The calculation of NMR and ESR spectroscopy parameters using density functional theory

Computational 199 Hg NMR

Theoretical background and fundamental results dealing with the computation of mercury chemical shifts and spin-spin coupling constants are reviewed with a special emphasis on their stereochemical behavior and applications.

Quantum chemical calculations of 77 Se and 125 Te nuclear magnetic resonance spectral parameters and their structural applications

An accurate quantum chemical (QC) modeling of ⁷⁷ Se and ¹²⁵ Te nuclear magnetic resonance (NMR) spectra is deeply involved in the NMR structural assignment for selenium and tellurium compounds that are of utmost importance both in organic and inorganic chemistry nowadays due to their huge application potential in many fields, like biology, medicine, and metallurgy. The main interest of this review is focused on the progress in QC computations of ⁷⁷ Se and ¹²⁵ Te NMR chemical shifts and indirect spin-spin coupling constants involving these nuclei. Different computational methodologies that have been used to simulate the NMR spectra of selenium and tellurium compounds since the middle of the 1990s are discussed with a strong emphasis on their accuracy. A special accent is placed on the calculations resorting to the relativistic methodologies, because taking into account the relativistic effects appreciably influences the precision of NMR calculations of selenium and, especially, tellurium compounds. Stereochemical applications of quantum chemical calculations of ⁷⁷ Se and ¹²⁵ Te NMR parameters are discussed so as to exemplify the importance of integrated approach of experimental and computational NMR techniques.

The Design of "Neutral" Carbanions with Intramolecular Charge Compensation

Strategies to construct zwitterionic anions from the parent anions are proposed. Two principles are employed; the cationic counterpart is (a) attached as a substituent or (b) inserted as an integral part at a remote location in the assembly. The optimized geometries reveal that a striking similarity exists between the zwitterions and the respective precursor parent anion. The computed vibrational frequencies emphasize that these novel entities are minima on their respective potential energy surfaces. A substantial HOMO-LUMO gap indicates that the proposed structures do not show instability in their respective electronic states and that the higher energy configuration states do not contribute to the ground state viability. The separation of charge between the monopoles in these zwitterions is demonstrated by moderately large nonzero dipole moments. Significant large energy barriers for rearrangement to the closely related positional isomers, demonstrated in a few cases, advocate the thermal stability (associated with spectroscopic viability) of the novel molecules. The donor capacity (basicity) of the anionic subunit in these zwitterions is comparable to that of the respective parent anions. Since the qualitative and quantitative features in the designed charged compensated complexes are conserved as anions, these molecules may perhaps be employed in synthetic organic or organometallic chemistry.

Hybrid Density Functional Methods Empirically Optimized for the Computation of (13)C and (1)H Chemical Shifts in Chloroform Solution

Two hybrid generalized-gradient approximation density functionals, WC04 and WP04, are optimized for the prediction of (13)C and (1)H chemical shifts, respectively, using a training set of 43 molecules in chloroform solution. Tests on molecules not included in the training set, namely six stereoisomeric methylcyclohexanols and a β-lactam antibiotic, indicate the models to be robust and moreover to provide results more accurate than those from equivalent B3LYP, PBE1, or mPW1PW91 calculations, particularly for the prediction of downfield resonances in nuclear magnetic resonance spectra. However, linear regression of the B3LYP, PBE1, and mPW1PW91 predicted values on the experimental data improves the accuracy of those models so that they are comparable to WC04 and WP04.

Photoexcitation of adenine cation radical [A*+] in the near UV-vis region produces sugar radicals in adenosine and in its nucleotides

In this study, we report the formation of ribose sugar radicals in high yields (85-100%) via photoexcitation of adenine cation radical (A*+) in Ado and its ribonucleotides. Photoexcitation of A*+ at low temperatures in homogeneous aqueous glassy samples of Ado, 2'-AMP, 3'-AMP, and 5'-AMP forms sugar radicals predominantly at C5'- and also at C3'-sites. The C5'* and C3'* sugar radicals were identified employing Ado deuterated at specific carbon sites: C1', C2', and C5'. Phosphate substitution is found to deactivate sugar radical formation at the site of substitution. Thus, in 5'-AMP, C3'* is observed to be the main radical formed via photoexcitation at ca. 143 K, whereas, in 3'-AMP, C5'* is the only species found. These results were supported by results obtained employing 5'-AMP with specific deuteration at the C5'-site (i.e., 5',5'-D,D-5'-AMP). Moreover, contrary to the C5'* observed in 3'-dAMP, we find that C5'* in 3'-AMP shows a clear pH-dependent conformational change as evidenced by a large increase in the C4' beta-hyperfine coupling on increasing the pH from 6 to 9. Calculations performed employing DFT (B3LYP/6-31G*) for C5'* in 3'-AMP show that the two conformations of C5'* result from strong hydrogen bond formation between the O5'-H and the 3'-phosphate dianion at higher pHs. Employing time-dependent density functional theory [TD-DFT, B3LYP/6-31G(d)], we show that, in the excited state, the hole transfers to the sugar moiety and has significant hole localization at the C5'-site in a number of allowed transitions. This hole localization is proposed to lead to the formation of the neutral C5'-radical (C5'*) via deprotonation.

Studies on the Substitution and Temperature Effects in the Insertion Reactions of Singlet State Aluminium Monohalides (1Alx) with Hydrogen Halides (Hx) (X = F, Cl, Br)

The insertion reactions of singlet aluminium monohalides 1(AlX) (X = F, Cl, Br) with hydrogen halides (HX) have been investigated by the DFT/B3LYP method at the B3LYP/6-311 + G( d, p) level, which involve three-membered ring transition states (TS). In addition, general statistical thermodynamics and Eyring transition state theory with the Wigner correction were used to study the thermodynamic and kinetic properties of these reaction channels within the temperature range of 200-1200 K. It is concluded that with increasing temperature, the reaction equilibrium constant K decreases sharply, while the reaction rate constant k increases gradually for all these insertion reactions. The orders are K(F) > K(Cl) > K(Br) and k(Br) > k(Cl) > k(F) over the entire temperature range of 200-1200 K, while the differences of lg K and lg k at low temperature are larger than those at high temperature.

Analyzing Pt chemical shifts calculated from relativistic density functional theory using localized orbitals: the role of Pt 5d lone pairs

Pt chemical shifts were calculated from two-component relativistic density functional theory (DFT). The shielding tensors were analyzed by using a recently developed method to decompose the spin-orbit DFT results into contributions from spin-free localized orbitals (here: natural localized molecular orbitals (NLMOs) and natural bond orbitals (NBOs)). Seven chemical shifts in six Pt complexes with Pt oxidation states II, III, and IV; and halide, amino, and amidate ligands were analyzed, with particular focus on the role of nonbonding Pt 5d orbitals. A simple d-orbital 'rotation' model has been used to rationalize some of the observed trends such as the main difference between Pt(II) and Pt(IV) chemical shifts. The localized orbital analysis data showed that most of this difference as well as trends among different Pt complexes with similar coordination can be rationalized by comparing properties of the nonbonding Pt 5d orbitals. We have also analyzed the spin-orbit effects on the chemical shifts of [PtCl4](2-) compared to [PtBr4](2-).

Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA

Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.

Which NICS aromaticity index for planar pi rings is best?

Five increasingly sophisticated aromaticity indexes, based on nucleus-independent chemical shifts (NICS), were evaluated against a uniform set of aromatic stabilization energies (ASE) for 75 mono- and polyheterocyclic five-membered rings. While acceptable statistical correlations were given by all of the NICS methods, the most fundamentally grounded index, NICS(0)pizz (based on the pi contribution to the out-of-plane zz tensor component), performed best statistically (cc=0.980) and in practice. The easily computable NICS(1)zz index is a useful alternative (cc=0.968).

The existence of secondary orbital interactions

B3LYP/6-311+G** (and MP2/6-311+G**) computations, performed for a series of Diels-Alder (DA) reactions, confirm that the endo transition states (TS) and the related Cope-TSs are favored energetically over the respective exo-TSs. Likewise, the computed magnetic properties (nucleus-independent chemical shifts and magnetic susceptibililties) of the endo- (as well as the Cope) TS's reveal their greater electron delocalization and greater aromaticity than the exo-TS's. However, Woodward and Hoffmann's original example is an exception: their endo-TS model, involving the DA reaction of a syn- with an anti-butadiene (BD), actually is disfavored energetically over the corresponding exo-TS; magnetic criteria also do not indicate the existence of SOI delocalization in either case. Instead, a strong energetic preference for endo-TSs due to SOI is found when both BDs are in the syn conformations. This is in accord with Alder and Stein's rule of "maximum accumulation of double bonds:" both the dienophile and the diene should have syn conformations. Plots along the IRC's show that the magnetic properties typically are most strongly exalted close to the energetic TS. Because of SOI, all the points along the endo reaction coordinates are more diatropic than along the corresponding exo pathways. We find weak SOI effects to be operative in the endo-TSs involved in the cycloadditions of cyclic alkenes, cyclopropene, aziridine, cyclobutene, and cyclopentene, with cyclopentadiene. While the endo-TSs are only slightly lower in energy than the respective exo-TSs, the magnetic properties of the endo-TS's are significantly exalted over those for the exo-TS's and the Natural Bond Orbitals indicate small stabilizing interactions between the methylene cycloalkene hydrogen orbitals (and lone pairs in case of aziridine) with pi-character and the diene pi MOs.

Insights into the mobility of methyl-bearing side chains in proteins from (3)J(CC) and (3)J(CN) couplings

Side-chain dynamics in proteins can be characterized by the NMR measurement of (13)C and (2)H relaxation rates. Evaluation of the corresponding spectral densities limits the slowest motions that can be studied quantitatively to the time scale on which the overall molecular tumbling takes place. A different measure for the degree of side-chain order about the C(alpha)-C(beta) bond (chi(1) angle) can be derived from (3)J(C)(')(-)(C)(gamma) and (3)J(N)(-)(C)(gamma) couplings. These couplings can be measured at high accuracy, in particular for Thr, Ile, and Val residues. In conjunction with the known backbone structures of ubiquitin and the third IgG-binding domain of protein G, and an extensive set of (13)C-(1)H side-chain dipolar coupling measurements in oriented media, these (3)J couplings were used to parametrize empirical Karplus relationships for (3)J(C)(')(-)(C)(gamma) and (3)J(N)(-)(C)(gamma). These Karplus curves agree well with results from DFT calculations, including an unusual phase shift, which causes the maximum (3)J(CC) and (3)J(CN) couplings to occur for dihedral angles slightly smaller than 180 degrees, particularly noticeable in Thr residues. The new Karplus curves permit determination of rotamer populations for the chi(1) torsion angles. Similar rotamer populations can be derived from side-chain dipolar couplings. Conversion of these rotamer populations into generalized order parameters, S(J)(2) and S(D)(2), provides a view of side-chain dynamics that is complementary to that obtained from (13)C and (2)H relaxation. On average, results agree well with literature values for (2)H-relaxation-derived S(rel)(2) values in ubiquitin and HIV protease, but also identify a fraction of residues for which S(J,D)(2) < S(rel)(2). This indicates that some of the rotameric averaging occurs on a time scale too slow to be observable in traditional relaxation measurements.

Diels-Alder Reaction of phosphaethene with 1,3-dienes: an ab initio study

Computations on Diels-Alder (DA) reactions of phosphaethene with 1,3-butadiene and with isoprene reveal asynchronous transition structures. The DFT (B3LYP/6-311+G) activation energies of these reactions, 12-14 kcal/mol, are much lower than that of the parent ethene-butadiene reaction, 28 kcal/mol, even though the exothermicities of all lie in the same range, from -29 to -33 kcal/mol. The transition states (TSs) for the phosphethene-butadiene or isoprene DA reactions are earlier than the TSs of the butadiene-ethene cycloaddition. Due to the weakness of the C=P pi bond compared to the C=C pi bonds, the energies required to reach the phosphaethene TSs are much less than the carbocyclic cases. The computed (1)H NMR chemical shifts and nucleus independent chemical shifts (NICS) quantify the aromatic character of the transition states. Regioselectivities of the neutral phosphaethene-isoprene DA reactions are modest, at best. However, computations on radical cation DA reactions of phosphaethene with isoprene, which proceed stepwise with open chain intermediates, can account for the high regioselectivities that have been observed in some cases.

A silyl cation with a three-center si-h-si bond

The unusually high kinetic stability of the silyl cation 1 is due to the presence of a three-center, two-electron Si-H-Si bond. NMR data ((1) H, (2) H, (13) C, (29) Si) are consistent with the static, symmetrical structure shown, which was further corroborated by the results of density functional calculations.

Magnetic properties and aromaticity of o-, m-, and p-benzyne

The relative aromaticities of the three singlet benzyne isomers, 1,2-, 1,3-, and 1,4-didehydrobenzenes have been evaluated with a series of aromaticity indicators, including magnetic susceptibility anisotropies and exaltations, nucleus-independent chemical shifts (NICS), and aromatic stabilization energies (all evaluated at the DFT level), as well as valence-bond Pauling resonance energies. Most of the criteria point to the o-benzyne<m-benzyne<p-benzyne aromaticity order, whereas the relative aromaticity of each isomer with respect to benzene depends on the aromaticity criterion. An additional aromaticity evaluation involved the transition state of the Bergman cyclization of (Z)-hexa-1,5-diyn-3-ene which yields p-benzyne. Dissected NICS calculations reveal an aromatic transition state with a larger total NICS but a smaller NICS(pi) component and thus lower aromaticity than benzene.

Calculation of electronic g-tensors for transition metal complexes using hybrid density functionals and atomic meanfield spin-orbit operators

We report the first implementation of the calculation of electronic g-tensors by density functional methods with hybrid functionals. Spin-orbit coupling is treated by the atomic meanfield approximation. g-Tensors for a set of small main group radicals and for a series of ten 3d and two 4d transition metal complexes have been compared using the local density approximation (VWN functional), the generalized gradient approximation (BP86 functional), as well as B3-type (B3PW91) and BH-type (BHPW91) hybrid functionals. For main group radicals, the effect of exact-exchange mixing is small. In contrast, significant differences between the various functionals arise for transition metal complexes. As has been shown previously, local and in particular gradient-corrected functionals tend to underestimate the "paramagnetic" contributions to the g-tensors in these cases and thereby recover only about 40-50% of the range of experimental g-tensor components. This is improved to ca. 60% by the B3PW91 functional, which also gives slightly reduced standard deviations. The range increases to almost 100% using the half-and-half functional BHPW91. However, the quality of the correlation with experimental data worsens due to a significant overestimate of some intermediate g-tensor values. The worse performance of the BHPW91 functional in these cases is accompanied by spin contamination. Although none of the functionals tested thus appears to be ideal for the treatment of electronic g-tensors in transition metal complexes, the B3PW91 hybrid functional exhibited the overall most satisfactory performance. Apart from the validation of hybrid functionals, some aspects in the treatment of spin-orbit contributions to the g-tensor are discussed.

Relativistic spin-orbit coupling effects on secondary isotope shifts of (13)C nuclear shielding in CX(2) (X = O, S, Se, Te)

Rovibrational corrections, temperature dependence, and secondary isotope shifts of the (13)C nuclear shielding in CX(2) (X = O, S, Se, Te) are calculated taking into account the relativistic spin-orbit (SO) interaction. The SO effect is considered for the first time for the secondary isotope shifts. The nuclear shielding hypersurface in terms of nuclear displacements is calculated by using a density-functional theory method. Ab initio multiconfiguration self-consistent field calculations are done at the equilibrium geometry for comparison. (13)C NMR measurements are carried out for CS(2). The calculated results are compared with both present and earlier experimental data on CO(2), CS(2), and CSe(2). The heavy-atom SO effects on the rovibrational corrections of (13)C shielding are shown to be significant. For CSe(2) and CTe(2), reliable prediction of secondary isotope effects and their temperature dependence requires the inclusion of the SO corrections. In particular, earlier discrepancies of theory and experiment for CSe(2) are fully resolved by taking the SO interactions into account.

2-Deoxy-beta-D-erythro-pentofuranose: hydroxymethyl group conformation and substituent effects on molecular structure, ring geometry, and NMR spin-spin coupling constants from quantum chemical calculations

The effect of hydroxymethyl conformation (gg, gt, and tg rotamers about the C4-C5 bond) on the conformational energies and structural parameters (bond lengths, bond angles, bond torsions) of the 10 envelope forms of the biologically relevant aldopentofuranose, 2-deoxy-beta-D-erythro-pentofuranose (2-deoxy-D-ribofuranose) 2, has been investigated by ab initio molecular orbital calculations at the HF/6-31G level of theory. C4-C5 bond rotation induces significant changes in the conformational energy profile of 2 (2gt and 2tg exhibit one global energy minimum, whereas 2gg exhibits two nearly equivalent energy minima), and structural changes, especially those in bond lengths, are consistent with predictions based on previously reported vicinal, 1,3- and 1,4-oxygen lone pair effects. HF/6-31G-optimized envelope geometries of 2gg were re-optimized using density functional theory (DFT, B3LYP/6-31G), and the resulting structures were used in DFT calculations of NMR spin-spin coupling constants involving 13C (i.e., J(CH) and J(CC) over one, two, and three bonds) in 2gg according to methods described previously. The computed J-couplings were compared to those reported previously in 2gt to assess the effect of C4-C5 bond rotation on scalar couplings within the furanose ring and hydroxymethyl side chain. The results confirm prior predictions of correlations between 2J(CH), 3J(CH), 2J(CC) and 3J(CC), and ring conformation, and verify the usefulness of a concerted application of these couplings (both their magnitudes and signs) in assigning preferred ring and C4-C5 bond conformations in aldopentofuranosyl rings. The new calculated J-couplings in 2gg have particular relevance to related J-couplings in DNA (and RNA indirectly), where the gg rotamer, rather than the gt rotamer, is observed in most native structures. The effects of two additional structural perturbations on 2 were also studied, namely, deoxygenation at C5 (yielding 2,5-dideoxy-beta-D-erythro-pentofuranose 4) and methyl glycosidation at O1 (yielding methyl 2-deoxy-beta-D-erythro-pentofuranoside 5) at the HF/6-31G level. The conformational energy profile of 4 resembles that found for 2gt, not 2gg, indicating that 4 is an inappropriate structural mimic of the furanose ring in DNA. Glycosidation failed to induce differential stabilization of ring conformations containing an axial C1-O1 bond (anomeric effect), contrary to experimental data. The latter discrepancy indicates that either the magnitude of this differential stabilization depends on ring configuration or that solvent effects, which are neglected in these calculations, play a role in promoting this stabilization.