Integral Equation Formalism Polarizable Continuum Research Articles

Computational Study on Nonenzymatic Peptide Bond Cleavage at Asparagine and Aspartic Acid

Nonenzymatic peptide bond cleavage at asparagine (Asn) and glutamine (Gln) residues has been observed during peptide deamidation experiments; cleavage has also been reported at aspartic acid (Asp) and glutamic acid (Glu) residues. Although peptide backbone cleavage at Asn is known to be slower than deamidation, fragmentation products are often observed during peptide deamidation experiments. In this study, mechanisms leading to the cleavage of the carboxyl-side peptide bond of Asn and Asp residues were investigated using computational methods (B3LYP/6-31+G**). Single-point solvent calculations at the B3LYP/6-31++G** level were carried out in water, utilizing the integral equation formalism-polarizable continuum (IEF-PCM) model. Mechanism and energetics of peptide fragmentation at Asn were comparatively analyzed with previous calculations on deamidation of Asn. When deamidation proceeds through direct hydrolysis of the Asn side chain or through cyclic imide formationvia a tautomerization routeit exhibits lower activation barriers than peptide bond cleavage at Asn. The fundamental distinction between the mechanisms leading to deamidationvia a succinimideand backbone cleavage was found to be the difference in nucleophilic entities involved in the cyclization process (backbone versus side-chain amide nitrogen). If deamidation is prevented by protein three-dimensional structure, cleavage may become a competing pathway. Fragmentation of the peptide backbone at Asp was also computationally studied to understand the likelihood of Asn deamidation preceding backbone cleavage. The activation barrier for backbone cleavage at Asp residues is much lower (approximately 10 kcal/mol) than that at Asn. This suggests that peptide bond cleavage at Asn residues is more likely to take place after it has deamidated into Asp.

Excess polarizabilities upon the first dipole‐allowed excitation of some conjugated oligomers

AbstractThis paper presents theoretical predictions for the excess polarizabilities upon excitation from the ground state to the first dipole‐allowed excited state (11Bu) of some conjugated oligomers. The excess polarizability was obtained by simulating the Stark shift, which was predicted by the time‐dependent density functional theory (TDDFT) with the hybrid Becke‐3 Lee–Yang–Parr (B3LYP) potential. The Stark shift in solution was simulated by employing the non‐equilibrium integral equation formalism polarizable continuum model (IEFPCM). All the model molecules considered in this study were fully optimized by the Hartree–Fock (HF) method and the density functional theory (DFT) with the B3LYP potential, respectively. For diphenylpolyenes, the excess polarizabilities displayed by the DFT/B3LYP‐optimized geometries are more reasonable than those displayed by the HF‐optimized geometries when compared with the experimental results. However, this feature is not clearly demonstrated by our results in the cases of oligo(phenylenevinylene)s (OPVs). Copyright © 2008 John Wiley & Sons, Ltd.

Origin of Diastereoselectivity in the Synthesis of Chiral Bicyclic Lactams: π-Facial Selective Attack of Singlet Oxygen Induced by Hindered Internal Rotation

Previously reported experimental results indicate that photooxygenation of homochiral N-(hydroxyalkyl)-2-methylpyrroles with singlet oxygen yields trans-rather than cis-bicyclic lactams as the major product. In this study, the origin of selectivity in this reaction has been investigated with computational methods. Relative stabilities of homochiral N-(hydroxyalkyl)-2-methylpyrrole conformers and their effect on pi-facial selectivity of 1O2 were extensively studied. Stepwise and concerted reaction mechanisms, starting from the endoperoxide intermediates, were proposed and modeled in vacuum using the UB3LYP method with the 6-31+G** basis set. Solvent calculations were carried out in CH2Cl2, by means of the integral equation formalism-polarizable continuum model (IEF-PCM) at the UB3LYP/6-31+G** level of theory. Free energies of activation leading to both diastereomers were analyzed in an effort to explain the stereoselectivity and product distribution. Steric interactions among the pyrrole substituents were shown to lead to a rotational barrier higher than 10 kcal/mol. Hence, hindered internal rotation is suggested to cause one pyrrole conformer to be substantially overpopulated. This in turn has a major effect on pi-facial selectivity of 1O2, thereby favoring one endoperoxide over the other and leading to the diastereoselective synthesis of trans-pyrrolooxazolones. The importance of hindered internal rotors, for an accurate calculation of the frequency factors of a chemical reaction, has already been mentioned in the literature many times; however, in this work hindered internal rotors also seem to dictate the diastereoselective outcome of the reaction.

Sphingosine 1-phosphate p Ka and binding constants: Intramolecular and intermolecular influences

The dissociation constant for an ionizable ligand binding to a receptor is dependent on its charge and therefore on its environmentally-influenced p K a value. The p K a values of sphingosine 1-phosphate (S1P) were studied computationally in the context of the wild type S1P 1 receptor and the following mutants: E3.29Q, E3.29A, and K5.38A. Calculated p K a values indicate that S1P binds to S1P 1 and its site mutants with a total charge of −1, including a +1 charge on the ammonium group and a −2 charge on the phosphate group. The dissociation constant of S1P binding to these receptors was studied as well. The models of wild type and mutant proteins originated from an active receptor model that was developed previously. We used ab initio RHF/6-31+G(d) to optimize our models in aqueous solution, where the solvation energy derivatives are represented by conductor-like polarizable continuum model (C-PCM) and integral equation formalism polarizable continuum model (IEF-PCM). Calculation of the dissociation constant for each mutant was determined by reference to the experimental dissociation constant of the wild type receptor. The computed dissociation constants of the E3.29Q and E3.29A mutants are three to five orders of magnitude higher than those for the wild type receptor and K5.38A mutant, indicating vital contacts between the S1P phosphate group and the carboxylate group of E3.29. Computational dissociation constants for K5.38A, E3.29A, and E3.29Q mutants were compared with experimentally determined binding and activation data. No measurable binding of S1P to the E3.29A and E3.29Q mutants was observed, supporting the critical contacts observed computationally. These results validate the quantitative accuracy of the model.

A Study of Cysteamine Ionization in Solution by Raman Spectroscopy and Theoretical Modeling

Different cysteamine (H2N-CH2-CH2-SH) ionization forms have been studied by polarized Raman spectroscopy in solutions prepared with H2O and D2O and by DFT calculations at the B3LYP/6-31++G(d,p) level. To account for solvation effects, we employed the integral equation formalism polarizable continuum model (IEFPCM) option and explicit water molecules. Calculated relative energies and Raman spectra revealed that gauche rotamers around the C-C bond are the most stable conformers in solution. The experimental pKa values and Raman spectra of various ionization forms were best predicted by using a model with three explicit water molecules and the IEFPCM option. In general, the use of IEFPCM tends to lower the calculated frequencies for a few bands, but in some cases (S-H stretching mode) this effect is expressed very strongly. Potential energy distribution (PED) analysis of gauche conformers of various cysteamine ionization forms provided the possibility of discriminating spectroscopically methylene groups adjacent to sulfur, (CH2)S, and nitrogen, (CH2)N, sites. In general, stretching and scissoring modes as well as wagging and twisting vibrations of the (CH2)N group were found to be at higher frequencies. The influence of ionization of SH and NH2 groups on the vibrational spectrum is discussed, and Raman markers for further amine group ionization studies are suggested.

Ab Initio Procedure for Aqueous-Phase pKa Calculation: The Acidity of Nitrous Acid

We present an ab initio procedure for accurately calculating aqueous-phase pKa values and apply it to study the acidity of nitrous acid (HNO2, or HONO). The aqueous-phase pK(a) of nitrous acid was obtained from calculated gas-phase acidities and solvation free energies via a thermodynamic cycle and the solvation model chemistry of Barone et al. (J. Chem. Phys. 1997, 107, 3210). Solvation free energies were calculated at the HF/6-31G(d) level using the dielectric-polarizable continuum and the integral equation formalism-polarizable continuum solvent models (D-PCM and IEF-PCM, respectively), with the D-PCM model yielding the most accurate pKa values. For HF free energies of solvation, significant improvements in accuracy could be made by moving to the larger 6-311++G(3df,3pd) and aug-cc-pVQZ basis sets. Solvation free energies were also calculated using the density functional theory (DFT) methods B3LYP, TPSS, PBE0, B1B95, VSXC, B98 and O3LYP, with the most accurate methods being TPSS and VSXC, which provided average errors of less than 0.11 pKa units. Solvation free energies calculated with the different DFT methods were relatively insensitive to the basis set used. Our theoretical calculations are compared with experimental results obtained using stopped flow spectrophotometry. The pKa of nitrous acid was measured as 3.16 at 25 degrees C, and the enthalpy and entropy of nitrous acid dissociation were calculated from measurements as 6.7 kJ mol(-1) and -38.4 J mol(-1) K(-1), respectively, between 25 and 45 degrees C. The UV/visible absorption spectra of the nitrite ion and nitrous acid were also examined, and molar extinction coefficients were obtained for each.

Reaction Mechanism of Deamidation of Asparaginyl Residues in Peptides: Effect of Solvent Molecules

Deamidation of proteins occurs spontaneously under physiological conditions. Asparaginyl (Asn) residues may deamidate into aspartyl (Asp) residues, causing a change in both the charge and the conformation of peptides. It has been previously proposed by Capasso et al. that deamidation of relatively unrestrained Asn residues proceeds through a succinimide intermediate. This mechanism has been modeled by Konuklar et al. and the rate determining step for the deamidation process in neutral media has been shown to be the cyclization step leading to the succinimide intermediate. In the present study, possible water-assisted mechanisms, for both concerted and stepwise succinimide formation, were computationally explored using the B3LYP method with 6-31+G* basis set. Single point solvent calculations were carried out in water, by means of integral equation formalism-polarizable continuum model (IEF-PCM) at the B3LYP/6-31++G* level of theory. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality has been proposed. The energetics of these pathways have been subject to a comparative study to identify the most probable mechanism for the deamidation of peptides in solution.

Ab Initio Molecular Orbital and Density Functional Studies on the Solvolysis of Sarin and O,S-Dimethyl Methylphosphonothiolate, a VX-like Compound

[reaction: see text] Potential energy surfaces for the alkaline hydrolysis of sarin and O,S-dimethyl methylphosphonothiolate, a VX model compound, and the perhydrolysis of the latter have been computed at the MP2/6-31+G(d)//mPW1K/MIDI! level of theory. The effect of aqueous solvation was accounted for via the integral equation formalism polarizable continuum model (IEF-PCM) at the HF/6-31+G(d) level. Excellent agreement with the experimental enthalpy of activation for alkaline hydrolysis of sarin was found. For the alkaline hydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that the P-O and P-S bond cleavage processes are kinetically competitive but that the products of P-S bond cleavage are thermodynamically favored. For the perhydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that P-O bond cleavage is not kinetically competitive with P-S bond cleavage. In both cases, the data support initial formation of trigonal bipyramidal intermediates and demonstrate kinetic selectivity for nucleophilic attack on the face opposite the more apicophilic methoxide ligand.

Infrared linear dichroism in stretched films: Quantum mechanical approach within the polarizable continuum model

AbstractIn this work we discuss how environmental effects on vibrational transition moment directions for molecules dispersed in stretched films can be accounted for via the integral equation formalism polarizable continuum model (IEFPCM). In particular, effects related to the matrix polarization induced by the probing field (cavity field terms) are taken into account. Calculations are performed for three DNA‐related molecules (9‐methyladenine, 7‐methyladenine, and 2‐amino‐9‐methylpurine) for which infrared linear dichroism (IR LD) has been measured experimentally. By combining experimental data and calculations, different parameters of the film (Saupe order parameters and orientational axis direction) can be obtained and used to give “experimental” estimates of transition moment directions. The results show the importance of accounting for the environment surrounding the molecule in transition moment calculations. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation.

New equations are derived and implemented for efficient and accurate computation of solvation energy derivatives for the conductor-like polarizable continuum model (C-PCM) and the isotropic integral equation formalism polarizable continuum model (IEF-PCM). Two new molecular surface tessellation procedures GEPOL-RT and GEPOL-AS that generate near continuous potential energy surfaces are proposed for PCM geometry optimization. The combined use of these new techniques leads to efficient and convergent geometry optimizations with the PCMs.

Theoretical Study on the Alkaline and Neutral Hydrolysis of Succinimide Derivatives in Deamidation Reactions

The hydrolysis of a succinimide derivative in alkali and neutral media has been studied at the B3LYP/6-31+G* level. Stepwise and concerted mechanisms have been considered in a vacuum. Both mechanisms have been also studied in solution by means of integral equation formalism-polarizable continuum model with a single point calculation. In basic medium, the stepwise mechanism consists of a bond cleavage and a subsequent rotation of the hydroxyl group that require 8.6 and 3.0 kcal/mol, respectively. For the concerted hydrolysis in the same medium, the barrier is 9.8 kcal/mol. In neutral medium, the hydrolysis is facilitated by the presence of a polar continuum, whereas in basic medium, the polar environment hinders hydrolysis of succinimide.