Probing NMR parameters, structure and dynamics of 5-nitroimidazole derivatives. Density functional study of prototypical radiosensitizers

Insights into the value of statistical models, solvent, and relativistic effects for investigating Re complexes of 2-(4'-aminophenyl)benzothiazole: a potential spectroscopic probe

Cancer affects a major part of the worldwide population, and, to minimize deaths, the diagnosis in the early stages of the disease is fundamental. Thus, to improve diagnosis and treatment new potential spectroscopic probes are crucial. Benzothiazole derivates present antitumor properties and are highly selective and interact strongly with the enzyme phosphoinositide 3-kinase (PI3K), which was associated with cell proliferation and breast cancer cells. In this paper, the rhenium shielding tensors (¹⁸⁷Re(σ)) and hydrogen and carbon chemical shifts (¹H(δ) and ¹³C(δ)) of the Re(CO)₃(NNO) complex conjugated with 2-(4'-aminophenyl)benzothiazole (ReABT) were evaluated. A statistical HCA model was used to analyze the best DFT protocol to compute σ and δ values and to evaluate the relativistic effects, both in the basis set and Hamiltonian as well as the functionals M06L or PBE0. The best protocol was applied to obtain ¹⁸⁷Re(σ) of the ReABT complex in different environments (gas phase, solution, and in the active site of the PI3K enzyme). The results point out that ¹⁸⁷Re(σ) values of the ReABT complex change significantly when the complex is docked in the PI3K enzyme.

NMR Chemical Shift and Methylation of 4-Nitroimidazole: Experiment and Theory

Nitroimidazoles and derivatives are a class of active pharmaceutical ingredients (APIs) first introduced sixty years ago. As anti-infection agents, the structure–activity relationships of nitroimidazole compounds have been particularly difficult to study due to their low reduction potentials and unique electronic structures. In this study, we combine dynamic nuclear polarization (DNP)-enhanced solid-state (100K), solid-state (298K), and 1H-13C heteronuclear single quantum coherence (HSQC) solution-state NMR techniques (303K) with density functional theory (DFT) to study the 1H, 13C, and 15N chemical shifts of 4-nitroimidazole (4-NI) and 1-methyl-4-nitroimidazole (CH3-4NI). The 4-NI chemical shifts were observed at 119.4, 136.4, and 144.7ppm for 13C, and at 181.5, 237.4, and 363.0ppm for 15N. The measurements revealed that methylation (deprotonation) of the amino nitrogen N(1) of 4-NI had less effect (Δδ=−4.8ppm) on the N(1) chemical shift but was compensated by shielding of the N(3) (Δδ=11.6ppm) in CH3-4NI. The calculated chemical shifts using DFT for 4-NI and CH3-4NI agreed well with the experimental values (within 2%) for the imidazole carbons. However, larger discrepancies (up to 13%) were observed between the calculated and measured 15N NMR chemical shifts for the imidazole nitrogen atoms of both molecules, which indicate that effects such as imidazole ring resonant structures and molecular dynamics may also contribute to the nitrogen chemical environment.

Binding preference of nitroimidazolic radiosensitizers to nucleobases and nucleosides probed by electrospray ionization mass spectrometry and density functional theory

Nitroimidazolic radiosensitizers are used in radiation therapy to selectively sensitize cancer cells deprived of oxygen, and the actual mechanism of radiosensitization is still not understood. Selecting five radiosensitizers (1-methyl-5-nitroimidazole, ronidazole, ornidazole, metronidazole, and nimorazole) with a common 5-nitroimidazolic ring with different substitutions at N1 and C2 positions of the imidazole moiety, we investigate here their binding to nucleobases (A, T, G, and C) and nucleosides (As, Td, Gs, and Cd) via the positive electrospray ionization mass spectrometry experiments. In addition, quantum chemical calculations at the M062x/6-311+G(d,p) level of theory and basis set were used to determine binding energies of the proton bound dimers of a radiosensitizer and a nucleobase. The positive electrospray ionization leads to the formation of proton bound dimers of all radiosensitizers except 1-methyl-5-nitroimidazole in high abundance with C and smaller abundance with G. Ronidazole and metronidazole formed less abundant dimers also with A, while no dimers were observed to be formed at all with T. In contrast to the case of the nucleoside Td, the dimer intensity is as high as that with Cd, while the abundance of the dimer with Gs is smaller than that of the former. The experimental results are consistent with the calculations of binding energies suggesting proton bound dimers with C and G to be the strongest bound ones. Finally, a barrier-free proton transfer is observed when protonated G or C approaches the nitroimidazole ring.

Value of NMR Parameters and DFT Calculations for Quantum Information Processing Utilizing Phosphorus Heterocycles

Quantum computing is the field of science that uses quantum-mechanical phenomena, such as superposition and entanglement, to perform operations on data. The fundamental information unit used in quantum computing is the quantum bit or qubit. It is well-known that quantum computers could theoretically be able to solve problems much more quickly than any classical computers. Currently, the first and still the most successful implementations of quantum information processing (QIP) have been based on nuclear spins in liquids. However, molecules that enable many qubits NMR QIP implementations should meet some conditions: have large chemical shifts and be appropriately dispersed for qubit addressability, appreciable spin-spin coupling between any pair of spins, and a long relaxation time. In this line, benzyldene-2,3-dihydro-1H-[1,3]diphosphole (BDF) derivatives have been theoretically tested for maximizing large chemical shifts, spin-spin coupling, and minimizing the hyperfine coupling constant. Thus, the structures were optimized at the B3LYP/6-311G(d,p) level and showed a significant similarity with the experimental geometrical parameters. The NMR spectroscopic parameters (δ and J) were calculated with six different DFT functionals. The τ-HCTH/6-31G(2d) level is in better agreement with the experimental data of ³¹P and ¹³C chemical shifts, while PCM-B3LYP/cc-pVDZ level shows a decrease on deviation between calculated and experimental values for P-P and P-C SSCC. The surface response technique was employed to rationalize how the hyperfine constant varies with the chemical shifts and coupling constants values. From our findings, BDF-NO₂ was the best candidate for NMR quantum computations (NMR-QC) among the studied series.

Exploring EPR Parameters of 99Tc Complexes for Designing New MRI Probes: Coordination Environment, Solvent, and Thermal Effects on the Spectroscopic Properties

We have evaluated the solvent and thermal effects on spectroscopic parameters of 99Tc complexes coordinated to explicit water molecules. Molecular dynamics simulations were performed followed by hyperfine coupling constant calculations (Aiso). Our results show a significant increase of Aiso, which demonstrates that the studied compounds can be promising contrast agents in MRI.

(1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.

99Tc NMR as a promising technique for structural investigation of biomolecules: theoretical studies on the solvent and thermal effects of phenylbenzothiazole complex

The phenylbenzothiazole compounds show antitumor properties and are highly selective. In this paper, the (99)Tc chemical shifts based on the ((99m)Tc)(CO)3 (NNO) complex conjugated to the antitumor agent 2-(4'-aminophenyl)benzothiazole are reported. Thermal and solvent effects were studied computationally by quantum-chemical methods, using the density functional theory (DFT) (DFT level BPW91/aug-cc-pVTZ for the Tc and BPW91/IGLO-II for the other atoms) to compute the NMR parameters for the complex. We have calculated the (99)Tc NMR chemical shifts of the complex in gas phase and solution using different solvation models (polarizable continuum model and explicit solvation). To evaluate the thermal effect, molecular dynamics simulations were carried, using the atom-centered density matrix propagation method at the DFT level (BP86/LanL2dz). The results highlight that the (99)Tc NMR spectroscopy can be a promising technique for structural investigation of biomolecules, at the molecular level, in different environments.

COMPUTATIONAL NMR INVESTIGATION OF RADIOSENSITIZER IN SOLUTION

15 N and 13 C NMR chemical shifts for four radiosensitizers have been calculated and compared with experimental data. The thermal and solvent effects on NMR spectra were simulated with the polarizable continuum model and an alternative molecular dynamics/quantum mechanics methodology. Magnetic shielding tensors were evaluated at the GIAO-B3LYP and GIAO-OPBE level using II' and 6-311+(2D,P) basis sets, showing that it is essential to incorporate the dynamics and solvent effects on NMR calculations in condensed phases.

Thermal and solvent effects on NMR indirect spin-spin coupling constants of a prototypical Chagas disease drug

NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.

Prediction of 13C chemical shifts in methoxyflavonol derivatives using MIA-QSPR

The (13)C chemical shifts of 19 methoxyflavonol derivatives have been modeled through using a structure-based quantitative structure-property relationship approach, which is based on the treatment of 2D images. In MIA-QSPR (multivariate image analysis applied to quantitative-structure-property relationships), descriptors correlating with dependent variables are pixels (binaries) of 2D chemical structures; variant pixels in the structures (substituents) account for the explained variance in the chemical shifts. Thus, a predictive model may be built from the regression between descriptors and experimental data. The MIA-QSPR approach coupled to partial least squares (PLS) regression built for the series of flavonols revealed that the predictive ability of MIA descriptors is comparable, or even superior for the fused rings moiety, when compared to the well-known Gauge Included Atomic Orbital (GIAO) procedure for (13)C chemical shifts calculations.

The impact of the pi-electron conjugation on (15)N, (13)C and (1)H NMR chemical shifts in push-pull benzothiazolium salts. Experimental and theoretical study

The (15)N as well as (13)C and (1)H chemical shifts of eight push-pull benzothiazolium iodides with various pi-conjugated chains between dimethylamino group and benzothiazolium moiety have been determined by NMR spectroscopy at the natural-abundance level of all nuclei in DMSO-d(6) solution. In general, the quaternary benzothiazolium nitrogen is more shielded [delta((15)N-3) vary between - 241.3 and - 201.9 ppm] with respect to parent 3-methylbenzothiazolium iodide [delta((15)N-3) = - 183.8 ppm], depending on the length and constitution of the pi-conjugated bridge. A larger variation in (15)N chemical shifts is observed on dimethylamino nitrogen, which covers the range of - 323.3 to - 257.2 ppm. The effect of pi-conjugation degree has a less pronounced influence on (13)C and (1)H chemical shifts. Experimental data are interpreted by means of density functional theory (DFT) calculations. Reasonable agreement between theoretical and experimental (15)N NMR chemical shifts was found, particularly when performing calculations with hybrid exchange-correlation functionals. A better accord with experiment is achieved by utilizing a polarizable continuum model (PCM) along with an explicit treatment of hydrogen-bonding between the solute and the water present in dimethylsulfoxide (DMSO). Finally, (13)C and (1)H NMR spectra were computed and analysed in order to compare them with available experimental data.

First-Principles Molecular Dynamics Evaluation of Thermal Effects on the NMR1JLi,C Spin–Spin Coupling

Car-Parrinello (CP) molecular dynamics were applied to sample conformations of various models of organolithium aggregates which are chosen to estimate (1)J(Li,C) NMR coupling constants. The results show that the deviations from the values computed using static (optimized) geometries are small provided no large-amplitude motions occur within the timescale of the simulations. In the case of the vinyllithium dimer, for which rotation of the vinyl chain is observed, this approach allows analysis of the various contributions to the experimentally measured constants. For the trisolvated methyllithium monomer, partial decoordination of solvating dimethyl ether is observed and results in a significant shift of (1)J(Li,C). All these results highlight that a varied physicochemical machinery is hidden behind general empirical formulas, such as the Bauer-Winchester-Schleyer rule used experimentally.

Computational study of structures and properties of metallaboranes: cobalt bis(dicarbollide)

A density functional study at the BP86/AE1 level is presented for the cobalt bis(dicarbollide) ion [3-Co-(1,2-C2B9H11)2]- (1) and selected isomers and rotamers thereof. Rotation of the two dicarbollide moieties with respect to each other is facile, as judged by the small energetic separation of the three rotamers located (within 11 kJ mol(-1)) and by the low barriers for their interconversion (at most 41 kJ mol(-1)). Among the isomers differing in carbon atom positions that contain two equivalent dicarbollide ligands, the 1,7 ("carbon apart") form [2-Co-(1,7-C2B9H11)2]- is the most stable, 121 kJ mol(-1) below 1. The electronic structure of 1 is characterized in terms of molecular orbitals, population analysis, and excitation energies from time-dependent density functional theory, relevant to UV/Vis spectroscopy. Experimental 11B NMR chemical shifts of 1 are reproduced to better than 5 ppm at the GIAO-B3LYP/II' level, and the computed delta(11B) values are only little affected by rotational averaging or the presence of a polarizable continuum. Larger such effects are found for the as-yet unknown 59Co chemical shift, for which a value in the range between -1800 and -2400 ppm is predicted. Even though the accuracy achieved for the theoretical delta(11B) values is somewhat lower than that for heteroboranes at conventional ab initio levels, the level of density functional employed can afford qualitatively reliable chemical shifts, which can be useful in assignments and structural refinements of heteroboranes containing transition metal.

Berry Pseudorotation Mechanism for the Interpretation of the19F NMR Spectrum in PF5by Ab Initio Molecular Dynamics Simulations

For the first time, theoretical evidence that confirms the importance of the Berry pseudorotation process in the interpretation of the 19F NMR spectrum of phosphorus pentafluoride (PF5) is presented. Ab initio molecular dynamics simulations have been performed to generate a large number of configurations used for NMR parameter computations at the density functional theory level. Two different temperatures were set to highlight the effect of pseudorotation process on the NMR spectrum. Average 19F chemical shifts and spin-spin coupling constants calculated for the five fluorine atoms converge towards the NMR equivalence of the five atoms when the Berry pseudorotation mechanism is accounted for.

Thermal and solvent effects on the NMR and UV parameters of some bioreductive drugs

15N NMR chemical shifts and n-->pi* electronic transition energy for metronidazole (1) has been calculated and compared with experimental data. A detailed computational study of 1 is presented, with special attention to the performance of various theoretical methods for reproducing spectroscopic parameters in solution. The most sophisticated approach involves density functional based on the Car-Parrinello molecular dynamics simulations of 1 in aqueous solution (BP86 level) and averaging chemical shifts and deltaE(n-->pi*) over snapshots from the trajectory. In the NMR and UV calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A good agreement with experiment is also obtained using static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Further theoretical predictions are also reported for 17O NMR and deltaE(n-->pi*) of three hydroxycinnamic acid derivatives, which suggest that it is essential to incorporate the dynamics and solvent effects for NMR and UV calculations in the condensed phase.