Unperturbed Molecule Research Articles

Tuning the transport properties of tetracene-based single-molecule junctions with chemical or structural variation of side and anchoring groups.

This study aims to tune the transport properties of tetracene single-molecule junctions with the proper choice and placement of side and anchoring groups. For the operationalization of the molecule that was anchored with thiol or isocyanide groups, two different side groups, amine and nitro, in two different positions, were taken into consideration. For unperturbed tetracene molecule, a prominent negative differential resistance (NDR) feature at 1.8 V was observed with the isocyanide anchoring group while the thiol anchoring group exhibits a plateau region over a bias voltage of 2.2 to 3.2 V. At a bias voltage that is dependent on the chemical or structural change of side or anchoring groups, NDR feature of varying degree was seen in all configurations. Results show that the current flowing through the thiol-anchored molecule perturbed with the amine group at S' position is relatively larger than other configurations because of the smaller HOMO-LUMO gap and broader transmission peaks resulting in a peak to valley current ratio (PVCR) of 1.22. In addition, multiple NDR regions were realized in nitro-perturbed isocyanide-anchored molecule at S position. These results suggest their promising applications in switches, logic cells, and storage devices. The modeling and simulation of side-group mediated anchored tetracene molecule through two electrodic systems were studied using density functional theory (DFT) combined with non-equilibrium Green's function (NEGF) in Virtual NanoLab-AtomistixToolkit (ATK). The electron transport properties were calculated using Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) exchange-correlation function. To optimize computing time, gold electrodes were single zeta polarized whereas the molecule, anchor groups, and side groups were double zeta polarized.

Anchoring Groups Determine Conductance, Thermopower and Thermoelectric Figure of Merit of an Organic Molecular Junction

Transport properties of molecular junctions are prone to chemical or conformational modifications. Perturbation of the molecule-electrode coupling with anchoring groups or functionalization of the molecule with side groups is a well-characterized method to modulate the thermoelectric properties of molecular junctions. In this study, we used wide-band approximation combined with the non-equilibrium Green’s function (NEGF) formalism to inspect conductance, thermopower and figure of merit of an anthracene molecule coupled to gold (Au) electrodes. To provide a comparative study, three different anchoring groups were used, i.e., thiol, isocyanide and cyanide. The molecule was then perturbed with the amine side group in two positions to explore the interplay between anchoring groups and the side group. We showed that the introduction of side group alters transmission probability near the Fermi energy where transmission peaks are shifted relative to the Fermi level compared to the unperturbed molecule (i.e., without side group), ultimately leading to modified electrical and thermoelectric properties. The greatest value of electrical conductance was achieved when the side-group-perturbed molecule was anchored with isocyanide, whereas the thiol-terminated molecule perturbed with the side group yielded the greatest value of thermal conductance. We found that the Wiedemann-Franz law is violated in the Au-anthracene-Au device. Furthermore, the highest thermopower and figure of merit were attained in the cyanide-terminated perturbed molecule. Our results indicate that charge donating/accepting character of the anchoring group and its interplay with the side group position can modify temperature dependency of conductance, thermopower and figure of merit which is in agreement with experimental findings in organic molecular junctions. Such modifications may potentially contribute to the understanding of emerging conductance-based memory devices designed to mimic the behavior of brain-like synapses.

Side-group-mediated thermoelectric properties of anthracene single-molecule junction with anchoring groups

Charge transfer characteristics of single-molecule junctions at the nanoscale, and consequently, their thermoelectric properties can be dramatically tuned by chemical or conformational modification of side groups or anchoring groups. In this study, we used density functional theory (DFT) combined with the non-equilibrium Green’s function (NEGF) formalism in the linear response regime to examine the thermoelectric properties of a side-group-mediated anthracene molecule coupled to gold (Au) electrodes via anchoring groups. In order to provide a comparative inspection three different side groups, i.e. amine, nitro and methyl, in two different positions were considered for the functionalization of the molecule terminated with thiol or isocyanide anchoring groups. We showed that when the anchored molecule is perturbed with side group, the peaks of the transmission spectrum were shifted relative to the Fermi energy in comparison to the unperturbed molecule (i.e. without side group) leading to modified thermoelectric properties of the system. Particularly, in the thiol-terminated molecule the amine side group showed the greatest figure of merit in both positions which was suppressed by the change of side group position. However, in the isocyanide-terminated molecule the methyl side group attained the greatest thermoelectric efficiency where its magnitude was relatively robust to the change of side group position. In this way, different combinations of side groups and anchoring groups can improve or suppress thermopower and the figure of merit of the molecular junction depending on the interplay between charge donating/accepting nature of the functionals or their position.

The kernel energy method (KEM) delivers fast and accurate QTAIM electrostatic charge for atoms in large molecules

The kernel energy method (KEM) is a soft scaling fragment quantum chemical calculation method that proved very useful for the estimation of ab initio energies of very large biological molecules. In this approach, a large molecule is broken into computationally tractable pieces (kernels), which reduces the otherwise rapidly rising computational difficulty with the number of atoms. The formula which delivers the KEM approximation to the total molecular energy includes sums over the energies of double kernels corrected for over-counting by subtracting a sum over single kernels. KEM has been shown to deliver numerically accurate energies of unperturbed large molecules and the energies and dipole moments of large molecules under strong external perturbing electric fields. A recent study has also shown that the full molecular localization–delocalization matrix and the electron density at bond and ring critical point can also be reconstructed from formulae of the same form of the KEM master equation. It is shown that the KEM formula can also be used to reconstruct accurate approximations to the two-particle and one-particle reduced density matrices. This paper shows three numerical examples, of increasing complexity and size, that the atomic charge of an atom in a molecule, calculated from Bader’s quantum theory of atoms in molecules, is accurately predicted from the KEM formula. The error introduced by the KEM approximation is found to be smaller than 0.01 % of the total number of electrons as our calculations demonstrate on three interesting compounds that represent a variety of bonding situations: a highly explosive compound N,N′-dinitrourea (C3H6N4O5, 92 electrons), a strong chelating agent (pyridine-2-azo-p-phenyl)tetramethylguanidine (PAPT) (C16H20N6, 158 electrons), and the conformationally restricted synthetic peptide acetyl-Cα,α-dipropylglycine heptapeptide (Ac-Dpg-7) (C39H71N7O9, 426 electrons).

Magnetic spin imaging under ambient conditions with sub-cellular resolution

The detection of small numbers of magnetic spins is a significant challenge in the life, physical and chemical sciences, especially when room temperature operation is required. Here we show that a proximal nitrogen-vacancy spin ensemble serves as a high precision sensing and imaging array. Monitoring its longitudinal relaxation enables sensing of freely diffusing, unperturbed magnetic ions and molecules in a microfluidic device without applying external magnetic fields. Multiplexed charge-coupled device acquisition and an optimized detection scheme permits direct spin noise imaging of magnetically labelled cellular structures under ambient conditions. Within 20 s we achieve spatial resolutions below 500 nm and experimental sensitivities down to 1,000 statistically polarized spins, of which only 32 ions contribute to a net magnetization. The results mark a major step towards versatile sub-cellular magnetic imaging and real-time spin sensing under physiological conditions providing a minimally invasive tool to monitor ion channels or haemoglobin trafficking inside live cells.

Orbital Control of Single-Molecule Conductance Perturbed by π-Accepting Anchor Groups: Cyanide and Isocyanide

Electron transport properties through benzene molecules disubstituted with π-accepting cyanide and isocyanide anchor groups at their para and meta positions are investigated on the basis of a qualitative orbital analysis at the Hückel molecular orbital level of theory. The applicability of a previously derived orbital symmetry rule for electron transport is extended to the systems perturbed by the π-accepting anchor groups, where the HOMO–LUMO symmetry in the molecular orbital energies relative to the Fermi level is removed. The conservation of the HOMO–LUMO symmetry in the spatial distribution of the molecular orbitals between the unperturbed benzene molecule and the perturbed molecules with the anchor groups rationalizes symmetry-allowed electron transport through the para isomers. On the other hand, destructive interferences between the nearly 2-fold degenerate frontier orbitals constructed from the 2-fold degenerate orbitals of the unperturbed benzene molecule and the anchor groups lead to symmetry-forbidden electron transport through the meta isomers. The qualitative orbital thinking is supported by more quantitative density functional theory (DFT) calculations combined with the nonequilibrium Green’s function (NEGF) method. The orbital analysis is a powerful tool for the understanding and rational design of molecular devices composed of π-conjugated hydrocarbons and those perturbed by the π-accepting anchor groups.

Mixed-valence behavior and strong correlation effects of metal phthalocyanines adsorbed on metals

We investigate the hierarchy of local correlation and hybridization effects in metal-organic molecules adsorbed on metals. Using x-ray magnetic circular dichroism and ligand field multiplet calculations, we demonstrate that the 3$d$ electronic ground state of monolayer metal-phthalocyanine (CoPc, FePc) on Au(111) is given by the coherent superposition of two charge states, ${d}^{n}E+{d}^{n+1}$, where $E$ represents a substrate electron antiferromagnetically coupled to the central metal ion and ${d}^{n}$ the many-body ionic orbital configuration of the unperturbed molecule. These results differ from previous models of hybrid metal-organic systems and provide a consistent description of their magnetic moments and Kondo physics in terms of spin and orbital multiplicity.

Quasistationary resonances induced by intense infrared fields in HD+and their decay

The nature of a few low-lying laser-induced resonances of HD${}^{+}$ along with their linewidths due to dissociation, has been investigated in the intensity range of (1--6) $\ifmmode\times\else\texttimes\fi{}{10}^{13}\mathrm{W}/{\mathrm{cm}}^{2}$ for three different laser frequencies. In the length gauge representation of the interaction Hamiltonian used by us, these resonances for the lower intensities are basically the vibrational states of the unperturbed molecule, shifted and broadened by radiative interactions. At higher intensities the resonances are obtained as quasistationary states on different adiabatic potentials. They are formed by the mixing of various unperturbed vibrational states by multiphoton interactions. In this mixing, the proportion of vibrational states further away from the resonance energy increases with the increase in intensity. At high enough intensities, signature of dissociation through a nonresonant intermediate vibrational transition to the $v=6$ and $v=7$ state is observed for a laser frequency of 12 500 cm${}^{\ensuremath{-}1}$. The width of the lowest resonance increases sharply with intensity, while its shift from the $v=0$ state increases only linearly with intensity. The branching ratios to different photon absorption channels change with intensity and they can be interpreted using the adiabatic potential curves. For a frequency of 2000 cm${}^{\ensuremath{-}1}$, which is close to the frequency of $v=0$ to $v=1$ transition, the resonances arise from the mixing of various vibrational levels through stepwise transitions, resulting in a dissociation linewidth larger compared to that obtained for higher frequencies.

Possible origin of thickness‐dependent deviations from bulk properties of thin polymer films

Journal of Polymer Science Part B: Polymer PhysicsVolume 48, Issue 24 p. 2544-2547 Viewpoint Possible origin of thickness-dependent deviations from bulk properties of thin polymer films Günter Reiter, Corresponding Author Günter Reiter guenter.reiter@physik.uni-freiburg.de Physikalisches Institut, Universität Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, GermanyPhysikalisches Institut, Universität Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, GermanySearch for more papers by this authorSimone Napolitano, Simone Napolitano Laboratory for Acoustics and Thermal Physics, Department of Physics and Astronomy, Katholieke Universiteit Leuven, Celestijnenlaan 200D, B-3001 Leuven, BelgiumSearch for more papers by this author Günter Reiter, Corresponding Author Günter Reiter guenter.reiter@physik.uni-freiburg.de Physikalisches Institut, Universität Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, GermanyPhysikalisches Institut, Universität Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, GermanySearch for more papers by this authorSimone Napolitano, Simone Napolitano Laboratory for Acoustics and Thermal Physics, Department of Physics and Astronomy, Katholieke Universiteit Leuven, Celestijnenlaan 200D, B-3001 Leuven, BelgiumSearch for more papers by this author First published: 07 September 2010 https://doi.org/10.1002/polb.22134Citations: 60Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume48, Issue2415 December 2010Pages 2544-2547 RelatedInformation

Analysis of Complexes Pairing Hydroperoxyl Radical with Peroxyformic Acid

Ab initio quantum calculations are used to analyze the binding of complexes pairing OOH with HOOCHO. Six minima are located on the potential energy surface, all of cyclic geometry. Of particular interest are the OH...O and CH...O H-bonds that arise in the complexes and the manner in which these interactions influence the internal properties of the subunits. The analysis is complicated by the presence of an intramolecular H-bond in the unperturbed HOOCHO molecule, which must be broken in order to form the pair of intermolecular H-bonds that are responsible for the binding in the most stable complex. The CH bond of HOOCHO is contracted, and its stretching frequency undergoes a blue shift, when this group participates in a H-bond.

Quantum-chemical study of the effects of noncovalent interactions on the nuclear magnetic screening constants of pyrimidine base associates

The effects of weak noncovalent interactions on the nuclear magnetic screening (NMS) constants (σ 1H), (σ 13C) and charge distribution (qt) on atoms in van der Waals model associates of unsubstituted and substituted pyrimidines and substituted uracil are considered. The NMS constants were calculated by the UB3LYP/6-31G(d,p) with GIAO functions. The correlation dependences of the 1H and 13C σ constants on the charge q on atoms whre constructed. It were shown that they can be represented as polynomials that include the terms that are linear and quadratic relative to the charge. The relations obtained in this way are similar in form and close in magnitude to the coefficients of the known Buckingham and Augspurger functions that describe the electric field effects on the nuclear magnetic screening constants. It was found that the coefficients in these polynomials have a definite physical sense in that they characterize nuclear magnetic screening and the “screening polarizability” tensor in the unperturbed molecule and associate, respectively. The NMS constants and charge distribution in pyrimidine base associates and accordingly the coefficients that reflect their values in polynomials depend on the form, size, and composition of the associate and can vary significantly depending on the position of the pyrimidine base in the associate.

Contributions of the substrate electric field to the molecular adsorbate optical nonlinearities

The nonlinear optical response of an adsorbate, whose structure is altered by the inhomogeneous electrostatic field of the substrate, has been evaluated with a particular emphasis on the sum-frequency generation process. In the limiting case of an homogeneous electrostatic field, besides the contributions associated with the induced dipole moments, we have additional contributions which only exist if the adsorbed molecule has permanent dipole moments. Also, the Franck-Condon factors of the unperturbed molecule weight the internal couplings induced by the electrostatic field. For the more general inhomogeneous electrostatic field case, while the main observations remain valid, the Franck-Condon factors are modified by the molecular structure changes induced by the electrostatic field. In addition, we have a strong redistribution of the vibronic couplings resulting from the analytical $\mathbf{Q}$ dependence of the partial charge distribution which is a signature of the field inhomogeneities.

Residual stresses in thin polymer films cause rupture and dominate early stages of dewetting

In attempting to reduce the size of functional devices, the thickness of polymer films has reached values even smaller than the diameter of the unperturbed molecule. However, despite enormous efforts for more than a decade, our understanding of the origin of some puzzling properties of such thin films is still not satisfactory and several peculiar observations remain mysterious. For example, under certain conditions, such films show negative expansion coefficients or show undesirable rupture although energetically they are expected to be stable. Here, we demonstrate that many of these extraordinary effects can be related to residual stresses within the film, resulting from the preparation of these films from solution by fast evaporation of the solvent. Consequently, depending on thermal history and ageing time, such films show significant changes even in the glassy state, which we quantify by dewetting experiments and corresponding theoretical studies. Identifying the relevance of frozen-in polymer conformations gives us a handle for manipulating and controlling properties of nanometric thin polymer films.

Sum rules for nonlinear optical properties of molecules

It is explicitly shown, that calculated sum over all states of the nonlinear optical properties (NLO) of molecular system (polarizability, hyperpolarizability, etc.) is exactly zero when wave functions which satisfy the Hellmann–Feynman theorem is used. These sum rules are correct for sum over energy levels (i.e., translation, rotation, oscillation and electronic) in case of any one-electron properties which can be described by the Hamiltonian H 0 + λH (1), where H 0 is the Hamiltonian of the unperturbed molecule and λ and H (1) represent external perturbation and the one-electron operator of any physical property, respectively.

Electronic Density Approaches to the Energetics of Noncovalent Interactions

We present an overview of procedures that have been developed to compute several energetic quantities associated with noncovalent interactions. These formulations involve numerical integration over appropriate electronic densities. Our focus is upon the electrostatic interaction between two unperturbed molecules, the effect of the polarization of each charge distribution by the other, and the total energy of interaction. The expression for the latter is based upon the Hellmann-Feynman theorem. Applications to a number of systems are discussed; among them are dimers of uracil and interacting pairs of molecules in the crystal lattice of the energetic compound RDX.

Nanostructured Diblock Copolymer Films: A Grazing Incidence Small-Angle Neutron Scattering Study

The destabilization of confined ultrathin poly(styrene-block-paramethylstyrene) films with a fully deuterated polystyrene block in the strong segregation limit is investigated. Using the spin-coating technique, polymer films with thicknesses smaller than the radius of gyration of the unperturbed polymer molecule were prepared on top of solid substrates. Successively these films have been annealed by storage under a toluene atmosphere. The evolving surface topographies are investigated with atomic force microscopy. From grazing incidence small-angle neutron scattering (GISANS), the microphase separation structure is determined in addition. Although these ultrathin films are hardly detectable with reflectivity measurements, in GISANS a good signal was obtained. The time dependence of the characteristic lateral length of the nanostructures follows an Avrami growth law.

A direct simulation of EPR slow-motion spectra of spin labelled phospholipids in liquid crystalline bilayers based on a molecular dynamics simulation of the lipid dynamics

EPR line shapes can be calculated from the stochastic Liouville equation assuming a stochastic model for the reorientation of the spin probe. Here we use instead and for the first time a detailed molecular dynamics (MD) simulation to generate the stochastic input to the Langevin form of the Liouville equation. A 0.1 μs MD simulation at T = 50°C of a small lipid bilayer formed by 64 dipalmitoylphosphatidylcholine (DPPC) molecules at the water content of 23 water molecules per lipid was used. In addition, a 10 ns simulation of a 16 times larger system consisting of 32 DPPC molecules with a nitroxide spin moiety attached at the sixth position of the sn2 chain and 992 ordinary DPPC molecules, was used to investigate the extent of the perturbation caused by the spin probe. Order parameters, reorientational dynamics and the EPR FID curve were calculated for spin probe molecules and ordinary DPPC molecules. The timescale of the electron spin relaxation for a spin-moiety attached at the sixth carbon position of a DPPC lipid molecule is 11.9 × 107 rad s−1 and for an unperturbed DPPC molecule it is 3.5 × 107 rad s−1.

Quantum-Chemical Modeling and Analysis of the Vibrational Structure in the Phosphorescence Spectrum of C60

The phosphorescence spectrum of C60, recently obtained in alkane and in Xe matrixes at low temperature, has been modeled by means of semiempirical quantum chemical calculations. The T1 → S0 transition in the unperturbed molecule is symmetry as well as spin multiplicity forbidden. The intensities of the false origins due to inducing modes have been calculated in terms of the Herzberg−Teller mechanism combined with an expansion over spin−orbit perturbations. To date, this is the first modeling of the phosphorescence spectrum of C60 entirely based on computed molecular parameters. Thus, the analysis of the spectrum is based not only on vibrational frequencies, but also on the comparison between computed and observed vibronic intensities. The calculations indicate that the vibrational structure is dominated by false origins due to modes of hu, gu, and t1u symmetry, but contains also a number of combination bands based mainly on the Jahn−Teller active hg(1) mode.

Convergence of the Electrostatic Interaction Based on Topological Atoms

An atom−atom partitioning of the electrostatic energy between unperturbed molecules is proposed on the basis of the topology of the electron density. Atom−atom contributions to the electrostatic energy are computed exactly, i.e., via a novel six-dimensional integration over two atomic basins, and by means of the spherical tensor multipole expansion, up to total interaction rank L = lA + lB + 1 = 6. The convergence behavior of the topological multipole expansion is compared with that using distributed multipole analysis (DMA) multipole moments for a set of van der Waals complexes at the B3LYP/6-311+G(2d,p) level. Within the context of the Buckingham−Fowler model it is shown that the topological and DMA multipole moments converge to a very similar interaction energy and geometry (average absolute discrepancy of 1.3 kJ/mol and 1.3°, respectively) and are both in good to excellent agreement with supermolecule calculations.

Dipole strengths in chlorophyll-a and bacteriochlorophyll-a

In principle, the dipole strength (D) of an optical transition of a chromophore in a given environment can be related to a vacuum dipole strength (d) of that transition. Such a vacuum strength refers to that of a completely unperturbed molecule and therefore to some unique theoretical value. In a given environment, characterized in practice by a refractive index n, it is possible to argue that D(n) = f(n)*d, where f(n) is a correction factor that is frequently taken to be that of Lorentz. By varying the solvent within broadly similar categories (polar or non-polar, for example), one might therefore expect to discover a unique value of d. However, it has been known for 70 years that even simple chromophores in simple solvents do not follow this prescription with a Lorentz factor. The chlorophylls also do not. More success has been achieved for the chlorophylls with an empty-cavity factor. The literature contains a confusing array of D values for the Qy transitions of both chlorophyll-a and bacteriochlorophyll-a. We analyze this problem and present a simplified procedure that should help to maintain consistency in comparing experimental results. In addition, we resolve some wide discrepancies among the predicted rates of Forster excitation transfer between chlorophyll-a molecules.