Gino A. DiLabio

Field regulation of single-molecule conductivity by a charged surface atom

Electrical transport through molecules has been much studied since it was proposed that individual molecules might behave like basic electronic devices, and intriguing single-molecule electronic effects have been demonstrated. But because transport properties are sensitive to structural variations on the atomic scale, further progress calls for detailed knowledge of how the functional properties of molecules depend on structural features. The characterization of two-terminal structures has become increasingly robust and reproducible, and for some systems detailed structural characterization of molecules on electrodes or insulators is available. Here we present scanning tunnelling microscopy observations and classical electrostatic and quantum mechanical modelling results that show that the electrostatic field emanating from a fixed point charge regulates the conductivity of nearby substrate-bound molecules. We find that the onset of molecular conduction is shifted by changing the charge state of a silicon surface atom, or by varying the spatial relationship between the molecule and that charged centre. Because the shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature.

Oscillations in meta-generalized-gradient approximation potential energy surfaces for dispersion-bound complexes.

Meta-generalized-gradient approximations (meta-GGAs) in density-functional theory are exchange-correlation functionals whose integrands depend on local density, density gradient, and also the kinetic-energy density. It has been pointed out by Johnson et al. [Chem. Phys. Lett. 394, 334 (2004)] that meta-GGA potential energy curves in dispersion-bound complexes are susceptible to spurious oscillations unless very large integration grids are used. This grid sensitivity originates from the saddle-point region of the density near the intermonomer midpoint. Various dimensionless ratios involving the kinetic-energy density, found in typical meta-GGAs, may be ill-behaved in this region. Grid sensitivity thus arises if the midpoint region is sampled by too sparse a grid. For most meta-GGAs, standard grids do not suffice. Care must be taken to avoid this problem when using, or constructing, meta-GGAs.

A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP

B3LYP is the most widely used density-functional theory (DFT) approach because it is capable of accurately predicting molecular structures and other properties. However, B3LYP is not able to reliably model systems in which noncovalent interactions are important. Here we present a method that corrects this deficiency in B3LYP by using dispersion-correcting potentials (DCPs). DCPs are utilized by simple modifications to input files and can be used in any computational package that can read effective-core potentials. Therefore, the technique requires no programming. DCPs (developed for H, C, N, and O) produce the best results when used in conjunction with 6-31+G(2d,2p) basis sets. The B3LYP-DCP approach was tested on the S66, S22, and HSG-A benchmark sets of noncovalently interacting dimers and trimers and was found to, on average, significantly outperform almost all other DFT-based methods that were designed to treat van der Waals interactions. Users of B3LYP who wish to model systems in which noncovalent interactions (viz., steric repulsion, hydrogen bonding, π-stacking) are present, should consider B3LYP-DCP.

Performance of conventional and dispersion-corrected density-functional theory methods for hydrogen bonding interaction energies

The approximate CCSD(T)/CBS binding energies for the set of 23 hydrogen-bonded dimers (HB23) of the S66 set reported by Řezáč et al. (J. Chem. Theory Comput. 2011, 7, 2427-2438) were expected to be under-estimated based on the known under-binding tendency of the counterpoise correction combined with small basis sets. In this work, we present binding energies for the HB23 set of dimers obtained using a composite approach recently described by Mackie and DiLabio (J. Chem. Phys. 2011, 135, 134318) that averages the counterpoise- and non-counterpoise-corrected energies, while utilizing standard approaches to obtain CCSD(T)/CBS-type energies. The binding energies for the HB23 set are revised upward by an average of 0.12 kcal mol(-1) and as much as 0.35 kcal mol(-1). We use these improved benchmark-level binding energies to evaluate the ability of pure, hybrid, long-range-corrected, and dispersion-corrected density-functional theory (DFT) methods to accurately predict the binding energies of hydrogen-bonded dimers. We find that, in general, the inclusion of dispersion into the DFT approach is required in order to obtain reasonable results for the HB23 set. We find that the dispersion-corrected DFT methods we tested produce results of variable quality, as measured by mean absolute deviation relative to the revised reference values we computed: B97D, 0.57 kcal mol(-1); B3LYP-D3, 0.44 kcal mol(-1); ωB97XD, 0.25 kcal mol(-1); LC-ωPBE-D3, 0.24 kcal mol(-1); M06-2X, 0.21 kcal mol(-1); B3LYP-DCP, 0.23 kcal mol(-1); B971-XDM, 0.18 kcal mol(-1).

Approximations to complete basis set-extrapolated, highly correlated non-covalent interaction energies

The first-principles calculation of non-covalent (particularly dispersion) interactions between molecules is a considerable challenge. In this work we studied the binding energies for ten small non-covalently bonded dimers with several combinations of correlation methods (MP2, coupled-cluster single double, coupled-cluster single double (triple) (CCSD(T))), correlation-consistent basis sets (aug-cc-pVXZ, X = D, T, Q), two-point complete basis set energy extrapolations, and counterpoise corrections. For this work, complete basis set results were estimated from averaged counterpoise and non-counterpoise-corrected CCSD(T) binding energies obtained from extrapolations with aug-cc-pVQZ and aug-cc-pVTZ basis sets. It is demonstrated that, in almost all cases, binding energies converge more rapidly to the basis set limit by averaging the counterpoise and non-counterpoise corrected values than by using either counterpoise or non-counterpoise methods alone. Examination of the effect of basis set size and electron correlation shows that the triples contribution to the CCSD(T) binding energies is fairly constant with the basis set size, with a slight underestimation with CCSD(T)∕aug-cc-pVDZ compared to the value at the (estimated) complete basis set limit, and that contributions to the binding energies obtained by MP2 generally overestimate the analogous CCSD(T) contributions. Taking these factors together, we conclude that the binding energies for non-covalently bonded systems can be accurately determined using a composite method that combines CCSD(T)∕aug-cc-pVDZ with energy corrections obtained using basis set extrapolated MP2 (utilizing aug-cc-pVQZ and aug-cc-pVTZ basis sets), if all of the components are obtained by averaging the counterpoise and non-counterpoise energies. With such an approach, binding energies for the set of ten dimers are predicted with a mean absolute deviation of 0.02 kcal/mol, a maximum absolute deviation of 0.05 kcal/mol, and a mean percent absolute deviation of only 1.7%, relative to the (estimated) complete basis set CCSD(T) results. Use of this composite approach to an additional set of eight dimers gave binding energies to within 1% of previously published high-level data. It is also shown that binding within parallel and parallel-crossed conformations of naphthalene dimer is predicted by the composite approach to be 9% greater than that previously reported in the literature. The ability of some recently developed dispersion-corrected density-functional theory methods to predict the binding energies of the set of ten small dimers was also examined.

Efficient silicon surface and cluster modeling using quantum capping potentials

A one-electron, silicon quantum capping potential for use in capping the dangling bonds formed by artificially limiting silicon clusters or surfaces is developed. The quantum capping potentials are general and can be used directly in any computational package that can handle effective core potentials. For silicon clusters and silicon surface models, we compared the results of traditional hydrogen atom capping with those obtained from capping with quantum capping potentials. The results clearly show that cluster and surface models capped with quantum capping potentials have ionization potentials, electron affinities, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps that are in very good agreement with those of larger systems. The silicon quantum capping potentials should be applied in cases where one wishes to model processes involving charges or low-energy excitations in silicon clusters and surfaces consisting of more than ca. 150 atoms.

Gas-Phase Thermolysis of a Guanidinate Precursor of Copper Studied by Matrix Isolation, Time-of-Flight Mass Spectrometry, and Computational Chemistry

The fragmentation of the copper(I) guanidinate [Me(2)NC(NiPr)(2)Cu](2) (1) has been investigated with time-of-flight mass spectrometry (TOF MS), matrix-isolation FTIR spectroscopy (MI FTIR spectroscopy), and density functional theory (DFT) calculations. Gas-phase thermolyses of 1 were preformed in the temperature range of 100-800 degrees C. TOF MS and MI FTIR gave consistent results, showing that precursor 1 starts to fragment at oven temperatures above 150 degrees C, with a close to complete fragmentation at 260 degrees C. Precursor 1 thermally fragments to Cu((s)), H(2)(g), and the oxidized guanidine Me(2)NC(=NiPr)(N=CMe(2)) (3). In TOF MS experiment, 3 was clearly indentified by its molecular ion at 169.2 u. Whereas H(2)(+) was detected, atomic Cu was not found in gas-phase thermolysis. In addition, the guanidine Me(2)NC(NiPr)(NHiPr) (2) was detected as a minor component among the thermolysis products. MI thermolysis experiments with precursor 1 were performed, and species evolving from the thermolysis oven were trapped in solid argon at 20 K. These species were characterized by FTIR spectroscopy. The most indicative feature of the resulting spectra from thermolysis above 150 degrees C was a set of intense and structured peaks between 1600 and 1700 cm(-1), an area where precursor 1 does not have any absorbances. The guanidine 2 was matrix-isolated, and a comparison of its FTIR spectrum with the spectra of the thermolysis of 1 indicated that species 2 was among the thermolysis products. However, the main IR bands in the range of 1600 and 1700 cm(-1) appeared at 1687.9, 1668.9, 1635.1, and 1626.6 cm(-1) and were not caused by species 2. The oxidized guanidine 3 was synthesized for the first time and characterized by (1)H NMR and FTIR spectroscopy. A comparison of an FTIR spectrum of matrix isolated 3 with spectra of the thermolysis of 1 revealed that the main IR bands in the range of 1600 and 1700 cm(-1) are due to the presence of 3. The isomers exhibit the NMe(2) group cis or trans to the iPr group, with cis-3 being significantly less stable than trans-3. At higher temperature secondary thermal fragments had been observed. For example at 700 degrees C, TOF MS and MI FTIR data showed that species 2 and 3 both eliminate HNMe(2) to give the carbodiimides iPrNCNiPr (CDI) and iPrNCN[C(=CH(2))Me] (4), respectively. A DFT study of the decomposition of compound 1 was undertaken at the B3LYP/6-31+G(d,p) level of theory employing dispersion-correcting potentials (DCPs). The DFT study rationalized both carbodiimide deinsertion and beta-hydrogen elimination as exergonic decomposition pathways (DeltaG = -44.4 kcal/mol in both cases), but experiment showed beta-hydrogen elimination to be the favorable route.

Extension of the B3LYP–dispersion-correcting potential approach to the accurate treatment of both inter- and intra-molecular interactions

Abstract We recently demonstrated that dispersion-correcting potentials (DCPs), which arexa0atom-centered Gaussian-type functions that were developed for use with B3LYP (Torres and DiLabio in J Phys Chem Lett 3:1738–1744, 2012), greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the recent application of the B3LYP–DCP approach to study the β-scission of the cumyloxyl radical led to a calculated barrier height that was over-estimated by ca. 8xa0kcal/mol. We demonstrate in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C–C covalent-bonding region. In this work, we developed a new C-DCP with a form that was expected to less strongly influence the electron density in the covalent bonding region. Tests of the new C-DCP, in conjunction with previously published H-, N-, and O-DCPs, with B3LYP–DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular interactions, giving mean absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18xa0kcal/mol, respectively. Additional testing on the S12L database of very large complexation systems gave an MAE of 2.6xa0kcal/mol, demonstrating that the B3LYP–DCP/6-31+G(2d,2p) approach to be one of the best-performing and most feasible methods for treating large systems containing significant non-covalent interactions. Finally, we showed that the modeling of C–C-making/C–C-breaking chemistry is well predicted using the newly developed DCPs. In addition to predicting a barrier height for the β-scission of the cumyloxyl radical, that is, within 1.7xa0kcal/mol of the high-level value, application of B3LYP–DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights and energies, isomerization energies, and relative conformation energies gives performance that is among the best of all available dispersion-corrected density-functional theory approaches.

Isomerization of Triphenylmethoxyl: The Wieland Free‐Radical Rearrangement Revisited a Century Later

yielded 2.3 g of a yellow oil from which benzophenone (almost 2 g) and phenol (0.2 g) were separated. Further heating gave a substantial, but not quantifiable, amount of Ph3COH. Wieland s interpretation was that triphenylmethoxyl radicals (Ph3COC, 2) had been formed and had isomerized to Ph2(PhO)CC radicals (3) which then coupled (Scheme 1). This was the first clearly demonstrated, and explicitly shown, free-radical rearrangement—a priority often overlooked. The rate constants and mechanisms of isomerization of triphenylmethoxyl (2) and the analogous isomerizations of Ph2C(Me)OC (5), [2–10] and related radicals (Scheme 2), have received considerable attention. Claims that discrete spiro intermediates (6) had been identified in the rearrangements of 2 and 5 3] have been disproven. However, computational studies on the rearrangement of 5 10] (and PhCH2OC) [11] do indicate stepwise processes with spiro radicals (6) as intermediates (Scheme 2). Consistent with these calculations, cumyloxyl radicals, PhC(Me)2OC, para substituted with a 2,2-diphenylcyclopropyl reporter group, have been demonstrated to be in equilibrium with spiro radicals 6. Rate constants (10 6 k2 s ) measured at room temperature by laser flash photolysis (LFP) in CH3CN were 2.5, [6]

Theoretical investigation of electron transport modulation through benzenedithiol by substituent groups.

Density functional theory combined with nonequilibrium Greens function techniques was used to model the conduction through disubstituted benzenedithiol molecules bonded to leads composed of 3x3, 5x5 gold and 3x3 aluminum. For the disubstituted 3x3 Au-benzenedithiol-Au systems, the small lead cross section results in a region of nearly zero transmission from -0.4 to -0.2 eV, relative to E(F), due to the absence of lead states. This feature results in negative differential resistance in the current-voltage curves and also causes the main peaks in the transmission spectra, which are dominated by the highest occupied molecular orbitals, to be centered near E(F). The zero-bias transmissions for the disubstituted benzenedithiol, as well as currents at applied biases, correlate very well with the Hammett parameter sigma(p), a quantity that relates the electron donating or withdrawing strength of a substituent. Calculations on disubstituted benzenedithiol connected to 5x5 Au leads produced transmission spectra that showed no gaps over the energy range considered and no negative differential resistance. The transmission in these cases also predominately involves the highest occupied molecular orbitals, and electron donating and withdrawing groups are able to increase and decrease current, respectively. However, there is no strong correlation between current and sigma(p) for this system. This suggests that the correlation observed in the 3x3 Au systems arises from the abrupt cutoff of the main transmission peaks near E(F). The disubstituted 3x3 Al-benzenedithiol-Al systems displayed markedly different behavior from the Au analogs. Electron donating groups and H benzenedithiol-substituted systems display almost no transmission over the energy range considered. However, electron withdrawing group disubstituted benzenedithiol systems had significant peaks in the transmission spectra near E(F), which are associated with the lowest-energy, unoccupied pi-type molecular orbitals. Higher currents are calculated for cases where the substituents have pi-type orbitals that are conjugated with the ring moiety of benzenedithiol. In all cases, the current through the 3x3 Al-benzenedithiol-Al systems is about a factor of 2 less than that through the analogous Au systems. These simulations reveal that the electrical conductance behavior through nanosystems of the type investigated in this work depends on the nature of the molecule as well as the size and composition of the leads to which it is connected. The results suggest that rational design of nanoelectronic systems might be possible under certain conditions but that structure-function relationships cannot be transferred from one system to another.