Publications by authors named "Tomasz Pawlak"

25 Publications

  • Page 1 of 1

Resolving Atomic-Scale Interactions in Non-Fullerene Acceptor Organic Solar Cells with Solid-State NMR Spectroscopy, Crystallographic Modelling, and Molecular Dynamics Simulations.

Adv Mater 2021 Nov 24:e2105943. Epub 2021 Nov 24.

University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181, Unité de Catalyse et Chimie du Solide, Lille, F-59000, France.

Fused-ring core non-fullerene acceptors (NFAs), designated "Y-series", have enabled high-performance organic solar cells (OSCs) achieving over 18% power conversion efficiency (PCE). Since the introduction of these NFAs, much effort has been expended to understand the reasons for their exceptional performance. While several studies have identified key optoelectronic properties that govern high PCEs, little is known about the molecular level origins of large variations in performance, spanning from 5 to 18% PCE, e.g., in the case of PM6:Y6 OSCs. Here, we introduce a combined solid-state NMR, crystallography, and molecular modelling approach to elucidate the atomic-scale interactions in Y6 crystals, thin films, and PM6:Y6 bulk heterojunction (BHJ) blends. We show the Y6 morphologies in BHJ blends are not governed by the morphology in neat films or single crystals. Notably, PM6:Y6 blends processed from different solvents self-assemble into different structures and morphologies, whereby the relative orientations of the sidechains and end groups of the Y6 molecules to their fused-ring cores play a crucial role in determining the resulting morphology and overall performance of the solar cells. The molecular-level understanding of BHJs enabled by this approach will guide the engineering of next-generation NFAs for stable and efficient OSCs. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1002/adma.202105943DOI Listing
November 2021

Synergy of Solid-State NMR, Single-Crystal X-ray Diffraction, and Crystal Structure Prediction Methods: A Case Study of Teriflunomide (TFM).

Cryst Growth Des 2021 Jun 10;21(6):3328-3343. Epub 2021 May 10.

Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.

In this work, for the first time, we present the X-ray diffraction crystal structure and spectral properties of a new, room-temperature polymorph of teriflunomide (TFM), CSD code 1969989. As revealed by DSC, the low-temperature TFM polymorph recently reported by Gunnam et al. undergoes a reversible thermal transition at -40 °C. This reversible process is related to a change in value, from 2 to 1, as observed by variable-temperature H-C cross-polarization (CP) magic-angle spinning (MAS) solid-state NMR, while the crystallographic system is preserved (triclinic). Two-dimensional C-H and H-H double-quantum MAS NMR spectra are consistent with the new room-temperature structure, including comparison with GIPAW (gauge-including projector augmented waves) calculated NMR chemical shifts. A crystal structure prediction procedure found both experimental teriflunomide polymorphs in the energetic global minimum region. Differences between the polymorphs are seen for the torsional angle describing the orientation of the phenyl ring relative to the planarity of the TFM molecule. In the low-temperature structure, there are two torsion angles of 4.5 and 31.9° for the two = 2 molecules, while in the room-temperature structure, there is disorder that is modeled with ∼50% occupancy between torsion angles of -7.8 and 28.6°. These observations are consistent with a broad energy minimum as revealed by DFT calculations. PISEMA solid-state NMR experiments show a reduction in the C-H dipolar coupling in comparison to the static limit for the aromatic CH moieties of 75% and 51% at 20 and 40 °C, respectively, that is indicative of ring flips at the higher temperature. Our study shows the power of combining experiments, namely DSC, X-ray diffraction, and MAS NMR, with DFT calculations and CSP to probe and understand the solid-state landscape, and in particular the role of dynamics, for pharmaceutical molecules.
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http://dx.doi.org/10.1021/acs.cgd.1c00123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273857PMC
June 2021

Cytotoxic Activity against A549 Human Lung Cancer Cells and ADMET Analysis of New Pyrazole Derivatives.

Int J Mol Sci 2021 Jun 22;22(13). Epub 2021 Jun 22.

Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Poland.

Two new pyrazole derivatives, namely compound and compound have been synthesized, and their biological activity has been evaluated. Monocrystals of the obtained compounds were thoroughly investigated using single-crystal X-ray diffraction analysis, FTIR spectroscopy, and NMR spectroscopy. The results gathered from all three techniques are in good agreement, provide complete information about the structures of and , and confirm their high purity. Thermal properties were studied using thermogravimetric analysis; both and are stable at room temperature. In order to better characterize and , some physicochemical and biological properties have been evaluated using ADMET analysis. The cytotoxic activity of both compounds was determined using the MTT assay on the A549 cell line in comparison with etoposide. It was determined that compound was effective in the inhibition of human lung adenocarcinoma cell growth and may be a promising compound for the treatment of lung cancer.
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http://dx.doi.org/10.3390/ijms22136692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269030PMC
June 2021

Porous Molecular Capsules as Non-Polymeric Transducers of Mechanical Forces to Mechanophores.

Chemistry 2020 Feb 7;26(7):1558-1566. Epub 2020 Jan 7.

Institute of Organic Chemistry, Polish Academy of Sciences, M. Kasprzaka 44/52, 01-224, Warsaw, Poland.

Mechanical grinding/milling can be regarded as historically the first technology for changing the properties of matter. Mechanically activated molecular units (mechanophores) can be present in various structures: polymers, macromolecules, or small molecules. However, only polymers have been reported to effectively transduce energy to mechanophores, which induces breakage of covalent bonds. In this paper, a second possibility is presented-molecular capsules as stress-sensitive units. Mechanochemical encapsulation of fullerenes in cystine-based covalent capsules indicates that complexation takes place in the solid state, despite the fact that the capsules do not possess large enough entrance portals. By using a set of solvent-free MALDI (sf-MALDI) and solid-state NMR (ss-NMR) experiments, it has been proven that encapsulation proceeds during milling and in this process hydrazones and disulfides get activated for breakage, exchange, and re-forming. The capsules are porous and therefore prone to collapse under solvent-free conditions and their conformational rigidity promotes the collapse by the breaking of covalent bonds.
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http://dx.doi.org/10.1002/chem.201904024DOI Listing
February 2020

The influence of the stereochemistry and C-end chemical modification of dermorphin derivatives on the peptide-phospholipid interactions.

Biochim Biophys Acta Biomembr 2020 02 18;1862(2):183066. Epub 2019 Oct 18.

Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Łódź, Sienkiewicza 112, Poland. Electronic address:

In this work the conformation of dermorphin, Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH, an opioid peptide and its analogues with different stereochemistry of alanine and different C-terminus is studied in aqueous and membrane environments. Using two-dimensional NMR techniques we demonstrate that in DO/HO peptides with D-alanine have extended conformation, while for the L-isomers more compact conformation is preferred. The analysis of ROESY HR MAS spectra of the peptides interacting with the DMPC bilayer indicates that both stereoisomers have still more extended conformation compared to aqueous phase, as shown by much weaker intermolecular interactions. The influence of Ala residue stereochemistry is also reflected in the interactions of the studied peptides with model membranes, as shown by the P NMR static spectra, in which the shapes of the phosphorus NMR signals originating from D-isomers correspond to spherically shaped vesicles in the presence of external magnetic field, in comparison to a more elongated ones observed for L-isomers, while TEM photographs shows that upon addition of D-isomers larger lipid vesicles are formed, in contrast to smaller ones for L-isomers. The location of aromatic fragments of dermorphins in the membrane is determined based on static H NMR and HH RFDR MAS experiments. All aromatic rings were found to be inserted in the hydrophobic part of the bilayer, with the exception of the Tyr5 rings of D-Ala dermorphins. The influence of the C-terminal modification was found to be almost imperceptible.
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http://dx.doi.org/10.1016/j.bbamem.2019.183066DOI Listing
February 2020

The use of variable temperature C solid-state MAS NMR and GIPAW DFT calculations to explore the dynamics of diethylcarbamazine citrate.

Magn Reson Chem 2019 05 15;57(5):200-210. Epub 2018 Oct 15.

Department of Physics, University of Warwick, Coventry, UK.

Experimental C solid-state magic-angle spinning (MAS) Nuclear Magnetic Resonance (NMR) as well as Density-Functional Theory (DFT) gauge-including projector augmented wave (GIPAW) calculations were used to probe disorder and local mobility in diethylcarbamazine citrate, (DEC) (citrate) . This compound has been used as the first option drug for the treatment of filariasis, a disease endemic in tropical countries and caused by adult worms of Wuchereria bancrofti, which is transmitted by mosquitoes. We firstly present 2D C─ H dipolar-coupling-mediated heteronuclear correlation spectra recorded at moderate spinning frequency, to explore the intermolecular interaction between DEC and citrate molecules. Secondly, we investigate the dynamic behavior of (DEC) (citrate) by varying the temperature and correlating the experimental MAS NMR results with DFT GIPAW calculations that consider two (DEC) conformers (in a 70:30 ratio) for crystal structures determined at 293 and 235 K. Solid-state NMR provides insights on slow exchange dynamics revealing conformational changes involving particularly the DEC ethyl groups.
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http://dx.doi.org/10.1002/mrc.4790DOI Listing
May 2019

Simple and Robust Study of Backbone Dynamics of Crystalline Proteins Employing H-N Dipolar Coupling Dispersion.

J Phys Chem B 2018 08 20;122(34):8146-8156. Epub 2018 Aug 20.

Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland.

We report a new solid-state multidimensional NMR approach based on the cross-polarization with variable-contact pulse sequence [ Paluch , P. ; Pawlak , T. ; Amoureux , J.-P. ; Potrzebowski , M. J. J. Magn. Reson. 233 , 2013 , 56 ], with H inverse detection and very fast magic angle spinning (ν = 60 kHz), dedicated to the measurement of local molecular motions of H-N vectors. The introduced three-dimensional experiments, H-N-H and hCA(N)H, are particularly useful for the study of molecular dynamics of proteins and other complex structures. The applicability and power of this methodology have been revealed by employing as a model sample the GB-1 small protein doped with NaCuEDTA. The results clearly prove that the dispersion of H-N dipolar coupling constants well correlates with higher order structure of the protein. Our approach complements the conventional studies and offers a fast and reasonably simple method.
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http://dx.doi.org/10.1021/acs.jpcb.8b04557DOI Listing
August 2018

Correction: Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations.

Phys Chem Chem Phys 2017 08;19(31):21210

Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.

Correction for 'Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations' by Piotr Paluch et al., Phys. Chem. Chem. Phys., 2015, 17, 28789-28801.
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http://dx.doi.org/10.1039/c7cp90168bDOI Listing
August 2017

Competent Geometric Semantic Genetic Programming for Symbolic Regression and Boolean Function Synthesis.

Evol Comput 2018 16;26(2):177-212. Epub 2017 Feb 16.

Institute of Computing Science, Poznan University of Technology, Poznań, Poland

Program semantics is a promising recent research thread in Genetic Programming (GP). Over a dozen semantic-aware search, selection, and initialization operators for GP have been proposed to date. Some of these operators are designed to exploit the geometric properties of semantic space, while others focus on making offspring effective, that is, semantically different from their parents. Only a small fraction of previous works aimed at addressing both of these features simultaneously. In this article, we propose a suite of competent operators that combine effectiveness with geometry for population initialization, mate selection, mutation, and crossover. We present a theoretical rationale behind these operators and compare them experimentally to operators known from literature on symbolic regression and Boolean function synthesis benchmarks. We analyze each operator in isolation as well as verify how they fare together in an evolutionary run, concluding that the competent operators are superior on a wide range of performance indicators, including best-of-run fitness, test-set fitness, and program size.
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http://dx.doi.org/10.1162/EVCO_a_00205DOI Listing
November 2018

Understanding the Electronic Factors Responsible for Ligand Spin-Orbit NMR Shielding in Transition-Metal Complexes.

J Chem Theory Comput 2015 Apr 17;11(4):1509-17. Epub 2015 Mar 17.

CEITEC-Central European Institute of Technology, Masaryk University , Kamenice 5/A4, CZ-62500 Brno, Czech Republic.

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 platinum and gold compounds in the magnitude and the sign of spin-orbit-induced (SO) nuclear magnetic shielding at the vicinal light atom ((13)C, (15)N), σ(SO)(LA), are explained by the contractions of 6s and 6p atomic orbitals in Au complexes, originating in the larger Au nuclear charge and stronger scalar relativistic effects in gold complexes. This leads to the chemical activation of metal 6s and 6p atomic orbitals in Au complexes and their larger participation in bonding with the ligand, which modulates the propagation of metal-induced SO effects on the NMR signal of the LA via the Spin-Orbit/Fermi Contact (SO/FC) mechanism. The magnitude of the σ(SO)(LA) in these square-planar complexes can be understood on the basis of a balance between various metal-based 5d → 5d* and 6p → 6p* orbital magnetic couplings. The large and positive σ(SO)(LA) in platinum complexes is dominated by the shielding platinum-based 5d → 5d* magnetic couplings, whereas small or negative σ(SO)(LA) in gold complexes is related to the deshielding contribution of the gold-based 6p → 6p* magnetic couplings. Further, it is demonstrated that σ(SO)(LA) correlates quantitatively with the extent of M-LA electron sharing that is the covalence of the M-LA bond (characterized by the QTAIM delocalization index, DI). The present findings will contribute to further understanding of the origin and propagation of the relativistic effects influencing the experimental NMR parameters in heavy-element systems.
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http://dx.doi.org/10.1021/ct501089zDOI Listing
April 2015

Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations.

Phys Chem Chem Phys 2015 Nov;17(43):28789-801

Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.

We report a new multidimensional magic angle spinning NMR methodology, which provides an accurate and detailed probe of molecular motions occurring on timescales of nano- to microseconds, in sidechains of proteins. The approach is based on a 3D CPVC-RFDR correlation experiment recorded under fast MAS conditions (ν(R) = 62 kHz), where (13)C-(1)H CPVC dipolar lineshapes are recorded in a chemical shift resolved manner. The power of the technique is demonstrated in model tripeptide Tyr-(d)Ala-Phe and two nanocrystalline proteins, GB1 and LC8. We demonstrate that, through numerical simulations of dipolar lineshapes of aromatic sidechains, their detailed dynamic profile, i.e., the motional modes, is obtained. In GB1 and LC8 the results unequivocally indicate that a number of aromatic residues are dynamic, and using quantum mechanical calculations, we correlate the molecular motions of aromatic groups to their local environment in the crystal lattice. The approach presented here is general and can be readily extended to other biological systems.
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http://dx.doi.org/10.1039/c5cp04475hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890705PMC
November 2015

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

Solid State Nucl Magn Reson 2015 Feb 8;65:2-11. Epub 2014 Sep 8.

Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Lodz, Poland. Electronic address:

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924.
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http://dx.doi.org/10.1016/j.ssnmr.2014.08.002DOI Listing
February 2015

Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

J Phys Chem B 2014 Mar 14;118(12):3298-309. Epub 2014 Mar 14.

Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Sienkiewicza 112, 90-363 Lodz, Poland.

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.
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http://dx.doi.org/10.1021/jp500379eDOI Listing
March 2014

Optimization of process parameters for microwave-vacuum puffing of black radish slices using the response surface method.

Acta Sci Pol Technol Aliment 2013 Jul-Sep;12(3):253-62

Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Poland.

Background: Due to the health-promoting value of black radish, authors decided to investigate the feasibility of forming - from its roots - chips, using the process of microwave-vacuum puffing. In order to produce desirable quality of chips, there is a need to determine the most advantageous values of process parameters. The main goal of the paper is to investigate the possibility of determining the best processing conditions for microwave-vacuum formation of black radish chips that can maximize the chips expansion ratio while maintaining consumer acceptability of sensory quality of chips.

Material And Methods: The raw material for analyses comprised fresh roots of black radish {raphanns sativus linne varietas niger). A three-level, one-factor central composite experimental design (DOE) was applied. The response surface method (RSM) was used as a part of the Statistica software and the R computer program for optimization. Response surfaces were built using the second degree polynomial that includes principal effects of processing parameters values and their interactions.

Results: A regression model was derived, based on results of natural experiments, that give a satisfactory prediction level (R² = 0.96) of the expansion ratio of black radish chips as a function of processing conditions. Then, the best values of process parameters were found using the RSM. The best processing parameters values were determined to be 0.39 kg kg⁻¹ wb (wet basis) moisture content of pre-dehydrated radish slices, 14.5 kPa vacuum absolute pressure and 80 s of microwave heating time during puffing (for the 650 W power output of the microwave generator).

Conclusion: Optimized process of puffing of black radish slices using the RSM provided a satisfactory high value of the sensory quality index of chips. In this paper we do not analyze the physical structure of chips. In the future more research needs to be done in this area.
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October 2014

Study of the mechanism of thermal chemical processes in the crystals of YAF tripeptides by means of mass spectrometry and solid state NMR.

J Phys Chem B 2013 Oct 10;117(43):13481-9. Epub 2013 Oct 10.

Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Sienkiewicza 112, 90-363 Lodz, Poland.

Thermal reactions in two Tyr-Ala-Phe (YAF) tripeptide crystals with different molecular packing (monoclinic and hexagonal), distinct stereochemistry of central amino acid (D or L alanine) and specific arrangement of molecules in the crystal lattice (head-to-tail) were investigated. Samples were heated up to 180 °C, while the melting point for YAF crystals is above the 220 °C. Below the melting temperature, in both cases the chemical reactions leading to formation of cyclic dipeptides (YA diketopiperazine) and leaving of phenylalanine were observed. Two possible mechanisms of chemical reaction in the crystal lattice assuming intra- and/or intermolecular pathways were considered. (13)C and (15)N enriched YAF samples were employed to study of mechanism of solid state reactivity using mass spectrometry and advanced solid state NMR techniques (2D DARR (Dipolar Assisted Rotational Resonance) and 2D Double CP (Cross-Polarization) correlations).
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http://dx.doi.org/10.1021/jp407080qDOI Listing
October 2013

Simple and accurate determination of X-H distances under ultra-fast MAS NMR.

J Magn Reson 2013 Aug 13;233:56-63. Epub 2013 May 13.

Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Lodz, Poland.

We demonstrate that a very simple experiment, Cross-Polarization with Variable Contact-time (CP-VC), is very efficient at ultra-fast MAS (νR ≥ 60 kHz) to measure accurately the C-H and N-H distances, and to analyze the dynamics of bio-molecules. This experiment can be performed with samples that are either (13)C or (15)N labeled or without any labeling. The method is very robust experimentally with respect to imperfect Hartman-Hahn setting, and presents a large scaling factor allowing a better dipolar determination, especially for long C-H or N-H distances, or for CH3 or NH3 moieties with three-site hopping. At ultra-fast MAS, it can be used quantitatively in a 2D way, because its scaling factor is then little dependent on the offsets. This robustness with respect to offset is related to the ultra-fast spinning speed, and hence to the related small rotor diameter. Indeed, these two specifications lead to efficient n = ±1 zero-quantum Hartman-Hahn CP-transfers with large RF-fields on proton and carbon or nitrogen channels, and large dipolar scaling factor.
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http://dx.doi.org/10.1016/j.jmr.2013.05.005DOI Listing
August 2013

NMR crystallography of α-poly(L-lactide).

Phys Chem Chem Phys 2013 Mar 22;15(9):3137-45. Epub 2013 Jan 22.

Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.

A complementary approach that combines NMR measurements, analysis of X-ray and neutron powder diffraction data and advanced quantum mechanical calculations was employed to study the α-polymorph of L-polylactide. Such a strategy, which is known as NMR crystallography, to the best of our knowledge, is used here for the first time for the fine refinement of the crystal structure of a synthetic polymer. The GIPAW method was used to compute the NMR shielding parameters for the different models, which included the α-PLLA structure obtained by 2-dimensional wide-angle X-ray diffraction (WAXD) at -150 °C (model M1) and at 25 °C (model M2), neutron diffraction (WAND) measurements (model M3) and the fully optimized geometry of the PLLA chains in the unit cell with defined size (model M4). The influence of changes in the chain conformation on the (13)C σ(ii) NMR shielding parameters is shown. The correlation between the σ(ii) and δ(ii) values for the M1-M4 models revealed that the M4 model provided the best fit. Moreover, a comparison of the experimental (13)C NMR spectra with the spectra calculated using the M1-M4 models strongly supports the data for the M4 model. The GIPAW method, via verification using NMR measurements, was shown to be capable of the fine refinement of the crystal structures of polymers when coarse X-ray diffraction data for powdered samples are available.
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http://dx.doi.org/10.1039/c2cp43174bDOI Listing
March 2013

Magic angle spinning NMR study of interaction of N-terminal sequence of dermorphin (Tyr-d-Ala-Phe-Gly) with phospholipids.

Biochim Biophys Acta 2012 Nov 27;1818(11):2579-87. Epub 2012 Jun 27.

Polish Academy of Sciences, Lodz, Poland.

Two modifications of the Tyr-d-Ala-Phe-Gly tetrapeptide with different C-terminal groups (Tyr-d-Ala-Phe-Gly-OH 1 and Tyr-d-Ala-Phe-Gly-NH(2)2) were investigated by various nuclear magnetic resonance sequences under magic angle spinning. The structural constraints obtained from the magic angle spinning nuclear magnetic resonance measurements suggest that both peptides are aligned on the surface of the membrane and that the sandwich-like π-CH(3)-π arrangement of the pharmacophore is preserved. The influence of the chemical modification of the C-terminal residue of 1 and 2 on their interaction with phosphate group of the phospholipid in the subgel phase L(c) and the conformation of the peptides in the liquid crystalline phase L(α) are discussed. The correlation between the X-ray structure of 1 in the solid state and 1 embedded into a membrane in the L(c) phase is presented on the basis of the comparative analysis of the two-dimensional (13)C-(13)C dipolar-assisted rotational resonance cross-peaks and the (13)C isotropic chemical shifts.
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http://dx.doi.org/10.1016/j.bbamem.2012.06.013DOI Listing
November 2012

Computed and experimental chemical shift parameters for rigid and flexible YAF peptides in the solid state.

J Phys Chem B 2012 Feb 6;116(6):1974-83. Epub 2012 Feb 6.

Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, PL-90-363 Lodz, Poland.

DFT methods were employed to compute the (13)C NMR chemical shift tensor (CST) parameters for crystals of YAF peptides (Tyr-Ala-Phe) with different stereochemistry for the Ala residue. Tyr-D-Ala-Phe 1 crystallizes in the C2 space group while Tyr-L-Ala-Phe crystallizes in either the P2(1)2(1)2 space group (2a) or the P6(5) space group (2b). PISEMA MAS measurements for samples with a natural abundance of (1)H and (13)C nuclei and (2)H QUADECHO experiments for samples with deuterium labeled aromatic rings were used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 1 is rigid and the phenylalanine ring undergoes a π-jump, both rings in sample 2a are static, and both rings in sample 2b undergo a fast regime exchange. The theoretical values of the CST were obtained for isolated molecules (IM) and clusters employing the ONIOM approach. The experimental (13)C δ(ii) parameters for all of the samples were measured via a 2D PASS sequence. Significant scatter of the computed versus the experimental (13)C CST parameters was observed for 1 and 2b, while the observed correlation was very good for 2a. In this report, we show that the quality of the (13)C σ(ii)/(13)C δ(ii) correlations, when properly interpreted, can be a source of important information about local molecular motions.
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http://dx.doi.org/10.1021/jp2111567DOI Listing
February 2012

Validation of Relativistic DFT Approaches to the Calculation of NMR Chemical Shifts in Square-Planar Pt(2+) and Au(3+) Complexes.

J Chem Theory Comput 2011 Dec 29;7(12):3909-23. Epub 2011 Nov 29.

Faculty of Chemistry, Nicholas Copernicus University , Gagarina 7, PL-87100 Toruń, Poland.

Recently implemented hybrid density functional methods of calculating nuclear magnetic shielding using the two-component zeroth-order regular approximation approach (J. Phys. Chem. A2009, 113, 11495) have been employed for a series of compounds containing heavy transition-metal atoms. These include Pt(2+), Pd(2+), and Au(3+) organometallics and metal complexes with azines, some of which exhibit interesting biological and catalytic activities. In this study we investigate the effects of geometry, exchange-correlation functional, solvent, and scalar relativistic and spin-orbit corrections on the nuclear magnetic shielding-mainly for (13)C and (15)N atoms connected to a heavy-atom center. Our calculations demonstrate that the B3LYP method using effective core potentials and a cc-pwCVTZ-PP/6-31G** basis set augmented with the polarizable continuum model of the dimethylsulfoxide solvent provides geometries for the complexes in question which are compatible with the experimental NMR results in terms of both the trends and the absolute values of the (13)C shifts. The important role of the exact exchange admixture parameter for hybrid functionals based on B3LYP and PBE0 is investigated systematically for selected Pt(2+) and Au(3+) complexes. The (13)C and (15)N NMR chemical shifts are found to be best reproduced by using a B3LYP or PBE0 approach with 30% and 40-50% exact exchange admixtures for the Pt(2+) and Au(3+) complexes, respectively. The spin-orbit contributions to the (15)N NMR chemical shifts reflect metal-ligand bonding that is much more ionic for the Au(3+) than for the Pt(2+) complex. Finally, an optimized density functional method is applied to a series of transition-metal complexes to estimate the scope and the limitations of the current approach.
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http://dx.doi.org/10.1021/ct200366nDOI Listing
December 2011

1H, 13C, 15N NMR coordination shifts in Fe(II), Ru(II) and Os(II) cationic complexes with 2,2':6',2″-terpyridine.

Magn Reson Chem 2011 May 29;49(5):237-41. Epub 2011 Mar 29.

Faculty of Chemistry, Nicholas Copernicus University, Gagarina 7, PL-87100 Toruń, Poland.

(1)H, (13)C and (15)N NMR studies of iron(II), ruthenium(II) and osmium(II) bis-chelated cationic complexes with 2,2':6',2″-terpyridine ([M(terpy)(2) ](2+) ; M = Fe, Ru, Os) were performed. Significant shielding of nitrogen-adjacent H(6) and deshielding of H(3'), H(4') protons were observed, both effects being mostly expressed for Fe(II) compounds. The metal-bonded nitrogens were shielded, this effect being much larger for the outer N(1), N(1″) than the inner N(1') atoms, and enhanced in the Fe(II) → Ru(II) → Os(II) series.
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http://dx.doi.org/10.1002/mrc.2739DOI Listing
May 2011

1H, 13C, 195Pt and 15N NMR structural correlations in Pd(II) and Pt(II) chloride complexes with various alkyl and aryl derivatives of 2,2'-bipyridine and 1,10-phenanthroline.

Magn Reson Chem 2011 Feb 3;49(2):59-64. Epub 2011 Jan 3.

Faculty of Chemistry, Nicholas Copernicus University, Gagarina 7, PL-87100 Toruń, Poland.

(1)H, (13)C, (195)Pt and (15)N NMR studies of platinide(II) (M = Pd, Pt) chloride complexes with such alkyl and aryl derivatives of 2,2'-bipyridine and 1,10-phenanthroline as LL = 6,6'-dimethyl-bpy, 5,5'-dimethyl-bpy, 4,4'-di-tert-butyl-bpy, 2,9-dimethyl-phen, 2,9-dimethyl-4,7-diphenyl-phen, 3,4,7,8-tetramethyl-phen, having the general [M(LL)Cl(2)] formula were performed and the respective chemical shifts (δ(1H), δ(13C), δ(195Pt), δ(15N)) reported. (1)H high-frequency coordination shifts (Δ(coord)(1H) = δ(complex)(1H)-δ(ligand)(1H)) mostly pronounced for nitrogen-adjacent protons and methyl groups in the nearest adjacency of nitrogen, as well as (15)N low-frequency coordination shifts (Δ(coord)(15H) = δ(complex)(15H)-δ(ligand)(15H)) were discussed in relation to the molecular structures.
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http://dx.doi.org/10.1002/mrc.2704DOI Listing
February 2011

(1)H NMR assignment corrections and (1)H, (13)C, (15)N NMR coordination shifts structural correlations in Fe(II), Ru(II) and Os(II) cationic complexes with 2,2'-bipyridine and 1,10-phenanthroline.

Magn Reson Chem 2010 Jun;48(6):450-7

Faculty of Chemistry, Nicholas Copernicus University, Gagarina 7, PL-87100 Toruń, Poland.

(1)H, (13)C and (15)N NMR studies of iron(II), ruthenium(II) and osmium(II) tris-chelated cationic complexes with 2,2'-bipyridine and 1,10-phenanthroline of the general formula [M(LL)(3)](2+) (M = Fe, Ru, Os; LL = bpy, phen) were performed. Inconsistent literature (1)H signal assignments were corrected. Significant shielding of nitrogen-adjacent protons [H(6) in bpy, H(2) in phen] and metal-bonded nitrogens was observed, being enhanced in the series Ru(II) --> Os(II) --> Fe(II) for (1)H, Fe(II) --> Ru(II) --> Os(II) for (15)N and bpy --> phen for both nuclei. The carbons are deshielded, the effect increasing in the order Ru(II) --> Os(II) --> Fe(II).
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http://dx.doi.org/10.1002/mrc.2600DOI Listing
June 2010

Structural correlations for (1)H, (13)C and (15)N NMR coordination shifts in Au(III), Pd(II) and Pt(II) chloride complexes with lutidines and collidine.

Magn Reson Chem 2010 Jun;48(6):417-26

Faculty of Chemistry, Nicholas Copernicus University, Gagarina 7, PL-87100 Toruń, Poland.

(1)H, (13)C and (15)N NMR studies of gold(III), palladium(II) and platinum(II) chloride complexes with dimethylpyridines (lutidines: 2,3-lutidine, 2,3lut; 2,4-lutidine, 2,4lut; 3,5-lutidine, 3,5lut; 2,6-lutidine, 2,6lut) and 2,4,6-trimethylpyridine (2,4,6-collidine, 2,4,6col) having general formulae [AuLCl(3)], trans-[PdL(2)Cl(2)] and trans-/cis-[PtL(2)Cl(2)] were performed and the respective chemical shifts (delta(1H), delta(13C), delta(15N)) reported. The deshielding of protons and carbons, as well as the shielding of nitrogens was observed. The (1)H, (13)C and (15)N NMR coordination shifts (Delta(1H) (coord), Delta(13C) (coord), Delta(15N) (coord); Delta(coord) = delta(complex) - delta(ligand)) were discussed in relation to some structural features of the title complexes, such as the type of the central atom [Au(III), Pd(II), Pt(II)], geometry (trans- or cis-), metal-nitrogen bond lengths and the position of both methyl groups in the pyridine ring system.
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http://dx.doi.org/10.1002/mrc.2594DOI Listing
June 2010

1H, 13C, 15N and 195Pt NMR studies of Au(III) and Pt(II) chloride organometallics with 2-phenylpyridine.

Magn Reson Chem 2009 Nov;47(11):932-41

Faculty of Chemistry, Nicholas Copernicus University, Gagarina 7, PL-87100, Toruń, Poland.

(1)H, (13)C, (15)N and (195)Pt NMR studies of gold(III) and platinum(II) chloride organometallics with N(1),C(2')-chelated, deprotonated 2-phenylpyridine (2ppy*) of the formulae [Au(2ppy*)Cl(2)], trans(N,N)-[Pt(2ppy*)(2ppy)Cl] and trans(S,N)-[Pt(2ppy*)(DMSO-d(6))Cl] (formed in situ upon dissolving [Pt(2ppy*)(micro-Cl)](2) in DMSO-d(6)) were performed. All signals were unambiguously assigned by HMBC/HSQC methods and the respective (1)H, (13)C and (15)N coordination shifts (i.e. differences between chemical shifts of the same atom in the complex and ligand molecules: Delta(1H)(coord) = delta(1H)(complex) - delta(1H)(ligand), Delta(13C)(coord) = delta(13C)(complex) - delta(13C)(ligand), Delta(15N)(coord) = delta(15N)(complex) - delta(15N)(ligand)), as well as (195)Pt chemical shifts and (1)H-(195)Pt coupling constants discussed in relation to the known molecular structures. Characteristic deshielding of nitrogen-adjacent H(6) protons and metallated C(2') atoms as well as significant shielding of coordinated N(1) nitrogens is discussed in respect to a large set of literature NMR data available for related cyclometallated compounds.
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http://dx.doi.org/10.1002/mrc.2491DOI Listing
November 2009
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