Investigations of hydrogen-bonded systems: Local density approximation and gradient corrections

The applicability of the local density approximation (LDA ) and of corresponding gradient corrections (for the exchange and correlation energy) for the treatment of the hydrogen bond is investigated. As test systems, we consider the water dimer and the H₂O…?HX complexes (X = F, Cl, Br): Using an LCAO scheme, their equilibrium geometries and interaction energies are ?alculated and compared with experimental data and with other calculations. We obtain that the LDA gives the geometries in qualitative agreement with other data, whereas the energies are overestimated. The use of the gradient corrections (GC ) according to Becke and Perdew leads to a significant improvement of the geometry, and especially of the interaction energies. The calculations indicate further that LDA + GC should also be able to describe weaker intermolecular interactions than the usual hydrogen bond. Finally, a short discussion of the charge distribution and the dipole moments of the H₂O…?HX complexes is performed. © 1994 John Wiley & Sons, Inc.     

Open shell organometallics: a general analysis of their electronic structure and reactivity

Transition metal organometallic compounds that contain fewer than 18-electrons and two or more unpaired electrons are generally excluded from treatises of either Werner-type coordination compounds or organometallic chemistry. However, they can be seen as the bridge filling the gap between these two traditional areas of coordination chemistry. Their magnetic and optical properties are reminiscent of the Werner-type complexes, whereas their chemical reactivity parallels that of the lower-valent organometallics. Spin state change phenomena are of paramount importance in this area. This paper provides a broad perspective of this area, with particular attention to: (i) how the ground state properties can be related to the metal and ligands nature; (ii) under which circumstances the often inappropriately invoked concept of “spin block” is meaningful; (iii) the spin acceleration concept; (iv) how the coordination sphere affects the topology of the reaction coordinate in the vicinity of spin crossing points; and (v) the effect of spin state changes on reaction selectivities.     

Heterobimetallic Mn/Co hybrid complexes composed of proximate organometallic and classical coordination sites

A series of highly unsymmetric heterobinuclear Mn/Co complexes is reported, in which an organometallic CpMn(CO)₂ fragment and a classical Werner-type cobalt(II) subunit are arranged in close proximity by means of a bridging pyrazolate. Two ligand scaffolds are employed that differ by the chelate size of the tripodal tetradentate {N4} binding site for cobalt. Molecular structures of three complexes with either nitrate or acetate coligands have been characterized by X-ray crystallography. IR and UV-Vis-spectroelectrochemistry reveals that oxidation of the heterobimetallic systems is highly localized at the organometallic manganese site, while electrochemical reduction occurs at cobalt. Structural and spectroscopic features as well as trends for the redox potentials of the Mn^I/Mn^II couple suggest that changes at the cobalt(II) Werner-type subunit have only minor effects on the properties of the organometallic site.     

Factors affecting d-block metal-ligand bond lengths: toward an automated library of molecular geometry for metal complexes

Metal-ligand (M-L) bond lengths for a range of ligands (carboxylates, chlorides, pyridines, water, tertiary phosphines, and alkenes) and a variety of metals have been retrieved from the Cambridge Structural Database, CSD. Analysis of the factors which affect M-L bond lengths (for example, ligand coordination mode, oxidation state, metal coordination number and geometry, spin and Jahn-Teller effects, and ligand trans to M-L bond) shows that it is generally possible to subdivide the M-L data sets systematically to obtain better defined, unimodal, bond length distributions with means and sample standard deviations (SSDs) which reflect the nature of the bond in question. Typically, the SSDs for the M-L data sets can be reduced to 0.04-0.05 A by these methods. This work is an extension to tables of bond lengths in organometallic compounds and coordination complexes published in 1989. The importance of the factors which affect M-L bond lengths for particular metal-ligand groups are discussed. From the case studies reported, an algorithm is proposed by which compilation of a library of molecular geometry for metal complexes may be automated. The points that need to be considered to produce such a molecular library from the data stored in the CSD are discussed. The development of such a library would allow users to retrieve chemically well-defined geometric data rapidly and accurately. This should be of use, for example, to crystallographers and molecular modelers.     

Novel method of self‐interaction corrections in density functional calculations

It is demonstrated that the commonly applied self‐interaction correction (SIC) used in density functional theory does not remove all self‐interaction. We present as an alternative a novel method that, by construction, is totally free from self‐interaction. The method has the correct asymptotic 1/r dependence. We apply the new theory to localized f electrons in praseodymium and compare with the old version of SIC, the local density approximation (LDA) and with an atomic Hartree–Fock calculation. The results show a lowering of the f level, a contraction of the f electron cloud and a lowering of the total energy by 13 eV per 4 f electron compared to LDA. The equilibrium volume of the new SIC method is close to the ones given by LDA and the older SIC method and is in good agreement with experiment. The experimental cohesive energy is in better agreement using the new SIC method, both compared to LDA and another SIC method. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 247–252, 2001     

On the evaluation of molecular electron affinities by approximate density functional theory

The ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH₃, NH₂, OH, and HC₂ as well as the multibonded species CN, BO, N₃, OCN, and NO₂. The simple Hartree–Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EA_ad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimates EA_ad by 0.2 eV. It is concluded that the LDA/NL method affords EA_ad's in as good agreement with experiment as ab initio techniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anions.     

Energy bands and bond alternation potential in poly(para-phenylene vinylene): a comparative ab initio quantum chemical and density functional theory study

We present calculations of the total energy per unit cell for different bond alternations of the C-C bonds bridging the distance between two aromatic rings in poly(para-phenylene vinylene) (PPV), using two different parametrizations of the energy functional in the local density approximation (LDA) and the ab initio Hartree-Fock (HF) method. For the application of correlation corrections to the HF results the system is already too large. We find that even simple LDA methods are reliable alternatives to the ab initio HF method for the calculation of potential surfaces in polymers with large unit cells. The results in turn can be used to determine parameters for model Hamiltonians necessary for theoretical studies of the dynamics of nonlinear quasiparticles in the polymers. We further present the LDA band structures of PPV together with their HF and correlation (many body perturbation theory of 2^nd order in Møller-Plesset partitioning, MP2) corrected counterparts. We find that the fundamental gap obtained is too large both with HF and with the correlation corrected band structure compared to experiment. However, we use only a modest correlation method and a small basis set, which already brings us to the limits of the computers available to us. The LDA gaps on the other hand are too small which, however, could be corrected with the help of self interaction corrections. None of the latter methods would lead to exceedingly large computation times.     

Analytical gradients for subsystem density functional theory within the slater‐function‐based amsterdam density functional program

We present a new implementation of analytical gradients for subsystem density‐functional theory (sDFT) and frozen‐density embedding (FDE) into the Amsterdam Density Functional program (ADF). The underlying theory and necessary expressions for the implementation are derived and discussed in detail for various FDE and sDFT setups. The parallel implementation is numerically verified and geometry optimizations with different functional combinations (LDA/TF and PW91/PW91K) are conducted and compared to reference data. Our results confirm that sDFT‐LDA/TF yields good equilibrium distances for the systems studied here (mean absolute deviation: 0.09 Å) compared to reference wave‐function theory results. However, sDFT‐PW91/PW91k quite consistently yields smaller equilibrium distances (mean absolute deviation: 0.23 Å). The flexibility of our new implementation is demonstrated for an HCN‐trimer test system, for which several different setups are applied. © 2016 Wiley Periodicals, Inc.     

Modeling halogen bonding with planewave density functional theory: Accuracy and challenges

Inspired by the recent interest of halogen bonding (XB) in the solid state, we detail a comprehensive benchmark study of planewave DFT geometry and interaction energy of lone-pair (LP) type and aromatic (AR) type halogen bonded complexes, using PAW and USPP pseudopotentials. For LP-type XB dimers, PBE-PAW generally agrees with PBE/aug-cc-pVQZ(−pp) geometries but significantly overbinds compared to CCSD(T)/aug-cc-pVQZ(-pp). Grimme's D3 dispersion corrections to PBE-PAW gives better agreement to the MP2/cc-pVTZ(-pp) results for AR-type dimers. For interaction energies, PBE-PAW may overbind or underbind for weaker XBs but clearly overbinds for stronger XBs. D3 dispersion corrections exacerbate the overbinding problem for LP-type complexes but significantly improves agreement for AR-type complexes compared to CCSD(T)/CBS. Finally, for periodic XB crystals, planewave PBE methods slightly underestimate the XB lengths by 0.03 to 0.05 Å. © 2019 Wiley Periodicals, Inc.     

Shape and symmetry of heptacoordinate transition-metal complexes: structural trends

The stereochemistries of heptacoordinate transition-metal complexes are analyzed by using continuous symmetry and shape measures of their coordination spheres. The distribution of heptacoordination through the transition-metal series is presented based on structural database searches including organometallic and Werner-type molecular complexes, metalloproteins, and extended solids. The most common polyhedron seems to be the pentagonal bipyramid, while different preferences are found for specific families of compounds, as in the complexes with three or four carbonyl or phosphine ligands, which prefer the capped octahedron or the capped trigonal prism rather than the pentagonal bipyramid. The symmetry maps for heptacoordination are presented and shown to be helpful for detecting stereochemical trends. The maximal symmetry interconversion pathways between the three most common polyhedra are defined in terms of symmetry constants and a large number of experimental structures are seen to fall along those paths.     

Redox site confinement in highly unsymmetric dimanganese complexes

A set of highly preorganized pyrazolate-bridged dimanganese complexes L(Mn)MnX have been prepared and structurally characterized. They can be described as hybrid organometallic/Werner-type systems that consist of a low-spin CpMn(I)(CO)2 subunit (Mn1) and a proximate tripodal tetradentate {N4} binding pocket accommodating a high-spin Mn(II) ion (Mn2), with Mn...Mn distances of approximately 4.3 A and different coligands bound to Mn2. Density functional theory (DFT) calculations (both the hybrid B3LYP and the pure BP86 functionals and the all-electron basis sets 6-311G and 6-311G*) confirm that the valence alpha and beta Kohn-Sham molecular orbitals (MOs) of these mixed-valent Mn(I)Mn(II) compounds have predominant Mn(3d) character and an almost perfectly localized nature: all five unpaired electrons are essentially localized at the Werner-type Mn2, whereas Mn1 possesses an effective closed-shell structure with the MOs of highest energy centered there. One-electron oxidation occurs in a clean process at approximately E(1/2) = -0.6 V (versus ferrocene/ferrocinium), giving the low-spin/high-spin Mn(II)Mn(II) species. UV/vis and IR spectroelectrochemistry as well as a detailed theoretical analysis reveal that the redox process takes place with strict site control at the organometallic subunit, while it does not significantly influence the spin and charge distribution on the Werner-type site. Positions and shifts of the nu(C[triple bond]O) absorptions are largely reproduced by the DFT calculations. These systems thus represent an exceptional example of the effect the unsymmetry of a dinucleating ligand scaffold has on the spin and charge distribution in homobimetallic complexes and might offer interesting prospects for the study of the cooperative effects of bimetallic arrays.     

High-Fidelity,Narcissistic Self-Sorting in the Synthesis of Organometallic Assemblies from Poly-NHC Ligands

Highly selective, narcissistic self-sorting has been observed in the one-pot synthesis of three organometallic molecular cylinders of type [M₃{L-(NHC)₃}₂](PF₆)₃ (M=Ag⁺, Au⁺; L=1,3,5-benzene, triphenylamine, or 1,3,5-triphenylbenzene) from L-(NHC)₃ and silver(I) or gold(I) ions. The molecular cylinders contain only one type of tris-NHC ligand with no crossover products detectable. Transmetalation of the tris-NHC ligands from Ag⁺ to Au⁺ in a one-pot reaction with retention of the supramolecular structures is also demonstrated. High-fidelity self-sorting was also observed in the one-pot reaction of benzene-bridged tris-NHC and tetrakis-NHC ligands with Ag₂O. This study for the first time extends narcissistic self-sorting in metal–ligand interactions from Werner-type complexes to organometallic derivatives.     

QuEChERS-同位素稀释-液相色谱-高分辨飞行时间质谱法高通量筛查化妆品中86种糖皮质激素

建立了QuEChERS-同位素稀释-液相色谱-四极杆串联飞行时间质谱同时快速筛查化妆品中86种糖皮质激素(Glucocorticoids, GCs)的高通量方法.样品经乙腈提取,改进的QuEChERS法净化,待测物选用具有多重色谱保留机理的新型色谱柱Poroshell 120 PFP (100 mm×2.1 mm,2.7 μm),以0.2% (V/V)乙酸和乙腈为流动相进行梯度洗脱分离,在电喷雾离子源的正离子模式下建立了一级精确质量数及二级碎片离子质谱图数据库,无需标准品即可完成化妆品中86种GCs的全面筛查与确证.所有待测物在2~200 μg/L浓度范围内线性良好,相关系数均大于0.99, 3个添加水平的平均回收率为66.2%~112.8%,相对标准偏差(RSD)为4.6%~13.9%,检出限(LOD,S/N≥3) 为0.006~0.015 mg/kg,定量限(LOQ,S/N≥10)为0.02~0.05 mg/kg.本方法简便高效、定性可靠、定量准确,适用于化妆品中非法添加GCs的高通量筛查.     

Basis set and correlation energy dependence of geometry and harmonic frequencies of difluoroethane,CHF2CH3

Optimum geometries and harmonic frequencies calculated at the Hartree–Fock and the MP2 level are reported for the fluorohydrocarbon CHF₂CH₃; basis sets employed range from STO-3G to 6-311G**. The significantly shortened C? C distance of 1.50 Å is reproduced already with the simplest split-valence basis set; the C? F distance of 1.36 Å on the other hand needs MP2 correction at least at the double-ζ or 6-311G* level. Symmetry coordinates defined in terms of internal coordinates are in qualitative agreement with available experimental evidence. Even the best basis set yields frequencies that differ from experimental (anharmonic) values by up to 200 cm^?1 indicating the well-known necessity of including higher-order force constants if quantitative agreement with experiment is to be achieved.     

The determination of intrinsic reaction coordinates by density functional theory

The first implementation of the intrinsic reaction coordinate (IRC ) method within the density functional theory (DFT ) framework is presented. The implementation has been applied to four different types of chemical reactions represented by the isomerization process, HCN ? HNC (A); the S_N2 process, H^? + CH₄ ? CH₄ + H^? (B); the exchange process, H˙ + HX ? HX + H˙ (X ? F,Cl) (C); and the elimination process, C₂H₅Cl ? C₂H₄ + HCl (D). The present study presents for each process optimized structures and calculated harmonic vibrational frequencies for the reactant(s), the transition state, and the product(s) along with the IRC path connecting the stationary points. The calculations were carried out within the local density approximation (LDA ) as well as the LDA/NL scheme where the LDA energy expression is augmented by Perdew's and Becke's nonlocal (NL ) corrections. The LDA and LDA/NL results are compared with each other as well as the best available ab initio calculations and experimental data. For reaction (D), ab initio calculations based on MP 2 geometries and MP 4SDTQ energies have been added due to the lack of accurate published post-HF calculations on this process. A detailed discussion is provided on the efficiency of the IRC algorithms, the relative accuracy of the DFT and ab initio schemes, as well as the reaction mechanisms of the four reactions. It is concluded that the LDA/NL scheme affords the same accuracy as does the MP 4 method. The post-HF methods seem to overestimate activation energies, whereas the corresponding LDA/NL estimates are too low. The LDA activation energies are even lower than the LDA/NL counterparts. The incorporation of the IRC method into the DFT framework provides a promising and reliable tool for probing the chemical reaction path on the potential energy surfaces, even for large-size systems. IRC calculations by ab initio methods of an accuracy similar to the LDA/NL scheme, such as the MP 4 scheme, are not feasible. © John Wiley & Sons, Inc.     

A Density Functional Study of Active Site Models for Xanthine Oxidase

The suggestion that hydroxide is coordinated to the oxidised molybdenum site in xanthine oxidase (XnO) is tested theoretically by computing the structures of a range of four-, five-, and six-coordinate active site models. The local density approximation of density functional theory has been used with the two experimentally verified singly bonded sulfur ligands modeled by both dithiolene, [SRCCRS](2-) (R = H and CH(3)), and thiolate, [CH(3)S](-) groups. Both ligand types give virtually identical results for analogous species. Based on a comparison of the computed M-L distances and those reported in recent EXAFS studies, it is concluded that both four- and six-coordination are unlikely since the optimized Mo-S contacts are too short or too long respectively. Of the five-coordinate MoOS(SR)(2)X models, the ones with X = [OH](-) give computed M-L bond lengths in excellent agreement with the reported EXAFS data while X = H(2)O, NH(3), [CH(3)S](-), and O(2-) give relatively poor agreement. The theoretical results imply that the active site represents a stable, preferred geometry rather than some imposed entatic state.     

103Rh NMR chemical shifts in organometallic complexes: a combined experimental and density functional study

Experimental 103Rh NMR chemical shifts of mono- and binuclear rhodium(I) complexes containing s- or as-hydroindacenide and indacenediide bridging ligands with different ancillary ligands (1,5-cyclooctadiene, ethylene, carbonyl) are presented. A protocol, based on density functional theory calculations, was established to determine 103Rh NMR shielding constants in order to rationalise the effects of electronic and structural variations on the spectroscopic signal, and to gain insight into the efficiency of this computational method when applied to organometallic systems. Scalar and spin-orbit relativistic effects based on the ZORA (zeroth order regular approximation) level have been taken into account and discussed. A good agreement was found for model compounds over a wide range of chemical shifts of rhodium (approximately 10,000 ppm). This allowed us to discuss the experimental and calculated delta(103Rh) in larger complexes and to relate it to their electronic structure.     

Vibrational spectroscopy and density functional theory of transition-metal ion-benzene and dibenzene complexes in the gas phase

Metal-benzene complexes of the form M(benzene)(n) (M = Ti, V, Fe, Co, Ni) are produced in the gas-phase environment of a molecular beam by laser vaporization in a pulsed nozzle cluster source. These complexes are photoionized with an ArF excimer laser, producing the corresponding cations. The respective mono- and dibenzene complex ions are isolated in an ion-trap mass spectrometer and studied with infrared resonance enhanced multiple-photon dissociation (IR-REMPD) spectroscopy using a tunable free electron laser. Photodissociation of all complexes occurs by the elimination of intact neutral benzene molecules, and this process is enhanced on resonances in the vibrational spectrum, making it possible to measure vibrational spectroscopy for size-selected complexes. Vibrational bands in the 600-1700 cm(-1) region are characteristic of the benzene molecular moiety with systematic shifts caused by the metal bonding. The spectra in this solvent-free environment exhibit periodic trends in band shifts and intensities relative to the free benzene molecule that varies with the metal. Density functional theory calculations are employed to investigate the structures, energetics, and vibrational frequencies of these complexes. The comparison between experiment and theory provides fascinating new insight into the bonding in these prototypical organometallic complexes.     

Relativistic density functional theory study of dioxoactinide(VI) and -(V) complexation with alaskaphyrin and related Schiff-base macrocyclic ligands

Formation of complexes of alaskaphyrin 1, bi-pyen 2 and bi-tpmd 3 ligands with actinyl ions AnO2(n+), An = U, Np, Pu and n = 1, 2, was studied using density functional theory (DFT) within the scalar relativistic four-component approximation. The alaskaphyrin complexes of the uranyl are predicted to have a bent conformation, in contrast to the experimentally available X-ray data. This deviation is likely due to crystal packing effects. Apart from these conformational differences, calculated geometry parameters and vibrational frequencies are in agreement with the available experimental data. The character of bonding in the complexes is investigated using bond order analysis and extended transition states (ETS) energy decomposition. Metal-to-ligand bonds can be described as primarily ionic although substantial charge transfer is observed as well. Based on ETS analysis, it is shown that steric and/or fit/misfit requirements of actinyl cations to the ligand cavities, among the studied complexes, are the most favorable for the bi-pyen ligand 2, because its flexibility allows for optimal metal-to-donor-atom distances. Planarity of the equatorial coordination sphere of the actinide atom is found to be less important than the ability of a ligand to provide optimal uranium-to-nitrogen bond lengths. Experimental differences in demetalation rates between similar alaskaphyrin, bi-pyen and bi-tpmd uranyl complexes are explained as a result of easier protonation of the Schiff-base nitrogen of the latter. Reduction potentials calculated for the uranium complexes show a good agreement with the experiment, both in relative and in absolute terms.     

A theoretical study on the effect of intercalating sulfur atom and doping boron atom on the adsorption of hydrogen molecule on (10,0) single-walled carbon nanotubes

Adsorption of molecular hydrogen on single-walled carbon nanotube (SWCNT), sulfur-intercalated SWCNT (S-SWCNT), and boron-doped SWCNT (BSWCNT), have been studied by means of density functional theory (DFT). Two methods KMLYP and local density approximation (LDA) were used to calculate the binding energies. The most stable configuration of H₂ on the surface of pristine SWCNT was found to be on the top of a hexagonal at a distance of 3.54 Å in good agreement with the value of 3.44 Å reported by Han and Lee (Carbon, 2004, 42, 2169). KMLYP binding energies for the most stable configurations in cases of pristine SWCNT, S-SWCNT, and BSWCNT were found to be ?2.2 kJ mol^?1, ?3.5 kJ mol^?1, and ?3.5 kJ mol^?1, respectively, while LDA binding energies were found to be ?8.8 kJ mol^?1, ?9.7 kJ mol^?1, and ?4.1 kJ mol^?1, respectively. Increasing the polarizability of hydrogen molecule due to the presence of sulfur in sulfur intercalated SWCNT caused changes in the character of its bonding to sulfur atom and affected the binding energy. In H₂-BSWCNT system, stronger charge transfer caused stronger interaction between H₂ and BSWCNT to result a higher binding energy relative to the binding energy for H₂-SWCNT.