Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach.

We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of l-lysine-H and its side-chain methylated analogues, -methyl-l-lysine-H (Me-lysine-H), ,-dimethyl-l-lysine-H (Me-lysine-H), and ,,-trimethyl-l-lysine-H (Me-lysine-H). The major pathways observed in the experimental measurements were / 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The / 130 peak corresponds to loss of N(CH)H, while / 84 has the additional loss of HCO likely in the form of HO + CO.

AutoMeKin2021: An open-source program for automated reaction discovery.

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem.

Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces.

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface.

Modeling the Effects of -Sulfonation on the CID of Serine.

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of -sulfonation on the collision-induced dissociation for serine. Toward this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems.

tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics.

A new software, called tsscds2018, has been developed to discover reaction mechanisms and solve the kinetics in a fully automated fashion. The program employs algorithms based on Graph Theory to find transition state (TS) geometries from accelerated semiempirical dynamics simulations carried out with MOPAC2016. Then, the TSs are connected to the corresponding minima and the reaction network is obtained.

A Computational Comparison of Soft Landing of α-Helical vs Globular Peptides.

The effect of secondary structure on the soft landing process is investigated through direct dynamics simulations of AcAK and AcKA colliding with a fluorinated, organic self-assembled monolayer (FSAM) surface. The α-helical (AcAK) and globular (AcKA) peptides each exhibited a similar probability of soft landing with normal incidence at all collision energies considered. Rapid conformational changes were quantified through the calculation of the time dependent, conformational entropy production that took place during the collision events, which is consistent with the prior structural measurements made by Laskin and co-workers on these systems.

Direct Chemical Dynamics Simulations.

In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular S2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra.

Model Simulations of the Thermal Dissociation of the TIK(H) Tripeptide: Mechanisms and Kinetic Parameters.

Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine-isoleucine-lysine ion, TIK(H), for temperatures of 1250-2500 K, corresponding to classical energies of 1778-3556 kJ/mol. The number of different fragmentation pathways increases with increase in temperature. At 1250 K there are only three fragmentation pathways, with one contributing 85% of the fragmentation.

Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment.

In this Perspective, mass spectrometry experiments and chemical dynamics simulations are described that have explored the atomistic dynamics of protonated peptide ions, peptide-H(+), colliding with organic surfaces. These studies have investigated the energy transfer and fragmentation dynamics for peptide-H(+) surface-induced dissociation (SID), peptide-H(+) physisorption on the surface, soft landing (SL), and peptide-H(+) reaction with the surface, reactive landing (RL). SID provides primary structures of biological ions and information regarding their fragmentation pathways and energetics.

Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces.

There are two components to the review presented here regarding simulations of collisions of protonated peptide ions peptide-H(+) with organic surfaces. One is a detailed description of the classical trajectory chemical dynamics simulation methodology. Different simulation approaches are used, and identified as MM, QM + MM, and QM/MM dependent on the potential energy surface used to represent the peptide-H(+) + surface collision.

Energy and temperature dependent dissociation of the Na(+)(benzene)1,2 clusters: importance of anharmonicity.

Chemical dynamics simulations were performed to study the unimolecular dissociation of randomly excited Na(+)(Bz) and Na(+)(Bz)2 clusters; Bz = benzene. The simulations were performed at constant energy, and temperatures in the range of 1200-2200 K relevant to combustion, using an analytic potential energy surface (PES) derived in part from MP2/6-311+G* calculations. The clusters decompose with exponential probabilities, consistent with RRKM unimolecular rate theory.

Time dependent quantum thermodynamics of a coupled quantum oscillator system in a small thermal environment.

Simulations are performed of a small quantum system interacting with a quantum environment. The system consists of various initial states of two harmonic oscillators coupled to give normal modes. The environment is "designed" by its level pattern to have a thermodynamic temperature.

Visualizing the zero order basis of the spectroscopic Hamiltonian.

Recent works have shown that a generalization of the spectroscopic effective Hamiltonian can describe spectra in surprising regions, such as isomerization barriers. In this work, we seek to explain why the effective Hamiltonian is successful where there was reason to doubt that it would work at all. All spectroscopic Hamiltonians have an underlying abstract zero-order basis (ZOB) which is the "ideal" basis for a given form and parameterization of the Hamiltonian.

Effective Hamiltonian for femtosecond vibrational dynamics.

Time propagation of zero-order states of an effective spectroscopic Hamiltonian is tested against femtosecond time dependent dynamics of adiabatic wavepackets evolving on a model potential energy surface for two coupled modes of the radical HO(2) with multiple potential wells and above barrier motion. A generalized Hamiltonian which breaks the usual conserved polyad action by including extra resonance couplings (V(2:1) and V(3:1)) successfully describes the time evolution after the further addition of two "ultrafast" couplings. These new couplings are a nonresonant coupling a(1)a(2)+a(1)(†)a(2)(†) and a resonant coupling V(1:1) that functions as an ultrafast term because the system is far from 1:1 frequency resonance.

Fragmentation and reactivity in collisions of protonated diglycine with chemically modified perfluorinated alkylthiolate-self-assembled monolayer surfaces.

Direct dynamics simulations are reported for quantum mechanical (QM)/molecular mechanical (MM) trajectories of N-protonated diglycine (gly(2)-H(+)) colliding with chemically modified perfluorinated octanethiolate self-assembled monolayer (SAM) surfaces. The RM1 semiempirical theory is used for the QM component of the trajectories. RM1 activation and reaction energies were compared with those determined from higher-level ab initio theories.

Detailed analysis of polyad-breaking spectroscopic Hamiltonians for multiple minima with above barrier motion: isomerization in HO2.

We present a two-dimensional model for isomerization in the hydroperoxyl radical (HO(2)). We then show that spectroscopic fitting Hamiltonians are capable of reproducing large scale vibrational structure above isomerization barriers. Two resonances, the 2:1 and 3:1, are necessary to describe the pertinent physical features of the system and, hence, a polyad-breaking Hamiltonian is required.

Communication: Effective spectroscopic Hamiltonian for multiple minima with above barrier motion: Isomerization in HO(2).

We present a two-dimensional potential surface for the isomerization in the hydroperoxyl radical HO(2) and calculate the vibrational spectrum. We then show that a simple effective spectroscopic fitting Hamiltonian is capable of reproducing large scale vibrational spectral structure above the isomerization barrier. Polyad breaking with multiple resonances is necessary to adequately describe the spectral features of the system.

Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer.

Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang, J.

Energy transfer, unfolding, and fragmentation dynamics in collisions of N-protonated octaglycine with an H-SAM surface.

Results are reported for PM3 and RM1 QM+MM direct dynamics simulations of collisions of N-protonated octaglycine (gly(8)-H(+)) with an octanethiol self-assembled monolayer (H-SAM) surface. Detailed analyses of the energy transfer, fragmentation, and conformational changes induced by the collisions are described. Extensive comparisons are made between the simulations and previously reported experimental studies.

NH4(+) + CH4 gas phase collisions as a possible analogue to protonated peptide/surface induced dissociation.

Results are reported for a direct dynamics simulation of NH(4)(+) + CH(4) gas phase collisions. We interpret the results with protonated peptide/hydrogenated alkanethiolate self-assembled monolayer (H-SAM) surface collisions in mind. Previous theoretical studies of such systems have made use of nonreactive surfaces, and therefore, our goal is to investigate the types and likelihood of peptide/H-SAM reactions.

The effects of asymmetric motions on the tunneling splittings in formic acid dimer.

We extend the reaction surface Hamiltonian model for double proton tunneling in formic acid dimer to include all in-plane modes, except the two CH stretch modes. Zero point corrections for the out-of-plane modes are also incorporated. Transition state and equilibrium normal mode representations for the description of the asymmetric modes are developed and compared.

Micro-computed tomography assessment of fracture healing: relationships among callus structure, composition, and mechanical function.

Non-invasive characterization of fracture callus structure and composition may facilitate development of surrogate measures of the regain of mechanical function. As such, quantitative computed tomography- (CT-) based analyses of fracture calluses could enable more reliable clinical assessments of bone healing. Although previous studies have used CT to quantify and predict fracture healing, it is unclear which of the many CT-derived metrics of callus structure and composition are the most predictive of callus mechanical properties.

Stimulation of fracture-healing with systemic intermittent parathyroid hormone treatment.

Over the past several years, there has been an increasing interest in the biology of bone repair and potential technologies for enhancing fracture-healing. Part of this interest is derived from the growing age of the population and the recognition that increased age carries an increased risk of complications after fracture. Although use of locally implanted or injected growth factors has received the most attention, systemic treatments for the enhancement of bone repair, especially for situations in which bone repair may be diminished or delayed, are now under investigation.

Symmetric double proton tunneling in formic acid dimer: a diabatic basis approach.

A model of double proton tunneling in formic acid dimer is developed using a reaction surface Hamiltonian. The surface includes the symmetric OH stretch plus the in-plane stretch and bend interdimer vibrations. The surface Hamiltonian is coupled to a bath of five A1g and B3g normal modes obtained at the D2h transition state structure.