DFT Calculations of the Ionization Potential and Electron Affinity of Alaninamide

Adiabatic and vertical ionization potentials (IPs) and valence electron affinities (EAs) of alaninamide in gas phase have been determined using density functional theory (BLYP,B3LYP,B3P86) methods with 6-311++G(d,p) basis set,respectively. IPs and EAs of alaninamide in solutions have been calculated at the B3LYP/6-311++G(d,p) level. Five possible conformers of alaninamide and their charged states have been optimized employing density functional theory B3LYP method with 6-311++(d,p) basis set,respectively.     

Cyclic vinyl p-tolyl sulfilimines as chiral dienophiles: theoretical study on the stereoselectivity, Lewis acid catalysis, and solvent effects in their Diels-Alder reactions

The theoretical study reported in the present work deals with chiral cyclic vinyl sulfilimines and their reactivity as dienophiles in [4 + 2] cycloaddition reactions, using B3LYP/6-31G(d)//AM1 and B3LYP/6-31G(d)//B3LYP/6-31G(d) model chemistries. Consideration of Lewis acid catalysis, illustrated by BF(3), decreases the activation energies of the cycloaddition process while the charge transfer from the diene to the sulfilimine is augmented. The [4 + 2] cycloaddition reactions of sulfilimines with both furan and cyclopentadiene occur in the gas phase with endo stereoselectivity, which is more pronounced with the latter diene. Endo-exo energy differences in the gas phase with the B3LYP/6-31+G(d)//B3LYP/6-31+G(d), B3LYP/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31G(d)//AM1 model chemistries are almost the same. Solvent effects are responsible for the inversion of the stereoselectivity in the reactions of sulfilimines with furan because of the great difference in the dipole moments in endo and exo approaches.     

Comparative studies on the structures,infrared spectrum,and thermodynamic properties of phthalocyanine using ab initio Hartree–Fock and density functional theory methods

The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3‐21G, 6‐31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin‐based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3‐21G and LANL2DZ basis sets are very close to those produced using the medium 6‐31G* basis set. The geometry of Pc obtained at the B3LYP level has D_2h symmetry and the diameter of the central macrocycle is about 4 Å. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6‐311G(2d,2p)//B3LYP/6‐31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Study of conformational and optical rotation for the alaninamide

Six stationary points of alaninamide have been located on the potential surface energy (PES) at the B3LYP/6‐311++G(2d,2p) level of theory both in the gas phase and in aqueous solution. In the aqueous solution, to take the water solvent effect into account, the polarizable continuum model (PCM) method has been used. Accurate geometric structures and their relative stabilities have been investigated. The results show that the intramolecular hydrogen bond plays a very important role in stabilizing the global minimum of the alaninamide. Moreover, the consistent result in relative energy using high‐level computations, including the MP2 and MP3 methods with the same basis set [6‐311++G(2d,2p)], indicates that the B3LYP/6‐311++G(d,p) level may be applied to the analogue system. More importantly, the optical rotation of the optimized conformers (both in the gas phase and in aqueous solution) of alaninamide have been calculated using the density functional theory (DFT) and Hartree–Fock (HF) method at various basis sets (6‐31+G*, 6‐311++G(d,p), 6‐311++G(2d,2p) and aug‐cc‐pvdz). The results show that the selection of the computation method and the basis set in calculation has great influence on the results of the optical rotations. The reliability of the HF method is less than that of DFT, and selecting the basis set of 6‐311++G(2d,2p) and aug‐cc‐pvDZ produces relative reliable results. Analysis of the computational results of the structure parameters and the optical rotations yields the conclusion that just the helixes in molecules caused the chiral molecules to be optical active. The Boltzmann equilibrium distributions for the six conformers (both in the gas phase and in the aqueous solution) are also carried out. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Understanding selenocysteine through conformational analysis,proton affinities,acidities and bond dissociation energies

Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6‐31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6‐311++G*//B3LYP/6‐31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

An approach to estimate the energy and strength of the intramolecular hydrogen bond in different conformers of 4‐methylamino‐3‐penten‐2‐one

The molecular structure and intramolecular hydrogen bond energy of 32 conformers of 4‐methylamino‐3‐penten‐2‐one were investigated at MP2 and B3LYP levels of theory using the standard 6–31G** basis set and AIM analyses. Furthermore, calculations for all the possible conformations of 4‐methylamino‐3‐penten‐2‐one in water solution were also carried out at B3LYP/6–31G** level of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the ketoamine conformers of this compound are more stable than the other conformers (i.e., enolimine and ketoimine). This stability is mainly due to the formation of a strong N? H···O intramolecular hydrogen bond, which is assisted by π‐electrons resonance. Hydrogen bond energies for all conformers of 4‐methylamino‐3‐penten‐2‐one were obtained from the related rotamers method. The nature of intramolecular hydrogen bond existing within 4‐methylamino‐3‐penten‐2‐one has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. The results of these calculations support the results which obtained by related rotamers method. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Assessment of density functionals with long‐range and/or empirical dispersion corrections for conformational energy calculations of peptides

Density functionals with long‐range and/or empirical dispersion corrections, including LC‐ωPBE, B97‐D, ωB97X‐D, M06‐2X, B2PLYP‐D, and mPW2PLYP‐D functionals, are assessed for their ability to describe the conformational preferences of Ac‐Ala‐NHMe (the alanine dipeptide) and Ac‐Pro‐NHMe (the proline dipeptide) in the gas phase and in water, which have been used as prototypes for amino acid residues of peptides. For both dipeptides, the mean absolute deviation (MAD) is estimated to be 0.22–0.40 kcal/mol in conformational energy and 2.0–3.2° in torsion angles ? and ψ using these functionals with the 6‐311++G(d,p) basis set against the reference values calculated at the MP2/aug‐cc‐pVTZ//MP2/aug‐cc‐pVDZ level of theory in the gas phase. The overall performance is obtained in the order B2PLYP‐D ≈ mPW2PLYP‐D > ωB97X‐D ≈ M06‐2X > MP2 > LC‐ωPBE > B3LYP with the 6–311++G(d,p) basis set. The SMD model at the M06‐2X/6‐31+G(d) level of theory well reproduced experimental hydration free energies of the model compounds for backbone and side chains of peptides with MADs of 0.47 and 4.3 kcal/mol for 20 neutral and 5 charged molecules, respectively. The B2PLYP‐D/6‐311++G(d,p)//SMD M06‐2X/6‐31+G(d) level of theory provides the populations of backbone and/or prolyl peptide bond for the alanine and proline dipeptides in water that are consistent with the observed values. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

DFT calculations of the ionization potentials and electron affinities of serinamide

Adiabatic and vertical ionization potentials (IPs) and valence electron affinities (EAs) of serinamide in the gas phase have been determined using density functional theory (DFT) B3LYP, B3P86, and B3PW91 methods with the 6‐311++G** and 6‐311G** basis sets, respectively. IPs and EAs of serinamide in solution have been calculated with the B3LYP method using the 6‐311++G** and 6‐311G** basis sets. Eight possible conformers of serinamide and its charged states in the gas phase have been optimized employing the DFT B3LYP method with 6‐311++G** and 6‐311G** basis sets, respectively. All the adiabatic and vertical ionization potentials (AIPs and VIPs) of eight serinamide conformers in our work are positive values, whether in the gas phase or in solutions; the IPs in solutions are smaller than the results in the gas phase and decrease with increased dielectric constants in solutions. This finding indicates that the cationic states in solutions are more stable than those in the gas phase. All EAs of eight serinamide conformers are negative values in the gas phase, indicating that the anionic states are unstable with respect to electron autodetachment, both adiabatically and vertically. In contrast, all other adiabatic electron affinities (AEAs) are negative values in solutions except for 6S in water; 7S in chloroform, acetone, and water; and 8S in acetone and water, and increase with increasing of dielectric constants in solutions. All vertical electron affinities (VEAs) are negative values in solutions; however, no good rule has been found for these values in solutions. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates

An extensive quantum mechanical study of a water dimer suggests that the introduction of a diffuse function into the basis set, which significantly reduces the basis set superposition error (BSSE) in the hydrogen bonding energy calculation, is the key to better calculations of the potential energy surfaces of carbohydrates. This article examines the potential energy surfaces of selected d -aldo- and d -ketohexoses (a total of 82 conformers) by quantum mechanics (QM) and molecular mechanics (MM) methods. In contrast to the results with a smaller basis set (B3LYP/6-31G** 5d), we found at the higher level calculation (B3LYP/6-311++G(2d,2p)//B3LYP/6-31G** 5d) that, in most cases, the furanose forms are less stable than the pyranose forms. These discrepancies are mainly due to the fact that intramolecular hydrogen bonding energies are overestimated in the lower level calculations. The higher level QM calculations of the potential energy surfaces of d -aldo- and d -ketohexoses now are more comparable to the MM3 results. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1593–1603, 1999     

Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Combined experimental and computational modeling studies on 4‐[(2‐hydroxy‐3‐methylbenzylidene) amino]‐1,5‐dimethyl‐2‐phenyl‐1,2‐dihydro‐3H‐pyrazol‐3‐one

The Schiff base compound, 4‐[(2‐hydroxy‐3‐methylbenzylidene)amino]‐1,5‐dimethyl‐2‐phenyl‐1,2‐dihydro‐3H‐pyrazol‐3‐one, has been synthesized and characterized by IR, UV–vis, and X‐ray single‐crystal determination. Molecular geometry from X‐ray experiment of the title compound in the ground state have been compared using the density functional method (B3LYP) with 6‐31G(d,p) basis set. Calculated results show that density functional theory (DFT) can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6‐31G(d,p) basis set by applying the Onsager and the polarizable continuum model (PCM). The results obtained with these methods reveal that the PCM method provided more stable structure than Onsager's method. By using TD‐DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD‐DFT method and the experimental one is determined. The predicted nonlinear optical properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential and NBO analysis were performed at B3LYP/6‐31G(d,p) level of theory. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A theoretical study of medium effects on the structure of the glycine analogue aminomethylphosphonic acid

alpha-Aminophosphonic acids are analogues of natural alpha-aminoacids and very promising agents for use in various pharmaceutical applications. However, in contrast to the numerous theoretical investigations on the structure of natural alpha-aminoacids, only very few studies on alpha-aminophosphonic acids have been performed. In the present work, we report a detailed investigation of the simplest compound, the glycine analogue aminomethylphosphonic acid (AMPA), by means of quantum mechanical calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) and MP2/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) levels. We focus on the structure of the neutral species looking at the evolution of non-ionized and ionized forms from gas phase to non-polar solvents and aqueous media. Continuum and discrete-continuum solvent models have been employed to account for the effects of the environment. The discussion is centered on: (1) the geometry and relative stability of possible conformers in gas phase and aqueous solution, (2) the free energy of tautomerization in different media, (3) the role of hydrogen bonds in liquid water, and (4) the free energy of transfer from water to a hydrophobic solvent such as cyclohexane. Systematic comparison between AMPA and Gly is performed. Though both systems exhibit many similarities, some important differences have also been found that may be explained, at least in part, by the higher acidity of phosphonic acids compared to carboxylic acids. In particular, in solvents lacking hydrogen-bond formation capability, Gly derivatives should mainly exist as non-ionized molecules while the equivalent AMPA derivatives should adopt a zwitterionic structure in media with dielectric constant above 10. This might have significant environmental or biological consequences that will need to be addressed.     

Theoretical studies on the formation mechanism and explosive performance of nitro‐substituted 1,3,5‐triazines

To develop new highly energetic materials, we have considered the design of molecules with high nitrogen content. Possible candidates include 1,3,5‐triazine derivatives. In this work, we studied potential synthetic routes for melamine using the MP2/6‐31+G(d,p)//B3LYP/6‐31G(d) level of theory. The mechanisms studied here are stepwise mechanism beginning with the dimerization of cyanamide and one‐step termolecular mechanism. The same type of mechanism is also applied to nitro‐substituted 1,3,5‐triazines. Values for the heat of formation in the solid phase were predicted from density functional theory calculations. Densities were estimated from a regression equation obtained by molecular surface electrostatic potentials. The Cheetah program was used to study the explosive performance of these compounds. In this study, we found that the explosive properties of 2‐amino‐4, 6‐dinitro‐1, 3,5‐triazine (ADNTA), and 2,4,6‐trinitro‐1,3,5‐triazine (TNTA) are similar to those of RDX and HMX, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

On the origin of cis selectivity in the cyclization of N-protected 2-substituted 3-aza-5-hexenyl radicals: a density functional study

Cyclization of the N-dimethylphosphinoyl-2-methyl-3-aza-5-hexenyl radical has been studied at the UB3LYP/6-31+G(d)//UB3LYP/6-31G(d) hybrid density functional level. The corresponding radical precursor has been synthesized and found to give cis/trans ratios of up to 10/1 in reductive radical cyclizations. The relative energies of reactant and transition state conformers were determined. In discord with the Beckwith-Houk model, it has been found that chair-axial transition states, which lead to cis products, are lowest in energy, rationalizing the observed experimental diastereoselectivity.     

Cycloadditions of Aryl‐Substituted 1,2,4‐Triazines with 2‐Cyclopropylidene‐1,3‐dimethylimidazolidine – Zwitterions as Discrete Intermediates

Cycloadditions of 2‐cyclopropylidene‐1,3‐dimethylimidazolidine ( 1 ), a strong, electron‐rich C‐nucleophile, with a variety of aryl‐substituted 1,2,4‐triazines occur at temperatures between ?100 and +100°, depending on the substitution pattern. At low temperatures, zwitterions, formed by nucleophilic attack of 1 on the triazines, could be detected spectroscopically and, in some cases, isolated. Two types of zwitterions were found: 1) those where the new bond was linked to C(5) of the triazine and which were formed in a reversible dead‐end equilibrium, and 2) those where the new bond was linked either to C(3) or C(6). The latter exhibited the same regiochemistry as the final cycloadducts, and might be intermediates of a two‐step Diels–Alder reaction. Energies and structural characteristics for stationary points in the reaction of monosubstituted triazines with 1 in the gas phase and in CH₂Cl₂ solution were calculated at the Becke3LYP/6‐311+G(d,p)//Becke3LYP/6‐31G(d) level of theory. Different reaction mechanisms are discussed on the basis of steric, electronic, and solvent effects.     

Extending the acidity ladder of neutral organic superacids—a DFT-B3LYP study of deprotonation of nonacyanofluorene

It was shown by a carefully selected B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) model that nonacyanofluorene and its most stable prototropic tautomer represent very powerful neutral organic acids both in the gas phase and in DMSO.     

Addition reaction of adamantylideneadamantane with Br2 and 2Br2: a computational study

Ab initio calculations were carried out for the reaction of adamantylideneadamantane (Ad=Ad) with Br2 and 2Br2. Geometries of the reactants, transition states, intermediates, and products were optimized at HF and B3LYP levels of theory using the 6-31G(d) basis set. Energies were also obtained using single point calculations at the MP2/6-31G(d)//HF/6-31G(d), MP2/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31+G(d)//B3LYP/6-31G(d) levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Only one pathway was found for the reaction of Ad=Ad with one Br2 producing a bromonium/bromide ion pair. Three mechanisms for the reaction of Ad=Ad with 2Br2 were found, leading to three different structural forms of the bromonium/Br3- ion pair. Activation energies, free energies, and enthalpies of activation along with the relative stability of products for each reaction pathway were calculated. The reaction of Ad=Ad with 2Br2 was strongly favored over the reaction with only one Br2. According to B3LYP/6-31G(d) and single point calculations at MP2, the most stable bromonium/Br3- ion pair would form spontaneously. The most stable of the three bromonium/Br3- ion pairs has a structure very similar to the observed X-ray structure. Free energies of activation and relative stabilities of reactants and products in CCl4 and CH2ClCH2Cl were also calculated with PCM using the united atom (UA0) cavity model and, in general, results similar to the gas phase were obtained. An optimized structure for the trans-1,2-dibromo product was also found at all levels of theory both in gas phase and in solution, but no transition state leading to the trans-1,2-dibromo product was obtained.     

二氯亚甲基锗烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet dichloromethylene germylene and ethylene has been investigated with B3LYP/6-31G＊ method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD（T）//B3LYP/6-31G＊ method. On the basis of the surface energy profile obtained with CCSD（T）// B3LYP/6-31G＊ method for the cycloaddition reaction between singlet dichloromethylene germylene and ethylene, it can be predicted that the dominant reaction pathway is that an intermediate INT1 is firstly formed between the two reactants through a barrier-free exothermic reaction of 61.7 kJ/mol, and the intermediate INT1 then isomerizes to an active four-membered ring product P2.1 via a transition state TS2, an intermediate INT2 and a transition state TS2.1, in which energy barriers are 57.7 and 42.2 kJ/mol, respectively.