Sourav Saha - Academia.edu (original) (raw)
Papers by Sourav Saha
Engineering with Computers
The advent of Cloud Computing has opened up newer avenues for business. Traditional industry vert... more The advent of Cloud Computing has opened up newer avenues for business. Traditional industry verticals like the healthcare are yet to reap the benefits of such cutting-edge technology in India. In an age of collaboration over virtual medium, the lack of coordination and an effective communication mechanism is creating information “silos” that are not propagated at other levels. In this paper we briefly discuss the state of Health Information Management Systems (HIMS) in India, the challenges faced en-route deployment of the solution. We then introduce some interesting aspects of cloud computing to show that how a cloudbased system can help reduce the technical barriers to HIMS acceptance and endorsement. Our contribution lies in addressing issues for HIMS deployment in an Indian scenario and arguing for a cutting-edge technology like Cloud Computing as an agent of change.
DNA Repair, 2020
Topoisomerases are essential enzymes solving DNA topological problems such as supercoils, knots a... more Topoisomerases are essential enzymes solving DNA topological problems such as supercoils, knots and catenanes that arise from replication, transcription, chromatin remodeling and other nucleic acid metabolic processes. They are also the targets of widely used anticancer drugs (e.g. topotecan, irinotecan, enhertu, etoposide, doxorubicin, mitoxantrone) and fluoroquinolone antibiotics (e.g. ciprofloxacin and levofloxacin). Topoisomerases manipulate DNA topology by cleaving one DNA strand (TOP1 and TOP3 enzymes) or both in concert (TOP2 enzymes) through the formation of transient enzyme-DNA cleavage complexes (TOPcc) with phosphotyrosyl linkages between DNA ends and the catalytic tyrosyl residue of the enzymes. Failure in the selfresealing of TOPcc results in persistent TOPcc that threaten genome integrity and lead to cancers and neurodegenerative diseases. The cell prevents the accumulation of topoisomerase-mediated DNA damage by excising the topoisomerase DNA-protein crosslinks (TOP-DPC) and ligating the associated breaks using multiple pathways conserved in eukaryotes. Tyrosyl-DNA phosphodiesterase (TDP1 and TDP2) cleave the tyrosyl-DNA bonds whereas structure-specific endonucleases such as Mre11 and XPF (Rad1) incise the DNA phosphodiester backbone to remove the TOP-DPC along with the adjacent DNA segment. The proteasome and metalloproteases of the WSS1/Spartan family typify proteolytic repair pathways that debulk TOP-DPC to make the peptide-DNA bonds accessible to the TDPs and endonucleases. The purpose of this review is to summarize our current understanding of how the cell excises TOP-DPC and why, when and where the cell recruits one specific mechanism for repairing topoisomerase-mediated DNA damage, acquiring resistance to therapeutic topoisomerase inhibitors and avoiding genomic instability, cancers and neurodegenerative diseases.
Antimicrobial Agents and Chemotherapy, 2016
Visceral leishmaniasis is a fatal parasitic disease, and there is an emergent need for developmen... more Visceral leishmaniasis is a fatal parasitic disease, and there is an emergent need for development of effective drugs against this neglected tropical disease. We report here the development of a novel spirooxindole derivative, N -benzyl-2,2′α-3,3′,5′,6′,7′,7α,α′-octahydro-2methoxycarbonyl-spiro[indole-3,3′-pyrrolizidine]-2-one (compound 4c), which inhibits Leishmania donovani topoisomerase IB (LdTopIB) and kills the wild type as well as drug-resistant parasite strains. This compound inhibits catalytic activity of LdTopIB in a competitive manner. Unlike camptothecin (CPT), the compound does not stabilize the DNA-topoisomerase IB cleavage complex; rather, it hinders drug-DNA-enzyme covalent complex formation. Fluorescence studies show that the stoichiometry of this compound binding to LdTopIB is 2:1 (mole/mole), with a dissociation constant of 6.65 μM. Molecular docking with LdTopIB using the stereoisomers of compound 4c produced two probable hits for the binding site, one in the smal...
P (proportional), PI (proportional-integral), and PID (proportional-integral-derivative) controll... more P (proportional), PI (proportional-integral), and PID (proportional-integral-derivative) controllers are popular means of controlling industrial processes. Due to superior response, accuracy, and stable performance, PID controllers are mostly used in control systems. This paper presents a mathematical model and subsequent response analysis regarding regulation of flow in mixed convection through a T-shaped open cavity by temperature dependent controllers. The T-shaped cavity has cold top and hot bottom walls, while air is flowing through the inlet at surrounding temperature. The inflow is regulated by a controlled gate which operates according to the signal received from the controller. Values of proportional gain (kp), integral gain (ki), and derivative gain (kd) are varied to obtain the desired system response and to ensure a stable system with fastest response. At first, only P controller is used and eventually PI and finally PID control scheme is applied for controller tuning. Tuning of different cont...
2015 28th International Conference on VLSI Design, 2015
A new power optimization perspective based on constraint based library access in physical synthes... more A new power optimization perspective based on constraint based library access in physical synthesis is presented in this paper. Power constraints are modelled and applied at the terminals of designs or sub designs based on relative power criticality of terminals. These constraints are then used in Physical Synthesis to selectively mask or expose different drive strength or threshold voltage variants of a given cell type. This constrained library access approach is compared with regular library access approach using a state-of-the-art power optimization engine. Experimental data shows it is possible to claim additional power savings in proposed approach with no or minimal performance impact. Also, it is possible to modulate this methodology to have selective focus on dynamic or leakage power if necessary.
Lecture Notes in Computer Science, 2002
This paper reports a Cellular Automata Machine (CAM) as a general purpose pattern recognizer. The... more This paper reports a Cellular Automata Machine (CAM) as a general purpose pattern recognizer. The CAM is designed around a general class of CA known as Generalized Multiple Attractor Cellular Automata (GM ACA). Experimental results confirm that the sparse network of CAM is more powerful than conventional dense network of Hopfield Net for memorizing unbiased patterns.
2007 2nd International Conference on Communication Systems Software and Middleware, 2007
based location management are critically analyzed to detect their advantages and future developme... more based location management are critically analyzed to detect their advantages and future development scopes. Then we Locating mobile nodes and delivery of inward calls to that node in selective paging"
ChemInform, 2007
Richard Feynman [1], in his seminal lecture in 1959, noted that I can hardly doubt that when we ... more Richard Feynman [1], in his seminal lecture in 1959, noted that I can hardly doubt that when we have some control of the arrangement of the things on a mo-lecular scale, we will get an enormously greater range of possible properties that substances can have and of ...
Supramolecular Chemistry, 2014
ABSTRACT Dipyridyl-naphthalenediimide (DPNDI) ligand has been employed to construct a dumbbell-sh... more ABSTRACT Dipyridyl-naphthalenediimide (DPNDI) ligand has been employed to construct a dumbbell-shaped Zn(II)–DPNDI–Zn(II) complex (1) comprised of two solvent-capped trigonal bipyramidal Zn(II) ions and a linear [Zn(II)/DPNDI]n coordination polymer (2) in which octahedral Zn(II) centres are threaded by axially coordinated DPNDI ligands. X-ray crystal structures of these complexes reveal that charge-diffused [Inline formula] counterions bind with the π-acidic DPNDI ligands through anion–π and CH···anion interactions, which in turn play an important role in crystal packing. These insights could be exploited for the sequestration of soft anions through complementary soft–soft interactions with hydrophobic, yet polarisable receptors.
Organic Letters, 2008
A [2]catenane, composed of a pi-electron-rich bis-1,5-dioxynaphthalene[38]crown10 (BDNP38C10) rin... more A [2]catenane, composed of a pi-electron-rich bis-1,5-dioxynaphthalene[38]crown10 (BDNP38C10) ring, mechanically interlocked with a large macrocycle containing two disubstituted tetraarylmethane "speed bumps" and two different pi-electron-deficient units--namely, naphthalene dimide (NpI) and bipyridinium (BIPY(2+)) units--has been synthesized from a [2]rotaxane, containing the former recognition unit, after performing two sequential Cu(I)-catalyzed azide-alkyne cycloadditions with a linker containing the latter recognition unit. The product, which exists as a single co-conformer, wherein the BDNP38C10 ring encircles the NpI unit, undergoes equilibration to give approximately equal amounts of the other co-conformer in which the BDNP38C10 ring encircles the BIPY(2+) unit.
Journal of the American Chemical Society, 2012
The recent emergence of anion−π interactions has added a new dimension to supramolecular chemistr... more The recent emergence of anion−π interactions has added a new dimension to supramolecular chemistry of anions. Yet, after a decade since its inception, actual mechanisms of anion−π interactions remain highly debated. To elicit a complete and accurate understanding of how different anions interact with π-electron-deficient 1,4,5,8-naphthalenediimides (NDIs) under different conditions, we have extensively studied these interactions using powerful experimental techniques. Herein, we demonstrate that, depending on the electron-donating abilities (Lewis basicity) of anions and electron-accepting abilities (π-acidity) of NDIs, modes of anion−NDI interactions vary from extremely weak non-chromogenic anion−π interactions to chromogenic anion-induced charge-transfer (CT) and electron-transfer (ET) phenomena. In aprotic solvents, electron-donating abilities of anions generally follow their Lewis basicity order, whereas π-acidity of NDIs can be fine-tuned by installing different electron-rich and electron-deficient substituents. While strongly Lewis basic anions (OH − and F −) undergo thermal ET with most NDIs, generating NDI •− radical anions and NDI 2− dianions in aprotic solvents, weaker Lewis bases (AcO − , H 2 PO 4 − , Cl − , etc.) often require the photoexcitation of moderately π-acidic NDIs to generate the corresponding NDI •− radical anions via photoinduced ET (PET). Poorly Lewis basic I − does not participate in thermal ET or PET with most NDIs (except with strongly π-acidic core-substituted dicyano-NDI) but forms anion/NDI CT or anion−π complexes. We have looked for experimental evidence that could indicate alternative mechanisms, such as a Meisenheimer complex or CH•••anion hydrogen-bond formation, but none was found to support these possibilities.
Journal of the American Chemical Society, 2007
Redox-controllable molecular nanovalves based on mesoporous silica nanoparticles have been fabric... more Redox-controllable molecular nanovalves based on mesoporous silica nanoparticles have been fabricated, using two bistable [2]rotaxanes with different spacer lengths between their recognition sites as the gatekeepers. Three different linkers with varying chain lengths have been employed to attach the bistable [2]rotaxane molecules covalently to the silica substrate. These nanovalves can be classified as having IN or OUT locations, based on the positions of the tethered bistable [2]rotaxanes with respect to the entrances to the nanopores. The nanovalves are more efficient when the bistable [2]rotaxane-based gatekeepers are anchored deep within (IN) the pores than when they are attached closer to (OUT) the pores' orifices. The silica nanopores can be closed and opened by moving the mechanically interlocked ring component of the bistable [2]rotaxane closer to and away from the pores' orifices, respectively, a process which allows luminescent probe molecules, such as coumarins, tris(2-phenylpyridine)iridium, and rhodamine B, to be loaded into or released from the mesoporous silica substrate on demand. The lengths of the linkers between the surface and the rotaxane molecules also play a critical role in determining the effectiveness of the nanovalves. The shorter the linkers, the less leaky are the nanovalves. However, the distance between the recognition units on the rod section of the rotaxane molecules does not have any significant influence on the nanovalves' leakiness. The controlled release of the probe molecules was investigated by measuring their luminescence intensities in response to ascorbic acid, which induces the ring's movement away from the pores' orifices, and consequently opens the nanovalves.
Journal of the American Chemical Society, 2007
A multicomponent [2]rotaxane designed to operate as a molecular shuttle driven by light energy ha... more A multicomponent [2]rotaxane designed to operate as a molecular shuttle driven by light energy has been constructed, and its properties have been investigated. The system is composed of (1) a lightfueled power station, capable of using the photon energy to create a charge-separated state, and (2) a mechanical switch, capable of utilizing such a photochemically generated driving force to bring about controllable molecular shuttling motions. The light-fueled power station is, in turn, a dyad comprising (i) a π-electron-accepting fullerene (C 60) component and (ii) a light-harvesting porphyrin (P) unit which acts as an electron donor in the excited state. The mechanical switch is a redox-active bistable [2]rotaxane moiety that consists of (i) a tetrathiafulvalene (TTF) unit as an efficient π-electron-donor station, (ii) a dioxynaphthalene (DNP) unit as a second π-electron-rich station, and (iii) a tetracationic cyclobis(paraquat-p-phenylene) (CBPQT 4+) π-electron-acceptor cyclophane, which encapsulates the better π-electron-donating TTF station. Diethylene glycol spacers were conveniently introduced between the electroactive components in the dumbbell-shaped thread to facilitate the template-directed synthesis of the [2]rotaxane. A modular synthetic approach was undertaken for the overall synthesis of this multicomponent bistable [2]rotaxane, beginning with the syntheses of the P-C 60 dyad unit and the two-station TTF-DNP-based [2]rotaxane separately, using conventional synthetic methodologies. These two components were finally stitched together by an esterification to afford the target rotaxane. Its structure was characterized by 1 H NMR spectroscopy and mass spectrometry as well as by UV-vis-NIR absorption spectroscopy and voltammetry. The observations reflect remarkable electronic interactions between the various units, pointing to the existence of folded conformations in solution. The redox-driven shuttling process of the CBPQT 4+ ring between the two competitive electron-rich recognition units, namely, TTF and DNP, was investigated by electrochemistry and spectroelectrochemistry as a means to verify its operational behavior prior to the photophysical studies related to light-driven operation. The oxidation process of the TTF unit is dramatically hampered in the rotaxane, thereby reducing the efficiency of the shuttling motion. These results confirm that, as the structural complexity increases, the overall function of the system no longer depends simply on its "primary" structure but also on higher-level effects which are reminiscent of the secondary and tertiary structures of biomolecules.
![Research paper thumbnail of Functionally Rigid Bistable [2]Rotaxanes](https://attachments.academia-assets.com/102428018/thumbnails/1.jpg)
](Journal of the American Chemical Society, 2007
Journal of the American Chemical Society, 2010
We report the discovery of a supramolecular interaction (anion-π and charge/electron transfer, CT... more We report the discovery of a supramolecular interaction (anion-π and charge/electron transfer, CT/ET) involving fluoride ion and π-electron deficient colorless naphthalene diimide (NDI) receptors. Strong electronic interactions between lone-pair electrons of Fion and π*-orbitals of the NDI unit lead to an unprecedented F-fNDI ET event, which produces an orange colored NDI •radical anion. Further reduction of NDI •by another Fion produces a pink colored NDI 2dianion, rendering NDI a colorimetric Fsensor. Preorganization of two NDI units in overlapping positions using folded linkers improves their selectivity and sensitivity for the Fion significantly, allowing Fdetection at nM concentration in 85:15 DMSO/H 2 O solutions.
Journal of Biological Chemistry, 2014
Background: Leishmania donovani adopts several defense mechanisms to become resistant to antileis... more Background: Leishmania donovani adopts several defense mechanisms to become resistant to antileishmanial agents. Results: Laboratory-grown flavone (baicalein)-resistant parasites exhibit efflux of drug by LdABCC2 transporter. Inside the host macrophage, this parasite up-regulates host MRP2 transporter by an Nrf2-dependent pathway. Conclusion: Resistant Leishmania parasite exploits ABC transporter in the parasite and inside the host. Significance: The mechanism of drug resistance in clinical isolates can be probed.
ELECTROPHORESIS, 2004
Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in... more Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions We study the effect of matrix chain molecular weight M w and concentration c on the electrophoretic mobility m of large linear and star-like, branched DNA in polymer solutions. Polyethylene oxide (PEO) with narrow molecular weight distributions form the main focus of this study. For PEO concentrations ranging from one half the overlap concentration, c*, to 3c*, the effective drag coefficient, z m 0 m À 1, satisfies the following approximate scaling relationship, z $ cM 0:7 w. Here, m 0 is the electrophoretic mobility in free solution. While the concentration dependence is consistent with predictions from the transient entanglement coupling (TEC) model, the molecular weight dependence is significantly weaker. Although a similar dependence of mobility on M w can be predicted when nonentangling collisions are the dominant source of drag, a model based on these collisions alone cannot reproduce the experimental observations. We also find that the architecture of large DNA does not affect either the concentration dependence or molecular weight dependence of the electrophoretic mobility.
ELECTROPHORESIS, 2003
Electrophoretic dynamics of large DNA stars in polymer solutions and gels We have developed a pro... more Electrophoretic dynamics of large DNA stars in polymer solutions and gels We have developed a procedure for synthesizing large stable branched DNA structures that enables visualization via fluorescence microscopy. Using this procedure we have synthesized large DNA stars and observed their electrophoretic behavior in polymer solutions and gels. In dilute polyacrylamide solutions, the DNA stars move as random coils and appear to experience only brief collisions with the polymer chains in solution. The effect of polymer solution concentration on the electrophoretic mobility of stars in the dilute regime is found to be in good accord with predictions of the transient entanglement coupling (TEC) model. In semidilute polymer solutions, the star arms extend in the field direction and drag the core through the matrix. The star arms form several U-shaped conformations as they collide and engage with polyacrylamide chains. The U-shaped conformations occasionally evolve into J-shaped conformations as the star arms slide off the matrix chains they engage during electrophoretic migration. In concentrated polymer solutions, the arms of the star extend and form V-shaped structures with the core as the apex. The arms then pull the core through the matrix. These V-shaped conformations are much longer-lived than U-shaped ones and, unlike the latter, do not transform to J-shaped conformations. In polyacrylamide and agarose gels, where matrix entanglements are fixed, DNA stars become trapped when entanglements with matrix molecules prevent the core from being pulled through the matrix by the extended arms. This trapping was observed at all gel concentrations and electric fields studied.
Engineering with Computers
The advent of Cloud Computing has opened up newer avenues for business. Traditional industry vert... more The advent of Cloud Computing has opened up newer avenues for business. Traditional industry verticals like the healthcare are yet to reap the benefits of such cutting-edge technology in India. In an age of collaboration over virtual medium, the lack of coordination and an effective communication mechanism is creating information “silos” that are not propagated at other levels. In this paper we briefly discuss the state of Health Information Management Systems (HIMS) in India, the challenges faced en-route deployment of the solution. We then introduce some interesting aspects of cloud computing to show that how a cloudbased system can help reduce the technical barriers to HIMS acceptance and endorsement. Our contribution lies in addressing issues for HIMS deployment in an Indian scenario and arguing for a cutting-edge technology like Cloud Computing as an agent of change.
DNA Repair, 2020
Topoisomerases are essential enzymes solving DNA topological problems such as supercoils, knots a... more Topoisomerases are essential enzymes solving DNA topological problems such as supercoils, knots and catenanes that arise from replication, transcription, chromatin remodeling and other nucleic acid metabolic processes. They are also the targets of widely used anticancer drugs (e.g. topotecan, irinotecan, enhertu, etoposide, doxorubicin, mitoxantrone) and fluoroquinolone antibiotics (e.g. ciprofloxacin and levofloxacin). Topoisomerases manipulate DNA topology by cleaving one DNA strand (TOP1 and TOP3 enzymes) or both in concert (TOP2 enzymes) through the formation of transient enzyme-DNA cleavage complexes (TOPcc) with phosphotyrosyl linkages between DNA ends and the catalytic tyrosyl residue of the enzymes. Failure in the selfresealing of TOPcc results in persistent TOPcc that threaten genome integrity and lead to cancers and neurodegenerative diseases. The cell prevents the accumulation of topoisomerase-mediated DNA damage by excising the topoisomerase DNA-protein crosslinks (TOP-DPC) and ligating the associated breaks using multiple pathways conserved in eukaryotes. Tyrosyl-DNA phosphodiesterase (TDP1 and TDP2) cleave the tyrosyl-DNA bonds whereas structure-specific endonucleases such as Mre11 and XPF (Rad1) incise the DNA phosphodiester backbone to remove the TOP-DPC along with the adjacent DNA segment. The proteasome and metalloproteases of the WSS1/Spartan family typify proteolytic repair pathways that debulk TOP-DPC to make the peptide-DNA bonds accessible to the TDPs and endonucleases. The purpose of this review is to summarize our current understanding of how the cell excises TOP-DPC and why, when and where the cell recruits one specific mechanism for repairing topoisomerase-mediated DNA damage, acquiring resistance to therapeutic topoisomerase inhibitors and avoiding genomic instability, cancers and neurodegenerative diseases.
Antimicrobial Agents and Chemotherapy, 2016
Visceral leishmaniasis is a fatal parasitic disease, and there is an emergent need for developmen... more Visceral leishmaniasis is a fatal parasitic disease, and there is an emergent need for development of effective drugs against this neglected tropical disease. We report here the development of a novel spirooxindole derivative, N -benzyl-2,2′α-3,3′,5′,6′,7′,7α,α′-octahydro-2methoxycarbonyl-spiro[indole-3,3′-pyrrolizidine]-2-one (compound 4c), which inhibits Leishmania donovani topoisomerase IB (LdTopIB) and kills the wild type as well as drug-resistant parasite strains. This compound inhibits catalytic activity of LdTopIB in a competitive manner. Unlike camptothecin (CPT), the compound does not stabilize the DNA-topoisomerase IB cleavage complex; rather, it hinders drug-DNA-enzyme covalent complex formation. Fluorescence studies show that the stoichiometry of this compound binding to LdTopIB is 2:1 (mole/mole), with a dissociation constant of 6.65 μM. Molecular docking with LdTopIB using the stereoisomers of compound 4c produced two probable hits for the binding site, one in the smal...
P (proportional), PI (proportional-integral), and PID (proportional-integral-derivative) controll... more P (proportional), PI (proportional-integral), and PID (proportional-integral-derivative) controllers are popular means of controlling industrial processes. Due to superior response, accuracy, and stable performance, PID controllers are mostly used in control systems. This paper presents a mathematical model and subsequent response analysis regarding regulation of flow in mixed convection through a T-shaped open cavity by temperature dependent controllers. The T-shaped cavity has cold top and hot bottom walls, while air is flowing through the inlet at surrounding temperature. The inflow is regulated by a controlled gate which operates according to the signal received from the controller. Values of proportional gain (kp), integral gain (ki), and derivative gain (kd) are varied to obtain the desired system response and to ensure a stable system with fastest response. At first, only P controller is used and eventually PI and finally PID control scheme is applied for controller tuning. Tuning of different cont...
2015 28th International Conference on VLSI Design, 2015
A new power optimization perspective based on constraint based library access in physical synthes... more A new power optimization perspective based on constraint based library access in physical synthesis is presented in this paper. Power constraints are modelled and applied at the terminals of designs or sub designs based on relative power criticality of terminals. These constraints are then used in Physical Synthesis to selectively mask or expose different drive strength or threshold voltage variants of a given cell type. This constrained library access approach is compared with regular library access approach using a state-of-the-art power optimization engine. Experimental data shows it is possible to claim additional power savings in proposed approach with no or minimal performance impact. Also, it is possible to modulate this methodology to have selective focus on dynamic or leakage power if necessary.
Lecture Notes in Computer Science, 2002
This paper reports a Cellular Automata Machine (CAM) as a general purpose pattern recognizer. The... more This paper reports a Cellular Automata Machine (CAM) as a general purpose pattern recognizer. The CAM is designed around a general class of CA known as Generalized Multiple Attractor Cellular Automata (GM ACA). Experimental results confirm that the sparse network of CAM is more powerful than conventional dense network of Hopfield Net for memorizing unbiased patterns.
2007 2nd International Conference on Communication Systems Software and Middleware, 2007
based location management are critically analyzed to detect their advantages and future developme... more based location management are critically analyzed to detect their advantages and future development scopes. Then we Locating mobile nodes and delivery of inward calls to that node in selective paging"
ChemInform, 2007
Richard Feynman [1], in his seminal lecture in 1959, noted that I can hardly doubt that when we ... more Richard Feynman [1], in his seminal lecture in 1959, noted that I can hardly doubt that when we have some control of the arrangement of the things on a mo-lecular scale, we will get an enormously greater range of possible properties that substances can have and of ...
Supramolecular Chemistry, 2014
ABSTRACT Dipyridyl-naphthalenediimide (DPNDI) ligand has been employed to construct a dumbbell-sh... more ABSTRACT Dipyridyl-naphthalenediimide (DPNDI) ligand has been employed to construct a dumbbell-shaped Zn(II)–DPNDI–Zn(II) complex (1) comprised of two solvent-capped trigonal bipyramidal Zn(II) ions and a linear [Zn(II)/DPNDI]n coordination polymer (2) in which octahedral Zn(II) centres are threaded by axially coordinated DPNDI ligands. X-ray crystal structures of these complexes reveal that charge-diffused [Inline formula] counterions bind with the π-acidic DPNDI ligands through anion–π and CH···anion interactions, which in turn play an important role in crystal packing. These insights could be exploited for the sequestration of soft anions through complementary soft–soft interactions with hydrophobic, yet polarisable receptors.
Organic Letters, 2008
A [2]catenane, composed of a pi-electron-rich bis-1,5-dioxynaphthalene[38]crown10 (BDNP38C10) rin... more A [2]catenane, composed of a pi-electron-rich bis-1,5-dioxynaphthalene[38]crown10 (BDNP38C10) ring, mechanically interlocked with a large macrocycle containing two disubstituted tetraarylmethane "speed bumps" and two different pi-electron-deficient units--namely, naphthalene dimide (NpI) and bipyridinium (BIPY(2+)) units--has been synthesized from a [2]rotaxane, containing the former recognition unit, after performing two sequential Cu(I)-catalyzed azide-alkyne cycloadditions with a linker containing the latter recognition unit. The product, which exists as a single co-conformer, wherein the BDNP38C10 ring encircles the NpI unit, undergoes equilibration to give approximately equal amounts of the other co-conformer in which the BDNP38C10 ring encircles the BIPY(2+) unit.
Journal of the American Chemical Society, 2012
The recent emergence of anion−π interactions has added a new dimension to supramolecular chemistr... more The recent emergence of anion−π interactions has added a new dimension to supramolecular chemistry of anions. Yet, after a decade since its inception, actual mechanisms of anion−π interactions remain highly debated. To elicit a complete and accurate understanding of how different anions interact with π-electron-deficient 1,4,5,8-naphthalenediimides (NDIs) under different conditions, we have extensively studied these interactions using powerful experimental techniques. Herein, we demonstrate that, depending on the electron-donating abilities (Lewis basicity) of anions and electron-accepting abilities (π-acidity) of NDIs, modes of anion−NDI interactions vary from extremely weak non-chromogenic anion−π interactions to chromogenic anion-induced charge-transfer (CT) and electron-transfer (ET) phenomena. In aprotic solvents, electron-donating abilities of anions generally follow their Lewis basicity order, whereas π-acidity of NDIs can be fine-tuned by installing different electron-rich and electron-deficient substituents. While strongly Lewis basic anions (OH − and F −) undergo thermal ET with most NDIs, generating NDI •− radical anions and NDI 2− dianions in aprotic solvents, weaker Lewis bases (AcO − , H 2 PO 4 − , Cl − , etc.) often require the photoexcitation of moderately π-acidic NDIs to generate the corresponding NDI •− radical anions via photoinduced ET (PET). Poorly Lewis basic I − does not participate in thermal ET or PET with most NDIs (except with strongly π-acidic core-substituted dicyano-NDI) but forms anion/NDI CT or anion−π complexes. We have looked for experimental evidence that could indicate alternative mechanisms, such as a Meisenheimer complex or CH•••anion hydrogen-bond formation, but none was found to support these possibilities.
Journal of the American Chemical Society, 2007
Redox-controllable molecular nanovalves based on mesoporous silica nanoparticles have been fabric... more Redox-controllable molecular nanovalves based on mesoporous silica nanoparticles have been fabricated, using two bistable [2]rotaxanes with different spacer lengths between their recognition sites as the gatekeepers. Three different linkers with varying chain lengths have been employed to attach the bistable [2]rotaxane molecules covalently to the silica substrate. These nanovalves can be classified as having IN or OUT locations, based on the positions of the tethered bistable [2]rotaxanes with respect to the entrances to the nanopores. The nanovalves are more efficient when the bistable [2]rotaxane-based gatekeepers are anchored deep within (IN) the pores than when they are attached closer to (OUT) the pores' orifices. The silica nanopores can be closed and opened by moving the mechanically interlocked ring component of the bistable [2]rotaxane closer to and away from the pores' orifices, respectively, a process which allows luminescent probe molecules, such as coumarins, tris(2-phenylpyridine)iridium, and rhodamine B, to be loaded into or released from the mesoporous silica substrate on demand. The lengths of the linkers between the surface and the rotaxane molecules also play a critical role in determining the effectiveness of the nanovalves. The shorter the linkers, the less leaky are the nanovalves. However, the distance between the recognition units on the rod section of the rotaxane molecules does not have any significant influence on the nanovalves' leakiness. The controlled release of the probe molecules was investigated by measuring their luminescence intensities in response to ascorbic acid, which induces the ring's movement away from the pores' orifices, and consequently opens the nanovalves.
Journal of the American Chemical Society, 2007
A multicomponent [2]rotaxane designed to operate as a molecular shuttle driven by light energy ha... more A multicomponent [2]rotaxane designed to operate as a molecular shuttle driven by light energy has been constructed, and its properties have been investigated. The system is composed of (1) a lightfueled power station, capable of using the photon energy to create a charge-separated state, and (2) a mechanical switch, capable of utilizing such a photochemically generated driving force to bring about controllable molecular shuttling motions. The light-fueled power station is, in turn, a dyad comprising (i) a π-electron-accepting fullerene (C 60) component and (ii) a light-harvesting porphyrin (P) unit which acts as an electron donor in the excited state. The mechanical switch is a redox-active bistable [2]rotaxane moiety that consists of (i) a tetrathiafulvalene (TTF) unit as an efficient π-electron-donor station, (ii) a dioxynaphthalene (DNP) unit as a second π-electron-rich station, and (iii) a tetracationic cyclobis(paraquat-p-phenylene) (CBPQT 4+) π-electron-acceptor cyclophane, which encapsulates the better π-electron-donating TTF station. Diethylene glycol spacers were conveniently introduced between the electroactive components in the dumbbell-shaped thread to facilitate the template-directed synthesis of the [2]rotaxane. A modular synthetic approach was undertaken for the overall synthesis of this multicomponent bistable [2]rotaxane, beginning with the syntheses of the P-C 60 dyad unit and the two-station TTF-DNP-based [2]rotaxane separately, using conventional synthetic methodologies. These two components were finally stitched together by an esterification to afford the target rotaxane. Its structure was characterized by 1 H NMR spectroscopy and mass spectrometry as well as by UV-vis-NIR absorption spectroscopy and voltammetry. The observations reflect remarkable electronic interactions between the various units, pointing to the existence of folded conformations in solution. The redox-driven shuttling process of the CBPQT 4+ ring between the two competitive electron-rich recognition units, namely, TTF and DNP, was investigated by electrochemistry and spectroelectrochemistry as a means to verify its operational behavior prior to the photophysical studies related to light-driven operation. The oxidation process of the TTF unit is dramatically hampered in the rotaxane, thereby reducing the efficiency of the shuttling motion. These results confirm that, as the structural complexity increases, the overall function of the system no longer depends simply on its "primary" structure but also on higher-level effects which are reminiscent of the secondary and tertiary structures of biomolecules.
Journal of the American Chemical Society, 2007
Journal of the American Chemical Society, 2010
We report the discovery of a supramolecular interaction (anion-π and charge/electron transfer, CT... more We report the discovery of a supramolecular interaction (anion-π and charge/electron transfer, CT/ET) involving fluoride ion and π-electron deficient colorless naphthalene diimide (NDI) receptors. Strong electronic interactions between lone-pair electrons of Fion and π*-orbitals of the NDI unit lead to an unprecedented F-fNDI ET event, which produces an orange colored NDI •radical anion. Further reduction of NDI •by another Fion produces a pink colored NDI 2dianion, rendering NDI a colorimetric Fsensor. Preorganization of two NDI units in overlapping positions using folded linkers improves their selectivity and sensitivity for the Fion significantly, allowing Fdetection at nM concentration in 85:15 DMSO/H 2 O solutions.
Journal of Biological Chemistry, 2014
Background: Leishmania donovani adopts several defense mechanisms to become resistant to antileis... more Background: Leishmania donovani adopts several defense mechanisms to become resistant to antileishmanial agents. Results: Laboratory-grown flavone (baicalein)-resistant parasites exhibit efflux of drug by LdABCC2 transporter. Inside the host macrophage, this parasite up-regulates host MRP2 transporter by an Nrf2-dependent pathway. Conclusion: Resistant Leishmania parasite exploits ABC transporter in the parasite and inside the host. Significance: The mechanism of drug resistance in clinical isolates can be probed.
ELECTROPHORESIS, 2004
Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in... more Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions We study the effect of matrix chain molecular weight M w and concentration c on the electrophoretic mobility m of large linear and star-like, branched DNA in polymer solutions. Polyethylene oxide (PEO) with narrow molecular weight distributions form the main focus of this study. For PEO concentrations ranging from one half the overlap concentration, c*, to 3c*, the effective drag coefficient, z m 0 m À 1, satisfies the following approximate scaling relationship, z $ cM 0:7 w. Here, m 0 is the electrophoretic mobility in free solution. While the concentration dependence is consistent with predictions from the transient entanglement coupling (TEC) model, the molecular weight dependence is significantly weaker. Although a similar dependence of mobility on M w can be predicted when nonentangling collisions are the dominant source of drag, a model based on these collisions alone cannot reproduce the experimental observations. We also find that the architecture of large DNA does not affect either the concentration dependence or molecular weight dependence of the electrophoretic mobility.
ELECTROPHORESIS, 2003
Electrophoretic dynamics of large DNA stars in polymer solutions and gels We have developed a pro... more Electrophoretic dynamics of large DNA stars in polymer solutions and gels We have developed a procedure for synthesizing large stable branched DNA structures that enables visualization via fluorescence microscopy. Using this procedure we have synthesized large DNA stars and observed their electrophoretic behavior in polymer solutions and gels. In dilute polyacrylamide solutions, the DNA stars move as random coils and appear to experience only brief collisions with the polymer chains in solution. The effect of polymer solution concentration on the electrophoretic mobility of stars in the dilute regime is found to be in good accord with predictions of the transient entanglement coupling (TEC) model. In semidilute polymer solutions, the star arms extend in the field direction and drag the core through the matrix. The star arms form several U-shaped conformations as they collide and engage with polyacrylamide chains. The U-shaped conformations occasionally evolve into J-shaped conformations as the star arms slide off the matrix chains they engage during electrophoretic migration. In concentrated polymer solutions, the arms of the star extend and form V-shaped structures with the core as the apex. The arms then pull the core through the matrix. These V-shaped conformations are much longer-lived than U-shaped ones and, unlike the latter, do not transform to J-shaped conformations. In polyacrylamide and agarose gels, where matrix entanglements are fixed, DNA stars become trapped when entanglements with matrix molecules prevent the core from being pulled through the matrix by the extended arms. This trapping was observed at all gel concentrations and electric fields studied.