Molecules in electric fields

Finite field perturbation theory coupled with configuration interaction techniques have been used to evaluate the components of the polarisability tensor of H₂ at and near its equilibrium internuclear separation. The values are fitted to a polynomial which then yields the derivatives of the polarisability with respect to internuclear distance. Our results compare favourably with theoretical values obtained by the use of highly accurate correlated wavefunctions.     

Modeling the bacterial photosynthetic reaction center. 4. The structural, electrochemical, and hydrogen-bonding properties of 22 mutants of Rhodobacter sphaeroides

Site-directed mutagenesis has been employed by a number of groups to produce mutants of bacterial photosynthetic reaction centers, with the aim of tuning their operation by modifying hydrogen-bond patterns in the close vicinity of the "special pair" of bacteriochlorophylls P identical with P(L)P(M). Direct X-ray structural measurements of the consequences of mutation are rare. Attention has mostly focused on effects on properties such as carbonyl stretching frequencies and midpoint potentials to infer indirectly the induced structural modifications. In this work, the structures of 22 mutants of Rhodobacter sphaeroides have been calculated using a mixed quantum-mechanical molecular-mechanical method by modifying the known structure of the wild type. We determine (i) the orientation of the 2a-acetyl groups in the wild type, FY(M197), and FH(M197) series mutants of the neutral and oxidized reaction center, (ii) the structure of the FY(M197) mutant and possible water penetration near the special pair, (iii) that significant protein chain distortions are required to assemble some M160 series mutants (LS(M160), LN(M160), LQ(M160), and LH(M160) are considered), (iv) that there is competition for hydrogen-bonding between the 9-keto and 10a-ester groups for the introduced histidine in LH(L131) mutants, (v) that the observed midpoint potential of P for HL(M202) heterodimer mutants, including one involving also LH(M160), can be correlated with the change of electrostatic potential experienced at P(L), (vi) that hydrogen-bond cleavage may sometimes be induced by oxidation of the special pair, (vii) that the OH group of tyrosine M210 points away from P(M), and (viii) that competitive hydrogen-bonding effects determine the change in properties of NL(L166) and NH(L166) mutants. A new technique is introduced for the determination of ionization energies at the Koopmans level from QM/MM calculations, and protein-induced Stark effects on vibrational frequencies are considered.     

Binding energies of π- and “lone-pair”-levels in mono- and diaza-phenanthrenes and anthracenes: An He(I) photoelectron spectroscopic study

The He(I) photoelectron spectra of a number of monoaza and diaza derivatives of anthracene and phenanthrene, and also of the parent hydrocarbons, have     

Comparison of the effects of symmetric versus asymmetric H bonding on 2H and 17O nuclear quadrupole coupling constants: Application to formic acid and the hydrogen diformate anion

In this paper, we analyse the effects on the nuclear quadrupole coupling behaviour of ²H and ¹⁷O nuclei of a shift in H-bond character from asymmetric to symmetric. Using ab initio methods, the coupling amplitudes (nuclear quadrupole coupling constant e²_qQ/h) coupling anisotropies (asymmetry parameter η), and orientations of the electric field gradient (EFG) principal axis (PA) system of the H-bonded deuterium and oxygen nuclei in the formic acid dimer and related monomers, and the deuterium diformate anion are calculated. In addition, the relative contributions to the ²H and ¹⁷O EFGs of nuclear and electronic terms, and also the convergence of the EFG as a function of contributions from increasingly distant nuclei in the molecule are investigated. The trends in the calculated ¹⁷O EFGs on going from an asymmetric to a symmetric H-bonded environment are correlated with experimental nqr data in order to establish the hitherto unknown e²qQ/h sign, EFG assignments and PA orientation of symmetrically H-bonded oxygen. The possibility that the e²qQ/h value of deuterium is negative for symmetric H bonds is discussed, and difficulties in the computation of ²H EFGs for symmetric - as distinct from asymmetric - H-bonded systems are pointed out. In strong disagreement with assumptions in the literature, it is found that nearest neighbour terms do not dominate the ²H EFG in symmetrically H-bonded systems.     

Single molecule conductivity: the role of junction-orbital degeneracy in the artificially high currents predicted by ab initio approaches

A priori evaluations, using Hartree-Fock self-consistent-field (SCF) theory or density-functional theory (DFT), of the current passing between two electrodes through a single bridging molecule result in predicted conductivities that may be up to one to two orders of magnitude larger than observed ones. We demonstrate that this is, in part, often due to the improper application of the computational methods. Conductivity is shown to arise from tunneling between junction states of the electrodes through the molecule; these states are inherently either quasi two-fold or four-fold degenerate and always comprise the (highest occupied molecular orbital) HOMO band at the Fermi energy of the system. Frequently, in previous cluster based molecular conduction calculations, closed-shell SCF or Kohn-Sham DFT methods have been applied to systems that we demonstrate to be intrinsically open shell in nature. Such calculations are shown to induce artificial HOMO-LUMO (LUMO-lowest unoccupied molecular orbital) band splittings that Landauer-based formalisms for steady-state conduction interpret as arising from extremely rapid through-molecule tunneling at the Fermi energy, hence, overestimating the low-voltage conductivity. It is demonstrated that these shortcomings can be eliminated, dramatically reducing calculated current magnitudes, through the alternate use of electronic-structure calculations based on the spin-restricted open-shell formalism and related multiconfigurational SCF of DFT approaches. Further, we demonstrate that most anomalies arising in DFT implementations arise through the use of hybrid density functionals such as B3LYP. While the enhanced band-gap properties of these functionals have made them the defacto standard in molecular conductivity calculations, we demonstrate that it also makes them particularly susceptible to open-shell anomalies.     

Ionization potentials and donor properties of nucleic acid bases and related compounds

The first vertical ionization potentials of guanine, adenine, hypoxanthine, xanthine, cytosine, thymine, uracil and purine have been determined by HeI photoelectron spectroscopy. The potentials increase in the above order and are assigned to ionization from the highest π level. The experimental results are compared with valence shell SCF calculations, and the correlation between the association constants of these molecules with riboflavin and their donor properties is discussed. Detailed spectra will be presented and discussed in a forthcoming paper.     

An atomic diffraction theory of molecular photoionization cross sections

A theory of molecular photoionization cross sections is developed on the basis of locally atomic character of the one-electron final state in the Golden Rule expression for the molecular orbital cross section. Ionization amplitudes from several atomic centres are added and rotationally averaged to produce molecular orbital cross sections displaying a sum of pseudo-atomic cross sections weighted according to the LCAO composition of the orbital and also two-centre products reflecting interference effects. The atomic ionization amplitudes are obtained by use of an atomic central potential constructed by an inversion procedure from the form of the ground state orbital. The theory is of a simple chemical nature but usually of at least semi-quantitative accuracy. In this work we illustrate the nature of the two-centre interference effects in small diatomic molecules (H₂, HF, N₂).     

CeO<Subscript>2</Subscript> nanoparticle-modified electrode as a novel electrochemical interface in the quantification of Zn<Superscript>2+ </Superscript>ions at trace level: application to real sample analysis

A simple strategy has been proposed to quantify Zn²⁺ ions using CeO₂ nanoparticle-modified glassy carbon electrode. The CeO₂ nanoparticles were prepared by sucrose-nitrate decomposition method, and it was characterized by X-ray diffraction (XRD), FT-IR, TEM, and surface area analyzer. The synthesized CeO₂ nanoparticles were used as modifier molecules as a thin film on glassy carbon electrode (GCE) in the trace level quantification of Zn²⁺ by using cyclic voltammetry (CV) and differential pulse anodic stripping voltammetry (DPASV) techniques. The fabricated sensor exhibited a good analytical response towards Zn²⁺ ions. The modified electrode showed a wide linearity in the concentration range 20–380 μg L^?1 with a limit of detection 0.36 μg L^?1. The proposed electrochemical sensor was successfully applied to trace level Zn²⁺ quantification from real sample matrices.     

Ground-state energies of mono-, di-, tri- and tetranegative ions of porphins and their metal complexes

From a range of porphin and metal porphin molecules, mono-, di-, tri- and tetranegative ions can be formed in solution. The disproportionation energies of these ions, measured byHush andClack [6] in dimethylformamide, show similar patterns. For the mononegative and trinegative ions, the disproportion of energies are of comparable magnitudes, but the disproportionation energy of the dinegative ion is 0.3 – 0.4 eV more positive. If it is assumed that the electrons are successively filling the lowest vacant orbital (e _g inD _4h ) these results can be rationalized. In particular, if it is assumed that the dinegative ion is spin-paired, with ground-state electronic symmetryB _1g inD _4h , the average difference of 0.3 – 0.4 eV mentioned above should approximate to twice the exchange integral in the antibondinge _g orbital. Calculation of this integral for a number of porphin structures gives good agreement with experiment.

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Zusammenfassung Von einer Reihe von Porphin- und Metallporphinmolekülen können ein-, zwei-, drei- und vierfach negativ geladene Ionen in Lösung hergestellt werden. Die Disproportionierungsenergien dieser Ionen, vonHush undClack [6] in Dimethylformamid gemessen, zeigen ähnliche Struktur. Für die ein- und dreifach negativ geladenen Ionen ist die Disproportionierungsenergie etwa gleich, dagegen für das zweifach negativ geladene Ion 0,3 – 0,4 eV positiver. Wenn man annimmt, daß die Elektronen nacheinander das tiefste unbesetzte Orbital (e _g inD _4h) auffüllen, können diese Ergebnisse erklärt werden. Wenn man insbesondere annimmt, daß das zweifach negativ geladene Ion als Grundzustand einen Singulettzustand der SymmetrieB _1g inD _4h besitzt, ist die oben erwähnte mittlere Differenz von 0,3 – 0,4 eV angenähert doppelt so groß wie das Austauschintegral im antibindendene _g-Orbital. Berechnung dieses Integrals für eine Anzahl Porphinstrukturen ergibt gute Übereinstimmung mit dem Experiment.

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Résumé Une série de porphines et porphines métallés forment des ions mono-, di, tri- et tétranégatifs en solution. Les énergies de disproportionation dans dimethylformamide, présentant de similitudes [6], sont comparables pour les ions mono- et trinégatifs, mais 0,3 – 0,4 eV plus positif pour l'ion dinégatif. Ces résultats sont compréhensibles dans un schéma où les électrons occupent successivement l'orbitale vide la plus basse (e _g en symétrieD _4h ). En particulier, si l'on adopte l'état fondamentalB _1g (enD _4h) aux spins antiparallèles, pour l'ion dinégatif, les 0,3 – 0,4 eV valent approximativement deux fois l'intégrale d'échange pour l'orbitalee _g antiliante. Le calcul de cette intégrale pour une série de porphines s'accorde bien à l'expérience.

     

Finite-field method calculations. IV. Higher-order moments,dipole moment gradients,polarisability gradients and field-induced shifts in molecular properties: Application to N2, CO,CN−, HCN and HNC

In this paper, theoretical methods developed in III are applied in calculating polarisabilities, polarisability gradients and field-induced shifts, by the finite-field method. Values of dipole moment gradients and higher-order moments, calculated from the unperturbed wavefunctions, are also reported. Results for N₂, CO, CN^?, HCN and HNC have been obtained at the SCF level; some CI results for the N₂ polarisability components and moments and for the dipole moment gradients of HCN are also given. The calculated polarisability gradients and dipole moment gradients have been used to estimate the Raman scattering intensities and depolarisation ratios and the IR absorption intensities. Model calculations of field-induced shifts in bond length, vibrational levels, spectroscopic constants, force constants and dipole moment gradient are reported for N₂ and CO.The discrepancy between the SCF and experimental bond dipole moment gradients for HCN, previously noted in the literature, has been re-examined and resolved by our CI results.