Matti Hanni | Oulu University Hospital (original) (raw)
Papers by Matti Hanni
Physical Chemistry Chemical Physics, 2011
Nuclear spin relaxation provides detailed dynamical information on molecular systems and material... more Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic 129 Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an ''NMR force field''. By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T 1 . The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T 1 . Persistent dimers Xe 2 are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings. 1312, +358-(0)8-553 1343 w Electronic supplementary information (ESI) available: Details of Redfield theory for CSA relaxation; computational details; error sources and antisymmetric terms in CSA-induced nuclear spin relaxation; supporting figures and tables. See
Physical Chemistry Chemical Physics, 2014
Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic res... more Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.
The Journal of Chemical Physics, 2007
Relativistic effects on the 129 Xe nuclear magnetic resonance shielding and 131 Xe nuclear quadru... more Relativistic effects on the 129 Xe nuclear magnetic resonance shielding and 131 Xe nuclear quadrupole coupling ͑NQC͒ tensors are examined in the weakly bound Xe 2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock ͑DHF͒ method. The intermolecular interaction-induced binary chemical shift ␦, the anisotropy of the shielding tensor ⌬, and the NQC constant along the internuclear axis ʈ are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory ͑BPPT͒ is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic ͑NR͒ coupled-cluster singles and doubles with perturbational triples ͓CCSD͑T͔͒ level of theory. The fully relativistic second-order Møller-Plesset many-body perturbation ͑DMP2͒ theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for ␦ and ⌬ by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for ␦ and ⌬ in Xe 2 . For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For ʈ , the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the 129 Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe 2 , are in excellent agreement with the experiment for the first time.
![Research paper thumbnail of Calculation of binary magnetic properties and potential energy curve in xenon dimer: Second virial coefficient of [sup 129]Xe nuclear shielding](https://attachments.academia-assets.com/45060767/thumbnails/1.jpg)
](The Journal of Chemical Physics, 2004
Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling te... more Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift ␦, the anisotropy of the shielding tensor ⌬, the nuclear quadrupole coupling tensor component along the internuclear axis ʈ , and the spin-rotation constant C Ќ are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction ͑CP͒ method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles ͑CCSD͒ theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD͑CP͒ binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of ␦, ⌬, ʈ , and C Ќ in the ϭ0, Jϭ0 rovibrational ground state of the xenon dimer are also reported.
Physical Chemistry Chemical Physics, 2009
Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the struct... more Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.
Ni2+(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic reson... more Ni2+(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the 17O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for 1H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s−1 of relaxation rates (R1 and R2 respectively) for the 1H nuclei of water molecules bonded to the Ni2+ center, in a magnetic field of 11.7 T. The corresponding 17O relaxation rates are around 33 and 38 s−1. We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni2+ in water.
Nuclear spin relaxation provides detailed dynamical information on molecular systems and material... more Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic 129Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an “NMR force field”. By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin–lattice relaxation times T1. The quality requirements on both the Xe–Xe interaction potential and binary shielding tensor are investigated in the context of CSA T1. Persistent dimers Xe2 are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.
Nuclear magnetic resonance (NMR) of atomic 129/131Xe is used as a versatile probe of the structur... more Nuclear magnetic resonance (NMR) of atomic 129/131Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xen (n = 2–12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe2 at different internuclear distances were obtained at the nonrelativistic Hartree–Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xen (n = 2–12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe2 can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xen clusters. Particularly, the chemical shift in Xen is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.
Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling te... more Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift δ, the anisotropy of the shielding tensor Δσ, the nuclear quadrupole coupling tensor component along the internuclear axis χ ∥ , and the spin-rotation constant C ⊥ are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree–Fock, complete active space self-consistent field, second-order Møller–Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of δ, Δσ, χ ∥ , and C ⊥ in the ν=0, J=0 rovibrational ground state of the xenon dimer are also reported.
Relativistic effects on the Xe 129 nuclear magnetic resonance shielding and Xe 131 nuclear qua... more Relativistic effects on the Xe 129 nuclear magnetic resonance shielding and Xe 131 nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe 2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shiftδ , the anisotropy of the shielding tensorΔσ , and the NQC constant along the internuclear axis χ ‖ are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlationeffects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Møller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for δ and Δσ by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for δ and Δσ in Xe 2 . For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlationeffects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For χ ‖ , the fully relativistic DMP2 results obtain a correction for NR correlationeffects beyond MP2. The computed temperature dependence of the second virial coefficient of the Xe 129 nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe 2 , are in excellent agreement with the experiment for the first time.
Journal of Chemical Theory and Computation, 2014
The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is comp... more The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.
The Journal of Organic Chemistry, 2014
A short total synthesis of the published structure of racemic trichodermatide A is reported. Our ... more A short total synthesis of the published structure of racemic trichodermatide A is reported. Our synthesis involves a Knoevenagel condensation/Michael addition sequence, followed by the formation of tricyclic hexahydroxanthene-dione and a diastereoselective bis-hydroxylation. The final product, the structure of which was confirmed by X-ray crystallography, has NMR spectra that are very similar, but not identical, to those of the isolated natural product. Quantum chemically computed (13)C shifts agree well with the present NMR measurements.
The Journal of Organic Chemistry, 2013
Selective binding of the phosphate-substituted molecular tweezer 1a to protein lysine residues wa... more Selective binding of the phosphate-substituted molecular tweezer 1a to protein lysine residues was suggested to explain the inhibition of certain enzymes and the aberrant aggregation of amyloid petide Aβ42 or α-synuclein, which are assumed to be responsible for Alzheimer's and Parkinson's disease, respectively. In this work we systematically investigated the binding of four water-soluble tweezers 1a−d (substituted by phosphate, methanephosphonate, sulfate, or O-methylenecarboxylate groups) to amino acids and peptides containing lysine or arginine residues by using fluorescence spectroscopy, NMR spectroscopy, and isothermal titration calorimetry (ITC). The comparison of the experimental results with theoretical data obtained by a combination of QM/MM and ab initio 1 H NMR shift calculations provides clear evidence that the tweezers 1a−c bind the amino acid or peptide guest molecules by threading the lysine or arginine side chain through the tweezers' cavity, whereas in the case of 1d the guest molecule is preferentially positioned outside the tweezer's cavity. Attractive ionic, CH-π, and hydrophobic interactions are here the major binding forces. The combination of experiment and theory provides deep insight into the host−guest binding modes, a prerequisite to understanding the exciting influence of these tweezers on the aggregation of proteins and the activity of enzymes.
Journal of Chemical Theory and Computation, 2014
An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts... more An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.
The Journal of Chemical Physics, 2013
Nuclear spin-spin coupling over van der Waals bond has recently been observed via the frequency s... more Nuclear spin-spin coupling over van der Waals bond has recently been observed via the frequency shift of solute protons in a solution containing optically hyperpolarized (129)Xe nuclei. We carry out a first-principles computational study of the prototypic van der Waals-bonded xenon dimer, where the spin-spin coupling between two magnetically non-equivalent isotopes, J((129)Xe - (131)Xe), is observable. We use relativistic theory at the four-component Dirac-Hartree-Fock and Dirac-density-functional theory levels using novel completeness-optimized Gaussian basis sets and choosing the functional based on a comparison with correlated ab initio methods at the nonrelativistic level. J-coupling curves are provided at different levels of theory as functions of the internuclear distance in the xenon dimer, demonstrating cross-coupling effects between relativity and electron correlation for this property. Calculations on small Xe clusters are used to estimate the importance of many-atom effects on J((129)Xe - (131)Xe). Possibilities of observing J((129)Xe - (131)Xe) in liquid xenon are critically examined, based on molecular dynamics simulation. A simplistic spherical model is set up for the xenon dimer confined in a cavity, such as in microporous materials. It is shown that the on the average shorter internuclear distance enforced by the confinement increases the magnitude of the coupling as compared to the bulk liquid case, rendering J((129)Xe - (131)Xe) in a cavity a feasible target for experimental investigation.
Physical Chemistry Chemical Physics, 2011
Nuclear spin relaxation provides detailed dynamical information on molecular systems and material... more Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic 129 Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an ''NMR force field''. By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T 1 . The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T 1 . Persistent dimers Xe 2 are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings. 1312, +358-(0)8-553 1343 w Electronic supplementary information (ESI) available: Details of Redfield theory for CSA relaxation; computational details; error sources and antisymmetric terms in CSA-induced nuclear spin relaxation; supporting figures and tables. See
Physical Chemistry Chemical Physics, 2014
Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic res... more Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.
The Journal of Chemical Physics, 2007
Relativistic effects on the 129 Xe nuclear magnetic resonance shielding and 131 Xe nuclear quadru... more Relativistic effects on the 129 Xe nuclear magnetic resonance shielding and 131 Xe nuclear quadrupole coupling ͑NQC͒ tensors are examined in the weakly bound Xe 2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock ͑DHF͒ method. The intermolecular interaction-induced binary chemical shift ␦, the anisotropy of the shielding tensor ⌬, and the NQC constant along the internuclear axis ʈ are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory ͑BPPT͒ is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic ͑NR͒ coupled-cluster singles and doubles with perturbational triples ͓CCSD͑T͔͒ level of theory. The fully relativistic second-order Møller-Plesset many-body perturbation ͑DMP2͒ theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for ␦ and ⌬ by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for ␦ and ⌬ in Xe 2 . For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For ʈ , the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the 129 Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe 2 , are in excellent agreement with the experiment for the first time.
The Journal of Chemical Physics, 2004
Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling te... more Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift ␦, the anisotropy of the shielding tensor ⌬, the nuclear quadrupole coupling tensor component along the internuclear axis ʈ , and the spin-rotation constant C Ќ are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction ͑CP͒ method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles ͑CCSD͒ theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD͑CP͒ binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of ␦, ⌬, ʈ , and C Ќ in the ϭ0, Jϭ0 rovibrational ground state of the xenon dimer are also reported.
Physical Chemistry Chemical Physics, 2009
Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the struct... more Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.
Ni2+(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic reson... more Ni2+(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the 17O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for 1H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s−1 of relaxation rates (R1 and R2 respectively) for the 1H nuclei of water molecules bonded to the Ni2+ center, in a magnetic field of 11.7 T. The corresponding 17O relaxation rates are around 33 and 38 s−1. We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni2+ in water.
Nuclear spin relaxation provides detailed dynamical information on molecular systems and material... more Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic 129Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an “NMR force field”. By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin–lattice relaxation times T1. The quality requirements on both the Xe–Xe interaction potential and binary shielding tensor are investigated in the context of CSA T1. Persistent dimers Xe2 are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.
Nuclear magnetic resonance (NMR) of atomic 129/131Xe is used as a versatile probe of the structur... more Nuclear magnetic resonance (NMR) of atomic 129/131Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xen (n = 2–12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe2 at different internuclear distances were obtained at the nonrelativistic Hartree–Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xen (n = 2–12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe2 can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xen clusters. Particularly, the chemical shift in Xen is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.
Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling te... more Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift δ, the anisotropy of the shielding tensor Δσ, the nuclear quadrupole coupling tensor component along the internuclear axis χ ∥ , and the spin-rotation constant C ⊥ are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree–Fock, complete active space self-consistent field, second-order Møller–Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of δ, Δσ, χ ∥ , and C ⊥ in the ν=0, J=0 rovibrational ground state of the xenon dimer are also reported.
Relativistic effects on the Xe 129 nuclear magnetic resonance shielding and Xe 131 nuclear qua... more Relativistic effects on the Xe 129 nuclear magnetic resonance shielding and Xe 131 nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe 2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shiftδ , the anisotropy of the shielding tensorΔσ , and the NQC constant along the internuclear axis χ ‖ are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlationeffects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Møller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for δ and Δσ by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for δ and Δσ in Xe 2 . For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlationeffects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For χ ‖ , the fully relativistic DMP2 results obtain a correction for NR correlationeffects beyond MP2. The computed temperature dependence of the second virial coefficient of the Xe 129 nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe 2 , are in excellent agreement with the experiment for the first time.
Journal of Chemical Theory and Computation, 2014
The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is comp... more The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.
The Journal of Organic Chemistry, 2014
A short total synthesis of the published structure of racemic trichodermatide A is reported. Our ... more A short total synthesis of the published structure of racemic trichodermatide A is reported. Our synthesis involves a Knoevenagel condensation/Michael addition sequence, followed by the formation of tricyclic hexahydroxanthene-dione and a diastereoselective bis-hydroxylation. The final product, the structure of which was confirmed by X-ray crystallography, has NMR spectra that are very similar, but not identical, to those of the isolated natural product. Quantum chemically computed (13)C shifts agree well with the present NMR measurements.
The Journal of Organic Chemistry, 2013
Selective binding of the phosphate-substituted molecular tweezer 1a to protein lysine residues wa... more Selective binding of the phosphate-substituted molecular tweezer 1a to protein lysine residues was suggested to explain the inhibition of certain enzymes and the aberrant aggregation of amyloid petide Aβ42 or α-synuclein, which are assumed to be responsible for Alzheimer's and Parkinson's disease, respectively. In this work we systematically investigated the binding of four water-soluble tweezers 1a−d (substituted by phosphate, methanephosphonate, sulfate, or O-methylenecarboxylate groups) to amino acids and peptides containing lysine or arginine residues by using fluorescence spectroscopy, NMR spectroscopy, and isothermal titration calorimetry (ITC). The comparison of the experimental results with theoretical data obtained by a combination of QM/MM and ab initio 1 H NMR shift calculations provides clear evidence that the tweezers 1a−c bind the amino acid or peptide guest molecules by threading the lysine or arginine side chain through the tweezers' cavity, whereas in the case of 1d the guest molecule is preferentially positioned outside the tweezer's cavity. Attractive ionic, CH-π, and hydrophobic interactions are here the major binding forces. The combination of experiment and theory provides deep insight into the host−guest binding modes, a prerequisite to understanding the exciting influence of these tweezers on the aggregation of proteins and the activity of enzymes.
Journal of Chemical Theory and Computation, 2014
An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts... more An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.
The Journal of Chemical Physics, 2013
Nuclear spin-spin coupling over van der Waals bond has recently been observed via the frequency s... more Nuclear spin-spin coupling over van der Waals bond has recently been observed via the frequency shift of solute protons in a solution containing optically hyperpolarized (129)Xe nuclei. We carry out a first-principles computational study of the prototypic van der Waals-bonded xenon dimer, where the spin-spin coupling between two magnetically non-equivalent isotopes, J((129)Xe - (131)Xe), is observable. We use relativistic theory at the four-component Dirac-Hartree-Fock and Dirac-density-functional theory levels using novel completeness-optimized Gaussian basis sets and choosing the functional based on a comparison with correlated ab initio methods at the nonrelativistic level. J-coupling curves are provided at different levels of theory as functions of the internuclear distance in the xenon dimer, demonstrating cross-coupling effects between relativity and electron correlation for this property. Calculations on small Xe clusters are used to estimate the importance of many-atom effects on J((129)Xe - (131)Xe). Possibilities of observing J((129)Xe - (131)Xe) in liquid xenon are critically examined, based on molecular dynamics simulation. A simplistic spherical model is set up for the xenon dimer confined in a cavity, such as in microporous materials. It is shown that the on the average shorter internuclear distance enforced by the confinement increases the magnitude of the coupling as compared to the bulk liquid case, rendering J((129)Xe - (131)Xe) in a cavity a feasible target for experimental investigation.