Deep learning-based size prediction for optical trapped nanoparticles and extracellular vesicles from limited bandwidth camera detection.

Due to its ability to record position, intensity, and intensity distribution information, camera-based monitoring of nanoparticles in optical traps can enable multi-parametric morpho-optical characterization at the single-particle level. However, blurring due to the relatively long (10s of microsecond) integration times and aliasing from the resulting limited temporal bandwidth affect the detected particle position when considering nanoparticles in traps with strong stiffness, leading to inaccurate size predictions. Here, we propose a ResNet-based method for accurate size characterization of trapped nanoparticles, which is trained by considering only simulated time series data of nanoparticles' constrained Brownian motion. Experiments prove the method outperforms state-of-art sizing algorithms such as adjusted Lorentzian fitting or CNN-based networks on both standard nanoparticles and extracellular vesicles (EVs), as well as maintains good accuracy even when measurement times are relatively short (<1s per particle). On samples of clinical EVs, our network demonstrates a well-generalized ability to accurately determine the EV size distribution, as confirmed by comparison with gold-standard nanoparticle tracking analysis (NTA). Furthermore, by combining the sizing network with still frame images from high-speed video, the camera-based optical tweezers have the unique capacity to quantify both the size and refractive index of bio-nanoparticles at the single-particle level. These experiments prove the proposed sizing network as an ideal path for predicting the morphological heterogeneity of bio-nanoparticles in optical potential trapping-related measurements.

Multicomponent Raman spectral regression using complete and incomplete models and convolutional neural networks.

With the advent of hyperspectral Raman imaging technology, especially the rapid and high-resolution imaging schemes, datasets with thousands to millions of spectra are now commonplace. Standard preprocessing and regression methods such as least squares approaches are time consuming and require input from highly trained operators. Here we propose a solution to this analytic bottleneck through a convolutional neural network trained fully on synthetic data and then applied to experimental measurements, including cases where complete spectral information is missing (i.e. an underdetermined model). An advantage of the model is that it combines background correction and regression into a single step, and does not require user-selected parameters. We compare our results with traditional least squares methods, including the popular asymmetric least squares (AsLS) approach. Our results demonstrate that the proposed CNN model boasts less sensitivity to parameter selection, and with a rapid processing speed, with performance equal to or better than comparison methods. The performance is validated on synthetic spectral mixtures, as well as experimentally measured single-vesicle liposome data.

Coherent Control of Molecular Dissociation by Selective Excitation of Nuclear Wave Packets.

We report on pump-probe control schemes to manipulate fragmentation product yields in p-nitrotoluene (PNT) cation. Strong field ionization of PNT prepares the parent cation in the ground electronic state, with coherent vibrational excitation along two normal modes: the C-C-N-O torsional mode at 80 cm-1 and the in-plane ring-stretching mode at 650 cm-1. Both vibrational wave packets are observed as oscillations in parent and fragment ion yields in the mass spectrum upon optical excitation. Excitation with 650 nm selectively fragments the PNT cation into C 7 H 7 + , whereas excitation with 400 nm selectively produces C 5 H 5 + and C 3 H 3 + . In both cases the ion yield oscillations result from torsional wave packet excitation, but 650 and 400 nm excitation produce oscillations with opposite phases. Ab initio calculations of the ground and excited electronic potential energy surfaces of PNT cation along the C-C-N-O dihedral angle reveal that 400 nm excitation accesses an allowed transition from D0 to D6 at 0° dihedral angle, whereas 650 nm excitation accesses a strongly allowed transition from D0 to D4 at a dihedral angle of 90°. This ability to access different electronic excited states at different locations along the potential energy surface accounts for the selective fragmentation observed with different probe wavelengths. The ring-stretching mode, only observed using 800 nm excitation, is attributed to a D0 to D2 transition at a geometry with 90° dihedral angle and elongated C-N bond length. Collectively, these results demonstrate that strong field ionization induces multimode coherent excitation and that the vibrational wave packets can be excited with specific photon energies at different points on their potential energy surfaces to induce selective fragmentation.

Ultrafast Dynamics of Nitro-Nitrite Rearrangement and Dissociation in Nitromethane Cation.

We report new insights into the ultrafast rearrangement and dissociation dynamics of nitromethane cation (NM+) using pump-probe measurements, electronic structure calculations, and ab initio molecular dynamics simulations. The "roaming" nitro-nitrite rearrangement (NNR) pathway involving large-amplitude atomic motion, which has been previously described for neutral nitromethane, is demonstrated for NM+. Excess energy resulting from initial population of the electronically excited D2 state of NM+ upon strong-field ionization provides the necessary energy to initiate NNR and subsequent dissociation into NO+. Both pump-probe measurements and molecular dynamics simulations are consistent with the completion of NNR within 500 fs of ionization with dissociation into NO+ and OCH3 occurring ∼30 fs later. Pump-probe measurements indicate that NO+ formation is in competition with the direct dissociation of NM+ to CH3+ and NO2. Electronic structure calculations indicate that a strong D0 → D1 transition can be excited at 650 nm when the C-N bond is stretched from its equilibrium value (1.48 Å) to 1.88 Å. On the other hand, relaxation of the NM+ cation after ionization into D0 occurs in less than 50 fs and results in observation of intact NM+. Direct dissociation of the equilibrium NM+ to produce NO2+ and CH3 can be induced with 650 nm excitation via a weakly allowed D0 → D2 transition.

Quantitative Analysis of Nitrotoluene Isomer Mixtures Using Femtosecond Time-Resolved Mass Spectrometry.

Discrimination of isomers in a mixture is a subject of ongoing interest in biology, pharmacology, and forensics. We demonstrate that femtosecond time-resolved mass spectrometry (FTRMS) effectively quantifies mixtures of ortho-, para-, and meta-nitrotoluenes, the first two of which are common explosive degradation products. The key advantage of the FTRMS approach to mixture quantification lies in the ability of the pump-probe laser control scheme to capture distinct fragmentation dynamics of each nitrotoluene cation isomer on femtosecond timescales, thereby allowing for discrimination of the isomers using only the signal of the parent molecular ion at m/z 137. Upon measurement of reference dynamics of each individual isomer, the molar fractions of binary and ternary mixtures can be predicted to within ∼5 and ∼7% accuracy, respectively.

Using computational chemistry to design pump-probe schemes for measuring nitrobenzene radical cation dynamics.

The electronic potential energy surfaces of the nitrobenzene cation obtained from time-dependent density functional theory and coupled cluster calculations are used to predict the most efficient excitation wavelength for femtosecond time-resolved mass spectrometry measurements. Both levels of theory identify a strongly-coupled transition from the ground state of the nitrobenzene cation with a geometry-dependent oscillator strength, reaching a maximum at 90° C-C-N-O dihedral angle with a corresponding energy gap of ∼2 eV. These results are consistent with the experimental observation in the nitrobenzene cation of a coherent superposition of vibrational states: a vibrational wave packet. Time-resolved measurements using a probe wavelength of 650 nm, nearly resonant with the strong transition, result in enhanced ion yield oscillation amplitudes as compared to excitation with the nonresonant 800 nm wavelength. Analogous behavior is found for the closely related molecules 2- and 4-nitrotoluene. These results demonstrate that computational chemistry can predict the best choice of probe wavelength in time-resolved measurements of vibrational coherent states in molecular cations.

Dissociation of Singly and Multiply Charged Nitromethane Cations: Femtosecond Laser Mass Spectrometry and Theoretical Modeling.

Dissociation pathways of singly- and multiply charged gas-phase nitromethane cations were investigated with strong-field laser photoionization mass spectrometry and density functional theory computations. There are multiple isomers of the singly charged nitromethane radical cation, several of which can be accessed by rearrangement of the parent CH3-NO2 structure with low energy barriers. While direct cleavage of the C-N bond from the parent nitromethane cation produces NO2+ and CH3+, rearrangement prior to dissociation accounts for fragmentation products including NO+, CH2OH+, and CH2NO+. Extensive Coulomb explosion in fragment ions observed at high laser intensity indicates that rapid dissociation of multiply charged nitromethane cations produces additional species such as CH2+, H+, and NO22+.  On the basis of analysis of Coulomb explosion in the mass spectral signals and pathway calculations, sufficiently intense laser fields can remove four or more electrons from nitromethane.

Identification and characterization of potent and selective inhibitors targeting protein tyrosine phosphatase 1B (PTP1B).

Protein tyrosine phosphatase 1B (PTP1B) plays an important role in the negative regulation of insulin and leptin signaling. The development of small molecular inhibitors targeting PTP1B has been validated as a potential therapeutic strategy for Type 2 diabetes (T2D). In this work, we have identified a series of compounds containing dihydropyridine thione and particular chiral structure as novel PTP1B inhibitors. Among those, compound 4b showed moderate activity with IC50 value of 3.33 µM and meanwhile with good selectivity (>30-fold) against TCPTP. The further MOA study of PTP1B demonstrated that compounds 4b is a substrate-competitive inhibitor. The binding mode analysis suggested that compound 4b simultaneously occupies the active site and the second phosphotyrosine (pTyr) binding site of PTP1B. Furthermore, the cell viability assay of compound 4b showed tolerable cytotoxicity in L02 cells, thus 4b may be prospectively used to further in vivo study.

Probing Coherent Vibrations of Organic Phosphonate Radical Cations with Femtosecond Time-Resolved Mass Spectrometry.

Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs ( 732 ± 28 cm - 1 ) oscillations with a weak feature at 610⁻650 cm - 1 , while DIMP exhibits bimodal oscillations with a period of ∼55 fs and two frequency features at 554 ± 28 and 670⁻720 cm - 1 . In contrast, the oscillations in DEMP decay too rapidly for effective resolution. The low- and high-frequency oscillations in DMMP and DIMP are assigned to coherent excitation of the symmetric O⁻P⁻O bend and P⁻C stretch, respectively. The observation of the same ionization-induced coherently excited vibrations in related molecules suggests a possible common excitation pathway in ionized organophosphorus compounds of biological relevance, while the distinct oscillatory dynamics in each molecule points to the potential use of FTRMS to distinguish among fragment ions produced by related molecules.

Conserved Vibrational Coherence in the Ultrafast Rearrangement of 2-Nitrotoluene Radical Cation.

2-Nitrotoluene (2-NT) is a good model for both photolabile protecting groups for organic synthesis and the military explosive 2,4,6-trinitrotoluene (TNT). In addition to the direct C-NO2 bond-cleavage reaction that initiates detonation in TNT, 2-NT undergoes an H atom attack reaction common to the photolabile 2-nitrobenzyl group, which forms the aci-nitro tautomer. In this work, femtosecond pump-probe measurements with mass spectrometric detection and density functional theory (DFT) calculations demonstrate that the initially prepared vibrational coherence in the 2-NT radical cation (2-NT+) is preserved following H atom attack. Strong-field adiabatic ionization is used to prepare 2-NT+, which can overcome a modest 0.76 eV energy barrier to H atom attack to form the aci-nitro tautomer as soon as ∼20-60 fs after ionization. Once formed, the aci-nitro tautomer spontaneously loses -OH to form C7H6NO+, which exhibits distinctly faster oscillations in its ion yield (290 fs period) as compared to the 2-NT+ ion (380 fs period). The fast oscillations are attributed to the coherent torsional motion of the aci-nitro tautomer, which has a significantly faster computed torsional frequency (86.9 cm-1) than the 2-NT+ ion (47.9 cm-1). Additional DFT calculations identify reaction pathways leading to the formation of the dissociation products C7H6NO+, C7H7+, and C6H6N+. Collectively, these results reveal a rich picture of coherently and incoherently driven dissociation pathways in 2-NT+.

Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization.

We present a pump-probe method for preparing vibrational coherences in polyatomic radical cations and probing their ultrafast dynamics. By shifting the wavelength of the strong-field ionizing pump pulse from the commonly used 800 nm into the near-infrared (1200-1600 nm), the contribution of adiabatic electron tunneling to the ionization process increases relative to multiphoton absorption. Adiabatic ionization results in predominant population of the ground electronic state of the ion upon electron removal, which effectively prepares a coherent vibrational state ("wave packet") amenable to subsequent excitation. In our experiments, the coherent vibrational dynamics are probed with a weak-field 800 nm pulse and the time-dependent yields of dissociation products measured in a time-of-flight mass spectrometer. We present the measurements on the molecule dimethyl methylphosphonate (DMMP) to illustrate how using 1500 nm pulses for excitation enhances the amplitude of coherent oscillations in ion yields by a factor of 10 as compared to 800 nm pulses. This protocol may be implemented in existing pump-probe setups through the incorporation of an optical parametric amplifier (OPA) for wavelength conversion.

Dissociation dynamics of 3- and 4-nitrotoluene radical cations: Coherently driven C-NO2 bond homolysis.

Monosubstituted nitrotoluenes serve as important model compounds for nitroaromatic energetic molecules such as trinitrotoluene. This work investigates the ultrafast nuclear dynamics of 3- and 4-nitrotoluene radical cations using femtosecond pump-probe measurements and the results of density functional theory calculations. Strong-field adiabatic ionization of 3- and 4-nitrotoluene using 1500 nm, 18 fs pulses produces radical cations in the ground electronic state with distinct coherent vibrational excitations. In both nitrotoluene isomers, a one-photon excitation with the probe pulse results in NO2 loss to form C7H7+, which exhibits out-of-phase oscillations in yield with the parent molecular ion. The oscillations in 4-nitrotoluene with a period of 470 fs are attributed to the torsional motion of the NO2 group based on theoretical results showing that the dominant relaxation pathway in 4-nitrotoluene radical cations involves the rotation of the NO2 group away from the planar geometry. The distinctly faster oscillation period of 216 fs in 3-nitrotoluene is attributed to an in-plane bending motion of the NO2 and CH3 moieties based on analysis of the normal modes. These results demonstrate that coherent nuclear motions determine the probability of C-NO2 homolysis in the nitrotoluene radical cations upon optical excitation within several hundred femtoseconds of the initial ionization event.

Ultrafast coherent vibrational dynamics in dimethyl methylphosphonate radical cation.

Femtosecond pump-probe measurements of the nerve agent simulant dimethyl methylphosphonate (DMMP) demonstrate the preparation of a robust coherent vibrational state in the corresponding radical cation. The oscillations in the transient ion yields have a period of 45 fs (750 cm-1), which is at least 3 times faster than any previously observed oscillations in polyatomic radical cations. Use of 1200-1600 nm, as opposed to 800 nm, wavelengths for ionization increases the oscillation amplitude by a factor of 5 and doubles the number of visible oscillation periods from 6 to 12, indicating that an adiabatic ionization mechanism significantly enhances preparation of the coherent state. The coherent motion is assigned to a bending mode in DMMP+ with frequency in the range of 742.2-754.7 cm-1 based on the results of DFT calculations. The observation of coherent nuclear dynamics in the dissociation of DMMP+ suggests the potential utility of coherent control schemes for controlling the dissociation of DMMP and related molecules, which has important implications for developing detection and decontamination technologies for organophosphorus chemical warfare agents.

A Theoretical and Mass Spectrometry Study of Dimethyl Methylphosphonate: New Isomers and Cation Decay Channels in an Intense Femtosecond Laser Field.

Using both mass spectrometry with intense femtosecond laser ionization and high-level computational methods, we have explored the structure and fragmentation patterns of dimethyl methylphosphonate (DMMP) cation. Extensive search of the geometries of both neutral and positively charged DMMP yields new isomers that are appreciably lower in total energy than those commonly synthesized using the Michaelis-Arbuzov reaction. The stability of the standard isomer with CH3PO(OCH3)2 topology is found to be due to the presence of high barriers to isomer interconversion that involves several transition states. Our femtosecond laser ionization experiments show that the relative yields of the major dissociation products as a function of peak laser intensity correlate well with the theoretical estimates for the energies of the DMMP+ decay via various channels. In contrast, the peak laser intensities required for observation of minor dissociation products exhibit no correlation with the computed decay energies, which suggests that barrier heights and/or excited electronic states of DMMP+ determine its preferred fragmentation pathways in an intense femtosecond laser field.

DNA damage by the sulfate radical anion: hydrogen abstraction from the sugar moiety versus one-electron oxidation of guanine.

The products of oxidative damage to double-stranded (ds) DNA initiated by photolytically generated sulfate radical anions SO4(•-) were analyzed using reverse-phase (RP) high-performance liquid chromatography (HPLC). Relative efficiencies of two major pathways were compared: production of 8-oxoguanine (8oxoG) and hydrogen abstraction from the DNA 2-deoxyribose moiety (dR) at C1,' C4,' and C5' positions. The formation of 8oxoG was found to account for 87% of all quantified lesions at low illumination doses. The concentration of 8oxoG quickly reaches a steady state at about one 8oxoG per 100 base pairs due to further oxidation of its products. It was found that another guanine oxidation product identified as 2-amino-5-(2'-alkylamino)-4H-imidazol-4-one (X) was released in significant quantities from its tentative precursor 2-amino-5-[(2'-deoxy-ß-d-erythro-pentofuranosyl)amino]-4H-imidazol-4-one (dIz) upon treatment with primary amines in neutral solutions. The linear dose dependence of X release points to the formation of dIz directly from guanine and not through oxidation of 8oxoG. The damage to dR was found to account for about 13% of the total damage, with majority of lesions (33%) originating from the C4' oxidation. The contribution of C1' oxidation also turned out to be significant (17% of all dR damages) despite of the steric problems associated with the abstraction of the C1'-hydrogen. However, no evidence of base-to-sugar free valence transfer as a possible alternative to direct hydrogen abstraction at C1' was found.