Effect of axial ligand on the electronic configuration, spin states, and reactivity of iron oxophlorin

Iron-oxophlorin is an intermediate in heme degradation, and the nature of the axial ligand can alter the spin, electron distribution, and reactivity of the metal and the oxophlorin ring. The structure and reactivity of iron-oxophlorin in the presence of imidazole, pyridine, and t-butyl isocyanide as axial ligands was investigated using the B3LYP and OPBE methods with the 6-31+G* and 6-311+G** basis sets. OPBE/6-311+G** has shown that the doublet state of [(Py)(2)Fe(III)(PO)] (where pyridines are in perpendicular planes and PO is the oxophlorin trianion) is 3.45 and 5.27 kcal/mol more stable than the quartet and sextet states, respectively. The ground-state electronic configuration of the aforementioned complex is π(xz)(2) π(yz)(2) a(2u)(2) d(xy)(1) at low temperatures and changes to π(xz)(2) π(yz)(2) d(xy)(2) a(2u)(1) at high temperatures. This latter electronic configuration is consistently seen for the [(t-BuNC)(2)Fe(II)(PO(?))] complex (where PO(?) is the oxophlorin dianion radical). The complex [(Im)(2)Fe(III)(PO)] adopted the d(xy)(2) (π(xz) π(yz))(3) ground state and has low-lying quartet excited state which is readily populated when the temperature is increased.     

Host-guest inclusion complex between β-cyclodextrin and paeonol: A theoretical approach

Host-guest interactions of β-cyclodextrin (β-CD) with paeonol (PAE) were simulated using semi-empirical PM3 and both ONIOM2 [(B3LYP/6-31G*:PM3), (HF/6-31G*:PM3)] methods. The results obtained with PM3 method clearly indicate that the complexes formed are energetically favored with or without solvent, the model 1 (PAE entering into the cavity of β-CD from its wide side by OCH3 group) is found more favored than the model 2 (PAE entering into the cavity of β-CD from its wide side by COCH3 group). Finally, natural bonding orbital (NBO) analysis was performed based on ONIOM2 optimized complexes to quantify the donor–acceptor interactions between PAE and β-CD.     

Cluster expansion reactions of group 6 and 8 metallaboranes using transition metal carbonyl compounds of groups 7-9

The reinvestigation of an early synthesis of heterometallic cubane-type clusters has led to the isolation of a number of new clusters which have been characterized by spectroscopic and crystallographic techniques. The thermolysis of [(Cp*Mo)(2)B(4)H(4)E(2)] (1: E = S; 2: E = Se; Cp* = η(5)-C(5)Me(5)) in presence of [Fe(2)(CO)(9)] yielded cubane-type clusters [(Cp*Mo)(2)(μ(3)-E)(2)B(2)H(μ-H){Fe(CO)(2)}(2)Fe(CO)(3)], 4 and 5 (4: E = S; 5: E = Se) together with fused clusters [(Cp*Mo)(2)B(4)H(4)E(2)Fe(CO)(2)Fe(CO)(3)] (8: E = S; 9: E = Se). In a similar fashion, reaction of [(Cp*RuCO)(2)B(2)H(6)], 3, with [Fe(2)(CO)(9)] yielded [(Cp*Ru)(2)(μ(3)-CO)(2)B(2)H(μ-H){Fe(CO)(2)}(2)Fe(CO)(3)], 6, and an incomplete cubane cluster [(μ(3)-BH)(3)(Cp*Ru)(2){Fe(CO)(3)}(2)], 7. Clusters 4-6 can be described as heterometallic cubane clusters containing a Fe(CO)(3) moiety exo-bonded to the cubane, while 7 has an incomplete cubane [Ru(2)Fe(2)B(3)] core. The geometry of both compounds 8 and 9 consist of a bicapped octahedron [Mo(2)Fe(2)B(3)E] and a trigonal bipyramidal [Mo(2)B(2)E] core, fused through a common three vertex [Mo(2)B] triangular face. In addition, thermolysis of 3 with [Mn(2)(CO)(10)] permits the isolation of arachno-[(Cp*RuCO)(2)B(3)H(7)], 10. Cluster 10 constitutes a diruthenaborane analogue of 8-sep pentaborane(11) and has a structural isomeric relationship to 1,2-[{Cp*Ru}(2)(CO)(2)B(3)H(7)].     

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.     

Theoretical study of geometrical effect on the deoxygenation of epoxide by singlet carbenes

The mechanism of the abstraction of oxygen from epoxide by carbenes has been investigated using the B3LYP/6-31G* and MP2/6-311++G(d,p)//B3LYP/6-31G* levels of theory. According to our model calculations, the reactivity of carbene decreases in the order: four-membered ring carbene > six-membered ring carbene > three-membered ring carbene > five-membered ring carbene vinylidene. Moreover, the present work shows that the singlet–triplet splitting of a carbene can be used as a guide for the prediction of its reactivity.     

Theoretical Study of Heterocyclic Nitro Compounds for Use as Novel Explosives and Propellants

The heats of formation (HOFs) of heterocyclic nitro compounds were obtained by using a density functional theory B3LYP method with 6‐31G* and 6‐311+G** basis sets. The isodesmic reactions designed for the evaluation of HOFs keep most of the basic ring structures of the title compounds and thus ensure the credibility of the results. The values of HOFs are 567.90, 874.29 and 975.83 kJ/mol at the B3LYP/6‐31G* level for hexanitrohexazaadamantane ( A ), nonanitrononaza‐tetracyclo[7.3.1.1^3,7.1^5,11] pentadecane ( B ) and tetranitrotetrazacubane ( C ) respectively. The predicted detonation velocities of the title compounds are larger than, and detonation pressures are much larger than that of the widely used 1,3,5,7‐tetranitro‐1,3,5,7‐tetraazacyclooctane (HMX). The dissociation energy for the weakest C‐N bonds in the cage skeleton of the title compounds are 137‐144 kJ/mol at the B3LYP/6‐31G* level.     

2,3,7,8-四氯苯并二英分子结构与热力学性质的理论研究

用密度泛函理论(DFT)和从头算(ab initio)方法,在B3LYP/6-31G、 B3LYP/6-31G*、 B3LYP/6-311G*和MP2/6-31G*水平上全优化计算了2,3,7,8-四氯苯并二英(2,3,7,8-TCDD)的几何构型、电子结构和振动频率,并用校正后的频率计算了298～1500 K的标准热力学函数,同时用半经验的PM3 SCF-MO进行了同样的计算,计算结果与实验值及文献值较好地吻合.     

Efficient blue-emitting Ir(III) complexes with phosphine carbanion-based ancillary ligand: a DFT study

We report a theoretical study on a series of heteroleptic cyclometalated Ir(III) complexes for OLED application. The geometries, electronic structures, and the lowest-lying singlet absorptions and triplet emissions of [(fppy)(2)Ir(III)(PPh(2)Np)] (1), and theoretically designed models [(fppy)(2)Ir(III)(PH(2)Np)] (2) and [(fppy)(2)Ir(III)Np](-)(3) were investigated with density functional theory (DFT)-based approaches, where, fppyH = 4-fluorophenyl-pyridine and NpH = naphthalene. The ground and excited states were, respectively, optimized at the M062X/LanL2DZ;6-31G* and CIS/LanL2DZ:6-31G* level of theory within CH(2)Cl(2) solution provided by PCM. The lowest absorptions and emissions were evaluated at M062X/Stuttgart;cc-pVTZ;cc-pVDZ level of theory. Though the lowest absorptions and emissions were all attributed as the ligand-based charge-transfer transition with slight metal-to-ligand charge-transfer transition character, the subtle differences in geometries and electronic structures result in the different quantum yields and versatile emission color. The newly designed molecular 3 is expected to be highly emissive in deep blue region.     

Structure and electronic properties for a newly synthesized red fluorescent material

The ground-state structure and electronic properties of a newly synthesized red fluorescent material, 2-[3-(2-{4-[(2-hydroxy-ethyl)-methyl-amino]-phenyl}-vinyl)-5, 5-dimethyl-cyclohex-2-enylidene]-malononitrile (A31), are investigated using a hybrid density-functional theory (DFT) approach, B3LYP, and the 6-31G* basis set. We have obtained four geometrical isomers. The theoretical infrared (IR) spectrum calculated by B3LYP/6-31G* level of theory is in very good agreement with our experimental measurement. The cation and anion are optimized to clarify the effects of the hole and electron injections and the energies needed by injections are estimated.     

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 on the hydrogen bonding of five-membered heteroaromatics with water

The hydrogen-bonding ability of five-membered heteroaromatic molecules containing one chalcogen and two heteroatoms with nitrogen in addition to chalcogen, respectively, have been analyzed using density functional and molecular orbital methods through adduct formation with water. The stabilization energies for all the adducts are established at B3LYP/6-31+G* and MP2/6-31+G* levels after correcting for the basis set superposition error by using the counterpoise method and also corrected for zero-point vibrational energies. A natural bond orbital analysis at B3LYP/6-31+G* level and natural energy decomposition analysis at HF/6-31+G* using MP2/6-31+G* geometries have been carried out to understand the nature of hydrogen-bonding interaction in monohydrated heterocyclic adducts. Nucleus-independent chemical shift have been evaluated to understand the correlation between hydrogen bond formation and aromaticity.     

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: comparison of semiempirical, ab initio, and density functional results

The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium-bacteriochlorin, magnesium-chlorin, magnesium-porphin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree-Fock/6-31G* ab initio and density functional B3LYP/6-31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c(1), and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self-consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6-31G* or Hartree-Fock/6-31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree-Fock/6-31G* and B3LYP/6-31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin-like molecules.     

Cubane-type heterometallic sulfido clusters: incorporation of two metal fragments into a dinuclear ReS(mu-S)2ReS core affording bimetallic M2Re2(mu 3-S)4 clusters (M = Ru,Pt, Cu) or trimetallic MM'Re2(mu 3-S)4 clusters via incomplete cubane-type MRe2(mu 3-S)(mu 2-S)3 intermediates (M = Ru,Rh, Ir; M' = Mo,W, Pd,Ru, Rh)

Reactions of a dirhenium tetra(sulfido) complex [PPh(4)](2)[ReS(L)(mu-S)(2)ReS(L)] (L = S(2)C(2)(SiMe(3))(2)) with a series of group 8-11 metal complexes in MeCN at room temperature afforded either the cubane-type clusters [M(2)(ReL)(2)(mu(3)-S)(4)] (M = CpRu (2), PtMe(3), Cu(PPh(3)) (4); Cp = eta(5)-C(5)Me(5)) or the incomplete cubane-type clusters [M(ReL)(2)(mu(3)-S)(mu(2)-S)(3)] (M = (eta(6)-C(6)HMe(5))Ru (5), CpRh (6), CpIr (7)), depending on the nature of the metal complexes added. It has also been disclosed that the latter incomplete cubane-type clusters can serve as the good precursors to the trimetallic cubane-type clusters still poorly precedented. Thus, treatment of 5-7 with a range of metal complexes in THF at room temperature resulted in the formation of novel trimetallic cubane-type clusters, including the neutral clusters [[(eta(6)-C(6)HMe(5))Ru][W(CO)(3)](ReL)(2)(mu(3)-S)(4)], [(CpM)[W(CO)(3)](ReL)(2)(mu(3)-S)(4)] (M = Rh, Ir), [(Cp*Ir)[Mo(CO)(3)](ReL)(2)(mu(3)-S)(4)], [[(eta(6)-C(6)HMe(5))Ru][Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)], and [(Cp*Ir)[Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)] (13) along with the cationic clusters [(Cp*Ir)(CpRu)(ReL)(2)(mu(3)-S)(4)][PF(6)] (14) and [(Cp*Ir)[Rh(cod)](ReL)(2)(mu(3)-S)(4)][PF(6)] (cod = 1,5-cyclooctadiene). The X-ray analyses have been carried out for 2, 4, 7, 13, and the SbF(6) analogue of 14 (14') to confirm their bimetallic cubane-type, bimetallic incomplete cubane-type, or trimetallic cubane-type structures. Fluxional behavior of the incomplete cubane-type and trimetallic cubane-type clusters in solutions has been demonstrated by the variable-temperature (1)H NMR studies, which is ascribable to both the metal-metal bond migration in the cluster cores and the pseudorotation of the dithiolene ligand bonded to the square pyramidal Re centers, where the temperatures at which these processes proceed have been found to depend upon the nature of the metal centers included in the cluster cores.     

Theoretical Study on Hydrogen Interaction between 5-Fluorouracil and Glycine

The geometries,electronic structure,IR spectrum and other properties of hydrogen interaction between 5-fluorouracil and glycine were studied at the B3LYP/6-31+G* level.Single point energy calculations were executed at the B3LYP/6-311++G** and B3LYP/aug-cc-pvdz levels,and natural bond orbital (NBO) analysis was carried out at the B3LYP/6-31+G* level.Finally,the hydrogen bonds were discussed via AIM electronic density topology analysis.     

Ab initio and DFT calculations on the initial step in thiamin catalysis

The diphosphate ester (ThDP) of thiamin (vitamin B₁) is an important cofactor of enzymes within the carbohydrate metabolism. The initial reaction step shared by all ThDP-dependent enzymes is the deprotonation of the C2–H of the thiazolium ring. The replacement of the 4′-amino group by a hydroxyl one in the pyrimidine ring leads to the oxy-ThDP analogue which is known as an antagonist in thiamin catalysis.

Ab initio and DFT calculations on the MP2/6-31G* and B3LYP/6-31G* level were performed to study the proton relay function in thiamin and oxythiamin systems. Both MP2 and B3LYP calculations show significant differences of the reaction coordinate of the ylide formation in the systems. Tautomers, protonated and deprotonated species of both systems show different trends regarding their stability. The influence of correlation effects on the results is discussed by comparison with the HF-SCF/6-31G* data. Frequency calculations on the B3LYP/6-31G* level were performed to characterize the minima and transition state structures, respectively.     

Opto-electronic properties and molecular design of new materials based on pyrrole studied by DFT

In this work, we investigate oligopyrroles and derivatives, which serve as models for corresponding polymers. In order to discuss these materials, we carried out DFT calculations and used DFT methods to calculate ground state electronic structures. We are particularly interested in exploring the potential of several substituent groups as electron donors with numerous ties to electronic materials by exploring and comparing the energies of HOMO, LUMO, Gap energies, and structural properties. Results are discussed in comparison with the properties of the doped oligomers. The theoretical ground-state geometry and electronic structure of the studied molecules were obtained by the DFT method at B3LYP level with 6-31G(d) basis set. The opto-electronic properties of these materials were determined by ZINDO/s and TD//B3LYP/6-31G(d) calculations performed on the B3LYP/6-31(d) optimized geometries. The results of this study demonstrate how electronic properties can be tuned by the backbone ring or side group and suggest these compounds as good candidates for opto-electronic applications.     

Synthesis, characterization, and electronic structure of new type of heterometallic boride clusters

The reaction of [Cp*TaCl(4)], 1 (Cp* = η(5)-C(5)Me(5)), with [LiBH(4)·THF] at -78 °C, followed by thermolysis in the presence of excess [BH(3)·THF], results in the formation of the oxatantalaborane cluster [(Cp*Ta)(2)B(4)H(10)O], 2 in moderate yield. Compound 2 is a notable example of an oxatantalaborane cluster where oxygen is contiguously bound to both the metal and boron. Upon availability of 2, a room temperature reaction was performed with [Fe(2)(CO)(9)], which led to the isolation of [(Cp*Ta)(2)B(2)H(4)O{H(2)Fe(2)(CO)(6)BH}], 3. Compound 3 is an unusual heterometallic boride cluster in which the [Ta(2)Fe(2)] atoms define a butterfly framework with one boron atom lying in a semi-interstitial position. Likewise, the diselenamolybdaborane, [(Cp*Mo)(2)B(4)H(4)Se(2)], 4 was treated with an excess of [Fe(2)(CO)(9)] to afford the heterometallic boride cluster [(Cp*MoSe)(2)Fe(6)(CO)(13)B(2)(BH)(2)], 5. The cluster core of 5 consists of a cubane [Mo(2)Se(2)Fe(2)B(2)] and a tricapped trigonal prism [Fe(6)B(3)] fused together with four atoms held in common between the two subclusters. In the tricapped trigonal prism subunit, one of the boron atoms is completely encapsulated and bonded to six iron and two boron atoms. Compounds 2, 3, and 5 have been characterized by mass spectrometry, IR, (1)H, (11)B, (13)C NMR spectroscopy, and the geometric structures were unequivocally established by crystallographic analysis. The density functional theory calculations yielded geometries that are in close agreement with the observed structures. Furthermore, the calculated (11)B NMR chemical shifts also support the structural characterization of the compounds. Natural bond order analysis and Wiberg bond indices are used to gain insight into the bonding patterns of the observed geometries of 2, 3, and 5.     

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.