Theoretical study of the highly diastereoselective 1,3-dipolar cycloaddition of 1,4-dihydropyridine-containing azomethine ylides to [60]fullerene (Prato's reaction)

The 1,3-dipolar cycloaddition of azomethine ylides bearing the biologically active 1,4-dihydropiridine ring to C(60) was investigated by means of quantum mechanical calculations at the semiempirical AM1 and DFT (B3LYP/6-31G) methods. The presence of two chiral centers and one chiral axis in the resulting fulleropyrrolidines leads to four possible [6,6] cycloaddition products. Formation of atropoisomers has also been considered. The transition-state structures were computed for the four different cycloaddition pathways to find out the lowest activation energy stereoisomer. In all cases, a frequency analysis and an IRC calculation were carried out to fully characterize the located transition-state structures. AM1 results and single-point energy calculations at the B3LYP/6-31G//AM1 level for the four transition-state structures yield activation energies values below 5 kcal/mol.     

Conformational space of 4,4′-methoxypropylstilbene molecule

Quantum-chemical simulation of the ground state [the density function B3LYP/6-31G, B3LYP/6-31G(d), and B3LYP/6-31+G(d,p) and the perturbation theory MP2/6-31G(d) methods] and the transition states [the B3LYP/6-31G(d) method] of 4,4′-methoxypropylstilbene molecule has been performed. Using the Ellinger MM2 force field method, the potentials of internal rotation have been obtained for each rotational degree of freedom of the molecule. The B3LYP simulation has revealed the planarity of the conjugated system and the orthogonal position of the alkyl substituent, whereas the benzene rings have deviated by about 20° with respect to the double bond plane according to the MP2 data. Three transition states of the molecule corresponding to the saddle points of the first and the second orders have been revealed. The stationary points have been identified by means of vibrational analysis.     

DFT study of the electronic and charge transfer properties of perfluoroarene–thiophene oligomers

The ground state structures of 5,5″-diperfluorophenyl-2,2′:5′,2″:5″,2‴-quaterthiophene (1), 5,5′-bis{1-[4-(thien-2-yl)perfluorophenyl]}-2,2′-dithiophene (2), 4,4′-bis[5-(2,2′-dithiophenyl)]-perfluorobiphenyl (3), 5,5″-diperfluorophenyl-2,2′:5′,2″-tertthiophene (4), 5,5′-diperfluorophenyl-2,2′-dihiophene (5), and 5,5-diperfluorophenylthiophene (6) have been optimized at the B3LYP/6-31G(d), B3LYP/6-31G(d,p), PBE0/6-31G(d), and PBE0/6-31G(d,p) level of theories. The B3LYP/6-31+G(d) and PBE0/6-31+G(d) level of theories have been applied to investigate the absorption spectra. The PBE0 functional is good to predict the C–S bond lengths while the C–F bond lengths are good envisaged with B3LYP functional. The increment of thiophene rings between two perfluoroarene rings leads to red shift in absorption spectra. The electron affinities are energetically destabilized while energetic stabilization of the radical-cation increases by decreasing the thiophene rings from four to one. The perfluoroarene rings leads to enhance the electron injection.     

Structures, stabilities, and electronic and optical properties of C62 fullerene isomers

The 2385 classical isomers and four nonclassical isomers of fullerene C62 have been studied by PM3, HCTH/3-21G//SVWN/STO-3G, B3LYP/6-31G(d)//HCTH/3-21G, and B3LYP/6-31G(d)//B3LYP/6-31G(d). The Cs:7mbr isomer, with a chain of four adjacent pentagons surrounding a heptagon, is predicted to be the most stable isomer, followed by C2v:4mbr which is 3.15 kcal/mol higher in energy. C2:0032 with three pairs of adjacent pentagons is the most stable isomer in the classical framework. To clarify the relative stabilities of C62 isomers at high temperatures, the entropy contributions are taken into account on the basis of the Gibbs energy at the B3LYP/6-31G(d) level. Analyses reveal that Cs:7mbr prevails in a wide temperature range. The vibrational frequencies of the five most stable C62 fullerene isomers are also predicted at the B3LYP/6-31G(d) level, and the simulated IR spectra show important differences in positions and intensities of the vibrational modes for different isomers. The nucleus-independent chemical shift and the density of states of the three most stable isomers show that the square in C2v:4mbr and the adjacent pentagons in Cs:7mbr and C2:0032 possess high chemical reactivity. In addition, the electronic spectra and second-order hyperpolarizabilities are determined by means of ZINDO and the sum-over-states mode. The intensity-dependent refractive index gamma(-omega; omega, omega, -omega) at omega = 2.3305 eV of Cs:7mbr is very large because of resonance with the external field. The second-order hyperpolarizabilities of the five most stable isomers of C62 are predicted to be larger than those of C60.     

基于噻吩和亚苯基合成的新物质的结构和电子性质

Theoretical study on the geometries and electronic properties of new conjugated compounds based on thiophene and phenylene was carried out. The theoretical ground-state geometries and electronic structures of the studied molecules were obtained using the density functional theory (DFT) method at B3LYP level with 6-31G(d) basis set. The electronic properties were determined by ZINDO/s, CIS/3-21G(d), and TD//B3LYP/3-21G(d) calculations performed on the B3LYP/6-31(d) optimized geometries. The effects of the ring structure and the substituents on the geometries and electronic properties of these materials were discussed. The results of this study indicate how the electronic properties can be tuned by the backbone ring or side group and suggest these compounds as good candidates for opro-electronic applications.     

Structural and Electronic Properties of New Materials Based on Thiophene and Phenylene

Theoretical study on the geometries and electronic properties of new conjugated compounds based on thiophene and phenylene was carried out. The theoretical ground-state geometries and electronic structures of the studied molecules were obtained using the density functional theory (DFT) method at B3LYP level with 6-31G(d) basis set. The electronic properties were determined by ZINDO/s, CIS/3-21G(d), and TD//B3LYP/3-21G(d) calculations performed on the B3LYP/6-31(d) optimized geometries. The effects of the ring structure and the substituents on the geometries and electronic properties of these materials were discussed. The results of this study indicate how the electronic properties can be tuned by the backbone ring or side group and suggest these compounds as good candidates for opto-electronic applications.     

DFT studies on endohedral fullerene C@C60: C centers the C60 cage

Structural and electronic properties of C@C₆₀ were studied via Hartree–Fock self-consistent field (SCF) and density functional B3LYP levels of theory with the STO-3G, 6-31G(d) and 6-31G(d, p) basis sets. Both singlet and triplet were considered. The triplet structure with C on the center of the C₆₀ cage was proved to be global minimum on the C@C₆₀ molecular potential energy surface. The calculated HOMO-LUMO gaps as well as the electron affinity (EA) and the ionization potential (IP) were also presented as an indicator of the kinetic stability.     

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.     

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。     

一种天然产物Wangzaozin A的细胞毒活性

从总序香茶菜Isodon racemosa (Hemsl) Hara植物中分离得到一个对人类肿瘤细胞Bel-7402和HD-8910具有毒活性的对映-贝壳衫烷型二萜Wangzaozin A化合物(1). 应用密度泛函理论(DFT)B3LYP方法, 对该分子的几何构型进行优化, 结果表明用B3LYP/6-31G(d)优化的几何参数与它的X射线衍射结构参数基本一致. 在优化的几何构型基础上, 采用规范不变原子轨道(GIAO)法, 在B3LYP理论水平分别用6-31G(d), 6-31G(d,p), 6-31+G(d,p)和6-31++G(d,p)基组进行核磁共振(NMR)化学位移值计算, 预测的1H和13CNMR化学位移值与实验值吻合; 统计误差分析表明, 用B3LYP/6-31G(d)优化的分子构型接近实际的分子构型. 因此, DFT方法适用这一类型化合物的构型和NMR参数进行预测. 在几何优化的基础上, 在B3LYP/6-31G(d)水平上, 对Wangzaozin A分子的静电位(MEP)进行理论计算. MEP三维图表明, 在Wangzaozin A分子中α-亚甲基环戊酮的羰基和羟基附近出现富电子区域(负电位), 起着供电子作用, 与受体的正电子区域结合. 这些结果从理论上支持了α-亚甲基环戊酮结构是一种抗肿瘤活性中心的看法.     

Quantum chemical calculations based on ONIOM and the DFT methods in the inclusion complex: doxycycline/2-O-Me-β-cyclodextrin

A computational study of inclusion complexes of 2-methyl-βCD with Doxycycline tautomeric (enol and keto form) has been performed with several combinations of ONIOM hybrid calculations. The reliability of the ONIOM2 calculations at the integrated level, ONIOM2 (M05-2X/6-31G(d): M05-2X/3-21G*), ONIOM2 (M05-2X/6-31G(d):HF/3-21G*), ONIOM2 (B3LYP/6-31G(d):HF/3-21G*), ONIOM2 (B3LYP/6-31G(d):B3LYP/3-21G*) and ONIOM2 (B3PW91/6-31G(d):B3PW91/3-21G*) was examined. Their complexation, binding, deformation and stabilization energies, and geometrical data were compared with those of the target geometry structure optimized at the M05-2X/6-31G(d) level of theory. Mixed combinations ONIOM2 (M05-2X 6-31G(d):HF 3-21G*) and ONIOM2 (B3LYP 6-31G(d):HF 3-21G*) reproduces nearly the target geometry structure and provides realistic energetic results at a relatively low computational cost.     

已烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p),6-31+G(d,p),6-311G(d,p)及6- 311+G(d,p)基组,分别对1-C_6H_(12)~+,2-C_6H_(12)~+和3-C_6H_(12)~+的各种构 象进行了几何构型优化,并在B3LYP/6-311G(d,p)水平上进行了频率分析计算,在 各优化构型上,使用B3LYP和MP2(full)方法进行了超精细结构的计算。计算的3- C_6H_(12)~+的超精细偶合常数比以往的计算结果更好;1-C_6H_(12)~+和2-C_6H_ (12)~+的超精细偶合常数目前尚无实验数据报道,本计算预言了它们的超精细偶合 常数和最稳定构型。     

Reaction of ketenyl radical with acetylene: a promising route for cyclopropenyl radical

The reaction of the ketenyl radical (HCCO) with acetylene (C(2)H(2)) is very relevant to the oxygen-acetylene flames and fuel-rich combustion process for nitrogen-containing compounds. Unfortunately, except for several rate constant measurements, the mechanism is completely unknown for this reaction. In this paper, detailed theoretical investigations are performed for the HCCO + C(2)H(2) reaction at the G3B3 level using the B3LYP/6-31G(d), B3LYP/6-311++G(d,p), and QCISD/6-31G(d) geometries. The exclusive fragmentation channel is the formation of the cyclopropenyl radical (c-C(3)H(3)) and carbon monoxide (CO) via the chainlike OCCHCHCH and three-membered ring OC-cCHCHCH intermediates. Thus, the mass spectroscopic peak of C(3)H(3)(+) in a previous experiment can be explained. The calculated overall reaction barrier is 4.4, 4.4, and 5.3 kcal/mol at the G3B3//B3LYP/6-31G(d), G3B3//B3LYP/6-311++G(d,p), and G3B3//QCISD/6-31G(d) levels, respectively. The title reaction may provide an effective route for generating the long-sought cyclopropenyl radical in the laboratory, which has been the long-standing subject of numerous theoretical studies as the simplest cyclic conjugate radical, and its bulky derivatives were already known. Future experimental investigations for the HCCO + C(2)H(2) reaction are greatly desired to test the predicted fragmentation channel. The implication of the present study in combustion and interstellar processes is discussed.     

Fused five-membered rings determine the stability of C60F60

The structure and stability of a set of (CF)60 isomers have been computed at the B3LYP/6-31G(d) density functional theory level. The most stable isomer (6, F4@C60F56) has tube-like structure with four endo C-F bonds and fused five-membered rings at the end of the tube, while the reported most stable cage structure (2, F8@C60F52) with eight endo C-F bonds is higher in energy by 22.6 kcal/mol. This is in contrast to the isolated pentagon rule for the stability of fullerenes. The mean bond dissociation energy of 6 is larger than those of the experimental known C60F36, C60F48, and graphite fluoride. The relative energy per CF unit of 6 to graphite fluoride (CF)n is 3.7 kcal/mol, which is smaller than that of C60 fullerene per carbon to graphite (about 9-10 kcal/mol).     

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     

DFT Study on the Heterofullerene C48O12 with Rare Th Symmetry

The molecule with T_h symmetry is rare. A novel C60-like molecule C48O12 with rare Th symmetry has been studied at the B3LYP/6-31G(d) level of theory. Its structural, electronic, vibrational, NMR, and thermodynamic properties have been calculated at the B3LYP/6-31G(d) level of theory. Vibrational modes have been assigned according to their symmetry. There are 73 independent vibrational modes: 22 IR-active modes with T u symmetry and 37 Raman-active modes with Ag , Eg and Tg symmetry, respectively. The heat of formation has been calculated by using isodesmic reactions, 765.7 kJ mol-1 . According to the heat of formation and the HOMO-LUMO gap, C48O12 with rare Th symmetry is more stable than C60 .     

Prediction of the 13C NMR Chemical Shifts of Fluorenone Analogues by the GIAO Method

After the geometry optimization at B3LYP/6-31+G(d,p) level,the NMR calcula-tions of a series of fluorenone analogues have been carried out by GIAO method at HF/6-31+G(d) level and B3LYP/6-311G+(2d,p) level,respectively.The 13C NMR chemical shifts calculated at HF/6-31+G(d) level show better agreement with the observed values.By a series of linear correction equations (δpred=a + bδcalc),accurate prediction of 13C chemical shifts was achieved for the new fluorenone compound.The linear correlation of δpred with δexptl is excellent,and the square of correlation coefficient,r2,is up to 0.994.The maximum absolute difference between δpred and δexptl,Δδ,is 4.6 ppm,and the root-mean-square error between δpred and δexptl is only 2.6 ppm.     

Molecular structure and vibrational spectra of 3-chloro-4-fluoro benzonitrile by ab initio HF and density functional method

In this work, the experimental and theoretical spectra of 3-chloro-4-fluoro benzonitrile (3C4FBN) were studied. The Fourier transform infrared and Fourier transform Raman spectra of 3C4FBN were recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods with 6-311++G(d,p) basis set. The harmonic-vibrational frequencies, infrared intensities and Raman scattering activities of the title compound were performed at and HF/B3LYP/6-311++G(d,p) level of theories. The scaled theoretical wave number showed very good agreement with the experimental values. The thermodynamic functions of the title compound was also performed at HF/6-31G(d,p) and B3LYP/6-311++G(d,p) level of theories. A detailed interpretation of the infrared and Raman spectra of 3C4FBN was reported. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

Computational study of the deamination reaction of cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.     

Neutral homoaromaticity in some heterocyclic systems

[reaction: see text] Neutral homoaromaticity has been evaluated in heterocyclic systems related to the bicyclo[3.2.1]octane skeleton with replacement of CH(2) at C-2 in bicyclo[3.2.1]octa-3,6-diene with X = BH, AlH, Be, Mg, O, S, PH, NH (12); replacement of CH at C-3 in bicyclo[3.2.1]octa-3,6-dien-2-yl anion with PH, S, NH, O (13); and replacement at C-2 and C-3 with N and O (14). Stabilization energies (SE) are evaluated using density functional theory and homodesmotic equations at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level for series 12-14. Stabilization energies are compared with diamagnetic susceptibility exaltations, Lambda, CSGT-B3LYP/6-31G(d)//B3LYP/6-31G(d), and nucleus-independent chemical shifts (NICS), GIAO-B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d). Analysis of frontier orbitals and geometries, B3LYP/6-31G(d)//B3LYP/6-31G(d), and proton affinities of 2-azabicyclo[3.2.1]octa-3,6-diene, pyrrole, and related model systems, B3LYP/6-311+G(2d,2p)//B3LYP/6-31G(d), provide complementary evidence supporting the division of the substrates evaluated into antihomoaromatic (12, X = BH, AlH, and Be), nonhomoaromatic (12, X = O, S, NH, PH), and homoaromatic (13, X = S, PH, NH, O and 14 X = ON), with 12 (X = Mg) appearing as transitional between anti- and nonhomoaromatic.