Geometry prediction of hafnocenes by quantum chemical methods

The performance of quantum chemical methods for geometry prediction of hafnocenes was evaluated. HF, B3LYP and MP2 in combination with nonrelativistic (MHF) and relativistic (MWB and LANL2DZ) basis sets for hafnium together with standard basis sets 3-21G*, 6-31G* and 6-311G** for other elements were applied. Five basic structural parameters of the optimized structures of the hafnocenes were compared with experimental crystal structures obtained from the Cambridge structural database. Altogether 80 hafnocenes were included in the analysis. The results show that relativistic corrections are necessary for Hf atom. However, even the Hartree–Fock (HF) method, when combined with relativistic pseudopotentials, reproduces the experimental crystal structures with significant accuracy. The good performance of the HF method can be understood to originate from the absence of significant near-degeneracy correlations for hafnium. On average, the B3LYP and MP2 methods provide structural parameters somewhat closer to the experimental ones.     

The role of the basis set and the level of quantum mechanical theory in the prediction of the structure and reactivity of cisplatin

In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis‐diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all‐electron basis sets (ABS). In addition, a modified all‐electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6‐31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol^?1, which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol^?1. For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol^?1, respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree‐Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6‐31+G(d) or B3PW91/mDZP/6‐31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP‐DNA complex), the lower levels B3LYP/LANL2DZ/6‐31+G(d) and B3LYP/SBKJC‐VDZ/6‐31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol^?1, respectively, which is only 13% higher than the actual value. © 2012 Wiley Periodicals, Inc.     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

C24团簇结构与稳定性的理论研究

采用量子化学HF, B3LYP和MP2方法,选用6-31G^*, 6-311G^*, cc-pVDZ和cc-pVTZ基组,对C₂₄团簇的6种异构体进行了优化,并对它们的几何构型、振动频率、核独立化学位移(NICS)和稳定性进行了讨论,比较C₂₄团簇各种异构体的稳定性.研究表明:在6-311G^*和cc-pVDZ水平上,B3LYP方法给出的稳定性大小顺序分别为c＞f＞b＞e＞a＞d和c＞b＞f＞a＞e＞d, MP2方法给出的稳定性大小顺序为b＞c＞a＞e＞f＞d.     

Density functional study of platinum polyyne monomer,oligomer, and polymer: Ground state geometrical and electronic structures

Geometries of monomers and oligomers of a platinum polyyne and its free ligands were optimized using density functional theory with B3LYP hybrid functional. The LANL2DZ basis set was used for Pt and the 6‐31G* for other atoms in geometry optimizations. The electronic structures of these compounds were analyzed using Stuttgart/Dresden ECPs (SDD) basis set for metal atoms and 6‐311G* for others. The polymerization has very little effect on the bond lengths and by introducing the metal, the acetylide bond length increases slightly. The strong overlap between metal sp_x orbitals and σp_x orbitals of acetylides results in localized σ bonding. The hybridization between the ligand pπ orbitals and the platinum dπ orbital resulted in the π‐conjugation enhancement. This conjugation enhancement causes some effects such as the highest‐occupied molecular orbital–lowest‐unoccupied molecular orbital gap reduction and charge transfer characteristic of low‐energy vertical transitions. © 2013 Wiley Periodicals, Inc.     

Chromium Bis(anthracene‐η6) Complexes – A DFT Study

Chromium bisanthracene‐η⁶ complexes are considered within the framework of density functional theory using LANL2DZ and 6‐31+G(d) basis sets and B3LYP functional. The complexation with both the same types of rings of anthracene decks (AA‐ and BB‐type complexes) and with different rings (AB‐type complex) are considered. The optimized geometries and the associated quantum chemical properties are comparatively discussed for the both types of basis sets used. LANL2DZ basis set yielded some unreasonable results. B3LYP/6‐31+G(d) level of calculations yielded the stability order as AA > BB > AB. IR spectra of AA and BB‐type complexes resemble each other. The C–H frequencies are almost the same for both of the anthracene decks, whereas they differ in the case of AB‐type complex. UV/Vis spectra of the complexes all absorb above 500 nm. AA and AB‐type complexes in contrast to BB‐type display rather complex pattern. The NICS(0) values of various rings in the complexes considered are obtained and discussed.     

Investigation of structural and biological properties of N-heterocyclic carbene silver(I) and palladium(II) complexes

abstract

Computational investigations were done on bis(1-allyl-3-benzyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)silver(I), bis(1-benzyl-3-butyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)silver(I), bis(1-allyl-3-benzyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)dibromidepalladium(II), and bis(1-benzyl-3-butyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)dibromidepalladium(II) complexes. Related complexes were optimized at different six calculation levels which are HF/6-31G(LANL2DZ), HF/6-31G(d,p)(LANL2DZ), B3LYP/6-31G(LANL2DZ), B3LYP/6-31G(d,p)(LANL2DZ), M062X/6-31G(LANL2DZ) and M062X/6-31G(d,p)(LANL2DZ) levels in vacuo. IR and NMR spectrum are calculated and examined in detail. Energy diagram of molecular orbitals, contour diagram of frontier molecular orbitals, molecular electrostatic potential maps and the harmonic surface of related molecules are examined in detail. Finally, interactions between mentioned complexes and related proteins (1BNA, 1JNX, and 2ING) are investigated in detail. As a result, it is found that biological and anti-cancer properties of silver N-heterocyclic carbene complexes are higher than those of palladium complexes.     

Theoretical and Experimental Studies on the Metal Complex of Diethylenetriamino-trioxo-molybdenum(Ⅵ)[MoO3(NH2C2H4NHC2H4NH2)]

For diethylenetriamino-trioxo-molybdenum(VI), density functional theory (DFT) method calculations of the structure, atomic charge distributions, electronic spectra, natural po- pulation analyses and thermodynamic properties at different temperatures have been performed by B3LYP method using LANL2DZ, CEP-121G and CEP-31G basis sets, respectively. The calculated results show that B3LYP/LANL2DZ method can best reproduce the molecular structure. The atomic charge distribution analyses indicate that during forming the complex, the ligand of diethyl- enetriamine donates negative charges to MoO3 and these charges are accepted by molybdenum(VI) atom as well as three oxygen atoms. The electronic spectra calculations indicate that B3LYP/ LANL2DZ results are nearest to experimental data among the three methods and electronic tran- sitions are mainly derived from the contribution of bands π→π*. The calculation of the second order optical nonlinearity was carried out, and the molecular hyperpolarizability was 0.7881*10-30 esu.     

Theoretical and Experimental Studies on the Metal Complex of Diethylenetriamino-trioxo-molybdenum(VI) [MoO_3(NH_2C_2H_4NHC_2H_4NH_2)]

1 INTRODUCTION Molybdenum is a biologically important trace ele- ment that occurs in the redox-active sites of moly- bdoenzymes involving in nitrogen, sulfur or carbon metabolism. The structural chemistry of molybde- num complexes has aroused considerable interest in view of its higher oxidation states to form a number of compounds containing MoO groups, and informa- tion on these is very useful in understanding the behavior of MO groups generally[1~3]. Molybdenum oxide-based solids hav…     

Geometry prediction of bridged zirconocene dichlorides by quantum chemical methods

The ab initio Hartree–Fock theory has been demonstrated to give accurate geometry predictions for bridged zirconocene dichlorides. Equilibrium geometries of crystallographically characterized bridged zirconocene dichlorides were optimized by Hartree–Fock, MP2, BLYP, and B3LYP methods, with basis sets ranging from 3‐21G* to 6‐311G**. Selected geometrical parameters were compared with experimental crystal structures. The least expensive HF/3‐21G* method proved to be notably accurate. The accuracy of HF/3‐21G* was verified by a comprehensive data set of 62 bridged zirconocene dichlorides. Furthermore, experimental corrections were applied to the optimized geometry parameters to eliminate systematic deviations. Corrections resulted in considerably improved accuracy for systematically overestimated metal–ligand distances, with maximum deviation falling from 0.081 to 0.039 Å, and absolute average deviations from 0.048 to 0.012 Å. Ligand–metal–ligand angles were predicted accurately with absolute average deviations of 0.7–1.3°. Zirconium–chlorine distances and chlorine–zirconium–chlorine angles are relatively constant in the studied molecules. Zirconium–cyclopentadienyl distances can be influenced mainly by modifying the ligand structure, whereas cyclopentadienyl–zirconium– cyclopentadienyl angles and cyclopentadienyl–cyclopentadienyl plane angles can be controlled by bridge modifications. The HF/3‐21G* method can be applied for the estimation of steric effects in zirconocene catalyzed polymerization reactions, therefore being suitable for the construction of structure–polymerization property correlations. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 51–64, 2001     

Conformations and rotational barriers of 2,2′‐bithiazole and 4,4′‐dimethyl‐2,2′‐bithiazole semiemperical,ab initio,and density functional theory calculations

Conformational properties of 2,2′‐bithiazole and 4,4′‐dimethyl‐2,2′‐ bithiazole have been studied by using AM1 and PM3 semiemperical methods and ab initio HF/6‐311+G* and B3LYP/6‐311+G* calculations. All methods agree that the planar s‐trans conformation is the global minimum and the perpendicular conformation is the transition state. Additional local minima were found using the Hartree–Fock (HF) and B3LYP levels for 2,2′‐bithiazole while for 4,4′‐dimethyl derivative the minima was located only at the MP2//B3LYP level. The barrier heights for rotation are 1.72, 7.69, and 7.88 kcal/mol at the PM3, HF, and B3LYP levels, respectively, and methyl substitution did not affect appreciably this value. Fourier expansion terms and bond orders were used to explain the origins of the rotational barrier in terms of π conjugation, electrostatic interaction, and steric effects, which represent the main factors in the shape of the rotational barrier. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 367–377, 2000     

Structure,stability, and aromaticity of M?SubPc (MB,Al, and Ga): Computational study

A theoretical investigation on the structure, stability, and aromaticity of M‐subphthalocyanine (M? SubPc; M?B, Al, and Ga) was performed at the B3LYP/6‐31+G*//B3LYP/6‐31G* level. The comparison between M? SubPc and the corresponding M? phthalocyanine (M? Pc) was considered. The geometry optimization of the M? SubPc shows that in the Al? SubPc and Ga? SubPc, the steric repulsions among the three azacoupled isoindole moieties increase, as to their macrocycles tend to be far from planarity. The binding energies of Cl? M … aza‐coupled isoindole corrected by the basis set superposition error (BSSE), and the nucleus‐independent chemical shift (NICS) values at the ring center, which are a simple and effective local aromaticity probe, were calculated. The results show that Al? SubPc is less stable than both B? SubPc and Al? Pc for larger steric repulsion, smaller binding energy, and weaker aromaticity. In the same way, Ga? SubPc is less stable than both B? SubPc and Ga? Pc. In addition, the ring expansion reactivity occurring in B? SubPc was confirmed by the global aromaticity mirrored by the electrophilicity index ω values. Therefore, the Al? SubPc and Ga? SubPc remain unknown, while the corresponding compounds Al? Pc and Ga? Pc are known experimentally. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Intramolecular Hypervalent X←X Interaction in Mono- and Bicyclic Heteroelement Compounds Containing Se and Te Atoms

Chalcogen-containing heterapentalene and quasimonocyclic compounds having SeÄSeÄSe and TeÄTeÄTe triads or SeÄSe and TeÄTe diads were studied by the ab initio [MP2(full)/6-31G**, MP2(fc)/6-31+G**, and MP2(fc)/LANL2DZ] and DFT methods (B3LYP/6-31G^**, B3LYP/6-31+G^**, and B3LYP/LANL2DZ). Heterapentalene compounds were found to be stable as planar bicyclic structures having a C _2v symmetry. The stability of quasimonocycic -chalcogenovinyl aldehydes increases with increase in the electron-acceptor power of the substituent at the X atom.     

DFT studies on the tetranuclear cubane complex [Ni4(ampd)4(Cl4)]·MeCN

Density functional theory (DFT) is used to investigate the structural properties of Ni(II) cubane [Ni₄(ampdH)₄Cl₄]·MeCN. The structural features and ground state geometry calculations are computed at the B3LYP/6-31G* (LANL2DZ) level of theory. We shed light on the highest occupied molecular orbital and lowest unoccupied molecular orbital. The absorption spectrum is calculated using time-dependent DFT. The absorption wavelengths are calculated using different functionals, i.e., pw91pw91, B3LYP, BHandHLYP, CAM-B3LYP, LC-BLYP, and M06. The LC-BLYP is in good agreement with the experimental data.     

Density functional theory studies on the dissociation energies of metallic salts: relationship between lattice and dissociation energies

The formation and physicochemical properties of polymer electrolytes strongly depend on the lattice energy of metal salts. An indirect but efficient way to estimate the lattice energy through the relationship between the heterolytic bond dissociation and lattice energies is proposed in this work. The heterolytic bond dissociation energies for alkali metal compounds were calculated theoretically using the Density Functional Theory (DFT) of B3LYP level with 6‐311+G(d,p) and 6‐311+G(2df,p) basis sets. For transition metal compounds, the same method was employed except for using the effective core potential (ECP) of LANL2DZ and SDD on transition metals for 6‐311+G(d,p) and 6‐311+G(2df,p) calculations, respectively. The dissociation energies calculated by 6‐311+G(2df,p) basis set combined with SDD basis set were better correlated with the experimental values with average error of ca. ±1.0% than those by 6‐311+G* combined with the LANL2DZ basis set. The relationship between dissociation and lattice energies was found to be fairly linear (r>0.98). Thus, this method can be used to estimate the lattice energy of an unknown ionic compound with reasonably high accuracy. We also found that the dissociation energies of transition metal salts were relatively larger than those of alkaline metal salts for comparable ionic radii. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 827–834, 2001     

Comparison of DFT methods for molecular structure and vibration spectra of ofloxacin calculations

Comparison of the performance of different density functional theory (DFT) methods at various basis sets in predicting molecular and vibration spectra of ofloxacin was reported. The methods employed in this study comprise six functionals, namely, mPW1PW91, HCTH, LSDA, PBEPBE, B3PW91 and B3LYP. Different basis sets including LANL2DZ, SDD, LANL2MB, 6-31g, 6-311g and 3-21g were also examined. Comparison between the calculated and experimental data indicates that the mPW1PW91/6-311g level afford the best quality to predict the structure of ofloxacin. The results also indicate that B3LYP/LANL2DZ level show better performance in the vibration spectra prediction of ofloxacin than other DFT methods.     

Experimental and theoretical investigation of the molecular and electronic structure of N′‐benzylidene‐N‐[4‐(3‐methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐chloro‐acetic acid hydrazide

The title compound, N′‐benzylidene‐N‐[4‐(3‐methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐chloro‐acetic acid hydrazide, has been synthesized and characterized by elemental analysis, IR, ¹H and ¹³C NMR, and X‐ray single crystal diffraction. The compound crystallizes in the orthorhombic space group P 21 21 21 with a = 5.8671 (3) Å, b = 17.7182 (9) Å, and c = 20.6373 (8) Å. Moreover, the molecular geometry from X‐ray experiment, the molecular geometry, vibrational frequencies, and gauge‐including atomic orbital ¹H and ¹³C chemical shift values of the title compound in the ground state have been calculated by using the Hartree–Fock and density functional methods (B3LYP) with 6‐31G(d) and 6‐31G(d,p) basis sets. The results of the optimized molecular structure are exhibited and compared with the experimental X‐ray diffraction. Besides, molecular electrostatic potential, Frontier molecular orbitals, and thermodynamic properties of the title compound were determined at B3LYP/6‐31G(d) levels of theory. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

DFT studies of temperature effect on coordination chemistry of Cu(II)-trimethoprim complexes

The computational analysis of geometrically different copper-trimethoprim complexes, experimentally formed at two different temperatures, was performed using Density Functional Theory (DFT) method. Initial geometries of copper-trimethoprim complexes 1, 2, and 3 were obtained from crystallographic data. These three geometries of complexes 1, 2, and 3 were fully optimized using B3LYP/BLYP hybrid density functional methods along with 6-31G and LANL2DZ basis sets at two temperatures, 298 and 352 K. The results obtained were compared with the experimental data and show that complex 1 is the most stable geometry while complex 3 is unstable/intermediate geometry and can be converted to stable form after the recrystallization process. Moreover, LANL2DZ basis set gives more accurate (with respect to experimental) results as compared to 6-31G.     

Equilibrium geometry and gas‐phase proton affinity of 2‐thiouracil derivatives

The ground‐state geometries of uracil, 6‐hydroxy‐uracil, and 6‐hydroxy‐, 6‐amino‐, 6‐methyl‐, 6‐trifluoro‐, and 6‐phenyl‐2‐thiouracil were optimized at the Hartree–Fock level. The molecular structures were fully optimized using the 6‐31G and 6‐31G* basis sets. The effect of substituents on the geometry and electronic structural features of 2‐thiouracils were examined. The perturbation effects of the OH and NH₂ groups are by far more pronounced on the geometric features and the dipole moment magnitude and direction of 2‐thiouracil. The potential energy per atom criteria was used to compare the relative tightness of binding in the studied series. Proton affinity and deprotonation enthalpy on each of the possible sites in 2‐thiouracil and its derivatives have been calculated at the 6‐31G/MP2 level of theory. The obtained results show that thiouracils behave as bases where they possess a high tendency to abstract protons. Substituents in the 6‐position have the general effect of enhancing the basicity strength of the thiocabonyl site in the order Ph < CH3 ≈ NH2 < OH. The CF3 group has the effect of reducing considerably the basicity strength and enhances the acidity strength at both N1 and N3. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

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。