Molecular orbital and DFT studies of the alimemazine radical cation

Semiempirical molecular orbital methods including CNDO, MNDO, AM1 and PM3, and density function theory method B3LYP/3-21G(d) were employed in the study of the alimemazine radical cation. It was found that PM3 was much better than CNDO, MNDO and AM1 in the structural optimization. The bond lengths and bond angles by PM3 were close to the experimental data, and comparable with the results by the density function theory method.     

Molecular conformation of bilirubin from semiempirical molecular orbital calculations

Semiempirical methods were utilized in the computation of a fully optimized structure of bilirubin. Bond lengths and bond angles obtained using either AM1 or PM3 calculations showed excellent agreement with those obtained by X-ray diffraction. This indicated that molecular orbital methods satisfactory reproduced the complex conjugation found in bilirubin. Dihedral angles of the crucial “hinge” and the dihedral angles of the propionic acid side chains agreed well with those found by X-ray diffraction. Calculated hydrogen- bond parameters (distance and angles) showed substantial differences from experimental values, probably due to inherent weakness in the parameterization of the molecular orbital techniques. Conformational studies were carried out using AM1 by rotating the C9? C10 bond in 5° increments showed that the most stable structure exhibited a minimum at about 125° and exhibited a structure similar to those postulated from X-ray and NMR experiments. The hydrogen bonds showed remarkable tenacity during rotation of the C9? C10 bond and resisted breaking until the molecule was under extreme strain. © 1992 John Wiley & Sons, Inc.     

Comparative parametric method 5 (PM5) study of trans-stilbene

In this work we report a comparative Austin method 1 (AM1), parametric method 3 (PM3), and parametric method 5 (PM5) studies for trans-stilbene in its ground, excited (singlet and triplet), and ionic (positive and negative polarons and bipolarons) states. We evaluated the accuracy of the recently developed PM5 method. PM5 and AM1 predict a non-planar ground and singlet states for trans-stilbene, while PM3 predicts planar ones, which is in agreement with the available experimental data. In general the PM3 and PM5 bond lengths are superior to AM1 while AM1 bond angles are superior to PM3 and PM5 when compared with available experimental data. The PM5 underestimates the cis–trans isomerization energy and and it is not a quite reliable method for the calculation of relative IP values. The presumed PM5 superior performance against AM1 and PM3 was not observed for the stilbene structures.     

Polycyclic aromatic hydrocarbons with five-membered rings: Modeling of experimental X-ray and neutron-diffraction structures

Several of the readily available theoretical programs are evaluated as tools for modeling the structures of polycyclic aromatic hydrocarbons with five-membered rings (CPAHs). The experimentally determined bond lengths and angles are compared to calculated values. Experimental bond lengths are also compared to Pauling and Huckel molecular orbital (HMO) bond orders. Previously published experimental X-ray and neutron-diffraction structures of acenaphthene, acenaphthylene, fluoranthene, cyclopent[o,p,q,r]benz[c]phenanthrene, and corannulene are modeled by the programs MMX, AM1, MNDO, and PM3, and previously reported STO-3G and 6-31G * data are also evaluated. In general, the error differences between the experimental and calculated results for all of the semiempirical programs were small. However, PM3 performed slightly better than AM1 and MMX, while MNDO generated structures which exhibited the largest deviation from experiment. Although the standard deviations for all programs are shown to be of comparable magnitude, a particular bond length or bond angle in any given theoretical calculation can exhibit significant error from the experimental data. The scatter in the bond order data computed from Huckel molecular orbital theory and valence bond theory is contrary to results obtained with alternant systems. It appears that these approaches are less successful at modeling accurately the nonalternant hydrocarbon systems described in this paper.     

Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules

Extensive testing of the SCC-DFTB method has been performed, permitting direct comparison to data available for NDDO-based semiempirical methods. For 34 diverse isomerizations of neutral molecules containing the elements C, H, N, and O, the mean absolute errors (MAE) for the enthalpy changes are 2.7, 3.2, 5.0, 5.1, and 7.2 kcal/mol from PDDG/PM3, B3LYP/6-31G(d), PM3, SCC-DFTB, and AM1, respectively. A more comprehensive test was then performed by computing heats of formation for 622 neutral, closed-shell H, C, N, and O-containing molecules; the MAE of 5.8 kcal/mol for SCC-DFTB is intermediate between AM1 (6.8 kcal/mol) and PM3 (4.4 kcal/mol) and significantly higher than for PDDG/PM3 (3.2 kcal/mol). Similarly, SCC-DFTB is found to be less accurate for heats of formation of ions and radicals; however, it is more accurate for conformational energetics and intermolecular interaction energies, though none of the methods perform well for hydrogen bonds with strengths under ca. 7 kcal/mol. SCC-DFTB and the NDDO methods all reproduce MP2/cc-pVTZ molecular geometries with average errors for bond lengths, bond angles, and dihedral angles of only ca. 0.01 A, 1.5 degrees , and 3 degrees . Testing was also carried out for sulfur containing molecules; SCC-DFTB currently yields much less accurate heats of formation in this case than the NDDO-based methods due to the over-stabilization of molecules containing an SO bond.     

Comparison of computational studies of internal stabilization of 1‐butadienyllithiums and representative 1‐chloro‐1‐lithio‐2‐phenylalkenes

Comparison of molecular orbital calculations of 1‐butadienyllithiums and representative 1‐chloro‐1‐lithio‐2‐phenylalkenes, carried out by using MNDO and AM1, reveals that the major stabilizing interaction with lithium in these systems is predicted to be agostic bonding between lithium and hydrogen. MNDO and AM1 calculations for 1‐chloro‐1‐lithio‐2‐phenylethenes give evidence for agostic bonding between lithium and the ortho H, such as compressed pertinent bond angles and increased pertinent bond lengths. © 2002 Wiley Periodicals, Inc. Heteroatom Chem 13:263–269, 2002; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/hc.10027     

3D comparative structural study of 6-hydroxy-4-methyl-5,7-dinitrocoumarin using experimental and theoretical approaches

The compound 6-hydroxy-4-methyl-5,7-dinitrocoumarin (2) was synthesized with high yield by the nitration of compound 1. Its molecular structure was determined using X-ray diffractometry and compared with the structure obtained from semiempirical, HF, and B3LYP methods. B3LYP calculations offer the best conformity with X-ray diffractometry for bond lengths and bond angles, whereas AM1 results are significantly close to them and provide the best superimposition with the entire 3D crystal structure.     

硝酸酯分子几何构型的量子化学研究

运用MINDO / 3、MNDO 和AM1 三种半经验分子轨道(MO)方法, 通过SCF计算, 首次系统地获得了32个硝酸酯化合物分子的全优化几何构型。三种方法的计算结果与已报道的四个化合物(硝酸甲酯、吉纳、硝化甘油和太安)的实验结果相比, AM1法较好。所有硝酸酯的酯基(-ONO~2)具有近似不变的几何参数。直链烷基硝酸酯的键长和键角极为相近, 全部重原子均共平面。二元直链和四元硝酸酯具有对称的分子构型。     

Optimization of parameters for semiempirical methods II. Applications

MNDO/AM1-type parameters for twelve elements have been optimized using a newly developed method for optimizing parameters for semiempirical methods. With the new method, MNDO-PM3, the average difference between the predicted heats of formation and experimental values for 657 compounds is 7.8 kcal/mol, and for 106 hypervalent compounds, 13.6 kcal/mol. For MNDO the equivalent differences are 13.9 and 75.8 kcal/mol, while those for AM1, in which MNDO parameters are used for aluminum, phosphorus, and sulfur, are 12.7 and 83.1 kcal/mol, respectively. Average errors for ionization potentials, bond angles, and dipole moments are intermediate between those for MNDO and AM1, while errors in bond lengths are slightly reduced.     

尿酸分子互变异构体平面构象的理论研究

使用半经验量子化学中的AM1方法、从头计算Hartree-Fock理论(在3-21G*水平)和密度泛函理论中的B3LYP方法(使用6-31G(d)基组),研究了尿酸分子的所有35种互变异构体。计算结果表明,三羰基互变异构体是所有异构体中能量最低的,其次为单羟基异构体和双羟基异构体,而含有三羟基的互变异构体相对能量最高。随着羟基数的增加, C-N键的平均键长从1.395逐渐缩短到1.351,而CC键的平均键长基本保持不变(1.400~1.406)。     

How H-bonding modifies molecular structure and pi-electron delocalization in the ring of pyridine/pyridinium derivatives involved in H-bond complexation

[structure: see text] Analysis of the experimental geometry of 397 variously substituted pyridine and pyridinium derivatives has shown very little variation of all bond lengths in the ring and substantial changes in the values of alpha and beta angles, being in line with theoretically modeled data (at the B3LYP/6-311+G level of theory). No dependence of bond lengths and pi-electron delocalization in the ring measured by HOMA index on the changes in bond angle at the N-atom is observed. This is at variance with the patterns observed in substituted phenolate/phenol systems involved in H-bonding. Due to significant differences in magnitude of the ipso angle at the nitrogen atom that depend on the location of hydrogen atom in pyridine/pyridinium systems (N, N...H, and N-H), this angle may be used as a valuable indicator of N...H interactions since the X-ray structural analysis does not give a reliable position for the proton.     

RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I

Twenty years ago, the landmark AM1 was introduced, and has since had an increasingly wide following among chemists due to its consistently good results and time-tested reliability--being presently available in countless computational quantum chemistry programs. However, semiempirical molecular orbital models still are of limited accuracy and need to be improved if the full potential of new linear scaling techniques, such as MOZYME and LocalSCF, is to be realized. Accordingly, in this article we present RM1 (Recife Model 1): a reparameterization of AM1. As before, the properties used in the parameterization procedure were: heats of formation, dipole moments, ionization potentials and geometric variables (bond lengths and angles). Considering that the vast majority of molecules of importance to life can be assembled by using only six elements: C, H, N, O, P, and S, and that by adding the halogens we can now build most molecules of importance to pharmaceutical research, our training set consisted of 1736 molecules, representative of organic and biochemistry, containing C, H, N, O, P, S, F, Cl, Br, and I atoms. Unlike AM1, and similar to PM3, all RM1 parameters have been optimized. For enthalpies of formation, dipole moments, ionization potentials, and interatomic distances, the average errors in RM1, for the 1736 molecules, are less than those for AM1, PM3, and PM5. Indeed, the average errors in kcal x mol(-1) of the enthalpies of formation for AM1, PM3, and PM5 are 11.15, 7.98, and 6.03, whereas for RM1 this value is 5.77. The errors, in Debye, of the dipole moments for AM1, PM3, PM5, and RM1 are, respectively, 0.37, 0.38, 0.50, and 0.34. Likewise, the respective errors for the ionization potentials, in eV, are 0.60, 0.55, 0.48, and 0.45, and the respective errors, in angstroms, for the interatomic distances are 0.036, 0.029, 0.037, and 0.027. The RM1 average error in bond angles of 6.82 degrees is only slightly higher than the AM1 figure of 5.88 degrees, and both are much smaller than the PM3 and PM5 figures of 6.98 degrees and 9.83 degrees, respectively. Moreover, a known error in PM3 nitrogen charges is corrected in RM1. Therefore, RM1 represents an improvement over AM1 and its similar successor PM3, and is probably very competitive with PM5, which is a somewhat different model, and not fully disclosed. RM1 possesses the same analytical construct and the same number of parameters for each atom as AM1, and, therefore, can be easily implemented in any software that already has AM1, not requiring any change in any line of code, with the sole exception of the values of the parameters themselves.     

Hybridization in fulvene and some related cycloalkenes by the iterative maximum overlap approximation

The hybrid orbitals in cyclopentadiene, fulvene and 6,6-dimethylfulvene were calculated by the iterative maximum overlap method. The hybridization parameters obtained were then used for the calculation of the proton chemical shifts and spin-spin coupling constants J(¹³C-¹H) of the directly bonded carbon and hydrogen nuclei. They can be favourably compared with available experimental data. The predicted bond lengths and bond angles are compared with the results of the more sophisticated semiempirical MINDO/2 and MINDO/3 methods. It is shown that the iterative maximum overlap method gives equally good, or sometimes even better, agreement with experiment. The calculated bond lengths and angles have been used for prediction of molecular diamagnetic susceptibilities by using the additivity formulae of Maksi? and Bloor. The results are within experimental error.     

Hydrogen Bonding in Phosphine Oxide/Phosphate–Phenol Complexes

To develop a new solvent‐impregnated resin (SIR) system for the removal of phenols and thiophenols from water, complex formation by hydrogen bonding of phosphine oxides and phosphates is studied using isothermal titration calorimetry (ITC) and quantum chemical modeling. Six different computational methods are used: B3LYP, M06‐2X, MP2, spin component‐scaled (SCS) MP2 [all four with 6‐311+G(d,p) basis set], a complete basis set extrapolation at the MP2 level (MP2/CBS), and the composite CBS‐Q model. This reveals a range of binding enthalpies (ΔH) for phenol–phosphine oxide and phenol–phosphate complexes and their thio analogues. Both structural (bond lengths/angles) and electronic elements (charges, bond orders) are studied. Furthermore, solvent effects are investigated theoretically by the PCM solvent model and experimentally via ITC. From our calculations, a trialkylphosphine oxide is found to be the most promising extractant for phenol in SIRs, yielding ΔH=?14.5 and ?9.8 kcal mol^?1 with phenol and thiophenol, respectively (MP2/CBS), without dimer formation that would hamper the phenol complexation. In ITC measurements, the ΔH of this complex was most negative in the noncoordinating solvent cyclohexane, and slightly less so in π–π interacting solvents such as benzene. The strongest binding is found for the dimethyl phosphate–phenol complex [?15.1 kcal mol^?1 (MP2/CBS)], due to the formation of two H‐bonds (P?O???H‐O‐ and P‐O‐H???O‐H); however, dimer formation of these phosphates competes with complexation of phenol, and would thus hamper their use in industrial extractions. CBS‐Q calculations display erroneous trends for sulfur compounds, and are found to be unsuitable. Computationally relatively cheap SCS‐MP2 and M06‐2X calculations did accurately agree with the much more elaborate MP2/CBS method, with an average deviation of less than 1 kcal mol^?1.     

Theoretical studies on the structure and electronic properties of aryl sulfides and sulfones

Molecular orbital calculations are reported on the structure and electronic properties of diphenyl sulfide using both semiempirical and ab initio methods. Neither the MNDO nor AM1 methods give satisfactory structures, but better results are obtained with the PM3 method. At the ab initio level, the 4-31G basis set with polarization functions on sulfur alone (4-31G/S*) gives comparable results to those obtained with the 6-31G** basis set. The corresponding bond lengths and angles at the sulfur atom of 4-aminophenyl-4′-nitrophenyl sulfide and related derivatives of diphenyl sulfone, diphenyl disulfide, and phenylthiosulfonate calculated at the 4-31 G/S* level show a good correlation with crystallographic data where available. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 141–147, 1998     

Synthesis and Structure of [4.5.5.5]Fenestranes ( = tetracyclo[5.4.1.04, 12.09, 12]dodecanes)

The preparation and the X-ray structure analysis of cis, trans, cis, cis-10-hydroxy-[4.5.5.5]fenestrane-1-methanol ( 8b ) is reported. The measured bond angles and bond lengths of the central C(C)₄ fragment are better reproduced by calculations with the AM 1 than by the MNDO method.     

Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D

We demonstrate that the ONIOM method can be used to optimize a conical intersection between the ground and first excited-state potential energy surfaces of previtamin D (precalciferol), with excitation localized in a small part of the molecule: the hexatriene chromophore. These calculations were up to 100 times faster with little loss of accuracy compared to a full non-ONIOM Target calculation. The most accurate ONIOM method combination was CASSCF/4-31G//ROHF/STO-3G(Triplet): in comparison to the Target (CASSCF/4-31G), bond lengths and angles in the hexatriene model region were calculated to within 0.02 A and 0.7 degrees , respectively, and the energy difference between the conical intersection and nearest associated S 1 minimum to within 0.5 kcal x mol (-1). All of the low-level methods selected produced accurate geometries, including the UFF molecular mechanics and AM1 semiempirical methods, suggesting a cheap and efficient way of initially optimizing conical intersections geometries. Furthermore, ONIOM allows for an assessment of the localization of excited states, providing some fundamental insight into the physical processes involved.     

Theoretical study of the molecular structure and normal coordinate analysis of hydrogen cyanide addition compound with boron trifluoride, HCN-BF(3)

An extensive HF, MP2, B3LYP and CCSD study of the molecular structure and normal vibrations have been performed for the HCN-BF(3) molecule. Calculations with a wide range of basis sets were classified into two groups based on the optimized N-B bond distance. The results for Group A are compared with the experimental structure of the solid phase molecules. The N-B lengths of Group A are approximately linear related to the N-B-F valence angles and also to the N-B stretching frequencies. HF/DZV calculation was used to represent the solid phase model. The N-B lengths of Group B are close to those of the gas phase molecule and both N-B-F angles and N-B sensitive frequencies have roughly the same values. Differences in the chemical bond between gaseous and solid phase HCN-BF(3) are discussed based on the calculated force constants, vibrational frequencies and potential energy distributions. Vibration mode analysis indicates that the nu(4) mode in the 600-700 cm(-1) region can be assigned to the BF(3) symmetric deformation, which shifts upon (10)B/(11)B isotopic substitution. The nu(5) mode which is insensitive to isotope substitution and changes band position with the N-B distance is assigned to the N-B bond stretching vibration.     

Structure determination of triplet diphenylcarbenes by in situ X-ray crystallographic analysis

Crystalline-state photoreactions of the following diphenyldiazomethanes were investigated by in situ X-ray crystallography, spectroscopy, and theoretical calculations: bis(2,4,6-trichlorophenyl)diazomethane (1-N2), bis(2,4,6-tribromophenyl)diazomethane (2-N2), bis(2,6-dibromo-4-methylphenyl)diazomethane (3-N2), bis(2,6-dibromo-4-tert-butylphenyl)diazomethane (4-N2), (2,4,6-tribromophenyl)-(2,6-dimethyl-4-tert-butylphenyl)diazomethane (5-N2), bis(4-bromophenyl)diazomethane(6-N2), and diazofluorene (7-N2). Crystal structures of photoinduced triplet diphenylcarbenes (DPCs) of 1, 2, and 4 were determined. We found remarkable differences between their structural information obtained in the crystalline state and that previously obtained spectroscopically in a glass matrix. Although the triplet DPCs of 1, 2, and 4 have significantly different stabilities in solution, only subtle differences in their structural parameters, except for their C(:)-Ar bond lengths, are observed. It is noteworthy that the average bond length of C(:)-Ar for 4 (1.374 A) is considerably shorter than those for (3)1 and (3)2 (1.430 and 1.428 A, respectively), provided that the two C(:)-Ar bonds being compared were chemically equivalent. The most likely explanations for the small and large differences in bond lengths in 1, 2, and 4 may be derived from the packing effect. The packing patterns of 1 and 2 are identical, but that of 4 is totally different from those of 1 and 2. Moreover, these results are interpreted as indicating that triplet DPCs undergo relaxation upon softening of the environments. Theoretical calculations indicate that the potential energy surface of triplet DPCs in terms of the carbene angle is extremely flat and changes in the angles have little effect on the energies. Triplet DPCs with a sterically congested carbene center are trapped in a structure dictated by the precursor structure in a rigid matrix, even if this is not the thermodynamically most stable geometry, but undergo geometrical relaxation upon softening the matrix to relieve steric compression. ESR studies indicate that the interplanar angles are more flexible than the bond angles.     

The molecular structure of different species of cuprous chloride from gas-phase electron diffraction and quantum chemical calculations

The molecular geometry of gaseous cuprous chloride oligomers was determined by gas-phase electron diffraction at two different temperatures. Quantum chemical calculations were also performed for Cu(n)Cl(n) (n=1-4) molecules. A complex vapor composition was found in both experiments. Molecules of Cu(3)Cl(3) and Cu(4)Cl(4) were present at the lower temperature (689 K), while dimeric molecules (Cu(2)Cl(2)) were found in addition to the trimers and tetramers at the higher temperature (1333 K). All Cu(n)Cl(n) species were found to have planar rings by both experiment and computation. The bond lengths from electron diffraction (r(g)) at 689 K are 2.166+/-0.008 A and 2.141+/-0.008 A and the Cu-Cl-Cu bond angles are 73.9+/-0.6 degrees and 88.0+/-0.6 degrees for the trimer and the tetramer, respectively. At 1333 K the bond lengths are 2.254+/-0.011 A, 2.180+/-0.011 A, and 2.155+/-0.011 A, and the Cu-Cl-Cu bond angles 67.3+/-1.1 degrees, 74.4+/-1.1 degrees, and 83.6+/-1.1 degrees for the dimer, trimer, and tetramer, respectively.