Papers by Frank Blockhuys
The teraHertz range (60 GHz - 4 THz = 2-130 cm -1 )i s a relatively unexplored, but information-r... more The teraHertz range (60 GHz - 4 THz = 2-130 cm -1 )i s a relatively unexplored, but information-rich part of the vibrational spectrum of molecular crystals. The motions in this frequency range are at lower energies than most of the internal vibrations of molecules (e.g., bond stretching and angle bending), but correspond instead to translations and librations of molecules. Thus, spectroscopic and computational investigations of this frequency range are a source of information on the intermolecular interactions in molecular crystals. Lattice dynamics calculations are being developed within the crystal structure modelling program DMAREL[1-2], for the use of elaborate model intermolecular potentials. Such calculations have been performed to characterise the measured teraHertz spectra of several molecular organic crystals, correlating regions of the spectra to distortions of certain intermolecular interactions. One of the systems studied is the polymorphic pharmaceutical molecule carbam...
Molecules, 2020
A uniform derivation of the self-consistent field equations in a finite basis set is presented. B... more A uniform derivation of the self-consistent field equations in a finite basis set is presented. Both restricted and unrestricted Hartree–Fock (HF) theory as well as various density functional approximations are considered. The unitary invariance of the HF and density functional models is discussed, paving the way for the use of localized molecular orbitals. The self-consistent field equations are derived in a non-orthogonal basis set, and their solution is discussed also in the presence of linear dependencies in the basis. It is argued why iterative diagonalization of the Kohn–Sham–Fock matrix leads to the minimization of the total energy. Alternative methods for the solution of the self-consistent field equations via direct minimization as well as stability analysis are briefly discussed. Explicit expressions are given for the contributions to the Kohn–Sham–Fock matrix up to meta-GGA functionals. Range-separated hybrids and non-local correlation functionals are summarily reviewed.
Acta Crystallographica Section A Foundations and Advances, 2018
Rapid Communications in Mass Spectrometry, 2020
RATIONALE Amide bond protonation triggering peptide fragmentations and the controversial b2 -ion ... more RATIONALE Amide bond protonation triggering peptide fragmentations and the controversial b2 -ion structures have both been subjects of intense research. The involvement of histidine (H), with its imidazole side-chain which induces specific dissociation patterns involving inter-side-chain (ISC) interactions, on b2 -ion formation was investigated, focusing on the QHS model tripeptide. METHODS To pinpoint the effect of histidine on fragmentations issued from ISC interactions, QHS was selected for a comprehensive analysis of the pathways leading to the three possible b2 -ion structures, using quantum chemical calculations performed at the DFT/B3LYP/6-311+G* level of theory. In addition, electrospray ionization ion trap mass spectrometry allowed recording MS2 and MS3 tandem mass spectra, while the Quantum Chemical Mass Spectrometry for Materials Science (QCMS2 ) method was used as tool to predict fragmentation patterns. RESULTS Whereas it is probably very difficult to unambiguously differentiate between protonated oxazolone, diketopiperazine or lactam b2 -ions from MS2 and MS3 mass spectra alone, the calculations indicated that the QH b2 -ion (detected at m/z 266) is probably a mixture of the lactam and oxazolone structures formed after amide nitrogen protonation, making the diketopiperazine form less likely to occur as it requires an additional step in its formation. CONCLUSIONS In contrast to glycine-histidine-containing b2 -ions known to be issued from backbone-imidazole cyclization, we found that interactions between the side chains were not that obvious to perceive, neither from a thermodynamics nor from a fragmentation perspective, emphasizing the importance of the whole sequence on the dissociation behavior usually demonstrated from simple glycine-containing tripeptides.
Surface Science, 2017
A DFT study on the adsorption of a series of phosphonic acids (PAs) on the TiO2 anatase ( ) and (... more A DFT study on the adsorption of a series of phosphonic acids (PAs) on the TiO2 anatase ( ) and (001) surfaces was performed. The adsorption energies and geometries of the most stable binding modes were compared to literature data and the effect of the inclusion of dispersion forces in the energy calculations was gauged. As the (101) surface is the most exposed surface of TiO2 anatase, the calculated chemical shifts and vibrational frequencies of PAs adsorbed on this surface were compared to experimental 31 P and 17 O NMR and IR data in order to assign the two possible binding modes (mono-and bidentate) to peaks and bands in these spectra; due to the corrugated nature of anatase (101) tridentate binding is not possible on this surface. Analysis of the calculated and experimental 31 P chemical shifts indicates that both monodentate and bidentate binding modes are present. For the reactive (001) surface, the results of the calculations indicate that both bi-and tridentate binding modes are possible. Due to the particular sensitivity of 17 O chemical shifts to hydrogen bonding and solvent effects, the model used is insufficient to assign these spectra at present. Comparison of calculated and experimental IR spectra leads to the conclusion that IR spectroscopy is not suitable for the characterization of the different binding modes of the adsorption complexes.
Letters in Applied Microbiology, 2006
To evaluate the electronic nose (EN) as method for the identification of ten clinically important... more To evaluate the electronic nose (EN) as method for the identification of ten clinically important micro-organisms. A commercial EN system with a series of ten metal oxide sensors was used to characterize the headspace of the cultured organisms. The measurement procedure was optimized to obtain reproducible results. Artificial neural networks (ANNs) and a k-nearest neighbour (k-NN) algorithm in combination with a feature selection technique were used as pattern recognition tools. Hundred percent correct identification can be achieved by EN technology, provided that sufficient attention is paid to data handling. Even for a set containing a number of closely related species in addition to four unrelated organisms, an EN is capable of 100% correct identification. The time between isolation and identification of the sample can be dramatically reduced to 17 h.
Acta crystallographica. Section C, Crystal structure communications, 2010
Three substituted triphenyl(phenylimino)phosphoranes, namely (4-cyanophenylimino)triphenylphospho... more Three substituted triphenyl(phenylimino)phosphoranes, namely (4-cyanophenylimino)triphenylphosphorane, C(25)H(19)N(2)P, (I), (4-nitrophenylimino)triphenylphosphorane, C(24)H(19)N(2)O(2)P, (II), and (3-nitrophenylimino)triphenylphosphorane, C(24)H(19)N(2)O(2)P, (III), were synthesized as precursors for the preparation of substituted diphenylcarbodiimides. All three compounds display a supramolecular arrangement in which the substituted benzene rings are organized in an antiparallel fashion. The nitro group on the ring participates in C-H...O and O...pi interactions, forming intermolecular dimers. Compound (III) shows disorder which involves the rotation of one of the phenyl rings of the triphenylphosphine group.
Theoretical Chemistry Accounts, 2012
A quantum chemical study was performed on ten different self-doping PPV oligomers. The geometry a... more A quantum chemical study was performed on ten different self-doping PPV oligomers. The geometry and the different weak intramolecular interactions were studied. The atomic spin populations were calculated using the FOHI method and related to the calculated EPR parameters. The effects of the removal of methoxy groups, the introduction of nitrogen atoms, and the relocation of the self-doping sidechain on the geometry, the spin distribution, and the EPR parameters have been described.
Journal of Chemical Theory and Computation, 2011
In this work, a new partitioning method is presented which allows one to calculate properties of ... more In this work, a new partitioning method is presented which allows one to calculate properties of radicals, in particular, atomic spin populations. The method can be seen as an extension of the Hirshfeld-I method [ Bultinck , P. et al. J. Chem. Phys. 2007 , 126 , 144111 ], in which the atomic weight functions, defining the atoms-in-molecules, are constructed by means of an iterative scheme in which the charges of the atoms-in-molecules are altered but the spin remains fixed. The Hirshfeld-I method is therefore not suitable for the calculation of atomic spin populations of open-shell systems. The new fractional occupation Hirshfeld-I (FOHI) uses an iterative scheme in which both the atomic charge and spin are optimized, resulting in a self-consistent method for the calculation of atomic spin populations. The results obtained with the FOHI method are compared with experimental results obtained using polarized neutron diffraction, thus serving as a validation of the FOHI method as well as the Hirshfeld definition of atoms-in-molecules in general.
The Journal of Chemical Physics, 2014
In this work, a new partitioning method based on the FOHI method (fractional occupation Hirshfeld... more In this work, a new partitioning method based on the FOHI method (fractional occupation Hirshfeld-I method) will be discussed. The new FOHI-D method uses an iterative scheme in which both the atomic charge and atomic dipole are calculated self-consistently. In order to induce the dipole moment on the atom, an electric field is applied during the atomic SCF calculations. Based on two sets of molecules, the atomic charge and intrinsic atomic dipole moment of hydrogen and chlorine atoms are compared using the iterative Hirshfeld (HI) method, the iterative Stockholder atoms (ISA) method, the FOHI method, and the FOHI-D method. The results obtained are further analyzed as a function of the group electronegativity of Boyd et al. [J. Am. Chem. Soc. 110, 4182 (1988); Boyd et al., J. Am. Chem. Soc. 114, 1652 (1992)] and De Proft et al. [J. Phys. Chem. 97, 1826 (1993)]. The molecular electrostatic potential (ESP) based on the HI, ISA, FOHI, and FOHI-D charges is compared with the ab initio ESP. Finally, the effect of adding HI, ISA, FOHI, and FOHI-D atomic dipoles to the multipole expansion as a function of the precision of the ESP is analyzed.
Inorganic Chemistry, 2006
A synthetic, spectroscopic, and theoretical study of Ex(CN)2 (E = S, Se; x = 1-3) is described. T... more A synthetic, spectroscopic, and theoretical study of Ex(CN)2 (E = S, Se; x = 1-3) is described. The X-ray structures of Se2(CN)2 and Se3(CN)2 have been determined. Se2(CN)2 crystallizes in a chiral space group with the CN groups approximately gauche.
European Journal of Inorganic Chemistry, 2009
Cp*Rh(S 2 N 2 ) was prepared as a microcrystalline solid using [S 4 N 3 ]Cl in liquid ammonia or ... more Cp*Rh(S 2 N 2 ) was prepared as a microcrystalline solid using [S 4 N 3 ]Cl in liquid ammonia or [nBu 2 Sn(S 2 N 2 )] 2 . It was characterised by NMR, IR and Raman spectroscopy and mass spectrometry. Low-temperature crystal structures of Cp*Co(S 2 N 2 ) and Cp*Ir(S 2 N 2 ) were determined. The experimental characterisation of the Cp*M(S 2 N 2 ) complexes is complemented by calculated geometries and bond orders at the DFT/B1B95 level of theory.
European Journal of Inorganic Chemistry, 2008
This review highlights the most important advances in the heteroatom chemistry of 1,3,2,4-benzodi... more This review highlights the most important advances in the heteroatom chemistry of 1,3,2,4-benzodithiadiazines (π-excessive and formally antiaromatic heterocycles), covering methods for synthesis, nontrivial features of the molecular and π-electronic structure, spectral properties, and reactivity, in particular the transformations into persistent π-radicals.
Environmental Science & Technology, 2014
Additonal information on the time-resolved α-pinene/NOx/air irradiation experiment, Figures S1 to... more Additonal information on the time-resolved α-pinene/NOx/air irradiation experiment, Figures S1 to S16, and explanation of the Figures.
Crystal Growth & Design, 2011
E, E-2,5-bis[2-(4-methoxyphenyl)ethenyl]pyrazine (2) A round-bottomed flask was charged with 3.4 ... more E, E-2,5-bis[2-(4-methoxyphenyl)ethenyl]pyrazine (2) A round-bottomed flask was charged with 3.4 g (25 mmol) of 3,4-dimethoxybenzaldehyde and 1.4 g (12.5 mmol) of 2,5-dimethylpyrazine in 20 mL of DMF. After 30 min. 2.8 g (50 mmol) of KOH was added. The mixture was heated to 100°C and stirred at this temperature for 3 days. After cooling to room temperature the mixture was cooled in an ice bath and 60 mL of cold methanol was added. The mixture was stored overnight in the refrigerator and the resulting orange precipitate was washed with water (2 × 20 mL) and ethanol (2 × 20 mL). The crude product was isomerized for 4 h in refluxing p-xylene containing a catalytic amount of I 2 . The precipitate was collected by filtration
Acta Crystallographica Section E Structure Reports Online, 2010
In the title compound, C 11 H 12 O 6 , the aldehyde group is disordered over two sites in a 0.79:... more In the title compound, C 11 H 12 O 6 , the aldehyde group is disordered over two sites in a 0.79:0.21 ratio. The carboxylic acid chain is found in the [ap,ap] conformation due to two intramolecular O-HÁ Á ÁO hydrogen bonds.
Acta Crystallographica Section A Foundations of Crystallography, 2006
We have been using the UK's synchrotron source at Daresbury Laboratory for 10 years. We first col... more We have been using the UK's synchrotron source at Daresbury Laboratory for 10 years. We first collected data during the commissioning phase and have obtained beam time regularly ever since. We wish to present a users perspective on the development of the small molecule crystallography stations, our experiences of using the facility as a whole, and some key results including those most recently obtained. Key aspects will be: c Detector advances and effects on data collection. c Computing developments (hardware and software). c The opening of the second station 16.2 SMX. c Key structures and publications in the fields of calixarene chemistry and supramolecular structures.
Journal of Mass Spectrometry
Journal of The American Society for Mass Spectrometry
The quantum chemical mass spectrometry for materials science (QCMS 2 ) method is used to verify t... more The quantum chemical mass spectrometry for materials science (QCMS 2 ) method is used to verify the proposed mechanism for proton transferthe Mobile Proton Model (MPM)by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS 2 framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of fivemembered ring intermediates to include larger-ring intermediates.
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Papers by Frank Blockhuys