Malgorzata Biczysko

Shanghai University | SHU · College of Sciences

Quantum refinement (Q|R) of crystallographic or cryo-EM derived structures of biomolecules within the Q|R project aims at using ab initio computations instead of library-based chemical restraints. An atomic model refinement requires the calculation of the gradient of the objective function. While it is not a computational bottleneck in classic refi...

Quantum refinement (Q|R) of crystallographic or cryo-EM derived structures of biomolecules within the Q|R project aims at using ab initio computations instead of library-based chemical restraints. An atomic model refinement requires the calculation of the gradient of the objective function. While it is not a computational bottleneck in classic refi...

The effect of the presence of a deuterium (D) or tritium (T) isotope bonded to the alpha carbon of glycine is determined without the need to apply external forces, for example, electric fields or using normal mode analysis. Isotopic effects were accounted for using the mass‐dependent diagonal Born‐Oppenheimer energy correction (DBOC) at the CCSD le...

Nitroxide radicals are characterized by a long-lived spin-unpaired electronic ground state and are strongly sensitive to their chemical surroundings. Combined with electron paramagnetic resonance spectroscopy, these electronic features have led to the widespread application of nitroxide derivatives as spin labels for use in studying protein structu...

The effect of the presence of a deuterium (D) or tritium (T) isotope bonded to the alpha carbon of glycine is determined without the need to apply external forces e.g. electric fields or using normal mode analysis. Isotopic effects were accounted for using the mass-dependent diagonal Born-Oppenheimer energy correction (DBOC) at the CCSD level of th...

Spectroscopic techniques can probe molecular systems non-invasively and investigate their structure, properties and dynamics in different environments and physico-chemical conditions. Different spectroscopic techniques (spanning different ranges of the electromagnetic field) and their combination can lead to a more comprehensive picture of investig...

Increased importance of vibrational fingerprints in the identification of molecular systems, can be highlighted by the upcoming interstellar medium (ISM) observations by the James Webb Space Telescope, or in a context of other astrochemical environments as meteorites or exoplanets, Mars robotic missions, such as instruments on board of Perseverance...

Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is...

The search for molecular biosignatures at the surface of Mars is complicated by an intense irradiation in the mid- and near-ultraviolet (UV) spectral range for several reasons: (i) many astrobiologically relevant molecules are electronically excited by efficient absorption of UV radiation and rapidly undergo photochemical reactions; (ii) even thoug...

This work provides the accurate reference data for structural and energetic properties relevant for computational studies of amino acids and polypeptides. Glycine due to its small size allows for detailed theoretical explorations of its whole conformational space. The reference energies are computed at the CCSD(T)/CBS+CV level on the best estimated...

Electron cryo-microscopy (cryo-EM) is fast becoming a major competitor to X-ray crystallography especially for large structures that are difficult or impossible to crystallize. While recent spectacular technology improvements are leading to significantly higher resolution of three-dimensional reconstructions, the average quality of cryo-EM maps is...

The search for molecular biosignatures at the surface of Mars is complicated by an intense irradiation in the mid- and near- ultraviolet (UV) spectral range for several reasons: (i) many astrobiologically relevant molecules are electronically excited by efficient absorption of UV radiation and rapidly undergo photochemical reactions; (ii) even thou...

The simplest molecule with a disulfide bond, hydrogen disulfide (HSSH), represents an ideal test model for the determination of accurate gas-phase equilibrium structures for molecules containing third-row elements. First, pure theoretical composite schemes based on the coupled-cluster (CC) theory, which take into account the extrapolation to the co...

Three-dimensional structure models refined using low-resolution data from crystallographic or electron cryo-microscopy experiments can benefit from high-quality restraints derived from quantum-chemical methods. However, nonperiodic atom-centered quantum-chemistry codes do not inherently account for nearest-neighbor interactions of crystallographic...

The conformations and molecular structures of diisopropyl disulfide have been studied by high-resolution microwave spectroscopy and quantum chemical calculations. Three conformers, G'GG', G'GT, and GGG', have been observed in the jet expansion. The global minimum, G'GG', adopts a configuration with the G' orientation of H-C-S-S and S-S-C-H and the...

Three-dimensional structure models refined using low-resolution data from crystallographic or electron cryo-microscopy experiments can benefit from high quality restraints derived from quantum chemical methods. However, non-periodic atom-centered quantum chemistry codes do not inherently account for nearest neighbor interactions of crystallographic...

The vibrational structure of the optical absorption and fluorescence spectra of the two lowest-energy singlet electronic states (Qy and Qx) of pheophytin a were carefully studied by combining low-resolution and high-resolution spectroscopy with quantum chemical analysis and spectral modeling. Large asymmetry was revealed between the vibrational str...

In this work, we study the structural changes of the polar [NH4][Cd(HCOO)3] hybrid perovskite under external hydrostatic pressure. We report a reversible framework rearrangement as a function of pressure characterized by: (i) a gradual modification of one formate ligand, which changes its coordination mode from a bridging syn-anti mode at atmospher...

Conformational changes of the monomeric safrole (5-(2-propenyl)-1,3-benzodioxole) isolated in low temperature xenon matrices were induced thermally or using narrow-band UV radiation. The rotation of the allyl group taking place in the studied matrices was followed by FTIR spectroscopy. Safrole represents a challenging example of a flexible molecule...

Open‐chain versus hemiaminal and macrocycle forms of the condensation product of 2,6‐diformylpyridine and opposite enantiomers of trans‐1,2‐diaminocyclopentane have been studied using DFT methods to reveal that the macrocycle (with a water molecule co‐product) is the thermochemically preferred form. The mechanistic picture of formation of 2+2 Schif...

Interaction of weakly bonded complexes of atmospheric constituents with the electromagnetic spectrum available in Earth's atmosphere can induce direct excitation to electronic excited states as well as to higher vibrational state (overtones) of the electronic ground state. The better understanding of these phenomena requires improved theoretical su...

The cover image, by Malgorzata Biczysko et al., is based on the Advanced Review Computational challenges in Astrochemistry, DOI: 10.1002/wcms.1349. The cover image, by Malgorzata Biczysko et al., is based on the Advanced Review Computational challenges in Astrochemistry, DOI: 10.1002/wcms.1349.

Context. To date, several complex organic molecules have been detected in the interstellar medium, and they have been suggested as precursors of biologically important species. Propargylamine (HC ≡C−CH 2 −NH 2 ) is structurally similar to a number of other organic molecules which have already been identified by radioastronomy, making it a good cand...

Electron Localization Function analysis reveals the details of a Charge Induced Hydrogen Detachment mechanism of 3-amino-1,2,4-triazole, identified recently as responsible for phototautomerization of the molecule. . In this process the vertical excitation to 1πσ* state is followed by the barrier-less migration of H atom along the N-H bond toward th...

Unusual local arrangements of protein in Ramachandran space is not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. By contrast, quantum chemical computations using small poly-peptide molecular models ca...

Cosmic evolution is the tale of progressive transition from simplicity to complexity. The newborn universe starts with the simplest atoms formed after the Big Bang and proceeds toward ‘astronomical complex organic molecules’ (astroCOMs). Understanding the chemical evolution of the universe is one of the main aims of Astrochemistry, with the startin...

A combined study of the vibrational spectroscopy of iodopentafluorobenzene by new Raman and Fourier-Transform infrared (FTIR) spectroscopies, over the spectral range 300 to 3200 cm-1 (Raman) and 50 to 3400 cm-1 (FTIR), with a state-of-the-art theoretical investigation is reported. This has enabled reliable identification of numerous fundamental, ov...

A set of accurate spectroscopic parameters for the detection of the atmospherically important HOC(O)O radical has been obtained by means of state-of-the-art ab initio computations. These include advanced coupled cluster treatments, involving both standard and explicitly correlated approaches, to correctly account for basis set incompleteness and co...

A new ultraviolet (UV) and vacuum ultraviolet (VUV) spectrum for iodopentafluorobenzene (C 6 F 5 I) using synchrotron radiation is reported. The measurements have been combined with those from a recent high-resolution photoelectron spectroscopic study. A major theoretical study, which includes both Franck-Condon (FC) and Herzberg-Teller (HT) analys...

The medium-resolution gas-phase infrared (IR) spectra of 1-bromo-1-fluoroethene (BrFC=CH2, 1,1-C2H2BrF) were investigated in the range 300 - 6500 cm(-1) , and the vibrational analysis led to the assignment of all fundamentals as well as many overtone and combination bands up to three quanta, thus giving an accurate description of its vibrational st...

A new ultraviolet (UV) and vacuum ultraviolet (VUV) spectrum for iodopentafluorobenzene (C6F5I) using synchrotron radiation is reported. The measurements have been combined with those from a recent high-resolution photoelectron spectroscopic (PES) study. A major theoretical study, which includes both Franck-Condon (FC) and Herzberg-Teller (HT) anal...

In this tutorial review, we present some effective methodologies available for the simulation of vibrational and vibrationally resolved electronic spectra of medium-to-large molecules. They have been integrated into a unified platform and extended to support a wide range of spectroscopies. The resulting tool is particularly useful in assisting the...

While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be cr...

New photoelectron spectra (PES) and ultra violet (UV) and vacuum UV (VUV) absorption spectra of fluorobenzene recorded at higher resolution than previously, have been combined with mass-resolved (2 + 1) and (3 + 1) resonance enhanced multiphoton ionization (REMPI) spectra; this has led to the identification of numerous Rydberg states. The PES have...

Vibrationally resolved one-photon absorption and electronic circular dichroism spectra of (R)-methyl oxirane were calculated with different electronic and vibronic models selecting, through an analysis of the convergence of the results, the best compromise between reliability and computational cost. Linear-response TD-DFT/CAM-B3LYP/SNST electronic...

New photoelectron (PE) and ultra violet (UV) and vacuum UV (VUV)spectra have been obtained for chlorobenzene by synchrotron study with higher sensitivity and resolution than previous work and are subjected to detailed analysis. In addition, we report on the mass-resolved (2 + 1) resonance enhanced multiphoton ionization (REMPI) spectra of a jet-coo...

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values, needs to be compensated by reliable co...

Thanks to significant improvements in hardware and the development of efficient algorithms, computational spectroscopy can now be routinely used to a simulate spectra of medium-to-large molecular systems, offering valuable help in the analysis or prediction of experimental spectra. This is the case for infrared and Raman spectroscopies, commonly us...

The aim of this paper is twofold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman Optical Activity (ROA) with the full inclusion of first- and second-order resonances for both frequencies and intensities in the framework of the generalized second-order vibrational perturbat...

A cost-effective, robust and reliable computational strategy is applied to simulate peak positions and band shapes of UV–Vis spectra together with the dye colours perceived by human eyes. The features of our virtual multifrequency spectrometer (VMS) relevant to this topic are sketched with special focus on the selection of density functional, vibro...

The possibilities offered by organic fluorophores in the preparation of advanced plastic materials have been increased by designing novel alkynylimidazole dyes, featuring different push and pull groups. This new family of fluorescent dyes was synthesized by means of a one-pot sequential bromination-alkynylation of the heteroaromatic core, and their...

Infrared spectra of [Re(X)(CO)3(α-diimine)] (α-diimine= 2,2'-bipyridine, X = Cl, NCS or pyridylimidazo[1,5-a]pyridine, X=Cl) in the ground and the lowest triplet electronic states were calculated by a global hybrid density functional going beyond the harmonic level by means of second-order vibrational perturbation theory (VPT2) and including bulk s...

New photoelectron, ultraviolet (UV), and vacuum UV (VUV) spectra have been obtained for bromobenzene by synchrotron study with higher sensitivity and resolution than previous work. This, together with use of ab initio calculations with both configuration interaction and time dependent density functional theoretical methods, has led to major advance...

The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer...

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of...

For many years, scientists suspected that the interstellar medium was too hostile for organic species and that only a few simple molecules could be formed under such extreme conditions. However, the detection of approximately 180 molecules in interstellar or circumstellar environments in recent decades has changed this view dramatically. A rich che...

Hydrogen-bonding interactions lead to significant changes in the infrared (IR) spectrum, like frequency-shifts of the order of magnitude of hundreds of wavenumbers and increases of IR intensity for bands related to vibrational modes of functional groups directly involved in the hydrogen-bonded bridges. We are actively developing a comprehensive and...

New valence electron photoelectron spectra of iodobenzene obtained using synchrotron radiation have been recorded. Ionization energies (IEs) determined using multi-configuration SCF calculation (MCSCF) procedures confirmed the adiabatic IE order as: X2B1<A2A2<B2B2<C2B1. Although it is convenient to retain C2v labelling, there is an evidence that mi...

Identification of many Rydberg states in iodobenzene, especially from the first and fourth ionization energies (IE1 and IE4, X2B1 and C2B1), has become possible using a new ultraviolet (UV) and vacuum-ultraviolet (VUV) absorption spectrum, in the region 29 000-87 000 cm−1 (3.60-10.79 eV), measured at room temperature with synchrotron radiation. A f...

This work aims at extending the semi-experimental (SE) approach for deriving accurate equilibrium structures to large molecular systems of organic and biological interest. SE equilibrium structures are derived by a least-squares fit of the structural parameters to the experimental ground-state rotational constants of several isotopic species correc...

An overview of the theoretical background and computational requirements needed for molecular structure analysis by means of spectroscopic techniques is provided. Different types of spectroscopy are considered: the account spans across rotational motion to electronic transitions. Particular emphasis is given to the interplay of experiment and theor...

Microsolvation of 2-Thiouracil: Molecular Structure and Spectroscopic Parameters of the Thiouracil–Water Complex Equilibrium structure information: the Z-matrix employed in our calculations together with the geometrical parameters obtained for all the computational levels considered.

State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-zeta basis set has been considered...

Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra- and inter-molecular interactions which may take place, the interpretation of experimental data becomes more and more difficult as the system under stu...

This article presents the setup and implementation of a graphical user interface (VMS-Draw) for a virtual multifrequency spectrometer. Special attention is paid to ease of use, generality and robustness for a panel of spectroscopic techniques and quantum mechanical approaches. Depending on the kind of data to be analyzed, VMS-Draw produces differen...

The subtle interplay of several different effects means that the interpretation and analysis of experimental spectra in terms of structural and dynamic characteristics is a challenging task. In this context, theoretical studies can be helpful, and as such, computational spectroscopy is rapidly evolving from a highly specialized research field towar...

Monomers of pyruvic acid (PA) isolated in cryogenic argon and nitrogen matrices were characterized by mid- and near-infrared spectroscopy. Interpretation of the experiments was aided by fully anharmonic calculations of the fundamental modes, overtones and combinations up to two quanta, including their infrared intensities. The initially dominating...

In this chapter we will review the main methodological aspects providing the background for the computational study of thermochemical and spectroscopic properties of molecular systems. A variety of spectroscopies covering a large interval of the electromagnetic spectrum, from the radiofrequencies to the UV–Vis zones, have been applied to a selected...

An accurate spectroscopic characterization of protonated oxirane has been carried out by means of state-of-the-art computational methods and approaches. The calculated spectroscopic parameters from our recent computational investigation of oxirane together with the corresponding experimental data available were used to assess the accuracy of our pr...

Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been ev...

The main building blocks of a virtual spectrometer aimed at the vis-a-vis comparison between computed and experimental electronic spectra of large-size molecules in condensed phases are shortly analyzed with special attention to stereo-electronic, dynamic and environmental effects. The combined use of time-dependent and time-independent models allo...

The main building blocks of a virtual spectrometer aimed at the vis-a-vis comparison between computed and experimental electronic spectra of large-size molecules in condensed phases are shortly analyzed with special attention to stereo-electronic, dynamic and environmental effects. The combined use of time-dependent and time-independent models allo...

A comprehensive study of the molecular structure and IR spectrum of cis and trans acrolein has been performed by an integrated computational approach coupling methods rooted into the coupled cluster ansatz and the density functional theory. From the one side, DFT anharmonic force elds allow to determine very reliable semi-experimental structures fo...

In an effort to provide an accurate spectroscopic characterization of oxirane, state-of-the-art computational methods and approaches have been employed to determine highly accurate fundamental vibrational frequencies and rotational parameters. Available experimental data were used to assess the reliability of our computations, and an accuracy on av...

Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising res...

In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor () and alizarin acceptor () moieties are linked to a triazole...