LIVIVO - Search results -

Search results

Result 1 - 10 of total 68

Search options

Article ; Online: Spin Coupling Effect on Geometry-Dependent X-Ray Absorption of Diradicals.

Garner, Scott M / Haugen, Eric A / Leone, Stephen R / Neuscamman, Eric

Journal of the American Chemical Society

2024 Volume 146, Issue 4, Page(s) 2387–2397

Abstract: We theoretically investigate the influence of diradical electron spin coupling on the time-resolved X-ray absorption spectra of the photochemical ring opening of furanone. We predict geometry-dependent carbon K-edge signals involving transitions from ... ...

Abstract	We theoretically investigate the influence of diradical electron spin coupling on the time-resolved X-ray absorption spectra of the photochemical ring opening of furanone. We predict geometry-dependent carbon K-edge signals involving transitions from core orbitals to both singly and unoccupied molecular orbitals. The most obvious features of the ring opening come from the carbon atom directly involved in the bond breaking through its transition to both the newly formed singly occupied and the available lowest unoccupied molecular orbitals (SOMO and LUMO, respectively). In addition to this primary feature, the singlet spin coupling of four unpaired electrons that arises in the core-to-LUMO states creates additional geometry dependence in some spectral features with both oscillator strengths and relative excitation energies varying observably as a function of the ring opening. We attribute this behavior to a spin-occupancy-induced selection rule, which occurs when singlet spin coupling is enforced in the diradical state. Notably, one of these geometry-sensitive core-to-LUMO transitions excites core electrons from a backbone carbon not involved in the bond breaking, providing a novel nonlocal X-ray probe of chemical dynamics arising from electron spin coupling.
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c08002
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Bonn / Germany

Z 4' 55/32: Show issues
Z 7.3: Show issues

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron-Withdrawing Groups.

Haugen, Eric A / Hait, Diptarka / Scutelnic, Valeriu / Xue, Tian / Head-Gordon, Martin / Leone, Stephen R

The journal of physical chemistry. A

2023 Volume 127, Issue 3, Page(s) 634–644

Abstract: Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at ... ...

Abstract	Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. We observe the excited state dynamics following excitation with 266 nm UV light to the
Language	English
Publishing date	2023-01-13
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.2c06044
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Femtosecond symmetry breaking and coherent relaxation of methane cations via x-ray spectroscopy.

Ridente, Enrico / Hait, Diptarka / Haugen, Eric A / Ross, Andrew D / Neumark, Daniel M / Head-Gordon, Martin / Leone, Stephen R

Science (New York, N.Y.)

2023 Volume 380, Issue 6646, Page(s) 713–717

Abstract: Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic-level insight into photochemistry. We performed a time-resolved study of ultrafast molecular symmetry breaking through geometric relaxation (Jahn-Teller ... ...

Abstract	Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic-level insight into photochemistry. We performed a time-resolved study of ultrafast molecular symmetry breaking through geometric relaxation (Jahn-Teller distortion) on the methane cation. Attosecond transient absorption spectroscopy with soft x-rays at the carbon K-edge revealed that the distortion occurred within 10 ± 2 femtoseconds after few-femtosecond strong-field ionization of methane. The distortion activated coherent oscillations in the asymmetric scissoring vibrational mode of the symmetry-broken cation, which were detected in the x-ray signal. These oscillations were damped within 58 ± 13 femtoseconds because vibrational coherence was lost with the energy redistributing into lower-frequency vibrational modes. This study completely reconstructs the molecular relaxation dynamics of this prototypical example and opens avenues for exploring complex systems.
Language	English
Publishing date	2023-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adg4421
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 77: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases.

Breeze, Charles E / Haugen, Eric / Gutierrez-Arcelus, María / Yao, Xiaozheng / Teschendorff, Andrew / Beck, Stephan / Dunham, Ian / Stamatoyannopoulos, John / Franceschini, Nora / Machiela, Mitchell J / Berndt, Sonja I

Genome biology

2024 Volume 25, Issue 1, Page(s) 3

Abstract: The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for ... ...

Abstract	The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.cancer.gov/ https://forge2.altiusinstitute.org/files/forgedb.html and https://doi.org/10.5281/zenodo.10067458 ), a standalone and web-based tool that integrates multiple datasets, delivering information on associated regulatory elements, transcription factor binding sites, and target genes for over 37 million variants. FORGEdb scores provide researchers with a quantitative assessment of the relative importance of each variant for targeted functional experiments.
MeSH term(s)	Genome-Wide Association Study ; Regulatory Sequences, Nucleic Acid ; Protein Binding ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-03126-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Single-molecule regulatory architectures captured by chromatin fiber sequencing.

Stergachis, Andrew B / Debo, Brian M / Haugen, Eric / Churchman, L Stirling / Stamatoyannopoulos, John A

Science (New York, N.Y.)

2020 Volume 368, Issue 6498, Page(s) 1449–1454

Abstract: Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach ... ...

Abstract	Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using nonspecific DNA N
MeSH term(s)	Animals ; Chromatin/chemistry ; Chromatin Assembly and Disassembly ; DNA/chemistry ; DNA/genetics ; Drosophila melanogaster ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Humans ; K562 Cells ; Nucleosomes/chemistry ; Promoter Regions, Genetic ; Single Molecule Imaging/methods ; Site-Specific DNA-Methyltransferase (Adenine-Specific)/chemistry ; Transcription Factors/chemistry
Chemical Substances	Chromatin ; Nucleosomes ; Transcription Factors ; DNA (9007-49-2) ; Site-Specific DNA-Methyltransferase (Adenine-Specific) (EC 2.1.1.72)
Language	English
Publishing date	2020-06-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aaz1646
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 77: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.

Breeze, Charles E / Haugen, Eric / Reynolds, Alex / Teschendorff, Andrew / van Dongen, Jenny / Lan, Qing / Rothman, Nathaniel / Bourque, Guillaume / Dunham, Ian / Beck, Stephan / Stamatoyannopoulos, John / Franceschini, Nora / Berndt, Sonja I

Genome biology

2022 Volume 23, Issue 1, Page(s) 13

Abstract: Background: Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further characterisation of associated ... ...

Abstract	Background: Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further characterisation of associated cell type-specific regulation can broaden our understanding of how GWAS signals may contribute to disease risk. Results: To gain insight into potential functional mechanisms underlying GWAS associations, we developed FORGE2 ( https://forge2.altiusinstitute.org/ ), which is an updated version of the FORGE web tool. FORGE2 uses an expanded atlas of cell type-specific regulatory element annotations, including DNase I hotspots, five histone mark categories and 15 hidden Markov model (HMM) chromatin states, to identify tissue- and cell type-specific signals. An analysis of 3,604 GWAS from the NHGRI-EBI GWAS catalogue yielded at least one significant disease/trait-tissue association for 2,057 GWAS, including > 400 associations specific to epigenomic marks in immune tissues and cell types, > 30 associations specific to heart tissue, and > 60 associations specific to brain tissue, highlighting the key potential of tissue- and cell type-specific regulatory elements. Importantly, we demonstrate that FORGE2 analysis can separate previously observed accessible chromatin enrichments into different chromatin states, such as enhancers or active transcription start sites, providing a greater understanding of underlying regulatory mechanisms. Interestingly, tissue-specific enrichments for repressive chromatin states and histone marks were also detected, suggesting a role for tissue-specific repressed regions in GWAS-mediated disease aetiology. Conclusion: In summary, we demonstrate that FORGE2 has the potential to uncover previously unreported disease-tissue associations and identify new candidate mechanisms. FORGE2 is a transparent, user-friendly web tool for the integrative analysis of loci discovered from GWAS.
MeSH term(s)	Epigenomics ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Phenotype ; Polymorphism, Single Nucleotide ; Regulatory Sequences, Nucleic Acid
Language	English
Publishing date	2022-01-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02560-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Jahn-Teller distortion and dissociation of CCl

Ross, Andrew D / Hait, Diptarka / Scutelnic, Valeriu / Haugen, Eric A / Ridente, Enrico / Balkew, Mikias B / Neumark, Daniel M / Head-Gordon, Martin / Leone, Stephen R

Chemical science

2022 Volume 13, Issue 32, Page(s) 9310–9320

Abstract: X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculations are used to study ... ...

Abstract	X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculations are used to study CCl
Language	English
Publishing date	2022-07-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d2sc02402k
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Correction: Jahn-Teller distortion and dissociation of CCl

Ross, Andrew D / Hait, Diptarka / Scutelnic, Valeriu / Haugen, Eric A / Ridente, Enrico / Balkew, Mikias B / Neumark, Daniel M / Head-Gordon, Martin / Leone, Stephen R

Chemical science

2022 Volume 13, Issue 35, Page(s) 10581

Abstract: This corrects the article DOI: 10.1039/D2SC02402K.]. ...

Abstract	[This corrects the article DOI: 10.1039/D2SC02402K.].
Language	English
Publishing date	2022-08-24
Publishing country	England
Document type	Published Erratum
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d2sc90172b
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations

Breeze, Charles E. / Haugen, Eric / Reynolds, Alex / Teschendorff, Andrew / van Dongen, Jenny / Lan, Qing / Rothman, Nathaniel / Bourque, Guillaume / Dunham, Ian / Beck, Stephan / Stamatoyannopoulos, John / Franceschini, Nora / Berndt, Sonja I.

Genome biology. 2022 Dec., v. 23, no. 1

2022

Abstract: BACKGROUND: Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further characterisation of associated ... ...

Abstract	BACKGROUND: Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further characterisation of associated cell type-specific regulation can broaden our understanding of how GWAS signals may contribute to disease risk. RESULTS: To gain insight into potential functional mechanisms underlying GWAS associations, we developed FORGE2 (https://forge2.altiusinstitute.org/), which is an updated version of the FORGE web tool. FORGE2 uses an expanded atlas of cell type-specific regulatory element annotations, including DNase I hotspots, five histone mark categories and 15 hidden Markov model (HMM) chromatin states, to identify tissue- and cell type-specific signals. An analysis of 3,604 GWAS from the NHGRI-EBI GWAS catalogue yielded at least one significant disease/trait-tissue association for 2,057 GWAS, including > 400 associations specific to epigenomic marks in immune tissues and cell types, > 30 associations specific to heart tissue, and > 60 associations specific to brain tissue, highlighting the key potential of tissue- and cell type-specific regulatory elements. Importantly, we demonstrate that FORGE2 analysis can separate previously observed accessible chromatin enrichments into different chromatin states, such as enhancers or active transcription start sites, providing a greater understanding of underlying regulatory mechanisms. Interestingly, tissue-specific enrichments for repressive chromatin states and histone marks were also detected, suggesting a role for tissue-specific repressed regions in GWAS-mediated disease aetiology. CONCLUSION: In summary, we demonstrate that FORGE2 has the potential to uncover previously unreported disease-tissue associations and identify new candidate mechanisms. FORGE2 is a transparent, user-friendly web tool for the integrative analysis of loci discovered from GWAS.
Keywords	Markov chain ; chromatin ; epigenome ; etiology ; genome-wide association study ; heart ; histones ; risk ; world wide web
Language	English
Dates of publication	2022-12
Size	p. 13.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02560-3
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article ; Online: Accurate prediction of core-level spectra of radicals at density functional theory cost via square gradient minimization and recoupling of mixed configurations.

Hait, Diptarka / Haugen, Eric A / Yang, Zheyue / Oosterbaan, Katherine J / Leone, Stephen R / Head-Gordon, Martin

The Journal of chemical physics

2020 Volume 153, Issue 13, Page(s) 134108

Abstract: State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted due to the risk of "variational collapse" down to the ground state. We employ ...

Abstract	State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted due to the risk of "variational collapse" down to the ground state. We employ the recently developed square gradient minimization [D. Hait and M. Head-Gordon, J. Chem. Theory Comput. 16, 1699 (2020)] algorithm to reliably avoid variational collapse and study the effectiveness of orbital optimized density functional theory (DFT) at predicting second period element 1s core-level spectra of open-shell systems. Several density functionals (including SCAN, B3LYP, and ωB97X-D3) are found to predict excitation energies from the core to singly occupied levels with high accuracy (≤0.3 eV RMS error) against available experimental data. Higher excited states are, however, more challenging by virtue of being intrinsically multiconfigurational. We thus present a configuration interaction inspired route to self-consistently recouple single determinant mixed configurations obtained from DFT, in order to obtain approximate doublet states. This recoupling scheme is used to predict the C K-edge spectra of the allyl radical, the O K-edge spectra of CO
Language	English
Publishing date	2020-10-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0018833
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Bonn / Germany

Z 4' 49/16: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED