Theoretical Study on the Tautomerization Reaction of Formamide to Formamidic Acid Encapsulated in a Nano-sized Molecular Container

The hybrid calculations with ONIOM(B3LYP/6-31G*:AM1) method were carried out on the tautomerization reaction of formamide to formamidic acid in the microcontainer-encapsulated state. The free-state tautomerization process was also investigated with B3LYP/6-31G**//B3LYP/6-31G* method for the purpose of comparison. Bare tautomerization, H2O-assisted(single-H2O or multiple-H2O) and self-assisted mechanisms were all taken into consideration for the encapsulated state. The results show that only bare tautomerization and single-H2O catalysis mechanisms are possible to the encapsulated for-mamide tautomerization owing to the container's size confinement effect. Geometrical changes in the complexed container and guest molecules are discussed to deeply understand the complex's structural properties. The bare tautomerization barrier in the encapsulated state increases by 23.826 kJ/mol, ac-counting for 12% of the corresponding total energy barrier in the free state, and the increased values for the single-H2O catalysis process are 12.958 kJ/mol, accounting for 16% of the corresponding total energy barrier, respectively. This finding suggests that the encapsulation can make the tautomerization process slightly difficult.     

Ab initio studies of molecules with N-C-C=O units Part 1. 2-Aminoethanal

A complete conformational analysis of 2-aminoethanal (2AE) has been carried out using the 6-31G^** basis set. The curve corresponding to the barrier of rotation of the N-C-C=O torsion was obtained and compared with the MM392 and the previously reported 4-21 G curves. Geometrical trends relating to intramolecular hydrogen bonding were found and quantitatively discussed. Full geometry optimization MP2/6-31G^**//6-31G^** was performed for the stable conformers found along the N-C-C=O curve with different arrangements of the NH₂ group.     

Prediction of geometries and interaction energies of complexes formed by small molecules using semiempirical and ab initio methods

The accuracy of the semiempirical quantum mechanics methods (AM1 and PM3), and the ab initio methods (6-31G^** and MP2/6-31G^**) in predicting intermolecular geometries and interaction energies have been evaluated by detailed studies of 17 bimolecular complexes formed by small molecules. Comparisons between calculated and experimental geometries for 12 complexes are presented. It was found that AM1 gave reasonably good predictions of the geometries of complexes such as CH₄ · CH₄, which have very weak interactions, but it is not as good as other methods in predicting intermolecular geometry for complexes where hydrogen bonding interactions play an important role. This is consistent with its inability to reproduce the charge transfer in the formation of hydrogen bonds in these complexes.

PM3 is able to predict intermolecular geometries for most complexes, including those with hydrogen bonding; its major flaw is its tendency to overestimate the strength of the interactions between hydrogen atoms. Care should be taken therefore in using PM3 to study complicated molecular systems with multiple hydrogen atom interactions and the method's weakness in handling complexes in which electrostatic forces are important should also be noted.

Among ab initio methods, both the 6-31G^** and the MP2/6-31G^** were found to outperform AM1 and PM3 in prediction of intermolecular geometry. Both of these ab initio methods showed excellent consistency in geometry prediction for most of the complexes studied, although MP2/6-31G^** is better than 6-31G^**. It is noted that the MP2/6-31G^** did not produce the correct geometry for the CO₂· HF complex.

For 12 complexes for which experimental geometry data are available, AM1, PM3, 6-31G^**, and MP2/6-31G^** successfully predicted the geometry in 10, 12, 12, and 11 cases, respectively. The average errors given by AM1 in the predicted intermolecular distances were 0.264, 0.272, 0.091, and 0.061 Å, respectively. In comparison to the ab initio methods, AM1 and PM3 commonly underestimated the molecular interaction energy in such complexes by ˜ 1–2 kcal mol⁻¹.     

Binding mechanism of RGD and its mimetics to receptor GPIIb/IIIa. A theoretical study

In order to better understand, at a sub-molecular level, the minimal structural requirements for the recognition process in the platelet aggregation inhibitory activity, a series of RGD mimetics were examined as fibrinogen receptor antagonists variants. We simulate the electronic interactions between RGD with its biological receptor in terms of smaller molecules. MeCOO⁻ was used to mimic the side chain of deprotonated Asp and Meguanidinium group mimicked the side chain of the protonated Arg. Alternative moieties present on the RGD mimetics were also studied in this report. AM1; RHF/3-21G; B3LYP/6-31++G^** in the gas phase. Also, B3LYP/6-31++G^** calculations using the IPCM solvation model were carried out for all the complexes. Our results indicate that high level of theory calculations and the inclusion of solvent effects are crucial in order to obtain satisfactory of accuracy in the electronic distributions of these compounds.     

Investigation of the use of B3LYP zero-point energies and geometries in the calculation of enthalpies of formation

The use of B3LYP/6–31G^* zero-point energies and geometries in the calculation of enthalpies of formation has been investigated for the enlarged G2 test set of 148 molecules [J. Chem. Phys. 106 (1997) 1063]. A scale factor of 0.96 for the B3LYP zero-point energies gives an average absolute deviation nearly the same as scaled HF/6–31G^* zero-point energies for G2, G2(MP2), and B3LYP/6–311 + G(3df,2p) enthalpies. A scale factor of 0.98, which has been recommended in some studies, increases the average absolute deviation by about 0.2 kcal/mol. Geometries from B3LYP/6–31G^* are found to do as well as MP2/6–31G^* geometries in the calculation of the enthalpies of formation.     

Structure and conformational stability of CH2CHCH2X (X=F, Cl and Br) molecules—post Hartree–Fock and density functional theory methods

The molecular structure and conformational stability of CH₂CHCH₂X (X=F, Cl and Br) molecules were studied using ab initio and density functional theory (DFT) methods. The molecular geometries of 3-fluoropropene were optimized employing BLYP and B3LYP levels of theory of DFT method implementing 6-311+G(d,p) basis set. The MP2/6-31G^*, BLYP and B3LYP levels of theory of ab initio and DFT methods were used to optimize the 3-chloropropene and 3-bromopropene molecules. The structural and physical parameters of the molecules are discussed with the available experimental values. The rotational potential energy surface of the above molecules were obtained at MP2/6-31G^* and B3LYP/6-311+G(d,p) levels of theory. The Fourier decomposition of the rotational potentials were analyzed. The HF/6-31G^* and MP2/6-31G^* levels of theory have predicted the cis conformer as the minimum energy structure for 3-fluoropropene, which is in agreement with the experimental values, whereas the BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory reverses the order of conformation. The ΔE values calculated for 3-chloropropene at MP2/6-31G^*, BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory show that the gauche form is more stable than the cis form, which is in agreement with the experimental value. The same levels of theory have also predicted that the gauche form is stable than cis for 3-bromopropene molecule. The maximum hardness principle has been able to predict the stable conformer of 3-fluoropropene at HF/6-31G^* level of theory, but the same level of theory reverses the conformational stability of 3-chloropropene and 3-bromopropene molecules and MP2/6-31G^* level of theory predicted the stable conformer correctly.     

Theoretical study of some 1,3-substituted (1,3-diketonato)borondifluorides. Potential energy curve relevant to the barrier crossing reaction

Ab initio Hartree-Fock calculations utilising STO-3G, 3-21G^* and 6-31G^* basis sets have been performed on three neutral and highly polar molecules, (diformylmethine)borondifluoride, (acetylacetonato)borondifluoride and (dibenzylmethine) borondifluoride. The calculated and experimental structures are well correlated when using the HF/3-21G^* basis set, except for the structure parameters involving the boron atom. The HF/6-31G^* basis set does not improve the accuracy in structure calculations. The conformational analysis is in agreement with the experimentally observed C_2v symmetrical structures, where the boron atom is tetrahedrally coordinated. The calculations support a one-dimensional ground state barrier crossing reaction for (dibenzylmethine)borondifluoride, where the phenyl torsion is the most likely reaction coordinate. Both HF/6-31G^* calculations and the second-order Møller-Plesset correction with the 3-21G^* basis set suggest an activation energy of the ground state reaction of about 30 kJ mol⁻¹. The ground state barrier crossing reaction kinetics is evaluated by the Kramers theory. The calculated ground state parameters relevant to the barrier crossing reaction are compared with the experimentally observed excited state values.     

DFT study of the EPR spectral pattern of propagating methacrylic radicals

The EPR spectral pattern observed in the bulk polymerization of methacrylic monomers was theoretically investigated by DFT methodology. The conformational analysis of the propagating radical by the rotation around the C–C_β bond, was performed using the B3LYP/6-31G^* computational scheme. To obtain accurate values of the isotropic hyperfine coupling constants (hfccs) a higher level protocol, B3LYP/TZVP//B3LYP/6-31G^*, was applied. The experimental 13-line spectrum registered at the first stage of the polymerization was assumed to correspond to a free rotating radical in a fluid medium and it was simulated just considering the most stable conformation. The 9-line spectrum registered at high conversions was interpreted in terms of highly hindered rotational conformers frozen in the very viscous medium. This spectrum was well reproduced by a model which considers the sum of the individual spectra of the conformations spread around the most probable. Each of these contributing spectra was obtained on the basis of the computed hfccs for the considered conformations and weighted by his relative Boltzmann population according to the DFT analysis. Besides, the calculated hfccs showed an excellent agreement with those predicted by the Heller–McConnell relationship, which confirms the coherence of the DFT methodology for this kind of calculations.     

Vibrational spectra and density functional study of propylgermane

Raman and infrared spectra of propylgermane, CH₃CH₂CH₂GeH₃, and its Ge-deuterated analog, CH₃CH₂CH₂GeD₃, were investigated in their gaseous, liquid and solid states. The normal coordinate treatment was carried out by density functional theory (DFT) calculation, using B3LYP/6-31G^* and 6-311++G^** basis sets, and the corresponding fundamental vibrations were assigned. The trans (T) and gauche (G) forms around the central C–C bond coexisted in the gaseous and liquid states and only the T form existed in the solid state. From the temperature dependent measurements of the Raman spectra in the liquid state, the enthalpy difference was found to be ΔH(T−G)=−0.36±0.02 kcalmol⁻¹ with the T form being more stable. The energy differences between the isomers obtained by DFT calculations were ΔE(T−G)=−0.46 kcalmol⁻¹ and ΔE(T−G)=−0.87 kcalmol⁻¹ by the 6-31G^* basis set and 6-311++G^** basis set, respectively.     

A semi-empirical and ab initio combined approach for the full conformational searches of gaseous lysine and lysine–H2O complex

A full structural search of the canonical, zwitterionic, protonated and deprotonated lysine conformers in gas phase is presented. A total of 17,496 canonical, 972 zwitterionic, 11,664 protonated and 1458 trial deprotonated structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were initially optimized at the AM1 level, and the resulting structures were determined at the B3LYP/6-311G^* level. A total of 927 canonical, 730 protonated and 193 deprotonated conformers were found, but there were no stable zwitterionic structures in the gas phase. The most stable conformers of the canonical, protonated and deprotonated lysine were further optimized at the B3LYP/6-311++G^** level. The energies of the most stable structures were determined at the MP2/6-311G(2df,p) level and the vibrational frequencies were calculated at the B3LYP/6-311++G^** level. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, vertical ionization energies, enthalpies, Gibbs free energies and conformational distributions of gaseous lysine were presented. Numerous new structures are found and the lowest-energy lysine conformer is more stable than the existing one by 1.1 kcal/mol. Hydrogen bonds are classified and may cause significant red-shifts to the associated vibrational frequencies. The calculated proton affinity/dissociation energy and gas-phase basicity/acidity are in good agreement with the experiments. Calculations are also presented for the canonical lysine–H₂O and zwitterionic lysine–H₂O clusters. Interaction between lysine and H₂O significantly affects the relative conformational stabilities. Only one water molecule is sufficient to produce the stable zwitterionic structures in gas phase. The lowest-energy structure is found to be zwitterions when applying the conductor-like polarized continuum solvent model (CPCM) to the lysine–H₂O complexes.     

Intermolecular Interaction of HMX： an Application of ONIOM Methodology

IntroductionExtensive studies on intermolecular interac-tions have been made in the past decades due totheir importance in a wide range of physical,chem-ical and biological fields.Researches on the weakintermolecular interactions began with hydrogenbonds.Scheiner summarized the ab initio investiga-tions on hydrogen bonding in detail[1] .With the abinitio method supermolecular structures and bind-ing energies can be predicted notonly for H- bondedsystems but also for other systems[2 _ 5] when …     

Molecular structure and conformational stability of allylisocyanate—post-Hartree–Fock and density functional theory studies

The molecular structure and conformational stability of allylisocyanate (CH₂CHCH₂NCO) molecule was studied using the ab initio and DFT methods. The geometries of possible conformers, C-gauche (δ=120°, θ=0°) (δ=C=C–C–N and θ=C–C–N=C) and C-cis N-trans (δ=0° and θ=180°) were optimized employing HF/6-31G^*, MP2/6-31G^* levels of theory of ab initio and BLYP, B3LYP, BPW91 and B3PW91 methods of DFT implementing the atomic basis set 6-311+G(d,p). The structural and physical parameters of the above conformers were discussed with the experimental and theoretical values of the related molecules, methylisocyanate and 3-fluoropropene. It has been found that the N=C=O bond angle is not linear as the experimental result for both the conformers and the theoretical bond angle is 173°. The rotational potential energy surfaces have been performed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The Fourier decomposition potentials were analysed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The HF/6-31G^* level of theory predicted that the C-gauche conformer is more stable than the C-cis N-trans conformer by 0.41 kJ/mol, but the MP2 and DFT methods predicted the C-cis N-trans conformer is found to be more stable than the C-gauche conformer. The calculated chemical hardness value at the HF/6-31G^* level of theory predicted the C-cis N-trans form is more stable than C-gauche form, whereas the chemical hardness value at the MP2/6-31G^* level of theory favours the slight preference towards the C-gauge conformer.     

双环金属铱(Ⅲ)异腈配合物的二阶非线性光学性质

采用密度泛函理论(DFT)方法对双环金属Ir(III)异腈配合物的非线性光学(NLO)性质进行计算研究。用B3PW91(UB3PW91)(金属原子采用LANL2DZ基组,非金属原子采用6-31G*基组)方法对配合物进行几何结构优化。在优化构型基础上,采用B3PW91(UB3PW91)和B3LYP(UB3LYP)方法计算了配合物的第一超极化率(βtot),并用CAM-B3LYP(UCAM-B3LYP)(金属原子采用LANL2DZ基组,非金属原子采用6-31G**基组)方法模拟配合物的吸收光谱。结果表明,主配体的取代基(R1)和副配体的取代基(R2)对第一超极化率值贡献不大。配合物发生氧化还原反应,电荷转移方式增多,电荷转移程度增大,使βtot值显著增加,其中1a+([(C∧N)2Ir(CNR)2]+(R=CH3))发生氧化反应和还原反应的βtot值分别增大了75倍和144倍。因此,这类双环金属铱(III)异腈配合物的氧化还原反应可以有效地调节其二阶NLO性质。     

Non-empirical molecular orbital studies of the possibility of ferromagnetic ordering in isoelectron-substituted ferrocarbon modifications

The vertical singlet-triplet (ST) splitting in the C₃H₆ molecule and C₂BH⁻₆ and C₂NH⁺₆ ions has been investigated by means of ab initio calculations. The molecular geometry was either taken as that corresponding to the UHF/6-31G^* or UHF/6-31+G^* energy minimum of the triplet configuration (for C₃H₆, C₂BH⁻₆, C₂NH⁺₆), or was extracted from the ferrocarbon crystal (for C₃H₆). Polarized split-valence basis sets (6-31G^*, 6-31+G^* and 6-311G^**) and fourth-order Møller-Plesset perturbation theory at the MP4SDTQ level of approximation provides more reliable ST splitting values, than the MP4SDQ level, the latter being the most accurate method used in our previous work. These calculations prove the presence of ferromagnetic ordering within the same quasi-graphite plane of ferrocarbon crystal. The presence of such ordering has been shown within the same quasi-graphite plane upon substitution of sp³ carbon atoms by ions B⁻, N⁺ and so on.     

Influence of DFT-calculated electron correlation on energies and geometries of retinals and of retinal derivatives related to the bacteriorhodopsin and rhodopsin chromophores

DFT-calculations were performed on retinal in the all-trans, 1, 11-cis-12-s-cis, 2, and 11-cis-12-s-trans configuration, 3, and on the corresponding N-methyl Schiff base and protonated N-methyl Schiff base derivatives; for the latter, the corresponding 6-s-trans conformations and the 6-s-trans-13-cis-14-s-trans isomer which play a role in the bacteriorhodopsin photocycle were also studied. All geometries were fully optimized using the Becke- three-parameter Lee-Yang-Parr method in conjunction with the 6-31G^** basis set (B3LYP/6-31G^**). The stabilities in order of increasing energy are 1, 3 and 2 regardless of the type of substitution of the end group. While the energy of 3 relative to 1 is almost constant (5 ± 0.2 kcal mol⁻¹), the relative energy of 2 depends somewhat on the nature of the functional group: it is highest in the protonated Schiff base derivative 2-SBH + with its steric congestion along the C12-C13 bond. Comparison with results previously obtained on the basis of RHF/6-31G^** ab initio calculations reveals that the B3LYP method is more biased towards π-electron delocalization. This is indicated by the reduced degree of double bond fixation along the chromophore and also in the increased tendency towards planarization as manifest, e.g. by the change of the C5-C6-C7-C8 dihedral angle between the cyclohexene ring and the open chain double bond system.     

Computational studies of the structure and vibrational spectra of hexafluorodisilane

Ab initio calculations predict that D_3d symmetry of Si₂F₆ is more stable than D_3h symmetry. The calculated potential barrier to internal rotation was 0.77, 0.73 and 0.78 kcal/mol using HF/6-31G*, B3LYP/6-31G* and MP2/6-31G* methods respectively, which was in good agreement with the experimental value between 0.51±0.10 and 0.73±0.14 kcal/mol. The optimized geometries, harmonic force fields, infrared intensities, Raman activities, and vibrational frequencies are reported for D_3d symmetry of Si₂F₆ from HF/6-31G* and B3LYP/6-31G*. A normal coordinate analysis was carried out. The average error between the scaled DFT frequencies obtained from the B3LYP/6-31G* calculation and observed frequencies was 4.2 cm⁻¹ and the average error between the scaled HF and observed frequencies was 2.2 cm⁻¹.     

DFT法研究3-羟基丙烯醛的双键旋转异构反应机理

利用密度泛函理论(DFT)分别在B3LYP/6-31G**和B3LYP/6-311＋＋G**的计算水平上优化了基态3-羟基丙烯醛分子在双键旋转异构反应过程中的平衡态以及过渡态的几何构型，分析了反应过程中键参数的变化，计算了该反应的内禀反应坐标(IRC)，发现在重排反应途径上存在一个四元环骨架的中间体.通过振动分析对平衡态和过渡态进行了确认，并得到了零点能.计算结果表明，基态3-羟基丙烯醛分子的双键旋转异构反应经过两步完成，第一步反应位垒稍高，第二步反应位垒较低，存在着发生重排反应的可能性.     

Ab initio studies of methanol, methanethiol and methylamine dimer

Quantum chemical calculations are used to provide structural, vibrational and energetical information on the dimers of the methanol, methylamine and methanethiol systems. These systems were studied employing the DFT(B3LYP) and MP2 methods together with the 6-31+G^** and 6-311+G^** basis sets. We found two distinct potential minima for methylamine (one of them is a transition structure) and methanethiol, and one for the methanol dimer. The properties of these dimers are compared with those of the dimers (H₂O)₂, (NH₃)₂ and (CH₃SH)₂. The interactions in these dimers were analyzed using electron density properties at the bond critical point.     

Structure and stability of ammonium-sulfate and guanidium-sulfate complex

Ab initio (HF/6-31G^** and B3LYP/6-31 + + G^**) methods have been used to study the stability and structure of complexes between CH₃SO⁻₃ and CH₃NH⁺₃ or C(NH₂)⁺₃. Results show that no hydrogen jump is involved in the complex formations, which is different from previous work studying complexes between CH₃COO⁻ and CH₃NH⁺₃. In addition, we have studied complexes between CH₃SO⁻₃ and HC(NH₂)⁺₃ or ⁺H₃NC(NH₂)₃, all of which have a cage structure.