Publications by authors named "Matthias Hennemann"

25 Publications

  • Page 1 of 1

An electrically conducting three-dimensional iron-catecholate porous framework.

Angew Chem Int Ed Engl 2021 Mar 29. Epub 2021 Mar 29.

Ludwig-Maximilians-Universitat Munchen, Chemistry, Butenandtstrasse 11, 81377, München, GERMANY.

Here, we report the synthesis of a unique cubic metal-organic framework (MOF), the Fe-HHTP-MOF, comprising hexahydroxytriphenylene (HHTP) supertetrahedral units and FeIII ions, arranged in a diamond topology. The MOF is synthesized under solvothermal conditions, yielding a highly crystalline, deep black powder, with crystallites of 300-500 nm size and tetrahedral morphology. Nitrogen sorption analysis indicates a highly porous material with a surface area exceeding 1400 m2 g-1. Furthermore, Fe-HHTP-MOF shows broadband absorption from 475 nm up to 1900 nm with excellent absorption capability of 98.5% of the incoming light over the visible spectral region. Electrical conductivity measurements of pressed pellets reveal a high intrinsic electrical conductivity of up to 10-3 S cm-1. Quantum mechanical calculations predict Fe-HHTP-MOF to be an efficient electron conductor, exhibiting continuous charge-carrier pathways throughout the structure. This report expands the paradigm of intrinsically electroactive MOFs, serving as a solid basis for the development of highly porous, ordered frameworks with enhanced electrical conductivity.
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http://dx.doi.org/10.1002/anie.202102670DOI Listing
March 2021

Energy Efficient Ultrahigh Flux Separation of Oily Pollutants from Water with Superhydrophilic Nanoscale Metal-Organic Framework Architectures.

Angew Chem Int Ed Engl 2021 Mar 18;60(10):5519-5526. Epub 2021 Jan 18.

Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität (LMU), Butenandtstr. 5-13, 81377, Munich, Germany.

The rising demand for clean water for a growing and increasingly urban global population is one of the most urgent issues of our time. Here, we introduce the synthesis of a unique nanoscale architecture of pillar-like Co-CAT-1 metal-organic framework (MOF) crystallites on gold-coated woven stainless steel meshes with large, 50 μm apertures. These nanostructured mesh surfaces feature superhydrophilic and underwater superoleophobic wetting properties, allowing for gravity-driven, highly efficient oil-water separation featuring water fluxes of up to nearly one million L m  h . Water physisorption experiments reveal the hydrophilic nature of Co-CAT-1 with a total water vapor uptake at room temperature of 470 cm  g . Semiempirical molecular orbital calculations shed light on water affinity of the inner and outer pore surfaces. The MOF-based membranes enable high separation efficiencies for a number of liquids tested, including the notorious water pollutant, crude oil, affording chemical oxygen demand (COD) concentrations below 25 mg L of the effluent. Our results demonstrate the great impact of suitable nanoscale surface architectures as a means of encoding on-surface extreme wetting properties, yielding energy-efficient water-selective large-aperture membranes.
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http://dx.doi.org/10.1002/anie.202012428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7986099PMC
March 2021

EMPIRE: a highly parallel semiempirical molecular orbital program: 3: Born-Oppenheimer molecular dynamics.

J Mol Model 2020 Feb 3;26(3):43. Epub 2020 Feb 3.

Computer-Chemie-Centrum, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany.

Direct NDDO-based Born-Oppenheimer molecular dynamics (MD) have been implemented in the semiempirical molecular orbital program EMPIRE. Fully quantum mechanical MD simulations on unprecedented time and length scales are possible, since the calculation of self-consistent wavefunctions and gradients is performed in a massively parallel manner. MD simulations can be performed in the NVE and NVT ensembles, using either deterministic (Berendsen) or stochastic (Langevin) thermostats. Furthermore, dynamics for condensed-phase systems can be performed under periodic boundary conditions. We show three exemplary applications: the dynamics of molecular reorganization upon ionization, long timescale dynamics of an endohedral fullerene, and calculation of the vibrational spectrum of a nanoparticle consisting of more than eight hundred atoms. Graphical AbstractA snapshot from an MNDO-H simulation of NH@C at 4000 K shortly before a proton crosses the fullerene wall to give NH@CH.
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http://dx.doi.org/10.1007/s00894-020-4293-zDOI Listing
February 2020

Propagation of Holes and Electrons in Metal-Organic Frameworks.

J Chem Inf Model 2019 12 20;59(12):5057-5064. Epub 2019 Nov 20.

Computer-Chemistry-Center, Department of Chemistry and Pharmacy , Friedrich-Alexander-University Erlangen-Nuremberg , Naegelsbachstr. 25 , 91052 Erlangen , Germany.

Charge transport in two zinc metal-organic frameworks (MOFs) has been investigated using periodic semiempirical molecular orbital calculations with the AM1* Hamiltonian. Restricted Hartree-Fock calculations underestimate the band gap using Koopmans theorem (ca. 2 eV compared to the experimental value of 2.8 eV). However, it almost doubles when the constraint on the wave function to remain spin-restricted is removed and the energies of the UHF Natural Orbitals are used. Charge-transport simulations using propagation of the electron- or hole-density in imaginary time allow charge-transport paths and mechanisms to be determined. The calculated relative mobilities in the directions of the three crystal axes agree with experimental expectations, but the absolute values are not reliable using the current technique. Hole-mobility along the crystal -axis (along the metal stacks) is found to be 13 times higher in the zinc MOF with anthracene linker (Zn-ANMOF-74) than in the other directions, whereas the factor is far smaller (1.7) for electron mobility. Directional preferences are far less distinct in the equivalent structure with phenyl linkers (Zn-MOF-74). The imaginary-time simulation technique does not give quantitative mobilities. The simulations reveal a change in mechanism between the different directions: Coherent polaron migration is observed along the stacks but tunneling hops between them.
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http://dx.doi.org/10.1021/acs.jcim.9b00461DOI Listing
December 2019

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties.

J Phys Chem A 2019 Oct 18;123(43):9403-9412. Epub 2019 Oct 18.

Lehrstuhl für Theoretische Chemie/Computer Chemie Centrum Friedrich-Alexander Universität Erlangen-Nürnberg Nägelsbachstraße 25 , 91052 Erlangen , Germany.

We present atomic scale models of differently sized eumelanin nanoaggregates from molecular dynamics simulations combined with a simulated annealing procedure. The analysis reveals the formation of secondary structures due to π-stacking on one hand, but on the other hand a broad distribution of stack geometries in terms of stack size, horizontal displacement angles, and relative torsion angles. The displacement angle distribution, which is a measure of the occurrence of zigzag and linear stacking motives, respectively, strongly depends on the aggregate size-and is hence controlled by the interplay of surface and bulk energy terms. Semiempirical spectra calculations of small stacks (up to five protomolecules) reveal a strong dependence on the precise stack structure and allow for a direct structure-property correlation. The observed spectral shifts result in an overall spectral broadening and, hence, further support the geometric disorder model, which complements the chemical disorder model in the interpretation of eumelanin's monotonically increasing broad-band absorption.
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http://dx.doi.org/10.1021/acs.jpca.9b08722DOI Listing
October 2019

Correction to: The Feynman dispersion correction for MNDO extended to F, Cl, Br and I.

J Mol Model 2019 Aug 5;25(9):257. Epub 2019 Aug 5.

Computer-Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany.

A small coding error in the development version of EMPIRE led to some inconsistencies in the above article. They are corrected in this erratum.
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http://dx.doi.org/10.1007/s00894-019-4142-0DOI Listing
August 2019

The Feynman dispersion correction for MNDO extended to F, Cl, Br and I.

J Mol Model 2019 May 11;25(6):156. Epub 2019 May 11.

Computer-Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany.

The recently introduced "Feynman" dispersion correction for MNDO (MNDO-F) has been extended to include the elements fluorine, chlorine, bromine and iodine and the original parameterization for hydrogen, carbon, nitrogen and oxygen improved by allowing individual damping radii for the elements. MNDO-F gives a root-mean-square deviation to reference interaction energies of 0.35 kcal mol for the complete parameterization dataset of H, C, N, O, F, Cl, Br and I containing compounds. Graphical Abstract The electrostatic potential at the 0.001 a.u. isodensity surface of the π-complex between benzene and 1,3,5-triodobenzene calculated at the MNDO-F optimized geometry.
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http://dx.doi.org/10.1007/s00894-019-4038-zDOI Listing
May 2019

Solvatochromic covalent organic frameworks.

Nat Commun 2018 09 18;9(1):3802. Epub 2018 Sep 18.

Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.

Covalent organic frameworks (COFs) are an emerging class of highly tuneable crystalline, porous materials. Here we report the first COFs that change their electronic structure reversibly depending on the surrounding atmosphere. These COFs can act as solid-state supramolecular solvatochromic sensors that show a strong colour change when exposed to humidity or solvent vapours, dependent on vapour concentration and solvent polarity. The excellent accessibility of the pores in vertically oriented films results in ultrafast response times below 200 ms, outperforming commercially available humidity sensors by more than an order of magnitude. Employing a solvatochromic COF film as a vapour-sensitive light filter, we demonstrate a fast humidity sensor with full reversibility and stability over at least 4000 cycles. Considering their immense chemical diversity and modular design, COFs with fine-tuned solvatochromic properties could broaden the range of possible applications for these materials in sensing and optoelectronics.
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http://dx.doi.org/10.1038/s41467-018-06161-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6143592PMC
September 2018

The hpCADD NDDO Hamiltonian: Parametrization.

J Chem Inf Model 2017 08 2;57(8):1907-1922. Epub 2017 Aug 2.

Computer-Chemie-Centrum, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg , Nägelsbachstr. 25, 91052 Erlangen, Germany.

A neglect of diatomic differential overlap (NDDO) Hamiltonian has been parametrized as an electronic component of a polarizable force field. Coulomb and exchange potentials derived directly from the NDDO Hamiltonian in principle can be used with classical potentials, thus forming the basis for a new generation of efficiently applicable multipolar polarizable force fields. The new hpCADD Hamiltonian uses force-field-like atom types and reproduces the electrostatic properties (dipole moment, molecular electrostatic potential) and Koopmans' theorem ionization potentials closely, as demonstrated for a large training set and an independent test set of small molecules. The Hamiltonian is not intended to reproduce geometries or total energies well, as these will be controlled by the classical force-field potentials. In order to establish the hpCADD Hamiltonian as an electronic component in force-field-based calculations, we tested its performance in combination with the 3D reference interaction site model (3D RISM) for aqueous solutions. Comparison of the resulting solvation free energies for the training and test sets to atomic charges derived from standard procedures, exact solute-solvent electrostatics based on high-level quantum-chemical reference data, and established semiempirical Hamiltonians demonstrates the advantages of the hpCADD parametrization.
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http://dx.doi.org/10.1021/acs.jcim.7b00080DOI Listing
August 2017

EMPIRE: a highly parallel semiempirical molecular orbital program: 2: periodic boundary conditions.

J Mol Model 2015 Jun 17;21(6):144. Epub 2015 May 17.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany.

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http://dx.doi.org/10.1007/s00894-015-2692-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435633PMC
June 2015

EMPIRE: a highly parallel semiempirical molecular orbital program: 1: self-consistent field calculations.

J Mol Model 2014 Jul 20;20(7):2331. Epub 2014 Jun 20.

Computer-Chemie-Centrum der Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052, Erlangen, Germany.

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http://dx.doi.org/10.1007/s00894-014-2331-4DOI Listing
July 2014

Quantum-mechanics-based molecular interaction fields for 3D-QSAR.

J Cheminform 2014 Mar 11;6(Suppl 1):O10. Epub 2014 Mar 11.

Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe 25, 91052 Erlangen, Germany ; Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nӓgelsbachstraβe 49, 91052 Erlangen, Germany ; Centre for Molecular Design, University of Portsmouth, King Henry Building, Portsmouth, PO1 2DY UK.

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http://dx.doi.org/10.1186/1758-2946-6-S1-O10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980143PMC
March 2014

Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes.

J Mol Model 2014 Mar 28;20(3):2159. Epub 2014 Feb 28.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052, Erlangen, Germany.

Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbitals are localized compared to "normal" conjugated semiconductors. The frontier orbitals are thus likely to be separated in space so that they are close to, but not quite, orthogonal during the SCF iterations. We report full SCF calculations using the massively parallel EMPIRE code and linear scaling localized-molecular-orbital (LMO) calculations using Mopac2009. The LMO procedure can lead to artificially over-polarized wavefunctions in gas-phase proteins. The full SCF iteration procedure can be very slow to converge because many cycles are needed to overcome the over-polarization by inductive charge shifts. Example molecules have been constructed to demonstrate this behavior. The two approaches give identical results if solvent effects are included.
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http://dx.doi.org/10.1007/s00894-014-2159-yDOI Listing
March 2014

Quantum mechanics-based properties for 3D-QSAR.

J Chem Inf Model 2013 Jun 5;53(6):1486-502. Epub 2013 Jun 5.

Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany.

We have used a set of four local properties based on semiempirical molecular orbital calculations (electron density (ρ), hydrogen bond donor field (HDF), hydrogen bond acceptor field (HAF), and molecular lipophilicity potential (MLP)) for 3D-QSAR studies to overcome the limitations of the current force field-based molecular interaction fields (MIFs). These properties can be calculated rapidly and are thus amenable to high-throughput industrial applications. Their statistical performance was compared with that of conventional 3D-QSAR approaches using nine data sets (angiotensin converting enzyme inhibitors (ACE), acetylcholinesterase inhibitors (AchE), benzodiazepine receptor ligands (BZR), cyclooxygenase-2 inhibitors (COX2), dihydrofolate reductase inhibitors (DHFR), glycogen phosphorylase b inhibitors (GPB), thermolysin inhibitors (THER), thrombin inhibitors (THR), and serine protease factor Xa inhibitors (fXa)). The 3D-QSAR models generated were tested thoroughly for robustness and predictive ability. The average performance of the quantum mechanical molecular interaction field (QM-MIF) models for the nine data sets is better than that of the conventional force field-based MIFs. In the individual data sets, the QM-MIF models always perform better than, or as well as, the conventional approaches. It is particularly encouraging that the relative performance of the QM-MIF models improves in the external validation. In addition, the models generated showed statistical stability with respect to model building procedure variations such as grid spacing size and grid orientation. QM-MIF contour maps reproduce the features important for ligand binding for the example data set (factor Xa inhibitors), demonstrating the intuitive chemical interpretability of QM-MIFs.
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http://dx.doi.org/10.1021/ci400181bDOI Listing
June 2013

Improving the charge transport in self-assembled monolayer field-effect transistors: from theory to devices.

J Am Chem Soc 2013 Mar 18;135(12):4893-900. Epub 2013 Mar 18.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, University Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany.

A three-pronged approach has been used to design rational improvements in self-assembled monolayer field-effect transistors: classical molecular dynamics (MD) simulations to investigate atomistic structure, large-scale quantum mechanical (QM) calculations for electronic properties, and device fabrication and characterization as the ultimate goal. The MD simulations reveal the effect of using two-component monolayers to achieve intact dielectric insulating layers and a well-defined semiconductor channel. The QM calculations identify improved conduction paths in the monolayers that consist of an optimum mixing ratio of the components. These results have been used both to confirm the predictions of the calculations and to optimize real devices. Monolayers were characterized with X-ray reflectivity measurements and by electronic characterization of complete devices.
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http://dx.doi.org/10.1021/ja401320nDOI Listing
March 2013

Predicting the sites and energies of noncovalent intermolecular interactions using local properties.

J Chem Inf Model 2012 Apr 13;52(4):1061-71. Epub 2012 Apr 13.

Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraβe 25, 91052 Erlangen, Germany.

Feed-forward artificial neural nets have been used to recognize H-bond donor and acceptor sites on drug-like molecules based on local properties (electron density, molecular electrostatic potential and local ionization energy, electron affinity, and polarizability) calculated at grid points around the molecule. Interaction energies for training were obtained from B97-D and ωB97X-D/aug-cc-pVDZ density-functional theory calculations on a series of model central molecules and H-bond acceptor and donor probes constrained to the grid points used for training. The resulting models provide maps of both classical and unusual H- and halogen-bonding sites. Note that these reactions result even though only classical H-bond donors and acceptors were used as probes around the central molecules. Some examples demonstrate the ability of the models to take the electronics of the central molecule into consideration and to provide semiquantitative estimates of interaction energies at low computational cost.
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http://dx.doi.org/10.1021/ci300095xDOI Listing
April 2012

Polarization-induced σ-holes and hydrogen bonding.

J Mol Model 2012 Jun 21;18(6):2461-9. Epub 2011 Oct 21.

Computer-Chemie-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.

The strong collinear polarizability of the A-H bond in A-H···B hydrogen bonds is shown to lead to an enhanced σ-hole on the donor hydrogen atom and hence to stronger hydrogen bonding. This effect helps to explain the directionality of hydrogen bonds, the well known cooperative effect in hydrogen bonding, and the occurrence of blue-shifting. The latter results when significant additional electron density is shifted into the A-H bonding region by the polarization effect. The shift in the A-H stretching frequency is shown to depend essentially linearly on the calculated atomic charge on the donor hydrogen for all donors in which A belongs to the same row of the periodic table. A further result of the polarization effect, which is also expected for other σ-hole bonds, is that the strength of the non-covalent interaction depends strongly on external electric fields.
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http://dx.doi.org/10.1007/s00894-011-1263-5DOI Listing
June 2012

CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory.

ChemMedChem 2009 Apr;4(4):657-69

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany.

CypScore is an in silico approach for predicting the likely sites of cytochrome P450-mediated metabolism of druglike organic molecules. It consists of multiple models for the most important P450 oxidation reactions such as aliphatic hydroxylation, N-dealkylation, O-dealkylation, aromatic hydroxylation, double-bond oxidation, N-oxidation, and S-oxidation. Each of these models is based on atomic reactivity descriptors derived from surface-based properties calculated with ParaSurf and based on AM1 semiempirical molecular orbital theory. The models were trained with data derived from Bayer Schering Pharma's in-house MajorMetabolite Database with more than 2300 transformations and more than 800 molecules collected from the primary literature. The models have been balanced to allow the treatment of relative intramolecular, intra-chemotype, and inter-chemotype reactivities of the labile sites toward oxidation. The models were evaluated with promising hit rates on three public datasets of varying quality in the annotation of the experimental positions. For 39 well-characterized compounds from 14 in-house lead optimization programs, we could detect at least one major metabolite for the three highest-ranked positions in 87 % of the compounds and overall more than 62 % of all major metabolites, with promising true- to false-positive ratios of 0.9.
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http://dx.doi.org/10.1002/cmdc.200800384DOI Listing
April 2009

The effect of a complexed lithium cation on a norcarane-based radical clock.

Chemistry 2009 ;15(10):2425-33

Computer Chemie Centrum, Friedrich-Alexander Universität Erlangen-Nürnberg Nägelsbachstrasse 25, 91052 Erlangen, Germany.

Density-functional theory (DFT) and ab initio calculations have been used to investigate the effect of a complexed lithium cation on the radical-clock rearrangement of the 2-norcaranyl radical to the 3-cyclohexenylmethyl radical. As found earlier for ring-closing radical clocks, complexation with a metal ion leads to a significant lowering of the barrier to rearrangement. DFT calculations on a model for the norcaranyl clock in cytochrome P450 confirm the two-state reactivity proposal of Shaik et al. and indicate that the porphyrin exerts little or no electrostatic effect on the rearrangement barrier.
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http://dx.doi.org/10.1002/chem.200801076DOI Listing
June 2009

An ab initio and density functional theory study of radical-clock reactions.

J Org Chem 2008 Feb 23;73(4):1536-45. Epub 2008 Jan 23.

Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany.

Density functional theory (DFT) and ab initio (CBS-RAD) calculations have been used to investigate a series of "radical clock" reactions. The calculated activation energies suggest that the barriers for these radical rearrangements are determined almost exclusively by the enthalpy effect with no evidence of significant polar effects. The ring-closure reactions to cyclopentylmethyl radical derivatives and the ring opening of cyclopropylmethyl radicals give different correlations between the calculated heat of reaction and barrier, but the two types of reaction are internally consistent.
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http://dx.doi.org/10.1021/jo702421mDOI Listing
February 2008

Halogen bonding: the sigma-hole. Proceedings of "Modeling interactions in biomolecules II", Prague, September 5th-9th, 2005.

J Mol Model 2007 Feb 23;13(2):291-6. Epub 2006 Aug 23.

Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052, Erlangen, Germany.

Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the sigma-hole, on the outermost portion of the halogen's surface, centered on the R-X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF(3)X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the [Formula: see text] configuration, where the z-axis is along the R-X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the sigma-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the sigma-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a sigma-hole is observed for the Cl in CF(3)Cl, but not in CH(3)Cl.
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http://dx.doi.org/10.1007/s00894-006-0130-2DOI Listing
February 2007

In silico prediction of buffer solubility based on quantum-mechanical and HQSAR- and topology-based descriptors.

J Chem Inf Model 2006 Mar-Apr;46(2):648-58

Bayer Healthcare AG, Aprather Weg 18a, 42096 Wuppertal, Germany.

We present an artificial neural network (ANN) model for the prediction of solubility of organic compounds in buffer at pH 6.5, thus mimicking the medium in the human gastrointestinal tract. The model was derived from consistently performed solubility measurements of about 5000 compounds. Semiempirical VAMP/AM1 quantum-chemical wave function derived, HQSAR-derived logP, and topology-based descriptors were employed after preselection of significant contributors by statistical and data mining approaches. Ten ANNs were trained each with 90% as a training set and 10% as a test set, and deterministic analysis of prediction quality was used in an iterative manner to optimize ANN architecture and descriptor space, based on Corina 3D molecular structure and AM1/COSMO single point wave function. In production mode, a mean prediction value of the 10 ANNs is created, as is a standard deviation based quality parameter. The productive ANN based on Corina geometries and AM1/COSMO wave function gives an r2cv of 0.50 and a root-mean-square error of 0.71 log units, with 87 and 96% of the compounds having an error of less than 1 and 1.5 log units, respectively. The model is able to predict permanently charged species, e.g. zwitterions or quaternary amines, and problematic structures such as tautomers and unresolved diastereomers almost as well as neutral compounds.
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http://dx.doi.org/10.1021/ci0503210DOI Listing
September 2006

Ambiphilicity: a characteristic reactivity principle of pi-bound phosphorus heterocycles.

Angew Chem Int Ed Engl 2002 Nov;41(21):4047-52

Institut für Anorganische, Chemie der Universität, Egerlandstrasse 1, 91058, Erlangen, Germany.

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http://dx.doi.org/10.1002/1521-3773(20021104)41:21<4047::AID-ANIE4047>3.0.CO;2-4DOI Listing
November 2002

A QSPR-approach to the estimation of the pK(HB) of six-membered nitrogen-heterocycles using quantum mechanically derived descriptors.

J Mol Model 2002 Apr;8(4):95-101

Computer-Chemie-Centrum der Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91054 Erlangen, Germany.

Descriptors derived from semiempirical (AM1) molecular orbital calculations have been used to construct a quantitative structure-property relationship (QSPR) for the thermodynamic hydrogen-bond basicity, p K(HB), of a series of six-membered aromatic nitrogen-heterocycles. The resulting model uses four-descriptors (the Coulson charge on the nitrogen atom, the energy of the localized nitrogen lone-pair orbital, the p-orbital contribution to this MO and an accessibility angle). The model gives r2(cv)=0.95 for 51 compounds with a standard deviation between calculation and experiment of 0.13 log units.
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http://dx.doi.org/10.1007/s00894-002-0075-zDOI Listing
April 2002

Solvation largely accounts for the effect of N-alkylation on the properties of nickel(II/I) and chromium(III/II) cyclam complexes.

Inorg Chem 2002 Jun;41(11):2927-35

Computer-Chemie-Centrum der Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany.

The source of the effect of N-alkylation on the redox properties of Ni(II/I) and Cr(III/II) cyclam complexes has been investigated using DFT calculations. The structures of the anhydrous and hydrated complexes were optimized in the gas phase, and single point calculations were performed in a polarized continuum. The main results are the following: the decrease in outer sphere solvation upon N-alkylation is the major source of the relative stabilization of the lower oxidation state complexes by the tertiary amine ligands; tertiary amine nitrogen donors are stronger sigma-donors than the secondary amines, as predicted from the inductive effect of alkyls; steric strain elongates the metal-nitrogen bonds in the tertiary complexes and decreases the ligand strain energies; and the site of water binding to the complexes differs because of their different electronic structures (i.e., in the Ni complexes, the water molecules bind to the M[bond]N[bond]H sites, whereas in the Cr complexes they bind to the central metal cation). Outer sphere hydrogen bonding of water to the ligands in the coordination sphere lowers the ionization potentials by charge delocalization.
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http://dx.doi.org/10.1021/ic0113193DOI Listing
June 2002