Density functional theory calculations of novel Rh(I) diphosphinite catalysts

Novel Rh(I) diphosphinite catalysts [Rh((R,R)-3,4-(bis(O-diphenylphosphino)-1,2,5,6-tetra-O-methyl-chiro-inositol)]+ ([Rh-CANDYPHOS]+) and [Rh((R,R)-3,4-(bis(O-diphenylphosphino)-1,2,5,6-tetra-O-ethyl-chiro-inositol)]+ ([Rh-EtCP]+) have been prepared utilizing naturally-occurring resources. Potential energy surfaces for the catalyzed asymmetric hydrogenation of the prochiral enamides methyl-(Z)-α-acetamido cinnamate, methyl-(Z)-α-acetamido cinnamic acid and dimethyl itaconate have been surveyed using density function theory (DFT) methods. Key transition states were identified from previous [Rh((R,R)-DUPHOS)]+ studies for the two diastereoisomeric manifolds 1 and 2. Transition state energies were found starting from models based on (1) the X-ray structure of the active complex (CANDYPHOS)(η⁴-(Z,Z)-cyclo-octa-1,5-diene)-rhodium(I) tetrafluoroborate CHCl₃ solvate [3] and (2) models in which the complex (without substrate) started with C2 molecular symmetry. The difficulties encountered in calculations of the transition state energies of large cations are outlined and limitations noted. Transition state enthalpy values are compared with the observed experimental free energy differences results and previous studies 1 and 2. The predictive aspects of the calculations appear to be limited with the starting models playing an important part in the absolute value of the final energies.     

黄嘌呤及其互变异构体的密度泛函理论研究

嘌呤碱及其衍生物在生物系统中起重要作用。对人具有兴奋和利尿作用的茶碱和咖啡碱就是黄嘌呤的甲基衍生物。黄嘌呤存在多种互变异构体,从理论计算的角度研究这些互变异构体的几何结构、电子结构及相对稳定性,进一步研究溶剂对其结构和性质的影响是有意义旧。密度泛函理论方法既考虑了电子相关,又较其它CI（组态相互作用）或MPn（n级微扰）方法节省机时。其计算结果较好,被广泛应用于研究各种化合物。本文采用密度泛函B3LYP／6—311G方法对14种黄嘌呤可能的互变异构体（见图1）,分别在气相和水相中进行几何构型全自由度优化和能量计算,讨论了异构体的相对稳定性,水的溶剂化作用对异构体的能量、几何构型、电荷分布和偶极矩的影响,探讨了溶剂极性对异构体的能量和偶极矩的影响。     

Density functional response theory calculations of three-photon absorption

Three-photon absorption probabilities delta(3PA) have been calculated through application of a recently derived method for cubic response functions within density functional theory (DFT). Calculations are compared with Hartree-Fock (HF) and with a coupled cluster hierarchy of models in a benchmarking procedure. Except for cases having intermediate states near resonance, density functional theory is demonstrated to be in sufficient agreement with the highly correlated methods in order to qualify for predictions of delta(3PA). For the larger systems addressed, a set of acceptor A and donor D substituted pi-conjugated systems formed by trans-stilbene and dithienothiophene (DTT), we find noticeable differences in the magnitude of delta(3PA) between HF and DFT, although similar trends are followed. It is shown that the dipolar structures, TS-AD and DTT-AD, have substantially larger delta(3PA) than other types of modifications which is in accordance with observations for two-photon absorption. This is the first application of density functional theory to three-photon absorption beyond the use of few-state models.     

Density functional theory calculations for two-dimensional silicene with halogen functionalization

The electronic structures and band gaps of silicene (the Si analogue of graphene) adsorbed with halogen elements are studied using the density functional theory based screened exchange local density approximation method. It is found that the band gaps of silicene adsorbed with F, Cl, Br and I have a nonmonotonic change as the periodic number of the halogen elements increases. This is attributed to the transfer of contributions to band gaps from Si-Si bonding to Si-halogen bonding.     

Density functional calculations of a tetradecametallic iron(III) cluster with a very large spin ground state

Density functional theory (DFT) calculations and Monte Carlo (MC) simulations are used to calculate the exchange interactions in the Fe(III) cluster [Fe14(bta)6O6(OMe)18Cl6], impossible to determine by conventional methods--the results support a huge ground state spin arising from competing antiferromagnetic interactions.     

Density functional theory calculations of selected Ru(II) two ring diimine complex dications

Geometry optimization for a series of ten, two-ring diimine Ru(II) complexes was effected using the Gaussian 98 protocol at density functional theory (DFT) B3LYP level with basis sets 3-21G*and 3-21G**. HOMO-LUMO energy difference values compared favorably to the experimental data from electrochemistry [Delta E(1/2) = (E(1/2ox) - E(1/2red))] and the lowest energy absorption maxima, which for these complexes correspond to the metal-to-ligand charge transfer (MLCT) band. The HOMO and LUMO distributions from DFT support the idea that the lowest energy transitions are metal-to-ligand charge transfer and that the lowest energy LUMO for the mixed ligand complexes is located on 2,2'-bipyrazine (bpz), followed by 2,2'-bipyrimidine (bpm) and then 2,2'-bipyridine (bpy).     

Density functional theory calculations and vibrational spectral analysis of 3,5-(dinitrobenzoic acid)

The FT-IR and Raman spectra of 3,5-dinitrobenzoic acid (DNBA) have been recorded and analyzed. The equilibrium geometry, various bonding and harmonic vibrational wavenumbers have been calculated with the help of density functional theory (DFT) method. Most of the vibrational modes are observed in the expected range. Mulliken population analysis shows the interactions C-N-O?H-C and C-O?H-C. The most possible interaction is explained using natural bond orbital (NBO) analysis. The strengthening and polarization of the CO bond increases due to the degree of conjugation. HOMO-LUMO energy and the thermodynamic properties are also evaluated.     

Density functional calculations on triply excited states of lithium isoelectronic sequence

Triply excited states of many-electron atomic systems are characterized by the presence of strong electron correlation, closeness to more than one threshold, and degeneracy with many continua; therefore, they offer unusual challenges to theoretical methodologies. In the present article, we computed with reasonable accuracy all the n=2 intrashell triply excited states (2s²2p ²P; 2s2p^{2 2}D, ⁴P, ²P, ²S; and 2p^{3 2}D, ²P, ⁴S) of three-electron atomic systems (Z=2, 3, 4, 6, 8, 10) by using a density functional formalism developed recently in our laboratory, based on the nonvariational Harbola–Sahni exchange potential in conjunction with a parametrized local Wigner and Lee–Yang–Parr correlation potentials. Nonrelativistic energies and densities are obtained by solving a Kohn–Sham-type differential equation. The calculated results are compared with available experimental and other theoretical data. The 2p³(⁴S)→1s2p²(⁴P) transition wavelength for the isoelectronic series is also computed. The overall good agreement of our results with the literature data indicates the reliability of the present density functional methodology for excited states of many-electron systems. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65 : 317–332, 1997     

Ge_10O_28单元构建的两个三维锗酸盐结构：（H_3O)_4Ge_7O_16·3H_2O和K_4Ge_9O_20

在半水溶剂热条件下,采用不同的合成条件合成了两个锗酸盐微孔分子筛：（ H_3单晶结构解析表明,两个晶体结构具有相同的"火箭状"二级结构单元（SBU）, SBU的不同的连接方式导致了完全不间结构．H_4Ge_7O_(16)·7H_2O的结晶学数据 为M_r=894 ．27,Pλ=O．071073nm,R（F）=3．48％,wR（F~2）＝8．39％． K_4Ge_9O_(20)的结晶学数据为C=0.7383（2）nm,V=16618（7）nm~3,Z＝4,Mo Ka,R（F）=3．92%,wR(F~2)=11.97%.     

Vibrational spectra of mixed (phthalocyaninato)(porphyrinato) yttrium(III) double-decker complexes: Density functional theory calculations

The vibrational (IR and Raman) spectra of neutral and reduced mixed (phthalocyaninato)(porphyrinato) yttrium(III) double-decker complexes Y(Pc)(Por) and [Y(Pc)(Por)]⁻ [the simplified models of mixed (phthalocyaninato)(porphyrinato) rare earth(III) complexes] are studied using density functional theory (DFT) calculations. The simulated IR and Raman spectra of Y(Pc)(Por) are compared with the experimental IR spectrum of Tb(Pc)(TClPP) and Raman spectrum of Y(Pc)(TClPP), respectively, and many bands can acceptably fit in spite of the different species. On the basis of comparison with the simulated spectra of PbPc and PbPor together with the assistance of normal coordinate analysis, the calculated frequencies in their IR and Raman spectra are identified in terms of the vibrational mode of different ligand for the first time. The calculated frequency at 1048 cm⁻¹ in the IR spectrum of [Y(Pc)(Por)]⁻ with contribution from both Pc and Por vibrational modes is the characteristic IR vibrational mode of the reduced double-decker, while the characteristic IR vibrational mode of Y(Pc)(Por) attributed from the vibration of phthalocyanine monoanion radical Pc⁻ appears at 1257 cm⁻¹. In line with our previous experimental findings that the Raman spectra of M(Pc)(TPP) and M(Pc)(TClPP) are dominated by the Pc vibrational modes, theoretical calculations indicate that most of the Raman vibrational modes contributed from Por ring are covered up by those of Pc ring and thus are hard to be recognized in the Raman spectra of [Y(Pc)(Por)]⁻ and Y(Pc)(Por) due to their much weaker intensity in comparison with that of Pc ligand. Comparison in the IR and Raman spectra between [Y(Pc)(Por)]⁻ and Y(Pc)(Por) also suggests the localization of hole on the Pc ring in the neutral double-decker Y(Pc)(Por). The present work, representing the first detailed DFT study on the vibrational spectra of mixed (phthalocyaninato)(porphyrinato) rare earth(III) double-decker complexes, is useful in helping to understand the vibrational spectroscopic properties of this series of mixed tetrapyrrole ring complexes.     

Density functional theory calculations and vibrational circular dichroism of aromatic foldamers

Ab initio calculations together with vibrational circular dichroism (VCD) have been used for studying the conformations of a quinoline-derived oligoamide bearing a terminal chiral residue. Three helically folded conformers of the dimer, trimer, and tetramer forms of the oligomer were optimized at the density functional theory (DFT) level using the B3LYP functional and the 6-31G* basis set. For each form, the three conformers differ in their helical handedness and in the conformation of the chiral end group. The calculated structures of the tetramer and also the proportions predicted between them based on their calculated Gibbs free energies differences match remarkably well with experimental data collected on an octamer. Specifically, a R-phenethyl terminal group gives rise to a 91:9 ratio between left handed and right handed helices. The predicted VCD spectrum calculated from the Boltzmann population of the individual conformer reproduces very well the experimental VCD spectrum of the tetramer in CDCl3 solution. The DFT calculations performed for the trimer also allow one to assess the preferred handedness of the helix and the conformation of the chiral end group, but the calculated relative populations differ slightly from experimental data. Finally, this study shows that the dimer fragment is not sufficient to obtain valuable information on the conformation of this aromatic oligoamide foldamer.     

Density functional theory study of 10-atom germanium clusters: effect of electron count on cluster geometry

Density functional theory (DFT) at the hybrid B3LYP level has been applied to Ge10z germanium clusters (z = -6, -4, -2, 0, +2, +4, +6) starting from 12 different initial configurations. The D4d 4,4-bicapped square antiprism found experimentally in B10H102- and other 10-vertex clusters with 22 skeletal electrons is calculated for the isoelectronic Ge102- to be the global minimum by more than 15 kcal/mol. The global minima found for electron-rich clusters Ge104- and Ge106- are not those known experimentally. However, experimentally known structures for nido-B10H14 and the pentagonal antiprism of arachno-Pd@Bi104+ are found at higher but potentially accessible energies for Ge104- and Ge106-. The global minimum for Ge10 is the C3v 3,4,4,4-tetracapped trigonal prism predicted by the Wade-Mingos rules and found experimentally in isoelectronic Ni@Ga1010-. However, only slightly above this global minimum for Ge10 (+3.3 kcal/mol) is the likewise C3v isocloso 10-vertex deltahedron found in metallaboranes such as (eta6-arene)RuB9H9 derivatives. Structures found for more electron-poor clusters Ge102+ and Ge104+ include various capped octahedra and pentagonal bipyramids. This study predicts a number of 10-vertex cluster structures that have not yet been realized experimentally but would be interesting targets for future synthetic 10-vertex cluster chemistry using vertex units isolobal with the germanium vertices used in this work.     

Density functional based calculations for Fen (n⩽32)

We investigate magnetic and structural properties of iron clusters up to Fe₃₂, well extending into the size range accessible by experiment. A density-functional based tight-binding scheme fully incorporating the effects of spin polarisation and charge transfer in a self-consistent manner has been used. The potential hypersurfaces have been scanned by an unconstrained search using a genetic algorithm. Results for smaller clusters up to Fe₁₇ are validated against more sophisticated density functional theory calculations. Our magnetic moment data show a strong change around Fe₁₃ being unique in this size range. For the larger cluster sizes a smooth decrease of the clusters average spin magnetic moments is found in good agreement with experimental data.     

Density functional theory calculations on the molecular structures and vibration spectra of platinum(II) antitumor drugs

A comparison of six density functional theory (DFT) methods and six basis sets for predicting the molecular structures and vibration spectra of cisplatin is reported. The theoretical results are discussed and compared with the experimental data. It is remarkable that LSDA/SDD level is clearly superior to all the remaining density functional methods (including mPW1PW) in predicting the structures of cisplatin. Mean deviation between the calculated harmonic and observed fundamental vibration frequencies for each method is also calculated. The results indicate that PBE1PBE/SDD is the best method to predict all frequencies on average for cisplatin molecule in DFT methods.     

Density functional theory (DFT) calculations of the infrared absorption spectra of acetaminophen complexes formed with ethanol and acetone species

We have investigated the infrared (IR) vibrational spectra of acetaminophen (N(4-hydroxyphenyl) acetamide or paracetamol) complexes formed with ethanol and acetone in relation to the nature of the specific intermolecular interactions involved in the stabilization of the complexes. The structures and binding energies of the complexes have been determined using Hartree-Fock (HF) and DFT-B3PW91 procedures and different Pople's basis sets as well. The main results are presented and discussed by considering the hydroxyl (OH), amino (NH), and carbonyl (CO) chemical groups of acetaminophen interacting with the acetone or ethanol molecules either separately or in conjunction in the complex formation. The frequency shifts and IR intensity variations associated with the internal modes of acetaminophen (namely nu(OH), nu(NH), and nu(CO)) as well as the most pertinent vibrational probes of ethanol (nu(OH)) and acetone (symmetric nu(CO) and nu(CCC) stretching modes) interacting with acetaminophen have been analyzed. The predicted spectral changes have been critically discussed in comparison with IR absorption measurements of acetaminophen dissolved as a solute in ethanol or acetone CO2 expanded solutions. It is argued that the exchange-correlation contribution taken into account in DFT calculations is likely significant in determining the main IR spectral features of acetaminophen complexes formed with acetone or involving hydrogen-bonded as with ethanol.     

Density functional theory calculations and vibrational spectra of 6-methyl 1,2,3,4-tetrahyroquinoline

The solid phase FTIR and Raman spectra of 6-methyl 1,2,3,4-tetrahydroquinoline (MTHQ) have been recorded in the regions 4000-100 and 3500-100 cm(-1), respectively. The spectra were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6-311+G(**) basis set combination. A close agreement was achieved between the observed and calculated frequencies by refinement of the scale factors.     

Effects of solvent on weak halogen bonds: Density functional theory calculations

In recent years, many applications of solution‐phase halogen bonding in anion recognition, catalysis, and pseudorotaxane formation have been reported. Moreover, a number of thermodynamic data of halogen bonding interactions in organic solution are now available. To obtain detailed information of the influence of the surrounding medium on weak halogen bonds, a series of dimeric complexes of halobenzene (PhX) with three electron donors (H₂O, HCHO, and NH₃) were investigated by means of DFT/PBE calculations in this work. The PCM implicit solvation approach was utilized to include the effects of three solvents (cyclohexane, chloroform, and water) as representatives for a wide range of dielectric constant. In some cases, halogen‐bond distances are shown to shorten in solution, accompanied by concomitant elongation of the C? X bonds. For the remaining systems, the intermolecular distances tend to increase or remain almost unchanged under solvent effects. In general, the solvent has a slight destabilizing effect on weak halogen bonds; the strength order of halogen bonds observed in vacuum remains unchanged in liquid phases. Particularly, the interaction strength attenuates in the order I > Br > Cl in solution, consistent with the experimental measurements of weak halogen bond door abilities. The similarities between halogen and hydrogen bonding in solution were also elucidated. The results presented herein would be very useful in future applications of halogen bonding in molecular recognition and medicinal chemistry. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Coupled cluster and density functional theory calculations of atomic hydrogen chemisorption on pyrene and coronene as model systems for graphene hydrogenation

Ab initio coupled cluster and density functional theory studies of atomic hydrogen addition to the central region of pyrene and coronene as molecular models for graphene hydrogenation were performed. Fully relaxed potential energy curves (PECs) were computed at the spin-unrestricted B3LYP/cc-pVDZ level of theory for the atomic hydrogen attack of a center carbon atom (site A), the midpoint of a neighboring carbon bond (site B), and the center of a central hexagon (site C). Using the B3LYP/cc-pVDZ PEC geometries, we evaluated energies at the PBE density functional, as well as ab initio restricted open-shell ROMP2, ROCCSD, and ROCCSD(T) levels of theory, employing cc-pVDZ and cc-pVTZ basis sets, and performed a G2MS extrapolation to the ROCCSD(T)/cc-pVTZ level of theory. In agreement with earlier studies, we find that only site A attack leads to chemisorption. The G2MS entrance channel barrier heights, binding energies, and PEC profiles are found to agree well with a recent ab initio multireference wave function theory study (Bonfanti et al. J. Chem. Phys.2011, 135, 164701), indicating that single-reference open-shell methods including B3LYP are sufficient for the theoretical treatment of the interaction of graphene with a single hydrogen atom.