Dichotomy between Level Broadening and Level Coupling to Electrodes in Large Area EGaIn Molecular Junctions.

Choosing self-assembled monolayers (SAMs) of fluorine-terminated oligophenylenes adsorbed on gold as an illustration, we show that a single-level [molecular orbital (MO)] model can excellently reproduce full I-V curves measured for large area junctions fabricated with a top EGaIn contact. In addition, this model unravels a surprising dichotomy between MO coupling to electrodes and MO broadening. Importantly for the coherence of the microscopic description, the latter is found to correlate with the SAM coverage and molecular and π* orbital tilt angles.

Breakdown of Ohm's Law in Molecular Junctions with Electrodes of Single-Layer Graphene.

For sufficiently low biases, Ohm's law, the cornerstone of electricity, stating that current I and voltage V are proportional, is satisfied at low biases for all known systems ranging from macroscopic conductors to nanojunctions. In this study, we predict theoretically and demonstrate experimentally that in single-molecule junctions fabricated with single-layer graphene as electrodes the current at low V scales as the cube of V, thereby invalidating Ohm's law. The absence of the ohmic regime is a direct consequence of the unique band structure of the single-layer graphene, whose vanishing density of states at the Dirac points precludes electron transfer from and to the electrodes at low biases.

Can tunneling current in molecular junctions be so strongly temperature dependent to challenge a hopping mechanism? Analytical formulas answer this question and provide important insight into large area junctions.

Analytical equations like Richardson-Dushman's or Shockley's provided a general, if simplified conceptual background, which was widely accepted in conventional electronics and made a fundamental contribution to advances in the field. In the attempt to develop a (highly desirable, but so far missing) counterpart for molecular electronics, in this work, we deduce a general analytical formula for the tunneling current through molecular junctions mediated by a single level that is valid for any bias voltage and temperature. Starting from this expression, which is exact and obviates cumbersome numerical integration, in the low and high temperature limits we also provide analytical formulas expressing the current in terms of elementary functions. They are accurate for broad model parameter ranges relevant for real molecular junctions. Within this theoretical framework we show that: (i) by varying the temperature, the tunneling current can vary by several orders of magnitude, thus debunking the myth that a strong temperature dependence of the current is evidence for a hopping mechanism, (ii) real molecular junctions can undergo a gradual (Sommerfeld-Arrhenius) transition from a weakly temperature dependent to a strongly ("exponential") temperature dependent current that can be tuned by the applied bias, and (iii) important insight into large area molecular junctions with eutectic gallium indium alloy (EGaIn) top electrodes can be gained. E.g., merely based on transport data, we estimate that the current carrying molecules represent only a fraction of f ≈ 4 × 10-4 out of the total number of molecules in a large area Au-S-(CH2)13-CH3/EGaIn junction.

Comment on "A single level tunneling model for molecular junctions: evaluating the simulation methods" by E. M. Opodi, X. Song, X. Yu and W. Hu, Phys. Chem. Chem. Phys., 2022, 24, 11958".

The present Comment demonstrates important flaws of the paper Opodi et al. Phys. Chem. Chem. Phys., 2022, 24, 11958 Their crown result ("applicability map") aims at indicating parameter ranges wherein two approximate methods (called method 2 and 3) apply. My calculations reveal that the applicability map is a factual error. Deviations of I2 from the exact current I1 do not exceed 3% for model parameters where Opodi et al. claimed that method 2 is inapplicable. As for method 3, the parameter range of the applicability map is beyond its scope, as stated in papers cited by Opodi et al. themselves.

CP-AFM Molecular Tunnel Junctions with Alkyl Backbones Anchored Using Alkynyl and Thiol Groups: Microscopically Different Despite Phenomenological Similarity.

In this paper, we report results on the electronic structure and transport properties of molecular junctions fabricated via conducting probe atomic force microscopy (CP-AFM) using self-assembled monolayers (SAMs) of n-alkyl chains anchored with acetylene groups (CnA; n = 8, 9, 10, and 12) on Ag, Au, and Pt electrodes. We found that the current-voltage (I-V) characteristics of CnA CP-AFM junctions can be very accurately reproduced by the same off-resonant single-level model (orSLM) successfully utilized previously for many other junctions. We demonstrate that important insight into the energy-level alignment can be gained from experimental data of transport (processed via the orSLM) and ultraviolet photoelectron spectroscopy combined with ab initio quantum chemical information based on the many-body outer valence Green's function method. Measured conductance GAg < GAu < GPt is found to follow the same ordering as the metal work function ΦAu < ΦAu < ΦPt, a fact that points toward a transport mediated by an occupied molecular orbital (MO). Still, careful data analysis surprisingly revealed that transport is not dominated by the ubiquitous HOMO but rather by the HOMO-1. This is an important difference from other molecular tunnel junctions with p-type HOMO-mediated conduction investigated in the past, including the alkyl thiols (CnT) to which we refer in view of some similarities. Furthermore, unlike in CnT and other junctions anchored with thiol groups investigated in the past, the AFM tip causes in CnA an additional MO shift, whose independence of size (n) rules out significant image charge effects. Along with the prevalence of the HOMO-1 over the HOMO, the impact of the "second" (tip) electrode on the energy level alignment is another important finding that makes the CnA and CnT junctions different. What ultimately makes CnA unique at the microscopic level is a salient difference never reported previously, namely, that CnA's alkyne functional group gives rise to two energetically close (HOMO and HOMO-1) orbitals. This distinguishes the present CnA from the CnT, whose HOMO stemming from its thiol group is well separated energetically from the other MOs.

Gaining insight into molecular tunnel junctions with a pocket calculator without I-V data fitting. Five-thirds protocol.

The protocol put forward in the present paper is an attempt to meet the experimentalists' legitimate desire of reliably and easily extracting microscopic parameters from current-voltage measurements on molecular junctions. It applies to junctions wherein charge transport dominated by a single level (molecular orbital, MO) occurs via off-resonant tunneling. The recipe is simple. The measured current-voltage curve I = I(V) should be recast as a curve of V5/3/I versus V. This curve exhibits two maxima: one at positive bias (V = Vp+), another at negative bias (V = Vp-). The values Vp+ > 0 and Vp- < 0 at the two peaks of the curve for V5/3/I at positive and negative bias and the corresponding values Ip+ = I(Vp+) > 0 and Ip- = I(Vp-) < 0 of the current is all information needed as input. The arithmetic average of Vp+ and |Vp-| in volt provides the value in electronvolt of the MO energy offset ε0 = EMO - EF relative to the electrode Fermi level (|ε0| = e(Vp+ + |Vp-|)/2). The value of the (Stark) strength of the bias-driven MO shift is obtained as γ = (4/5)(Vp+ - |Vp-|)/(Vp+ + |Vp-|) sign (ε0). Even the low-bias conductance estimate, G = (3/8)(Ip+/Vp+ + Ip-/Vp-), can be a preferable alternative to that deduced from fitting the I-V slope in situations of noisy curves at low bias. To demonstrate the reliability and the generality of this "five-thirds" protocol, I illustrate its wide applicability for molecular tunnel junctions fabricated using metallic and nonmetallic electrodes, molecular species possessing localized σ and delocalized π electrons, and various techniques (mechanically controlled break junctions, STM break junctions, conducting probe AFM junctions, and large area junctions).

Can room-temperature data for tunneling molecular junctions be analyzed within a theoretical framework assuming zero temperature?

Routinely, experiments on tunneling molecular junctions report values of conductances (GRT) and currents (IRT) measured at room temperature. On the other hand, theoretical approaches based on simplified models provide analytic formulas for the conductance (G0K) and current (I0K) valid at zero temperature. Therefore, interrogating the applicability of the theoretical results deduced in the zero-temperature limit to real experimental situations at room temperature (i.e., GRT ≈ G0K and IRT ≈ I0K) is a relevant aspect. Quantifying the pertaining temperature impact on the transport properties computed within the ubiquitous single-level model with Lorentzian transmission is the specific aim of the present work. Comprehensive results are presented for broad ranges of the relevant parameters (level's energy offset ε0 and width Γa, and applied bias V) that safely cover values characterizing currently fabricated junctions. They demonstrate that the strongest thermal effects occur at biases below resonance (2|ε0| - δε0 - 0.3 ≲ |eV| - 0.3 ≲ 2|ε0|). At fixed V, they affect an ε0-range whose largest width δε0 is about nine times larger than the thermal energy (δε0 ≈ 3πkBT) at Γa → 0. The numerous figures included aim to convey a quick overview on the applicability of the zero-temperature limit to a specific real junction. In quantitative terms, the conditions of applicability are expressed as mathematical inequalities involving elementary functions. They constitute the basis of a proposed interactive data-fitting procedure, which aims to guide experimentalists interested in data processing in a specific case.

Estimating the Number of Molecules in Molecular Junctions Merely Based on the Low Bias Tunneling Conductance at Variable Temperature.

Temperature (T) dependent conductance G=G(T) data measured in molecular junctions are routinely taken as evidence for a two-step hopping mechanism. The present paper emphasizes that this is not necessarily the case. A curve of lnG versus 1/T decreasing almost linearly (Arrhenius-like regime) and eventually switching to a nearly horizontal plateau (Sommerfeld regime), or possessing a slope gradually decreasing with increasing 1/T is fully compatible with a single-step tunneling mechanism. The results for the dependence of G on T presented include both analytical exact and accurate approximate formulas and numerical simulations. These theoretical results are general, also in the sense that they are not limited, e.g., to the (single molecule electromigrated (SET) or large area EGaIn) fabrication platforms, which are chosen for exemplification merely in view of the available experimental data needed for analysis. To be specific, we examine in detail transport measurements for molecular junctions based on ferrocene (Fc). As a particularly important finding, we show how the present analytic formulas for G=G(T) can be utilized to compute the ratio f=Aeff/An between the effective and nominal areas of large area Fc-based junctions with an EGaIn top electrode. Our estimate of f≈0.6×10-4 is comparable with previously reported values based on completely different methods for related large area molecular junctions.

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 reaction­bond 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 mechanisms­direct 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.

Why Ortho- and Para-Hydroxy Metabolites Can Scavenge Free Radicals That the Parent Atorvastatin Cannot? Important Pharmacologic Insight from Quantum Chemistry.

The pharmaceutical success of atorvastatin (ATV), a widely employed drug against the "bad" cholesterol (LDL) and cardiovascular diseases, traces back to its ability to scavenge free radicals. Unfortunately, information on its antioxidant properties is missing or unreliable. Here, we report detailed quantum chemical results for ATV and its ortho- and para-hydroxy metabolites (o-ATV, p-ATV) in the methanolic phase. They comprise global reactivity indices, bond order indices, and spin densities as well as all relevant enthalpies of reaction (bond dissociation BDE, ionization IP and electron attachment EA, proton detachment PDE and proton affinity PA, and electron transfer ETE). With these properties in hand, we can provide the first theoretical explanation of the experimental finding that, due to their free radical scavenging activity, ATV hydroxy metabolites rather than the parent ATV, have substantial inhibitory effect on LDL and the like. Surprisingly (because it is contrary to the most cases currently known), we unambiguously found that HAT (direct hydrogen atom transfer) rather than SPLET (sequential proton loss electron transfer) or SET-PT (stepwise electron transfer proton transfer) is the thermodynamically preferred pathway by which o-ATV and p-ATV in methanolic phase can scavenge DPPH• (1,1-diphenyl-2-picrylhydrazyl) radicals. From a quantum chemical perspective, the ATV's species investigated are surprising because of the nontrivial correlations between bond dissociation energies, bond lengths, bond order indices and pertaining stretching frequencies, which do not fit the framework of naive chemical intuition.

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 HCnH chains are underproportionally represented in the interstellar medium in comparison with the isoelectronically equivalent HCnN 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 HCnH 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 HCnH- anion chains with sizes of astrochemical interest are unstable (i.e., not all calculated frequencies are real). Nonlinear cis and trans HCnH- 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.

Quantitative analysis of weak current rectification in molecular tunnel junctions subject to mechanical deformation reveals two different rectification mechanisms for oligophenylene thiols versus alkane thiols.

Metal-molecule-metal junctions based on alkane thiol (CnT) and oligophenylene thiol (OPTn) self-assembled monolayers (SAMs) and Au electrodes are expected to exhibit similar electrical asymmetry, as both junctions have one chemisorbed Au-S contact and one physisorbed, van der Waals contact. Asymmetry is quantified by the current rectification ratio RR apparent in the current-voltage (I-V) characteristics. Here we show that RR < 1 for CnT and RR > 1 for OPTn junctions, in contrast to expectation, and further, that RR behaves very differently for CnT and OPTn junctions under mechanical extension using the conducting probe atomic force microscopy (CP-AFM) testbed. The analysis presented in this paper, which leverages results from the previously validated single level model and ab initio quantum chemical calculations, allows us to explain the puzzling experimental findings for CnT and OPTn in terms of different current rectification mechanisms. Specifically, in CnT-based junctions the Stark effect creates the HOMO level shifting necessary for rectification, while for OPTn junctions the level shift arises from position-dependent coupling of the HOMO wavefunction with the junction electrostatic potential profile. On the basis of these mechanisms, our quantum chemical calculations allow quantitative description of the impact of mechanical deformation on the measured current rectification. Additionally, our analysis, matched to experiment, facilitates direct estimation of the impact of intramolecular electrostatic screening on the junction potential profile. Overall, our examination of current rectification in benchmark molecular tunnel junctions illuminates key physical mechanisms at play in single step tunneling through molecules, and demonstrates the quantitative agreement that can be obtained between experiment and theory in these systems.

What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?

A recent work indicates that temporarily splitting larger populations into smaller groups can efficiently mitigate the spread of SARS-CoV-2 virus. The fact that, soon afterward, the two million people Slovenia was the first European country proclaiming the end of COVID-19 epidemic within national borders may be relevant from this perspective. Motivated by this evolution, in this paper the time dynamics of coronavirus cases in Slovenia is investigated with emphasis on how efficient various containment measures act to diminish the number of COVID-19 infections. Noteworthily, the present analysis does not rely on any speculative theoretical assumption; it is solely based on raw epidemiological data. Out of the results presented here, the most important one is perhaps the finding that, while imposing drastic curfews and travel restrictions reduce the infection rate κ by a factor of four with respect to the unrestricted state, they only improve the κ-value by ≈15% as compared to the much bearable state of social and economic life wherein wearing face masks and social distancing rules are enforced/followed. Significantly for behavioral and social science, our analysis may reveal an interesting self-protection instinct of the population, which became manifest even before the official lockdown enforcement.

Suppression of Groups Intermingling as an Appealing Option for Flattening and Delaying the Epidemiological Curve While Allowing Economic and Social Life at a Bearable Level during the COVID-19 Pandemic.

The COVID-19 pandemic in a population modelled as a network wherein infection can propagate both via intra- and inter-group interactions is simulated. The results emphasize the importance of diminishing the inter-group infections in the effort of substantial flattening/delaying of the epi(demiologic) curve with concomitant mitigation of disastrous economy and social consequences. To exemplify, splitting a population into m (say, 5 or 10) noninteracting groups while keeping intra-group interaction unchanged yields a stretched epidemiological curve having the maximum number of daily infections reduced and postponed in time by the same factor m (5 or 10). More generally, the study suggests a practical approach to fight against SARS- CoV- 2 virus spread based on population splitting into groups and minimizing intermingling between them. This strategy can be pursued by large-scale infrastructure reorganization of activity at different levels in big logistic units (e.g., large productive networks, factories, enterprises, warehouses, schools, (seasonal) harvest work). Importantly, unlike total lockdown, the proposed approach prevents economic ruin and keeps social life at a more bearable level than distancing everyone from anyone. The declaration for the first time in Europe that COVID-19 epidemic ended in the two-million population Slovenia may be taken as support for the strategy proposed here.

Evidence That Molecules in Molecular Junctions May Not Be Subject to the Entire External Perturbation Applied to Electrodes.

Whether molecules forming molecular junctions are really subject to the entire external perturbation applied to electrodes is an important issue, but so far, it has not received adequate consideration in the literature. In this paper, we demonstrate that, out of the temperature difference ΔTelectr between electrodes applied in thermopower measurements, molecules only feel a significantly smaller temperature difference (ΔTmolec < ΔTelectr). Rephrasing, temperature drops at metal-molecule interfaces are substantial. Our theoretical analysis to address this problem of fundamental importance for surface science is based on experimental data collected via ultraviolet photoelectron spectroscopy, transition voltage spectroscopy, and Seebeck coefficient measurements. An important practical consequence of the presently reported finding is that the energetic alignment of the frontier molecular orbital (HOMO or LUMO) of the embedded molecules with respect to the metallic Fermi level position deduced from thermopower data-and this is frequently the case in current studies of molecular electronics-is substantially overestimated. Another important result presented here is that, unlike the exponential length dependence characterizing electric conduction (which is a fingerprint for quantum tunneling), thermal conduction through the molecules considered (oligophenylene thiols and alkane thiols) exhibits a length dependence compatible with classical physics.

Energy Level Alignment in Molecular Tunnel Junctions by Transport and Spectroscopy: Self-Consistency for the Case of Alkyl Thiols and Dithiols on Ag, Au, and Pt Electrodes.

We report here an extensive study of transport and electronic structure of molecular junctions based on alkyl thiols (CnT; n = 7, 8, 9, 10, 12) and dithiols (CnDT; n = 8, 9, 10) with various lengths contacted with different metal electrodes (Ag, Au, Pt). The dependence of the low-bias resistance (R) on contact work function indicates that transport is HOMO-assisted (p-type transport). Analysis of the current-voltage (I-V) characteristics for CnT and CnDT tunnel junctions with the analytical single-level model (SLM) provides both the HOMO-Fermi energy offset εhtrans and the average molecule-electrode coupling (Γ) as a function of molecular length (n), electrode work function (Φ), and the number of chemical contacts (one or two). The SLM analysis reveals a strong Fermi level (EF) pinning effect in all the junctions, i.e., εhtrans changes very little with n, Φ, and the number of chemical contacts, but Γ depends strongly on these variables. Significantly, independent measurements of the HOMO-Fermi level offset (εhUPS) by ultraviolet photoelectron spectroscopy (UPS) for CnT and CnDT SAMs agree remarkably well with the transport-estimated εhtrans. This result provides strong evidence for hole transport mediated by localized HOMO states at the Au-thiol interface, and not by the delocalized σ states in the C-C backbones, clarifying a long-standing issue in molecular electronics. Our results also substantiate the application of the single-level model for quantitative, unified understanding of transport in benchmark molecular junctions.

Determination of Energy-Level Alignment in Molecular Tunnel Junctions by Transport and Spectroscopy: Self-Consistency for the Case of Oligophenylene Thiols and Dithiols on Ag, Au, and Pt Electrodes.

We report detailed measurements of transport and electronic properties of molecular tunnel junctions based on self-assembled monolayers (SAMs) of oligophenylene monothiols (OPT n, n = 1-3) and dithiols (OPD n, n = 1-3) on Ag, Au, and Pt electrodes. The junctions were fabricated with the conducting probe atomic force microscope (CP-AFM) platform. Fitting of the current-voltage ( I-V) characteristics for OPT n and OPD n junctions to the analytical single-level tunneling model allows extraction of both the HOMO-to-Fermi-level offset (εh) and the average molecule-electrode coupling (Γ) as a function of molecular length ( n) and electrode work function (Φ). Significantly, direct measurements of εhUPS by ultraviolet photoelectron spectroscopy (UPS) for OPT n and OPD n SAMs on Ag, Au, and Pt agree remarkably well with the transport estimates εhtrans, providing strong support-beyond the high quality I-V simulations-for the relevance of the analytical single-level model to simple molecular tunnel junctions. Because the UPS measurements involve SAMs bonded to only one metal contact, the correspondence of εhUPS and εhtrans also indicates that the top contact has a weak effect on the HOMO energy. Corroborating ab initio calculations definitively rule out a dominant contribution of image charge effects to the magnitude of εh. Thus, the effective molecular tunnel barrier εh is determined, and essentially pinned, by the formation of a single metal-S covalent bond per OPT n or OPD n molecule.

Mechanical Deformation Distinguishes Tunneling Pathways in Molecular Junctions.

Developing a clearer understanding of electron tunneling through molecules is a central challenge in molecular electronics. Here we demonstrate the use of mechanical stretching to distinguish orbital pathways that facilitate tunneling in molecular junctions. Our experiments employ junctions based on self-assembled monolayers (SAMs) of homologous alkanethiols (C nT) and oligophenylene thiols (OPT n), which serve as prototypical examples of σ-bonded and π-bonded backbones, respectively. Surprisingly, molecular conductances ( Gmolecule) for stretched C nT SAMs have exactly the same length dependence as unstretched C nT SAMs in which molecular length is tuned by the number of CH2 repeat units, n. In contrast, OPT n SAMs exhibit a 10-fold-greater decrease in Gmolecule with molecular length for stretched versus unstretched cases. Experiment and theory show that these divergent results are explained by the dependence of the molecule-electrode electronic coupling Γ on strain and the spatial extent of the principal orbital facilitating tunneling. In particular, differences in the strain sensitivity of Γ versus the repeat-length ( n) sensitivity can be used to distinguish tunneling via delocalized orbitals versus localized orbitals. Angstrom-level tuning of interelectrode separation thus provides a strategy for examining the relationship between orbital localization or delocalization and electronic coupling in molecular junctions and therefore for distinguishing tunneling pathways.

A sui generis electrode-driven spatial confinement effect responsible for strong twisting enhancement of floppy molecules in closely packed self-assembled monolayers.

At present, it is widely accepted that properties (e.g., molecular conformation) of molecules adsorbed to form self-assembled monolayers (SAMs) on electrodes can be very different from isolated species because of a substantial charge transfer or specific chemical bonding at the interface. Contrary to this view, the theoretical results presented here predict that the strong twisting angle (φ) enhancement of floppy molecules adsorbed to form densely packed SAMs on most common electrodes (Pt, Au, Ag, and Cu) is neither due to charge transfer nor to specific bonding but rather to a sui generis electrode-driven spatial confinement effect that can be quantitatively described within an electrode-free two-dimensional model. We predict a logistic ("Fermi-Dirac") growth pattern of φ as the coverage approaches the value characteristic of a herringbone arrangement, which is twice the value for isolated molecules or low-coverage SAMs.

Why one can expect large rectification in molecular junctions based on alkane monothiols and why rectification is so modest.

Many attempts to obtain high current rectification ratios (RRs) in molecular electronics are triggered by a potentiometer rule argument, which predicts that a strongly asymmetric location of the dominant molecular orbital yields large RR-values. Invoking this argument, molecular junctions based on alkane monothiols (CnT) can be expected to exhibit high RRs; the HOMO of these molecules is localized on the thiol terminal group bonded to one electrode. The extensive current-voltage (I-V) results for CP-AFM (conducting probe atomic force microscope) CnT junctions of various molecular lengths (n = 7, 8, 9, 10, and 12) and different metallic contacts (Ag, Au, and Pt) are consistent with conduction dominated by the HOMO, but the measured RR ∼ 1.5 is much smaller than that predicted by the potentiometer rule framework. Further, the linear shift in the HOMO position with applied bias, γ, which gives rise to rectification, is also smaller than expected, and critically, γ has the opposite sign from potentiometer rule predictions. Companion ab initio OVGF (outer valence Green's function) quantum chemical calculations provide important insight. Namely, a linear Stark shift γm is calculated for the HOMO of CnT molecules for electric field strengths (106-107 V cm-1) typical of molecular junctions, and the sign of γm matches the sign of the experimental γ for junctions derived from transport measurements, suggesting that the Stark effect plays an important role. However, the magnitude of the measured γ is only 10-15% of the computed value γm. We propose that this implies that the contacts are far from optimal; they substantially screen the effect of the applied bias, possibly via molecule-electrode interface states. We predict that, with optimized contacts, the rectification ratios in CnT-based junctions can reach reasonably high values (RR ≈ 500). We believe that Stark shifts and limited current rectification due to non-ideal contacts discussed here for the specific case of alkane monothiol junctions are issues of general interest for molecular electronics that deserve further consideration.