Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

A density functional study of the hydrolysis reaction of phosphodiesters with a series of attacking nucleophiles in the gas phase and in solution is presented. The nucleophiles HOH, HO-, CH3OH, and CH3O- were studied in reactions with ethylene phosphate, 2'3'-ribose cyclic phosphate and in their neutral (protonated) and monoanionic forms. Stationary-point geometries for the reactions were determined at the density functional B3LYP/6-31++G(d,p) level followed by energy refinement at the B3LYP/6-311++G(3df,2p) level. Solvation effects were estimated by using a dielectric approximation with the polarizable continuum model (PCM) at the gas-phase optimized geometries. This series of reactions characterizes factors that influence the intrinsic reactivity of the model phosphate compounds, including the effect of nucleophile, protonation state, cyclic structure, and solvent. The present study of the in-line mechanism for phosphodiester hydrolysis, a reaction of considerable biological importance, has implications for enzymatic mechanisms. The analysis generally supports the associative mechanism for phosphate ester hydrolysis. The results highlight the importance for the reaction barrier of charge neutralization resulting from the protonation of the nonbridging phosphoryl oxygens and the role of internal hydrogen transfer in the gas-phase mechanism. It also shows that solvent stabilization has a profound influence on the relative barrier heights for the dianionic, monoanionic, and neutral reactions. The calculations provide a comprehensive data set for the in-line hydrolysis mechanisms that can be used for the development of improved semiempirical quantum models for phosphate hydrolysis reactions.     

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

Density functional calculations of thio effects on the in-line mechanism of methanolysis of ethylene phosphate (a reverse reaction model for RNA phosphate transesterification) are presented. A total of 12 reaction mechanisms are examined using the B3LYP functional with large basis sets, and the effects of solvation were treated using the PCM, CPCM, and SM5 solvation models. Single thio substitutions at all of the distinct phosphoryl oxygen positions (2', 3', 5', pro-R) and a double thio substitution at the nonbridging (pro-R/pro-S) positions were considered. Profiles for each reaction were calculated in the dianionic and monoanionic/monoprotic states, corresponding to reaction models under alkaline and nonalkaline conditions, respectively. These models provide insight into the mechanisms of RNA transesterification thio effects and serve as a set of high-level quantum data that can be used in the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations and linear-scaling electronic structure calculations.     

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions.     

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions     

Calculation of solvation free energy from quantum mechanical charge density and continuum dielectric theory

We have combined ultrasoft pseudopotential density functional theory utilizing plane wave basis with a Poisson-Boltzmann/solvent-accessible surface area (PB/SA) model to calculate the solvation free energy of small neutral organic compounds in water. The solute charge density obtained from density functional theory was directly used in solving the Poisson-Boltzmann equation to obtain the reaction field. The polarized electronic wave function of the solute in the solvent was solved by including the reaction field in the density functional Hamiltonian. The quantum mechanical and Poisson-Boltzmann equations were solved self-consistently until the charge density and reaction field converged. Using the solute charge density directly instead of a point-charge representation permitted asymmetric distortion and spreading out of the electron cloud. Because the electron density could leave the van der Waals surface to penetrate into the high-dielectric solvent, the reaction field generated by this density was generally smaller than that obtained by using the point-charge representation. In applying this model to calculate the solvation free energy of 31 small neutral organic molecules spanning a range of 25 kcal/mol, we obtained a root-mean-square error of only 1.3 kcal/mol if we allowed one adjustable parameter to shift the calculated solvation free energy.     

Electrostatic Interactions That Determine the Rate of Pseudorotation Processes in Oxyphosphorane Intermediates: Implications with Respect to the Roles of Metal Ions in the Enzymatic Cleavage of RNA

The enzymatic cleavage of RNA takes place via a cyclic pentacoordinate oxyphosphorane intermediate/transition state. We carried out ab initio investigations on the neutral cyclic oxyphosphorane, which exists as a stable intermediate. As a consequence of the conformational preferences of the pentacoordinate trigonal bipyramidal intermediates, the rotation of the P-OH bonds is strongly coupled with the reaction coordinate for the pseudorotation process. In addition, the neutral PF(4)OH species has a higher barrier to pseudorotation than the corresponding anionic species PF(4)O(-). These findings are related to the positive charge of the hydrogen atoms on the equatorial oxygens in the trigonal bipyramidal structures: the hydrogen atoms preferably adopt eclipsed positions relative to the axial ligands. Fixing the cationic species in these regions causes an increase in the barrier heights for pseudorotation processes and, thus, prevents isomerization by pseudorotation. Consequently, metal coordination in the double-metal ion mechanism for enzymatic cleavage of RNA should serve to exclusively stabilize the trigonal bipyramidal intermediate/transition state for the in-line attack and departure process.     

Photo absorption of ‐coumaric acid in aqueous solution: RISM‐SCF‐SEDD theory approach

Photo absorption properties of p‐coumaric acid, the chromophore of photoactive yellow protein, in aqueous solution were investigated by means of reference interaction site model self‐consistent field with spatial electron density distribution (RISM‐SCF‐SEDD) method. RISM‐SCF‐SEDD is a combination methodology of electronic structure theory and statistical mechanics for molecular liquids. Here, time‐dependent density functional theory was coupled with RISM equation to study the electronic structure of p‐coumaric acid in aqueous system. Excitation energies of the chromophore in its neutral, two monoanionic and dianionic forms were computed to elucidate the effect of the deprotonation and solvation on the spectroscopic properties. We found that solvation strongly affects the excitation character of the chromophore, especially for phenolate anion and dianion. The free energy difference among the four protonation states is also discussed. © 2017 Wiley Periodicals, Inc.     

Ion chemistry of OV(OCH3)3 in the gas phase: molecular cations and anions and their primary fragmentations

Trimethyl vanadate(V), OV(OCH(3))(3) (1), is examined by various mass spectrometric means. Photoionization experiments yield an ionization energy of IE(OV(OCH(3))(3)) = 9.54 +/- 0.05 eV for the neutral molecule. The primary fragmentation of the molecular cation 1(+), i.e., loss of neutral formaldehyde, can occur via two independent routes of hydrogen migrations to afford the formal V(IV) compounds HOV(OCH(3))(2)(+) and OV(OCH(3))(CH(3)OH)(+), respectively. These two pathways are associated with low-lying activation barriers of almost identical height. At elevated energies, direct V-O bond cleavage of 1(+) allows for expulsion of a methoxy radical concomitant with the generation of the cationic fragment OV(OCH(3))(2)(+), a formal V(V) compound. Trimethyl vanadate can also form a molecular anion, 1(-), whose most abundant dissociation channel involves loss of a methyl radical, thereby leading to the formal V(V) compound OV(OCH(3))(2)O(-). Various mass spectrometric experiments and extensive theoretical studies provide detailed insight into the ion structures and the relative energetics of the primary dissociation reactions of the molecular cations and anions of 1.     

Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy

We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.     

Ylidic radical-molecule reactions

The known reactions between a neutral radical and a neutral closed-shell sigma-type molecule are generally associated with the atom/group-abstraction (e.g., CN, OH reactions) or the carbenoid insertion processes (e.g., CH reactions). In this article, we describe a new type of neutral radical-molecule reaction that feature the nucleophilic addition and elimination mechanism based on the systematic Gaussian-3//MP2(full)/6-31G(d) investigations on the PH(3)CH+HX model reactions (X = CH(3), NH(2), OH, F, CH(2)F, CHF(2), CF(3), NHCH(3)/CH(2)NH(2), OCH(3)/CH(2)OH). The novel properties are found to benefit both from the radical and ylidic characters of PH(3)CH, and the type of reagent HX determines the nucleophilic addition reactivity. The present work is the first study on the chemical reactivity of the ylidic radicals.     

Charge-dependent cavity radii for an accurate dielectric continuum model of solvation with emphasis on ions: aqueous solutes with oxo, hydroxo, amino, methyl, chloro, bromo, and fluoro functionalities

Dielectric continuum solvation models are widely used because they are a computationally efficacious way to simulate equilibrium properties of solutes. With advances that allow for molecular-shaped cavities, they have reached a high level of accuracy, in particular for neutral solutes. However, benchmark tests show that existing schemes for defining cavities are unable to consistently predict accurately the effects of solvation on ions, especially anions. This work involves the further development of a protocol put forth earlier for defining the cavities of aqueous solutes, with resulting advances that are most striking for anions. Molecular cavities are defined as interlocked spheres around atoms or groups of atoms in the solute, but the sphere radii are determined by simple empirically based expressions involving the effective atomic charges of the solute atoms (derived from molecular electrostatic potential) and base radii. Both of these terms are optimized for the different types of atoms or functional groups in a training set of neutral and charged solutes. Parameters in these expressions for radii were fitted by minimizing residuals between calculated and measured standard free energies of solvation (DeltaG(s)*), weighted by the uncertainty in the measured value. The calculations were performed using density functional theory with the B3LYP functional and the 6-311+G** basis set and the COnductor-like Screening MOdel (COSMO). The optimized radii definitions reproduce DeltaG(s)* of neutral solutes and singly charged ions in the training set to within experimental uncertainty and, more importantly, accurately predict DeltaG(s)* of compounds outside the training set, in particular anions (J. Phys. Chem. A 2003, 107, 5778). Inherent to this approach, the cavity definitions reflect the strength of specific solute-water interactions. We surmise that this feature underlies the success of the model, referred to as the CD-COSMO model for Charge-Dependent (also Camaioni-Dupuis) COSMO model. These findings offer encouragement that we can keep extending this scheme to other functional groups and obtain better accuracy in using continuum solvation models to predict equilibrium properties of aqueous ionic solutes. The approach is illustrated for a number of test cases, including the determination of acidities of an amine base, a study of the tautomerization equilibrium of a zwitterionic molecule (glycine), and calculating solvation energies of transition states toward a full characterization of reaction pathways in aqueous phase, here in S(N)2 exchange reactions. The calculated reaction barriers in aqueous solution are in excellent agreement with experimental values.     

CYCLIC OXYPHOSPHORANES

Abstract

A review on pertinent information on cyclic oxyphosphoranes is presented. Recent X-ray structures and variable temperature ¹H NMR investigations of cyclic pentaoxyphosphoranes reveals a preference for a boat conformation for saturated six-membered rings in apical-equatorial orientations of trigonal bipyramids. These studies include five-, six-, and seven-membered rings and show that the solid state structures are retained in solution. Apical-equatorial ring pseudorotations are more facile for five-membered rings, whereas ligand exchange via diequatorial ring placement is more facile for the larger rings. The importance of the apical-equatorial ring orientation for phosphorinanes appearing as trigonal bipyramidal intermediates in enzymatic reactions of cyclic AMP analogs is emphasized.     

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

Density-functional and semiempirical quantum methods and continuum dielectric and explicit solvation models are applied to study the role of solvation on the stabilization of native and thio-substituted transphosphorylation reactions. Extensive comparison is made between results obtained from the different methods. For the semiempirical methods, explicit solvation was treated using a hybrid quantum mechanical/molecular mechanical (QM/MM) approach and the implicit solvation was treated using a recently developed smooth solvation model implemented into a d-orbital semiempirical framework (MNDO/d-SCOSMO) within CHARMM. The different quantum and solvation methods were applied to the transesterification of a 3'-ribose,5'-methyl phosphodiester that serves as a nonenzymatic model for the self-cleavage reaction catalyzed by the hammerhead and hairpin ribozymes. Thio effects were studied for a double sulfur substitution at the nonbridging phosphoryl oxygen positions. The reaction profiles of both the native and double sulfur-substituted reactions from the MNDO/d-SCOSMO calculations were similar to the QM/MM results and consistent with the experimentally observed trends. These results underscore the need for a d-orbital semiempirical representation for phosphorus and sulfur for the study of experimentally observed thio effects in enzymatic and nonenzymatic phosphoryl transfer reactions. One of the major advantages of the present approach is that it can be applied to model chemical reactions at a significantly lower computational cost than either the density-functional calculations with implicit solvation or the semiempirical QM/MM simulations with explicit solvent.     

Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers

We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA-Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.     

M(R-dmet)2] bis(1,2-dithiolenes): a promising new class intermediate between [M(dmit)2] and [M(R,R'-timdt)2] (M = Ni, Pd, Pt)

We report the first examples of metal dithiolenes belonging to the class [M(R-dmet)(2)] [R-dmet = formally monoreduced N-substituted thiazolidine-2,4,5-trithione; R = Et, M = Ni (1), Pd (2), Pt (3)]. A comparative spectroscopic, electrochemical, and density functional theory theoretical investigation indicates that [M(R-dmet)(2)] complexes show features intermediate between those of the dithiolenes belonging to the previously reported classes [M(R,R'-timdt)(2)] and [M(dmit)(2)] (R,R'-timdt = formally monoreduced N,N'-disubstituted imidazolidine-2,4,5-trithione; dmit = 2-thioxo-1,3-dithiole-4,5-dithiolato). UV-vis-near-IR spectroscopy and cyclic voltammetry/differential pulsed voltammetry measurements performed on 1 and 3 proved that the new dithiolenes are stable as neutral, monoanionic, and bianionic species and feature a near-IR electrochromic absorption falling at about 1000 and 1250 nm for neutral and monoanionic species, respectively.     

Hydroxyl radical and hydroxide ion in liquid water: a comparative electron density functional theory study

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.     

Origin of the SN2 benzylic effect

The S N2 identity exchange reactions of the fluoride ion with benzyl fluoride and 10 para-substituted derivatives (RC6H 4CH 2F, R = CH3, OH, OCH 3, NH2, F, Cl, CCH, CN, COF, and NO2) have been investigated by both rigorous ab initio methods and carefully calibrated density functional theory. Groundbreaking focal-point computations were executed for the C6H5CH 2F + F (-) and C 6H 5CH2Cl + Cl (-) SN2 reactions at the highest possible levels of electronic structure theory, employing complete basis set (CBS) extrapolations of aug-cc-pV XZ (X = 2-5) Hartree-Fock and MP2 energies, and including higher-order electron correlation via CCSD/aug-cc-pVQZ and CCSD(T)/aug-cc-pVTZ coupled cluster wave functions. Strong linear dependences are found between the computed electrostatic potential at the reaction-center carbon atom and the effective SN2 activation energies within the series of para-substituted benzyl fluorides. An activation strain energy decomposition indicates that the SN2 reactivity of these benzylic compounds is governed by the intrinsic electrostatic interaction between the reacting fragments. The delocalization of nucleophilic charge into the aromatic ring in the SN2 transition states is quite limited and should not be considered the origin of benzylic acceleration of SN2 reactions. Our rigorous focal-point computations validate the benzylic effect by establishing SN2 barriers for (F (-), Cl (-)) identity exchange in (C6H5CH2F, C6H 5CH2Cl) that are lower than those of (CH3F, CH3Cl) by (3.8, 1.6) kcal mol (-1), in order.     

Ab initio QM/MM simulation of Ag+ in 18.6% aqueous ammonia solution: structure and dynamics investigations

Structure and dynamics investigations of Ag(+) in 18.6% aqueous ammonia solution have been carried out by means of the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation method. The most important region, the first solvation shell, was treated by ab initio quantum mechanics at the Restricted Hartree-Fock (RHF) level using double-zeta plus polarization basis sets for ammonia and plus ECP for Ag(+). For the remaining region in the system, newly constructed three-body corrected potential functions were used. The average composition of the first solvation shell was found to be [Ag(NH(3))(2)(H(2)O)(2.8)](+). No ammonia exchange process was observed for the first solvation shell, whereas ligand exchange processes occurred with a very short mean residence time of 1.1 ps for the water ligands. No distinct second solvation shell was observed in this simulation.