Connecting Discrete Stereoclusters by Using DFT and NMR Spectroscopy: The Case of Nivariol

The structural determination of small organic molecules is mainly undertaken by using NMR techniques, although it is increasingly supplemented by using computational methods. NMR parameters, such as chemical shifts and coupling constants, are extremely sensitive indicators of local molecular conformation and are a source of structural evidence. However, their interpretation is fairly challenging in many circumstances, such as the case of the new polyether squalene derivative nivariol, the structure of which was elucidated by means of NMR spectroscopy and DFT calculations. The potential flexibility of this molecule and the high number of quaternary carbon atoms that it contains make its configurational assignment very difficult. Moreover, the relative configuration of four separated stereoclusters was established and subsequently connected by using NOE and J‐based analysis, as well as by a comparison of its experimental ¹³C NMR chemical shifts with the corresponding population‐weighted values, as calculated by using DFT methods. Limitations of these used approaches became apparent but were overcome by combining the two methods.     

Gas-phase infrared photodissociation spectroscopy of tetravanadiumoxo and oxo-methoxo cluster anions.

The infrared spectra of the binary vanadium oxide cluster anions V(4)O(9)(-) and V(4)O(10)(-) and of the related methoxo clusters V(4)O(9)(OCH(3))(-) and V(4)O(8)(OCH(3))(2)(-) are recorded in the gas phase by photodissociation of the mass-selected ions using an infrared laser. For the oxide clusters V(4)O(9)(-) and V(4)O(10)(-), the bands of the terminal vanadyl oxygen atoms, nu(V-O(t)), and of the bridging oxygen atoms, nu(V-O(b)-V), are identified clearly. The clusters in which one or two of the oxo groups are replaced by methoxo ligands show additional absorptions which are assigned to the C-O stretch, nu(C-O). Density functional calculations are used as a complement for the experimental studies and the interpretation of the infrared spectra. The results depend in an unusual way on the functional employed (BLYP versus B3LYP), which is due to the presence of both V-O(CH(3)) single and V=O double bonds as terminal bonds and to the strong multireference character of the latter.     

The Geometric Structure of Silver‐Doped Silicon Clusters

Cationic silver‐doped silicon clusters, Si_nAg⁺ (n=6–15), are studied using infrared multiple photon dissociation in combination with density functional theory computations. Candidate structures are identified using a basin‐hopping global optimizations method. Based on the comparison of experimental and calculated IR spectra for the identified low‐energy isomers, structures are assigned. It is found that all investigated clusters have exohedral structures, that is, the Ag atom is located at the surface. This is a surprising result because many transition‐metal dopant atoms have been shown to induce the formation of endohedral silicon clusters. The silicon framework of Si_nAg⁺ (n=7–9) has a pentagonal bipyramidal building block, whereas the larger Si_nAg⁺ (n=10–12, 14, 15) clusters have trigonal prism‐based structures. On comparing the structures of Si_nAg⁺ with those of Si_nCu⁺ (for n=6–11) it is found that both Cu and Ag adsorb on a surface site of bare Si_n⁺ clusters. However, the Ag dopant atom takes a lower coordinated site and is more weakly bound to the Si_n⁺ framework than the Cu dopant atom.     

Far‐Infrared Spectra of Yttrium‐Doped Gold Clusters AunY (n=1–9)

The geometric, spectroscopic, and electronic properties of neutral yttrium‐doped gold clusters Au_nY (n=1–9) are studied by far‐infrared multiple photon dissociation (FIR‐MPD) spectroscopy and quantum chemical calculations. Comparison of the observed and calculated vibrational spectra allows the structures of the isomers present in the molecular beam to be determined. Most of the isomers for which the IR spectra agree best with experiment are calculated to be the energetically most stable ones. Attachment of xenon to the Au_nY cluster can cause changes in the IR spectra, which involve band shifts and band splittings. In some cases symmetry changes, as a result of the attachment of xenon atoms, were also observed. All the Au_nY clusters considered prefer a low spin state. In contrast to pure gold clusters, which exhibit exclusively planar lowest‐energy structures for small sizes, several of the studied species are three‐dimensional. This is particularly the case for Au₄Y and Au₉Y, while for some other sizes (n=5, 8) the 3D structures have an energy similar to that of their 2D counterparts. Several of the lowest‐energy structures are quasi‐2D, that is, slightly distorted from planar shapes. For all the studied species the Y atom prefers high coordination, which is different from other metal dopants in gold clusters.     

Low-lying excited states and primary photoproducts of [Os3(CO)10(s-cis-L)] (L=cyclohexa-1,3-diene, buta-1,3-diene)] clusters studied by picosecond time-resolved UV/Vis and IR spectroscopy and by density functional theory

Combined picosecond transient absorption and time-resolved infrared studies were performed, aimed at characterising low-lying excited states of the cluster [Os(3)(CO)(10)(s-cis-L)] (L=cyclohexa-1,3-diene, 1) and monitoring the formation of its photoproducts. Theoretical (DFT and TD-DFT) calculations on the closely related cluster with L=buta-1,3-diene (2') have revealed that the low-lying electronic transitions of these [Os(3)(CO)(10)(s-cis-1,3-diene)] clusters have a predominant sigma(core)pi*(CO) character. From the lowest sigmapi* excited state, cluster 1 undergoes fast Os-Os(1,3-diene) bond cleavage (tau=3.3 ps) resulting in the formation of a coordinatively unsaturated primary photoproduct (1 a) with a single CO bridge. A new insight into the structure of the transient has been obtained by DFT calculations. The cleaved Os-Os(1,3-diene) bond is bridged by the donor 1,3-diene ligand, compensating for the electron deficiency at the neighbouring Os centre. Because of the unequal distribution of the electron density in transient 1 a, a second CO bridge is formed in 20 ps in the photoproduct [Os(3)(CO)(8)(micro-CO)(2)(cyclohexa-1,3-diene)] (1 b). The latter compound, absorbing strongly around 630 nm, mainly regenerates the parent cluster with a lifetime of about 100 ns in hexane. Its structure, as suggested by the DFT calculations, again contains the 1,3-diene ligand coordinated in a bridging fashion. Photoproduct 1 b can therefore be assigned as a high-energy coordination isomer of the parent cluster with all Os-Os bonds bridged.     

Two‐Dimensional Infrared Spectroscopy Reveals the Structure of an Evans Auxiliary Derivative and Its SnCl4 Lewis Acid Complex

Determining the structure of reactive intermediates is the key to understanding reaction mechanisms. To access these structures, a method combining structural sensitivity and high time resolution is required. Here ultrafast polarization‐dependent two‐dimensional infrared (P2D‐IR) spectroscopy is shown to be an excellent complement to commonly used methods such as one‐dimensional IR and multidimensional NMR spectroscopy for investigating intermediates. P2D‐IR spectroscopy allows structure determination by measuring the angles between vibrational transition dipole moments. The high time resolution makes P2D‐IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short‐lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei. Here we illustrate the strengths of P2D‐IR by determining the conformation of a Diels–Alder dienophile that carries the Evans auxiliary and its conformational change induced by the complexation with the Lewis acid SnCl₄, which is a catalyst for stereoselective Diels–Alder reactions. We show that P2D‐IR in combination with DFT computations can discriminate between the various conformers of the free dienophile N‐crotonyloxazolidinone that have been debated before, proving antiperiplanar orientation of the carbonyl groups and s‐cis conformation of the crotonyl moiety. P2D‐IR unequivocally identifies the coordination and conformation in the catalyst–substrate complex with SnCl₄, even in the presence of exchange that is fast on the NMR time scale. It resolves a chelate with the carbonyl orientation flipped to synperiplanar and s‐cis crotonyl configuration as the main species. This work sets the stage for future studies of other catalyst–substrate complexes and intermediates using a combination of P2D‐IR spectroscopy and DFT computations.     

A New Quantum Chemical Approach to the Magnetic Properties of Oligonuclear Transition‐Metal Complexes: Application to a Model for the Tetranuclear Manganese Cluster of Photosystem II

Broken‐symmetry DFT calculations on transition‐metal clusters with more than two centers allow the hyperfine coupling constants to be extracted. Application of the proposed theoretical scheme to a tetranuclear manganese complex that models the S₂ state of the oxygen‐evolving complex of photosystem II yields hyperfine parameters that can be directly compared with experimental data. The picture shows the metal–oxo core of the model and the following parameters; exchange coupling constant J_ij, the expectation value of the site‐spin operator , and the isotropic hyperfine coupling parameters.

     

Density Functional Calculations of 55Mn, 14N and 13C Electron Paramagnetic Resonance Parameters Support an Energetically Feasible Model System for the S2 State of the Oxygen‐Evolving Complex of Photosystem II

Metal and ligand hyperfine couplings of a previously suggested, energetically feasible Mn₄Ca model cluster ( SG2009^?1 ) for the S₂ state of the oxygen‐evolving complex (OEC) of photosystem II (PSII) have been studied by broken‐symmetry density functional methods and compared with other suggested structural and spectroscopic models. This was carried out explicitly for different spin‐coupling patterns of the S=1/2 ground state of the Mn^III(Mn^IV)₃ cluster. By applying spin‐projection techniques and a scaling of the manganese hyperfine couplings, computation of the hyperfine and nuclear quadrupole coupling parameters allows a direct evaluation of the proposed models in comparison with data obtained from the simulation of EPR, ENDOR, and ESEEM spectra. The computation of ⁵⁵Mn hyperfine couplings (HFCs) for SG2009^?1 gives excellent agreement with experiment. However, at the current level of spin projection, the ⁵⁵Mn HFCs do not appear sufficiently accurate to distinguish between different structural models. Yet, of all the models studied, SG2009^?1 is the only one with the Mn^III site at the Mn_C center, which is coordinated by histidine (D1‐His332). The computed histidine ¹⁴N HFC anisotropy for SG2009^?1 gives much better agreement with ESEEM data than the other models, in which Mn_C is an Mn^IV site, thus supporting the validity of the model. The ¹³C HFCs of various carboxylates have been compared with ¹³C ENDOR data for PSII preparations with ¹³C‐labelled alanine.     

Experimental and Theoretical Evidence for an Agostic Interaction in a Gold(III) Complex

The first agostic interaction in a gold complex is described. The presence of a bonding C?H???Au interaction in a cationic “tricoordinate” gold(III) complex was suggested by DFT calculations and was subsequently confirmed by NMR spectroscopy at low temperature. The agostic interaction was analyzed computationally using NBO and QTAIM analyses (NBO=natural bond orbital; QTAIM=quantum theory of atoms in molecules).     

1，2，5-噻重氮和1，4-二正戊氧基苯环化的自由四氮杂卟啉及其金属镁配合物的结构和性质：密度泛函理论计算

用DFT方法计算分析了1，2，5-噻重氮和1，4-二正戊氧基苯环化的自由四氮杂卟啉及其金属镁配合物的分子和电子结构，理论计算的键参数和单晶结构测定结果一致。进一步对1，2，5-噻重氮和1，4-二正戊氧基苯环化的自由四氮杂卟啉的红外光谱进行了正则坐标分析和光谱模拟，以及用TD-DFT方法对1，2，5-噻重氮和1，4-二正戊氧基苯环化的四氮杂卟啉金属镁配合物的电子吸收光谱进行了分析和谱峰归属，比较了四氮杂卟啉环上取代基的电子性质对四氮杂卟啉衍生物光谱性质的影响。     

Vibrational structure of endohedral fullerene Sc3N@C78 (D3h'): evidence for a strong coupling between the Sc3N cluster and C78 cage.

The vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) is studied by FTIR spectroscopy, Raman spectroscopy and DFT-based quantum chemical calculations. Remarkably good agreement between experimental and calculated spectra is achieved and a full assignment of the Sc(3)N-based vibrational modes is given. Significant differences in the vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) and the empty, charged C(78) (6-): 5 (D(3h)') are rationalized by the strong coupling between the Sc(3)N cluster and the fullerene cage. This coupling has its origin in a significant overlap of the Sc(3)N and C(78) molecular orbitals, and causes atomic-charge and bond-length redistributions compared to the neutral C(78) and the C(78) (6-) anion. An ionic model is not sufficient to describe the electronic, geometric and vibrational structure of the Sc(3)N@C(78) nitride cluster fullerene.     

Toward the complete prediction of the 1H and 13C NMR spectra of complex organic molecules by DFT methods: application to natural substances

The NMR parameters (1H and 13C chemical shifts and coupling constants) for a series of naturally occurring molecules have been calculated mostly with DFT methods, and their spectra compared with available experimental ones. The comparison includes strychnine as a test case, as well as some examples of recently isolated natural products (corianlactone, daphnipaxinin, boletunone B) featuring unusual and/or crowded structures and, in the case of boletunone B, being the subject of a recent revision. Whenever experimental spectra were obtained in polar solvents, the calculation of NMR parameters was also carried out with the Integral Equation-Formalism Polarizable Continuum Model (IEF-PCM) continuum method. The computed results generally show a good agreement with experiment, as judged not only by statistical parameters but also by visual comparison of line spectra. The origin of the remaining discrepancies is attributed to the incomplete modeling of conformational and specific solvent effects.