40 results on '"Pal, Sourav"'
Search Results
2. Activity-guided development of potent and selective toll-like receptor 9 antagonists.
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Roy, Swarnali, Pal, Sourav, Satish, Sohal, Goon, Sunny, Talukdar, Arindam, Paul, Barnali, Mukherjee, Ayan, Rahaman, Oindrila, Ganguly, Dipyaman, Ghosh, Amrit R., Raychaudhuri, Deblina, and Bhattacharya, Roopkatha
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INFLAMMATION , *DRUG design , *PHARMACOKINETICS , *ENDOSOMES , *QUINAZOLINE - Abstract
Abstract TLR9 is one of the major innate immune receptors expressed in the endosomes of pDCs and B cells in humans. Aberrant TLR9 activation is implicated in several autoimmune and metabolic disorders as well as in sepsis, making this receptor an important therapeutic target, though specific TLR9 antagonists are yet to be available for clinical use. Here we elucidate the importance of specific physiochemical properties through substitution patterns in quinazoline scaffold to achieve potent hTLR9 inhibition at < 50 nM as well as > 600 fold selectivity against hTLR7, another closely related TLR that shares downstream signaling with TLR9 but plays distinct roles in physiology and pathology. Assays were performed using hPBMC and reporter cell lines. Favorable in vitro ADME profile, pharmacokinetics as well as validation in a clinically relevant in vivo TLR9-inhibition efficacy model in mice establish these novel TLR9-antagonists as candidate therapeutic agents in relevant clinical contexts. Graphical abstract Image 1 Highlights • Substitutions in quinazoline that influence potency and specificity for hTLR9. • Favourable in vitro ADME and pharmacokinetics in rodent model. • In vivo TLR9-inhibition efficacy was investigated in a rodent model. • Development of potent TLR9 antagonist with excellent selectivity against TLR7. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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3. Probing non-classicality of primordial gravitational waves and magnetic field through quantum Poincare sphere.
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Maity, Debaprasad and Pal, Sourav
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GRAVITATIONAL waves , *MAGNETIC fields , *QUANTUM operators , *QUANTUM states , *INFLATIONARY universe , *POWER spectra , *PSEUDODIFFERENTIAL operators , *SPHERES - Abstract
The universe is believed to be originated from a quantum state. However, defining measurable quantities for the quantum properties in the present universe has gained interest recently. In this submission, we propose a quantum Poincare sphere as an observable quantity that can hint at the quantumness of primordial gravitational waves and large-scale magnetic fields. The Poincare sphere is defined in terms of quantum stokes operators associated with the polarization of those fields, which can be measured directly. We have further studied the effects of the initial non-BD vacuum on the power spectrum and squeezing parameter of the primordial gravitational waves and magnetic field. We have found that the initial non-BD vacuum increases the value of the squeezing parameter as expected at the end of inflation, which further enhances the possibility of measuring the quantumness of the fields under consideration. To support our results, we further explored the possible Bell violation test for a set of generalized pseudo spin operators defined in the polarization space of those fields. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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4. 2D MoS2-MoSe2 and MoS2-NbS2 lateral heterostructures as anode materials for LIBs/SIBs.
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Barik, Gayatree and Pal, Sourav
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HETEROSTRUCTURES , *ELECTRIC conductivity , *INTERFACE structures , *ANODES , *SEMICONDUCTOR junctions , *ENERGY storage , *METAL oxide semiconductor field-effect transistors , *OPEN-circuit voltage - Abstract
[Display omitted] • The MoS 2 -MoSe 2 lateral heterostructure is semiconducting, whereas the MoS 2 -NbS 2 lateral heterostructure is metallic. • The 2D MoS 2 -MoSe 2 and MoS 2 -NbS 2 LHS can withstand massive volume change during the charging-discharging processes. • The MoS 2 -MoSe 2 and MoS 2 -NbS 2 lateral heterostructures give high Li/Na storage capacities of 518 mAh/g and 677 mAh/g, respectively. • MoS 2 -NbS 2 LHS is more advantageous over MoS 2 -MoSe 2 LHS for anodes of LIBs/SIBs. The requirement of an efficient energy storage device has become an exclusive requisite for technological and scientific innovations. In the present work, by using the 2D monolayer semiconductor-semiconductor and semiconductor-metal lateral interface structures as the model structure, we performed periodic DFT calculations to examine the possibility of 2D MoS 2 -MoSe 2 and MoS 2 -NbS 2 lateral heterostructures (LHS) as the electrodes of a battery. The MoS 2 -MoSe 2 lateral interface is a semiconductor, whereas the MoS 2 -NbS 2 lateral interface preserves metallic character. Besides, we found that Li/Na ion adsorption is more influential on the lateral heterostructure and is exothermic, with ultrafast diffusion, and is comparable to their monolayers. Meanwhile, the calculated open-circuit voltage is enormously low, like other widely investigated pristine 2D materials. The enhanced electrical conductivity, short diffusion distances, minutely low equilibrium voltage with good stability, large theoretical capacity and ultrahigh mechanical strength offered bare 2D TMDs lateral heterostructures as a potential candidate for LIBs/SIBs applications. This work broadens the possibility of applications based on 2D TMD-based semiconductor-semiconductor and semiconductor-metal lateral heterostructures. The lateral heterostructures can give an exciting new paradigm and offer exciting opportunities for potential applications in portable electronic devices. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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5. Theoretical study of frequency and temperature dependence of dipole-quadrupole polarizability of P4 and adamantane
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Shedge, Sapana V., Pal, Sourav, and Köster, Andreas M.
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DIPOLE moments , *QUADRUPOLES , *ADAMANTANE , *POLARIZABILITY (Electricity) , *TEMPERATURE effect , *DENSITY functionals , *ELECTRON distribution - Abstract
Abstract: The frequency and temperature dependence of dipole-quadrupole polarizability of tetrahedral P4 and adamantane molecules have been studied using first-principle all-electron density functional theory calculation. The recently developed time-dependent auxiliary density functional theory is extended for the calculation of dynamic dipole-quadrupole polarizabilities. Temperature effects are incorporated by Born–Oppenheimer molecular dynamics (BOMD) simulations recorded up to 100ps. The dynamic dipole-quadrupole polarizabilities are calculated along these trajectories. The frequency and temperature effects can be significant for the accurate calculation of dipole-quadrupole polarizability. We have also identified the main reason for the observed discrepancy between experiment and theory in the case of adamantane. [Copyright &y& Elsevier]
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- 2012
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6. Validation and application of auxiliary density perturbation theory and non-iterative approximation to coupled-perturbed Kohn–Sham approach for calculation of dipole–quadrupole polarizability
- Author
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Shedge, Sapana V., Pal, Sourav, and Köster, Andreas M.
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QUANTUM perturbations , *QUADRUPOLES , *POLARIZABILITY (Electricity) , *DENSITY functionals , *ADAMANTANE , *PHYSICAL & theoretical chemistry , *MATRIX effect - Abstract
Abstract: Recently, two non-iterative approaches have been proposed to calculate response properties within density functional theory (DFT). These approaches are auxiliary density perturbation theory (ADPT) and the non-iterative approach to the coupled-perturbed Kohn–Sham (NIA-CPKS) method. Though both methods are non-iterative, they use different techniques to obtain the perturbed Kohn–Sham matrix. In this Letter, for the first time, both of these two independent methods have been used for the calculation of dipole–quadrupole polarizabilities. To validate these methods, three tetrahedral molecules viz., and adamantane have been used as examples. The comparison with MP2 and CCSD proves the reliability of the methodology. [Copyright &y& Elsevier]
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- 2011
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7. A model study of effect of M = Li+, Na+, Be2+, Mg2+, and Al3+ ion decoration on hydrogen adsorption of metal-organic framework-5
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Maark, Tuhina Adit and Pal, Sourav
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BINDING energy , *HYDROGEN , *GAS absorption & adsorption , *DENSITY functionals , *GRAVIMETRIC analysis , *CHARGE transfer , *ORGANOMETALLIC compounds , *BENZENE - Abstract
Abstract: The effect of light metal ion decoration of the organic linker in metal-organic framework MOF-5 on its hydrogen adsorption with respect to its hydrogen binding energy (ΔB.E.) and gravimetric storage capacity is examined theoretically by employing models of the form MC6H6:nH2 where M = Li+, Na+, Be2+, Mg2+, and Al3+. A systematic investigation of the suitability of DFT functionals for studying such systems is also carried out. Our results show that the interaction energy (ΔE) of the metal ion M with the benzene ring, ΔB.E., and charge transfer (Qtrans) from the metal to benzene ring exhibit the same increasing order: Na+ < Li+ < Mg2+ < Be2+ < Al3+. Organic linker decoration with the above metal ions strengthened H2-MOF-5 interactions relative to its pure state. However, amongst these ions only Mg2+ ion resulted in ΔB.E. magnitudes that were optimal for allowing room temperature hydrogen storage applications of MOF-5. A much higher gravimetric storage capacity (6.15 wt.% H2) is also predicted for Mg2+-decorated MOF-5 as compared to both pure MOF-5 and Li+-decorated MOF-5. [ABSTRACT FROM AUTHOR]
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- 2010
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8. Ionization potential and structure relaxation of adenine, thymine, guanine and cytosine bases and their base pairs: A quantification of reactive sites
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Mishra, Deepti and Pal, Sourav
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NUCLEOTIDES , *DENSITY functionals , *STRUCTURAL analysis (Science) , *RADICALS (Chemistry) , *IONIZATION (Atomic physics) , *CHARGE transfer , *HYDROGEN bonding - Abstract
Abstract: We present density functional theory (DFT) calculations using B3LYP/6-31++G∗∗ method to show relaxation in geometry of base pairs on cation radical formation. The changes in hydrogen bond length and angles show that in the cationic radical form the structure of the base pairs relaxes due to the distribution of charge. According to a recent study, it has been found that, upon excitation hole transfer from base to sugar occurs which results in sugar radical formation and leads to strand breakage [A. Kumar, M.D. Sevilla, J. Phys. Chem. B 110 (2006) 24181]. One hydrogen bond increases, while the other decreases in Adenine–Thymine (AT) base pair and in case of Guanine–Cytosine (GC) base pair, one bond increases and other two decrease. Same is the case with bond angles for both the base pairs. Analysis of the electron density map of Singly Occupied Molecular Orbital (SOMO) reveals that electron is transferred mainly from adenine and guanine bases in the cationic radical formation of AT and GC base pair, respectively. The reactive sites of bases have been analyzed using condensed Fukui functions in a relaxed and frozen core approximation. The effects of relaxation on the reactivity indices are also analyzed. [Copyright &y& Elsevier]
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- 2009
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9. Dipole moments and polarizabilities of some small radicals using constrained variational response to Fock-space multi-reference coupled-cluster theory
- Author
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Manohar, Prashant Uday and Pal, Sourav
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DIPOLE moments , *POLARIZABILITY (Electricity) , *CLUSTER theory (Nuclear physics) , *RADICALS (Chemistry) - Abstract
Abstract: In this Letter, we present dipole moments and polarizabilities of some open-shell doublet radicals, obtained analytically using constrained variational response to Fock-space (FS) multi-reference (MR) coupled cluster (CC) theory. These radicals can be treated as electron attached (EA) states of the corresponding closed-shell cations. Additionally, we also report analytical polarizabilities of some doublet radicals, which can be considered as ionized (IP) states of the corresponding anions. We compare our results with finite field FSMRCC response and the available benchmark results. [Copyright &y& Elsevier]
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- 2007
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10. Analytically continued Fock space multi-reference coupled-cluster theory: Application to the shape resonance
- Author
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Pal, Sourav, Sajeev, Y., and Vaval, Nayana
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QUANTUM theory , *MOLECULAR structure , *ATOMS , *CHEMICAL structure - Abstract
Abstract: The Fock space multi-reference coupled-cluster (FSMRCC) method is used for the study of the shape resonance energy and width in an electron–atom/molecule collision. The procedure is based upon combining a complex absorbing potential (CAP) with FSMRCC theory. Accurate resonance parameters are obtained by solving a small non-Hermitian eigen-value problem. We study the shape resonances in e−–C2H4 and e−–Mg. [Copyright &y& Elsevier]
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- 2006
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11. Effects of conjugation length and donor–acceptor functionalization on the non-linear optical properties of organic push–pull molecules using density functional theory
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Datta, Ayan and Pal, Sourav
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DENSITY functionals , *OPTICAL properties , *METABOLIC conjugation , *LINEAR systems - Abstract
Abstract: We consider a series of dipolar organic molecules where the donor groups and the acceptor groups are separated by π-conjugation like phenyl ring or alkene chains. We have performed extensive quantum chemical calculations based on density functional theory (DFT) to calculate their linear and non-linear optical coefficients. We show that though DFT is known to overestimate the polarizabilities of quasi-linear systems, the results with proper inclusion of exchange correlation compare well with the experimental studies. On increasing the π-conjugation length, the coefficients increase non-linearly. We also vary the donor and the acceptor groups and study the role of chemical modifications on the response properties. Herein we suggest experimental methods by which the molecules may be arranged in non-centrosymmetric fashion in the bulk for device integration. [Copyright &y& Elsevier]
- Published
- 2005
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12. A fully relaxed extended coupled-cluster approach for molecular properties
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Vaval, Nayana and Pal, Sourav
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MOLECULES , *CLUSTER analysis (Statistics) , *BORANES , *EQUILIBRIUM - Abstract
A fully relaxed analytic extended coupled cluster response method is presented for molecular properties. The inclusion of orbital relaxation in extended coupled cluster method is expected to improve molecular properties away from equilibrium. A fully relaxed model of extended coupled cluster method is tested using hydrogen fluoride and boron hydride at various geometries. [Copyright &y& Elsevier]
- Published
- 2004
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13. Electric properties of BH, CO and H2O molecules by density functional response approach
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Sophy, K.B. and Pal, Sourav
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MOLECULES , *DENSITY functionals , *FINITE fields , *FUNCTIONAL analysis - Abstract
In this paper, we present linear and non-linear electric properties of BH, CO and H2O using a density functional response approach, which is a combination of numerical and analytical technique and is thus a simplification of fully analytic method. In the framework of an analytic response approach using Kohn–Sham (KS) density functional theory, the derivative of the KS operator with respect to external field is evaluated numerically, while the orbital derivatives and the subsequent energy derivatives are obtained fully analytically. The method is tested using three molecules BH, CO and H2O, which are marked by high degree of electron correlation and for which extensive ab initio benchmark results are available. Further, we have made a study of possible incorporation of non-dynamical electron correlation by studying BH at several inter-nuclear distances. [Copyright &y& Elsevier]
- Published
- 2004
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14. DFT and local reactivity descriptor studies on the nitrogen sorption selectivity from air by sodium and calcium exchanged zeolite-A
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Chandrakumar, K.R.S. and Pal, Sourav
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ZEOLITES , *NITROGEN , *OXYGEN - Abstract
In the present paper, we have attempted to explain the sorption behavior of nitrogen and oxygen molecule in the sodium and calcium ion exchanged zeolite-A. We have specified the essential role of different cations in making the interaction of the molecules strongly with the cations present at the different reactive sites. All the studies are carried out through local density approximation (LDA). We have also used the recently developed density based global and local reactivity descriptors (GRD and LRD) to study the site reactivity and the energetic patterns of the nitrogen and oxygen molecule with all possible cationic sites. It is found that the calculated interaction energy from our reactivity descriptor model is in agreement with the experimental values. Our methodology can be considered as one of the important tools to investigate the effect of zeolite framework, charge and size of the cations on determining the sorption properties. [Copyright &y& Elsevier]
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- 2002
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15. Synthesis and characterization of new potent TLR7 antagonists based on analysis of the binding mode using biomolecular simulations.
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Pal, Sourav, Paul, Barnali, Bandopadhyay, Purbita, Preethy, Nagothy, Sarkar, Dipika, Rahaman, Oindrila, Goon, Sunny, Roy, Swarnali, Ganguly, Dipyaman, and Talukdar, Arindam
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SMALL molecules , *MOLECULAR dynamics , *MOLECULAR docking , *LIGAND binding (Biochemistry) , *HYDROGEN bonding interactions - Abstract
Aberrant activation of the endosomal Toll-like receptor 7 (TLR7) has been implicated in myriad autoimmune diseases and is an established therapeutic target in such conditions. Development of diverse TLR7 antagonists is mainly accomplished through random screening. To correlate human TLR7 (hTLR7) antagonistic activity with the structural features in different chemotypes, we derived a hypothetical binding model based on molecular docking analysis along with molecular dynamics (MD) simulations study. The binding hypothesis revealed different pockets, grooves and a central cavity where ligand-receptor interaction with specific residues through hydrophobic and hydrogen bond interactions take place, which correlate with TLR7 antagonistic activity thus paving the way for rational design using varied chemotypes. Based on the structural insight thus gained, TLR7 antagonists with quinazoline were designed to understand the effect of engagement of these pockets as well as boundaries of the chemical space associated with them. The newly synthesized most potent hTLR7 antagonist, i.e. compound 63 , showed IC 50 value of 1.03 ± 0.05 μM and was validated by performing primary assay in human plasmacytoid dendritic cells (pDC) (IC 50 pDC: 1.42 μM). The biological validation of the synthesized molecules was performed in TLR7-reporter HEK293 cells as well as in human plasmacytoid dendritic cells (pDCs). Our study provides a rational design approach thus facilitating further development of novel small molecule hTLR7 antagonists based on different chemical scaffolds. Image 1 • hTLR7 antagonist binding hypothesis based on docking analysis of known antagonists. • Significance of engaging different pockets and grooves for hTLR7 antagonism. • MD simulation showed ligand binding stability and protein conformational change. • Newly designed ligands based on binding model showed potent hTLR7 antagonism. • Interaction pattern can correlate the structural change in molecule with the activity. [ABSTRACT FROM AUTHOR]
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- 2021
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16. Structure theorems for operators associated with two domains related to μ-synthesis.
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Bisai, Bappa and Pal, Sourav
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CONTRACTION operators , *HILBERT space , *STEINER systems - Abstract
A commuting tuple of n operators (S 1 , ... , S n − 1 , P) defined on a Hilbert space H , for which the closed symmetrized polydisc Γ n = { (∑ i = 1 n z i , ∑ 1 ≤ i < j ≤ n z i z j , ... , ∏ i = 1 n z i) : | z i | ≤ 1 , i = 1 , ... , n } is a spectral set is called a Γ n -contraction. Also a triple of commuting operators (A , B , P) for which the closed tetrablock E ‾ is a spectral set is called an E -contraction, where E = { (x 1 , x 2 , x 3) ∈ C 3 : 1 − z x 1 − w x 2 + z w x 3 ≠ 0 ∀ z , w ∈ D ‾ }. There are several decomposition theorems for contraction operators in the literature due to Sz. Nagy, Foias, Levan, Kubrusly, Foguel and few others which reveal structural information of a contraction. In this article, we obtain analogues of six such major theorems for both Γ n -contractions and E -contractions. In each of these decomposition theorems, the underlying Hilbert space admits a unique orthogonal decomposition which is provided by the last component P. The central role in determining the structure of a Γ n -contraction or an E -contraction is played by positivity of some certain operator pencils and the existence of a unique operator tuple associated with a Γ n -contraction or an E -contraction. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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17. Dedication
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Pal, Sourav and Thakkar, Ajit J.
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- 2006
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18. Auger decay rates of core hole states using equation of motion coupled cluster method.
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Ghosh, Aryya, Vaval, Nayana, and Pal, Sourav
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AUGER effect , *EQUATIONS of motion , *MOLECULAR clusters , *COHERENCE (Optics) , *IONIZATION (Atomic physics) - Abstract
The recent development of Linac coherent light source high intense X-ray laser makes it possible to create double core ionization in the molecule. The generation of double core hole state and its decay is identified by Auger spectroscopy. The decay of this double core hole (DCH) states can be used as a powerful spectroscopic tool in chemical analysis. In the present work, we have implemented a promising approach, known as CAP-EOMCC method, which is a combination of complex absorbing potential (CAP) and equation-of-motion coupled cluster (EOMCC) approach to calculate the lifetime of single and double core hole states. We have applied this method to calculate the lifetime of the single core hole (K-LL) and double core hole (KK-KLL) states of CH 4 , NH 3 and HF molecules. The predicted lifetime is found to be extremely short. [ABSTRACT FROM AUTHOR]
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- 2017
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19. Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study.
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Dixit, Mudit, Major, Dan Thomas, and Pal, Sourav
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HYDROGEN absorption & adsorption , *DENSITY functional theory , *MOLECULAR dynamics , *ZEOLITES , *HYDROGEN storage - Abstract
Primary H 2 adsorption sites in a zeolitic imidazolate framework, ZIF-7, are identified using ab-initio density functional theory (DFT) based molecular dynamics annealing simulations. The simulations suggest several low energy adsorption sites. The effect of light transition metal decoration on hydrogen storage properties was studied. Our ab-intio DFT calculations illustrate that decorating the ZIF with Sc increases both the number of H 2 molecules, as well as the H 2 binding energy. The binding energy (∼25 kJ/mol per H 2 ) at 8H 2 loading in the pore, suggests that Sc-ZIFs can be potential candidates for hydrogen storage. [ABSTRACT FROM AUTHOR]
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- 2016
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20. Systematic comparison of DFT and CCSD dipole moments, polarizabilities and hyperpolarizabilities.
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Karne, Anagha S., Vaval, Nayana, Pal, Sourav, Vásquez-Pérez, José M., Köster, Andreas M., and Calaminici, Patrizia
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DENSITY functional theory , *COUPLED-cluster theory , *POLARIZABILITY (Electricity) , *DIPOLE moments , *COMPARATIVE studies , *ELECTRON configuration - Abstract
A comparative study of dipole moments, polarizabilities and hyperpolarizabilities of 16 different molecules is performed employing two completely different theoretical approaches namely, density functional theory (DFT) and coupled cluster singles and doubles (CCSD). Both methods include electron correlation. The CCSD method is more accurate but highly expensive. DFT with auxiliary density allows non-iterative solutions which is computational advantage and useful for large molecules. Dipole moments and polarizability calculations from DFT are in very good agreement with CCSD calculations. However, negative hyperpolarizability values from DFT differ significantly from their CCSD counterparts, whereas positive hyperpolarizabilities show reasonable agreement between these methodologies. [ABSTRACT FROM AUTHOR]
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- 2015
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21. Polarizability of few electron quantum dots: Extended coupled-cluster response approach
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Heidari, Ideh, Vaval, Nayana, Pal, Sourav, and Kanhere, D.G.
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POLARIZABILITY (Electricity) , *ELECTRONS , *QUANTUM dots , *DIPOLE moments , *GAUSSIAN processes , *NUMERICAL calculations - Abstract
Abstract: The dipole polarizability is studied for few electron quantum dots using extended coupled cluster linear response method (ECCLR). The polarizability of pure parabolic quantum dots depends only on the number of electrons and the parabolic confinement strength. We added impurity in a Gaussian form to the external parabolic potential and used ECCLR to calculate polarizability. To examine the effect of external potential, we changed the parabolic confinement to square-well and repeated all calculations. We mainly looked at eigenvalue spectrum and charge density specially when the system shifts towards lower density regions. [Copyright &y& Elsevier]
- Published
- 2013
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22. A first principle investigation on the thermal stability of a golden fullerene: A case study of Au32
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De, Himadri Sekhar, Krishnamurty, Sailaja, and Pal, Sourav
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CHEMICAL stability , *FULLERENES , *CASE studies , *DENSITY functionals , *CHEMICAL structure , *MOLECULAR dynamics - Abstract
Abstract: Structural and electronic properties of Au32 cluster are analyzed using relativistic density functional theory (DFT) based methods. Further, DFT based molecular dynamical (MD) simulations are performed on Au32 golden fullerene with an aim of understanding its thermal stability at various working temperatures. Various conformations being populated at different temperatures of a cluster are analyzed. The study shows that the ground state icosahedral conformation is stable only up to 300K and structure remains in a hollow conformation only up to 400K. This clearly explains the reasons for failure by experimentalists in trapping the unique fullerene conformation in spite of the theoretical predictions of it being a very stable one. The above MD study also indicates that the bare fullerene Au32 cluster (without any stabilizing ligands) can be used for potential catalytic applications only around room temperatures. [Copyright &y& Elsevier]
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- 2012
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23. Constrained variational approach for energy derivatives in Intermediate Hamiltonian Fock-space coupled-cluster theory
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Ghosh, Aryya, Gupta, Jitendra, Pal, Sourav, and Vaval, Nayana
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CLUSTER theory (Nuclear physics) , *HAMILTONIAN systems , *FORCE & energy , *ELECTRONIC structure , *DIPOLE moments , *RADICALS (Chemistry) , *STOCHASTIC convergence - Abstract
Abstract: Fock-space multi-reference coupled cluster theory is an efficient method for electronic structure of nearly degenerate cases. However, it suffers from the intruder state problem for large model space. The intermediate Hamiltonian formulation eliminates intruder state problem and helps in the convergence of equations. In this paper we have implemented intermediate Hamiltonian approach in Fock-space coupled cluster method for the response properties. We test our method for the dipole moments of doublet radicals. We report dipole moments of CN, SF and NS radicals. [Copyright &y& Elsevier]
- Published
- 2012
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24. Ab initio and periodic DFT investigation of hydrogen storage on light metal-decorated MOF-5
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Dixit, Mudit, Maark, Tuhina Adit, and Pal, Sourav
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HYDROGEN , *ENERGY storage , *DENSITY functionals , *LIGHT metals , *ORGANOMETALLIC compounds , *BINDING energy , *CHARGE transfer , *ELECTROSTATICS - Abstract
Abstract: The effect of light metal (M=Li, Be, Mg, and Al) decoration on the stability of metal organic framework MOF-5 and its hydrogen adsorption is investigated by ab initio and periodic density functional theory (DFT) calculations by employing models of the form BDC:M2:nH2 and MOF-5:M2:nH2, where BDC stands for the benzenedicarboxylate organic linker and MOF-5 represents the primitive unit cell. The suitability of the periodic DFT method employing the GGA-PBE functional is tested against MP2/6-311+G* and MP2/cc-pVTZ molecular calculations. A correlation between the charge transfer and interaction energies is revealed. The metal-MOF-5 interactions are analyzed using the frontier molecular orbital approach. Difference charge density plots show that H2 molecules get polarized due to the charge generated on the metal atom adsorbed over the BDC linker, resulting in electrostatic guest-host interactions. Our solid state results show that amongst the four metal atoms, Mg and Be decoration does not stabilize the MOF-5 to any significant extent. Li and Al decoration strengthened the H2-MOF-5 interactions relative to the pure MOF-5 exhibited by the enhanced binding energies. The hydrogen binding energies for the Li- and Al-decorated MOF-5 were found to be sensible for allowing reversible hydrogen storage at ambient temperatures. A high hydrogen uptake of 4.3wt.% and 3.9wt.% is also predicted for the Li- and Al-decorated MOF-5, respectively. [Copyright &y& Elsevier]
- Published
- 2011
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25. Probing Lewis acidity and reactivity of Sn- and Ti-beta zeolite using industrially important moieties: A periodic density functional study
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Kulkarni, Bhakti S., Krishnamurty, Sailaja, and Pal, Sourav
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ZEOLITE catalysts , *LEWIS acids , *REACTIVITY (Chemistry) , *DENSITY functionals , *MOLECULAR structure , *METAL complexes , *BASIS sets (Quantum mechanics) , *CHEMICAL bonds - Abstract
Abstract: The Lewis acidic nature and reactivity of two industrially important catalysts, viz., Sn and Ti substituted beta zeolite (T-BEA) are analyzed using a unique combination of structural parameters, energetics and reactivity descriptors. To achieve this purpose, we adsorb the industrially important moieties (L) namely NH3, H2O, CH3OH, CH3CN on the active sites of T-BEA. The calculations were performed using a periodic density functional method where the valence electrons are described using a plane wave basis set in conjunction with pseudo-potentials for the core electrons. The analysis of the structural properties of these complexes reveals that TO4 shows typical characteristic splitting 120°/90°, close to bipyramidal geometry as compared to tetrahedral symmetry observed in the bare T-BEA. This is associated with small variations in the framework bond lengths (≥0.08Å) and a substantially large variation of bond angles (≤10°) in all the ligand-zeolite complexes. Further in both cases of Sn and Ti substituted beta zeolite, ligand interacts at optimum inter-atomic bond distance. Our interaction energies show that adsorption of all ligand moieties is stronger at Sn center than that of Ti. In general, the order of stability of the different T-BEA adducts is NH3 >H2O>CH3OH>CH3CN. The ligand interaction is associated with the corresponding bond elongation and bond reduction of the adsorbed molecules on catalyst active site, which can be taken as measure of red or blue shifted frequencies. Finally, the global descriptors of reactivity justify the fact that soft acid, Sn-BEA, interacts strongly with soft bases following the Pearson''s HSAB principle. However, hard acid, Ti-BEA interacts with soft bases to form a stable Lewis adduct. Furthermore, the HOMO–LUMO gap of all Sn-BEA–L adducts is lower than that of Ti-BEA–L adducts indicating to its higher Lewis acidic nature compared to Ti-BEA. [Copyright &y& Elsevier]
- Published
- 2010
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26. Molecular electric dipole moments using the GVVPT2 variant of multireference perturbation theory
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Theis, Daniel, Khait, Yuriy G., Pal, Sourav, and Hoffmann, Mark R.
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DIPOLE moments , *ANALYSIS of variance , *NUMERICAL analysis , *POTENTIAL energy surfaces , *EXCITED state chemistry , *CHEMICAL equilibrium , *LITHIUM hydride , *QUANTUM perturbations - Abstract
Abstract: A Lagrangian approach for electric dipoles within second order Generalized Van Vleck Perturbation Theory (GVVPT2) is presented. The Lagrangian approach for this response property requires that only one, perturbation-independent, set of simultaneous equations needs to be solved. The presented formulation is demonstrated numerically on several well studied molecules at their equilibrium bond lengths and on the complete potential energy curves of the ground and first excited states of LiH. Numerical corroboration of the expected continuity for molecular properties for the GVVPT2 method is observed. It is seen that the GVVPT2 electric dipoles are in good agreement with experiment and with other high accuracy theoretical methods. [Copyright &y& Elsevier]
- Published
- 2010
- Full Text
- View/download PDF
27. Influence of plane wave cut-off on structural and electronic properties in Sn-BEA and Ti-BEA zeolite water molecule interaction
- Author
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Kulkarni, Bhakti S., Krishnamurty, Sailaja, and Pal, Sourav
- Subjects
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MOLECULAR structure , *ELECTRONIC structure , *ZEOLITES , *WATER , *MOLECULE-molecule collisions , *PSEUDOPOTENTIAL method , *SUBSTITUTION reactions - Abstract
Abstract: Periodic systems are best described by the pseudo-potential methods. However, the accuracy of its description depends on the cut-off of plane wave basis. This is much more critical in the case of weak interactions, where a clear understanding on the influence of plane wave cut-off on the structural and electronic properties is not readily available in the literature. In the present work, we have taken a metal substituted beta zeolite–H2O complex for understanding this objective. Our studies show that while a lower cut-off of 500eV is sufficient for the convergence of the structural parameters, description of energy-dependent properties necessitates a high cut-off value. [Copyright &y& Elsevier]
- Published
- 2010
- Full Text
- View/download PDF
28. Bond length variations: Electron number profiles and transferable atomic sizes
- Author
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Ganguly, Parthasarathy, Kulkarni, Bhakti S., and Pal, Sourav
- Subjects
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CHEMICAL bonds , *ELECTRON distribution , *DENSITY functionals , *CHARGE transfer , *HYDROGEN , *DIATOMIC molecules - Abstract
Abstract: A profile of the number of electrons with distance along the M–X bond in gas-phase diatomic molecules has been obtained from electron density plots calculated using DFT B3LYP 6-311G∗∗ method for some representative molecules. This “number profile” is compared with that expected from the partitioning of the 1D bond-distance into atom-specific transferable “hub” or core atomic sizes of the M and X atoms and another “axle” size which is associated with a pair of (bonding) electrons. The “hub” size is proportional to a core atom-specific size, rnZ c with rnZ c (M)⩾ rnZ c (X). For “single bonds”, the “hub” size for M atom is CMrnZ c (M) and for X atom is CXrnZ c (X). The “axle” size, DMX , is usually the ordinary (∼4aH /3 where aH is the Bohr radius of the hydrogen atom) or elongated (∼2aH ) bond length of the hydrogen molecule. The “hub” and “axle” sizes could be characterized “charge-transfer” (CM =π2/3 =2.144; CX =π4/3/2=2.300 and DMX = 4aH /3) or “neutral” (CM or CX =1, 2, … and DMX =2aH ). We use a new “static” or “peripatetic” classification for the core sizes which is derived from a new condition for metallization in elements based on atomic size. The charge-transfer distance, dMX ±, is usually found for “static” conditions while the “neutral” description is usually found when X=F or for “peripatetic” conditions. Such a partitioning is seen to agree with that from the plot of the total number of electrons, N el, vs r along a bond axis. The N el vs r plots from each atom are described by a simple hydrogen-atom-like function which differ away (“out”) or towards (“in”) the M–X bond. Thus N in,out(M,X)=(ZM,X ±1)exp(−r/B in,out) where the minus sign is associated with M and plus sign with X and B in,out being related inversely to the Slater orbital exponent. [Copyright &y& Elsevier]
- Published
- 2009
- Full Text
- View/download PDF
29. First principles calculations of thermal equations of state and thermodynamical properties of MgH2 at finite temperatures
- Author
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Kelkar, Tuhina, Kanhere, D.G., and Pal, Sourav
- Subjects
- *
EQUATIONS of state , *HARMONIC analysis (Mathematics) , *THERMODYNAMICS , *LINEAR free energy relationship - Abstract
Abstract: We present the first principles calculations of the thermodynamical properties of magnesium hydride (MgH2) over a temperature range of 0–1000K. The phonon dispersions are determined within the density functional framework and are used to calculate the free energy of MgH2 within the quasiharmonic approximation (QHA) at each cell volume and temperature T. Using the free energies the thermal equation of state (EOS) is derived at several temperatures. From the thermal EOS structural parameters such as the equilibrium cell volume (V 0) and elastic properties, namely, bulk modulus (K 0) and its pressure derivative are computed. The free energies are also used to calculate various thermodynamical properties within QHA. These include internal energy E, entropy S, specific heat capacity at constant pressure C P, thermal pressure P thermal(V, T) and volume thermal expansion ΔV/V (%). The good agreement of calculated values of S and C P with experimental data exhibits that QHA can be used as a tool for calculating the thermodynamical properties of MgH2 over a wide temperature range. P thermal(V,T) increases strongly with T at all the volumes but it is a slowly varying function of volume for T =298–500K. According to Karki [B.B. Karki, Am. Miner. 85 (2000) 1447] such volume based variations can be neglected and so it is possible to estimate the thermal EOS only with the knowledge of the measured P thermal(V, T) versus temperature at ambient pressure and isothermal compression data at ambient temperature. Temperature dependence of ΔV/V(%) shows that V 0 increased with increase in temperature. However, the percentage decrease in K 0 superseded this percentage increase in V 0 even at temperatures moderately higher than 298K. Therefore, we suggest application of temperature (T >298K) as an approach to enhance the hydrogen storage capacity of MgH2 because of its better compressibility at these temperatures. [Copyright &y& Elsevier]
- Published
- 2008
- Full Text
- View/download PDF
30. Constrained variational response to Fock-space multi-reference coupled-cluster theory: Some pilot applications
- Author
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Manohar, Prashant Uday, Vaval, Nayana, and Pal, Sourav
- Subjects
- *
PARTICLES (Nuclear physics) , *DIELECTRICS , *DIPOLE moments , *MAGNETIC dipoles - Abstract
Abstract: Fock space (FS) multi-reference (MR) coupled-cluster (CC) has been established to be state-of-the-art method for energies of open-shell radicals, ionized, electron attached states and excited states. Due to the multi-root nature of the method, the linear response of MRCC, however, is non-trivial. Constrained variation approach (CVA) makes it plausible to calculate response of the MRCC method efficiently. However, the approach is used for only one root of the problem at a time. In the present article, we make first implementation of the approach and present test results of dipole moments of small radicals. [Copyright &y& Elsevier]
- Published
- 2006
- Full Text
- View/download PDF
31. Extended coupled-cluster approach for magnetizabilities of small molecules
- Author
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Manohar, Prashant Uday, Vaval, Nayana, and Pal, Sourav
- Subjects
- *
MAGNETIZATION , *MOLECULES , *COUPLED mode theory (Wave-motion) , *THEORY of wave motion - Abstract
Extended coupled-cluster method has emerged as a compact method for study of energies and electric properties of molecules and extended systems. In this Letter, we present a linear response to the above method for study of magnetizabilities of small test molecules. Specifically, we have presented results of diamagnetic and paramagnetic magnetizabilities of HF and CO in appropriate basis sets and studied the gauge dependence and basis set dependence of the properties evaluated through the above method. The results have been compared with SCF and NCC values, as well as experimental values. [Copyright &y& Elsevier]
- Published
- 2004
- Full Text
- View/download PDF
32. Improvement of water quality of remnant from chemical retting of coconut fibre through electrocoagulation and activated carbon treatment.
- Author
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Jose, Seiko, Mishra, Leena, Debnath, Sayandeep, Pal, Sourav, Munda, Prabhat K., and Basu, Gautam
- Subjects
- *
WASTEWATER treatment , *WATER quality , *RETTING , *ELECTROCOAGULATION (Chemistry) , *BIOMASS energy , *COCONUT , *ACTIVATED carbon - Abstract
Abstract Remnant obtained from chemical retting of coconut fibre was found to have an exorbitant COD, BOD, TDS, sulphide content having blackish brown colour. Traditional (physico-chemical) treatment could not reduce its COD, TDS, colour substantially. Further, the traditional method was lengthy, consumed huge chemicals and time. Present paper reports a quicker, simpler, economic i.e., an industrially viable method to separate the chemicals and biomass by employing electrocoagulation (EC). The performance of EC was analyzed by keeping temperature, and pH of remnant constant, while varying current flow (100–2000 mA), time (15–90 min) and number of iron electrodes (2,4,6). Efficacy of EC was evaluated in terms of reduction in conductivity, pH, TDS, COD, TOC, colour and quantity of sludge generated from the wastewater. Six electrodes with 2000 mA current flow for 90 min were found to give noticeable reduction on COD (92.8%), TOC (56%), TDS (99%), and colour. To reduce pH, and TDS to an acceptable level, filtration with activated charcoal was attempted on recovered water from EC. Resultant water was also found to have acceptable LC 50 value for safe disposal. Carbon content (53%) in the sludge was high, contained lignin and cellulose whiskers also, as revealed from the EDX and FTIR, SEM respectively. Cost of EC ($ 0.087 USD/L) was found to be much less as compared to traditional method ($ 0.384 USD/L). Graphical abstract Image 1 Highlights • Remnant of chemical retting of coconut fibre was treated by electrocoagulation. • Optimum treatment condition is 6 electrodes, pH 7, 90 min and 2000 mA. • COD (80%), TOC (56%), TDS, darkness of colour were remarkably reduced. • Lethal concentration of 135 mg/L indicates its safer disposability. • Cost (USD/L) of electrolysis 0.087 as compared to chemical process 0.38. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
33. Corrigendum to “Systematic comparison of DFT and CCSD dipole moments, polarizabilities and hyperpolarizabilities” [Chem. Phys. Lett. 635 (2015) 168–173].
- Author
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Karne, Anagha S., Vaval, Nayana, Pal, Sourav, Vásquez-Pérez, José M., Köster, Andreas M., and Calaminici, Patrizia
- Subjects
- *
PERIODICAL articles , *DENSITY functional theory , *DIPOLE moments , *POLARIZABILITY (Electricity) , *PHYSICS research - Published
- 2015
- Full Text
- View/download PDF
34. Design and development of benzoxazole derivatives with toll-like receptor 9 antagonism.
- Author
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Roy, Swarnali, Mukherjee, Ayan, Paul, Barnali, Rahaman, Oindrila, Roy, Shounak, Maithri, Gundaram, Ramya, Bandaru, Pal, Sourav, Ganguly, Dipyaman, and Talukdar, Arindam
- Subjects
- *
BENZOXAZOLES , *TOLL-like receptors , *DRUG antagonism , *SMALL molecules , *LEUCINE , *BASICITY , *AMINO acids - Abstract
Toll-like receptor 9 (TLR9) is a major therapeutic target for numerous inflammatory disorders. Development of small molecule inhibitors for TLR9 remains largely empirical due to lack of structural understanding of potential TLR9 antagonism by small molecules and due to the unusual topology of the ligand binding surface of the receptor. To develop a structural model for rational design of small molecule TLR9 antagonists, an enhanced homology model of human TLR9 (hTLR9) was constructed. Binding mode analysis of a series of molecules having characteristic molecular geometry, flexibility and basicity was conducted based on crystal structure of the inhibitory DNA (iDNA) bound to horse and bovine TLR9. Interaction with specific amino acid residues in four leucine rich repeat (LRR) regions of TLR9 was identified to be critical for antagonism by small molecules. The biological validation of TLR9 antagonism and its correlation with probe-receptor interactions led to a reliable model that could be used for development of novel small molecules with potent TLR9 antagonism (IC 50 30–100 nM) with excellent selectivity against TLR7. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
35. Molecular recognition pattern of cytotoxic alkaloid vinblastine with multiple targets.
- Author
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Pandya, Prateek, Agarwal, Lokesh Kr, Gupta, Neelima, and Pal, Sourav
- Subjects
- *
ANTINEOPLASTIC agents , *MOLECULAR recognition , *ALKALOIDS , *VINBLASTINE , *TARGETED drug delivery - Abstract
Vinblastine (VLB), a cytotoxic alkaloid is used extensively against various cancer types and the crystal structure of its tubulin complex is already known. Multitarget affinity of vinblastine has been investigated and the nature of binding with biological receptors namely, duplex DNA and Human serum albumin (HSA) has been compared to the binding characteristics of its known complex with natural high affinity receptor tubulin using molecular docking and QM–MM calculations. VLB is found to interact with DNA as well as HSA protein, though, with weaker affinity as compared to tubulin. Analysis of various docked complexes revealed that the H-bonds and cation–pi bonds do not have significant contribution to the binding interactions and despite its large size, VLB remains in relaxed conformation and fits in the hydrophobic regions on the receptors. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
36. 1,8-Diazabicyclo[5.4.0]undec-7-ene (DBU): A highly efficient catalyst in glycerol carbonate synthesis.
- Author
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Munshi, Mudassir K., Gade, Swapna M., Mane, Manoj V., Mishra, Deepti, Pal, Sourav, Vanka, Kumar, Rane, Vilas H., and Kelkar, Ashutosh A.
- Subjects
- *
GLYCERIN , *CARBONATE synthesis , *TRANSESTERIFICATION , *AMINES , *CHEMICAL reactions , *NUCLEAR magnetic resonance spectroscopy - Abstract
Highlights: [•] Transesterification of DMC with glycerol was investigated using amines as catalysts. [•] Amidines like DBU and DBN were found to be the best catalysts for the reaction. [•] 98% conv. with 96% sel. to GC (TON: 9408), were obtained with DBU as a catalyst. [•] Mechanism was investigated with the help of NMR analysis and DFT calculations. [Copyright &y& Elsevier]
- Published
- 2014
- Full Text
- View/download PDF
37. Photoelectrochemical splitting of water with nanocrystalline Zn1−x Mn x O thin films: First-principle DFT computations supporting the systematic experimental endeavor.
- Author
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Sharma, Vidhika, Dixit, Mudit, Satsangi, Vibha R., Dass, Sahab, Pal, Sourav, and Shrivastav, Rohit
- Subjects
- *
PHOTOELECTROCHEMISTRY , *WATER , *ZINC oxide thin films , *NANOCRYSTALS , *DENSITY functional theory , *CHEMISTRY experiments , *X-ray diffraction - Abstract
Abstract: Photoelectrochemical splitting of water with nanocrystalline Zn1−x Mn x O thin films was investigated. ZnO thin films with 1, 3, 5 and 7% at. Mn incorporation were synthesized by sol–gel method and characterized by X-Ray Diffraction (XRD) analysis, Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), X-ray Photoelectron spectroscopy (XPS), High Resolution Transmission Electron Microscopy (HR-TEM) and UV–Vis spectroscopy. Mn incorporation coupled with variation in sintering temperature led to significant microstructural changes, which tentatively influenced the magnitude of optical absorption and charge carrier mobility, thereby impacting the performance of such systems towards photoelectrochemical splitting of water. Electronic structure computations based on first principle density functional theory (DFT) revealed electronic states of Mn being responsible for the marginally recorded red shift in bandgap energy. Photoelectrochemical measurements using thin films of 1% at. Mn:ZnO sintered at 600 °C yielded 3 times enhanced photocurrent at zero bias due to improved optical absorption. Plausible explanations for the effect have also been offered. [Copyright &y& Elsevier]
- Published
- 2014
- Full Text
- View/download PDF
38. Extended coupled cluster through nth perturbation order for molecular response properties: A comparative study.
- Author
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Gupta, Jitendra, Manohar, P.U., Ghosh, Aryya, Vaval, Nayana, and Pal, Sourav
- Subjects
- *
ENERGY function , *CHEMICAL equilibrium , *PERTURBATION theory , *DIPOLE moments , *MOLECULAR clusters , *COUPLING agents (Chemistry) - Abstract
Highlights: [•] Extended coupled cluster method is used for all calculations. [•] The energy functional is truncated up to nth perturbation order. [•] Dipole moments for all the molecules are calculated at both equilibrium and stretched geometry. [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
- View/download PDF
39. On the single-root approach within the framework of coupled-cluster theory in Fock space
- Author
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Horný, Ľuboš, Schaefer, Henry F., Hubač, Ivan, and Pal, Sourav
- Subjects
- *
NUMERICAL analysis , *MATHEMATICAL analysis , *CLUSTER analysis (Statistics) , *STATISTICAL correlation - Abstract
Abstract: A thorough formulation of Fock Space Brillouin–Wigner Coupled Cluster method is presented following previous developments [N.D.K. Petraco, Ľ. Horný, H.F. Schaefer, I. Hubač, J. Chem. Phys. 117 (2002) 9580]. The new method is designed to avoid the intruder states problem, and introduces the single-root solution feature which has not been considered yet within valence-universal methods. The explicit equations for the (0,1) sector of the Fock space are introduced. [Copyright &y& Elsevier]
- Published
- 2005
- Full Text
- View/download PDF
40. Development of a metabolically stable topoisomerase I poison as anticancer agent.
- Author
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Kundu, Biswajit, Sarkar, Dipayan, Chowdhuri, Srijita Paul, Pal, Sourav, Das, Subhendu K., Das, Benu Brata, and Talukdar, Arindam
- Subjects
- *
LIVER microsomes , *DYNAMIC simulation , *POISONS , *CELL lines , *LEAD compounds , *DNA topoisomerase I , *ANTINEOPLASTIC agents - Abstract
We have recently reported a new chemotype of a potent topoisomerase I poison with compound 1 as a potential anticancer chemotherapeutic agent. During further optimization, it has been observed that compound 1 suffers from high intrinsic clearance in human liver microsomes. To overcome the metabolic instability of compound 1 , we report design and synthesis of metabolically stable Top1 poison 3. Newly identified Top1 poison 3 exhibits t 1/2 of 69.1 min in human liver microsomes in comparison to compound 1 with t 1/2 of 9.9 min. Molecular dynamic study of the newly optimized Top1 poison 3 was performed to get the insight into the stability of the binding pose in the active site. Compound 3 was able to trap DNA-Top1 cleavage complex and found to be less cytotoxic in non-cancerous cell line as compared to compound 1. Image 1 • Strategic development of potent Top1 poison with enhanced metabolic stability. • Validation of compound 3 as Top1 poison by ex vivo plasmid DNA cleavage assay. • Molecular Dynamic simulations of compound 3 in the active site. • Lead compound 3 found to be less cytotoxic in non-cancerous cell line. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
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