Hydrogen bonds are of utmost importance in both chemistry and biology. As the applicability of de... more Hydrogen bonds are of utmost importance in both chemistry and biology. As the applicability of density functional theory and ab initio methods extends to ever larger systems and to liquids, an accurate description of such interactions is desirable. However, reference data are often lacking, and ab initio calculations are only possible and done in very small basis sets. Here, we present high level [CCSD(T)] ab initio reference calculations at the basis set limit on a large set of hydrogen-bonded systems and assess the accuracy of second-order perturbation theory (MP2). The possibilities of using basis set extrapolations for geometries and dissociation energies are discussed as well as the results of R12 methods and density functional and local correlation methods.
Distance measurements between spin labels by means of pulse EPR have attracted considerable atten... more Distance measurements between spin labels by means of pulse EPR have attracted considerable attention because of the applications to biological systems. 1,2 These determine the dipolar interaction between two electron spins, which for two S) 1 / 2 spins is In eq 1, g 1 and g 2 are the g values, r is the interspin distance, and θ is the angle between r and the external magnetic field, B 0. The accessible distance range, 1.5-6.0 nm, allows one to obtain structural information on biomolecules such as proteins, DNA and RNA, and their complexes. 3,4 Two nitroxide spin labels (NSL) are introduced in the biomolecule, and the measurements are usually carried out at X-band frequencies (∼9.5 GHz) on samples of ∼50 µL of 0.1-0.2 mM solutions (∼12 h accumulation time). Distance measurements, however, are not limited to organic radicals, and measurements involving metal ions were reported as well. 5-7 In principle, high field (HF)/high microwave frequency (HM-WF) 8,9 measurements can offer improvement in sensitivity over X-band. However, due to the g anisotropy, the width of the NSL EPR spectrum increases at HF, leading to a decrease in the spectral density and of the flip probability of the pumped spins. Therefore, excluding cases where the relative orientation of the g frames of the NSLs is of prime interest, HF measurements provide only moderate gain (if any). For HF distance measurements, a different class of spin labels, the spectrum of which narrows with increasing B 0 , such as high spin half integer systems (HSS) like Gd 3+ (S) 7/2) may be attractive. While the width of the entire spectrum of these ions is determined by the crystal field interaction (cfi), which is magnetic field independent, the sub-spectrum of the central |-1 / 2 〉 f | 1 / 2 〉 transition (CT) narrows as B 0 increases. Here we present first results on the synthesis and pulse double electron-electron resonance (DEER) measurements between two Gd 3+ ions connected via a rigid linker, shown in Scheme 1. The bis-Gd 3+ complex comprises two units of a pyridine-based tetracarboxylate gadolinium complex, developed as an MRI contrast agent. 10 Double Sonogashira coupling of the pyridine tetracarboxy-late ester 1 and 1,4-diethynylbenzene (2) provided the corresponding octa-ester 11 (Scheme 1). Deprotection of the octa-ester 11 and subsequent complexation of the octa-acid with excess of an aqueous solution of GdCl 3 ‚3H 2 O gave the desired bis-Gd 3+ complex 5 in 86% yield. The paramagnetic complex 5 was characterized by IR, MS (ESI), HRMS, and magnetic moment (p) 15.63(2) µ B) analyses. 11 The DEER measurements were carried out at Ka-(33.78 and 29.6 GHz) and W-(94.9 GHZ) bands. 12,13 The corresponding echo-detected (ED) EPR spectra are shown in Figure 1b. The width of the W-band CT is about 0.4 of that at Ka-band, as expected. 14 The broad background the CT is superimposed on is due to all other transitions, and their relative intensities are a function of the temperature and spectrometer frequency. The relative populations, P(M S), of the M S) (1 / 2 energy levels for the frequencies and temperatures at which the experiments were carried out are listed in Table 1. The four-pulse, 15 time domain DEER traces, shown in Figure 2a, exhibit a steep initial decay and shallow but clear
The conductance of a single molecule transport junction is investigated in the Landauer-Imry regi... more The conductance of a single molecule transport junction is investigated in the Landauer-Imry regime of coherent tunneling transport. Utilizing aromatic systems with thiol end groups, we have calculated using density functional theory the expected conductance of junctions containing molecules with different levels of conjugation and of different lengths. The calculated variations in transport junction conductance are explained in terms of the continuity of the conjugation path between leads. Molecular conjugation describes this continuity within the molecule, and the interfacial terms (spectral densities or imaginary parts of the self-energy) describe its continuity at the molecule/metal interface. We compare the results from junction conductance calculations with isolated molecule electronic structure calculations These density functional theory calculations suggest that for these dithiol molecules, transport occurs mostly through the occupied orbital manifold. The decay of the transport with length is found to be exponential for poly-Ph dithiol molecules. We compare the calculated conductance of conjugated aromatic molecules with their molecular orbital calculations and with the Green's function formulation and evaluate the relative significance of different factors (such as energetic alignment and spectral density) that control the conductance of molecules.
Basis set convergence of correlation effects on molecular atomization energies beyond the coupled... more Basis set convergence of correlation effects on molecular atomization energies beyond the coupled cluster with singles and doubles CCSD approximation has been studied near the one-particle basis set limit. Quasiperturbative connected triple excitations, T, converge more rapidly than L −3 where L is the highest angular momentum represented in the basis set, while higher-order connected triples, T 3 − T, converge more slowly—empirically, L −5/2. Quasiperturbative connected quadruple excitations, Q, converge smoothly as L −3 starting with the cc-pVTZ basis set, while the cc-pVDZ basis set causes overshooting of the contribution in highly polar systems. Higher-order connected quadruples display only weak, but somewhat erratic, basis set dependence. Connected quintuple excitations converge very rapidly with the basis set, to the point where even an unpolarized double-zeta basis set yields useful numbers. In cases where fully iterative coupled cluster up to connected quintuples CCSDTQ5 calculations are not an option, CCSDTQ5 i.e., coupled cluster up to connected quadruples plus a quasiperturbative connected quintuples correction cannot be relied upon in the presence of significant nondynamical correlation, whereas CCSDTQ5 represents a viable alternative. Connected quadruples corrections to the core-valence contribution are thermochemically significant in some systems. We propose an additional variant of W4 theory A. Karton et al., J. Chem. Phys. 125, 144108 2006, denoted W4.4 theory, which is shown to yield a rms deviation from experimental atomization energies active thermochemical tables, ATcT of only 0.05 kcal/ mol for systems for which ATcT values are available. We conclude that " 3 1 kJ/ mol " thermochemistry is feasible with current technology, but that the more ambitious goal of ±10 cm −1 accuracy is illusory, at least for atomization energies.
We examine the applicability of density functional theory (DFT) to the polarizability of C n-(n) ... more We examine the applicability of density functional theory (DFT) to the polarizability of C n-(n) 3-9) cluster anions. This was achieved by comparing DFT calculations using two different exchange-correlation functionals (the non-empirical local density approximation, LDA, and the semiempirical hybrid functional B97-1) to quantum chemical calculations using the coupled cluster method in the CCSD(T) " gold standard " approximation. We find that, unless the extra electron is not bound at all by DFT, both LDA and B97-1 agree with the CCSD(T) calculation to within 5-10%, allowing for a meaningful qualitative and semiquantitative analysis. Furthermore, the polarizability is found to increase monotonically with chain size, consistent with the trend inferred from electron detachment experiments.
Hydrogen bonds are of utmost importance in both chemistry and biology. As the applicability of de... more Hydrogen bonds are of utmost importance in both chemistry and biology. As the applicability of density functional theory and ab initio methods extends to ever larger systems and to liquids, an accurate description of such interactions is desirable. However, reference data are often lacking, and ab initio calculations are only possible and done in very small basis sets. Here, we present high level [CCSD(T)] ab initio reference calculations at the basis set limit on a large set of hydrogen-bonded systems and assess the accuracy of second-order perturbation theory (MP2). The possibilities of using basis set extrapolations for geometries and dissociation energies are discussed as well as the results of R12 methods and density functional and local correlation methods.
Distance measurements between spin labels by means of pulse EPR have attracted considerable atten... more Distance measurements between spin labels by means of pulse EPR have attracted considerable attention because of the applications to biological systems. 1,2 These determine the dipolar interaction between two electron spins, which for two S) 1 / 2 spins is In eq 1, g 1 and g 2 are the g values, r is the interspin distance, and θ is the angle between r and the external magnetic field, B 0. The accessible distance range, 1.5-6.0 nm, allows one to obtain structural information on biomolecules such as proteins, DNA and RNA, and their complexes. 3,4 Two nitroxide spin labels (NSL) are introduced in the biomolecule, and the measurements are usually carried out at X-band frequencies (∼9.5 GHz) on samples of ∼50 µL of 0.1-0.2 mM solutions (∼12 h accumulation time). Distance measurements, however, are not limited to organic radicals, and measurements involving metal ions were reported as well. 5-7 In principle, high field (HF)/high microwave frequency (HM-WF) 8,9 measurements can offer improvement in sensitivity over X-band. However, due to the g anisotropy, the width of the NSL EPR spectrum increases at HF, leading to a decrease in the spectral density and of the flip probability of the pumped spins. Therefore, excluding cases where the relative orientation of the g frames of the NSLs is of prime interest, HF measurements provide only moderate gain (if any). For HF distance measurements, a different class of spin labels, the spectrum of which narrows with increasing B 0 , such as high spin half integer systems (HSS) like Gd 3+ (S) 7/2) may be attractive. While the width of the entire spectrum of these ions is determined by the crystal field interaction (cfi), which is magnetic field independent, the sub-spectrum of the central |-1 / 2 〉 f | 1 / 2 〉 transition (CT) narrows as B 0 increases. Here we present first results on the synthesis and pulse double electron-electron resonance (DEER) measurements between two Gd 3+ ions connected via a rigid linker, shown in Scheme 1. The bis-Gd 3+ complex comprises two units of a pyridine-based tetracarboxylate gadolinium complex, developed as an MRI contrast agent. 10 Double Sonogashira coupling of the pyridine tetracarboxy-late ester 1 and 1,4-diethynylbenzene (2) provided the corresponding octa-ester 11 (Scheme 1). Deprotection of the octa-ester 11 and subsequent complexation of the octa-acid with excess of an aqueous solution of GdCl 3 ‚3H 2 O gave the desired bis-Gd 3+ complex 5 in 86% yield. The paramagnetic complex 5 was characterized by IR, MS (ESI), HRMS, and magnetic moment (p) 15.63(2) µ B) analyses. 11 The DEER measurements were carried out at Ka-(33.78 and 29.6 GHz) and W-(94.9 GHZ) bands. 12,13 The corresponding echo-detected (ED) EPR spectra are shown in Figure 1b. The width of the W-band CT is about 0.4 of that at Ka-band, as expected. 14 The broad background the CT is superimposed on is due to all other transitions, and their relative intensities are a function of the temperature and spectrometer frequency. The relative populations, P(M S), of the M S) (1 / 2 energy levels for the frequencies and temperatures at which the experiments were carried out are listed in Table 1. The four-pulse, 15 time domain DEER traces, shown in Figure 2a, exhibit a steep initial decay and shallow but clear
The conductance of a single molecule transport junction is investigated in the Landauer-Imry regi... more The conductance of a single molecule transport junction is investigated in the Landauer-Imry regime of coherent tunneling transport. Utilizing aromatic systems with thiol end groups, we have calculated using density functional theory the expected conductance of junctions containing molecules with different levels of conjugation and of different lengths. The calculated variations in transport junction conductance are explained in terms of the continuity of the conjugation path between leads. Molecular conjugation describes this continuity within the molecule, and the interfacial terms (spectral densities or imaginary parts of the self-energy) describe its continuity at the molecule/metal interface. We compare the results from junction conductance calculations with isolated molecule electronic structure calculations These density functional theory calculations suggest that for these dithiol molecules, transport occurs mostly through the occupied orbital manifold. The decay of the transport with length is found to be exponential for poly-Ph dithiol molecules. We compare the calculated conductance of conjugated aromatic molecules with their molecular orbital calculations and with the Green's function formulation and evaluate the relative significance of different factors (such as energetic alignment and spectral density) that control the conductance of molecules.
Basis set convergence of correlation effects on molecular atomization energies beyond the coupled... more Basis set convergence of correlation effects on molecular atomization energies beyond the coupled cluster with singles and doubles CCSD approximation has been studied near the one-particle basis set limit. Quasiperturbative connected triple excitations, T, converge more rapidly than L −3 where L is the highest angular momentum represented in the basis set, while higher-order connected triples, T 3 − T, converge more slowly—empirically, L −5/2. Quasiperturbative connected quadruple excitations, Q, converge smoothly as L −3 starting with the cc-pVTZ basis set, while the cc-pVDZ basis set causes overshooting of the contribution in highly polar systems. Higher-order connected quadruples display only weak, but somewhat erratic, basis set dependence. Connected quintuple excitations converge very rapidly with the basis set, to the point where even an unpolarized double-zeta basis set yields useful numbers. In cases where fully iterative coupled cluster up to connected quintuples CCSDTQ5 calculations are not an option, CCSDTQ5 i.e., coupled cluster up to connected quadruples plus a quasiperturbative connected quintuples correction cannot be relied upon in the presence of significant nondynamical correlation, whereas CCSDTQ5 represents a viable alternative. Connected quadruples corrections to the core-valence contribution are thermochemically significant in some systems. We propose an additional variant of W4 theory A. Karton et al., J. Chem. Phys. 125, 144108 2006, denoted W4.4 theory, which is shown to yield a rms deviation from experimental atomization energies active thermochemical tables, ATcT of only 0.05 kcal/ mol for systems for which ATcT values are available. We conclude that " 3 1 kJ/ mol " thermochemistry is feasible with current technology, but that the more ambitious goal of ±10 cm −1 accuracy is illusory, at least for atomization energies.
We examine the applicability of density functional theory (DFT) to the polarizability of C n-(n) ... more We examine the applicability of density functional theory (DFT) to the polarizability of C n-(n) 3-9) cluster anions. This was achieved by comparing DFT calculations using two different exchange-correlation functionals (the non-empirical local density approximation, LDA, and the semiempirical hybrid functional B97-1) to quantum chemical calculations using the coupled cluster method in the CCSD(T) " gold standard " approximation. We find that, unless the extra electron is not bound at all by DFT, both LDA and B97-1 agree with the CCSD(T) calculation to within 5-10%, allowing for a meaningful qualitative and semiquantitative analysis. Furthermore, the polarizability is found to increase monotonically with chain size, consistent with the trend inferred from electron detachment experiments.
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