Is the problem of molecular structure just the quantum measurement problem?

In a recent article entitled “The problem of molecular structure just is the measurement problem”, Alexander Franklin and Vanessa Seifert argue that insofar as the quantum measurement problem is solved, the problems of molecular structure are resolved as well. The purpose of the present article is to show that such a claim is too optimistic. Although the solution of the quantum measurement problem is relevant to how the problem of molecular structure is faced, such a solution is not sufficient to account for the structure of molecules as understood in the field of chemistry.

     

Is the FeC cluster linear? Theoretical study of the equilibrium structure and bonding of FeC

Ab initio electron correlation methods and density functional theory are used to investigate the structure, bonding, and stability of FeC. Theoretical calculations show that the ground state of the FeC anion strongly depends on the level of theory. The linear ⁴Σ^? state with an open configuration δ²σ¹ is predicted to be the ground state of FeC at the coupled‐cluster theory restricted to single, double, and noniterative triple excitations (CCSD[T])//CISD and multireference (MR) second‐order Moller–Plesset (MP2)//CAS self‐consistent field (SCF) levels. Next stable conformations are a C_2V ring structure II (⁴B₂) and a C_2V structure III (⁴A₂) in which Fe is bonded to one carbon atom of a triangular C₃. However, CISD and CCSD//CISD calculations show that the C_2V ring structure II and the C_2V structure III are more slightly stable than is the linear structure I of FeC. The harmonic vibrational frequencies and relevant vertical electron binding energies are reported. Possible detachment transitions in the photoelectron spectrum of FeC are discussed on the basis of current calculations. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 275–279, 2003     

Mini-review on the functionalization of C–H bond to C-X linkage via metalla-electrocatalyzed tool

To date, the C–H activation protocol and its functionalization of bonds via transition metal have witnessed major attention in coordination chemistry as they eliminate the pre-functionalization of the substrate. Conventional approaches use a stoichiometric amount of chemical oxidants which are toxic under mild conditions. This will create a major problem in C–H functionalization reactions that involve a selective issue of reductive elimination from metal center to form a significant amount of by-product (waste) in large amount which is difficult to separate and thus reduce atom economy and sustainability of the reaction medium. This will limit catalyst turnover and thus, decreases the reaction rate. To avoid this, there is an urgent need for renewable resources which bring about the functionalization of the C–H bond. Metalla-electro catalyzed is the cleanest tool on the platform of C–H activation chemistry. Here, electricity was being involved as a clean surrogate of chemical oxidant and holds unleashed potential for an oxidative protocol of C–H activation with unmet site selectivity. This mini-review pay attention to the C–H functionalization of the bond to C–C, C–N, and C-Miscellaneous (P, O, and S) bond linkage by employing different transition metal {precious (Pd, Rh, Ru, and Ir)} and {earth-abundant (Mn, Ni, Co, and Cu)} using the electrochemical tool. Such metalla-electro catalyzed tools are helpful to those who were not being trained electrochemists but can unleash this potential benefit in various sustainable organic transformations.     

Is the dynamical polarization a significant part of the contribution of the triples to the correlation energy?

One may call dynamical polarization of doubly excited configurations the energy lowering of these configurations under the response of the other electrons to the so-created fluctuation of the electric field. This contribution of triply excited configurations may be identified and calculated through a computation that only requires a computation time proportional to the sixth power of the number of molecular orbitals (MOs), instead of the seventh power for the total contribution of the triples. Its amplitude depends on the choice of the MOs and becomes important when localized MOs are used.     

What is the structure of the RecA-DNA filament?

The bacterial RecA protein has been a model system for understanding how a protein can catalyze homologous genetic recombination. RecA-like proteins have now been characterized from many organisms, from bacteriophage to humans. Some of the RecA-like proteins, including human RAD51, appear to function as helical filaments formed on DNA. However, we currently have high resolution structures of inactive forms of the protein, and low resolution structures of the active complexes formed by RecA-like proteins on DNA in the presence of ATP or ATP analogs. Within a crystal of the E. coli RecA protein, a helical polymer exists, and it has been widely assumed that this polymer is quite similar to the active helical filament formed on DNA. Recent developments have suggested that this may not be the case.     

Does the topological approach characterize the hydrogen bond?

 The topological analysis of the electron localization function has been applied to complexes representative of the weak, medium and strong hydrogen bond. For both the weak and the medium hydrogen bonds, the number of basins in the complexes is the sum of those of the moieties. In this case, the formation of a weak or a medium hydrogen-bonded complex does not involve a chemical reaction. In the weak hydrogen bond case, the reduction of the localization domain yields two domains in the first step, which can be partitioned afterwards into valence and core domains. In contrast, for medium complexes the core–valence separation is the first event which occurs during the reduction process and therefore the complex should be considered as a single molecular species. Moreover, the analysis of the basin population variance indicates in this case a noticeable delocalization between the V(A, H) and V(B) basins. Finally, the symmetrical strong hydrogen bond has a protonated basin V(H) at the bond midpoint. Such a topology corresponds to an incomplete proton transfer and to a rather covalent bond. Received: 19 April 1999 / Accepted: 22 July 1999 / Published online: 17 January 2000     

Development of sample preparation technique to characterize chemical structure of humin by synchrotron-radiation–based X-ray photoelectron spectroscopy

Carbon-binding state of humin (HM, a non-conductive insoluble organo-mineral humic substance) was successfully characterized for the first time by synchrotron-radiation–based X-ray photoelectron spectroscopy (XPS). Four sample preparation techniques—HM on double-sided carbon tape, indium sheet, copper mesh, and in pellet formed from the mixture of HM and copper powder (Cu) at different mixing ratios (1:1, 1:2, and 1:6 v/v)—were compared. The results show that HM samples prepared using the first three methods had significant charge buildup, which made the interpretation of the XPS spectra impossible because of the shifts in the binding energy of C 1s XPS spectra. Pellets of HM:Cu mixture enhanced the electrical conductivity and reduced charge buildup on the sample surface. Pellets prepared with HM:Cu ratio of 1:1 (v/v) provided the minimum charge buildup and high sensitivity with difference in C 1s spectra regardless of the observing position. The C 1s spectra, estimated by the subtraction of the carbon contamination in Cu, showed the resolution of CC (284.0 eV), C C/C H (285.1 eV), C O (286.3 eV), CO (287.3 eV), and OC O (288.3 eV) and three additional peaks of CF (289.3 eV), CF₂ (290.2 eV), and CF₃ (291.4 eV). Soft X-ray absorption spectroscopic (XAS) analysis further proved the existence of fluoride (F 1s) in HM structure. The detection of fluorinated carbon in HM showed a great advancement of XPS compared with other conventional analyses. X-ray with the incident angle of 0° provided the smallest (nearly negligible) energy shift in the C 1s spectra of HM and did not damage the surface of the sample.     

A synthetic approach to the phorboxazoles – Synthesis of the C20–C32 central core

An enantiospecific synthesis of the C20–C32 central core of the phorboxazole scaffold, including the non-macrocyclic oxazole is detailed in 17 steps (longest linear sequence) from methacrolein in 7.8% overall yield. All of the stereocenters are communicated from a single Evans aldol reaction, and the final compound is suitably functionalized for further elaboration to the natural products.     

Is the allylpalladium structure altered between solid and solutions?

Recent EXAFS measurements on [(Ph(2)PCH(2)CH(2)PPh(2))Pd(H(2)CCHCMe(2))]O(3)SCF(3) (Tromp et al. J. Am. Chem. Soc. 2002, 124, 14814) were interpreted as evidence that, when the complex is dissolved in THF, the allyl ligand adopts an eta(2) structure with a dangling allyl CH(2) substituent. DFT calculations of the Pd complex using H(2)P-CH(2)CH(2)-PH(2) as a model for Ph(2)P-CH(2)CH(2)-PPh(2) (dppe), in the absence or the presence of the triflate counteranion, and modeling the THF solvent by explicit Me(2)O molecules or by a continuum model give always a conventional eta(3)-H(2)CCHCMe(2) structure with equal Pd-C bonds to the terminal carbon centers of the allyl. QM/MM calculations using the dppe ligand also fail to support an eta(2)-allyl structure as a global minimum. The EXAFS parameter space is shown to have multiple minima. These have very similar overall EXAFS, but have very different structural parameters. The minimum that was the basis for the previous structural conclusion gives a slightly better fit but has unrealistic Debye-Waller factors and threshold energies.     

Is the mechanism of the proline-catalyzed enantioselective aldol reaction related to biochemical processes ?

The enantioselectivity shown by the title reaction is explained by an intramolecular hydrogen bond in an enamine intermediate resulting from nucleophilic catalysis by one molecule of proline and by a proton transfer mediated by a second molecule of proline.     

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations

Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches (“SP”, “only H”, “full”, “full+cell”) of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc.     

1H–13C HMBC NMR experiments as a structural and analytical tool for the characterization of elusive trans/cis hydroperoxide isomers from oxidized unsaturated fatty acids in solution

The radical-dependent oxidation of unsaturated fatty acids is a fundamental reaction in lipid chemistry, biochemistry, and technology. We report herein the first successful application of ¹H–¹³C HMBC NMR experiment for the identification and quantification of complex and minor (3.9% to 0.85%) components of cis and trans primary hydroperoxide isomers of oxidized oleate and linoleate methyl esters in solution, without the need of laborious isolation of the individual components.     

Is the stereomutation of methane possible?

Large basis set ab initio calculations at correlated levels, including MP2, single reference, as well as multireference configuration interaction, carried out on the methane potential energy surface, have located and characterized a transition structure for stereomutation (one imaginary frequency). This structure is best described as a pyramidal complex between singlet methylene and a side-on hydrogen molecule with C_s symmetry. At the single reference CI level, it lies 105 kcal/mol above the methane T_d-ground state but is stable relative to dissociation into CH₂(¹A₁) and H₂ by 13 kcal/mol at 0 K (with harmonic zero point energy (ZPE) corrections for all structures). Dissociation of the transition state into triplet methylene and hydrogen also is endothermic (by 4 kcal/mol), but single bond rupture to give CH and H^. is 3 kcal/mol exothermic. Thus, it does not appear likely that methane can undergo stereomutation classically beneath the dissociation limit. Confirming earlier conclusions, side-on insertion of ¹A₁ CH₂ into H₂ in a perpendicular geometry occurs without activation energy. Planar (D_4h) methane (130.5 kcal/mol) has four imaginary frequencies. Two of these are degenerate and lead to equivalent planar C_2v structures with one three-center, two-electron bond and two two-electron bonds and two imaginary frequencies. The remaining imaginary frequencies of the D_4h form lead to tetrahedral (T_d) and pyramidal (C_4v) methane. The latter has three negative eigenvalues in the force-constant matrix; one of these leads to the T_d global minimum and the other to the C_s (parallel) stereomutation transition structure. Multireference CI calculations with a large atomic natural orbitals basis set produce similar results, with the electronic energy of the C_s stereomutation transition state 0.7 ± 0.5 kcal/mol higher than that of CH + H^. dissociation products, and a ZPE-corrected energy which is 5 ± 1 kcal/mol higher. Also considered are photochemical pathways for stereomutation and the possible effects of nuclear spin, inversion tunneling, and the parity-violating weak nuclear interaction on the possibility of an experimental detection of stereomutation in methane. © 1995 by John Wiley & Sons, Inc.     

Theoretical investigation to characterize the inclusion complex of α-lipoic acid and β-cyclodextrin

We simulated the docking of α-lipoic acid (α-LA) in β-cyclodextrin (β-CD) using two models. We considered in this study complexes formed by 1:1 host–guest stoichiometry in vacuo and in aqueous phase, using PM6, DFT and ONIOM2 hybrid calculations. The results obtained with PM6 method clearly indicate that the complexes formed are energetically favored with or without solvent, model 2 (α-LA entering the cavity of β-CD from its wide side by COOH group) is found more favored than model 1 (α-LA entering into the cavity of β-CD from its wide side by cyclic group), the preference being greater in the case of ONIOM2 calculations. In addition, NBO analysis gives that mutual interactions between the donor and acceptor orbitals of α-lipoic acid and β-CD plays an important role to the stabilization of such a complex. Finally, ¹H nuclear magnetic resonance (NMR) chemical shifts of free and complexed α-LA were calculated by the Gauge-Including Atomic Orbital (GIAO) method and compared with available experimental data. The results of GIAO calculations were analyzed and discussed.     

Is the methanation reaction over Ru single crystals structure dependent?

The influence of monoatomic steps and defects on the methanation reaction over ruthenium has been investigated. The experiments are performed on a Ru(0 1 54) ruthenium single crystal, which contains one monoatomic step atom for each 27 terrace atoms. The methanation activity is measured at one bar of hydrogen and CO in a high pressure cell, which enables simultaneous measurements of the local reactivity of the well defined single crystal surface and the global reactivity of the entire crystal and its auxiliary support. By adding sulfur we observe that the measured activity from the well defined stepped front-side of the crystal is poisoned faster than the entire crystal containing more defects. We also observe that additional sputtering of the well-defined front-side increases the reactivity measured on the surface. Based on this, we conclude that the methanation reaction takes place on undercoordinated sites, such as steps and kinks, and that the methanation reaction is extremely structure dependent. Simulations of the flow, temperature, and product distributions in the high pressure cell are furthermore presented as supplementary information.     

Is the 31P chemical shift anisotropy of aluminophosphates a useful parameter for NMR crystallography?

The ³¹P chemical shift anisotropy (CSA) offers a potential source of new information to help determine the structures of aluminophosphate (AlPO) framework materials. We investigate how to measure the CSAs, which are small (span of ~20–30 ppm) for AlPOs, demonstrating the need for CSA-amplification experiments (often in conjunction with ²⁷Al and/or ¹H decoupling) at high magnetic field (20.0 T) to obtain accurate values. We show that the most shielded component of the chemical shift tensor, δ₃₃, is related to the length of the shortest P─O bond, whereas the more deshielded components, δ₁₁ and δ₂₂ can be related more readily to the mean P─O bond lengths and P─O─Al angles. Using the case of Mg-doped STA-2 as an example, the CSA is shown to be much larger for P(OAl)_4–n(OMg)_n environments, primarily owing to a much shorter P─O(Mg) bond affecting δ₃₃, however, because the mean P─O bond lengths and P─O─T (T = Al, Mg) bond angles do not change significantly between P(OAl)₄ and P(OAl)_4–n(OMg)_n sites, the isotropic chemical shifts for these species are similar, leading to overlapped spectral lines. When the CSA information is included, spectral assignment becomes unambiguous, therefore, although the specialist conditions required might preclude the routine measurement of ³¹P CSAs in AlPOs, in some cases (particularly doped materials), the experiments can still provide valuable additional information for spectral assignment.     

Is Curcumin the Answer to Future Chemotherapy Cocktail?

The rise in cancer cases in recent years is an alarming situation worldwide. Despite the tremendous research and invention of new cancer therapies, the clinical outcomes are not always reassuring. Cancer cells could develop several evasive mechanisms for their survivability and render therapeutic failure. The continuous use of conventional cancer therapies leads to chemoresistance, and a higher dose of treatment results in even greater toxicities among cancer patients. Therefore, the search for an alternative treatment modality is crucial to break this viscous cycle. This paper explores the suitability of curcumin combination treatment with other cancer therapies to curb cancer growth. We provide a critical insight to the mechanisms of action of curcumin, its role in combination therapy in various cancers, along with the molecular targets involved. Curcumin combination treatments were found to enhance anticancer effects, mediated by the multitargeting of several signalling pathways by curcumin and the co-administered cancer therapies. The preclinical and clinical evidence in curcumin combination therapy is critically analysed, and the future research direction of curcumin combination therapy is discussed.     

Topological transformation of the phase diagram of the lithium nitrate-water-acetonitrile ternary system within the range of −20 to 50°C

Phase equilibria and critical phenomena in the lithium nitrate-water-acetonitrile ternary system were studied by a visual polythermal method within the range of ?20 to 50°C. In this ternary system, the constituent liquid binary system is characterized by phase separation with an upper critical solution temperature. It was found that the ternary system undergoes phase separation at temperatures below 0.7°C. In the phase diagram within the range of ?1.1 to 0.7°C, a closed phase separation region with two critical points was revealed. The temperature of the formation of the critical tie line of the monotectic state the solid phase of which is the crystalline hydrate LiNO₃ · 3H₂O was determined (?18.7°C). Depending on the concentration, lithium nitrate has both salting-in and salting-out effect on aqueous acetonitrile mixtures. The plotted isothermal sections of the temperature-concentration prism of the system at fifteen temperatures showed the pattern of the topological transformation of its phase diagram with varying temperature.