Real-time dynamics of vibronic wavepackets within Rydberg and ion-pair states of molecular iodine

Real-time dynamics of vibrationally and electronically excited I2 molecules has been investigated experimentally using the pump-probe technique. A 2-photon excitation was performed either at 269 nm or 266 nm. An electronic and vibrational wavepacket was built as coherent superposition of a few (269 nm excitation) or many (266 nm excitation) Rydberg states of the and series partly coupled with ion-pair states. The probe operated by ionisation or photodetachement. The energy and angular distribution of the resulting photoelectrons, I+ photocations and I- photoanions were monitored. During the dynamics that is turned on by the pump excitation, the wavepacket splits and explores a variety of electronic states of Rydberg and ion-pair character. The experimental results were complemented by molecular dynamics calculations. This provided invaluable information to identify wavepacket motion along ion-pair potential energy curves.

Time-resolved photoelectron spectroscopy of 4-(dimethylamino)benzethyne - an experimental and computational study

We investigated the excited-state dynamics of 4-(dimethylamino)benzethyne (4-DMABE) in a combined theoretical and experimental study using surface-hopping simulations and time-resolved ionisation experiments. The simulations predict a decay of the initially excited S₂ state into the S₁ state in only a few femtoseconds, inducing a subsequent partial twist of the dimethylamino group within ∼100 fs. This leads to drastically reduced Franck-Condon factors for the ionisation transition to the cationic ground state, thus inhibiting the effective ionisation of the molecule, which leads to a vanishing photoelectron signal on a similar timescale as observed in our time-resolved photoelectron spectra. From the phototoelectron spectra, an adiabatic ionisation energy of 7.17 ± 0.02 eV was determined. The experimental decays match the theoretical predictions very well and the combination of both reveals the electronic characteristics of the molecule, namely the role of intramolecular charge transfer (ICT) states in the deactivation pathway of electronically excited 4-DMABE.

OS01.7.A Detection of methylation-based prognostic signatures in liquid biopsy specimens from patients with meningiomas

Background

Detection of distinct epigenetic biomarkers in circulating cell-free DNA (cfDNA) of liquid biopsy (LB) specimens (e.g. blood) fosters opportunity for prognostication of central nervous system (CNS) tumors and has not been thoroughly explored in patients with meningiomas.

Material and Methods

We profiled the cfDNA methylome (EPIC array) in serum specimens from patients with meningiomas (MNG; n= 63) and harnessed internal and external meningioma tissue methylome data with reported follow up (n=48). To predict recurrence risk (RR), we consolidated a tissue cohort with at least 5 years of follow up and divided them into confirmed recurrence (CR; either reported progressive disease in post-surgical imaging, or additional resections following initial surgery) and confirmed no-recurrence (CNR: no confirmed disease progression w/in at least 5-years of follow-up). Then through application of an iterative process consisting of multiple tissue- and serum-based supervised analyses, we identified risk-specific methylation markers with serum specific features which, when inputted into a random forest algorithm allowed for segregation of both tumor tissue and liquid biopsy specimens according to recurrence risk. We estimated immune cell composition using MethylCIBERSORT, where a reference methylome atlas of chosen immune cell types was utilized to deconvolute the MNG samples.

Results

The resulting recurrence risk classifier demonstrated an appreciable predictive power in classifying samples as high or low recurrence risk across the tumor tissue cohort (ACC: 87.5%, CUI+: 85.2%). When compared to another classifier, our model demonstrated statistically significant agreement across primary meningioma samples (κ=0.269, p=0.002), and more accurately predicted samples to recur across an expanded time window (time to recurrence >5yrs). Across resulting liquid biopsy classifications, recurrence risk subgroups were analogous with reported risk factors, including WHO grade, extent of resection, and tumor location. Recurrence risk subgroups (high and low) also demonstrated differential estimated immune cell contributions, with low-risk samples exhibiting a “hot” profile, or enrichment of B-Cells, CD56- and CD4 T-Cells, and natural killer cells. Notably, the estimated neutrophil to lymphocyte ratio, previously purported to be relevant to tumor prognosis, was appreciably higher for those meningioma samples with the highest recurrence risk.

Conclusion

DNA methylation markers identified in the serum are suitable for the development of machine learning-based models which present high predictive power to prognosticate patients with meningioma and estimate a differential immune profile across recurrence risk groups. After validation in an external cohort, this noninvasive approach may improve the presurgical therapeutic management of patients with meningiomas.

Excited state dynamics of normal dithienylethene molecules either isolated or deposited on an argon cluster

Real-time dynamics of the electronically excited open-ring isomer of 1,2-bis(2-methylbenzo[b]thiophen-3-yl)perfluorocyclopentene (BTF6) and 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (PTF6) molecules was investigated using a set-up that associates a molecular beam, femtosecond lasers and velocity map imaging. The molecules were either free in the gas phase or bound to an argon cluster. DFT and TDDFT calculations were performed on BTF6. The calculated vertical excitation energies indicate an excitation by the pump laser towards a superposition of S₅ and S₆ states. The free molecule dynamics was found to follow a three wavepacket model. One describes the parallel conformer (P) of these molecules. It is unreactive with respect to the ring closure reaction which is responsible for the photochromic property of these molecules. It has no observable decay at the experiment time scale (up to 350 ps). The other two wavepackets describe the reactive antiparallel conformer (AP). They are formed by an early splitting of the wavepacket that was launched initially by the pump laser. They can be considered as generated by excitation of different, essentially uncoupled, deformation modes. They subsequently evolve along independent pathways. One is directed ballistically towards a conical intersection (CI) and decays through the CI to a potential energy surface where it can no longer be detected. The other fraction of the wavepacket decays also towards undetected states but in this case the driving mechanism is a non-adiabatic electronic relaxation within a potential well of the energy surfaces where it was launched. When BTF6 and PTF6 molecules are bound to an argon cluster, the same three wavepacket model applies. The vibronic relaxation timespan is enhanced by a factor 5 and a larger fraction of AP conformers follows this pathway. In contrast, the time constant associated with the ballistic movement is enhanced by only a factor of 2.

Reaction dynamics within a cluster environment

This perspective article reviews experimental and theoretical works where rare gas clusters and helium nanodroplets are used as a nanoreactor to investigate chemical dynamics in a solvent environment. A historical perspective is presented first followed by specific considerations on the mobility of reactants within these reaction media. The dynamical response of pure clusters and nanodroplets to photoexcitation is shortly reviewed before examining the role of the cluster (or nanodroplet) degrees of freedom in the photodynamics of the guest atoms and molecules.

Anisotropic dynamics of two-photon ionization: An attosecond movie of photoemission

Imaging in real time the complete dynamics of a process as fundamental as photoemission has long been out of reach because of the difficulty of combining attosecond temporal resolution with fine spectral and angular resolutions. Here, we achieve full decoding of the intricate angle-dependent dynamics of a photoemission process in helium, spectrally and anisotropically structured by two-photon transitions through intermediate bound states. Using spectrally and angularly resolved attosecond electron interferometry, we characterize the complex-valued transition probability amplitude toward the photoelectron quantum state. This allows reconstructing in space, time, and energy the complete formation of the photoionized wave packet.

Photodissociation of the trichloromethyl radical: photofragment imaging and femtosecond photoelectron spectroscopy

Halogen-containing radicals play a key role in catalytic reactions leading to stratospheric ozone destruction, thus their photochemistry is of considerable interest. Here we investigate the photodissociation dynamics of the trichloromethyl radical, CCl₃ after excitation in the ultraviolet. While the primary processes directly after light absorption are followed by femtosecond-time resolved photoionisation and photoelectron spectroscopy, the reaction products are monitored by photofragment imaging using nanosecond-lasers. The dominant reaction is loss of a Cl atom, associated with a CCl₂ fragment. However, the detection of Cl atoms is of limited value, because in the pyrolysis CCl₂ is formed as a side product, which in turn dissociates to CCl + Cl. We therefore additionally monitored the molecular fragments CCl₂ and CCl by photoionisation at 118.2 nm and disentangled the contributions from various processes. A comparison of the CCl images with control experiments on CCl₂ suggest that the dissociation to CCl + Cl₂ contributes to the photochemistry of CCl₃.

Probing the dynamics of the photo-induced decarboxylation of neutral and ionic pyruvic acid

The dynamics of the electronically excited pyruvic acid (PA) and of its unimolecular decomposition upon single photon ionization are investigated by means of a table top fs laser and VUV...

Time-Resolved Observation of the Solvation Dynamics of a Rydberg Excited Molecule Deposited on an Argon Cluster. II. DABCO☆ at Long Time Delays

The real-time dynamics of DABCO-argon clusters is investigated in a femtosecond pump-probe experiment where the pump excites DABCO to the S₁ state within the argon cluster. The probe operates by photoionization and documents the energy and angular distributions of the resulting photoelectrons. The present work complements a previous work from our group [Awali Phys. Chem. Chem. Phys., 2014, 16, 516-526] where this dynamics was probed at short time, up to 4 ps after the pump pulse. Here, the dynamics is followed up to 500 ps. A multiscale dynamics is observed. It includes a jump between two solvation sites (time scale 0.27 ps) followed by the relaxation of the solvation cage excess vibrational energy (time scale 14 ps) and then by that of DABCO (time scale >150 ps). Polarization anisotropy, double polarization, and angular anisotropy effects are reported also. They are interpreted (quantitatively for the former effect) in terms of decoherence of rotational alignment, driven by the overall rotation of the DABCO-argon clusters. A tomographic view of the DABCO excited orbital, provided by the double anisotropy effect, is discussed on a qualitative basis.

Excited State Dynamics of Isolated 6- and 8-Hydroxyquinoline Molecules

The photoinduced dynamics of isolated n-hydroxyquinoline (nHQ) molecules (n=6,8) was investigated in femtosecond pump-probe experiments. A qualitative difference was found between 8HQ and 6HQ. After an initial rapid decay corresponding to the departure of the initial wavepacket out of the Franck-Condon region of the excitation, the 8HQ probe signal decays to zero in 0.37 ps whereas a much longer time constant of 10.4 ps is observed in 6HQ. This interrogates on the role played by the intramolecular H-bond N · · · HO which is at play the 8HQ molecule. Ab-initio were performed at the MCSCF/aug-cc-pVDZ level on the 8HQ molecule to help the discussion. A complex energy landscape was found, which includes a conical intersection.

Unimolecular decomposition of methyl ketene and its dimer in the gas phase: theory and experiment

We present a combined theoretical and experimental investigation on the single photoionization and dissociative photoionization of gas-phase methyl ketene (MKE) and its neutral dimer (MKE2). The performed experiments entail the recording of photoelectron photoion coincidence (PEPICO) spectra and slow photoelectron spectra (SPES) in the energy regime 8.7-15.5 eV using linearly polarized synchrotron radiation. We observe both dimerization and trimerization of the monomer which brings about significantly complex and abstruse dissociative ionization patterns. These require the implementation of theoretical calculations to explore the potential energy surfaces of the monomer and dimer's neutral and ionized geometries. To this end, explicitly correlated quantum chemical methodologies involving the coupled cluster with single, double and perturbative triple excitations (R)CCSD(T)-F12 method, are utilized. An improvement in the adiabatic ionization energy of MKE is presented (AIE = 8.937 ± 0.020 eV) as well as appearance energies for multiple fragments formed through dissociative ionization of either the MKE monomer or dimer. In this regard, the synergy of experiment and theory is crucial to interpreting the obtained results. We discuss the potential astrochemical implications of this work in the context of recent advances in the field of astrochemistry and speculate on the potential presence and eventual fate of interstellar MKE molecules.

OS1.5 Detection of glioma and prognostic subtypes by non-invasive circulating cell-free DNA methylation markers

BACKGROUND: Genome-wide DNA methylation profiling has shown that epigenetic abnormalities are biologically important in glioma and can be used to classify these tumors into distinct prognostic groups. Thus far, DNA profiling has required surgically resected glioma tissue; however, gliomas release tumoral material into biofluids providing an opportunity for a minimally invasive testing. While prior studies have shown that molecular markers can be detected in liquid biopsy (LB), there has been low sensitivity for tumor-specific markers. We hypothesize that the low sensitivity is due to the targeted assay methods. METHODS: Genome-wide CpG methylation levels in DNA of tumor tissue and cell-free DNA serum of glioma patients. RESULTS: We defined glioma-specific and IDH-specific epigenetic LB (eLB) signatures (Glioma-eLB and IDH-eLB, respectively) from serum cell-free DNA from patients diagnosed with glioma (N=15 IDH mutant and N=7 IDH wildtype) and with epilepsy (N=3). The epigenetic profiles of the matched tissue demonstrate that these eLB signatures reflected the signature of the tumor. Through cross-validation we show that Glioma-eLB can accurately predict a patient’s glioma from those with other neoplasias (N=6 Colon; N=14 Pituitary; N=3 Breast; N=4 Lung), non-neoplastic immunological conditions (N=22 sepsis; N=9 pancreatic islet transplantation), and from healthy individuals (sensitivity: 98%; specificity: 99%). Finally, IDH-eLB includes promoter methylated markers associated with genes known to be involved in glioma tumorigenesis (PVT1 and CXCR6). CONCLUSIONS: The application of the non-invasive eLB signature discovered in this study has the potential to complement the standard of care for patients harboring glioma.

This project is supported by the Henry Ford Health System, Department of Neurosurgery and the Hermelin Brain Tumor Center Foundation (A30935), United States National Institutes of Health (R01CA222146), and United States Department of Defense (CA170278)

P11.54 Identification of PDGFRA and MYC(N) as somatic driver genes in Glioblastoma

BACKGROUND

Somatic oncogene amplification happens frequently in glioblastoma (GBM). The second most frequently amplified gene encoding receptor tyrosine kinases in GBMs is platelet derived growth factor alpha (PDGFRA) (15%). In contrast, MYC and MYCN amplification occurs in 1.6% and 2.9%, respectively. Our goal was to characterize the role of PDGFRɑ and Myc in GBM.

MATERIAL AND METHODS

Neurosphere cultures were implanted in cohorts of 10–15 nude mice. 5 PDX lines, presenting median survival of 29–59 days were classified as short survivors, and 5 lines with median survival between 104–134 days classified as long survivors. Total RNA was extracted from PDX terminal tumors (3 biological replicates) and sequenced in a paired-end read format. Mouse reads were filtered out using Xenome. MYC and PDGFRA expression patterns were analyzed in tissue microarrays representing duplicated samples from 40 glioma neurosphere-derived PDX lines by IHC (1 anaplastic oligodendroglioma, 8 recurrent GBM with 2 newly diagnosed/recurrent pairs). Normalized staining intensity (MI) and area (A) were quantified using Fiji/ImageJ.

RESULTS

PDGFRA, MYC, MYCN gene amplifications were represented in a molecularly diverse panel of GBM patient-derived cancer stem-like cells (CSC) and orthotopic mouse xenografts (PDX). Transforming to a normal distribution (log10), 4/13 of cell lines had a PDGFRA mRNA expression (RPKM) higher than 1.5. Similarly, one PDX line had a staining index of greater than 10, 11 (27.5%) had an index between 5–10. The range of intra-tumoral variance, represented by standard deviation, was 0.09–24.25 highlighting the heterogeneity of PDGFRɑ expression. PDGFRɑ phosphorylation (Y754) did not differ between 8 cell lines cultured in NMGF, but deviated in alternate medias without growth factors, supplemented with FBS. In comparison, MYC(N) mRNA expression is only elevated in the context of a known amplification. Furthermore, a a MYC activity signature consisting of 18 target genes was only evident in the 5 amplified CSC lines. Taking advantage of genomic heterogeneity, we have isolated subclones lacking PDGFRA amplification from a PDGFRA amplified GBM CSC. The absence of PDGFRA amplification reduced the self-renewal potential to 37% of the PDGFRA amplified cell population (p=0.001) in clone 1 and 57% in clone 2 (p=0.013). Pertaining to determinants of in vivo survival, MYC was altered in 80% of short survivors (2/5 MYC, 2/5 MYCN amplification) and in 0% of long survivors. Myc signature was highly correlated with in vivo survival (Pearsons’ corr. = -0.77) and MYC gene expression was correlated with in vivo TMZ resistance (corr. = 0.7).

CONCLUSION

These results suggest that PDGFRɑ expression and activity can occur in the absence of gene amplification, while Myc activity is dependent on gene amplification. Both oncogenes drive oncogenic pathways that should be explored as therapeutic targets.

Energetics and ionization dynamics of two diarylketone molecules: benzophenone and fluorenone

Single photon ionization and subsequent unimolecular ion decomposition were studied on jet-cooled benzophenone and fluorenone separately, using VUV synchrotron radiation in a photoion/photoelectron coincidence setup. Slow PhotoElectron Spectra (SPES) were recorded in coincidence with either the parent or the fragment ions for hν < 12.5 eV. Dissociative ionization is observed for benzophenone only. The full interpretation of the measurements, including the identification of the neutral and ionic species when dissociative ionization is at play, benefits from high level ab initio computations for determining the equilibrium structures and the energetics of the neutral and ionized molecules and of their fragments. Electronically excited states of the parent molecular ions were calculated also. From this analysis, an accurate experimental determination of the energetics of the benzophenone and fluorenone ions and of their fragmentation channels is available: adiabatic ionization energies of benzophenone at 8.923 ± 0.005 eV and of fluorenone at 8.356 ± 0.007 eV; and appearance energies of benzophenone fragment ions at 11.04 ± 0.02 eV (loss of C₆H₅), 11.28 ± 0.02 eV (loss of H) and 11.45 ± 0.02 eV (loss of CO). The corresponding fragmentation mechanisms are explored, showing likely concerted bonds rearrangement. Possible pre-ionizing fragmentation is discussed in light of the spectra presented. The structural rigidity of fluorenone diarylketone seems to be the origin of the inhibition of the fragmentation of its cation.

Large amplitude motion within acetylene-rare gas complexes hosted in helium droplets

Near-infrared spectroscopy of the C2H2-Ar, Kr complexes was performed in the spectral region overlapping the ν3/ν2 + ν4 + ν5 Fermi-type resonance of C2H2. The experiment was conducted along the HElium NanoDroplet Isolation (HENDI) technique in order to study the coupling dynamics between a floppy molecular system (C2H2-Ar and C2H2-Kr) and a mesoscopic quantum liquid (the droplet). Calculations were performed using a spectral element based close-coupling program and state-of-the-art 2-dimensional potential energy surfaces to determine the bound states of the C2H2-Ar and C2H2-Kr complexes and simulate the observed spectra. This furnished a quantitative basis to unravel how the superfluid and non-superfluid components of the droplet affect the rotation and the deformation dynamics of the hosted complex.

Excited state dynamics and time-resolved photoelectron spectroscopy of para-xylylene

We investigated the excited-state dynamics of para-xylylene using a combination of field-induced surface hopping (FISH) simulations and time-resolved ionisation experiments. Our simulations predict an ultrafast decay of the initially excited bright state (S2/S3) to the S1 state on a sub-100 fs time scale, followed by return to the ground state within ∼1 ps. This is accompanied by a transient change of the biradical character of the molecule, as monitored by calculating natural orbital occupation numbers. Specifically, the initially low biradicality is increased by electronic excitation as well as by vibrational activation. Experimentally, para-xylylene was generated by pyrolysis from [2,2]paracyclophane and excited with 266 nm radiation into the S2/S3 bright state. The subsequent dynamics were followed using ionisation as the probe step, with both mass spectra and photoelectron spectra recorded as a function of pump-probe delay. The observed decay of photoelectron and photoion intensities closely matches the theoretical predictions and is consistent with the sequential mechanism found in the simulations. This mechanism exhibits characteristic signatures in both time-resolved mass and photoelectron spectra, in particular in the appearance of fragment ions that are exclusively generated from the S1 state. This allows for a separation of the S2 and S1 dynamics in the photoelectron and mass spectra. An excellent agreement between the observed and the simulated ion signal is observed.

Unveiling the complex vibronic structure of the canonical adenine cation

Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine). This isolated DNA base was ionized by single VUV photons from a synchrotron beamline and the corresponding slow photoelectron spectrum was compared to ab initio computations of the neutral and ionic species. We report the vibronic structure of the X+ 2A'' (D0), A+ 2A' (D1) and B+ 2A'' (D2) electronic states of the 9H adenine cation, from the adiabatic ionization energy (AIE) up to AIE + 1.8 eV. Accurate AIEs are derived for the 9H-adenine (X[combining tilde] 1A') + hν → 9H-adenine+ (X+ 2A'', A+ 2A', B+ 2A'') + e- transitions. Close to the AIE, we fully assign the rich vibronic structure solely to the 9H-adenine (X 1A') + hν → 9H-adenine+ (X+ 2A'') transition. Importantly, we show that the lowest cationic electronic states of canonical adenine are coupled vibronically. The present findings are important for understanding the effects of ionizing radiation and the charge distribution on this elementary building block of life, at ultrafast, short, and long timescales.

The surprisingly high ligation energy of CO to ruthenium porphyrins

A combined theoretical and experimental approach has been used to investigate the binding energy of a ruthenium metalloporphyrin ligated with CO, ruthenium tetraphenylporphyrin [RuII TPP], in the RuII oxidation degree. Measurements performed with VUV ionization using the DESIRS beamline at Synchrotron SOLEIL led to adiabatic ionization energies of [RuII TPP] and its complex with CO, [RuII TPP-CO], of 6.48 ± 0.03 eV and 6.60 ± 0.03 eV, respectively, while the ion dissociation threshold of [RuII TPP-CO]+ is measured to be 8.36 ± 0.03 eV using the ground-state neutral complex. These experimental data are used to derive the binding energies of the CO ligand in neutral and cationic complexes (1.88 ± 0.06 eV and 1.76 ± 0.06 eV, respectively) using a Born-Haber cycle. Density functional theory calculations, in very satisfactory agreement with the experimental results, help to get insights into the metal-ligand bond. Notably, the high ligation energies can be rationalized in terms of the ruthenium orbital structure, which is singular compared to that of the iron atom. Thus, beyond indications of a strengthening of the Ru-CO bond due to the decrease in the CO vibrational frequency in the complex as compared to the Fe-CO bond, high-level calculations are essential to accurately describe the metal ligand (CO) bond and show that the Ru-CO bond energy is strongly affected by the splitting of triplet and singlet spin states in uncomplexed [Ru TPP].

Self-trapping relaxation decay investigated by time-resolved photoelectron spectroscopy

The present work combines time-resolved photoelectron spectroscopy on isolated species with high-level data processing to address an issue which usually pertains to materials science: the electronic relaxation dynamics towards the formation of a self-trapped exciton (STE). Such excitons are common excited states in ionic crystals, silica and rare gas matrices. They are associated with a strong local deformation of the matrix. Argon clusters were taken as a model. They are excited initially to a Wannier exciton at 14 eV and their evolution towards the formation of an STE has showed an unusual type of vibronic relaxation where the electronic excitation of the cluster decreases linearly as a function of time with a 0.59 ± 0.06 eV ps-1 rate. The decay was followed for 3.0 ps, and the STE formation occurred in ∼5.1 ± 0.7 ps.

Abstract P3-16-01: Using the new pan-cancer clinical data resource (TCGA-CDR) to identify breast cancer genomic correlates associating with different survival outcome endpoints

Introduction The Cancer Genome Atlas (TCGA) generated abundant high quality molecular data, however its relatively short-term patient follow-up limited its immediate clinical utility. We led a PanCanAtlas effort to systematically collate, integrate, and quality check the large body of acquired clinicopathologic data, generated 4 primary clinical outcome endpoints for each case, and created a new Pan-Cancer Clinical Data Resource (TCGA-CDR) for public use. We report here on the utility and validity of this TCGA-CDR in relating breast cancer (BC) genomic information to survival endpoints.

Methods Clinicopathologic data from all data files were integrated and processed. Overall survival (OS), disease-specific survival (DSS, an approximation), progression-free interval (PFI), and disease-free interval (DFI)were derived.Tests of the adequacy of the follow-up intervals for each endpoint were performed, and quality evaluation of these endpoints was established by their comparison with different clinical features. As a case study we compared each survival endpoint for significant association (FDR &lt;0.2) with chromosomal aneuploidy.

Results The 4 endpoints were derived for 1097 TCGA BC cases having a median follow-up time of 27.7 months. Median times to events/censorship for OS, DSS, PFI, and DFI were 41.8/25.0, 32.6/26.0, 26.0/25.0, and 25.4/25.0 months respectively. PFI and DFI passed tests for adequate follow-up times; OS and DSS partially passed the same tests signaling some caution with their use in genomic associations.

Using the endpoints, outcomes of patients with ER+ and ER- tumors were compared, along with those of patients with low (I&II) and high (III&IV) stage breast tumors. Univariate analyses suggested patients with ER+ tumors had significantly better survival than patients with ER- tumors when using PFI (p=0.005), DFI (p=0.001), and DSS (p=0.009), with OS not reaching significance (p=0.09). Patients with low stage tumors showed significantly better outcomes than patients with high stage tumors for each endpoint (p&lt;0.001). The 4 endpoints were also evaluated for their significant associations with chromosomal arm aneuploidy. Adjusted for patient age and AJCC stage, tumors with a loss of 8q and 8p (p=0.019, FDR=0.37) had worse PFI; and those with loss of 8q, 20q, and 8p had worse DFI. Tumors with gain of 11q or loss of 14, 7q, 12q, 18q, 20q, 3p, 7p, 8p, 18p, and 20p had worse OS. In contrast, tumors with loss of 16q had better DSS, while those with loss of 3q, 12q, 17q, 18q, 19q, 20q, 3p, 8p, 12p, 18p, 19p, and 20p had worse DSS. The finding that 8p loss associated with worse survival for all 4 endpoints, while 18p loss associated with worse OS and DSS, agrees with literature reports.

Conclusion These findings confirm that PFI and DFI, as extracted from the TCGA-CDR, are valid and appropriate BC survival endpoints, while OS and DSS may be recommended with some caution when employing TCGA data to evaluate new relationships between breast cancer genomic abnormalities and clinical outcomes.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Army/Navy/Air Force, the Department of Defense, or U.S. Government.

Citation Format: Liu J, Lichtenberg T, Hoadley KA, Cherniack A, Poisson L, Kovatich AJ, Benz C, Thorsson V, TCGA PanCanAtlas Research Network, Shriver CD, Hu H. Using the new pan-cancer clinical data resource (TCGA-CDR) to identify breast cancer genomic correlates associating with different survival outcome endpoints [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-16-01.

Direct observation of slow intersystem crossing in an aromatic ketone, fluorenone

Direct measurements of Single vibronic Level InterSystem Crossing (SLISC) have been performed on the fluorenone molecule in the gas phase, by time resolved photoelectron and photoion spectroscopy. Vibronic transitions above the S1 nπ* origin were excited in the 432-420 nm region and the decay of S1 and growth of T1(3)ππ* could be observed within a 10 ns time domain. The ionization potential is measured as 8.33 ± 0.04 eV. The energy of the first excited triplet state of fluorenone, T1 has been characterized directly at 18 640 ± 250 cm(-1). The internal conversion of S1 to S0 is found to amount to ∼15% of the population decay, thus ISC is the dominant electronic relaxation process. ISC, although favored by the S1(1)nπ*-T1(3)ππ* coupling scheme, is 3 orders of magnitude less efficient than in the similar molecule benzophenone. Thus, the planarity of the fluorenone molecule disfavors the exploration of the configuration space where surface crossings would create high ISC probability, which occurs in benzophenone through surface crossings. The time evolution of S1 fluorenone is well accounted for by the statistical decay of individual levels into a quasi-continuum of T1 vibronic levels.

A HElium NanoDroplet Isolation (HENDI) investigation of the weak hydrogen bonding in the propyne dimer (CH3CCH)2

A HElium Nanodroplet Isolation (HENDI) experiment was performed to explore the absorption spectra of the propyne monomer (CH₃CCH), dimer and (CH₃CCH)_≥3 multimers in the vicinity of the CH stretch region ν₁ of the monomer.

Dynamics of acetylene dimers hosted in helium droplets

The CH antisymmetric stretch of the C₂H₂ moieties in acetylene dimers was explored over the range 3270–3290 cm⁻¹ using the helium nanodroplet isolation (HENDI) technique.

Femtosecond dynamics of the 2-methylallyl radical: A computational and experimental study

We investigate the photodynamics of the 2-methylallyl radical by femtosecond time-resolved photoelectron imaging. The experiments are accompanied by field-induced surface hopping dynamics calculations and the simulation of time-resolved photoelectron intensities and anisotropies, giving insight into the photochemistry and nonradiative relaxation of the radical. 2-methylallyl is excited at 236 nm, 238 nm, and 240.6 nm into a 3p Rydberg state, and the subsequent dynamics is probed by multiphoton ionization using photons of 800 nm. The photoelectron image exhibits a prominent band with considerable anisotropy, which is compatible with the result of theory. The simulations show that the initially excited 3p state is rapidly depopulated to a 3s Rydberg state, from which photoelectrons of high anisotropy are produced. The 3s state then decays within several 100 fs to the D₁ (nπ) state, followed by the deactivation of the D₁ to the electronic ground state on the ps time scale.

Femtosecond time-resolved photoelectron spectroscopy of the benzyl radical

We present a joint experimental and computational study of the nonradiative deactivation of the benzyl radical, C₇H₇, after UV excitation. Femtosecond time-resolved photoelectron imaging was applied to investigate the photodynamics of the radical. The experiments were accompanied by excited state dynamics simulations using surface hopping. Benzyl has been excited at 265 nm into the D-band (ππ*) and the dynamics was probed using probe wavelengths of 398 nm or 798 nm. At a probe wavelength of 398 nm a single time constant of around 70-80 fs was observed. When the dynamics was probed at 798 nm, a second time constant τ₂ = 1.5 ps was visible, which can be attributed to further non-radiative deactivation to the lower-lying D₁/D₂ states.

Large amplitude motion of the acetylene molecule within acetylene-neon complexes hosted in helium droplets

Superfluid helium droplets provide an ideal environment for spectroscopic studies with rotational resolution. Nevertheless, the molecular rotation is hindered because the embedded molecules are surrounded by a non-superfluid component. The present work explores the dynamical role of this component in the hindered rotation of C2H2 within the C2H2-Ne complex. A HENDI experiment was built and near-infrared spectroscopy of C2H2-Ne and C2H2 was performed in the spectral region overlapping the ν3/ν2 + ν4 + ν5 Fermi-type resonance of C2H2. The comparison between measured and simulated spectra helped to address the above issue.

Multipronged mapping to the dynamics of a barium atom deposited on argon clusters

Dynamics of an electronically excited Ba atom at the surface of an Ar_≈500 cluster in a nanosecond frequency-resolved and femtosecond time-resolved multipronged approach.

Absorption Spectroscopy, a Tool for Probing Local Structures and the Onset of Large-Amplitude Motions in Small KAr(n) Clusters at Increasing Temperatures

Photoabsorption spectra of KArn (n = 1-10) are simulated at temperatures ranging between 5 and 25 K. The calculations associate a Monte Carlo (MC) method to sample cluster geometries at temperature T, with a one-electron ab initio model to calculate the ground-state and excited-state energies of the cluster. The latter model replaces the K(+) core electrons and all the electrons of the Ar atoms by appropriate pseudopotentials, complemented by core polarization potentials. It also provides the necessary oscillator strengths to simulate the spectra. Global optimization by basin-hopping is used in combination with MC simulation at low temperature (5 K) to identify the most stable isomer and remarkable isomers of ground-state KArn clusters, which are stable with respect to deformations of the order of those expected with Zero Point Energy motions. The absorption spectra calculated for each of these isomers at 5 K suggest that absorption spectroscopy can probe sensitively the local environment of K atom: surface location of K with respect to a close-packed Ar moiety, number of Ar atom in close vicinity, and local symmetry about K. Simulation at increasing temperatures, up to the evaporation limit of K out of the cluster, shows the onset of large amplitude motions above 20 K, when the K atom experiences a variety of local environments.

Photoionization of Benzophenone in the Gas Phase: Theory and Experiment

We report on the single photoionization of jet-cooled benzophenone using a tunable source of VUV synchrotron radiation coupled with a photoion/photoelectron coincidence acquisition device. The assignment and the interpretation of the spectra are based on a characterization by ab initio and density functional theory calculations of the geometry and of the electronic states of the cation. The absence of structures in the slow photoelectron spectrum is explained by a congestion of the spectrum due to the dense vibrational progressions of the very low frequency torsional mode in the cation either in pure form or in combination bands. Also a high density of electronic states has been found in the cation. Presently, we estimate the experimental adiabatic and vertical ionization energy of benzophenone at 8.80 ± 0.01 and 8.878 ± 0.005 eV, respectively. The ionization energy as well as the energies of the excited states are compared to the calculated ones.

Spectroscopy and Dynamics of K Atoms on Argon Clusters

We present a combined experimental and simulation study of the 4s → 4p photoexcitation of the K atom trapped at the surface of ArN clusters made of a few hundred Ar atoms. Our experimental method based on photoelectron spectroscopy allows us to firmly establish that one single K atom is trapped at the surface of the cluster. The absorption spectrum is characterized by the splitting of the atomic absorption line into two broad bands, a Π band associated with p orbitals parallel to the cluster surface and a Σ band associated with the perpendicular orientation. The spectrum is consistent with observations reported for K atoms trapped on lighter inert gas clusters, but the splitting between the Π and Σ bands is significantly larger. We show that a large amount of K atoms are transiently stuck and eventually lost by the Ar cluster, in contrast with previous observations reported for alkaline earth metal systems. The excitation in the Σ band leads systematically to the ejection of the K atom from the Ar cluster. On the contrary, excitation in the Π band leads to the formation of a bound state. In this case, the analysis of the experimental photoelectron spectrum by means of nonadiabatic molecular dynamics simulation shows that the relaxation drives the system toward a basin where the coordination of the K atom is 2.2 Ar atoms on the average, in a poorly structured surface.

Reactive and Inelastic Channels in the Ca*···FCH3 Transition State: A Simple Branching Mechanism

To study the excited state dynamics between a calcium atom and the CH3F molecule, a Ca···CH3F 1:1 complex has been prepared by a supersonic expansion with laser ablation of calcium metal in the gas phase. Tunable laser excitation of these complexes in molecular states correlating to Ca (1)P1(4s4p) + CH3F allows observing two competitive channels: the direct dissociation and the reactive channel into CaF* + CH3. The translational recoil, as well as the alignment of the fragments Ca* and CaF* have been analyzed by velocity map imaging and time-of-flight mass spectrometry. This revealed that both the dissociation and reaction processes are quasi direct and are of comparable intensity. We provide a simple interpretation for this process: the electronically excited potential surface of the Ca*···FCH3 complex initiates a fast predissociation from a suspended well to two repulsive surfaces that lead either to Ca (1)P1(4s4p) (Ω = 1) + CH3F or to CaF((2)Δ) + CH3.

Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA bases: application to the ã state of thymine cation

For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules. While ground state investigations are currently straightforward, those of electronic excited states are not. Here, we characterized the à electronic state of ionic thymine (T(+)) DNA base using explicitly correlated coupled cluster ab initio methods and state-of-the-art synchrotron-based electron/ion coincidence techniques. The experimental spectrum is composed of rich and long vibrational progressions corresponding to the population of the low frequency modes of T(+)(Ã). This work challenges previous numerous works carried out on DNA bases using common synchrotron and VUV-based photoelectron spectroscopies. We provide hence a powerful theoretical and experimental framework to study the electronic structure of ionized DNA bases that could be generalized to other medium-sized biologically relevant systems.

Observation in the gas phase of the ligation of 1-methylimidazole to hemoprotein mimics

Hemoprotein mimics, cobalt picket fence porphyrins have been prepared in the gas phase as neutral molecules for the first time. Their ligation properties have been studied with 1-methylimidazole and compared with those of other cobalt porphyrins, tetraphenyl porphyrin, and cobalt protoporphyrin IX chloride, in view of studying the sterical properties of the ligation. It is shown that the cobalt picket fence porphyrin can only accept one 1-methylimidazole ligand in contrast to less sterically crowded porphyrins like cobalt tetraphenylporphyrin that present two accessible ligation sites. The femtosecond dynamics of these ligated systems have been studied after excitation at 400 nm, in comparison with the unligated ones. The observed transients are formed in much shorter times, 30 fs for the ligated species, as compared to free species (100 fs), supporting the porphyrin to metal charge transfer nature of these transients. The similar decays of the ligated transients <1 ps reveal the absence of photodissociation of the cobalt-1-methylimidazole bond at this step of evolution.

VUV photoionization and dissociative photoionization of the prebiotic molecule acetyl cyanide: theory and experiment

The present combined theoretical and experimental investigation concerns the single photoionization of gas-phase acetyl cyanide and the fragmentation pathways of the resulting cation. Acetyl cyanide (AC) is inspired from both the chemistry of cyanoacetylene and the Strecker reaction which are thought to be at the origin of medium sized prebiotic molecules in the interstellar medium. AC can be formed by reaction from cyanoacetylene and water but also from acetaldehyde and HCN or the corresponding radicals. In view of the interpretation of vacuum ultraviolet (VUV) experimental data obtained using synchrotron radiation, we explored the ground potential energy surface (PES) of acetyl cyanide and of its cation using standard and recently implemented explicitly correlated methodologies. Our PES covers the regions of tautomerism (between keto and enol forms) and of the lowest fragmentation channels. This allowed us to deduce accurate thermochemical data for this astrobiologically relevant molecule. Unimolecular decomposition of the AC cation turns out to be very complex. The implications for the evolution of prebiotic molecules under VUV irradiation are discussed.

Coupled electronic and structural relaxation pathways in the postexcitation dynamics of Rydberg states of BaArN clusters

We investigate, theoretically, the joint relaxation of orbital and structure in postexcitation dynamics of Rydberg states of cluster BaArN (N=250). Mixed quantum-classical dynamics is used to account for the nonadiabatic transitions among more than 160 electronic states, represented via a diatomics-in-molecules Hamiltonian. The simulation illustrates the complex multistep relaxation processes and provides detailed insight in the mechanisms contributing to the final-time experimental photoelectron spectrum.