Search

Your search keyword '"Buma, Wybren J."' showing total 165 results
Start Over Author "Buma, Wybren J."
165 results on '"Buma, Wybren J."'

3. Ultrafast vibrational dynamics of rotaxanes

Author

Larsen, Olaf F.A., Buma, Wybren J., Leigh, David A., Woutersen, Sander, Castleman, A. W., Jr., editor, Toennies, J.P., editor, Zinth, W., editor, Kobayashi, Takayoshi, editor, Okada, Tadashi, editor, Kobayashi, Tetsuro, editor, Nelson, Keith A., editor, and De Silvestri, Sandro, editor

Published
2005
Full Text
View/download PDF

4. Femtosecond excited state studies of the two-center three-electron bond driven twisted internal charge transfer dynamics in 1,8-bis(dimethylamino)naphthalene

Author

Balkowshi, Grzegorz, Szemik-Hojniak, Anna, Stokkum, Ivo H. M. van, Hong Zang, and Buma, Wybren J.

Subjects
Naphthalene -- Chemical properties, Charge transfer -- Research, Excited state chemistry -- Research, Chemicals, plastics and rubber industries
Abstract

The femtosecond fluorescence upconversion and transient absorption experiments were performed to monitor the photoinduced electronic, geometry, and solvent relaxation dynamics of 1,8-bis(dimethylamino)naphthalene dissolved in methycyclohexane and acetonitrile. It is concluded that the solvent relaxation and vibrational cooling in the lpi* state cannot be seperated in polar solvents, but in apolar solvents a distinct vibrational cooling process in the lpi* state is discerned.

Published
2005

5. Towards developing novel and sustainable molecular light-to-heat converters

Author

Abiola, Temitope T., primary, Rioux, Benjamin, additional, Toldo, Josene M., additional, Alarcan, Jimmy, additional, Woolley, Jack M., additional, Turner, Matthew A. P., additional, Coxon, Daniel J. L., additional, Telles do Casal, Mariana, additional, Peyrot, Cédric, additional, Mention, Matthieu M., additional, Buma, Wybren J., additional, Ashfold, Michael N. R., additional, Braeuning, Albert, additional, Barbatti, Mario, additional, Stavros, Vasilios G., additional, and Allais, Florent, additional

Published
2021
Full Text
View/download PDF

8. Enantiospecific Brook Rearrangement of Tertiary Benzylic alpha-Hydroxysilanes

Author

Collados, Juan F., Ortiz, Pablo, Pérez, Juana M., Xia, Yiyin, Koenis, Mark A. J., Buma, Wybren J., Nicu, Valentin P., Harutyunyan, Syuzanna R., and Synthetic Organic Chemistry

Subjects
ABSOLUTE-CONFIGURATION, SILYLCARBINOL, Rearrangement, ALKOXYSILANE, Enantiospecific, CHIRAL MOLECULES, ACYLATION, CARBON, REDUCTION, Synthetic methods, Hydroxysilanes, Chirality, ACYLSILANES, ANIONIC REARRANGEMENTS, STEREOCHEMISTRY
Abstract

The Brook rearrangement of simple, chiral tertiary benzylic -hydroxysilanes is presented. The rearrangement followed by proton trapping is enantiospecific and proceeds with inversion of the configuration at the carbon center. Importantly, the [1,2]-Brook rearrangement can be followed by trapping of methyl or allyl electrophiles even in the protic environment, although with minimal retention of chirality.

Published
2018

12. Bimodal dynamics of mechanically constrained hydrogen bonds revealed by vibrational photon echoes.

Author

Bodis, Pavol, Yeremenko, Sergiy, Berná, José, Buma, Wybren J., Leigh, David A., and Woutersen, Sander

Subjects
CONSTRAINTS (Physics), HYDROGEN bonding, PHOTON echoes, ROTAXANES, SOLUTION (Chemistry), AMIDES, MACROCYCLIC compounds, FLUCTUATIONS (Physics), DISSOCIATION (Chemistry)
Abstract

We have investigated the dynamics of the hydrogen bonds that connect the components of a [2]rotaxane in solution. In this rotaxane, the amide groups in the benzylic-amide macrocycle and the succinamide thread are connected by four equivalent N-H···O=C hydrogen bonds. The fluctuations of these hydrogen bonds are mirrored by the frequency fluctuations of the NH-stretch modes, which are probed by means of three-pulse photon-echo peak shift spectroscopy. The hydrogen-bond fluctuations occur on three different time scales, with time constants of 0.1, 0.6, and >=200 ps. Comparing these three time scales to the ones found in liquid formamide, which contains the same hydrogen-bonded amide motif but without mechanical constraints, we find that the faster two components, which are associated with small-amplitude fluctuations in the strength of the N-H···O=C hydrogen bonds, are very similar in the liquid and the rotaxane. However, the third component, which is associated with the breaking and subsequent reformation of hydrogen bonds, is found to be much slower in the rotaxane than in the liquid. It can be concluded that the mechanical bonding in a rotaxane does not influence the amplitude and time scale of the small-amplitude fluctuations of the hydrogen bonds, but strongly slows down the complete dissociation of these hydrogen bonds. This is probably because in a rotaxane breaking of the macrocycle-axle contacts is severely hindered by the mechanical constraints. The hydrogen-bond dynamics in rotaxane-based molecular machines can therefore be regarded as liquidlike on a time scale 1 ps and less, but structurally frozen on longer (up to at least 200 ps) time scales. [ABSTRACT FROM AUTHOR]

Published
2011
Full Text
View/download PDF

13. Regional Susceptibility in VCD Spectra to Dynamic Molecular Motions: The Case of a Benzyl α-Hydroxysilane

Author

Xia, Yiyin, Koenis, Mark A.J., Collados, Juan F., Ortiz, Pablo, Harutyunyan, Syuzanna R., Visscher, Lucas, Buma, Wybren J., Nicu, Valentin P., Xia, Yiyin, Koenis, Mark A.J., Collados, Juan F., Ortiz, Pablo, Harutyunyan, Syuzanna R., Visscher, Lucas, Buma, Wybren J., and Nicu, Valentin P.

Abstract

Experimental and theoretical studies of the vibrational circular dichroism (VCD) spectrum of 3-methyl-1-(methyldiphenlsilyl)-1-phenylbutan-1-ol, whose absolute configuration is key to elucidating the Brook rearrangement of tertiary benzylic α-hydroxylsilanes, are presented. It is found that the entire OH-bending region in this spectrum—a region that provides important marker bands—cannot be reproduced at all by standard theoretical approaches even though other regions are well described. Using a novel approach to disentangle contributions to the rotational strength of these bands, internal coordinates are identified that critically influence the appearance of this part of the spectrum. We show that the agreement between experiment and theory is greatly improved when structural dynamics along these coordinates are explicitly taken into account. The general applicability of the approach underlines its usefulness for structurally flexible chiral systems, a situation that is more the rule rather than the exception.

Published
2018
Full Text
View/download PDF

14. Fluorescence Correlation Spectroscopy of Labeled Azurin Reveals Photoinduced Electron Transfer between Label and Cu Center

Author

Andreoni, Alessio, Sen, Saptaswa, Hagedoorn, Peter-Leon, Buma, Wybren J., Aartsma, Thijs J., Canters, Gerard W., Andreoni, Alessio, Sen, Saptaswa, Hagedoorn, Peter-Leon, Buma, Wybren J., Aartsma, Thijs J., and Canters, Gerard W.

Abstract

Fluorescent labeling of biomacromolecules enjoys increasing popularity for structural, mechanistic, and microscopic investigations. Its success hinges on the ability of the dye to alternate between bright and dark states. Forster resonance energy transfer (FRET) is an important source of fluorescence modulation. Photo-induced electron transfer (PET) may occur as well, but is often considered only when donor and acceptor are in van der Waals contact. In this study, PET is shown between a label and redox centers in oxidoreductases, which may occur over large distances. In the small blue copper protein azurin, labeled with ATTO655, PET is observed when the label is at 18.5 angstrom, but not when it is at 29.1 angstrom from the Cu. For Cu-II, PET from label to Cu occurs at a rate of (4.8 +/- 0.3) x 10(4) s(-1) and back at (0.7 +/- 0.1) x 10(3) s(-1). With Cu-I the numbers are (3.3 +/- 0.7) x 10(6) s(-1) and (1.0 +/- 0.1) x 10(4) s(-1). Reorganization energies and electronic coupling elements are in the range of 0.8-1.2 eV and 0.02-0.5 cm(-1), respectively. These data are compatible with electron transfer (ET) along a through-bond pathway although transient complex formation followed by ET cannot be ruled out. The outcome of this study is a useful guideline for experimental designs in which oxidoreductases are labelled with fluorescent dyes, with particular attention to single molecule investigations. The labelling position for FRET can be optimized to avoid reactions like PET by evaluating the structure and thermodynamics of protein and label., QC 20180131

Published
2018
Full Text
View/download PDF

15. IR spectroscopy of molecular ions by nonthermal ion ejection from helium nanodroplets

Author

Smokarek, Szymon, Brauer, Nils B., Buma, Wybren J., and Drabbels, Marcel

Subjects
Excited state chemistry -- Analysis, Helium -- Chemical properties, Helium -- Thermal properties, Infrared spectroscopy -- Usage, Solvation -- Analysis, Chemistry
Abstract

A novel spectroscopic method is described that has used superfluid helium nanodroplets to record IR spectra of cold molecular ions. The spectra are recorded with a high sensitivity, have displayed only a small matrix shift and the widths of the individual transitions have depended on the excited vibrational level.

Published
2010

16. High-resolution excitation and absorption spectroscopy of gas-phase p-coumaric acid: unveiling an elusive chromophore

Author

Smolarek, Szymon, Vdovin, Alexander, Perrier, Dayinta L., Smit, Jorrit P., Drabbels, Marcel, and Buma, Wybren J.

Subjects
Coumarins -- Structure, Coumarins -- Chemical properties, Coumarins -- Spectra, Excited state chemistry -- Analysis, Quantum chemistry -- Usage, Proteins -- Structure, Proteins -- Analysis, Chemistry
Abstract

Several high-resolution excitation and absorption spectroscopy studies are conducted to study the properties of the gas-phase p-coumaric acid. The analyses have been shown to be extremely useful for analyzing the light-induced signal transduction taking place in such complexes.

Published
2010

17. Stiff, and sticky in the right places: binding interactions in isolated mechanically interlocked molecules probed by mid-infrared spectroscopy

Author

Rijs, Anouk M., Compagnon, Isabelle, Oomens, Jos, Hannam, Jeffrey S., Leigh, David A., and Buma, Wybren J.

Subjects
Hydrogen bonding -- Analysis, Infrared spectroscopy -- Usage, Jets -- Usage, Macrocycles -- Structure, Macrocycles -- Spectra, Macrocycles -- Thermal properties, Chemistry
Abstract

The high-resolution spectroscopic studies on isolated, jet-cooled [2]rotaxanes are described. The infrared (IR) spectra of prototypical hydrogen-bond assembled rotaxanes as well as their associated threads and macrocycles have provided direct view on the effects of interlocking the macrocycle and thread.

Published
2009

18. Femtosecond spectroscopic studies of the one- and two-photon excited-state dynamics of 2,2,17,17-tetramethyloctadeca-5,9,13-trien-3,7,11,15-tetrayne: A trimeric oligodiacetylene

Author

Balkowski, Grzegorz M., Groeneveld, Michiel, Hong Zhang, Hendriks, Cindy C.J., Polhius, Michael, Zuilhof, Han, and Buma, Wybren J.

Subjects
Excited state chemistry -- Research, Oligomers -- Chemical properties, Chemicals, plastics and rubber industries
Abstract

The excited-state dynamics of an oligomer of polydiacerylene, 2,2,17,17-tetramethyloctadeca-5,9,13-trien-3,7,11,15-tetrayne, dissolved in n-hexane is studied by femtosecond fluorescence upconversion and polarized transient absorption experiments under one- and two-photon excitation conditions. Spectroscopically monitoring the population relaxation in the excited states in real time results in a distinct time separation of the dynamics.

Published
2006

25. Photophysics of 1,8-bis(dimethylamino)naphthalene in solution: Internal change transfer with a twist

Author

Szemik-Hojniak, Anna, Balkowski, Grzegorz, Wurpel, George W.H., Herbich, Jurek, Waals, Joan H. van der, and Buma, Wybren J.

Subjects
Quantum chemistry -- Research, Naphthalene -- Electric properties, Chemicals, plastics and rubber industries
Abstract

The photophysical properties of the excited states of 1,8-(bisdimethylamino)naphthalene are investigated by a combination of experimental spectroscopic methods and quantum chemical calculations. The experiments show that vertical excitation occurs to an (super 1)L(sub a)-type state from which internal conversion occurs to a state with dominant internal charge-transfer character.

Published
2004

28. GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra

Author

Koenis, Mark A. J., Visser, Olivier, Visscher, Lucas, Buma, Wybren J., and Nicu, Valentin P.

Abstract

As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments.

Published
2020
Full Text
View/download PDF

29. Self-Assembly of Supramolecular Polymers of N-Centered Triarylamine Trisamides in the Light of Circular Dichroism: Reaching Consensus between Electrons and Nuclei

Author

Koenis, Mark A. J., Osypenko, Artem, Fuks, Gad, Giuseppone, Nicolas, Nicu, Valentin P., Visscher, Lucas, and Buma, Wybren J.

Abstract

The self-assembly of chiral supramolecular polymers is an intricate process that spans a wide range of length scales. Circular dichroism techniques are ideal to study this process as they provide information on the molecular scale but are at the same time also sensitive probes of the long-range interactions that control the growth and morphology of these polymers. As yet, Electronic Circular Dichroism that uses electronic transitions as a probe has by far been the method of choice while Vibrational Circular Dichroism, which uses vibrational transitions to probe structure, is much less employed. Here, we report experimental and theoretical studies of the self-assembly of helical supramolecular polymers of (S)-triarylamine tris-amides ((S)-TATA) in which both techniques are applied in concert. Theoretical studies based on quantum chemical calculations and on simplified models that allow for extrapolation to “infinitely” long polymers provide a solid basis for interpreting results from each of the two techniques that on their own would appear to be contradictory. In the particular case of (S)-TATA it is shown that upon equilibration the initially formed fibers undergo a conformational transition that becomes only “visible” by the combination of the two techniques. Our studies thus show that combining electronic and vibrational domains offers a unique and complementary means to probe these polymers, precisely because they are sensitive to different aspects of molecular and polymeric structure.

Published
2020
Full Text
View/download PDF

30. Conformational Heterogeneity of Methyl 4-Hydroxycinnamate: A Gas-Phase UV–IR Spectroscopic Study

Author

Tan, Eric M. M., Amirjalayer, Saeed, Smolarek, Szymon, Vdovin, Alexander, Rijs, Anouk M., and Buma, Wybren J.

Abstract

UV excitation and IR absorption spectroscopy on jet-cooled molecules is used to study the conformational heterogeneity of methyl 4-hydroxycinnamate, a model chromophore of the Photoactive Yellow Protein (PYP), and to determine the spectroscopic properties of the various conformers. UV–UV depletion spectroscopy identifies four different species with distinct electronic excitation spectra. Quantum chemical calculations argue that these species are associated with different conformers involving the s-cis/s-transconfiguration of the ester with respect to the propenyl C–C single bond and the syn/antiorientation of the phenolic OH group. IR–UV hole-burning spectroscopy is used to record their IR absorption spectra in the fingerprint region. Comparison with IR absorption spectra predicted by quantum chemical calculations provides vibrational markers for each of the conformers, on the basis of which each of the species observed with UV–UV depletion spectroscopy is assigned. Although both DFT and wave function methods reproduce experimental frequencies, we find that calculations at the MP2 level are necessary to obtain agreement with experimentally observed intensities. To elucidate the role of the environment, we compare the IR spectra of the isolated conformers with IR spectra of methyl 4-hydroxycinnamate–water clusters, and with IR spectra of methyl 4-hydroxycinnamate in solution.

Published
2024
Full Text
View/download PDF

31. An investigation into the photochemistry of, and the electrochemically induced CO-loss from, [(CO)5MC(OMe)Me](M = Cr or W) using low-temperature matrix isolation, picosecond infrared spectroscopy, cyclic voltammetry, and time-dependent density functional theory

Author

McMahon, Suzanne, Amirjalayer, Saeed, Buma, Wybren J., Halpin, Yvonne, Long, Conor, Rooney, A. Denise, Woutersenc, Sander, Pryce, Mary T., McMahon, Suzanne, Amirjalayer, Saeed, Buma, Wybren J., Halpin, Yvonne, Long, Conor, Rooney, A. Denise, Woutersenc, Sander, and Pryce, Mary T.

Abstract

The photophysics and photochemistry of [(CO)5MC(OMe)Me] (M = Cr or W) were investigated using picosecond time-resolved infrared spectroscopy (M = Cr or W), low-temperature matrix isolation techniques (M = Cr), and time-dependent density functional calculations (M = Cr or W). These studies provide unambiguous evidence for the photochemical formation of a long-lived, 18-electron metallaketene species capable of acting as a synthetically useful intermediate. For the Cr complex, an intermediate metallacyclopropanone singlet excited state was detected on the reaction path to the metallaketene species. This metallacyclopropanone excited state species has a lifetime of less than 100 ps and a characteristic bridging carbonyl band at 1770 cm−1. The tungsten ketene species was also detected but in contrast to the chromium system, this forms directly from a low-lying triplet excited state. The electrochemical release of CO showed a greater efficiency for the chromium complex when compared to the tungsten.

Published
2015

33. Fluorescence Correlation Spectroscopy of Labeled Azurin Reveals Photoinduced Electron Transfer between Label and Cu Center.

Author

Aartsma, Thijs J., Canters, Gerard W., Andreoni, Alessio, Sen, Saptaswa, Hagedoorn, Peter‐Leon, and Buma, Wybren J.

Subjects
FLUORESCENCE spectroscopy, PHOTOINDUCED electron transfer, AZURINS, PSEUDOMONAS aeruginosa, CONFOCAL microscopy
Abstract

Abstract: Fluorescent labeling of biomacromolecules enjoys increasing popularity for structural, mechanistic, and microscopic investigations. Its success hinges on the ability of the dye to alternate between bright and dark states. Förster resonance energy transfer (FRET) is an important source of fluorescence modulation. Photo‐induced electron transfer (PET) may occur as well, but is often considered only when donor and acceptor are in van der Waals contact. In this study, PET is shown between a label and redox centers in oxidoreductases, which may occur over large distances. In the small blue copper protein azurin, labeled with ATTO655, PET is observed when the label is at 18.5 Å, but not when it is at 29.1 Å from the Cu. For CuII, PET from label to Cu occurs at a rate of (4.8±0.3)×104 s−1 and back at (0.7±0.1)×103 s−1. With CuI the numbers are (3.3±0.7)×106 s−1 and (1.0±0.1)×104 s−1. Reorganization energies and electronic coupling elements are in the range of 0.8–1.2 eV and 0.02–0.5 cm−1, respectively. These data are compatible with electron transfer (ET) along a through‐bond pathway although transient complex formation followed by ET cannot be ruled out. The outcome of this study is a useful guideline for experimental designs in which oxidoreductases are labelled with fluorescent dyes, with particular attention to single molecule investigations. The labelling position for FRET can be optimized to avoid reactions like PET by evaluating the structure and thermodynamics of protein and label. [ABSTRACT FROM AUTHOR]

Published
2018
Full Text
View/download PDF

34. An investigation into the photochemistry of, and the electrochemically induced CO-loss from, [(CO)5MC(OMe)Me](M = Cr or W) using low-temperature matrix isolation, picosecond infrared spectroscopy, cyclic voltammetry, and time-dependent density functional theory

Author

McMahon, Suzanne, primary, Amirjalayer, Saeed, additional, Buma, Wybren J., additional, Halpin, Yvonne, additional, Long, Conor, additional, Rooney, A. Denise, additional, Woutersen, Sander, additional, and Pryce, Mary T., additional

Published
2015
Full Text
View/download PDF

41. Critical Landau Velocity in Helium Nanodroplets

Author

Brauer, Nils B., primary, Smolarek, Szymon, additional, Loginov, Evgeniy, additional, Mateo, David, additional, Hernando, Alberto, additional, Pi, Marti, additional, Barranco, Manuel, additional, Buma, Wybren J., additional, and Drabbels, Marcel, additional

Published
2013
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results