The International Conference on Ultrafast Phenomena (UP) 2022
We explore with ultrafast infrared spectroscopy and molecular dynamics simulations how imidazole,... more We explore with ultrafast infrared spectroscopy and molecular dynamics simulations how imidazole, an amphoteric molecule that can act both as acid and as base, provides alternate proton transfer pathways in the tautomerization reaction of 7-hydroxyquinoline.
Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral m... more Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, i.e. the DFT based clusters-in-a-liquid solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations , which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.
We present an explicit solvation protocol for the calculation of electron affinity values of the ... more We present an explicit solvation protocol for the calculation of electron affinity values of the solvated nucleobases. The protocol uses a quantum mechanics/molecular mechanics (QM/MM) approach based on the newly implemented domain-based pair natural orbital EOM-CCSD (equation-of-motion coupled-cluster single-double) method. The stability of the solvated nucleobase anion is sensitive to the local distribution of the water molecules around the nucleobase, and the calculated electron affinity values converge slowly with respect to the number of snapshots and the size of the water box. The use of nonpolarizable water molecules leads to an overestimation of the electron affinity and makes the result sensitive to the size of the QM region in the QM/MM calculation. The electron affinity values, although sensitive to the size of the basis set, lead to an almost constant blue shift of the electron affinity upon the increase in the basis set. The present protocol allows for a controllable description of the various parameters affecting the electron affinity value, and the calculated adiabatic electron affinity values are in excellent agreement with experimental results.
We report on the thermodynamic, structural, and dynamic properties of a recently proposed deep eu... more We report on the thermodynamic, structural, and dynamic properties of a recently proposed deep eutectic solvent, formed by choline acetate (ChAc) and urea (U) at the stoichiometric ratio 1:2, hereinafter indicated as ChAc:U. Although the crystalline phase melts at 36-38 °C depending on the heating rate, ChAc:U can be easily supercooled at sub-ambient conditions, thus maintaining at the liquid state, with a glass-liquid transition at about -50 °C. Synchrotron high energy x-ray scattering experiments provide the experimental data for supporting a reverse Monte Carlo analysis to extract structural information at the atomistic level. This exploration of the liquid structure of ChAc:U reveals the major role played by hydrogen bonding in determining interspecies correlations: both acetate and urea are strong hydrogen bond acceptor sites, while both choline hydroxyl and urea act as HB donors. All ChAc:U moieties are involved in mutual interactions, with acetate and urea strongly interacting through hydrogen bonding, while choline being mostly involved in van der Waals mediated interactions. Such a structural situation is mirrored by the dynamic evidences obtained by means of 1H nuclear magnetic resonance techniques, which show how urea and acetate species experience higher translational activation energy than choline, fingerprinting their stronger commitments into the extended hydrogen bonding network established in ChAc:U.
We present a novel method for the computation of well-defined optimized atomic partial charges an... more We present a novel method for the computation of well-defined optimized atomic partial charges and radii from the total electron density. Our method is based on a two-step radical Voronoi tessellation of the (possibly periodic) system and subsequent integration of the total electron density within each Voronoi cell. First, the total electron density is partitioned into the contributions of each molecule, and subsequently the electron density within each molecule is assigned to the individual atoms using a second set of atomic radii for the radical Voronoi tessellation. The radii are optimized on-the-fly to minimize the fluctuation (variance) of molecular and atomic charges. Therefore, our method is completely free of empirical parameters. As a by-product, two sets of optimized atomic radii are produced in each run, which take into account many specific properties of the system investigated. The application of an on-the-fly interpolation scheme reduces discretization noise in the Vor...
In this work, we resolve a long-standing issue concerning the local structure of molten MgCl 2 by... more In this work, we resolve a long-standing issue concerning the local structure of molten MgCl 2 by employing a multimodal approach, including X-ray scattering and Raman spectroscopy, along with the theoretical modeling of the experimental spectra based on ab initio molecular dynamics (AIMD) simulations utilizing several density functional theory (DFT) methods. We demonstrate the reliability of AIMD simulations in achieving excellent agreement between the experimental and simulated spectra for MgCl 2 and 50 mol % MgCl 2 + 50 mol % KCl, and ZnCl 2 , thus allowing structural insights not directly available from experiment alone. A thorough computational analysis using five DFT methods provides a convergent view that octahedrally coordinated magnesium in pure MgCl 2 upon melting preferentially coordinates with five chloride anions to form distorted square pyramidal polyhedra that are connected via corners and to a lesser degree via edges. This is contrasted with the results for ZnCl 2 , which does not change its tetrahedral coordination on melting. Although the five-coordinate MgCl 5 3− complex was not considered in the early literature, together with an increasing tendency to form a tetrahedrally coordinated complex with decreasing the MgCl 2 content in the mixture with alkali metal chloride systems, current work reconciles the results of most previous seemingly contradictory experimental studies.
We present 1,2,3-triazolium- and imidazolium-based ionic liquids (ILs) with aromatic anions as a ... more We present 1,2,3-triazolium- and imidazolium-based ionic liquids (ILs) with aromatic anions as a new class of cellulose solvents. The two anions in our study, benzoate and salicylate, possess a lower basicity when compared to acetate and therefore should lead to a lower amount of N-heterocyclic carbenes (NHCs) in the ILs. We characterize their physicochemical properties and find that all of them are liquids at room temperature. By applying force field molecular dynamics (MD) simulations, we investigate the structure and dynamics of the liquids and find strong and long-lived hydrogen bonds, as well as significant π–π stacking between the aromatic anion and cation. Our ILs dissolve up to 8.5 wt.-% cellulose. Via NMR spectroscopy of the solution, we rule out chain degradation or derivatization, even after several weeks at elevated temperature. Based on our MD simulations, we estimate the enthalpy of solvation and derive a simple model for semi-quantitative prediction of cellulose solub...
TRAVIS ("Trajectory Analyzer and Visualizer") is a program package for post-processing and analyz... more TRAVIS ("Trajectory Analyzer and Visualizer") is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years.
We present BILFF, a force field for bio-polymers in ionic liquids, optimized to accurately descri... more We present BILFF, a force field for bio-polymers in ionic liquids, optimized to accurately describe hydrogen bonds. In the first part, we introduce force field parameters for mixtures of 1-ethyl-3-methylimidazolium acetate ([EMIm][OAc]) with water.
Bifunctional or amphoteric photoacids simultaneously present donor (acidic) and acceptor (basic) ... more Bifunctional or amphoteric photoacids simultaneously present donor (acidic) and acceptor (basic) properties making them useful tools to analyze proton transfer reactions. In protic solvents, the proton exchange between the acid and the base is controlled by the acidity or basicity strength and typically occurs on two different pathways known as protolysis and hydrolysis. We report here how the addition of a formate base will alter the relative importance of the possible reaction pathways of the bifunctional photoacid 7-hydroxyquinoline (7HQ), which has been recently understood to predominantly involve a hydroxide/methoxide transport mechanism between the basic proton-accepting quinoline nitrogen site toward the proton-donating OH group with a time constant of 360 ps in deuterated methanol (CD 3 OD). We follow the reaction dynamics by probing the IR-active marker modes of the different charged forms of photoexcited 7HQ, and of formic acid (HCOOD) in CD 3 OD solution. A comparison of the transient IR spectra as a function of formate concentration, and classical molecular dynamics simulations enables us to identify distinct contributions of "tight" (meaning "contact") and "loose" (i.e., "solvent-separated") 7HQ−formate reaction pairs in our data. Our results suggest that depending on the orientation of the OH group with respect to the quinoline aromatic ring system, the presence of the formate molecule in a proton relay pathway facilitates a net proton transfer from the proton-donating OH group of 7HQ-N* via the methanol/formate bridge toward the quinoline N site.
Abstract The liquid structure of a representative of the first water-in-salt (WiS) Natural Deep E... more Abstract The liquid structure of a representative of the first water-in-salt (WiS) Natural Deep Eutectic Solvents (NADES), hereinafter indicated as aquoline, a mixture of choline chloride (ChCl) and water with molar ratio 1:3.33, is explored at ambient conditions. Using Molecular Dynamics (MD) simulation tools, we extract structural information at atomistic level on the nature of inter-correlations between the different moieties. Despite being a very fluid liquid, with much lower viscosity than other common ChCl-based DES, aquoline turns out to be very structured. Computed X-ray and neutron weighted scattering patterns (the latter also on selectively deuterated mixtures) highlight the existence of mesoscopic organization that is rationalised in terms of choline vs. water/chloride structural alternation. The study shows that choline cations are highly coordinating the surrounding environment: strong hydrogen bonding mediated correlations between the hydroxyl group and water or chloride are detected. In addition, the ammonium group drives the formation of a complex solvating environment, with water, chloride and hydroxyl moieties approaching it, between the hindering methyl groups. Strong hydrogen-bonding interactions between water molecules and between water and anions are detected and, while water cannot create a bulk water-like environment around itself, its network with neighbour water or anions develops long chains across the bulk phase. This is a first study that will be extended based on complementary experimental work as a function of water content and temperature/pressure, to explore structural and dynamic properties of this class of materials.
We present a computational study on the enantioselectivity of organocatalytic proline-catalyzed a... more We present a computational study on the enantioselectivity of organocatalytic proline-catalyzed aldol reactions between aldehydes in dimethylformamide (DMF). To explore the free energy surface of the reaction, we apply two-dimensional metadynamics on top of ab initio molecular dynamics (AIMD) simulations with explicit solvent description on the DFT level of theory. We avoid unwanted side reactions by utilizing our newly developed hybrid AIMD (HyAIMD) simulation scheme, which adds a simple force field to the AIMD simulation to prevent unwanted bond breaking and formation. Our condensed phase simulation results are able to nicely reproduce the experimental findings, including the main stereoisomer that is formed, and give a correct qualitative prediction of the change in syn:anti product ratio with different substituents. Furthermore, we give a microscopic explanation for the selectivity. We show that both the explicit description of the solvent and the inclusion of entropic effects a...
Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo... more Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo-TEMPO (TEMPONE) in water and THF is studied. With electron paramagnetic resonance (EPR) spectroscopy at X- and Q-band as well as spectral simulations, the existence of pure water shells enclosing TEMPO in aqueous solution that lead to significantly reduced local polarity at the nitroxide is shown. These aqueous lower polarity solvation shells (ALPSS) offer TEMPO a local polarity that is similar to that in organic solvents like THF. Furthermore, using double electron-electron resonance (DEER) spectroscopy, local enrichment and inhomogenous distribution without collisions of dissolved TEMPO in water is found that can be correlated with potentially attractive interactions mediated through ALPSS. However, no local enrichment of TEMPO is found in organic solvents such as THF. These results are substantiated by MD and metadynamics simulations and physical methods like DLS and MS.
We derive a matrix formalism for the simulation of long range proton dynamics for extended system... more We derive a matrix formalism for the simulation of long range proton dynamics for extended systems and timescales. On the basis of an ab initio molecular dynamics simulation, we construct a Markov chain, which allows us to store the entire proton dynamics in an M × M transition matrix (where M is the number of oxygen atoms). In this article, we start from common topology features of the hydrogen bond network of good proton conductors and utilize them as constituent constraints of our dynamic model. We present a thorough mathematical derivation of our approach and verify its uniqueness and correct asymptotic behavior. We propagate the proton distribution by means of transition matrices, which contain kinetic data from both ultra-short (sub-ps) and intermediate (ps) timescales. This concept allows us to keep the most relevant features from the microscopic level while effectively reaching larger time and length scales. We demonstrate the applicability of the transition matrices for the description of proton conduction trends in proton exchange membrane materials.
An unexpected growth mechanism for organic semiconductors on gold where the molecules approach th... more An unexpected growth mechanism for organic semiconductors on gold where the molecules approach their bulk structure over several interfacial layers.
We present our novel approach for computing resonance Raman (RR) spectra of periodic bulk phase s... more We present our novel approach for computing resonance Raman (RR) spectra of periodic bulk phase systems from ab initio molecular dynamics, including solvent influence and some anharmonic effects. Based on real-time timedependent density functional theory, we obtain the RR spectra for all laser wavelengths in one pass. We compute the RR spectrum of uracil in aqueous solution, which is in good agreement with experiment. This is the first simulation of a bulk phase RR spectrum.
Salt bridges are elementary motifs of protein secondary and tertiary structure and are commonly a... more Salt bridges are elementary motifs of protein secondary and tertiary structure and are commonly associated with structural driving force that increases stability. Often found on the interface to the solvent, they are highly susceptible to solvent–solute interactions, primarily with water but also with other cosolvents (especially ions). We have investigated the interplay of an Arginine–Aspartic acid salt bridge with simple salt ions in aqueous solution by means of molecular dynamics simulations. Besides structural and dynamical features at equilibrium, we have computed the mean force along the dissociation pathway of the salt bridge. We demonstrate that solvated ions influence the behavior of the salt bridge in a very specific and local way, namely the formation of tight ionic pairs Li+/Na+–Asp−. Moreover, our findings show that the enthalpic relevance of the salt bridge is minor, regardless of the presence of solvated ions.
The International Conference on Ultrafast Phenomena (UP) 2022
We explore with ultrafast infrared spectroscopy and molecular dynamics simulations how imidazole,... more We explore with ultrafast infrared spectroscopy and molecular dynamics simulations how imidazole, an amphoteric molecule that can act both as acid and as base, provides alternate proton transfer pathways in the tautomerization reaction of 7-hydroxyquinoline.
Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral m... more Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, i.e. the DFT based clusters-in-a-liquid solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations , which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.
We present an explicit solvation protocol for the calculation of electron affinity values of the ... more We present an explicit solvation protocol for the calculation of electron affinity values of the solvated nucleobases. The protocol uses a quantum mechanics/molecular mechanics (QM/MM) approach based on the newly implemented domain-based pair natural orbital EOM-CCSD (equation-of-motion coupled-cluster single-double) method. The stability of the solvated nucleobase anion is sensitive to the local distribution of the water molecules around the nucleobase, and the calculated electron affinity values converge slowly with respect to the number of snapshots and the size of the water box. The use of nonpolarizable water molecules leads to an overestimation of the electron affinity and makes the result sensitive to the size of the QM region in the QM/MM calculation. The electron affinity values, although sensitive to the size of the basis set, lead to an almost constant blue shift of the electron affinity upon the increase in the basis set. The present protocol allows for a controllable description of the various parameters affecting the electron affinity value, and the calculated adiabatic electron affinity values are in excellent agreement with experimental results.
We report on the thermodynamic, structural, and dynamic properties of a recently proposed deep eu... more We report on the thermodynamic, structural, and dynamic properties of a recently proposed deep eutectic solvent, formed by choline acetate (ChAc) and urea (U) at the stoichiometric ratio 1:2, hereinafter indicated as ChAc:U. Although the crystalline phase melts at 36-38 °C depending on the heating rate, ChAc:U can be easily supercooled at sub-ambient conditions, thus maintaining at the liquid state, with a glass-liquid transition at about -50 °C. Synchrotron high energy x-ray scattering experiments provide the experimental data for supporting a reverse Monte Carlo analysis to extract structural information at the atomistic level. This exploration of the liquid structure of ChAc:U reveals the major role played by hydrogen bonding in determining interspecies correlations: both acetate and urea are strong hydrogen bond acceptor sites, while both choline hydroxyl and urea act as HB donors. All ChAc:U moieties are involved in mutual interactions, with acetate and urea strongly interacting through hydrogen bonding, while choline being mostly involved in van der Waals mediated interactions. Such a structural situation is mirrored by the dynamic evidences obtained by means of 1H nuclear magnetic resonance techniques, which show how urea and acetate species experience higher translational activation energy than choline, fingerprinting their stronger commitments into the extended hydrogen bonding network established in ChAc:U.
We present a novel method for the computation of well-defined optimized atomic partial charges an... more We present a novel method for the computation of well-defined optimized atomic partial charges and radii from the total electron density. Our method is based on a two-step radical Voronoi tessellation of the (possibly periodic) system and subsequent integration of the total electron density within each Voronoi cell. First, the total electron density is partitioned into the contributions of each molecule, and subsequently the electron density within each molecule is assigned to the individual atoms using a second set of atomic radii for the radical Voronoi tessellation. The radii are optimized on-the-fly to minimize the fluctuation (variance) of molecular and atomic charges. Therefore, our method is completely free of empirical parameters. As a by-product, two sets of optimized atomic radii are produced in each run, which take into account many specific properties of the system investigated. The application of an on-the-fly interpolation scheme reduces discretization noise in the Vor...
In this work, we resolve a long-standing issue concerning the local structure of molten MgCl 2 by... more In this work, we resolve a long-standing issue concerning the local structure of molten MgCl 2 by employing a multimodal approach, including X-ray scattering and Raman spectroscopy, along with the theoretical modeling of the experimental spectra based on ab initio molecular dynamics (AIMD) simulations utilizing several density functional theory (DFT) methods. We demonstrate the reliability of AIMD simulations in achieving excellent agreement between the experimental and simulated spectra for MgCl 2 and 50 mol % MgCl 2 + 50 mol % KCl, and ZnCl 2 , thus allowing structural insights not directly available from experiment alone. A thorough computational analysis using five DFT methods provides a convergent view that octahedrally coordinated magnesium in pure MgCl 2 upon melting preferentially coordinates with five chloride anions to form distorted square pyramidal polyhedra that are connected via corners and to a lesser degree via edges. This is contrasted with the results for ZnCl 2 , which does not change its tetrahedral coordination on melting. Although the five-coordinate MgCl 5 3− complex was not considered in the early literature, together with an increasing tendency to form a tetrahedrally coordinated complex with decreasing the MgCl 2 content in the mixture with alkali metal chloride systems, current work reconciles the results of most previous seemingly contradictory experimental studies.
We present 1,2,3-triazolium- and imidazolium-based ionic liquids (ILs) with aromatic anions as a ... more We present 1,2,3-triazolium- and imidazolium-based ionic liquids (ILs) with aromatic anions as a new class of cellulose solvents. The two anions in our study, benzoate and salicylate, possess a lower basicity when compared to acetate and therefore should lead to a lower amount of N-heterocyclic carbenes (NHCs) in the ILs. We characterize their physicochemical properties and find that all of them are liquids at room temperature. By applying force field molecular dynamics (MD) simulations, we investigate the structure and dynamics of the liquids and find strong and long-lived hydrogen bonds, as well as significant π–π stacking between the aromatic anion and cation. Our ILs dissolve up to 8.5 wt.-% cellulose. Via NMR spectroscopy of the solution, we rule out chain degradation or derivatization, even after several weeks at elevated temperature. Based on our MD simulations, we estimate the enthalpy of solvation and derive a simple model for semi-quantitative prediction of cellulose solub...
TRAVIS ("Trajectory Analyzer and Visualizer") is a program package for post-processing and analyz... more TRAVIS ("Trajectory Analyzer and Visualizer") is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years.
We present BILFF, a force field for bio-polymers in ionic liquids, optimized to accurately descri... more We present BILFF, a force field for bio-polymers in ionic liquids, optimized to accurately describe hydrogen bonds. In the first part, we introduce force field parameters for mixtures of 1-ethyl-3-methylimidazolium acetate ([EMIm][OAc]) with water.
Bifunctional or amphoteric photoacids simultaneously present donor (acidic) and acceptor (basic) ... more Bifunctional or amphoteric photoacids simultaneously present donor (acidic) and acceptor (basic) properties making them useful tools to analyze proton transfer reactions. In protic solvents, the proton exchange between the acid and the base is controlled by the acidity or basicity strength and typically occurs on two different pathways known as protolysis and hydrolysis. We report here how the addition of a formate base will alter the relative importance of the possible reaction pathways of the bifunctional photoacid 7-hydroxyquinoline (7HQ), which has been recently understood to predominantly involve a hydroxide/methoxide transport mechanism between the basic proton-accepting quinoline nitrogen site toward the proton-donating OH group with a time constant of 360 ps in deuterated methanol (CD 3 OD). We follow the reaction dynamics by probing the IR-active marker modes of the different charged forms of photoexcited 7HQ, and of formic acid (HCOOD) in CD 3 OD solution. A comparison of the transient IR spectra as a function of formate concentration, and classical molecular dynamics simulations enables us to identify distinct contributions of "tight" (meaning "contact") and "loose" (i.e., "solvent-separated") 7HQ−formate reaction pairs in our data. Our results suggest that depending on the orientation of the OH group with respect to the quinoline aromatic ring system, the presence of the formate molecule in a proton relay pathway facilitates a net proton transfer from the proton-donating OH group of 7HQ-N* via the methanol/formate bridge toward the quinoline N site.
Abstract The liquid structure of a representative of the first water-in-salt (WiS) Natural Deep E... more Abstract The liquid structure of a representative of the first water-in-salt (WiS) Natural Deep Eutectic Solvents (NADES), hereinafter indicated as aquoline, a mixture of choline chloride (ChCl) and water with molar ratio 1:3.33, is explored at ambient conditions. Using Molecular Dynamics (MD) simulation tools, we extract structural information at atomistic level on the nature of inter-correlations between the different moieties. Despite being a very fluid liquid, with much lower viscosity than other common ChCl-based DES, aquoline turns out to be very structured. Computed X-ray and neutron weighted scattering patterns (the latter also on selectively deuterated mixtures) highlight the existence of mesoscopic organization that is rationalised in terms of choline vs. water/chloride structural alternation. The study shows that choline cations are highly coordinating the surrounding environment: strong hydrogen bonding mediated correlations between the hydroxyl group and water or chloride are detected. In addition, the ammonium group drives the formation of a complex solvating environment, with water, chloride and hydroxyl moieties approaching it, between the hindering methyl groups. Strong hydrogen-bonding interactions between water molecules and between water and anions are detected and, while water cannot create a bulk water-like environment around itself, its network with neighbour water or anions develops long chains across the bulk phase. This is a first study that will be extended based on complementary experimental work as a function of water content and temperature/pressure, to explore structural and dynamic properties of this class of materials.
We present a computational study on the enantioselectivity of organocatalytic proline-catalyzed a... more We present a computational study on the enantioselectivity of organocatalytic proline-catalyzed aldol reactions between aldehydes in dimethylformamide (DMF). To explore the free energy surface of the reaction, we apply two-dimensional metadynamics on top of ab initio molecular dynamics (AIMD) simulations with explicit solvent description on the DFT level of theory. We avoid unwanted side reactions by utilizing our newly developed hybrid AIMD (HyAIMD) simulation scheme, which adds a simple force field to the AIMD simulation to prevent unwanted bond breaking and formation. Our condensed phase simulation results are able to nicely reproduce the experimental findings, including the main stereoisomer that is formed, and give a correct qualitative prediction of the change in syn:anti product ratio with different substituents. Furthermore, we give a microscopic explanation for the selectivity. We show that both the explicit description of the solvent and the inclusion of entropic effects a...
Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo... more Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo-TEMPO (TEMPONE) in water and THF is studied. With electron paramagnetic resonance (EPR) spectroscopy at X- and Q-band as well as spectral simulations, the existence of pure water shells enclosing TEMPO in aqueous solution that lead to significantly reduced local polarity at the nitroxide is shown. These aqueous lower polarity solvation shells (ALPSS) offer TEMPO a local polarity that is similar to that in organic solvents like THF. Furthermore, using double electron-electron resonance (DEER) spectroscopy, local enrichment and inhomogenous distribution without collisions of dissolved TEMPO in water is found that can be correlated with potentially attractive interactions mediated through ALPSS. However, no local enrichment of TEMPO is found in organic solvents such as THF. These results are substantiated by MD and metadynamics simulations and physical methods like DLS and MS.
We derive a matrix formalism for the simulation of long range proton dynamics for extended system... more We derive a matrix formalism for the simulation of long range proton dynamics for extended systems and timescales. On the basis of an ab initio molecular dynamics simulation, we construct a Markov chain, which allows us to store the entire proton dynamics in an M × M transition matrix (where M is the number of oxygen atoms). In this article, we start from common topology features of the hydrogen bond network of good proton conductors and utilize them as constituent constraints of our dynamic model. We present a thorough mathematical derivation of our approach and verify its uniqueness and correct asymptotic behavior. We propagate the proton distribution by means of transition matrices, which contain kinetic data from both ultra-short (sub-ps) and intermediate (ps) timescales. This concept allows us to keep the most relevant features from the microscopic level while effectively reaching larger time and length scales. We demonstrate the applicability of the transition matrices for the description of proton conduction trends in proton exchange membrane materials.
An unexpected growth mechanism for organic semiconductors on gold where the molecules approach th... more An unexpected growth mechanism for organic semiconductors on gold where the molecules approach their bulk structure over several interfacial layers.
We present our novel approach for computing resonance Raman (RR) spectra of periodic bulk phase s... more We present our novel approach for computing resonance Raman (RR) spectra of periodic bulk phase systems from ab initio molecular dynamics, including solvent influence and some anharmonic effects. Based on real-time timedependent density functional theory, we obtain the RR spectra for all laser wavelengths in one pass. We compute the RR spectrum of uracil in aqueous solution, which is in good agreement with experiment. This is the first simulation of a bulk phase RR spectrum.
Salt bridges are elementary motifs of protein secondary and tertiary structure and are commonly a... more Salt bridges are elementary motifs of protein secondary and tertiary structure and are commonly associated with structural driving force that increases stability. Often found on the interface to the solvent, they are highly susceptible to solvent–solute interactions, primarily with water but also with other cosolvents (especially ions). We have investigated the interplay of an Arginine–Aspartic acid salt bridge with simple salt ions in aqueous solution by means of molecular dynamics simulations. Besides structural and dynamical features at equilibrium, we have computed the mean force along the dissociation pathway of the salt bridge. We demonstrate that solvated ions influence the behavior of the salt bridge in a very specific and local way, namely the formation of tight ionic pairs Li+/Na+–Asp−. Moreover, our findings show that the enthalpic relevance of the salt bridge is minor, regardless of the presence of solvated ions.
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Papers by Martin Brehm