Isodensity Polarized Continuum Model Research Articles

The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.

A simple strategy to compose a new all-atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (E(TOTAL)) is divided into three components; a single amino acid potential term (E(SAAP)), an interamino acid nonbonded interaction term (E(INTER)), and a miscellaneous term (E(OTHERS)), which is ignored (or considered to be constant) at the current version of the force field. The E(INTER) term consists of electrostatic interactions (E(ES')) and van der Waals interactions (E(LJ')). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of For-Ala(2)-NH(2) in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for For-Gly(10)-NH(2) and For-Ala(10)-NH(2) showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (E(TOTAL)) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the E(SAAP) term) may play definitive roles on the topologies of protein secondary structures.

A way to compare experimental and SCRF electronic static dipole polarizability of pure liquids

When the polarizability tensor is computed through Self-Consistent Reaction Field Models (the interactions between solute and solvent are incorporated into calculation), there still exists a need to take into account the modifications of the applied macroscopic fields at the local site of the solvated molecule (the phenomenon historically indicated as ‘local field effects’). Another way is to remove local field factors from experimental mean polarizability ( α ̄ ) and polarizability anisotropy (Δ α) values. The present paper focuses on this way. Seven liquids (CS 2, C 6H 6, (CH 3) 2CO, CHCl 3, CH 2Cl 2, CH 3CN, CCl 4) have been studied. In a first step, the α tensor components have been computed at the B3LYP and HF levels with Sadlej basis set using a finite field procedure. The solvent effect is introduced into the calculation through the Self-Consistent Isodensity Polarizable Continuum Model (SCIPCM). In a second step, experimental literature values of refractive index, density, isothermal compressibility coefficient and depolarization ratio have been carefully chosen and introduced in modified experimental equations (where local field factors have been removed) to determine α ̄ and Δ α. Concerning α ̄ , there is a good agreement between experimental and B3LYP values for dipolar molecules. In the case of non-dipolar molecules calculated values are always lower than experimental ones. Such a behaviour had not been observed in a previous study concerning molecules in the gas state, therefore it seems that the SCIPCM induces a deficiency over calculated α ̄ (0) in the case of non-dipolar molecules.

Molecular orbital study on the reaction process of dimethylamine borane as a reductant for electroless deposition

The oxidation mechanism of dimethylamine borane (DMAB), which acts as a reductant in the electroless deposition process, was studied using ab initio molecular orbital approaches such as Hartree–Fock (HF) and second order Møller–Plesset (MP2) calculations. The overall oxidation process of the DMAB was divided into each elementary reaction in which OH − substitutes H one by one and eventually forms B(OH) 4 −. The oxidation mechanism of DMAB in the isolated state, which was previously proposed by us, was refined using more accurate basis sets, and the effects of solvation and interaction with metal surface sites on the oxidation mechanism were also studied. Taking the solvation effect into consideration using the self-consistent reaction field method with an isodensity polarized continuum model (SCRF-IPCM), the heat of oxidation was transferred to an exothermic reaction with decreasing dielectric constant. This indicated that the reaction preferably proceeds at the solid ∣ liquid interface. Combined with Cu(111) and Pd(111) neutral cluster models as metal surface sites, it was found that the oxidation reaction proceeds preferentially at the metal surface sites. It was also suggested that the catalytic activity of the deposited metal is caused by its electron acceptivity.

Theoretical study of aqueous uranyl carbonate (UO 2CO 3) and its hydrated complexes: UO 2CO 3· nH 2O ( n=1–3)

Extensive ab initio calculations have been carried out to study the structure and bonding of hydrated UO 2CO 3 complexes using state-of-the-art techniques. The structures of aqueous UO 2CO 3 and its hydrated complexes have been further studied by considering the solvent as a polarizable continuum dielectric. The calculations have been carried out using polarization continuum, self-consistent isodensity polarizable continuum model, and conductor like screen models. The calculated uranyl frequencies of the hydrated UO 2CO 3 have been compared with the available vibrational frequencies and the nature of water binding has been analyzed using energy decomposition techniques.

Electronic and steric substituent influences on the conformational equilibria of cyclohexyl esters: the anomeric effect is not anomalous!

The cyclohexyl esters of a series of carboxylic acids, RCO(2)H, spanning a range of electronegativities and quotients of steric hindrance for the R substituent (R=Me, Et, iPr, tBu, CF(3), CH(2)Cl, CHCl(2), CCl(3), CH(2)Br, CHBr(2), and CBr(3)) were prepared. Their conformational equilibria in CD(2)Cl(2) were examined by low-temperature (1)H NMR spectroscopy to study the axial or equatorial orientation of the ester functionality with respect to the adopted chair conformation of the cyclohexane ring. The ab initio and DFT geometry-optimized structures and relative free energies of the axial and equatorial conformers were also calculated at the HF/6-311G**, MP2/6-311G**, and B3LYP/6-31G** levels of theory, both in the gas phase and in solution. In the latter case, a self-consistent isodensity polarized continuum model was employed. Only by including electron correlation in the modeling calculations for the solvated molecules was it possible to obtain a reasonable correlation between DeltaG degrees (calcd) and DeltaG degrees (exp). Both the structures and the free energy differences of the axial and equatorial conformers were evaluated with respect to the factors normally influencing conformational preference, namely, 1,3-diaxial steric interactions in the axial conformer and hyperconjugation. It was assessed that hyperconjugative interactions, sigma(C-C)/sigma(C-H) and sigma*(C-O), together with a steric effect--the destabilization of the equatorial conformer with increasing bulk of the R group--were the determinant factors for the position of the conformational equilibria. Thus, because hyperconjugation is held responsible as the mitigating factor for the anomeric effect in 2-substituted, six-membered saturated heterocyclic rings, and since it is also similarly responsible, at least partly, in these monosubstituted cyclohexanes for a preferential shift towards the axial conformer, the question is therefore raised: can the anomeric effect really be construed as anomalous?

Vibrational Spectra of Lumazine in Water at pH 2−13: Ab Initio Calculation and FTIR/Raman Spectra

Harmonic vibrational frequencies and transition intensities of lumazine (2,4-(1H,3H)pteridinedione in the neutral state) have been calculated in a self-consistent reaction field of high dielectric medium (ε = 78.54) using ab initio Hartree−Fock (HF) and hybrid HF/density functional theory (DFT) methods. For the DFT method, the 4-31G basis set and the three parameter exchange functional of Becke combined with the Lee, Yang, and Parr correlational functional are used. The 6-31+G* basis set is used in the HF calculations. Both the spherical cavity model (SCM) and the self-consistent isodensity polarizable continuum model (SCIPCM) are used to simulate an aqueous environment for the N-protonated lumazines. For the N-deuterated lumazines, only the SCM is used. Simple scaling of the vibrational frequencies resulting from the DFT calculations incorporating the reaction field models of neutral lumazine, lumazine A1/N3-H monoanion, and lumazine A1,A3-dianion compare closely with Raman and Fourier transform infrared spectra of lumazine taken in aqueous media (both H2O and D2O) over a wide pH/pD range. The mean deviation between calculated and experimental vibrational frequencies is 9.10 cm-1 for neutral lumazine (9.37 cm-1 in D2O), 9.18 cm-1 for the monoanion (10.77 cm-1 in D2O), and 16.06 cm-1 for the dianion (16.00 cm-1 when prepared in D2O). Calculated vibrational energy shifts with changes in ionization exhibit many trends that are evident in the experimental data although the absolute magnitudes of many of the individual shifts do not agree exactly. The calculated H/D isotopic shifts for the neutral and monoanionic species of lumazine agree well with those seen experimentally. Correlating shifts with ionization and the H/D isotopic shifts of the vibrational modes of each species of lumazine investigated have resulted in normal mode assignments of all in-plane vibrational modes observed in the 300−1750 cm-1 range in aqueous solution.

Conformational and electronic study of N‐phenylalkyl‐3,4‐dichloromaleimides: Ab initio and DFT study

AbstractA conformational and electronic study on N‐phenylalkyl‐3,4‐dichloromaleimides, a new series of antifungal compounds, was carried out. In this study ab initio [RHF/3‐21G and RHF/6‐31G(d)] and density functional theory (B3LYP/6‐31G(d)) calculations were performed. The effect of solvent (water) was taken into account by performing calculations with the isodensity polarizable continuum model method. The electronic study of the compounds was carried out using molecular electrostatic potentials. The presence of two symmetrical aromatic systems reduces notably the conformational possibilities of these maleimides. The results permit the recognition of the minimal structural requirements for the production of the antifungal response; a 3,4‐dichloroimido ring and a benzene ring appear to be indispensable. Also, theoretical calculations suggest that the optimum interatomic distance between these moieties is about 3.5–5.0 Å. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

Theoretical Study of the aza-Wittig Reactions of X3PNH (X=H and Cl) with Formaldehyde in Gas Phase and in Solution

The aza-Wittig reaction of iminophosphoranes (X3PNH, X=H and Cl) with formaldehyde (H2CO) was investigated in gas phase and in water using ab initio MP2/6-31G** level of theory and the self-consistent reaction field theory (isodensity polarized continuum model, IPCM). In the gas phase, the aza-Wittig reaction was predicted to be a two-step process with two dipole−dipole complexes, one four-membered ring intermediate and two transition states. The potential energy profiles along the minima energy path in gas phase and in water were obtained. The solvent effects on the thermodynamic and kinetic properties of this reaction were discussed. This aza-Wittig reaction is more favorable for X=H than for X=Cl, both in the gas phase and in water.

Ab initio studies of solvent effect on conformational equilibria and vibrational spectra of dipropionamide

Systematic ab initio molecular orbital studies of the conformational equilibria and vibrational spectra of dipropionamide using the basis sets 6-31g(d) and 6-31++G(d,p) have been carried out. The vibrational spectra of dipropionamide have been satisfactorily interpreted taking into account the agreement between the calculated frequencies, infrared and Raman band intensities and the shifts in the spectra of deuterated molecules with those observed. The previous assignments of most of the vibrational bands are well confirmed, a few bands need reassignment, however. The solvent effects were investigated by self-consistent reaction field theory using dipole and self-consistent isodensity polarized continuum model methods. The introduction of a dielectric medium has only a marginal effect on the conformational equilibria and vibrational spectra. However, the calculated changes in geometry and vibrational spectra on going from the gas phase to the solution phase are in accord with the increasing weight of the dipolar resonance structure in polar solvents.

Solvent effects on the φ– ψ potential surfaces of glycine and alanine dipeptides studied by PCM and I-PCM methods

Two-dimensional φ– ψ potential surfaces of representative amino acid models, For-Gly-NH 2 ( 1) and For-Ala-NH 2 ( 2), were calculated at the HF/6-311++G(2d,2p)//HF/6-31G(d) level of theory in various solvents by applying the polarizable continuum model (PCM) and isodensity polarizable continuum model (I-PCM) methods. Three dielectric constants of medium (i.e. 4.335, 32.63, and 78.39) were selected corresponding to ether, methanol, and water, respectively. The PCM potential surfaces in the solvents were found to be significantly different from the corresponding I-PCM potential surfaces due presumably to the lower approximation level. However, the both methods commonly resulted in local energy minima at the α region for 1 and the α and β regions for 2. Thus, intrinsic conformational propensities of glycine and alanine residues to adopt folded secondary structures were suggested in the solvents. Comparison of the more reliable I-PCM potentials with the Ramachandran plots extracted from protein databank (PDB_SELECT) revealed that glycine and alanine residues in folded proteins roughly adopt random statistical structures in high energy ranges (Δ E>3 and 5 kcal/mol for 1 and 2, respectively). It was also proposed that the conformational space of a polypeptide molecule is significantly restricted in water compared with that in the gas phase.

Formaldehyde oxime nitrosomethane tautomerism.

Formaldehyde oxime <--> nitrosomethane tautomerism, isomeric nitrone, and their common cations and anions are studied with Gaussian-2 theory using MP2(full)/6-31G geometries and with density functional theory using B3LYP/6-311+G**. Geometrical parameters, harmonic vibrational frequencies, relative stabilities, conformational stabilities, and ionization energies are compared with experimental gas-phase data when available. The formaldehyde oxime <--> nitrosomethane tautomerism is compared with the amide <--> imidol, imine <--> enamine, keto <--> enol, and nitro <--> aci-nitro tautomeric processes. Solvent effects are estimated by the self-consistent isodensity polarizable continuum model (SCIPCM). The influence of hydrogen bonding interactions with the solvent is addressed by including two water molecules. In the final evaluation, formaldehyde oxime is 15.8 kcal/mol more stable than nitrosomethane when the aqueous solvation correction of 3.8 kcal/mol is applied to the G2 energies. Unsolvated formaldehyde oxime is estimated to be 11.1 kcal/mol more stable than nitrone. The estimated gas-phase ionization energies (G2) are 362.5 kcal/mol for formaldehyde oxime, 350.6 kcal/mol for nitrosomethane, and 351.4 kcal/mol for nitrone.

Self-Consistent Reaction Field Calculations of Aqueous Al3+, Fe3+, and Si4+: Calculated Aqueous-Phase Deprotonation Energies Correlated with Experimental ln(Ka) and pKa

Reaction energies for the deprotonation of Al3+·6(H2O), Fe3+·6(H2O), and Si(OH)4 were calculated using Hartree−Fock and density functional methods with 6-311+G(d,p) (for Al3+ and Si4+) and 6-311G(d) (for Fe3+) basis sets. Theoretical energies were calculated using a supermolecule approach (i.e., explicit hydration of the solute) combined with the Integral Equation Formalism Polarized Continuum Model (IEFPCM; Cancès et al., 1997, J. Chem. Phys. 107, 3032) and the Self-Consistent Isodensity Polarized Continuum Model (SCIPCM; Keith and Frisch, 1994, ACS Symp. Ser. 56, 22) in Gaussian 98. Tests on the effects of increasing the number of water molecules explicitly included in the supermolecule were also carried out. Additional water molecules in the energy minimizations of Al(OH)3, Fe(OH)3, and [Si(OH)3(OH2)]+ resulted in 5-coordinate complexes for all three species. Correlations of deprotonation energies with observed ln(Ka) values are good for individual cations. These correlations suggest that the combined supermolecule/continuum approach can give reliable pKa estimates, provided that the structural optimization reflects the aqueous-phase solute and that the basis set includes polarization and diffuse functions. An estimate is made of the pKa of the reaction[Si(OH)3(OH2)]+(aq) ↔ Si(OH)4(aq) + H+(aq)which has not yet been measured. A value of pKa ≈ −2 is predicted in this study.

Substrate Binding to DNA Photolyase Studied by Electron Paramagnetic Resonance Spectroscopy

Structural changes in Escherichia coli DNA photolyase induced by binding of a ( cis, syn)-cyclobutane pyrimidine dimer (CPD) are studied by continuous-wave electron paramagnetic resonance and electron-nuclear double resonance spectroscopies, using the flavin adenine dinucleotide (FAD) cofactor in its neutral radical form as a naturally occurring electron spin probe. The electron paramagnetic resonance/electron-nuclear double resonance spectral changes are consistent with a large distance (≥0.6 nm) between the CPD lesion and the 7,8-dimethyl isoalloxazine ring of FAD, as was predicted by recent model calculations on photolyase enzyme-substrate complexes. Small shifts of the isotropic proton hyperfine coupling constants within the FAD’s isoalloxazine moiety can be understood in terms of the cofactor binding site becoming more nonpolar because of the displacement of water molecules upon CPD docking to the enzyme. Molecular orbital calculations of hyperfine couplings using density functional theory, in conjunction with an isodensity polarized continuum model, are presented to rationalize these shifts in terms of the changed polarity of the medium surrounding the FAD cofactor.

Bisimide–Lactamimide ring contraction in six‐membered bisimides: a theoretical study

AbstractThe bisimide–lactamimide ring contraction reaction of six‐membered bisimides has been modeled at the B3PW91/6‐31 + G(d,p)//HF/3‐21G level of theory using the isodensity polarized continuum model to take into account the solvent effect. Basically, the results of molecular modeling support the validity of the proposed mechanism. However, the calculations suggest that the final reaction step involves the direct oxidation of dianions by molecular oxygen, instead of oxidation of the hydroaromatic intermediate as proposed previously. The reactivity difference between N‐alkyl and N‐phenyl bisimides in the ring contraction reaction has been explained. Copyright © 2001 John Wiley &amp; Sons, Ltd.

The Cluster−Continuum Model for the Calculation of the Solvation Free Energy of Ionic Species

A hybrid approach using a combination of explicit solvent molecules and the isodensity polarizable continuum model (IPCM) method is proposed for the calculation of the solvation thermodynamic prope...

Tautomerism in 4‐substituted 1‐phenyl‐3‐methyl‐pyrazolin‐5‐ones—a theoretical ab initio and 13C NMR study

AbstractThe tautomeric equilibria between the CH, OH and NH forms in a series of 4‐substituted 1‐phenyl‐3‐methyl‐pyrazolin‐5‐ones have been studied using ab initio calculations at various levels of theory and comparison made with the experimental results obtained from NMR measurements. Quantitative comparison of both the relative energies and the 13C chemical shifts of the tautomers constituting the tautomeric equilibria were made by calculation of both sets of parameters. The influence of the solvent was included by employing various models of the self‐consistent reaction field theory. Initially, the solvent was included in the calculations by applying a continuum of differing polarity over the surface of isolated tautomers (self‐consistent isodensity polarized continuum model method), then later by assuming formation of an adduct between the solute and the solvent (thereby simulating effectively the hydrogen bonding in the OH and NH tautomers) and finally by calculating dimer or trimer complexes of the various tautomers. In this manner, the agreement between the theoretically calculated and the experimentally determined tautomeric equilibria was improved significantly. The theoretically calculated 13C chemical shifts of the tautomers were found to be viable for the assignment of the tautomers, particularly the preferred tautomer in the OH/NH equilibrium, which remains fast on the NMR time scale even at low temperatures. Copyright © 2001 John Wiley &amp; Sons, Ltd.

Solvent effects on methyl transfer reactions. 2. The reaction of amines with trimethylsulfonium salts.

The reaction of ammonia and pyridine with trimethylsulfonium ion has been studied in gas phase and solution. Density functional theory at the B3LYP/6-31+G level was used to describe the energy changes along the reaction coordinate in the gas phase, and the self-consistent isodensity polarizable continuum model (SCI-PCM) was used to calculate the effect of cyclohexane and dimethyl sulfoxide as the solvent on the energy changes. The effect of water as the solvent was studied using the Monte Carlo free energy perturbation method. The reaction with both ammonia and pyridine follows a similar rather convoluted path in gas phase, with the formation of several reaction complexes before and after the formation of the transition state. All the species found in gas phase persist in cyclohexane, yielding a reaction path very similar to that in gas phase but with significant differences in the relative energy of the critical points. In DMSO, the energy profile is greatly simplified by the disappearance of several of the species found in gas phase and in cyclohexane. The activation free energy increases with the polarity of the solvent in both reactions. Increasing the polarity of the solvent also increases the exothermicity of the reaction of trimethylsulfonium ion with ammonia and reduces it in the reaction with pyridine. In water, the free energy profile follows the same trend as found for DMSO, and free energy of activation is calculated to be larger by about 2-3 kcal/mol. This is in good agreement with an experimental measurement of the effect of solvent on the rate of reaction.

Protonation-induced paramagnetism. Structures and stabilities of six- and seven-coordinate complexes of Os(II) in singlet and triplet states: a density functional study.

Li, Yeh, and Taube in 1993 (J. Am. Chem. Soc. 1993, 115, 10384) synthesized a number of complexes which can be formally regarded as protonated Os(II) species. Some of these were paramagnetic, in contrast to the diamagnetism of the closed shell 5d(6) Os(II) ions. This intriguing phenomenon is investigated theoretically using density functional theory. The geometries, stabilities, and electronic structures of a series of six- and seven-coordinate osmium complexes were studied in gas phase and aqueous solution using the B3P86 functional, in conjunction with the isodensity-polarized continuum model of solvation. The general formula for these complexes is [Os(NH(3))(4)H(L(1)(x)())(m)()(L(2)(y)())(n)()](()(x)()(+)(y)()(+3)+), where L(1) and L(2) = H(2)O, NH(3), CH(3)OH, CH(3)CN, Cl(-), and CN(-), which could be regarded as protonated Os(II) species or hydrides of Os(IV), although according to this work the osmium-hydrogen interaction is best described as a covalent Os(III)-H bond, in which the hydrogen is near-neutral. The ground states are generally found to be singlets, with low-lying triplet excited states. Solvation tends to favor the singlet states by as much as approximately 18 kcal mol(-)(1) in the 3+ ions, an effect which is proportional to the corresponding difference in molecular volumes. To have realistic estimates of the importance of spin-orbit coupling in these systems, the spin-orbit energy corrections were computed for triplet [Os(NH(3))(4)](2+), [Os(NH(3))(4)H](3+), and [Os(NH(3))(4)H(H(2)O)](3+), along with gas-phase Os and its ions as well as [Os(H(2)O)(6)](3+). The seven-coordinate triplet-state complex [Os(NH(3))(5)H(CH(3)OH)](3+), which had been successfully isolated by Li, Yeh, and Taube, is predicted to be a stable six-coordinate complex which strongly binds to a methanol molecule in the second coordination shell. The calculations further suggest that the singlet-triplet splitting would be very small, a few kilocalories per mole at most. The geometries and the electronic structures of the complexes are interpreted and rationalized in terms of Pauling's hybridization model in conjunction with conventional ligand field theory that effectively precludes the existence of true seven-coordinate triplet-state complexes of the above formula.

Solvent Effects on Electrophilicity

Continuum solvent effect on the electrophilicity index recently proposed by Parr and co-workers (Parr, R. G.; von Szentpaly, L.; Liu, S. J. Am. Chem. Soc. 1999, 121, 1922) is discussed in detail. Solvent effect is introduced using the self-consistent isodensity polarized continuum model (SCI-PCM). A linear relationship is found between the change in electrophilicity index and the solvation energy as represented in the frame of the reaction field theory. The effect of a polarizable environment on the global electrophilicity is examined for a series of 18 well-known electrophiles presenting a wide diversity in structure and bonding properties. It is found that solvation enhances the electrophilicity power of neutral electrophilic ligands but attenuates this power in charged and ionic electrophiles.

Solvent effect on DNA base stacked dimers: An isodensity polarizable continuum model approach

The role of solvent on the base stacking properties of various stacked dimers has been analyzed. Ab initio calculations have been performed on the various stacked dimers using the isodensity polarizable continuum model (IPCM), in the framework of the HF/6-31G** level. It is observed that the stacked dimers undergo different levels of stabilization for different rotated conformations, and the total energy of stacked dimers depends on the twist angle. The results reveal that DNA stacked dimers prefer the twisted (rotated conformation) conformation in water environment, so as to escape from water, due to their hydrophobic nature. In addition, the presence of solvent stabilizes the stacking interaction between bases. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001