Michal Straka

• Doc. Ph.D. Mgr.
• present at The Czech Academy of Sciences

The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic-structure and SO-HALA effect have been missing. By analyzing 1H NMR chemical...

Copper isotopes and their complexes are intensively studied due to their high potential for the application in radiodiagnosis and radiotherapy. Here we study the Cu II complex of 1,8-bis(2-hydroxybenzyl)-cyclam (H 2 L) that...

Coordination compounds of lanthanides are indispensable in biomedical applications as MRI contrast agents and radiotherapeutics. However, since the introduction of the chelator DOTA four decades ago, there has been only limited progress on improving their thermodynamic stability and kinetic inertness, which are essential for safe in vivo use. Here,...

Since their discovery, fullerenes represent a fascina­ting type of molecule with many unusual properties. One of these is the existence of a cavity into which other atoms and molecules can be enclosed to form the so-called endohedral fullerenes. In terms of fundamental research, endohedral fullerenes provide a platform for studying exotic chemical...

Coordination compounds of lanthanides are indispensable in biomedical applications as MRI contrast agents and radiotherapeutics. However, since the introduction of the chelator DOTA four decades ago, there has been only limited progress on improving their thermodynamic stability and kinetic inertness, which are essential for safe in-vivo use. Here,...

Two different docked poses of two diastereoisomers accommodated in the PBLG helix. Conformational change caused by PBLG was used for generation of new ensembles of conformers for RDC analysis.

Actinide-actinide bonding poses a challenge for both experimental and theoretical chemists because of both the scarcity of experimental data and the exotic nature of actinide bonding due to the involvement and mixing of actinide 7s-, 6p-, 6d-, and particularly 5f-orbitals. Only a few experimental examples of An-An bonding have been reported so far....

Abstract In this paper, an in silico proof of concept of a spinristor is proposed and provided; a new electronic component that combines a spin‐filter and a memristor in a single molecule, useful for in‐memory processing. It builds on the idea of an open‐shell transition metal ion enclosed within an elliptical fullerene connected to a pair of elect...

Borane and heteroborane clusters have been known as neutral or anionic species. In contrast to them, several ten-vertex monocationic nido and closo dicarbaborane-based systems have recently emerged from the reaction of the parent bicapped-square antiprismatic dicarbaboranes with N-heterocyclic carbenes followed by the protonization of the correspon...

Endohedral fullerenes with a dipolar molecule enclosed in the fullerene cage have great potential in molecular electronics, such as diodes, switches, or molecular memristors. Here, we study a series of model systems based on MX@D5h(1)-C70 (M = a metal or hydrogen, X = a halogen or a chalcogen) endohedral fullerenes to identify potential molecular m...

The 3He atom is an excellent NMR probe, particularly when enclosed in endohedral helium fullerenes. The 3He chemical shift, δ(3He), in fullerenes spans a range from ca. -50 to +10 ppm, and changes sensitively between different cages, isomers, and external substituents. Reduction of the fullerenes to anions changes the δ(3He) dramatically and unexpe...

Gold(I) centers can form moderately strong (Au⋅⋅⋅H) hydrogen bonds with tertiary ammonium groups, as has been demonstrated in the 3AuCl⁺ (3⁺=1‐(tert‐butyl)‐3‐phenyl‐4‐(2‐((dimethylammonio)methyl)phenyl)‐1,2,4‐triazol‐5‐ylidene) complex. However, similar hydrogen bonding interactions with isoelectronic silver(I) or copper(I) centers are unknown. Her...

Gold(II) complexes are rare, and their application to the catalysis of chemical transformations is underexplored. The reason is their easy oxidation or reduction to more stable gold(III) or gold(I) complexes, respectively. We explored the thermodynamics of the formation of [AuII(L)(X)]⁺ complexes (L=ligand, X=halogen) from the corresponding gold(II...

Excitation energies of the lowest singlet and triplet state of molecules whose first excited singlet state lies energetically below the first triplet state have been studied computationally at (time-dependent) density functional theory, coupled-cluster, and second-order multiconfiguration perturbation theory levels. The calculations at the ab initi...

The Cover Feature illustrates thorough and extensive examination of bis‐μ‐oxo/μ‐η2 : η2‐peroxo Cu2O2 equilibrium by employing different levels of theory and perusing various physicochemical contributions to this “enigmatic” equilibrium, including calibrations of computed vibrational spectra of the [Cu2O2] (bio)inorganic systems. This may provide a...

Gold(II) complexes are rare and their application for catalysis of chemical transformations is unexplored. The reason is their easy oxidation or reduction to the more stable gold(III) or gold(I) complexes, respectively. We explored the thermodynamics of the formation of the [(L)AuIIX]+ complexes (L = ligand, X = halogen) from their gold(III) precur...

Coupled binuclear copper (CBC) sites are employed by many metalloenzymes to catalyze a broad set of biochemical transformations. Typically, the CBC catalytic sites are activated by the O2 molecule to form various [Cu2O2] reactive species. This has also inspired synthesis and development of various biomimetic inorganic complexes featuring the CBC co...

Here, we propose and provide in silico proof of concept of a spinristor; a new molecular electronic component that combines a spin-filter, a rectifier, and a switch, in a single molecule for in-memory processing. It builds on the idea of an open-shell transition metal ion enclosed within an elliptical fullerene connected to the source, drain, and a...

Here, we propose and provide in silico proof of concept of a spinristor; a new molecular electronic component that combines a spin-filter, a rectifier, and a switch, in a single molecule for in-memory processing. It builds on the idea of an open-shell transition metal ion enclosed within an elliptical fullerene connected to the source, drain, and a...

A robust method based on NMR traceable cyclic intermediates clearly distinguished self-immolation from other cargo-release processes.

Al(III) complexes are extensively studied as [¹⁸F]fluoride carriers in positron emission tomography. However, our limited knowledge on their thermodynamic and kinetic properties has hindered efforts to easily prepare radiochemically pure compounds while simultaneously reducing the overall labeling time. Thus, to improve our understanding of fluorid...

Actinide-actinide bonds are rare. Only a few experimental systems with An-An bonds have been described so far. Recent experimental characterization of the U2@I h (7)-C80 (J. Am. Chem. Soc.2018, 140, 3907) system with one-electron two-center (OETC) U-U bonds as was predicted by some of us (Phys. Chem. Chem. Phys.2015, 17, 24182) encourages the searc...

Chemical shifts present crucial information about an NMR spectrum. They show the influence of the chemical environment on the nuclei being probed. Relativistic effects caused by the presence of an atom of a heavy element in a compound can appreciably, even drastically, alter the NMR shifts of the nearby nuclei. A fundamental understanding of such r...

Chemical Reviews features on its cover an insightful review on relativistic effects exerted by heavy atoms on neighboring light atoms and how such effects manifest in NMR spectra, coauthored by Michal Straka of #IOCBPrague, in collaboration with Jan Vícha of Centrum polymerních systémů, Univerzita Tomáše Bati ve Zlíně, Jan Novotný and Radek Marek o...

Spin‐orbit (SO) heavy‐atom on the light‐atom (SO‐HALA) effect is the largest relativistic effect caused by a heavy atom on its light‐atom neighbors, leading, for example, to unexpected NMR chemical shifts of ¹H, ¹³C, and ¹⁵N nuclei. In this study, a combined experimental and theoretical evidence for the SO‐HALA effect transmitted through hydrogen b...

Observation of through‐space (or through‐hydrogen bond) relativistic effects between a heavy element (iodine) and a hydrogen atom is reported in this work. The artwork represents a neutron star (an extremely heavy space object) that causes relativistic time effects (a connotation of Einstein's theory of relativity). A stylized spacecraft with the s...

“We show that the inclusion of relativistic SO‐HALA contribution in the calculations of chemical shift of the hydrogen atom included in H⋅⋅⋅I⁻ hydrogen bond is necessary to obtain good agreement with experiment.” Read more about the story behind the cover in the Cover Profile and about the research itself on page 8698 ff. (DOI: 10.1002/chem.2020015...

Heavy atoms influence their surroundings by relativistic effects, such as spin-orbit heavy atom on the light-atom (SO-HALA) effect, causing, among others, chemical-shift changes of the light atom in NMR experiments. Scientists from IOCB Prague - Institute of Organic Chemistry and Biochemistry, Univerzita Tomáše Bati ve Zlíně, and Univerzita Pardub...

Employing multi-scale in silico modeling we propose switching molecular diodes on the basis of endohedral fullerenes (fullerene switching diode, FSD), encapsulated with polar molecules of general type MX (M: metal, X: non-metal) to be used for data storage and processing. Here, we demonstrate for [email protected] systems that the relative orientat...

Polar diatomic molecules encapsulated in asymmetric fullerene cages (here C70) may act as molecular diodes, predicted Adam Jaroš & Michal Straka from #IOCBPrague, and Esmaeil Farajpour Bonab & Cina Foroutan-Nejad from C E I T E C in their paper published in @Journal of the American Chemical Society. Theoretical calculations of MX@C70 systems (M -...

Despite substantial evidence of short Au⋅⋅⋅H−X contacts derived from a number of X‐ray structures of AuI compounds, the nature of AuI⋅⋅⋅H bonding in these systems has not been clearly understood. Herein, we present the first spectroscopic evidence for an intramolecular AuI⋅⋅⋅H⁺−N hydrogen bond in a [Cl−Au−L]⁺ complex, where L is a protonated N‐hete...

Despite substantial evidence of short Au···H–X contacts derived from a number of X‐ray structures of Au(I) compounds, the nature of Au(I)···H bonding has not been clearly understood. Herein, we present the first spectroscopic evidence for intramolecular Au(I)···H+–N hydrogen bond in a [Cl Au L]+ complex, where L is protonated N–heterocyclic carbene...

Illusive Au^I/III···H hydrogen bonds and their effect on structure and dynamics of molecules have been a matter of debate. While a number of X-ray studies reported gold compounds with short Au^I/III···H contacts, a solid spectroscopic evidence for Au^I/III···H bonding has been missing. Recently , Bakar et al. (NATURE C...

We report the F2@C60 system as the first example of an endohedral fullerene in which C60 acts as a cation C60+ interacting with endohedral anion, F2-. Our state-of-the-art computations reveal that in F2@C60, despite of the known high electron affinity of C60, an electron is transferred from C60 to F2 resulting in the F2-@C60+ system. The F-F bond l...

We report the F2@C60 system as the first example of an endohedral fullerene in which C60 acts as a cation C60+ interacting with endohedral anion, F2–. Our state‐of‐the‐art computations reveal that in F2@C60, despite of the known high electron affinity of C60, an electron is transferred from C60 to F2 resulting in the F2–@C60+ system. The F–F bond l...

Resveratrol is antioxidant naturally occurring in wine grapes. It is thought to have a preventive biological activity against number of diseases. However, it has been recently shown that in the presence of metal ions, such as Cu²⁺, resveratrol forms oxidative radicals. Cu²⁺ is usually present in wine due to former usage of bluestone in vineyards. F...

A recent study (Sci. Adv. 2017, 3, e1602833) has shown that FH…OH2 hydrogen bond in a HF·H2O pair substantially shortens and the H-F bond elongates upon encapsulation of the cluster in C70 fullerene. This has been attributed to compression of the HF·H2O pair inside the cavity of C70. Here we present theoretical evidence that the effect is not cause...

Besides their technological applications, endohedral fullerenes provide ideal conditions for investigating molecular dynamics in restricted geometries. A representative of this class of systems, Sc3C2@C80 displays complex intramolecular dynamics. The motion of the ⁴⁵Sc trimer has a remarkable effect on its electron paramagnetic resonance (EPR) spec...

Relativistic effects significantly affect various spectroscopic properties of compounds containing heavy elements. Particularly in Nuclear Magnetic Resonance (NMR) spectroscopy, the heavy atoms strongly influence the NMR shielding constants of neighboring light atoms. In this account we analyze paramagnetic contributions to NMR shielding constants...

Only a single thorium fullerene, Th@C84, has been reported up to date (K. Akiyama et al. J. Nucl. Radiochem. Sci., 3, 2002). Although the system was characterized by UV/vis and XANES spectra, its structure and properties remain unknown. In this work we used the density functional calculations to identify molecular and electronic structure of the Th...

We propose a two-state electric field-driven room-temperature single-molecule switch based on a dipolar molecule enclosed inside ellipsoidal fullerene C70. We show that the two low-energy minima of the molecular dipole inside the C70 cage provide distinguishable molecular states of the system that can be switched by application of an external elect...

The role of relativistic effects on 1H NMR chemical shifts of Sn(II) and Pb(II) hydrides is investigated by using fully relativistic DFT calculations. The stability of possible Pb(II) hydride isomers is studied together with their 1H NMR chemical shifts, which are predicted in the high-frequency region, up to 90 ppm. These 1H signals are dictated b...

Fullerenes are carbon-based materials that exhibit unique chemical and physical properties. They can be conveniently characterized with spectroscopic methods combined with quantum-chemical computations. We review some aspects of quantum-chemical and moleculardynamics simulations of the nuclear magnetic resonance (NMR) and magnetic circular dichrois...

The (13)C and (29)Si NMR signals of ligand atoms directly bonded to Tl(I) or Pb(II) heavy-element centers are predicted to resonate at very high frequencies, up to 400 ppm for (13)C and over 1000 ppm for (29)Si, outside the typical experimental NMR chemical-shift ranges for a given type of nuclei. The large (13)C and (29)Si NMR chemical shifts are...

Magnetic circular dichroism (MCD) spectra of C60Cl6, C70Cl10 and C60Cl24 were measured and interpreted using a sum-over-state (SOS) protocol exploring time dependent density functional theory (TDDFT). Unlike for plain absorption, the MCD spectra exhibited easily recognizable features specific for each chlorinated molecule and appear as a useful too...

The role of various factors (structure, solvent, and relativistic treatment) was evaluated for square-planar 4d and 5d transition-metal complexes. The DFT approach for calculating the structures was calibrated using a cluster approach and compared to X-ray geometries, with the PBE0 functional (def2-TZVPP basis set) providing the best results, follo...

Endohedral actinide fullerenes are rare and a little is known about their molecular properties. Here we characterize the U2@C80 system, which was recently detected experimentally by means of mass spectrometry (Akiyama et al., JACS, 2001, 123, 181). Theoretical calculations predict a stable endohedral system, 7U2@C80, derived from the C80:7 IPR full...

The significant role of relativistic effects in altering the NMR chemical shifts of light nuclei in heavy-element compounds has been recognized for a long time; however, full understanding of this phenomenon in relation to the electronic structure has not been achieved. In this study, the recently observed qualitative differences between the platin...

Applications of liquid crystals (LCs), such as smart windows and the ubiquitous display devices, are based on controlling the orientational and translational order in a small volume of LC medium. Hence, understanding the effects of confinement to the liquid crystal phase behaviour is essential. The NMR shielding of 129Xe atoms dissolved in LCs cons...

In the recently proposed phenomenon, Nuclear Spin-Induced Circular Dichroism (NSCD), collective magnetisation of nuclei induces circular dichroism in a light beam passing through a molecular sample. Here we present the first computational predictions of NSCD for fullerenes C60 and C70. We show that the NSCD signal is nucleus-specific, like in NMR s...

Relativistic effects play an essential role in understanding the nuclear magnetic resonance (NMR) chemical shifts in heavy-atom compounds. Particularly interesting from the chemical point of view are the relativistic effects due to heavy atom (HA) on the NMR chemical shifts of the nearby light atoms (LA), referred to as the HALA effects. The effect...

The isotropic (129) Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C60 dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the (129) Xe NMR CS. The (129) Xe shielding constant was obtained by averagi...

A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with a Hg(II) ion, which results in the formation of a (T)N3-Hg(II) -N3(T) metal-mediated base pair was proposed and calculated. The mechanism assumes two key steps: The formation of the first Hg(II) N3(T) bond is triggered...

The nuclear magnetic resonance (NMR) spectroscopy combined with theoretical calculations is an important tool for fullerene identification. However, the accuracy of available theoretical methods is often not adequate. Therefore, in this work, different computational aspects needed to simulate realistically chemical shifts in the C70 molecule are in...

The similarity in shape makes separation and identification of fullerenes difficult. In this work, the magnetic circular dichroism (MCD) spectroscopy is presented as a useful tool for this purpose. Experimental C60 and C70 spectra were obtained and reproduced with the aid of density functional computations and the complex polarization propagator me...

The interpretation of Nuclear Magnetic Resonance (NMR) parameters is essential to understanding experimental observations at the molecular and supramolecular levels and to designing new and more efficient molecular probes. In many aromatic natural compounds, unusual (13)C NMR chemical shifts have been reported for out-of-plane methoxy groups bonded...

The isotropic 129 Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C 60 dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimen-tal conditions and to evaluate the role of different physical fac-tors influencing the 129 Xe NMR CS. The 129 Xe shielding constant was obtained by averaging...

The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT...

Among rare gases, xenon features an unusually broad nuclear magnetic resonance (NMR) chemical shift range in its compounds and as a non-bonded Xe atom introduced into different environments. In this work we show that (129)Xe NMR chemical shifts in the recently prepared, matrix-isolated xenon compounds appear in new, so far unexplored (129)Xe chemic...

Determination of nucleic acid (NA) structure with NMR spectroscopy is limited by the lack of restraints on conformation of NA phosphate. In this work, the (31)P chemical shielding tensor, the Γ(P,C5'H5'1) and Γ(P,C5'H5'2) cross-correlated relaxation rates, and the (2)J(P,C3'), (2)J(P,C5'), and (3)J(P,C4') coupling constants were calculated in depen...

A range of purine derivatives modified at position 6 of the basic purine skeleton exhibit a variety of biological activities. Several derivatives are used or tested nowadays for pharmacological treatments. The present work aims to analyze the effects of substituents on the electron distribution in the purine core as reflected by NMR chemical shifts...

The isotropic 129Xe NMR chemical shift of atomic Xe dissolved in liquid benzene was simulated by combining classical molecular dynamics and quantum chemical calculations of 129Xe nuclear magnetic shielding. Snapshots from the molecular dynamics trajectory of xenon atom in a periodic box of benzene molecules were used for the quantum chemical calcul...

For Abstract see ChemInform Abstract in Full Text.

The (3)He chemical shifts were calculated for He(n)@C(84) (n = 1, 2) fullerenes to obtain characteristic NMR patterns for distinguishing their isomers in a mixture. The density functional methods were calibrated on experimental data. Accuracy within 1 ppm could be reached without further fitting of individual shifts. Such precision allows for a sem...

Metal atoms with a closed-shell electronic structure and positive charge as for example the Au(I), Pt(II), Ag(I), Tl(I) or Hg(II) atoms do not in some compounds repel each other due to the so-called metallophilic attraction (P. Pyykkö, Chem. Rev., 1997, 97, 597-636). Here we highlight the role of the Hg(II)Hg(II) metallophilic attraction between th...

The compounds I–IV derived from α-D-cyclodextrin moiety by bridging and/or interconnecting with various patterns of disulfide bonds were chosen as models for the spectroscopic study of conformation of the disulfide bridge. The energy gap between the disulfide and cyclodextrin's electronic transitions allows us to investigate absorption and electron...

The formation and structure of the potassium complex with valinomycin in solution were studied by means of Raman and Raman optical activity (ROA) spectroscopy. The complexation caused significant spectral changes, particularly in the region 1200-1400 cm(-1). The experimental spectra were interpreted using first principles computations. A complete c...

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An attempt is made to express the interaction energy in an endohedral A@B system starting from a one-center (r(<))(l)/(r(>))(l+1) expansion. Electrostatic, induction, and dispersion contributions are obtained from Rayleigh-Schrödinger perturbation theory. New electric polarizabilities with r(-l-1) radial integrals are calculated for l = 0, 1 and 2...

A prototypical study of NMR chemical shifts in biologically relevant heteroaromatic compounds containing a heavy halogen atom is presented for two isomers of halogen-substituted purines. Complete sets of (1)H-, (13)C- and (15)N-NMR chemical shifts are determined experimentally in solution. Experimental results are complemented by quantum-chemical c...

The recently observed nonintuitive pH dependence of methylene (1)H chemical shifts in cobalt(III) polyamine complexes upon deprotonation of coordinated aqua or (poly)alcohol coligands (J. Am. Chem. Soc. 2004, 126, 6728) was attributed to differential spin-orbit effects on the (1)H shifts transmitted over three bonds from the cobalt low-spin d(6) ce...

We report density functional theory (DFT) studies on the endohedral scandium carbide fullerene Sc3C2@C80 and its monoanion [Sc3C2@C80](-). The system consisting of a Sc3C2 moiety inside the Ih C80 fullerene has been studied by using first principles molecular dynamics simulations at the DFT level. On the picosecond time scale, the triangle defined...

We perform a computational mapping study of a family of new inorganic species, based on idea of donor-acceptor type bonding between N+ and a ligand L with a terminal electron lone pair. The nitrogen ion is seen as being in an atomic D-1 state, with empty 2p acceptor orbitals [I.S.K. Kerkines., A. Papakondylis, A. Mavridis, Journal of Physical Chemi...

The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define t...

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and t...

We calibrate the methodology for the calculation of nuclear magnetic resonance (NMR) properties in novel organo-xenon compounds. The available state-of-the-art quantum-chemical approaches are combined and applied to the HXeCCH molecule as the model system. The studied properties are (129)Xe, (1)H, and (13)C chemical shifts and shielding anisotropie...

A London-type formula is derived for endohedral systems. It involves the static dipole polarisability, alpha(1)(A) of the inner system, A, and a new type of dipole polarisability, alpha(-2)(B) with an r(-2) radial operator, for the outer system, B. The new formula has no explicit dependence on the radius, R, of B. The predicted interaction energies...

We present constant-pressure Monte Carlo simulations of nuclear magnetic resonance (NMR) spectral parameters, nuclear magnetic shielding relative to the free atom as well as nuclear quadrupole coupling, for atomic xenon dissolved in a model thermotropic liquid crystal. The solvent is described by Gay-Berne (GB) molecules with parametrization kappa=...

We report density functional calculations of 3He nuclear magnetic resonance chemical shifts in a series of experimentally known endohedral helium fullerenes, He(n)@Cm(q) (n = 1, 2; m = 60, 70, 76, 78; q = 0, 6-), including for the first time anionic and di-helium species. Despite the lack of dispersion in the density functional model, the results a...

The title systems, including EThE', are treated at DFT level using a B3LYP functional and small-core quasirelativistic pseudopotentials. Most of the studied systems are bent, like their isoelectronic ThO2, analogue, except for some anionic systems containing Ir. The bond lengths vary considerably and can lie above or below the sum of triple-bond co...

While the thermochemical stability of gas-phase HgF4 against F2 elimination was predicted by accurate quantum chemical calculations more than a decade ago, experimental verification of "truly transition-metal" mercury(IV) chemistry is still lacking. This work uses detailed density functional calculations to explore alternative species that might pr...

The acetylene-like linear HThThH structure is calculated to lie almost degenerate to its rhombic alternative. Its unsupported Th-Th triple bond would be the first one of its kind.