Theoretical Study of Molecular Structure, Tautomerism, and Geometrical Isomerism of N-Methyl- and N-Phenyl-Substituted Cyclic Imidazolines, Oxazolines, and Thiazolines

The geometries of various tautomers and isomers of 2-methylamino-2-imidazoline, 2-methylamino-2-oxazoline, 2-methylamino-2-thiazoline, 2-phenylamino-2-imidazoline, 2-phenylamino-2-oxazoline, and 2-phenylamino-2-thiazoline have been studied using the Becke3LYP/6–31+G(d,p) DFT, ONIOM(Becke3LYP/6–31+G(d,p):HF/3–21G^*) and ONIOM(Becke3LYP/6–31+G(d,p):AM1) methods. The optimized geometries indicate that these molecules show a distinctly nonplanar configuration of the cyclic moieties. In the gas phase, the amino tautomers (with exception of 2-phenylamino-2-imidazoline) are computed to be more stable than the imino tautomers. Of the two possible (E and Z) isomers of methyl and phenyl derivatives of imino-oxazolidine and imino-thiazolidine species, the (Z) isomers have the lowest energy. The iminozation free energies in the gas phase were found to be 5 – 15 kJ/mol. Absolute values of K _T depend strongly on the accuracy of the method used for calculation of free energy. Solvation (using the MD simulations) causes, in most cases, a shift in tautomeric preference toward the imino species.     

Theoretical investigation on the GaCl3-catalyzed ring-closing metathesis reaction of N-2,3-butadienyl-2-propynyl-1-amine: three-membered ring versus four-membered ring mechanism

The gallium chloride (GaCl(3))-catalyzed ring-closing metathesis reaction mechanism of N-2,3-butadienyl-2-propynyl-1-amine has been studied at the Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional (B3LYP)/6-31G(d), B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p)//B3LYP/ 6-31G(d) and the second-order M?ller-Plesset perturbation (MP2)/6-311++G(d,p)//B3LYP/6-31+G(d,p) levels. It was found that the final metathesis product can be yielded via a three-membered or four-membered ring mechanism. The three-membered ring pathway is favorable due to its low energy barrier at the rate determining step. The whole reaction is stepwise and strongly exothermic.     

Theoretical study of structure and properties of hexuronic acid and <Emphasis Type="SmallCaps">d</Emphasis>-glucosamine structural units of glycosaminoglycans

The Becke3LYP functional of DFT theory was used to investigate molecular structure and sodium affinity of the systems CH₃CO₂Na (1), CH₃–O–SO₃Na (2), CH₃–NH–SO₃Na (3), saccharide_1Na₂ (4), saccharide_2Na (5), saccharide_3Na₃ (6), saccharide_4Na₂ (7), and saccharide_5Na₂ (8), respectively, which are models of N- and O-sulfate glycosaminoglycans. Interaction enthalpies, entropies and Gibbs energies of the sodium-coordinated systems in the gas phase were determined with the B3LYP/6-311+G(d,p) and B3LYP/6-31+G(d) methods. The computed Gibbs energies, ΔG ^o , of model systems 1–3 are negative and span a rather broad energy interval (from −500 to −1,500 kJ mol⁻¹). Gibbs interaction energies for sodium acetate, sodium sulfate and sodium sulfamate functions of the five saccharides, systems 4–8 are always lower than those values found for the model compounds 1–3. The ionization of sodium salts of saccharides studied in gas phase is in most cases connected with considerable conformational rearrangement of the ionic species. This rearrangement causes an additional energetic stabilization of anionic species and is connected with the substantial release of entropy.     

Experimental and computational studies on (<Emphasis Type="Italic">Z</Emphasis>)-1-((4-phenylamino)phenylamino)-methylene)naphthalen-2(1<Emphasis Type="Italic">H</Emphasis>)-one

The Schiff base compound (Z)-1-((4-phenylamino)phenylamino)methylene)naphthalen-2(1H)-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 Hartree–Fock (HF) and density functional method (B3LYP) with 6−31G(d,p) basis set. Calculated results show that density functional theory DFT and HF can well reproduce the structure of the title compound. Using the time-dependent density functional theory (TD-DFT) and Hartree–Fock (TD-HF) methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and experimental ones is determined. 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 polarizable continuum model (PCM). The total energy of the title compound decreases with increasing polarity of the solvent. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), natural bond orbital analysis (NBO), and non-linear optical (NLO) properties were performed at B3LYP/6−31G(d,p) level of theory.     

NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.     

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.     

One-electron reduction potential for oxygen- and sulfur-centered organic radicals in protic and aprotic solvents

We estimated one-electron reduction potentials of redox-active organic molecules for a spectrum of eight different functional groups (phenoxyl, p-benzoquinone, phenylthiyl, p-benzodithiyl, carboxyl, benzoyloxyl, carbthiyl, and benzoylthiyl) in protic (water) and aprotic (acetonitrile, N,N-dimethylacetamide) solvents. Electron affinities (EA) were evaluated in a vacuum with high level quantum chemical methods using Gaussian3-MP2 (G3MP2) and Becke 3 Lee, Yang, and Parr functional B3LYP with aug-cc-pVTZ basis set. To evaluate one-electron redox potentials, gas-phase free energies were combined with solvation energies obtained in a two-step computational approach. First, atomic partial charges were determined in a vacuum by the quantum chemical method B3LYP/6-31G(d,p). Second, solvation energies were determined, solving the Poisson equation with these atomic partial charges. Redox potentials computed this way, compared to experimental data for the 21 considered organic compounds in different solvents, yielded overall root-mean-square deviations of 0.058 and 0.131 V using G3MP2 or B3LYP to compute electronic energies, respectively, while B3LYP/6-31G(d,p) was used to compute solvation energies.     

Theoretical Study of Gas-Phase Acidities of Selected Angiotensin-Converting Enzyme Inhibitors

The structure and gas-phase acidities of six members of large angiotensin-converting enzyme (ACE) inhibitor family [cilazaprilat, silanediol, fosinoprilat, AcSDKP, angiotensin_I (terminal part), and RXP_407] have been studied using the ONIOM Becke3LYP/6-311+G(d,p):HF/3-21G^∗ method. The investigated ACE inhibitors are weak acids with calculated acidity of about 1270–1650 kJ mol⁻¹. Of acids studied the highest gas-phase acidity (1273 kJ mol⁻¹) possesses experimental ACE inhibitor RXP_407. This drug, according to the computed pK_a value (3.2), is also in water solution the most acidic compound of the ACE inhibitors investigated.     

Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans

This study reports in detail the results of systematic large-scale theoretical investigations of the acidic dimeric structural units (D–E, E–F, F–G, and G–H) and pentamer D–E–F–G–H (fondaparinux) of the glycosaminoglycan heparin, and their anionic forms. The geometries and energies of these oligomers have been computed using HF/6–31G(d), Becke3LYP/6–31G(d), and Becke3LYP/6–311+G(d,p) methods. The optimized geometries indicate that the most stable structure of these units in the neutral state is stabilized via a system of intramolecular hydrogen bonds. The equilibrium structure of these species changed appreciably upon dissociation. Water has a remarkable effect on the geometry of the anions studied. Because of high negative charge, the solvent effect also resulted in an appreciable energetic stabilization of biologically active anionic forms of these glycosaminoglycans. The stable energy conformations around glycosidic bonds found for dimers and pentamer investigated are compared and discussed with the available experimental X-ray structural data for the structurally related heparin-derived pentasaccharides in cocrystals with proteins.     

Thermochemical properties for n‐propyl,iso‐propyl,and tert‐butyl nitroalkanes,alkyl nitrites,and their carbon‐centered radicals

Density functional theory (DFT) based calculations are performed on a series of alkyl nitrites and nitroalkanes representing large‐scale primary, secondary, and tertiary nitro compounds and their radicals resulting from the loss of their skeletal hydrogen atoms. Geometries, vibration frequencies, and thermochemical properties [S°(T) and C°_p(T) (10 K ? T ? 5000 K)] are calculated at the B3LYP/6‐31G(d,p) DFT level. Δ_fH°₂₉₈ values are from B3LYP/6‐31G(d,p), B3LYP/6‐31+G(2d,2p), and the composite CBS‐QB3 levels. Potential energy barriers for the internal rotations have been computed at the B3LYP/6‐31G(d,p) level of theory, and the lower barrier contributions are incorporated into entropy and heat capacity data. The standard enthalpies of formation at 298 K are evaluated using isodesmic reaction schemes with several work reactions for each species. Recommended values derived from the most stable conformers of respective nitro‐ and nitrite isomers include ?30.57 and ?28.44 kcal mol^?1 for n‐propane‐, ?33.89 and ?32.32 kcal mol^?1 for iso‐propane‐, ?42.78 and ?41.36 kcal mol^?1 for tert‐butane‐nitro compounds and nitrites, respectively. Entropy and heat capacity values are also reported for the lower homologues: nitromethane, nitroethane, and corresponding nitrites. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 181–199, 2010     

Theoretical and experimental studies of the electrochemistry of <Emphasis Type="Italic">p</Emphasis>-aminophenol on a golden electrode

The geometric parameters, vibrational frequencies, and thermochemical values of p-quinonimine (p-AQ) and p-aminophenol (p-AP) were computed ab initio (IIF) and by the density functional theory (DFT) method with the 6-31G(d, p) basis set. Cyclic voltammetry with a golden electrode of p-AP solutions in phosphate buffers at pH 7.30 showed that the standard electrode potential of half reaction for p-QI and p-AP was 0.728 V. The standard electrode potentials of half reactions for p-QI and p-AP were calculated using the free energies and solvation energies of p-QI, p-AP, p-benzoquinone (p-BQ), and hydroquinone (p-HQ). The results showed that the standard electrode potential of half reaction for p-QI and p-AP was 0.743 V at the B3LYP/6-31G(d, p) level and 0.755 V at the HF/6-31G(d, p) level. The standard electrode potentials computed at the B3LYP/6-31G(d, p) and HF/6-31G(d, p) levels were close to their experimental values. The article is published in the original.     

Experimental and theoretical studies on the reactions of 1-amino-5-benzoyl-4-phenyl-1<Emphasis Type="Italic">H</Emphasis>-pyrimidine-2-one/-thione compounds with ethyl acetoacetate

The reaction of 1-amino-5-(4-methylbenzoyl)-4-(4-methylphenyl)pyrimidin-2(1H)-one/-thione (1a,b) with ethyl acetoacetate (EA) afforded moderate to good yields (59–63%) of ethyl 2-methyl-4-(4-methylbenzoyl)-5-(4-methylphenyl)-7-oxo/-thioxo-3,3a-dihydropyrazolo[1,5-c]pyrimidine-3-carboxylate (2a,b). The newly synthesized compounds were characterized by elemental analyses, IR, ¹H and ¹³C NMR spectral data. All were compared with their previous analogues. The reaction mechanism of 1 with EA was studied by means of the B3LYP/6-31G(d,p) method. In addition, for reactants Fukui functions were performed using the data calculated with the Becke3–Lee–Yang–Parr (B3LYP) hybrid function.     

Molecular structure, barriers to internal rotation, and the enthalpy of formation of cumene hydroperoxide PhCMe2OOH: a DFT study

Conformational analysis of cumene hydroperoxide PhCMe₂OOH (1) has been carried out using the density functional methods B3LYP/6-31G(d,p) and B3LYP/6-311+G(3df,2p). Ignoring rotation of methyl groups, molecule 1 has seven conformers differing in orientation of the — CMe₂OOH fragment relative to the benzene ring and in mutual position of atoms in this fragment. The molecular structures, relative energies, and statistical distribution of the conformers were determined, and intramolecular rotational barriers were estimated. The enthalpies of formation of all conformers of molecule 1 were calculated using two approximations with inclusion of zero-point vibrational energy and temperature correction. Calculations using the isodesmic reaction (IDR) scheme made it possible to reduce the systematic error of the determination of the enthalpy of reactions. The total enthalpy of formation of compound 1 calculated with inclusion of statistical distribution of rotamers equals −19.7±3.6 kcal mol⁻¹. The combination of the B3LYP/6-31G(d,p) approximation and the IDR scheme gives fairly accurate results (relative error is ±0.4 kcal mol⁻¹) as compared to those obtained with the extended basis set 6-311+G(3df,2p). Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1157–1164, June, 2008.     

A density functional theory study of the structure and vibrational spectra of beta-carotene, capsanthin, and capsorubin

A theoretical study of the structure and the vibrational spectra of the beta-carotene molecule and its derivatives capsanthin and capsorubin is carried out. We first investigate systematically the theoretical method which provides the best results for beta-carotene by performing ab initio calculations at the HF/6-31G(d), SVWN/6-31G(d), PBE0/6-31G(d), BLYP/6-31G(d), B3LYP/6-31G(d), B3LYP/6-31G(d,p), B3LYP/6-311G(d), and B3LYP/6-311G(d,p) levels and by using previous theoretical results available in the literature obtained at the AM1 and BPW91/6-31G(d) levels. The influence of both the level of calculation and the size of the basis set used in the geometry optimization and in the determination of the IR and Raman spectra of this molecule is thus analyzed. It is confirmed that the hybrid functional B3LYP with the basis 6-31G(d) is the method that gives the best results as a whole. By use of this level of calculation, we next optimize the molecular geometries of related molecules of capsanthin and capsorubin, which to the best of our knowledge have only been studied at the semiempirical AM1 level. In addition we calculate the IR and Raman spectra of these molecules at the B3LYP/6-31G(d) level of theory. The results obtained for capsanthin show on the one hand that the double bond of the beta-ionone ring is outside the polyene chain plane, due to the repulsion between the hydrogen atoms of the ring methyl groups and the hydrogen atoms of the polyene chain, and on the other hand that the carbonyl double bond in the other headgroup is very close to planarity with the polyene chain, since in this case such a repulsion does not exist. For the molecule of capsorubin the two carbonyl groups also take the same coplanar orientation relative to the polyene chain. The IR and Raman spectra theoretically computed for these two molecules are finally compared with their experimental spectra and the vibrational normal modes of the main signals are interpreted.     

C_3O_2分子结构和光谱的密度泛函理论研究

使用密度泛函理论,在B3LYP/6-31G(d)和B3LYP/6-311G(2d)水平上,研究了C_3O_2分子的可能几何构型,并在6-31G(d)水平上计算了其中2种总能量最小的构型的振动频率,同时与实验观察值进行了比较, 计算结果当C_3O_2分子具有C2v对称性的W型弯曲结构（键角C－C－C和C－C－O分别为162.3°和178.8°）时,振动频率的计算值和实验观察值非常吻合。     

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.     

Molecular structure of 6-(N,N-dimethylamino)fulvene from a joint gas-phase electron diffraction and quantum-chemical study

The molecular structure of 6-(N,N-dimethylamino)fulvene was studied by gas-phase electron diffraction and quantum-chemical methods (HF/6-31G(d), MP2/3Z, MP2/4Z, density functional theory with the B3LYP/6-31G(d) and PBE/3Z functionals). Pronounced flattening of the nitrogen atom and equalization of the intracyclic C—C bonds were found to be a consequence of the electron delocalization in the molecule.     

Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl

The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out     

The structure and energetics of pyrrolidinones, tetrahydrofuranones, piperidinones, and tetrahydropyranones: a computational study

We have performed high level ab initio quantum chemical calculations for 2- and 3-pyrrolidinone; tetrahydro-2- and -3-furanone; 2-, 3-, and 4-piperidinone; and tetrahydro-2-, -3-, and -4-pyranone. The most stable molecular structures were obtained from DFT calculations using the B3LYP density functional and the 6-31G(d) and 6-311+G(3df,2p) basis sets. The respective enthalpies of formation have been computed by the G3(MP2)//B3LYP composite method and appropriately chosen reactions. The calculated results are in excellent agreement with experimental data reported in the literature.     

Computational studies on acyclic amidyl radicals: Π and Σ states and conformations

Restricted open and unrestricted Becke3LYP/6-31+G(d) calculations on Π and Σ states as well as equilibrium geometries of the formamidyl radical (1) and four of its dialkyl substituted derivatives 2–5 have been carried out. While all radicals studied are significantly twisted about the RN–C(O) bond and show a Π-type total spin density, the calculations confirm the special status of N-tert-butyl acetamidyl (4) that was found with EPR spectroscopy. Each of the torsional double-minimum potentials of N-methyl and N-isopropyl radicals 2, 3, and 5 shows a low barrier to interconversion for two equivalent conformers whereas 4 is situated in a steeper well with a larger twist angle which explains reported EPR ¹³C hyperfine splittings.