Steric effects on alkyl cation affinities of maingroup-element hydrides

We have carried out an extensive exploration of gas‐phase alkyl cation affinities (ACA) of archetypal anionic and neutral bases across the periodic system using zeroth order regular approximation‐relativistic density functional theory at BP86/QZ4P//BP86/TZ2P. ACA values were computed for the methyl, ethyl, i‐propyl and t‐butyl cations and compared with the corresponding proton affinities (PA). One purpose of this work is to provide an intrinsically consistent set of values of the 298 K ACA of all anionic (XH) and neutral bases (XH_n) constituted by maingroup‐element hydrides of groups 14–17 and the noble gases (group 18) along the periods 1–6. Another purpose is to determine and rationalize the trend in affinity for a cation as the latter varies from proton to t‐butyl cation. This undertaking is supported by quantitative bond energy decomposition analyses. Correlations are established between PA and ACA values. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Alkali Metal Cation Affinities of Anionic Main Group‐Element Hydrides Across the Periodic Table

We have carried out an extensive exploration of gas‐phase alkali metal cation affinities (AMCA) of archetypal anionic bases across the periodic system using relativistic density functional theory at ZORA‐BP86/QZ4P//ZORA‐BP86/TZ2P. AMCA values of all bases were computed for the lithium, sodium, potassium, rubidium and cesium cations and compared with the corresponding proton affinities (PA). One purpose of this work is to provide an intrinsically consistent set of values of the 298 K AMCAs of all anionic (XH_{n ‐1}⁻) constituted by main group‐element hydrides of groups 14–17 along the periods 2–6. In particular, we wish to establish the trend in affinity for a cation as the latter varies from proton to, and along, the alkali cations. Our main purpose is to understand these trends in terms of the underlying bonding mechanism using Kohn–Sham molecular orbital theory together with a quantitative bond energy decomposition analyses (EDA).     

Understanding the reactivity and basicity of zeolites: a periodic DFT study of the disproportionation of N(2)O(4) on alkali-cation-exchanged zeolite Y

The disproportionation of N(2)O(4) into NO(3)(-) and NO(+) on Y zeolites has been studied through periodic DFT calculations to unravel 1) the role of metal cations and the framework oxygen atoms and 2) the relationship between the NO(+) stretching frequency and the basicity of zeolites. We have considered three situations: adsorption on site II cations with and without a cation at site III and adsorption on a site III cation. We observed that cations at sites II and III cooperate to stabilize N(2)O(4) and that the presence of a cation at site III is necessary to allow the disproportionation reaction. The strength of the stabilization is due to the number of stabilizing interactions increasing with the size of the cation and to the Lewis acidity of the alkali cations, which increases as the size of the cations decreases. In the product, NO(3)(-) interacts mainly with the cations and NO(+) with the basic oxygen atoms of the tetrahedral aluminium through its nitrogen atom. As the cation size increases, the NO(3)(-)...cation interaction increases. As a result, the negative charge of the framework is less well screened by the larger cations and the interaction between NO(+) and the basic oxygen atoms becomes stronger. NO(+) appears to be a good probe of zeolite basicity, in agreement with experimental observations.     

Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

Excited-state properties and environmental effects for protonated schiff bases: a theoretical study.

Complete active space self-consistent field (CASSCF), multireference configuration interaction (MRCI), density functional theory (DFT), time dependent DFT (TDDFT) and the singles and doubles coupled-cluster (CC2) methodologies have been used to study the ground state and excited states of protonated and neutral Schiff bases (PSB and SB) as models for the retinal chromophore. Systems with two to four conjugated double bonds are investigated. Geometry relaxation effects are studied in the excited pipi* state using the aforementioned methods. Taking the MRCI results as reference we find that CASSCF results are quite reliable even though overshooting of geometry changes is observed. TDDFT does not reproduce bond alternation well in the pipi* state. CC2 takes an intermediate position. Environmental effects due to solvent or protein surroundings have been studied in the excited states of the PSBs and SBs using a water molecule and solvated formate as model cases. Particular emphasis is given to the proton transfer process from the PSB to its solvent partner in the excited state. It is found that its feasibility is significantly enhanced in the excited state as compared to the ground state, which means that a proton transfer could be initiated already at an early step in the photodynamics of PSBs.     

Understanding the acid-base properties of adenosine: the intrinsic basicities of N1, N3 and N7

Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H(3) (Ado)(3+) , and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H(+) and (N7)H(+). However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, pK(H)(H(3))((Ado)) = -4.02 and pK(H)(H(2))((Ado)) = -1.53; the third one was re-measured as pK(H)(H)((Ado)) = 3.64 ± 0.02 (25 °C; I=0.5 M, NaNO(3)), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H(+) site; this constant has now been determined in an unequivocal manner, and that of the (N3)H(+) site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H(+) site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order pk(N7-N1)(N7(Ado)N1·H)) = 3.63 ± 0.02 > pk(N7-N1)(H·N7(Ado)N1) = 2.15 ± 0.15 > pk(N3-N1,N7)(H·N3(Ado)N1,N7) =1.5 ± 0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above-mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)(+) , in aqueous solution; the results are 96.1, 3.2, and 0.7% for N7(Ado)N1·H(+), (+)H·N7(Ado)N1, and (+)H·N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)(+) exists to the largest part as N7(Ado)N1·H(+) having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion-binding properties; these aspects are briefly discussed.     

On the accuracy of DFT methods in reproducing ligand substitution energies for transition metal complexes in solution: the role of dispersive interactions

The performance of a series of density functionals when tested on the prediction of the phosphane substitution energy of transition metal complexes is evaluated. The complexes Fe-BDA and Ru-COD (BDA=benzylideneacetone, COD=cyclooctadiene) serve as reference systems, and calculated values are compared with the experimental values in THF as obtained from calorimetry. Results clearly indicate that functionals specifically developed to include dispersion interactions usually outperform other functionals when BDA or COD substitution is considered. However, when phosphanes of different sizes are compared, functionals including dispersion interactions, at odd with experimental evidence, predict that larger phosphanes bind more strongly than smaller phosphanes, while functionals not including dispersion interaction reproduce the experimental trends with reasonable accuracy. In case of the DFT-D functionals, inclusion of a cut-off distance on the dispersive term resolves this issue, and results in a rather robust behavior whatever ligand substitution reaction is considered.     

Adsorption of uranyl species onto the rutile (110) surface: a periodic DFT study

To model the structures of dissolved uranium contaminants adsorbed on mineral surfaces and further understand their interaction with geological surfaces in nature, we have performed periodic density funtional theory (DFT) calculations on the sorption of uranyl species onto the TiO₂ rutile (110) surface. Two kinds of surfaces, an ideal dry surface and a partially hydrated surface, were considered in this study. The uranyl dication was simulated as penta‐ or hexa‐coordinated in the equatorial plane. Two bonds are contributed by surface bridging oxygen atoms and the remaining equatorial coordination is satisfied by H₂O, OH^?, and CO₃^2? ligands; this is known to be the most stable sorption structure. Experimental structural parameters of the surface–[UO₂(H₂O)₃]²⁺ system were well reproduced by our calculations. With respect to adsorbates, [UO₂(L1)_x(L2)_y(L3)_z]ⁿ (L1=H₂O, L2=OH^?, L3=CO₃^2?, x≤3, y≤3, z≤2, x+y+2z≤4), on the ideal surface, the variation of ligands from H₂O to OH^? and CO₃^2? lengthens the U? O_surf and U? Ti distances. As a result, the uranyl–surface interaction decreases, as is evident from the calculated sorption energies. Our calculations support the experimental observation that the sorptive capacity of TiO₂ decreases in the presence of carbonate ions. The stronger equatorial hydroxide and carbonate ligands around uranyl also result in U?O distances that are longer than those of aquouranyl species by 0.1–0.3 Å. Compared with the ideal surface, the hydrated surface introduces greater hydrogen bonding. This results in longer U?O bond lengths, shorter uranyl–surface separations in most cases, and stronger sorption interactions.     

Ab initio molecular dynamics free-energy study of microhydration effects on the neutral-zwitterion equilibrium of phenylalanine.

The structures and relative energies of the most stable conformers of both naked and microsolvated phenylalanine, Phe.(H(2)O)(n)(n=0-3), are calculated by density functional theory. For selected structures, coordination-constrained ab initio molecular dynamics simulations determine the proton-transfer mechanism connecting neutral and zwitterionic forms of Phe. The associated free-energy profiles are calculated by thermodynamic integration. While no zwitterionic free-energy minimum is found for naked Phe, microsolvation is found to stabilize the zwitterionic form. For cluster sizes n > or = 3, the proton-transfer equilibrium shifts towards the zwitterionic structure for specific proton-transfer pathways. The energetically most favourable interconversion path between the neutral and zwitterionic forms is through a H(2)O bridge with free-energy barriers as low as 14.4 kJ mol(-1) for Phe.(H(2)O)(3). The free energy required for breaking a carboxylic OH bond involved in intramolecular hydrogen bonding is typically lower than in the water-assisted case. However, the resulting zwitterion turns out to be unstable with respect to the backward proton-transfer reaction.     

Solvent/base effects in the selective domino synthesis of phenanthridinones that involves high-valent palladium species: experimental and theoretical studies

The domino reaction of o-bromobenzamides 1a-m in the presence of K(2)CO(3) and the [PdCl(2)(PPh(3))(2)] catalyst granted a selective access to phenanthridinones 2 or to the new 1-carboxamide phenanthridinones 3 depending on the solvent, DMF or 1,4-dioxane, respectively. Investigations of the reaction parameters provided the first example of a direct correlation between the base dissociation and the solvent polarity on the selectivity observed. Moreover, mechanistic studies (NMR spectroscopy and ESI-MS monitoring) allowed us to characterize Pd(II) palladacycle 4 and biaryl species as common intermediates for these two domino processes. On that basis, C(sp(2))-C(sp(2)) bond formation is envisaged by generation of a Pd(IV) complex after oxidative addition of 1 into Pd(II) palladacycle 4, a rationale that is supported by DFT calculations. A general catalytic cycle is proposed to account for these observations.     

Proton Affinities of Cationic Carbone Adducts [AC(PPh3)2]+ (A=Halogen,Hydrogen, Methyl) and Unusual Electronic Structures of the Cations and Dications [AC(H)(PPh3)2]2+

This work reports the syntheses and the first crystal structures of the cationic carbone adducts [FC(PPh₃)₂]⁺ and [BrC(PPh₃)₂]⁺ and the protonated dication [FC(H)(PPh₃)₂]²⁺, which are derived from the carbone C(PPh₃)₂. Quantum chemical calculations and bonding analyses were carried out for the series of cations [AC(PPh₃)₂]⁺ and dications [AC(H)(PPh₃)₂]²⁺, where A=H, Me, F, Cl, Br, I. The bonding analysis suggests that the cations are best described as phosphane complexes L→(CA)⁺←L (L=PPh₃), which are related to the neutral borylene adducts L→(BA)←L (L=cyclic carbene; A=H, aryl) that were recently isolated. The carbone adducts [AC(PPh₃)₂]⁺ possess a π electron lone pair at carbon and they can easily be protonated to the dications [AC(H)(PPh₃)₂]²⁺. The calculations of the dications indicate that the molecules are best represented as complexes L→(CHA)²⁺←L (L=PPh₃) where a carbene dication is stabilized by the ligands. The central carbon atom in the cations and even in the dications carries a negative partial charge, which is larger than the negative charge at fluorine. There is also the peculiar situation in which the carbon–fluorine bonds in [FC(PPh₃)₂]⁺ and [FC(H)(PPh₃)₂]²⁺ exhibit the expected polarity with the negative end at fluorine, but the carbon atom has a larger negative charge than fluorine. Given the similarity of carbodiphosphorane C(PPh₃)₂ and carbodicarbene C(NHC)₂, we expect that analogous compounds [AC(NHC)₂]⁺ and [AC(H)(NHC)₂]²⁺ with similar features as [AC(PPh₃)₂]⁺ and [AC(H)(PPh₃)₂]²⁺ can be isolated.