Two Theorems and Important Insight on How the Preferred Mechanism of Free Radical Scavenging Cannot Be Settled. Comment on Pandithavidana, D.R.; Jayawardana, S.B. Comparative Study of Antioxidant Potential of Selected Dietary Vitamins; Computational Insights. Molecules 2019, 24, 1646

Totally ignoring that the five enthalpies of reaction—bond dissociation enthalpy (BDE), adiabatic ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE)—characterizing the three free radical scavenging mechanisms—direct hydrogen atom transfer (HAT), sequential electron transfer proton transfer (SET-PT), and stepwise proton loss electron transfer (SPLET)—are not independent of each other, a recent publication on the antioxidant activity of dietary vitamins compared various vitamins and “found” different quantities, which should be strictly equal by virtue of energy conservation. Aiming to clarify this point, as well as to avoid such mistakes in future studies and to unravel errors in the previous literature, in the present paper we formulate two theorems that any sound results on antioxidation should obey. The first theorem states that the sums of the enthalpies characterizing the individual steps of SET-PT and SPLET are equal: IP+PDE = PA+ETE (=H2). This is a mathematical identity emerging from the fact that both the reactants and the final products of SET-PT and SPLET are chemically identical. The second theorem, which is also a mathematical identity, states that H2 − BDE = IPH > 0, where IPH is the ionization potential of the H-atom in the medium (e.g., gas or solvent) considered. Due to their general character, these theorems may/should serve as necessary sanity tests for any results on antioxidant activity, whatever the method employed in their derivation. From a more general perspective, they should represent a serious word of caution regarding attempts to assign the preferred free radical scavenging pathway based merely on thermochemical descriptors.

HCnH- Anion Chains with n ≤ 8 Are Nonlinear and Their Permanent Dipole Makes Them Potential Candidates for Astronomical Observation

To be detectable in space via radio astronomy, molecules should have a permanent dipole moment. This is the plausible reason why HC_nH chains are underproportionally represented in the interstellar medium in comparison with the isoelectronically equivalent HC_nN chain family, which is the most numerous homologous series astronomically observed so far. In this communication, we present results of quantum chemical calculations for the HC_nH family at several levels of theory: density functional theory (DFT/B3LYP), coupled-cluster expansions (ROCCSD(T)), and G4 composite model. Contradicting previous studies, we report here that linear HC_nH⁻ anion chains with sizes of astrochemical interest are unstable (i.e., not all calculated frequencies are real). Nonlinear cis and trans HC_nH⁻ anion chains turn out to be stable both against molecular vibrations (i.e., all vibrational frequencies are real) and against electron detachment (i.e., positive electroaffinity). The fact that the cis anion conformers possess permanent dipole is the main encouraging message that this study is aiming at conveying to the astrochemical community, as this makes them observable by means of radio astronomy.

Environmental Control of Single-Molecule Junction Evolution and Conductance: A Case Study of Expanded Pyridinium Wiring

Environmental control of single-molecule junction evolution and conductance was demonstrated for expanded pyridinium molecules by scanning tunneling microscopy break junction method and interpreted by quantum transport calculations including solvent molecules explicitly. Fully extended and highly conducting molecular junctions prevail in water environment as opposed to short and less conducting junctions formed in non-solvating mesitylene. A theoretical approach correctly models single-molecule conductance values considering the experimental junction length. Most pronounced difference in the molecular junction formation and conductance was identified for a molecule with the highest stabilization energy on the gold substrate confirming the importance of molecule-electrode interactions. Presented concept of tuning conductance through molecule-electrode interactions in the solvent-driven junctions can be used in the development of new molecular electronic devices.

Mono- and Di-Quaternized 4,4'-Bipyridine Derivatives as Key Building Blocks for Medium- and Environment-Responsive Compounds and Materials

Mono- and di-quaternized 4,4'-bipyridine derivatives constitute a family of heterocyclic compounds, which in recent years have been employed in numerous applications. These applications correspond to various disciplines of research and technology. In their majority, two key features of these 4,4'-bipyridine-based derivatives are exploited: their redox activity and their electrochromic aptitude. Contemporary materials and compounds encompassing these skeletons as building blocks are often characterized as multifunctional, as their presence often gives rise to interesting phenomena, e.g., various types of chromism. This research trend is acknowledged, and, in this review article, recent examples of multifunctional chromic materials/compounds of this class are presented. Emphasis is placed on solvent-/medium- and environment-responsive 4,4'-bipyridine derivatives. Two important classes of 4,4'-bipyridine-based products with solvatochromic and/or environment-responsive character are reviewed: viologens (i.e., N,N'-disubstituted derivatives) and monoquats (i.e., monosubstituted 4,4'-bipyridine derivatives). The multifunctional nature of these derivatives is analyzed and structure-property relations are discussed in connection to the role of these derivatives in various novel applications.

Floppy molecules as candidates for achieving optoelectronic molecular devices without skeletal rearrangement or bond breaking

Molecular species investigated as possible candidates for molecular photoswitches often toggle between two (low and high conductance) conformations implying skeletal rearrangement, bond breaking, and substantial changes of molecular length. All these represent shortcomings that impede the switching speed and straightforward incorporation in nanodevices. In the present paper we propose a mechanism wherein the photoinduced switching is from a nonplanar conformation to a planar conformation, and involves neither skeletal rearrangement nor bond breaking or significant molecular length changes. Specifically, by choosing typical floppy molecules consisting of two benzene or benzene-like rings that can easily rotate relative to each other, we present results of both ab initio and DFT quantum chemical calculations demonstrating that the lowest electronic excitation corresponds to a planar molecular conformation (φ = 0), in contrast to the nonplanar ground state characterized by φ ≠ 0. Because the low bias conductance scales as G ∝ cos² φ, the planar conformation has a higher conductance than the non-planar conformation, acting therefore as ON and OFF states of the molecular switch, respectively. We analyze recent experimental data on illuminated single-molecule junctions (E.-D. Fung et al., Nano Lett., 2017, 17, 1255) and show that the measured photoinduced conductance enhancement is consistent with the presently proposed mechanism. Furthermore, based on recent results demonstrating the substantial impact of the SAM coverage on the twisting angle (I. Bâldea, Faraday Discuss., 2017, 204, 35) we show that a photoinduced conductance enhancement can be much stronger than the rather modest enhancement obtained in the aforementioned experiment.

Vibrational Frequencies of Fractionally Charged Molecular Species: Benchmarking DFT Results against ab Initio Calculations

Recent advances in nano/molecular electronics and electrochemistry made it possible to continuously tune the fractional charge q of single molecules and to use vibrational spectroscopic methods to monitor such changes. Approaches to compute vibrational frequencies ω(q) of fractionally charged species based on the density functional theory (DFT) are faced with an important issue: the basic quantity used in these calculations, the total energy, should exhibit piecewise linearity with respect to the fractional charge, but approximate, commonly utilized exchange correlation functionals do not obey this condition. In this paper, with the aid of a simple and representative example, we benchmark results for ω(q) obtained within the DFT against ab initio methods, namely, coupled cluster singles and doubles and also second- and third-order Møller-Plesset perturbation) expansions. These results indicate that, in spite of missing the aforementioned piecewise linearity, DFT-based values ω(q) can reasonably be trusted.

Fractional molecular charge studied via molecular vibrational properties. Specific aspects in Jahn–Teller active molecular species

Jahn–Teller active and inactive vibrational modes are affected in a different manner by charge removal.

Tuning the conformation of floppy molecules by charge transfer

Recent advances in electrochemistry and nano- and molecular electronics made it possible to prepare and study molecular species having fractional charges (q ≠ 0, ±1, …) that can be continuously tuned by biases.

Experimental and Theoretical Analysis of Nanotransport in Oligophenylene Dithiol Junctions as a Function of Molecular Length and Contact Work Function

We report the results of an extensive investigation of metal-molecule-metal tunnel junctions based on oligophenylene dithiols (OPDs) bound to several types of electrodes (M1-S-(C6H4)n-S-M2, with 1 ≤ n ≤ 4 and M1,2 = Ag, Au, Pt) to examine the impact of molecular length (n) and metal work function (Φ) on junction properties. Our investigation includes (1) measurements by scanning Kelvin probe microscopy of electrode work function changes (ΔΦ = ΦSAM - Φ) caused by chemisorption of OPD self-assembled monolayers (SAMs), (2) measurements of junction current-voltage (I-V) characteristics by conducting probe atomic force microscopy in the linear and nonlinear bias ranges, and (3) direct quantitative analysis of the full I-V curves. Further, we employ transition voltage spectroscopy (TVS) to estimate the energetic alignment εh = EF - EHOMO of the dominant molecular orbital (HOMO) relative to the Fermi energy EF of the junction. Where photoelectron spectroscopy data are available, the εh values agree very well with those determined by TVS. Using a single-level model, which we justify via ab initio quantum chemical calculations at post-density functional theory level and additional UV-visible absorption measurements, we are able to quantitatively reproduce the I-V measurements in the whole bias range investigated (∼1.0-1.5 V) and to understand the behavior of εh and Γ (contact coupling strength) extracted from experiment. We find that Fermi level pinning induced by the strong dipole of the metal-S bond causes a significant shift of the HOMO energy of an adsorbed molecule, resulting in εh exhibiting a weak dependence with the work function Φ. Both of these parameters play a key role in determining the tunneling attenuation factor (β) and junction resistance (R). Correlation among Φ, ΔΦ, R, transition voltage (Vt), and εh and accurate simulation provide a remarkably complete picture of tunneling transport in these prototypical molecular junctions.

Adsorption-Induced Solvent-Based Electrostatic Gating of Charge Transport through Molecular Junctions

Recent experiments have shown that transport properties of molecular-scale devices can be reversibly altered by the surrounding solvent. Here, we use a combination of first-principles calculations and experiment to explain this change in transport properties through a shift in the local electrostatic potential at the junction caused by nearby conducting and solvent molecules chemically bound to the electrodes. This effect is found to alter the conductance of 4,4'-bipyridine-gold junctions by more than 50%. Moreover, we develop a general electrostatic model that quantitatively relates the conductance and dipoles associated with the bound solvent and conducting molecules. Our work shows that solvent-induced effects can be used to control charge and energy transport at molecular-scale interfaces.

Negative differential resistance devices by using N-doped graphene nanoribbons

Recently, extensive efforts have been devoted to the investigations of negative differential resistance (NDR) behavior in graphene. Here, by performing fully self-consistent density functional theory calculations combined with non-equilibrium Green's function technique, we investigate the transport properties of three molecules from conjugated molecule, one-dimension alkane chain, and single molecule magnet, which are sandwiched between two N-doped zigzag and armchair graphene nanoribbons (GNRs). We observe robust NDR effect in all examined molecular junctions including benzene, alkane, and planar four-coordinated Fe complex. Through the analyses of the calculated electronic structures and the bias-dependent transmission coefficients, we find that the narrow density of states of N-doped GNRs and the bias-dependent effective coupling between the discrete frontier molecular orbitals and the subbands of N-doped GNRs are responsible for the observed NDR phenomenon. These theoretical findings imply that N-doped GNRs hold great potential for building NDR devices based on various molecules.

Quantifying the relative molecular orbital alignment for molecular junctions with similar chemical linkage to electrodes

Estimating the relative alignment between the frontier molecular orbitals (MOs) that dominates the charge transport through single-molecule junctions represents a challenge for theory. This requires approaches beyond the widely employed framework provided by the density functional theory, wherein the Kohn-Sham 'orbitals' are treated as if they were real MOs, which is not the case. In this paper, we report results obtained by means of quantum chemical calculations, including the equation-of-motion coupled-cluster singles and doubles, which is the state-of-the-art of quantum chemistry for medium-size molecules like those considered here. These theoretical results are validated against data on the MO energy offset relative to the electrodes' Fermi energy extracted from experiments for junctions based on 4,4'-bipyridine and 1,4-dicyanobenzene.

A quantum chemical study from a molecular transport perspective: ionization and electron attachment energies for species often used to fabricate single-molecule junctions

The accurate determination of the lowest electron attachment (EA) and ionization (IP) energies for molecules embedded in molecular junctions is important for correctly estimating, for example, the magnitude of the currents (I) or the biases (V) where an I-V curve exhibits significant non-Ohmic behavior. Benchmark calculations for the lowest electron attachment and ionization energies of several typical molecules utilized to fabricate single-molecule junctions characterized by n-type conduction (4,4'-bipyridine, 1,4-dicyanobenzene and 4,4'-dicyano-1,1'-biphenyl) and p-type conduction (benzenedithiol, biphenyldithiol, hexanemonothiol and hexanedithiol) based on the EOM-CCSD (equation-of-motion coupled-cluster singles and doubles) state-of-the-art method of quantum chemistry are presented. They indicate significant differences from the results obtained within current approaches to molecular transport. The present study emphasizes that, in addition to a reliable quantum chemical method, basis sets much better than the ubiquitous double-zeta set employed for transport calculations are needed. The latter is a particularly critical issue for correctly determining EAs, which is impossible without including sufficient diffuse basis functions. The spatial distribution of the dominant molecular orbitals (MOs) is another important issue, on which the present study draws attention, because it sensitively affects the MO energy shifts Φ due to image charges formed in electrodes. The present results cannot substantiate the common assumption of a point-like MO midway between electrodes, which substantially affects the actual Φ-values.

Transition voltage spectroscopy reveals significant solvent effects on molecular transport and settles an important issue in bipyridine-based junctions

Results of a seminal study (B. Xu and N. J. Tao, Science, 2003, 301, 1221) on the single-molecule junctions based on bipyridine placed in a solvent have been challenged recently (S. Y. Quek et al., Nat. Nano, 2009, 4, 230) by implicitly assuming a negligible solvent impact on the molecular transport and by merely considering low bias conductance data. In this paper we demonstrate that solvent effects on the molecular transport are important, and to show this we focus our attention on the energy offset ε(0) of the dominant molecular orbital (LUMO) relative to the electrode Fermi level. To estimate the energy offset ε(0)(sol) from the full I-V curves presented by Xu and Tao for wet junctions, we resort to the recently proposed transition voltage spectroscopy (TVS). TVS, which plays a key role in the present analysis, emphasizes that data beyond the ohmic conductance regime are needed to reveal the solvent impact. We show that ε(0)(sol) significantly differs from the energy offset ε(0)(0)deduced for dry junctions (J. R. Widawsky et al., Nano Lett., 2012, 12, 354). The present work demonstrates that solvent effects on molecular transport are important and can be understood quantitatively. Results of ab initio calculations with and without solvent are reported that excellently explain the difference δε(0) = ε(0)(sol)-ε(0)(0). δε(0) = ΔΔG + δΦ + δW can be disentangled in contributions with a clear physical content: solvation energies (ΔΔG), image charges (δΦ), and work functions (δW). Accurate analytical formulae for ΔΔG and δΦ are reported, which provide experimentalists with a convenient framework to quantify solvent effects obviating demanding numerical efforts.