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1.
J Mol Graph Model ; 127: 108678, 2024 03.
Article in English | MEDLINE | ID: mdl-38064808

ABSTRACT

We examine the role of coadsorbents on dye-sensitized solar cells (DSSCs) with metal-containing and metal-free organic dyes to assess the performance computationally. The results corroborate well with the reported experimental results of Ru-containing dyes exhibiting that the co-adsorbent with longer alkyl chains anchored on the semiconductor surface lower the electron recombination process. The calculated results reveal that the co-adsorbents influence the conduction band energy level and that improve the effective density of states augmenting the forward electron transmission as well as reducing the electron recombination process. The role of co-adsorbents with metal-free organic dyes in DSSCs has also been examined. The computational results suggest that the metal-free organic dyes employed in DSSCs can achieve similar efficiency as reported with metal-organic sensitizers. The results revealed that co-adsorbents grafted through non-covalent interaction are more efficient in improving the efficiency of the DSSCs than co-adsorbents grafted through covalent bonds. The coadsorbents, 1-dimethoxyphosphoryloctadecane with long alkyl chains anchored on the semiconductor surface through hydrogen bonding interactions highly improve the effective density of states resulting in better forward electron transmission and may be one of the parameters to enhance the DSSCs efficiency.


Subject(s)
Coloring Agents , Solar Energy , Coloring Agents/chemistry , Electrons
2.
ACS Omega ; 8(41): 38546-38556, 2023 Oct 17.
Article in English | MEDLINE | ID: mdl-37867725

ABSTRACT

A set of carbon center-based P-ylidesubstituting bases have been exploited computationally with pentacyclo[5.4.0.02,6.03,10.05.9]undecane (PCU) and pentacyclo [6.4.0.02,7.03,11.06,10] dodecane (PCD) scaffolds using the B3LYP-D3/6-311+G(d,p) level of theory. The proton affinities calculated in the gas phase are in the range of superbases and hyperbases. The Atomsin-Molecules and Natural Bond Orbital calculations reveal that the -C-H···C- interaction plays a substantial role in improving the basicity, and tuning the -C-H···C- interaction can enhance the basicity of such systems. The free activation energy for proton exchange for PCD and PCU scaffolds substituted with P-ylide is substantially low. The computed results reveal the strength and nature of such - C-H···C- interactions compared to the -N-H···N- hydrogen bonds. The isodesmic reactions suggest that the superbasicity achieved using these frameworks arises from a combination of several factors, such as the ring strain of the bases in their unprotonated form, steric repulsion, and the intramolecular -C-H···C- interaction.

3.
J Mol Model ; 29(7): 211, 2023 Jun 15.
Article in English | MEDLINE | ID: mdl-37318621

ABSTRACT

CONTEXT: In contrast to un-catalyzed hydrolysis of organophosphorus (OP) compounds, metal ions or/and their complexes with chelating ligands show catalytic effects in several ways depending upon the nature of the metal, ligand, substrate, and medium. It is known that Cu(II)-en chelate containing copper complexes accelerate the hydrolysis of OP compounds. However, the mechanism for this rate enhancement in the Cu(II)-en chelate catalytic hydrolysis reaction of sarin remains unexplored. We have examined possible mechanisms involving a Cu(II)-en with hydroxide nucleophile for the reaction pathway of the hydrolysis of O-isopropyl methylphosphonofluoridate (sarin) computationally. The density functional (B3LYP) employed in this study has reproduced the experimental Gibb's free energy of activation value 15.5 kcal/mol for alkaline hydrolysis of sarin. Earlier proposal of push-pull mechanism for metal ion chelate-catalyzed hydrolysis of OP compounds has been found to be unfavorable in the present study. The role of water molecules in catalyzing the hydrolysis of sarin with Cu(II)-en chelate is crucial. The catalytic process involving Cu(II)-en chelate with one water molecule is the more plausible pathway to achieve the hydrolysis of sarin with Cu(II)-en chelate complexes. METHODS: The most popular B3LYP method was used for optimization of given geometries. Except LANL2DZ for Cu atom, all the atoms are described using the 6-31 + G(d) basis set. The stability test has been performed for the wave functions as we are dealing with the open-shell molecules in order to ensure stable electronic configuration form, and the stable wavefunction is used as the initial configuration for the subsequent optimization. Harmonic frequency calculations and thermodynamic corrections were performed at the same level of theory. PCM method has been used for solvation effects. In order to ensure that each saddle point is linked to a minimum, IRC calculations were performed in forward and reverse directions to ensure the eigenvectors associated with the unique negative eigenvalues of the Hessian matrix. All energies discussed are solvated Gibbs free energies corrected to 298.15 K for the relative stability of the chemical structure. All calculations were performed using the Gaussian 09 code.


Subject(s)
Copper , Sarin , Copper/chemistry , Hydrolysis , Metals/chemistry , Organophosphorus Compounds/chemistry , Water/chemistry , Catalysis
4.
J Antibiot (Tokyo) ; 76(9): 503-510, 2023 09.
Article in English | MEDLINE | ID: mdl-37208457

ABSTRACT

Three new 22-membered polyol macrolides, dactylides A-C (1-3), were isolated from Dactylosporangium aurantiacum ATCC 23491 employing repeated chromatographic separations, and their structures were established based on detailed analysis of NMR and MS data. The relative configurations at the stereocenters were established via vicinal 1H-1H coupling constants, NOE correlations, and by application of Kishi's universal NMR database. In order to get insights into the biosynthetic pathway of 1-3, the genome sequence of the producer strain D. aurantiacum was obtained and the putative biosynthetic gene cluster encoding their biosynthesis was identified through bioinformatic analysis using antiSMASH. Compounds 1-3 showed significant in-vitro antimycobacterial and cytotoxic activity.


Subject(s)
Macrolides , Micromonosporaceae , Macrolides/chemistry , Anti-Bacterial Agents/chemistry , Magnetic Resonance Spectroscopy
5.
Dalton Trans ; 52(14): 4336-4348, 2023 Apr 04.
Article in English | MEDLINE | ID: mdl-36912042

ABSTRACT

The electronic structure of hexasilaprismane (HSP) was examined with different computational techniques to elucidate the bonding features and the electrostatic surface potential of HSP. The carbon dioxide adsorption and separation capacities of metal-ion-decorated hexasilaprismane (HSP) were examined with DFT and CBS-QB3. Furthermore, the 1,2,3,4,5,6-hexaphenylprismasilane (HPPS) molecule was examined for its binding with metal ions and gas adsorption capacity. The Mg2+ ion complexed HPPS molecule adsorbs 15CO2 molecules with an average binding free energy of -0.98 eV per molecule. The calculated gravimetric densities of 45.1 and 48.4 wt% show that these systems can be employed for CO2 capture. The substantial difference in the affinity of the designed systems for CO2 gas molecules compared to N2 and CH4 molecules show the potential of the systems for CO2 separation from N2 and CH4 gas molecules.

6.
Chemistry ; 29(24): e202203953, 2023 Apr 25.
Article in English | MEDLINE | ID: mdl-36757149

ABSTRACT

The synthesis of spiroketals has gained attention because of their importance in chemical and biological reactions. Yet, the mechanistic investigation of mild acid-catalyzed spiroketalization remains elusive and less explored in the literature and speculated that such transformations may proceed through the oxocarbenium ion intermediate; however, the existence of such species in mild acid-catalyzed spiroketalization is not documented. The computational study has been performed at M06-2X/6-31+G(d) level to examine the kinetically controlled product formation for such reactions and the intrinsic reaction coordinates of 1 d suggest that the reaction proceeds via a "one-step, two-stage" mechanism with the formation of transient oxocarbenium as a "hidden intermediate" in the reaction. This study reveals that stereoelectronic interactions devoid the formation of stable oxocarbenium ion intermediate after the proton transfer transition state in the mild acid catalyzed spiroketalization process.

7.
Wiley Interdiscip Rev RNA ; 14(4): e1774, 2023.
Article in English | MEDLINE | ID: mdl-36594112

ABSTRACT

During the last decade, riboswitches emerged as new small-molecule sensing RNA in bacteria. Thiamine pyrophosphate (TPP) riboswitch is widely distributed and occurs in plants, bacteria, fungi, and archaea. Extensive biochemical, structural, and genetic studies have been carried out to elucidate the recognition mechanism of TPP riboswitches. However, a comprehensive report summarizing all information on recognition principles and newly designed ligands for TPP riboswitch is scarce in the literature. This review gives a comprehensive understanding of the TPP riboswitch's structure, mechanism, and methods applied to design ligands for the TPP riboswitch. The ligand-bound TPP riboswitch was studied with various experimental and theoretical techniques to elucidate the conformational dynamics. The mutation studies shed light on the significance of pyrimidine sensing helix for the binding of ligands. Further, the structure-activity relationship study and fragment-based approach lead to the development of ligands with Kd values at the sub-micromolar level. However, there is a need to design more potent inhibitors for TPP riboswitch for therapeutic applications. The recent advancements in ligand design highlight the TPP riboswitch as a promising target for developing new antibiotics. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Riboswitches Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.


Subject(s)
Riboswitch , Thiamine Pyrophosphate , Thiamine Pyrophosphate/chemistry , Thiamine Pyrophosphate/genetics , Thiamine Pyrophosphate/metabolism , Ligands , RNA , Nucleic Acid Conformation , Anti-Bacterial Agents/pharmacology
8.
Sci Rep ; 12(1): 17119, 2022 10 12.
Article in English | MEDLINE | ID: mdl-36224315

ABSTRACT

Globally 3 billion people are consuming water with moderately high concentrations of fluoride and arsenic. The development of a simple point of care (PoC) device or home device for the detection of fluoride/arsenic ensures safety before consuming water. Till date, lateral flow assay (LFA) based PoC devices can detect nucleic acids, viruses and diseases. An aluminium complex of rhodamine B functionalized oxacalix[4]arene (L) was designed to execute the LFA-based PoC device. Initially, Al3+ and Fe3+ ions were involved in complexation with the rhodamine B functionalized oxacalix[4]arene (L), resulting C1 (L-Al3+) and C2 (L-Fe3+) complexes respectively. The receptor L, as well as the probes (C1, C2), were characterized thoroughly using mass spectroscopy, FTIR, NMR, and EA. C1 and C2 were further utilized as recyclable probes for the detection of aqueous fluoride (21 ppb) and arsenate (1.92 ppb) respectively. The computational calculation indicates that upon complexation, the spirolactam ring opening at the rhodamine B site leads to optoelectronic changes. The consistency of LFA-based portable sensing device has been tested with water samples, synthetic fluoride standards and dental care products like toothpaste and mouthwash with concentrations ≥ 3 ppm. Moreover, fixed cell imaging experiments were performed to ascertain the in-vitro sensing phenomena.


Subject(s)
Arsenic , Nucleic Acids , Aluminum , Arsenates , Colorimetry/methods , Fluorides , Humans , Mouthwashes , Toothpastes , Water/chemistry
9.
J Org Chem ; 87(15): 10366-10371, 2022 08 05.
Article in English | MEDLINE | ID: mdl-35852799

ABSTRACT

A monoprotected amino acid Bz-Gly-OH assists in the allylic alkylation of a variety of ketones, ß-keto esters, aldehydes, etc., during enamine-palladium catalysis. Density functional theory calculations reveal that Bz-Gly-OH assists in the formation of an enamine that attacks the π-allylpalladium complex via an outer sphere mechanism. The preliminary result points to an asymmetric allylic alkylation under a new mode of bifunctional catalysis.


Subject(s)
Palladium , Alkylation , Alkynes , Catalysis , Ligands , Palladium/chemistry , Stereoisomerism
10.
J Mol Model ; 28(5): 131, 2022 Apr 27.
Article in English | MEDLINE | ID: mdl-35476166

ABSTRACT

In this work, we report the lower stability of dyes containing cyanoacrylic acid anchoring group on semiconductor TiO2 surface compared to the corresponding silyl unit in dye-sensitized solar cell. Density functional theory (DFT) calculations have been performed with simple donor (N,N diphenylamine) and π-conjugated spacers, with silyl anchoring groups to examine the efficiency of DSSCs. The calculated results in CAM-B3LYP/6-31G(d)/CPCM(THF) reveal that the cyanoacrylic acid anchoring group would have weaker coordination on semiconductor TiO2 surface compared to the silyl anchoring group on the same surface. The designed dyes 1-7 exhibit comparable or in cases superior optical properties than that of the reference dye molecule with cyanoacrylic acid as an anchoring group. All designed dyes have lower ΔGrejection values implying efficient and faster electron recombination between the dye and electrolyte. The electron transition coefficient for these dyes is higher enough (~72-87%) suggesting successful electron propagation from dye to the semiconductor. The electron-donating methyl and ethyl groups show lower ΔGrejection values than the commonly studied -OEt substitution with the silyl anchoring group. The extended π conjugation for better electronic propagation and higher λmax values have been achieved with simple ethylene and butadiene units in the dye molecules. Dye 7 with butadiene as π-spacer unit shows superior oscillatory strength (f) of 2.19 and light-harvesting efficiency (LHE) of 0.99 than the other studied dyes and reference dye with carboxylic anchoring group (TA-ST-CA). The lowest ΔGrejection value (0.53 eV) of dye 7 suggests better electronic recombination than all the other dyes studied here. Transition Density matrix and PDOS calculations with the representative dye 7 suggest a good electronic propagation from the dye to the semiconductor. The incorporation of a highly π-conjugated spacer 4,8-di(thiophen-2-yl)-1H,5H-benzo[1,2-c:4,5-c']bis([1,2,5]thiadiazole) in dye 7 (7-BBT) showed remarkable enhancement in the absorption maxima ~800 nm corresponds to the UV-vis and NIR regions. The DFT calculated results shed light on designing new DSSCs with silyl anchoring groups for enhanced stability and superior efficiency.

11.
J Mol Graph Model ; 113: 108150, 2022 06.
Article in English | MEDLINE | ID: mdl-35227971

ABSTRACT

Frustrated Lewis pair (FLP) chemistry is an alternative strategy in the area of metal-free organic catalysis. This study reports adamantane as FLP molecular scaffold used to design new FLP (ambiphilic molecule) for the metal-free catalytic reduction of CO2 to methoxy borane (CH3O[B]) via hydroboration process. The DFT [B97D/6-31G(d,p), (SMD,benzene)//B3PW91/6-31G(d,p),SDD] calculations have been employed to examine the reaction. The saturated hydrocarbon showed a marked improvement in the energetics of the reduction process compared to the unsaturated phenylene FLPs employed for such reactions. The saturated scaffold improves the Lewis acid and base characters in adamantyl-derived FLPs. The gauche arrangement of Lewis pairs in the adamantyl FLP system is critical to lower the energy barriers in the potential energy surfaces compared to the unsaturated phenylene FLPs. The adamantyl scaffold FLP lowered the activation barriers by ∼6.0 kcal/mol in the key steps of the reduction of CO2 with the reducing agent compared to the phenylene FLPs. These calculated results corroborate the activation of the reducing agent and carbon dioxide to function as efficient catalysis in all steps. The enhancement in the Lewis characters of FLPs with adamantane scaffold was elucidated with conceptual density functional theory (CDFT) calculations.

12.
J Phys Chem B ; 126(5): 1076-1084, 2022 02 10.
Article in English | MEDLINE | ID: mdl-35089046

ABSTRACT

The thiamine pyrophosphate (TPP) riboswitch has emerged as the new target for designing new ligands for antibiotic purpose. Binding of the natural ligand TPP to the TPP riboswitch causes downregulation of the genes responsible for its biosynthesis. We have reported the role of π-stacking energy contributions to ligand binding with a TPP riboswitch. In conjunction with the docking study, the higher-level quantum chemical calculations performed with the wB97XD and Def2TZVPP basis set in the aqueous phase revealed that the optimum ring size is crucial to attain the effective binding efficiency of ligands with a TPP riboswitch. The π-stacking energy contributions observed for the ligands studied are largely similar; however, the cases studied with higher π-stacking energies with larger rings have a weaker ability to displace the radiolabeled thiamine from the riboswitch. The EDA and NCI analyses suggest the role of larger dispersive interactions in stabilizing the π-stacking rings. The contribution from hydrogen-bonding interactions of the hydrogen-bond donor groups on the A ring augments the binding affinity of the ligand. This study sheds light on various factors that contribute to the design of new ligands for efficient binding with a TPP riboswitch and inhibition of gene expression.


Subject(s)
Riboswitch , Ligands , Nucleic Acid Conformation , Thiamine , Thiamine Pyrophosphate/genetics , Thiamine Pyrophosphate/metabolism , Thiamine Pyrophosphate/pharmacology
13.
J Biomol Struct Dyn ; 40(11): 5100-5111, 2022 07.
Article in English | MEDLINE | ID: mdl-33382027

ABSTRACT

Galantamine is one of the approved drugs based on the cholinergic hypothesis for the symptomatic treatment of mild to moderate Alzheimer's disease (AD). The etiology of AD is not fully known; however, the reported cholinergic hypothesis suggests the inadequate synthesis of the neurotransmitter acetylcholine (ACh) is responsible for this disease. The crystal structure of galantamine bound human acetylcholinesterase (hAChE) has been reported; however, the inhibition mechanism of hAChE by galantamine is not well understood. A Well-tempered metadynamics (WTMtD) simulation study has been performed with the crystal structure of galantamine bound hAChE. The reported mechanism for the degradation of ACh is suggested through a proton transfer process from a carboxylic group of Glu334 to the hydroxyl group of Ser203, which attacks ACh for the degradation to acetic acid and choline. Such proton transfer process is lowered in the presence of galantamine due to the separation of catalytic triad inside the gorge of AChE as observed with WTMtD. A docking study has been performed to examine the ACh's binding with the catalytic triad of galantamine bound hAChE. The docking results reveal that the approach of ACh to the catalytic triad is interrupted due to the galantamine's presence in the gorge of the enzyme.


Subject(s)
Alzheimer Disease , Cholinesterase Inhibitors , Galantamine , Acetylcholinesterase/metabolism , Alzheimer Disease/drug therapy , Cholinesterase Inhibitors/chemistry , Cholinesterase Inhibitors/pharmacology , Galantamine/chemistry , Galantamine/pharmacology , Humans , Protons
14.
Phys Chem Chem Phys ; 24(2): 817-828, 2022 Jan 04.
Article in English | MEDLINE | ID: mdl-34928280

ABSTRACT

The FMN riboswitch is a novel drug target for the design of new antibiotics, and efforts have been made to design new charged and uncharged ligands. Uncharged ligands have shown advantages of not requiring any transporter for intracellular transport or proteins for their phosphorylation. 5FDQD (5-(3-(4-fluorophenyl)butyl)-7,8-dimethylpyrido(3,4-b)quinoxaline-1,3(2H,5H)-dione) is a recently reported neutral ligand for the FMN riboswitch active against Clostridium difficile infection in mice. However, the crystal structure of the 5FDQD bound FMN riboswitch is not available, and the mechanism of ligand binding and triggering the function of the riboswitch is not well understood. We have examined 5FDQD for its binding affinity with the FMN riboswitch using the well-tempered metadynamics (WT-MtD) simulation technique. The crystal structure of the FMN riboswitch shows that the FMN interacts with the J4/5 region through the phosphate group with G62; however, the uncharged ligands take advantage of π-π stacking interactions with the same residue of the riboswitch observed from the WT-MtD simulation results. The simulation results show that the presence of fluorine on the phenyl ring in 5FDQD is important to enhance the binding affinity of the neutral ligands with the FMN riboswitch. The WT-MtD results showed that the 1,2-difluoro substitution on the phenyl ring in 5FDQD (FMN-difluoro2) and the 1,3 positions in the phenyl ring (FMN-difluoro1) showed weaker binding energy with the FMN riboswitch compared to 5FDQD. The substitution of another fluorine atom at the 5-position of the phenyl ring (FMN-trifluoro) showed a comparable binding affinity (∼-31.4 kcal mol-1) to 5FDQD. Electron-donating substitution on the phenyl ring such as the amino group also lowered the binding affinity (-28.8 kcal mol-1) with the riboswitch compared to 5FDQD. The computed results suggest that the position and nature of substitution in the phenyl ring of the uncharged ligands affect the overall binding and such a delicate balance is important to achieve superior binding affinity with the FMN riboswitch.

15.
Phys Chem Chem Phys ; 24(2): 829-841, 2022 Jan 04.
Article in English | MEDLINE | ID: mdl-34928284

ABSTRACT

Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.


Subject(s)
Aluminum/chemistry , Benzoxazoles/chemistry , Boron Compounds/chemistry , Density Functional Theory , Fluorescent Dyes/chemistry , Molecular Dynamics Simulation , Adenine/chemistry , Adsorption , Cytosine/chemistry , Guanine/chemistry , Thymine/chemistry
16.
J Org Chem ; 87(1): 884-891, 2022 01 07.
Article in English | MEDLINE | ID: mdl-34941241

ABSTRACT

An efficient protocol involving the transformation of sequentially generated recursive anions from heterocyclic precursors to orthogonally strap diynones through one pot transition-metal-free spirocyclopentannulation has been devised, employing oxindoles and pyrazolones as prototypical platforms. Insights into these regioselective tandem Michael-anti-Michael processes have been gleaned through DFT calculations.


Subject(s)
Pyrazolones , Catalysis , Molecular Structure , Oxindoles
17.
Org Biomol Chem ; 19(28): 6353-6367, 2021 07 21.
Article in English | MEDLINE | ID: mdl-34231642

ABSTRACT

Synthesis of linearly fused aromatic systems using a glycal-based diene with an aryne is a long-standing topic of interest in glycal chemistry. We have examined the mechanistic pathways for the transformation of substituted glycals to chiral fused aromatic cores via Diels-Alder (DA) reaction using the SMDACN-M06-2X/6-31G(d) level of theory. The DA reactions of E (1a) and Z (1a') forms of C-2 alkenyl glycal and an aryl glycal (1b) as a diene were examined with a benzyne intermediate generated as a dienophile. The computational results reveal that 1a and 1b can only be transformed into the fused aromatic cores by the base-catalyzed reaction because a [1,5] sigmatropic hydrogen shift is not feasible. The activation free energy barrier for the base-catalyzed proton abstraction process is 4.2 kcal mol-1 and there is almost no barrier for stereoisomeric 1a DA-complexes. The activation free energy barrier values for stereoisomeric 1b DA-complexes for the base-catalyzed proton abstraction process are 10.8 and 12.4 kcal mol-1. The appropriate orientation of glycal-ring-oxygen and hydrogen at the 5th position of Z (1a') forms of C-2 alkenyl glycal facilitates the [1,5] sigmatropic hydrogen shift; however, the base-catalyzed reaction is energetically more favored than the former case. The rate-determining step for 1a and 1a' is the ring-opening step (18.2 and 19.5 kcal mol-1 for the S-stereoisomer), whereas the DA adduct formation step is the rate-determining step for 1b (16.1 kcal mol-1 for the S-stereoisomer). The structural analysis reveals the formation of the preferred S-stereoisomer over the R-stereoisomer with the respective dienes.

18.
J Mol Graph Model ; 104: 107849, 2021 05.
Article in English | MEDLINE | ID: mdl-33545607

ABSTRACT

Riboswitches are metabolite sensing aptamer domains present in non-coding regions in RNA and act as gene-regulating elements. Thiamine pyrophosphate (TPP) riboswitch is evolved as a new target for developing antibiotics against many pathogenic bacteria. The earlier reports suggest that the modification of the pyrophosphate group in the ligand molecule can enhance gene expression. In this work, we have examined the binding affinity and efficacy of TPP and two recently reported ligands, CH2-TPP, and CF2-TPP, using Well-tempered metadynamics (WT-MtD) simulations. The experimental in vitro assays show that both TPP and CH2-TPP repress the gene expression to the same extent. The calculated binding energies correlate well with the experimental study and show the same trend of binding affinity of ligands for the TPP riboswitch. The root mean square fluctuation profiles suggest that the CH2-TPP and TPP trigger higher fluctuations in P1 and L3 region, and such fluctuations in the P1 region is involved in the gene regulation process. The metal ion mediated contact of TPP ligand with pyrophosphate binding helix is found to be critical in the gene regulation process. The simulation results corroborate the experimental observations that the role of conformational changes occurring in different riboswitch regions upon ligand binding is essential to repress the gene expression process. This work sheds light on the subtle change in the ligand structure that can induce a more considerable impact on binding affinity and efficacy of ligands with riboswitch.


Subject(s)
Riboswitch , Diphosphates , Gene Expression , Nucleic Acid Conformation , Riboswitch/genetics , Thiamine , Thiamine Pyrophosphate/metabolism
19.
ACS Appl Bio Mater ; 4(8): 6430-6440, 2021 08 16.
Article in English | MEDLINE | ID: mdl-35006925

ABSTRACT

Environmental remediation with a single platform for selective sensing and removal of toxic analytes with recyclability of the material has always been a desirable system for sustainability. However, materials comprising all the abovementioned advantages are rarely known for oxoanions. We herein developed a fluorogenic napthalimide-based functionalized mesoporous silica material (SiO2@NBDBIA) as a signaling and remediation system for oxoanions (CrO42-, Cr2O72-, and MnO4-) from a pool of several anions. The fluorescence quenching of the SiO2@NBDBIA material in the presence of CrO42-, Cr2O72-, and MnO4- ions gives the limit of detection (LOD) values of 6.23, 25.2, and 20.32 ppb, respectively, which are well below the maximum contaminant level demarcated by the United States Environmental Protection Agency. The maximum adsorption capacities of the material for the abovementioned oxoanions are found to be 352, 363, and 330 mg/g, respectively, which are well above those mentioned in the literature reports. Contrary to the literature-dominated irreversible ion-exchange mechanism, the reversible hydrogen-bonded binding of the material with the oxoanions leads to the recyclability of the material easily, which is very rare in the literature. The DFT calculations were performed to examine the interactions between the material and oxoanions. For real applications, this material was also used as a fluorescence probe to detect these oxoanions in the actual water samples, and more interestingly, used as a biosensing probe for these oxoanions in the living organism Artemia salina through fluorescence imaging. Thus, the SiO2@NBDBIA material is a unique example of recyclable material for detecting and remediating oxoanions.


Subject(s)
Chromium , Silicon Dioxide , Ions , Manganese Compounds , Oxides , Silicon Dioxide/chemistry , United States
20.
ACS Omega ; 5(48): 31146-31155, 2020 Dec 08.
Article in English | MEDLINE | ID: mdl-33324823

ABSTRACT

Selective adsorption of CO2 from flue gas is extremely significant because of its increasing concentration in air and its deleterious effect on the environment. In this work, we have explored metal-ion-bound prismane molecules for selective CO2 adsorption from the flue gas mixture. The Ca2+-bound prismane complex exhibits superior CO2 selectivity and adsorption capacity. The calculated binding energy and molecular electrostatic potential (MESP) analysis showed that the rectangular face of prismane binds strongly with metal ions as compared to its triangular face. The CBS-QB3 and density functional theory-based functional M06-2X/6-311+G(d) calculations show that the prismane molecule can bind to one Li+, K+, Mg2+, and Ca2+ ion with favorable binding energy. The metal-ion-bound prismane complexes have been examined for their CO2, N2, and CH4 adsorption capacity. Prismane-Ca2+ can bind with six CO2 molecules strongly with an average binding energy of -18.1 kcal/mole as compared to six N2 (-12.6) and five CH4 (-13.4) gas molecules. The gravimetric density calculated for the CO2-adsorbed prismane-Ca2+ complex has been found to be 69.1 wt %. The discrete hydrocarbon structure for selective separation of CO2 is rare in the literature and can have potential applications for cost-effective CO2 capture from the flue gas mixture.

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