Molecular Fragmentation Dynamics Research Articles

A recoil ion momentum spectrometer for probing ionization, e-capture, and capture-ionization induced molecular fragmentation dynamics.

The development of a recoil ion momentum spectrometer (RIMS) along with a post-collision projectile charge state analyzer (CSA) and its performance for carrying out studies of molecular fragmentation following direct ionization, electron-capture, and capture-ionization have been demonstrated here. This is a two-stage Wiley-McLaren type spectrometer with slight modification introduced by adding a lens to achieve higher momentum resolution as well as larger angular acceptance. Along with the time and position sensitive detector, it can measure all the three momentum components of singly charged recoil ions of energy up to 10 eV emitted in all directions. The CSA assembly is designed for separating out any neutral or singly or doubly charged post-collision projectiles typically of keV energy. The RIMS with initial trigger ("start") from CSA or an ionized electron can uniquely determine the dynamics of molecular fragmentation following different electron-capture or direct ionization events, respectively. To check the performance of the setup, we carried out an experimental study of the fragmentation of N2 molecules under the impact of 250 keV protons. Apart from the single-electron-capture channel, we could clearly identify three more capture-ionization channels, which lead to fragmentation. The essential features of the momentum distributions and the kinetic energy release distributions of all three fragmentation channels are discussed in detail. These results are compared with the findings from the ionization induced fragmentation experiments and with the available results from theoretical calculations as well as high resolution experiments. The branching ratios of these fragmentation channels are determined.

Time-Dependent Electronic Populations in Fragment-Based Time-Dependent Density Functional Theory

Conceiving a molecule as being composed of smaller molecular fragments, or subunits, is one of the pillars of the chemical and physical sciences and leads to productive methods in quantum chemistry. Using a fragmentation scheme, efficient algorithms can be proposed to address problems in the description of chemical bond formation and breaking. We present a formally exact time-dependent density functional theory for the electronic dynamics of molecular fragments with a variable number of electrons. This new formalism is an extension of previous work [Phys. Rev. Lett. 111, 023001 (2013)]. We also introduce a stable density-inversion method that is applicable to time-dependent and ground-state density functional theories and their extensions, including those discussed in this work.

Coulomb-explosion imaging using a pixel-imaging mass-spectrometry camera

Femtosecond laser-induced Coulomb-explosion imaging of 3,5-dibromo-$3{}^{\ensuremath{'}},5{}^{\ensuremath{'}}$-difluoro-$4{}^{\ensuremath{'}}$-cyanobiphenyl molecules prealigned in space is explored using a pixel-imaging mass-spectrometry (PImMS) camera. The fast-event-triggered camera allows the concurrent detection of the correlated two-dimensional momentum images, or covariance maps, of all the ionic fragments resulting from fragmentation of multiple molecules in each acquisition cycle. Detailed simulation of the covariance maps reveals that they provide rich information about the parent molecular structure and fragmentation dynamics. Future opportunities for imaging the real-time dynamics of intramolecular processes are considered.

Mesoscopic simulation of phospholipid membranes, peptides, and proteins with molecular fragment dynamics.

Molecular fragment dynamics (MFD) is a variant of dissipative particle dynamics (DPD), a coarse-grained mesoscopic simulation technique for isothermal complex fuids and soft matter systems with particles that are chosen to be adequate fluid elements. MFD choses its particles to be small molecules which may be connected by harmonic springs to represent larger molecular entities in order to maintain a comparatively accurate representation of covalent bonding and molecular characteristics. For this study the MFD approach is extended to accomplish long-term simulations (up to the microsecond scale) of large molecular ensembles (representing millions of atoms) containing phospholipid membranes, peptides, and proteins. For peptides and proteins a generally applicable fragmentation scheme is introduced in combination with specific backbone forces that keep native spatial shapes with adequate levels of flexibility or rigidity. The new approach is demonstrated by MFD simulations of the formation and characteristics of phospholipid membranes and vesicles, vesicle-membrane fusion, the backbone force dependency of the overall structural flexibility of dumbbell-shaped Calmodulin, the stability of subunit-aggregation of tetrameric hemoglobin, and the collaborative interaction of Kalata B1 cyclotides with a phospholipid membrane. All findings are in reasonable agreement with experimental as well as alternative simulation results. Thus, the extended MFD approach may become a new tool for biomolecular system studies to allow for comparatively fast simulative investigations in combination with a comparatively high chemical granularity.

A recoil ion momentum spectrometer for molecular and atomic fragmentation studies.

We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented.

Characterization of Tenofovir Disoproxil Fumarate and Its Behavior under Heating

Tenofovir disoproxil fumarate (TDF) is a nucleotide reverse transcriptase inhibitor used worldwide to treat AIDS. The aim of this study was to investigate the structural and dynamic properties of the polymorphic form I of the drug by thermal analysis, Fourier transform infrared spectroscopy, solid-state NMR, and powder X-ray diffraction. A full assignment of 13C NMR resonances was achieved for the first time. Variable-temperature studies were conducted, and the results were related to changes in the TDF structure and dynamics of specific molecular fragments, especially of the fumarate portion of the molecule. It was found that, under heating, the 13C NMR signals related to the carbon atoms of the disoproxil fumarate moiety split into two resonances. The region of the phosphonate vicinity also changes. This can reflect the lack of symmetry of the two molecules in the asymmetric unit after heating. This solid–solid transformation was related to DSC and XRD observations.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

BackgroundMesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application.ResultsThe molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted fSMILES) with connected molecular fragments to represent a molecular structure. The fSMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software.ConclusionsMesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences.Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-014-0045-3) contains supplementary material, which is available to authorized users.

Study of structural response of chlorpropamide polymorphs to external stress

Polymorphism in molecular crystals is a remarkable property of Nature to create a wide range of various combinations of limited amount of components. Studies of the polymorphic crystals upon different types of external influence could be very useful in terms of analysis of molecular packing, nature and dynamics of the intermolecular interactions. When applied to pharmaceuticals, crystal structure may noticeably affect on stability, solubility, bioavailability, etc. which are essential for drug development. Sulfonyl urea derivatives represent a great example of compounds which are potentially inclined to conformational polymorphism. In particular generation drug chlorpropamide could be crystallized in a five different polymorphs. Chlorpropamide molecule is highly flexible in the crystal structure whereby we obtain various types of molecular conformations and their relative arrangements within the main structural forming motif – directed hydrogen bonded chains. Although polymorphic properties of chlorpropamide have been well-known for a decade there are still a lot of open questions regarding relative stability and crystallization conditions of the polymorphs as well as their behavior under extreme conditions such as cryogenic temperatures, hydrostatic pressure and mechanical stress. In order to follow dynamics of molecular fragments and to observe possible phase transitions on cooling and compression polarized Raman spectroscopy was used. Low temperature spectra were recorded in a wide temperature (5-300 K) range. The effect of hydrostatic pressure was studied using diamond anvil cell up to 5 – 5.5 GPa. Nanoindentation was applied to five polymorphs of chlorpropamide to examine and compare their mechanical properties. Experimental results were also supported by quantum-mechanical calculations. The research was supported by a grant for Russia-Slovenia collaboration BI-RU-12-13-038, a grant from RFBR and the Integration project 108 of the SB RAS.

Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants

Molecular Fragment Dynamics (MFD) is a mesoscopic simulation technique based on Dissipative Particle Dynamics (DPD). Whereas DPD beads in general may not necessarily be identified with chemical compounds at all the MFD variant uses specific molecules or molecular fragments as its basic coarse-grained interacting entities (rather than the fine-grained atom types of Molecular Mechanics). MFD can be used to study formulations of drugs and active agents in oil, water and emulsions. MFD simulations of the nonionic polyoxyethylene alkyl ether surfactants C6E6, C10E6, C12E6 and C16E6 at the water-air interface are performed to study their nanoscale structures and surface properties. The simulations of the self-aggregation of the polyoxyethylene alkyl ether surfactants lead to equilibrium nanoscale structures and computationally determined surface tensions which are in agreement with experimental data for different surfactant concentrations [1]. Figure 1

Covariance imaging experiments using a pixel-imaging mass-spectrometry camera

The ``pixel imaging mass spectrometry'' camera is used to perform femtosecond laser-induced Coulomb explosion imaging of 3,5-dibromo-3${}^{\ensuremath{'}}$,5${}^{\ensuremath{'}}$-difluoro-4${}^{\ensuremath{'}}$-cyanobiphenyl molecules prealigned in space. The experiment allows the concurrent detection of the correlated two-dimensional momentum images of all the ionic fragments resulting from fragmentation of multiple molecules in each acquisition cycle. The Coulomb explosion studies provide rich information about the parent molecular structure and fragmentation dynamics, and open new opportunities for real-time imaging of intramolecular processes.

Momentum imaging spectrometer for molecular fragmentation dynamics induced by pulsed electron beam

A momentum imaging spectrometer has been built for studying the electron impact molecular fragmentation dynamics. The setup consists of a pulsed electron gun and a time of flight system as well as a two-dimensional time and position sensitive multi-hit detector. The charged fragments with kinetic energy up to 10 eV can be detected in 4π solid angles and their three-dimensional momentum vectors can be reconstructed. The apparatus is tested by electron impact ionization of Ar and dissociative ionization of CO2. By analyzing the ion-ion coincidence spectra, the complete and incomplete Coulomb fragmentation channels for CO2(2+) and CO2(3+) are identified. The kinetic energy release (KER) and angular correlation for the two-body breakup channel CO2(2+*) → O(+) + CO(+) are reported. The peak value of total KER is found to be 6.8 eV which is consistent with the previous photoion-photoion coincidence studies, and the correlation angle of O(+) and CO(+) is also explicitly determined to be 172.5°.

Molecular fragment dynamics study on the water–air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants

Molecular fragment dynamics (MFD) is a mesoscopic simulation technique based on dissipative particle dynamics (DPD). MFD simulations of the self-aggregation of the polyoxyethylene alkyl ether surfactants C6E6, C10E6, C12E6 and C16E6 at the water–air surface lead to equilibrium nanoscale structures and computationally determined surface tensions which are in agreement with experimental data for different surfactant concentrations. Thus, molecular fragment dynamics is a well-suited predictive technique to study the behavior of new surfactant systems.

Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD)

Molecular Fragment Dynamics (MFD) is a mesoscopic simulation technique based on dissipative particle dynamics. The method has been shown to successfully describe the phase behaviour and interfacial tensions of large chemical systems in good agreement with experimental results [1]. Unlike molecular mechanics a MFD simulation is based on coarse-grained molecular fragments rather than fine-grained atom types. The current MFD fragment definition is based on a SMILES like one-dimensional line notation which is visualized with the Structure Diagram Generator of the Chemistry Development Kit (CDK) [2]. For an extension of the MFD technique to chemical ensembles containing peptides and proteins an appropriate molecular fragment cheminformatics tool for their design is in need. This work provides an editor for the construction of peptides and proteins from molecular fragments. It includes building blocks for all 20 proteinogenic amino acids, their charged species and disulfide bonds. A flexible input of one-letter and three-letter amino acid codes is supported. Additionally, the editor has the capability to set charges of side chains manually or automatically.

Ultrafast probing of ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets

The ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets are studied with time-resolved extreme ultraviolet ion imaging spectroscopy. At excitation energies of 23.6 ± 0.2 eV, Rydberg atoms in n = 3 and n = 4 states are ejected on different time scales and with significantly different kinetic energy distributions. Specifically, n = 3 Rydberg atoms are ejected with kinetic energies as high as 0.85 eV, but their appearance is delayed by approximately 200 fs. In contrast, n = 4 Rydberg atoms appear within the time resolution of the experiment with considerably lower kinetic energies. Major features in the Rydberg atom kinetic energy distributions for both principal quantum numbers can be described within a simple elastic scattering model of localized perturbed atomic Rydberg atoms that are expelled from the droplet due to their repulsive interaction with the surrounding helium bath. Time-dependent kinetic energy distributions of He(2) (+) and He(3) (+) ions are presented that support the formation of molecular ions in an indirect droplet ionization process and the ejection of neutral Rydberg dimers on a similar time scale as the n = 3 Rydberg atoms.

Strong-field ionization of molecular iodine traced with XUV pulses from a free-electron laser

Ultrafast dynamics of a molecular wave packet created by a strong 120-fs near-infrared (800 nm) laser pulse in iodine has been probed by synchronized 13.4-nm, 35-fs extreme-ultraviolet pulses delivered by the free-electron laser facility in Hamburg, FLASH. The kinetic energy release of the multiply charged ionic fragments reveals three essential steps of strong-field-induced molecular fragmentation dynamics: (i) The creation of I${}_{2}$${}^{2+}$ and (I${}_{2}$${}^{2+}$)${}^{*}$ molecular ions proceeds within (75 $\ifmmode\pm\else\textpm\fi{}$ 15) fs full-width-at-half-maximum. (ii) With the onset of the I${}_{2}$${}^{2+}$ fragmentation the probability to lose a further electron within the same optical laser pulse rises with increasing I${}^{+}$---I${}^{+}$ internuclear separation and reaches its maximum after $\ensuremath{\sim}$30 fs with respect to the pulse maximum. (iii) Charge separation into the I${}_{2}$${}^{2+}\ensuremath{\rightarrow}{\mathrm{I}}^{2+}+\mathrm{I}$ dissociative channel with an asymmetric charge distribution is completed after (121 $\ifmmode\pm\else\textpm\fi{}$ 22) fs.

Biomaterialcoatings - a challenging task studied by the molecular fragment dynamics

A special and important task in medicinal implant technology is to prevent the material from fouling or make it compatible for tissues by coating the material with functionalized lipid biomolecules. In order to rationalize the design of such new materials structural information about the film is needed. In this presentation we give an account on the investigation of coating of the tetraetherlipid GDNT on a borofluorate surface in different solvents. To gain insights into the dynamic process on the microsecond and micrometer scale we applied our recently developed Molecular Fragment Dynamics method (MFD) [1]. Aside of the size of the system and the duration of the simulation, the challenging task of the investigation lies in the divers chemical functionality of the compounds. The applied MFD algorithm is developed to resolve especially these problems. The MFD algorithm is based on the Dissipative-Particle-Dynamics method (DPD). Whereas in the DPD method the system is divided into different regions of fluid subsystems, the MFD algorithm calculates the interaction of molecular fragments. Consequently, the MFD method is well suited for the molecular modelling simulation of systems having a diverse variety of chemical functionalities thus allowing for investigation of biocoatings, polymers and tensids. Figure ​Figure11. Figure 1

Molecular fragments chemoinformatics

The description of chemical structures as a collection of connected molecular fragments is a basic requirement of coarse grained simulation methods like molecular fragment dynamics. These methods use molecular fragments as their basic interacting entities (atoms) and allow the modelling and investigation of very large chemical systems. Therefore a molecular fragments chemoinformatics is in need that supports the fragment-based representation of chemical structures as well as the elementary operations upon them. The poster outlines definitions and approaches to tackle these issues from an adequate molecular line notation up to the graphical representation of simulation boxes.

Revealing femtosecond multiphoton induced multichannel molecular ionization and fragmentation dynamics by photoelectron–photoion coincidence imaging

We report on photoelectron–photoion coincidence imaging after single-color (400 nm) multiphoton excitation of CF 3 I at laser intensities of about 10 12 Watt / cm 2 . The dominant ionic species are the parent CF 3 I + and the CF 3 + fragment from four-photon excitation. Photoelectrons are ejected leaving the parent ion at an internal energy above the dissociation limit leading to fragmentation in CF 3 + + I with low kinetic energy. Weaker dissociation channels of fast CF 3 + + I fragments or fast I + + CF 3 fragments result from the absorption of a fifth photon by the ionized CF 3 I + parent. We propose a new assignment of 7s, 8s intermediate Rydberg levels in CF 3 I resonant at the three-photon level.

High-resolution inner-shell coincidence spectroscopy

The present review article gives a historical overview of high-resolution inner-shell coincidence spectroscopies followed by selected examples showing their scientific impact in studying molecular fragmentation dynamics. The development of such spectroscopies was intimately related to the last 20 years spectacular advances of the instrumentation. They include the construction of high-performance soft X-ray beamlines at the newest synchrotron radiation facilities, but also the remarkable improvement of charged particles analyzers and detectors and the extensive use of multidimensional coincidence techniques allowing for simultaneous recording and further correlation of several physical parameters. From the examples shown, it clearly appears the importance of using coincidence measurements in addition to pure electron spectroscopy methods in order to fully characterize the complex decay processes of inner-shell excited species leading for instance to site-selective fragmentation, vibrational motion mediated dissociation or ultrafast intramolecular recombination processes. The perspectives of the field will be briefly drawn in the end.

MFD-simulation of surface coatings – an extension to solid/fluid molecular modelling models

Molecular Fragment Dynamics (MFD) is a new method for mesoscopic molecular modelling computer simulations derived from Dissipative Particle Dynamics (DPD) [1]. It can be used to simulate dynamical processes at a microsecond timescale and up to micrometer scales and can handle up to 1.500.000 particles. This unique technique so far has been successfully applied to surfactants, adjuvants, polymers, nanoparticles and complex mixtures thereof in materials and life science simulation studies [2]. MFD has been applied to a system of different glyceroldialkylnomizoltetraetherlipid (GDNT) concentrations at different solvent / solid borofloate substrate interfaces. GDNT is a tetraetherlipid won from archaebacteria and known for its antifouling capabilities. This scheme was applied in order to find out at which concentration and in which solvent the best levels of GDNT aggregation could be reached and how such coated glass surfaces look like. A brief introduction to the MFD theory and the procedure will be given. From the simulation results the aggregation of GDNT at the solvent / borofloat interface can be shown. The influence of the different solvents and concentrations on the aggregation process is discussed in detail. The simulations reveal differences of the molecular conformations of the GDNT at the interface and the effect demonstrated on a molecular level. By considering these calculations we show the transfer of real surface structures to a molecular model used in MFD simulations.