Somes K. Das - Academia.edu (original) (raw)
Papers by Somes K. Das
nano-channel labeled with sequence specific fluorescent probes
Bulletin of the Chemical Society of Japan, 1997
Journal of the Chemical Society Faraday Transactions, Jan 7, 1998
ABSTRACT
The Journal of Physical Chemistry C, 2015
The emissive properties of both doped and nondoped graphene quantum dots (GQDs) with sizes rangin... more The emissive properties of both doped and nondoped graphene quantum dots (GQDs) with sizes ranging from 3 to 11 nm were analyzed at the single particle level. Both doped and nondoped GQDs are a composite of particles exhibiting green, red, or NIR fluorescence on excitation at 488, 561, and 640 nm, respectively. Nitrogen-doped GQDs (N-GQDs) with diameters ranging from 3.4 to 5.2 nm show a larger proportion of particles with NIR emission as compared to nondoped particles. Doping of GQDs also resulted in changes in the photostability and the fluorescence intermittency seen in single GQD particles. While milliseconds to seconds time scale blinking was regularly observed for red-emitting nondoped GQDs, nitrogen doping significantly reduced blinking. Both doped and nondoped particles also exhibit moderate size dependent photophysical properties.
Journal of the Chemical Society, Perkin Transactions 2, 1998
The absorption, fluorescence and fluorescence excitation spectra of 2-(2′-methoxyphenyl)-3H-imida... more The absorption, fluorescence and fluorescence excitation spectra of 2-(2′-methoxyphenyl)-3H-imidazo[4,5-b]pyridine (2-MPIP) have been studied in five different solvents and at different acid–base concentrations. Semi-empirical quantum mechanical calculations have been carried out to supplement the experimental results. Spectral characteristics of 2-MPIP in different solvents and semi-empirical quantum mechanical calculations suggest the presence of both a-1 and b-1 isomers. The observation of a single exponential decay and one lifetime suggests an equilibrium between the isomers. Out of five monocations two kinds of monocations (MC’s) are possible, one from protonation of N1 (MC1) and the second from protonation of N4 (MC2) atoms. Spectral characteristics and semi-empirical calculations carried out on MC’s neglect the presence of isomer b-1. Only one kind of dication and one kind of monoanion are formed by protonating both the nitrogen atoms (N1 and N4) and deprotonating the >NH atom respectively. pKa and pKa* values for the various prototropic reactions are determined and discussed.
Photosynthesis research, 2005
Chlorosomes are the light-harvesting organelles in photosynthetic green bacteria and typically co... more Chlorosomes are the light-harvesting organelles in photosynthetic green bacteria and typically contain large amounts of bacteriochlorophyll (BChl) c in addition to smaller amounts of BChl a, carotenoids, and several protein species. We have isolated vestigial chlorosomes, denoted carotenosomes, from a BChl c-less, bchK mutant of the green sulfur bacterium Chlorobium tepidum. The physical shape of the carotenosomes (86 +/- 17 nm x 66 +/- 13 nm x 4.3 +/- 0.8 nm on average) was reminiscent of a flattened chlorosome. The carotenosomes contained carotenoids, BChl a, and the proteins CsmA and CsmD in ratios to each other comparable to their ratios in wild-type chlorosomes, but all other chlorosome proteins normally found in wild-type chlorosomes were found only in trace amounts or were not detected. Similar to wild-type chlorosomes, the CsmA protein in the carotenosomes formed oligomers at least up to homo-octamers as shown by chemical cross-linking and immunoblotting. The absorption spec...
Nano Letters, 2014
Fluorescent carbon nanodots (CNDs) were synthesized in oxidized and reduced forms and were analyz... more Fluorescent carbon nanodots (CNDs) were synthesized in oxidized and reduced forms and were analyzed at the single-particle level. Images of single CNDs at different excitation energies revealed significant heterogeneity in the lower energy trap sites between particles. We observed that a high percentage of reduced CND particles transitioned between multiple fluorescence intensity levels indicative of multichromophoric systems. Despite this behavior, individual CNDs exhibit single-step photobleaching and transient blinking to the background level suggesting single-molecule behavior.
Journal of Colloid and Interface Science, 1998
Spectral characteristics and prototropic reactions of 2-(2-hydroxyphenyl)benzimidazole (HPBI) in ... more Spectral characteristics and prototropic reactions of 2-(2-hydroxyphenyl)benzimidazole (HPBI) in Tween-20, Tween-40, Tween-60, Tween-80, and dioxane-water mixtures of different compositions have been studied. Comparison of the fluorescence band maxima of the tautomer band in nonionic micelles with the correlation diagram, drawn between the fluorescence band maxima and the dielectric constants of the dioxane-water mixtures, have shown that the effective dielectric constant (⑀ eff) at the binding site of HPBI is 18 ؎ 2 for all the Tweens. Fluorescence lifetimes (f) and fluorescence quantum yields (fl) have shown that the hydrophobicity of these micelles is maximum for Tween-80 and at a minimum for Tween-20. Similar results have also been observed from the pK a values for the deprotonation of HPBI, whereas the protonation reaction of HPBI occurs at the site in nonionic micelles which is more hydrophilic than that where the deprotonation reaction takes place. The protonation reaction in 2-(2-methoxyphenyl)benzimidazole (MPBI) has shown that the value of ⑀ eff in Tweens where this reaction occurs is less hydrophobic than the site where the same reaction occurs in HPBI.
Biochemistry, 2001
The steady state absorption and fluorescence spectroscopic properties of the xanthophylls, violax... more The steady state absorption and fluorescence spectroscopic properties of the xanthophylls, violaxanthin, zeaxanthin, and lutein, and the efficiencies of singlet energy transfer from the individual xanthophylls to chlorophyll have been investigated in recombinant CP26 protein overexpressed in Escherichia coli and then refolded in vitro with purified pigments. Also, the effect of the different xanthophylls on the extents of static and dynamic quenching of chlorophyll fluorescence has been investigated. Absorption, fluorescence, and fluorescence excitation demonstrate that the efficiency of light harvesting from the xanthophylls to chlorophyll a is relatively high and insensitive to the particular xanthophyll that is present. A small effect of the different xanthophylls is observed on the extent of quenching of Chl fluorescence. The data provide the precise wavelengths of the absorption and fluorescence features of the bound pigments in the highly congested spectral profiles from these light-harvesting complexes. This information is important in assessing the mechanisms by which higher plants dissipate excess energy in light-harvesting proteins.
Biochemistry, 2002
Absorption, fluorescence, and fluorescence excitation spectra have been measured from CP26, CP29,... more Absorption, fluorescence, and fluorescence excitation spectra have been measured from CP26, CP29, and monomeric and trimeric LHCIIb light-harvesting complexes isolated from Photosystem II subchloroplast particles from spinach. The complexes were purified using a combination of isoelectric focusing and sucrose gradient ultracentrifugation. The chlorophyll (Chl) and xanthophyll pigment compositions were measured using high-performance liquid chromatography (HPLC). Using the pigment compositions from the HPLC analysis as a starting point, the absorption spectral profiles of the complexes have been reconstructed from the individual absorption spectra obtained for each of the pigments. Also, the fluorescence excitation spectra of the complexes have been deconvoluted. The data reveal the energy transfer efficiencies between Chl b and Chl a and between specific xanthophylls and Chl a in the complexes. The spectral analyses reveal the underlying features of the highly congested spectral profiles associated with the complexes and are expected to be beneficial to researchers employing spectroscopic methods to investigate the mechanisms of energy transfer between the pigments bound in these complexes.
Nucleic Acids Research, 2010
Nature Biotechnology, 2012
Journal of the American Chemical Society, 2003
Thin film voltammetry was used to obtain direct, reversible, electron transfer between electrodes... more Thin film voltammetry was used to obtain direct, reversible, electron transfer between electrodes and spinach Photosystem I reaction center (PS I) in lipid films for the first time. This reaction center (RC) protein retains its native conformation in the films, and AFM showed that film structure rearranges during the first several minutes of rehydration of the film. Two well-defined chemically reversible reduction-oxidation peaks were observed for native PS I in the dimyristoylphosphatidylcholine films, and were assigned to phylloquinone, A1 (Em)-0.54 V) and iron-sulfur clusters, FA/FB (Em)-0.19 V) by comparisons with PS I samples selectively depleted of these cofactors. Observed Em values may be influenced by protein-lipid interactions and electrode double-layer effects. Voltammetry was consistent with simple kinetically limited electron transfers, and analysis of reduction-oxidation peak separations gave electrochemical rate constants of 7.2 s-1 for A1 and 65 s-1 for FA/FB. A catalytic process was observed in which electrons were injected from PS I in films to ferredoxin in solution, mimicking in vivo electron shuttle from the terminal FA/FB cofactors to soluble ferredoxin during photosynthesis.
![Research paper thumbnail of Inclusion complexation of 2-(4′-N,N-dimethylaminophenyl)-1H-naphth[2,3-d]imidazole by β-cyclodextrin: effect on the twisted intramolecular charge transfer emission](https://attachments.academia-assets.com/72704408/thumbnails/1.jpg)
](Chemical Physics Letters, 2002
Spectral characteristics of 2-(4 0-N; N-dimethylaminophenyl)-1H-naphth[2,3-d] imidazole (DMAPNI) ... more Spectral characteristics of 2-(4 0-N; N-dimethylaminophenyl)-1H-naphth[2,3-d] imidazole (DMAPNI) have been studied in aqueous b-cyclodextrin (b-CDx) solution. Enhancement in the fluorescence intensity of the normal band (B) is more than that of the twisted intramolecular charge transfer (TICT) band (A). pK a value for the protonation of @NA atom and the blue shifts observed in both the fluorescence bands suggest the encapsulation of DMAPNI in the hydrophobic cavity of b-CDx. Steady state and time resolved spectral analysis support the formation 1:2 complex between DMAPNI and b-CDx. Enhancement in the fluorescence intensity in aqueous b-CDx solution is due to the decrease in the non-radiative processes.
Biophysical Journal, 2008
Experimental determination of the free energy (DG) stabilizing the structure of membrane proteins... more Experimental determination of the free energy (DG) stabilizing the structure of membrane proteins (MPs) in their native environment has been hampered by the aggregation and precipitation of MPs outside the lipid bilayer. We recently demonstrated that the latter process can be prevented by the use of fluorinated surfactants, FTACs, that act as chaperones for MP insertion without partitioning in the membrane themselves. Here we combine the advantages of the chaperone-like ability of FTACs with the sensitivity of fluorescence correlation spectroscopy measurements to determine DG of bilayer insertion of model MPs. First, we calibrate our approach by examining the effects of chaperoned insertion on DG of transmembrane insertion of Annexin B12. We find that a shorter-chained surfactant, FTAC-C6, for which the working concentration range of 0.05-0.2 mM falls below CMC ¼ 0.33 mM, has a mild effect on an apparent DG. In contrast, additions of a longer-chained FTAC-C8 (CMC ¼ 0.03 mM) result in a steep and nonlinear concentration dependence of DG. We then apply the same methodology to the pH-triggered insertion of diphtheria toxin T-domain, which is known to be affected by nonproductive aggregation in solution. We find that the correction of the DG value needed to compensate for unchaperoned insertion of the T-domain exceeds 3 kcal/mole. A relatively shallow and linear dependence of the DG for Annexin B12 and T-domain insertion on FTAC-C6 concentration is encouraging for future applications of this surfactant in thermodynamic studies of the stability of other MPs.
Chemical Physics, 2011
Excited-state intramolecular proton transfer (ESIPT) reaction has been studied in a molecule show... more Excited-state intramolecular proton transfer (ESIPT) reaction has been studied in a molecule showing dual fluorescence, the 2,5-bis(2-benzoxazolyl)-4-methoxyphenol (BBMP), and its isotopomers, where the methoxy, and alternatively, the OH group has been deuterated. Attention is focused on the influence of electron donating OCH3 substituent on fast excited state reaction. Comparison between the resonance-enhanced multiphoton ionization spectrum and the laser-induced excitation of
nano-channel labeled with sequence specific fluorescent probes
Bulletin of the Chemical Society of Japan, 1997
Journal of the Chemical Society Faraday Transactions, Jan 7, 1998
ABSTRACT
The Journal of Physical Chemistry C, 2015
The emissive properties of both doped and nondoped graphene quantum dots (GQDs) with sizes rangin... more The emissive properties of both doped and nondoped graphene quantum dots (GQDs) with sizes ranging from 3 to 11 nm were analyzed at the single particle level. Both doped and nondoped GQDs are a composite of particles exhibiting green, red, or NIR fluorescence on excitation at 488, 561, and 640 nm, respectively. Nitrogen-doped GQDs (N-GQDs) with diameters ranging from 3.4 to 5.2 nm show a larger proportion of particles with NIR emission as compared to nondoped particles. Doping of GQDs also resulted in changes in the photostability and the fluorescence intermittency seen in single GQD particles. While milliseconds to seconds time scale blinking was regularly observed for red-emitting nondoped GQDs, nitrogen doping significantly reduced blinking. Both doped and nondoped particles also exhibit moderate size dependent photophysical properties.
Journal of the Chemical Society, Perkin Transactions 2, 1998
The absorption, fluorescence and fluorescence excitation spectra of 2-(2′-methoxyphenyl)-3H-imida... more The absorption, fluorescence and fluorescence excitation spectra of 2-(2′-methoxyphenyl)-3H-imidazo[4,5-b]pyridine (2-MPIP) have been studied in five different solvents and at different acid–base concentrations. Semi-empirical quantum mechanical calculations have been carried out to supplement the experimental results. Spectral characteristics of 2-MPIP in different solvents and semi-empirical quantum mechanical calculations suggest the presence of both a-1 and b-1 isomers. The observation of a single exponential decay and one lifetime suggests an equilibrium between the isomers. Out of five monocations two kinds of monocations (MC’s) are possible, one from protonation of N1 (MC1) and the second from protonation of N4 (MC2) atoms. Spectral characteristics and semi-empirical calculations carried out on MC’s neglect the presence of isomer b-1. Only one kind of dication and one kind of monoanion are formed by protonating both the nitrogen atoms (N1 and N4) and deprotonating the >NH atom respectively. pKa and pKa* values for the various prototropic reactions are determined and discussed.
Photosynthesis research, 2005
Chlorosomes are the light-harvesting organelles in photosynthetic green bacteria and typically co... more Chlorosomes are the light-harvesting organelles in photosynthetic green bacteria and typically contain large amounts of bacteriochlorophyll (BChl) c in addition to smaller amounts of BChl a, carotenoids, and several protein species. We have isolated vestigial chlorosomes, denoted carotenosomes, from a BChl c-less, bchK mutant of the green sulfur bacterium Chlorobium tepidum. The physical shape of the carotenosomes (86 +/- 17 nm x 66 +/- 13 nm x 4.3 +/- 0.8 nm on average) was reminiscent of a flattened chlorosome. The carotenosomes contained carotenoids, BChl a, and the proteins CsmA and CsmD in ratios to each other comparable to their ratios in wild-type chlorosomes, but all other chlorosome proteins normally found in wild-type chlorosomes were found only in trace amounts or were not detected. Similar to wild-type chlorosomes, the CsmA protein in the carotenosomes formed oligomers at least up to homo-octamers as shown by chemical cross-linking and immunoblotting. The absorption spec...
Nano Letters, 2014
Fluorescent carbon nanodots (CNDs) were synthesized in oxidized and reduced forms and were analyz... more Fluorescent carbon nanodots (CNDs) were synthesized in oxidized and reduced forms and were analyzed at the single-particle level. Images of single CNDs at different excitation energies revealed significant heterogeneity in the lower energy trap sites between particles. We observed that a high percentage of reduced CND particles transitioned between multiple fluorescence intensity levels indicative of multichromophoric systems. Despite this behavior, individual CNDs exhibit single-step photobleaching and transient blinking to the background level suggesting single-molecule behavior.
Journal of Colloid and Interface Science, 1998
Spectral characteristics and prototropic reactions of 2-(2-hydroxyphenyl)benzimidazole (HPBI) in ... more Spectral characteristics and prototropic reactions of 2-(2-hydroxyphenyl)benzimidazole (HPBI) in Tween-20, Tween-40, Tween-60, Tween-80, and dioxane-water mixtures of different compositions have been studied. Comparison of the fluorescence band maxima of the tautomer band in nonionic micelles with the correlation diagram, drawn between the fluorescence band maxima and the dielectric constants of the dioxane-water mixtures, have shown that the effective dielectric constant (⑀ eff) at the binding site of HPBI is 18 ؎ 2 for all the Tweens. Fluorescence lifetimes (f) and fluorescence quantum yields (fl) have shown that the hydrophobicity of these micelles is maximum for Tween-80 and at a minimum for Tween-20. Similar results have also been observed from the pK a values for the deprotonation of HPBI, whereas the protonation reaction of HPBI occurs at the site in nonionic micelles which is more hydrophilic than that where the deprotonation reaction takes place. The protonation reaction in 2-(2-methoxyphenyl)benzimidazole (MPBI) has shown that the value of ⑀ eff in Tweens where this reaction occurs is less hydrophobic than the site where the same reaction occurs in HPBI.
Biochemistry, 2001
The steady state absorption and fluorescence spectroscopic properties of the xanthophylls, violax... more The steady state absorption and fluorescence spectroscopic properties of the xanthophylls, violaxanthin, zeaxanthin, and lutein, and the efficiencies of singlet energy transfer from the individual xanthophylls to chlorophyll have been investigated in recombinant CP26 protein overexpressed in Escherichia coli and then refolded in vitro with purified pigments. Also, the effect of the different xanthophylls on the extents of static and dynamic quenching of chlorophyll fluorescence has been investigated. Absorption, fluorescence, and fluorescence excitation demonstrate that the efficiency of light harvesting from the xanthophylls to chlorophyll a is relatively high and insensitive to the particular xanthophyll that is present. A small effect of the different xanthophylls is observed on the extent of quenching of Chl fluorescence. The data provide the precise wavelengths of the absorption and fluorescence features of the bound pigments in the highly congested spectral profiles from these light-harvesting complexes. This information is important in assessing the mechanisms by which higher plants dissipate excess energy in light-harvesting proteins.
Biochemistry, 2002
Absorption, fluorescence, and fluorescence excitation spectra have been measured from CP26, CP29,... more Absorption, fluorescence, and fluorescence excitation spectra have been measured from CP26, CP29, and monomeric and trimeric LHCIIb light-harvesting complexes isolated from Photosystem II subchloroplast particles from spinach. The complexes were purified using a combination of isoelectric focusing and sucrose gradient ultracentrifugation. The chlorophyll (Chl) and xanthophyll pigment compositions were measured using high-performance liquid chromatography (HPLC). Using the pigment compositions from the HPLC analysis as a starting point, the absorption spectral profiles of the complexes have been reconstructed from the individual absorption spectra obtained for each of the pigments. Also, the fluorescence excitation spectra of the complexes have been deconvoluted. The data reveal the energy transfer efficiencies between Chl b and Chl a and between specific xanthophylls and Chl a in the complexes. The spectral analyses reveal the underlying features of the highly congested spectral profiles associated with the complexes and are expected to be beneficial to researchers employing spectroscopic methods to investigate the mechanisms of energy transfer between the pigments bound in these complexes.
Nucleic Acids Research, 2010
Nature Biotechnology, 2012
Journal of the American Chemical Society, 2003
Thin film voltammetry was used to obtain direct, reversible, electron transfer between electrodes... more Thin film voltammetry was used to obtain direct, reversible, electron transfer between electrodes and spinach Photosystem I reaction center (PS I) in lipid films for the first time. This reaction center (RC) protein retains its native conformation in the films, and AFM showed that film structure rearranges during the first several minutes of rehydration of the film. Two well-defined chemically reversible reduction-oxidation peaks were observed for native PS I in the dimyristoylphosphatidylcholine films, and were assigned to phylloquinone, A1 (Em)-0.54 V) and iron-sulfur clusters, FA/FB (Em)-0.19 V) by comparisons with PS I samples selectively depleted of these cofactors. Observed Em values may be influenced by protein-lipid interactions and electrode double-layer effects. Voltammetry was consistent with simple kinetically limited electron transfers, and analysis of reduction-oxidation peak separations gave electrochemical rate constants of 7.2 s-1 for A1 and 65 s-1 for FA/FB. A catalytic process was observed in which electrons were injected from PS I in films to ferredoxin in solution, mimicking in vivo electron shuttle from the terminal FA/FB cofactors to soluble ferredoxin during photosynthesis.
Chemical Physics Letters, 2002
Spectral characteristics of 2-(4 0-N; N-dimethylaminophenyl)-1H-naphth[2,3-d] imidazole (DMAPNI) ... more Spectral characteristics of 2-(4 0-N; N-dimethylaminophenyl)-1H-naphth[2,3-d] imidazole (DMAPNI) have been studied in aqueous b-cyclodextrin (b-CDx) solution. Enhancement in the fluorescence intensity of the normal band (B) is more than that of the twisted intramolecular charge transfer (TICT) band (A). pK a value for the protonation of @NA atom and the blue shifts observed in both the fluorescence bands suggest the encapsulation of DMAPNI in the hydrophobic cavity of b-CDx. Steady state and time resolved spectral analysis support the formation 1:2 complex between DMAPNI and b-CDx. Enhancement in the fluorescence intensity in aqueous b-CDx solution is due to the decrease in the non-radiative processes.
Biophysical Journal, 2008
Experimental determination of the free energy (DG) stabilizing the structure of membrane proteins... more Experimental determination of the free energy (DG) stabilizing the structure of membrane proteins (MPs) in their native environment has been hampered by the aggregation and precipitation of MPs outside the lipid bilayer. We recently demonstrated that the latter process can be prevented by the use of fluorinated surfactants, FTACs, that act as chaperones for MP insertion without partitioning in the membrane themselves. Here we combine the advantages of the chaperone-like ability of FTACs with the sensitivity of fluorescence correlation spectroscopy measurements to determine DG of bilayer insertion of model MPs. First, we calibrate our approach by examining the effects of chaperoned insertion on DG of transmembrane insertion of Annexin B12. We find that a shorter-chained surfactant, FTAC-C6, for which the working concentration range of 0.05-0.2 mM falls below CMC ¼ 0.33 mM, has a mild effect on an apparent DG. In contrast, additions of a longer-chained FTAC-C8 (CMC ¼ 0.03 mM) result in a steep and nonlinear concentration dependence of DG. We then apply the same methodology to the pH-triggered insertion of diphtheria toxin T-domain, which is known to be affected by nonproductive aggregation in solution. We find that the correction of the DG value needed to compensate for unchaperoned insertion of the T-domain exceeds 3 kcal/mole. A relatively shallow and linear dependence of the DG for Annexin B12 and T-domain insertion on FTAC-C6 concentration is encouraging for future applications of this surfactant in thermodynamic studies of the stability of other MPs.
Chemical Physics, 2011
Excited-state intramolecular proton transfer (ESIPT) reaction has been studied in a molecule show... more Excited-state intramolecular proton transfer (ESIPT) reaction has been studied in a molecule showing dual fluorescence, the 2,5-bis(2-benzoxazolyl)-4-methoxyphenol (BBMP), and its isotopomers, where the methoxy, and alternatively, the OH group has been deuterated. Attention is focused on the influence of electron donating OCH3 substituent on fast excited state reaction. Comparison between the resonance-enhanced multiphoton ionization spectrum and the laser-induced excitation of