the B3LYP approach to its consistent underestimation of the C-C bond energy. Other DFT models show this problem to lesser extents, while the MP2 method avoids it. As a consequence, we discourage the use of the B3LYP model for reaction energy calculations for organic compounds containing more than four carbon atoms. We advocate use of a collection of pure and hybrid DFT models (and ab initio models where possible) to provide computational "error bars".     

Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid

On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.     

Toward a small molecule, biomimetic carbonic anhydrase model: theoretical and experimental investigations of a panel of zinc(II) aza-macrocyclic catalysts

A panel of five zinc-chelated aza-macrocycle ligands and their ability to catalyze the hydration of carbon dioxide to bicarbonate, H(2)O + CO(2) → H(+) + HCO(3)(–), was investigated using quantum-mechanical methods and stopped-flow experiments. The key intermediates in the reaction coordinate were optimized using the M06-2X density functional with aug-cc-pVTZ basis set. Activation energies for the first step in the catalytic cycle, nucleophilic CO(2) addition, were calculated from gas-phase optimized transition-state geometries. The computationally derived trend in activation energies was found to not correspond with the experimentally observed rates. However, activation energies for the second, bicarbonate release step, which were estimated using calculated bond dissociation energies, provided good agreement with the observed trend in rate constants. Thus, the joint theoretical and experimental results provide evidence that bicarbonate release, not CO(2) addition, may be the rate-limiting step in CO(2) hydration by zinc complexes of aza-macrocyclic ligands. pH-independent rate constants were found to increase with decreasing Lewis acidity of the ligand-Zn complex, and the trend in rate constants was correlated with molecular properties of the ligands. It is suggested that tuning catalytic efficiency through the first coordination shell of Zn(2+) ligands is predominantly a balance between increasing charge-donating character of the ligand and maintaining the catalytically relevant pK(a) below the operating pH.     

Ferric superoxide and ferric hydroxide are used in the catalytic mechanism of hydroxyethylphosphonate dioxygenase: a density functional theory investigation

Hydroxyethylphosphonate dioxygenase (HEPD) is a mononuclear nonheme iron enzyme that utilizes an O(2) molecule to cleave a C-C bond in 2-hydroxyethylphosphonate and produce hydroxymethylphosphonate (HMP) and formic acid. Density functional theory calculations were performed on an enzyme active-site model of HEPD to understand its catalytic mechanism. The reaction starts with H-abstraction from the C2 position of 2-HEP by a ferric superoxide-type (Fe(III)-OO(?-)) intermediate, in a similar manner to the H-abstraction in the reaction of the dinuclear iron enzyme myo-inositol oxygenase. The resultant Fe(II)-OOH intermediate may follow either a hydroperoxylation or hydroxylation pathway, the former process being energetically more favorable. In the hydroperoxylation pathway, a ferrous-alkylhydroperoxo intermediate is formed, and then its O-O bond is homolytically cleaved to yield a complex of ferric hydroxide with a gem-diol radical. Subsequent C-C bond cleavage within the gem-diol leads to formation of an R-CH(2)(?) species and one of the two products (i.e., formic acid). The R-CH(2)(?) then intramolecularly forms a C-O bond with the ferric hydroxide to provide the other product, HMP. The overall reaction pathway does not require the use of a high-valent ferryl intermediate but does require ferric superoxide and ferric hydroxide intermediates.     

Comprehensive density functional theory study on serine and related ions in gas phase: conformations, gas phase basicities, and acidities

Density functional theory (DFT) calculations have been performed to investigate the gas-phase conformations of serine and its three related ions (serineH(+), serine(-), and serine(2-)). The full ensemble of possible conformations, 324 conformations for serine, 108 for serineH(+), 162 for serine(-) and 54 for serine(2-), were first surveyed at B3LYP/6-31G level, and then the obtained unique conformations were further refined at B3LYP/6-311+G level. From full optimizations, 74 unique conformations for seine, 14 for serineH(+), 11 for serine(-), and 4 for serine(2-) were located, and their relative energies were also determined at B3LYP/6-311+G level. Atoms in molecules (AIM) analysis was carried out to establish rigorous definition of hydrogen bonds. Six types of intramolecular H-bonds in conformers of serine, six types in serineH(+), three types in serine(-), and two types in serine(2-) were identified within the framework of AIM theory and their relative strengths were determined based on topological properties at bond critical points (BCPs) of H-bonds. The intramolecular H-bonds were demonstrated to play an important role in deciding the relative stability of conformations of amino acids and the related ions. The enthalpies and Gibbs free energies of protonation and deprotonation reactions of serine and its related ions were calculated at B3LYP/6-311+G//B3LYP/6-31G, and B3LYP/6-311+G//B3LYP/6-311+G level. The calculated results are both in excellent agreement with the experimental data. We demonstrate in this study that B3LYP is an efficient and accurate method to predict the thermochemical and structural parameters of amino acids and the related ions.     

Comparison of hydration reactions for "piano-stool" RAPTA-B and [Ru(η6-arene)(en)Cl]+ complexes: density functional theory computational study

The hydration process for two Ru(II) representative half-sandwich complexes: Ru(arene)(pta)Cl(2) (from the RAPTA family) and [Ru(arene)(en)Cl](+) (further labeled as Ru_en) were compared with analogous reaction of cisplatin. In the study, quantum chemical methods were employed. All the complexes were optimized at the B3LYP/6-31G(d) level using Conductor Polarizable Continuum Model (CPCM) solvent continuum model and single-point (SP) energy calculations and determination of electronic properties were performed at the B3LYP∕6-311++G(2df,2pd)/CPCM level. It was found that the hydration model works fairly well for the replacement of the first chloride by water where an acceptable agreement for both Gibbs free energies and rate constants was obtained. However, in the second hydration step worse agreement of the experimental and calculated values was achieved. In agreement with experimental values, the rate constants for the first step can be ordered as RAPTA-B > Ru_en > cisplatin. The rate constants correlate well with binding energies (BEs) of the Pt∕Ru-Cl bond in the reactant complexes. Substitution reactions on Ru_en and cisplatin complexes proceed only via pseudoassociative (associative interchange) mechanism. On the other hand in the case of RAPTA there is also possible a competitive dissociation mechanism with metastable pentacoordinated intermediate. The first hydration step is slightly endothermic for all three complexes by 3-5 kcal∕mol. Estimated BEs confirm that the benzene ligand is relatively weakly bonded assuming the fact that it occupies three coordination positions of the Ru(II) cation.     

Hydration and water-exchange mechanism of the UO2 2+ ion revisited: the validity of the "n + 1" model

Hydration and water-exchange mechanism of the UO2(2+) ion was studied by the B3LYP calculations. Relative Gibbs energies in aqueous phase of the 4-, 5-, and 6-fold uranyl(VI) hydrates were compared. A model with a complete first hydration shell and one water in the second shell was used (which is called "n + 1" model) to compare the energy of the UO2(2+) ion with different hydration numbers. The n + 1 model tends to overestimate the overall stability of the complex, and this type of model should be carefully used for the determination of the coordination number or the coordination mode such as unidentate or bidentate. A stable 5-fold uranyl(VI) hydrate goes through a very rapid water-exchange process via an associative (A-) mechanism keeping the 5-fold uranyl(VI) the dominant species.     

Experimental and DFT studies of the conversion of ethanol and acetic acid on PtSn-based catalysts

Reaction kinetics studies were conducted for the conversions of ethanol and acetic acid over silica-supported Pt and Pt/Sn catalysts at temperatures from 500 to 600 K. Addition of Sn to Pt catalysts inhibits the decomposition of ethanol to CO, CH4, and C2H6, such that PtSn-based catalysts are active for dehydrogenation of ethanol to acetaldehyde. Furthermore, PtSn-based catalysts are selective for the conversion of acetic acid to ethanol, acetaldehyde, and ethyl acetate, whereas Pt catalysts lead mainly to decomposition products such as CH4 and CO. These results are interpreted using density functional theory (DFT) calculations for various adsorbed species and transition states on Pt(111) and Pt3Sn(111) surfaces. The Pt3Sn alloy slab was selected for DFT studies because results from in situ (119)Sn M?ssbauer spectroscopy and CO adsorption microcalorimetry of silica-supported Pt/Sn catalysts indicate that Pt-Sn alloy is the major phase present. Accordingly, results from DFT calculations show that transition-state energies for C-O and C-C bond cleavage in ethanol-derived species increase by 25-60 kJ/mol on Pt3Sn(111) compared to Pt(111), whereas energies of transition states for dehydrogenation reactions increase by only 5-10 kJ/mol. Results from DFT calculations show that transition-state energies for CH3CO-OH bond cleavage increase by only 12 kJ/mol on Pt3Sn(111) compared to Pt(111). The suppression of C-C bond cleavage in ethanol and acetic acid upon addition of Sn to Pt is also confirmed by microcalorimetric and infrared spectroscopic measurements at 300 K of the interactions of ethanol and acetic acid with Pt and PtSn on a silica support that had been silylated to remove silanol groups.     

A computational study on addition of Grignard reagents to carbonyl compounds

The mechanism of stereoselective addition of Grignard reagents to carbonyl compounds has been investigated using B3LYP density functional theory calculations. The study of the reaction of methylmagnesium chloride and formaldehyde in dimethyl ether revealed a new reaction path involving carbonyl compound coordination to magnesium atoms in a dimeric Grignard reagent. The structure of the transition state for the addition step shows that an interaction between a vicinal-magnesium bonding alkyl group and C=O causes the C-C bond formation. The simplified mechanism shown by this model is in accord with the aggregation nature of Grignard reagents and their high reactivities toward carbonyl compounds. Concerted and four-centered formation of strong O-Mg and C-C bonds was suggested as a polar mechanism. When the alkyl group is bulky, C-C bond formation is blocked and the Mg-O bond formation takes precedence. A diradical is formed with the odd spins localized on the alkyl group and carbonyl moiety. Diradical formation and its recombination were suggested to be a single electron transfer (SET) process. The criteria for the concerted polar and stepwise SET processes were discussed in terms of precursor geometries and relative energies.     

Experimental and theoretical investigation of alkali metal cation interactions with hydroxyl side-chain amino acids

Absolute bond dissociation energies of serine (Ser) and threonine (Thr) to alkali metal cations are determined experimentally by threshold collision-induced dissociation of M+AA complexes, where M+=Li+, Na+, and K+ and AA=Ser and Thr, with xenon in a guided ion beam tandem mass spectrometer. Experimental results show that the binding energies of both amino acids to the alkali metal cations are very similar to one another and follow the order of Li+>Na+>K+. Quantum chemical calculations at three different levels, B3LYP, B3P86, and MP2(full), using the 6-311+G(2d,2p) basis set with geometries and zero-point energies calculated at the B3LYP/6-311+G(d,p) level show good agreement with the experimental bond energies. Theoretical calculations show that all M+AA complexes have charge-solvated structures (nonzwitterionic) with [CO, N, O] tridentate coordination.     

Catalytic C-C bond cleavage and C-Si bond formation in the reaction of RCN with Et3SiH promoted by an iron complex

Catalytic C-C bond cleavage of acetonitrile and C-Si bond formation have been attained in the photoreaction of MeCN with Et3SiH in the presence of an iron complex, Cp(CO)2FeMe. This catalytic system can be applied for arylnitrile C-C bond cleavage.     

Potential interstellar molecules. Formation of neutral C(6)CO from C(6)CO(-*) in the gas phase

Computations at the RCCSD(T)/aug-cc-pVDZ//B3LYP/6-31G* level of theory indicate that neutral C(6)CO is a stable species. The ground state of this neutral is the singlet cumulene oxide :C=C=C=C=C=C=C=O. The adiabatic electron affinity and dipole moment of singlet C(6)CO are 2.47 eV and 4.13 D, respectively, at this level of theory. The anion (C(6)CO)-* should be a possible precursor to this neutral. It has been formed by an unequivocal synthesis in the ion source of a mass spectrometer by the S(N)2(Si) reaction between (CH(3))(3)Si-C(triple bond)C-C(triple bond)C-C(triple bond)C-CO-CMe(3) and F(-) to form (-)C(triple bond)C-C(triple bond)C-C(triple bond)C-CO-Me(3) which loses Me(3)C* in the source to form C(6)CO(-)*. Charge stripping of this anion by vertical Franck-Condon oxidation forms C(6)CO, characterised by the neutralisation-reionisation spectrum (-NR(+)) of C(6)CO(-*), which is stable during the timeframe of this experiment (10(-6) s).     

Carbon-carbon bond cleavage of diynes through the hydroamination with transition metal catalysts

The C-C bond cleavage of terminal and internal diynes takes place readily in the presence of catalytic amounts of Ru3(CO)12 or Pd(NO3)2 and of 2-aminophenol, giving the corresponding benzoxazoles and ketones in good to high yields. There are two different modes of the bond cleavage: (a) an alkyne C-C triple bond is cleaved, and (b) the C-C single bond between the two alkyne groups is cleaved.     

取代氯苯化合物的电子结构和键离解能的理论研究

利用密度泛函（DFT）三种交换／相关函数（B3LYP,B3PW91,B3P86）结合6—31G^＊＊和 6-311G^＊＊基组,计算了13个取代氯苯化合物的键离解能．结果表明B3PS6／6—311G^＊＊方法是计算取代氯苯化合物键离解能的可信方法,研究发现C—Cl键的键离解能与所使用的基组和计算方法密切相关,取代基对C—Cl键的键离解能的影响不明显．研究了目标化合物的前线轨道能级差,并对取代氯苯化合物的热稳定性做了评估．     

The rotational barrier in ethane: a molecular orbital study

The energy change on each Occupied Molecular Orbital as a function of rotation about the C-C bond in ethane was studied using the B3LYP, mPWB95 functional and MP2 methods with different basis sets. Also, the effect of the ZPE on rotational barrier was analyzed. We have found that σ and π energies contribution stabilize a staggered conformation. The σ(s) molecular orbital stabilizes the staggered conformation while the stabilizes the eclipsed conformation and destabilize the staggered conformation. The π(z) and molecular orbitals stabilize both the eclipsed and staggered conformations, which are destabilized by the π(v) and molecular orbitals. The results show that the method of calculation has the effect of changing the behavior of the energy change in each Occupied Molecular Orbital energy as a function of the angle of rotation about the C-C bond in ethane. Finally, we found that if the molecular orbital energy contribution is deleted from the rotational energy, an inversion in conformational preference occurs.     

C-C and C-H bond activation reactions in N-heterocyclic carbene complexes of ruthenium

Thermolysis of Ru(PPh3)3(CO)H2 with the N-heterocyclic carbene bis(1,3-(2,4,6-trimethylphenyl)imidazol-2-ylidene) (IMes) results in C-C activation of an Ar-CH3 bond in one of the mesityl rings of the carbene ligand. Upon addition of IMes to Ru(PPh3)3(CO)H2 at room temperature in the presence of an alkene, C-H bond activation is observed instead. The thermodynamics of these C-C and C-H cleavage reactions have been probed using density functional theory.