Adam KubasPolish Academy of Sciences | PAN · Institute of Physical Chemistry
Adam Kubas
Dr. rer. nat.
About
70
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Introduction
Adam Kubas currently works at the Institute of Physical Chemistry, Polish Academy of Sciences. Adam does research in Physical Chemistry, Catalysis and Theoretical Chemistry. Their current project is 'Iron-sulfur clusters as natural switches: consequences of the unique iron atom coordination at a molecular level'.
Additional affiliations
September 2014 - March 2016
March 2016 - present
October 2009 - March 2010
BioInfoBank Institute
Position
- Coourse Author
Education
September 2009 - August 2012
October 2004 - June 2009
Publications
Publications (70)
Friedel oscillations are quantum mechanical phenomena observed as oscillatory variations in electron density due to the presence of impurity or defect in a media containing electron gas. FOs profoundly influence surface properties, including the ordering of adsorbates and surface-mediated interactions crucial for catalytic activity. We delve into b...
We present an efficient route to tetramethylalumoxane by the controlled hydrolysis of AlMe 3 in the presence of pyridine. The AlMe 3 (pyr) hydrolysis by 0.5 and 1 equiv. of H 2 O has been...
The capability of organic emitters to harvest triplet excitons via a thermally activated delayed fluorescence (TADF) process has opened a new era in organic optoelectronics. Nevertheless, low brightness, and consequently an insufficient roll-off ratio, constitutes a bottleneck for their practical applications in the domain of organic light-emitting...
Despite the design and proposal of several new structural motifs as thermally activated delayed fluorescent (TADF) emitters for organic light-emitting device (OLED) applications, the nature of their interaction with the host matrix in the emissive layer of the device and their influence on observed photophysical outputs remain unclear. To address t...
Despite promising optoelectronic features of N-doped polycyclic aromatic hydrocarbons (PAHs), their use as functional materials remains underdeveloped due to their limited post-functionalization. Facing this challenge, a novel design of N-doped PAHs with D-A-D electronic structure for thermally activated delayed fluorescence (TADF) emitters was per...
The domain-based local pair natural orbital (PNO) coupled-cluster DLPNO-CCSD(T) method has been proven to provide accurate single-point energies at a fraction of the cost of canonical CCSD(T) calculations. However, the desired "chemical accuracy" can only be obtained with a large PNO space and extended basis set. We present a simple yet accurate an...
We report the synthesis and characterization of a series of donor-acceptor TADF emitters with a new architecture, where the donor moiety and the dibenzazepine-based acceptor moiety are separated by a...
For sustained vision, photoactivated rhodopsin (Rho*) must undergo hydrolysis and release of all- trans -retinal, producing substrate for the visual cycle and apo-opsin available for regeneration with 11- cis -retinal. The kinetics of this hydrolysis has yet to be described for rhodopsin in its native membrane environment. We developed a method con...
Hyperfluorescence (HF), a relatively new phenomenon utilizing the transfer of excitons between two luminophores, requires careful pairwise tuning of molecular energy levels and is proposed to be the crucial step towards the development of new, highly effective OLED systems. To date, barely few HF yellow emitters with desired narrowband emission but...
Furylfulgides, a class of photochromic organic compounds, show a complex system of photoinduced reactions. In the present study, the excited-state dynamics of the E𝛼 and E𝛽 isomers of a representative furylfulgide is modelled with the use of nonadiabatic molecular dynamics simulations. Moreover, a pattern recognition algorithm is employed in order...
Hyperfluorescence (HF), a relatively new phenomenon utilizing excitons transfer between two luminophores, requires careful pairwise tuning of molecular energy levels and is proposed to be the crucial step toward the development of new, highly effective OLED systems. To date, barely a few HF yellow emitters with desired narrowband emission but moder...
Although bowl‐shaped N‐pyrrolic polycyclic aromatic hydrocarbons (PAHs) can achieve excellent electron‐donating ability, their application for optoelectronics is hampered by typically low photoluminescence quantum yields (PLQYs). To address this issue, we report the synthesis and characterization of a series of curved and fully conjugated nitrogen‐...
Although bowl‐shaped N‐pyrrolic polycyclic aromatic hydrocarbons (PAHs) can achieve excellent electron‐donating ability, their application for optoelectronics is hampered by typically low photoluminescence quantum yields (PLQYs). To address this issue, we report the synthesis and characterization of a series of curved and fully conjugated nitrogen‐...
The introduction of pyrrolic nitrogen dopants into the central sites of polycyclic aromatic hydrocarbons (PAHs) often gives rise to characteristic bowl-shaped structures due to the simultaneous introduction of 5- and/or 7-membered cycles. Although the incorporation of these heteroatoms achieves excellent electron-donating ability, the application o...
Polycyclic aromatic hydrocarbons (PAHs) with centrally positioned nitrogen dopants possess a unique curved structure and strong electron-donating features. However, the lack of tools to synthetically affect their bandgap engineering and charge-transfer (CT) characteristic is detrimental to their future optoelectronics use because of usually low PLQ...
A new molecular dataset called HAB79 is introduced to provide ab-initio reference values for electronic couplings (transfer integrals) and to benchmark density functional theory (DFT) and density functional tight-binding (DFTB) calculations. The HAB79 dataset is comprised of 79 planar heterocyclic polyaromatic hydrocarbon molecules frequently encou...
N‐heterocyclic carbene ligands (NHC) are widely utilized in catalysis and material science. They are characterized by their steric and electronic properties. Steric properties are usually quantified on the basis of their static structure, which can be determined by X‐ray diffraction. The electronic properties are estimated in the liquid state; for...
4-(N,N-Dimethylamino)benzonitrile (DMABN) is a well-known model compound for dual fluorescence—in sufficiently polar solvents, it exhibits two distinct fluorescence emission bands. The interpretation of its transient absorption (TA) spectrum in the visible range is the subject of a long-standing controversy. In the present study, we resolve this is...
The compound 9-cis-retinyl acetate (9-cis-RAc) is a precursor to 9-cis-retinal, which has potential application in the treatment of some hereditary diseases of the retina. An attractive synthetic route to 9-cis-RAc is based on the photoisomerization reaction of the readily available all-trans-RAc. In the present study, we examine the mechanism of t...
![(a) Quenching of the fluorescence of 1.0μM\documentclass[12pt]{minimal}...](publication/350810942/figure/fig3/AS:1012006614212613@1618292587770/a-Quenching-of-the-fluorescence-of-10mMdocumentclass12ptminimal_Q320.jpg)
![(a) Quenching of the fluorescence of 2.0μM\documentclass[12pt]{minimal}...](publication/350810942/figure/fig4/AS:1012006614228994@1618292587836/a-Quenching-of-the-fluorescence-of-20mMdocumentclass12ptminimal_Q320.jpg)
Graphene-based nanohybrids are good candidates for various applications. However, graphene exhibits some unwanted features such as low solubility in an aqueous solution or tendency to aggregate, limiting its potential applications. On the contrary, its derivatives, such as graphene oxide (GO) and reduced graphene oxide (RGO), have excellent propert...
The electronic coupling matrix element HAB is an essential ingredient of most electron-transfer theories. HAB depends on the overlap between donor and acceptor wave functions and is affected by the involved states' spin. We classify the spin-state effects into three categories: orbital occupation, spin-dependent electron density, and density deloca...
We present an efficient strategy for synthesising the PdAu catalysts with a homogeneous PdAu alloy phase for environmentally important hydrodechlorination of tetrachloromethane in the gas phase. The synthesis of carbon-supported catalysts involved two major steps: (i) incorporation of palladium and gold nanoparticles into carbon support and (ii) ac...
Solar energy‐driven processes for biomass valorization are priority for the growing industrialized society. To address this challenge, efficient visible light‐active photocatalyst for the selective oxidation of biomass‐derived platform chemical is highly desirable. Herein, selective oxidation of 5‐hydroxymethylfurfural (HMF) to 2,5‐diformylfuran (D...
Figure S1. a) X-ray diffraction pattern of SGH-TiO2. b) X-ray diffraction pattern of P25.
Figure S2. a) Nitrogen sorption isotherms of SGH-TiO2. b) Nitrogen sorption isotherms of P25. c) Pore width distribution of SGH-TiO2. d) Pore width distribution of P25.
Figure S3. a) Selected area electron diffraction image of SGH-TiO2. b) Particle size distri...
The effect of Pd doping on nano-Ni catalyst hydrogenation aptitude in sulcatone (6-methyl-5-hepten-2-one) hydrogenation was investigated. Obtained results demonstrated that the addition of non-catalytic amounts of Pd to the surface of parent Ni catalyst improves the activity to the extent that it surpassed the activity of 2.16 wt% Pd catalyst (mode...
The experimental UV–Vis spectra of the biologically relevant [2Fe–2S] iron–sulfur clusters feature typically three bands in the 300–800 nm range. Based on ground-state orbitals and using the one electron transition picture, these bands are said to be of charge transfer character. The key complication in the electronic structure calculations of thes...
The present study explores the influence of graphene oxide (GO) on deactivation pathways of the excited states of zinc 5,10,15,20-tetrakis(4-(hydroxyphenyl) porphyrin (ZnTPPH). The interaction of light with free ZnTPPH molecules and with ZnTPPH molecules adsorbed on graphene oxide sheets was probed via UV-Vis spectroscopy, fluorescence spectroscopy...
The effect of nano‐Ni catalyst post‐synthetic Zr‐modification on hydrogenation reaction of 6‐methyl‐5‐hepten‐2‐one was investigated in a fixed bed continuous‐flow micro‐reactor to produce fine chemicals. The catalytic performance revealed that Zr‐doping achieved by surface organometallic chemistry approach modifies the natural aptitude of nickel to...
Catalytic Z-isomerization of retinoids to their thermodynamically less stable Z-isomer remains a challenge. In this report, we present a photochemical approach for the catalytic Z-isomerization of retinoids using monochromatic wavelength UV irradiation treatment. We have developed a straightforward approach for the synthesis of Z-retinoids in high...
The regioselective Z-isomerization of thermodynamically stable all-trans retinoids remains challenging, and ultimately limits the availability of much needed therapeutics for the treatment of human diseases.1-3 We present here a novel, straightforward approach for the catalytic Z-isomerization of retinoids using conventional heat treatment or micro...
SALEN- and SALAN-based complexes with catalytically active metal centers are very promising small molecules to be utilized as part of antioxidant therapies. Here we discuss a modified SALAN-type molecule armed with two phosphonate groups that significantly increase its water solubility and aid to furnish mono- or dinuclear complexes with Cu ²⁺ ions...
Zinc oxide (ZnO) is one of the most versatile semiconductor material with multifarious potential applications. Easily accessible alkylzinc alkoxides have been widely exploited as single-source precursors of ZnO-based nanomaterials but their multi-step decomposition pathways have not been understood in detail. The formation mechanism of ZnO nanocrys...
Herein we report on the hydrolysis mechanism of [Pt{N(p-HC6F4)CH2}2(NC5H5)2(OH)2], a platinum(IV) complex that exhibits anti-cancer properties. Atomic telemetry, an in situ technique based on electron structure sensitive X-ray spectroscopy, revealed that hydrolysis preceded any reduction of the metal center. The obtained results are complemented wi...
In this study the M- and L-edge X-ray absorption spectra of a series of open- and closed-shell solids (TiO2 rutile, α-Fe2O3 hematite, FeS2 pyrite, and the spinel Co3O4) are investigated with the restricted open-shell configuration interaction singles methods (ROCIS/DFT and PNO-ROCIS/DFT) using the embedded cluster approach. ROCIS/DFT type of method...
[Fe4S4] iron‐sulfur clusters are typically anchored to the protein scaffold via four cysteine residues but in a number of proteins one of the Cys is replaced with other ligand. The biological role of such replacement is unknown although essential to maintain catalytic activity. Here, we explore the geometries and electronic structures of 3:1 site d...
Chemoselective flow hydrogenation of 6-methyl-5-hepten-2-one was performed over nano-nickel catalysts. The parent catalyst composed solely of nickel nanoparticles grafted on the polymeric resin exhibited high activity and selectivity towards C. C bond saturation but its modification with small quantities of tin significantly increased its ability t...
Absorption and multiwavelength resonance Raman spectroscopy are widely used to investigate the electronic structure of transition metal centers in coordination compounds and extended solid systems. In combination with computational methodologies that have predictive accuracy, they define powerful protocols to study the spectroscopic response of cat...
Coupled cluster theory with single, double and perturbative triple excitations (CCSD(T)) is widely considered to be the ‘gold standard’ of ab initio quantum chemistry. Using the domain-based pair natural orbital local correlation concept (DLPNO-CCSD(T)), these calculations can be performed on systems with hundreds of atoms at an accuracy of about 9...
FeFe hydrogenases are the most efficient H2-producing enzymes. However, inactivation by O2 remains an obstacle that prevents them being used in many biotechnological devices. Here, we combine electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to uncover the molecular mechanism of O2 diffusion within th...
We noted a few numerical mistakes in Tables VI, X, and XI of Ref. 1. Some of the FODFTB data were not correctly copied from the source spreadsheet. The statistical analysis was performed with the original data and is not affected along with the conclusions made in the manuscript. Corrected tables with updated values marked in bold are presented bel...
The pathways by which small molecules (substrates or inhibitors) access active sites are a key aspect of the function of enzymes and other proteins. A key problem in designing or altering such proteins is to identify sites for mutation that will have the desired effect on the substrate transport properties. While specific access channels have been...
We investigate laser-induced spin-dynamics scenarios on a nickel dimer at various interatomic distances. Successful spin-flip processes based on highly correlated abinitio calculations are established and analyzed. Switching is achieved through a laser-driven Λ-process and optimized with a genetic algorithm.
A new database (HAB7-) of electronic coupling matrix elements (Hab) for electron transfer in seven medium-sized negatively charged π-conjugated organic dimers is introduced. Reference data are obtained with spin-component scaled approximate coupled cluster method (SCS-CC2) and large basis sets. Assessed DFT-based approaches include constrained dens...
Simulation of charge transport in organic semiconducting materials requires the development of strategies for very fast yet accurate estimation of electronic coupling matrix elements for electron transfer between organic molecules (transfer integrals, H_ab). A well known relation that is often exploited for this purpose is the approximately linear...
We introduce a database (HAB11) of electronic coupling matrix elements (H
ab
) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory,
n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate cou...
[FeFe]-hydrogenases are the best natural hydrogen-producing enzymes but their biotechnological exploitation is hampered by their extreme oxygen sensitivity. The free energy profile for the chemical attachment of O2 to the enzyme active site was investigated by using a range-separated density functional re-parametrized to reproduce high-level ab ini...
![Figure 1: The active site of the [FeFe]-hydrogenases. The H-cluster is...](profile/Adam-Kubas/publication/260678698/figure/fig1/AS:267282366595086@1440736490379/The-active-site-of-the-FeFe-hydrogenases-The-H-cluster-is-shown-in-blue-and-red-along_Q320.jpg)
[FeFe]-hydrogenases are the best natural hydrogen-producing enzymes but their biotechnological exploitation is hampered by their extreme oxygen sensitivity. The free energy profile for the chemical attachment of O2 to the enzyme active site was investigated by using a range-separated density functional re-parametrized to reproduce high-level ab ini...
The 1,2- and 1,4-asymmetric additions of dialkylzinc reagents (ZnMe(2) and ZnEt(2)) to cinnamaldehyde and N-formylbenzylimine catalysed by [2.2]paracyclophane-based N,O-ligands were studied with quantum chemical methods. High level LPNO-CEPA/1 (local pair natural orbital coupled electron pair approximation 1) calculations were performed to obtain r...
N-Acyl-L-homoserine lactones (AHLs) are small cell-to-cell signaling molecules involved in the regulation of population density and local gene expression in microbial communities. Recent evidence shows that contact of this signaling system, usually referred to as quorum sensing, to living eukaryotes results in interactions of AHL with host cells in...
The heterolytic splitting of hydrogen by two types of [2.2]paracyclophane derived bisphosphines (1, 2a and 2b) in combination with tris(pentafluorophenyl)borane (3) at room temperature is described. The corresponding frustrated Lewis pairs (FLPs) exhibit different behavior in the activation of hydrogen. This results from diverse steric and electron...
N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechani...
The experimental charge density distribution was determined for 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitryle, using the Hansen-Coppens multipole model. Free R factor calculations were performed with MoPro software to find optimal restraints for a physically meaningful model. The crystal packing is determined to some extent by weak C-H···O...
We thank the Deutsche Forschungsgemeinschaft for financial support and Prof. Dr. H. Schnöckel, Dr. Christian Schenk, and Dr. E. Barnes for helpful discussions. A.K. and K.F. thank the Deutsche Forschungsgemeinschaft for financial support through SFB TRR88.
Kleine Ursache, große Wirkung: Die Umsetzung von SnIBr mit LiSi(SiMe3)3 ergibt die Titelverbindung, ein neues Mitglied der Singulett-Biradikaloide. Rechnungen zeigen, dass die Ligandenanordnung die Bindungssituation im Clusterkern beeinflusst und zu einem scharfen Übergang annähernd erster Ordnung zwischen gebundener und biradikaloider Form führt....
Cobalt(II) diketonate complexes, such as bis[trifluoroacetylacetonato(-1)]cobalt(II) [Co(tfa)(2)], catalyze the aerobic oxidation of alkenols into functionalized tetrahydrofurans. To gain insight into activation of triplet dioxygen by Co(tfa)(2) in a protic solvent, as used in oxidation catalysis, the electronic structure of aquabis[trifluoroacetyl...
The reaction of GeBr with LiSi(SiMe(3))(3) leads to the metalloid cluster compound [(THF)(2)Li](3)Ge(14)[Si(SiMe(3))(3)](5) (1). After the introduction of a first cluster of this type, in which 14 germanium atoms form an empty polyhedron, [(THF)(2)Li](3)Ge(14)[Ge(SiMe(3))(3)](5) (2), we present here further investigations on 1 to obtain preliminary...
We present herein the first indications for dimeric structures in cometal-free asymmetric conjugate addition reactions of dialkylzinc reagents with aldehydes. These are revealed by nonlinear effect (NLE) studies. A monomer-dimer equilibrium can be assumed which explains the increase of the ee value in the product over time. Also, DOSY NMR spectrosc...
Cartesian coordinates of the optimized structures discussed in the text are available as a Supplementary Material.
In this study quantum chemical calculations based on the density functional theory (DFT) have been carried out to examine the effects of methoxy substituent attached to a silicon atom on the reaction of silylative coupling of olefins. It has been shown, that substituted substrate undergoes the reaction according to the recently proposed insertion-r...
Questions
Question (1)
Hi All,
I have just read very recent paper "Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?" by Xuefei Xu, Wenjing Zhang, Mingsheng Tang and Donald Truhlar published in JCTC ("just accepted"). Here is the link:
They looked how few DFT functionals perform for the dissociation energies of a set of diatomic, transition metal-containing molecules and compared this to the performance of a hierarchy of CC approximations (CCSD, CCSD(T), CCSDT, CCSDT(Q)). They concluded that CC, although much more elaborate and time consuming, are not better than modern DFT functionals. They also questioned benchmarks of DFT methods against CC for TM systems.
With the results they presented the conclusions are right. Of course, as they properly noted, if the experimental data change the trends can also be changed. As I'm personally interested in TM compounds and do a lot of calculations on these systems (DFT, single- and multireference wavefunction-based methods), I'm quite surprise that they make such strong statements.
First of all, I would never use CC methods for the molecules in question. Multireference treatment would be preferred. Linear molecules tend to have near-degenerate states. Most of the complexes we deal in real life have stronger ligands and way lower symmetry and consequently highly single-reference character. The latter, as properly pointed by authors, is not well defined. In fact, T1, M and B1 diagnostics used in the paper do not seem to correlate between each other.
In larger systems weak interactions tend to have really large impact and consistent solution for this problem is still not definitely done in DFT. The DFT errors here can reach more than deviations presented in the paper.
Although the paper is very solid, I'm a bit sceptical about the generality of conclusions made. I would be curious to hear your feelings about this paper and about benchmarks for transition metals in general.
All the best,
Adam
