Response of the mechanical and chiral character of ethane to ultra-fast laser pulses.

A pair of simulated left and right circularly polarized ultra-fast laser pulses of duration 20 femtoseconds that induce a mixture of excited states are applied to ethane. The response of the electron dynamics is investigated within the next generation quantum theory of atoms in molecules (NG-QTAIM) using third-generation eigenvector-trajectories which are introduced in this work. This enables an analysis of the mechanical and chiral properties of the electron dynamics of ethane without needing to subject the C-C bond to external torsions as was the case for second-generation eigenvector-trajectories. The mechanical properties, in particular, the bond-flexing and bond-torsion were found to increase depending on the plane of the applied laser pulses. The bond-flexing and bond-torsion, depending on the plane of polarization, increases or decreases after the laser pulses are switched off. This is explainable in terms of directionally-dependent effects of the long-lasting superpositions of excited states. The chiral properties correspond to the ethane molecule being classified as formally achiral consistent with previous NG-QTAIM investigations. Future planned investigations using ultra-fast circularly polarized lasers are briefly discussed.

Low-Coordinate Magnesium Sulfide and Selenide Complexes.

The reactions of [{(iPrDipNacNac)Mg}2] 1 (iPrDipnacnac = HC(iPrCNDip)2) with Ph3P═O at 100 °C afforded the phosphinate complex [(iPrDipNacNac)Mg(OPPh3)(OPPh2)] 3. Reactions of 1 with Ph3P═E (E = S, Se) proceeded rapidly at room temperature to low-coordinate chalcogenide complexes [{(iPrDipNacNac)Mg}2(µ-S)] 4 and [{(iPrDipNacNac)Mg}2(µ-Se)] 5, respectively. Similarly, reactions of RNHC═S ((MeCNR)2C═S with R = Me, Et, or iPr) with 1 afforded NHC adducts of magnesium sulfide complexes, [{(iPrDipNacNac)Mg(RNHC)}(µ-S){Mg(iPrDipNacNac)}] 6, that could alternatively be obtained by adding the appropriate RNHC to sulfide complex 4. Complex 4 reacted with 1-adamantylazide (AdN3) to give [{(iPrDipNacNac)Mg}2(µ-SN3Ad)] 7 and can form various simple donor adducts in solution, of which [(iPrDipNacNac)Mg(OAd)}2(µ-S)] 8a (OAd = 2-adamantanone) was structurally characterized. The nature of the ionic Mg-E-Mg unit is described by solution and solid-state studies of the complexes and by DFT computational investigations.

Scoring molecular wires subject to an ultrafast laser pulse for molecular electronic devices.

A nonionizing ultrafast laser pulse of 20-fs duration with a peak amplitude electric-field ±E = 200 × 10-4 a.u. was simulated. It was applied to the ethene molecule to consider its effect on the electron dynamics, both during the application of the laser pulse and for up to 100 fs after the pulse was switched off. Four laser pulse frequencies ω = 0.2692, 0.2808, 0.2830, and 0.2900 a.u. were chosen to correspond to excitation energies mid-way between the (S1 ,S2 ), (S2 ,S3 ), (S3 ,S4 ) and (S4 ,S5 ) electronic states, respectively. Scalar quantum theory of atoms in molecules (QTAIM) was used to quantify the shifts of the C1C2 bond critical points (BCPs). Depending on the frequencies ω selected, the C1C2 BCP shifts were up to 5.8 times higher after the pulse was switched off compared with a static E-field with the same magnitude. Next generation QTAIM (NG-QTAIM) was used to visualize and quantify the directional chemical character. In particular, polarization effects and bond strengths, in the form of bond-rigidity vs. bond-flexibility, were found, for some laser pulse frequencies, to increase after the laser pulse was switched off. Our analysis demonstrates that NG-QTAIM, in partnership with ultrafast laser irradiation, is useful as a tool in the emerging field of ultrafast electron dynamics, which will be essential for the design, and control of molecular electronic devices.

Towards Computational Modeling of Ligand Binding to the ILPR G-Quadruplex.

Using a combination of unconstrained and constrained molecular dynamics simulations, we have evaluated the binding affinities between two porphyrin derivatives (TMPyP4 and TEGPy) and the G-quadruplex (G4) of a DNA fragment modeling the insulin-linked polymorphic region (ILPR). Refining a well-established potential of mean force (PMF) approach to selections of constraints based on root-mean-square fluctuations results in an excellent agreement between the calculated and observed absolute free binding energy of TMPyP4. The binding affinity of IPLR-G4 toward TEGPy is predicted to be higher than that toward TMPyP4 by 2.5 kcal/mol, which can be traced back to stabilization provided by the polyether side chains of TMPyP4 that can nestle into the grooves of the quadruplex and form hydrogen bonds through the ether oxygen atoms. Because our refined methodology can be applied to large ligands with high flexibility, the present research opens an avenue for further ligand design in this important area.

The Cis-Effect Explained Using Next-Generation QTAIM.

We used next-generation QTAIM (NG-QTAIM) to explain the cis-effect for two families of molecules: C2X2 (X = H, F, Cl) and N2X2 (X = H, F, Cl). We explained why the cis-effect is the exception rather than the rule. This was undertaken by tracking the motion of the bond critical point (BCP) of the stress tensor trajectories Tσ(s) used to sample the Uσ-space cis- and trans-characteristics. The Tσ(s) were constructed by subjecting the C1-C2 BCP and N1-N2 BCP to torsions ± θ and summing all possible Tσ(s) from the bonding environment. During this process, care was taken to fully account for multi-reference effects. We associated bond-bending and bond-twisting components of the Tσ(s) with cis- and trans-characteristics, respectively, based on the relative ease of motion of the electronic charge density ρ(rb). Qualitative agreement is found with existing experimental data and predictions are made where experimental data is not available.

Umpolung of an Aliphatic Ketone to a Magnesium Ketone-1,2-diide Complex with Vicinal Dianionic Charge.

The new ß-diketimine iPrDip nacnacH, HC(iPrCNDip)2 H, Dip=2,6-iPr2 -C6 H3 , was converted to the magnesium(I) complex [{(iPrDip nacnac)Mg}2 ] and reaction with 2-adamantanone (OAd) afforded the ketone-1,2-diide complex [{(iPrDip nacnac)Mg}2 (µ-OAd)]. The complex contains the first stable dianion of an aliphatic ketone with an electropositive metal and shows an OAd2- unit with long C-O bond and pyramidal carbon centre. DFT studies reveal an anionic charge on both neighbouring C and O atoms. Reductions of aliphatic ketones with magnesium(I) complexes show that these likely proceed via highly reactive dianions and afforded a 1 : 1 mixture of an alkoxide and an enolate when an enolisable ketone was used, and rapid CH activations reactions, e.g., of stabilising ligand moieties, when non-enolisable ketones were employed.

Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation.

The effect of a static electric (E)-field and an unchirped and chirped laser pulse field on the cycl[3.3.3]azine molecule was investigated using next-generation quantum theory of atoms in molecules (NG-QTAIM). Despite the magnitude of the E-field of the laser pulses being an order of magnitude lower than for the static E-field, the variation of the energy gap between the lowest lying singlet (S1 ) and triplet (T1 ) excited states was orders of magnitude greater for the laser pulse than for the static E-field. Insights into the response of the electronic structure were captured by NG-QTAIM, where differences in the inverted singlet-triplet gap due to the laser pulses were significant larger compared to those induced by the static E-field. The response of the S1 and T1 excited states, as determined by NG-QTAIM, switched discontinuously between weak and strong chemical character for the static E-field. In contrast, the response to the laser pulses, determined by NG-QTAIM, is to induce a continuous range of chemical character, indicating the unique ability of the laser pulses to induce polarization effects in the form of "mixed" bond types. Our analysis demonstrates that NG-QTAIM is a useful tool for understanding the response to laser irradiation of the lowest-lying singlet S1 and triplet T1 excited states of emitters exhibiting thermally activated delayed fluorescence. The chirped laser pulse led to more frequent instances of the desired outcome of an inverted singlet-triplet gap than the unchirped pulse, indicating its usefulness as a tool to design more efficient organic light-emitting diode devices.

Chirality without Stereoisomers: Insight from the Helical Response of Bond Electrons.

The association between molecular chirality and helical characteristics known as the chirality-helicity equivalence is determined for the first time by quantifying a chirality-helicity measure consistent with photoexcitation circular dichroism experiments. This is demonstrated using a formally achiral SN 2 reaction and a chiral SN 2 reaction. Both the achiral and chiral SN 2 reactions possess significant values of the chirality-helicity measure and display a Walden inversion, i. e. an inversion of the chirality between the reactant and product. We also track the chirality-helicity measure along the reaction path and discover the presence of chirality at the transition state and two intermediate structures for both reactions. We demonstrate the need for the chirality-helicity measure to differentiate between steric effects due to eclipsed conformations and chiral behaviors in formally achiral species. We explain the significance of this work for asymmetric synthetic reactions including the intermediate structures where the Cahn-Ingold-Prelog (CIP) rules cannot be used.

A quinone based single-molecule switch as building block for molecular electronics.

Using a model molecule, we show that it is possible to create molecules that show the required properties for use as elements in a molecular circuit or computer: two conformations with similar energy but different electric conductivity, and the possibility to switch between those by applying an external electric field.

Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons.

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine-guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).

Simulation of electrochemical properties of naturally occurring quinones.

Quinones are produced in organisms and are utilized as electron transfer agents, pigments and in defence mechanisms. Furthermore, naturally occurring quinones can also be cytotoxins with antibacterial properties. These properties can be linked to their redox properties. Recent studies have also shown that quinones can be utilized in flow battery technology, though naturally occurring quinones have not yet been investigated. Here, we have analyzed the properties of 990 different quinones of various biological sources through a computation approach to determine their standard reduction potentials and aqueous solubility. The screening was performed using the PBE functional and the 6-31G** basis set, providing a distribution of reduction potentials of the naturally occurring quinones varying from - 1.4 V to 1.5 V vs. the standard hydrogen electrode. The solvation energy for each quinone, which indicates the solubility in aqueous solution, was calculated at the same level. A large distribution of solubilities was obtained, containing both molecules that show tendencies of good solubilities and molecules that do not. The solubilities are dependent on the nature of the side groups and the size of the molecules. Our study shows that the group containing the quinones of fungal origin, which is also the largest of the groups considered, has the largest antimicrobial and electrochemical potential, when considering the distribution of reduction potentials for the compounds.

Next-generation QTAIM for scoring molecular wires in E-fields for molecular electronic devices.

The effect of a varying, directional E x , E y , and E z electric field on the ethene molecule was investigated using next-generation quantum theory of atoms in molecules (QTAIM). Despite using low E-field strengths that are within the realm of experiment and do not measurably alter the molecular geometry, significant changes to the QTAIM properties were observed. Using conventional QTAIM, the shifting of the C─C and C─H bond critical points (BCPs) demonstrates polarization through an interchange in the size of the atoms involved in a bond, since a BCP is located on the boundary between a pair of bonded atoms. Next-generation QTAIM, however, demonstrates the polarization effect more directly with a change in morphology of the 3-D envelope around the BCP. Modest increases of ≈ 2% in the ellipticity ε of the BCP were uncovered when the C─C bond was aligned parallel or anti-parallel to the applied E x -field. Significant asymmetries were found in the response of the next-generation QTAIM 3-D paths of the C─H bonds to the applied E-field. When the E-field coincided with the C─C bond, the BCP moved in response and was accompanied by the envelope constructed from 3-D next-generation paths. The response displayed a polarization effect that increased with increasing magnitude of the E x -field parallel and anti-parallel to the C─C bond. Our analysis demonstrates that next-generation QTAIM is a useful tool for understanding the response of molecules to E-fields, for example, for the screening of molecular wires for the design of molecular electronic devices. © 2019 Wiley Periodicals, Inc.

Halogen and Hydrogen Bonding in Halogenabenzene/NH3 Complexes Compared Using Next-Generation QTAIM.

Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.

Halogen bonding with the halogenabenzene bird structure, halobenzene, and halocyclopentadiene.

The ability of the "bird-like" halogenabenzene molecule, referred to as X-bird (XCl to At), to form halogen-bonded complexes with the nucleophiles H2 O and NH3 was investigated using double-hybrid density functional theory and the aug-cc-pVTZ/aug-cc-pVTZ-PP basis set. The structures and interaction energies were compared with 5-halocyclopenta-1,3-diene (halocyclopentadiene; an isomer of halogenabenzene) and halobenzene, also complexed with H2 O and NH3 . The unusual structure of the X-bird, with the halogen bonded to two carbon atoms, results in two distinct σ-holes, roughly at the extension of the C-X bonds. Based on the behavior of the interaction energy (which increases for heavier halogens) and van der Waals (vdW) ratio (which decreases for heavier halogens), it is concluded that the X-bird forms proper halogen bonds with H2 O and NH3 . The interaction energies are larger than those of the halogen-bonded complexes involving halobenzene and halocyclopentadiene, presumably due to the presence of a secondary interaction. © 2019 Wiley Periodicals, Inc.

The destabilization of hydrogen bonds in an external E-field for improved switch performance.

The effect of an electric field on a recently proposed molecular switch based on a quinone analogue was investigated using next-generation quantum theory of atoms in molecules (QTAIM) methodology. The reversal of a homogenous external electric field was demonstrated to improve the "OFF" functioning of the switch. This was achieved by destabilization of the H atom participating in the tautomerization process along the hydrogen bond that defines the switch. The "ON" functioning of the switch, from the position of the tautomerization barrier, is also improved by the reversal of the homogenous external electric field: this result was previously inaccessible. The "ON" and "OFF" functioning of the switch was visualized in terms of the response of the most preferred directions of motion of the electronic charge density to the applied external field. All measures from QTAIM and the stress tensor provide consistent results for the factors affecting the "ON" and "OFF" switch performance. Our analysis therefore demonstrates use for future design of molecular electronic devices. © 2019 Wiley Periodicals, Inc.

Halogen bonding in mono- and dihydrated halobenzene.

Density functional theory calculations were performed on halogen-bonded and hydrogen-bonded systems consisting of a halobenzene (XPh; X = F, Cl, Br, I, and At) and one or two water molecules, using the M06-2X density functional with the 6-31+G(d) (for C, H, F, Cl, and Br) and aug-cc-pVDZ-PP (for I, At) basis sets. The counterpoise procedure was performed to counteract the effect of basis set superposition error. The results show halogen bonds form in the XPh-H2 O system when X > Cl. There is a trend toward stronger halogen bonding as the halogen group is descended, as assessed by interaction energy and X•••Ow internuclear separation (where Ow is the water oxygen). For all XPh-H2 O systems hydrogen-bonded systems exist, containing a combination of CH•••Ow and Ow Hw •••X hydrogen bonds. For all systems except X = At the X•••Hw hydrogen-bonding interaction is stronger than the X•••Ow halogen bond. In the XPh-(H2 O)2 system halogen bonds form only for X > Br. The two water molecules prefer to form a water dimer, either located around the CH bond (for X = Br, At, and I) or located above the benzene ring (for all halogens). Thus, even in the absence of competing strong interactions, halogen bonds may not form for the lighter halogens due to (1) competition from cooperative weak interactions such as CH•••O and OH•••X hydrogen bonds, or (2) if the formation of the halogen bond would preclude the formation of a water dimer. © 2018 Wiley Periodicals, Inc.

13C-1H coupling constants as a conformational tool for structural assignment of quinic and octulosonic acid.

A complete set of NMR coupling constants (1JC-H, 2JC-H, 3JC-H, and 3JH-H) were calculated for the eight stereoisomers of quinic acid, at the B3LYP/6-311G(d,p)/PCM(methanol) level of theory. The Fermi contact term of the coupling constants was computed with a modified, uncontracted, version of the 6-311G(d,p) basis set, with additional tight polarization functions. 1H and 13C NMR chemical shifts were determined at the same level using the gauge-invariant atomic orbital (GIAO) method. The magnitude of the spin-spin coupling constants was found to be affected by the orientation (axial or equatorial) of the coupling proton and the orientation of the hydroxy group on the coupling carbon, whereas the chemical shifts depend on the presence or absence of electron-withdrawing hydroxy groups attached to the carbon atoms involved. Graphical Abstract Nuclear magnetic resonance coupling constants, computed with density functional theory, can be used to differentiate and identify the different stereoisomers of quinic acid.