9 results on '"Fareed Bhasha Sayyed"'
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2. Uncovering the Most Kinetically Influential Reaction Pathway Driving the Generation of HCN from Oxyma/DIC Adduct: A Theoretical Study
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Lingfeng Gui, Claire S. Adjiman, Amparo Galindo, Fareed Bhasha Sayyed, Stanley P. Kolis, and Alan Armstrong
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Technology ,Engineering, Chemical ,Science & Technology ,Engineering ,QUANTUM CONTRIBUTIONS ,General Chemical Engineering ,General Chemistry ,Chemical Engineering ,03 Chemical Sciences ,09 Engineering ,Industrial and Manufacturing Engineering - Abstract
The combination of ethyl (hydroxyimino)cyanoacetate (Oxyma) and diisopropylcarbodiimide (DIC) has demonstrated superior performance in amino acid activation for peptide synthesis. However, it was recently reported that Oxyma and DIC could react to generate undesired hydrogen cyanide (HCN) at 20 °C, raising safety concerns for the practical use of this activation strategy. To help minimize the risks, there is a need for a comprehensive investigation of the mechanism and kinetics of the generation of HCN. Here we show the results of the first systematic computational study of the underpinning mechanism, including comparisons with experimental data. Two pathways for the decomposition of the Oxyma/DIC adduct are derived to account for the generation of HCN and its accompanying cyclic product. These two mechanisms differ in the electrophilic carbon atom attacked by the nucleophilic sp2-nitrogen in the cyclization step and in the cyclic product generated. On the basis of computed “observed” activation energies, ΔGobs⧧, the mechanism that proceeds via the attack of the sp2-nitrogen at the oxime carbon is identified as the most kinetically favorable one, a conclusion that is supported by closer agreement between predicted and experimental 13C NMR data. These results can provide a theoretical basis to develop a design strategy for suppressing HCN generation when using Oxyma/DIC for amino acid activation.
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- 2023
3. Correlation and Prediction of Redox Potentials of Hydrogen Evolution Mononuclear Cobalt Catalysts via Molecular Electrostatic Potential: A DFT Study
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Bai Amutha Anjali, Cherumuttathu H. Suresh, and Fareed Bhasha Sayyed
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010405 organic chemistry ,Ligand ,Solvation ,Substituent ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Redox ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Electronic effect ,Physical chemistry ,Density functional theory ,Macrocyclic ligand ,Physical and Theoretical Chemistry ,human activities ,Cobalt - Abstract
Reduction potentials (E(0)) of six mononuclear cobalt catalysts (1-6) for hydrogen evolution reaction and electron donating/withdrawing effect of nine X-substituents on their macrocyclic ligand are reported at solvation effect-included B3P86/6-311+G** level of density functional theory. The electrostatic potential at the Co nucleus (V(Co)) is found to be a powerful descriptor of the electronic effect experienced by Co from the ligand environment. The V(Co) values vary substantially with respect to the nature of macrocycle, type of apical ligands, nature of substituent and oxidation state of the metal center. Most importantly, V(Co) values of both the oxidized and reduced states of all the six complexes show strong linear correlation with E(0). The correlation plots between V(Co) and E(0) provide an easy-to-interpret graphical interpretation and quantification of the effect of ligand environment on the reduction potential. Further, on the basis of a correlation between the relative V(Co) and relative E(0) values of a catalyst with respect to the CF3-substituted reference system, the E(0) of any X-substituted 1-6 complexes is predicted.
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- 2016
4. Appraisal of Through-Bond and Through-Space Substituent Effects via Molecular Electrostatic Potential Topography
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Fareed Bhasha Sayyed, Cherumuttathu H. Suresh, and Shridhar R. Gadre
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chemistry.chemical_classification ,Molecular Structure ,Stereochemistry ,Chemistry ,Static Electricity ,Substituent ,Resonance (chemistry) ,Ring (chemistry) ,Hydrocarbons, Aromatic ,Crystallography ,chemistry.chemical_compound ,Models, Chemical ,Quantitative assessment ,Physical and Theoretical Chemistry ,Alkyl - Abstract
Through-bond (TB) and through-space (TS) substituent effects in substituted alkyl, alkenyl, and alkynyl arenes are quantified separately using molecular electrostatic potential (MESP) topographical analysis. The deepest MESP point over the aromatic ring (V(min)) is considered as a probe for monitoring these effects for a variety of substituents. In the case of substituted alkyl chains, the TS effect (79.6%) clearly dominates the TB effect, whereas in the unsaturated analogues the TB effect (∼55%) overrides the TS effect.
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- 2010
5. Resonance enhancement via imidazole substitution predicts new cation receptors
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Cherumuttathu H. Suresh and Fareed Bhasha Sayyed
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chemistry.chemical_compound ,Chemistry ,Stereochemistry ,Substituent ,Imidazole ,Density functional theory ,Interaction energy ,Physical and Theoretical Chemistry ,Benzene ,Receptor ,Resonance (chemistry) ,Ring (chemistry) - Abstract
Design and development of cation receptors represent a fascinating area of research, particularly in dealing with chemical and biological applications that require fine-tuning of cation-π interactions. The electronic nature of a substituent is largely responsible for tuning the strength of cation-π interaction, and recent studies have shown that substituent resonance effect contributes significantly to such interactions. Using substituent resonance effect as a key electronic factor, we have proposed new cation-π receptors (1···M(+)-4···M(+); M(+) = Li(+), Na(+), K(+), NH4(+), and NMe4(+)). B3LYP/6-311+G(d,p) density functional theory (DFT) calculations show that by using a strategy of resonance donation from six nitrogen atoms via three substituted imidazole subunits, more than 4-fold increase in cation-π interaction energy (E(M)(+)) can be achieved for a single phenyl ring compared to benzene. The E(M)(+) (M(+) = NH4(+), NMe4(+)) of 4···M(+), wherein M(+) interacts with only one phenyl ring, is significantly higher than E(M)(+) of a known cation host with several aromatic rings (abstract figure). Our hypothesis on resonance enhancement of cation-π interaction is verified using several π-systems (5-10) containing a lone pair bearing six nitrogens and observed that a nitrogen lone pair attached to a double bond is more effective for donation than the lone pair that is directly attached to the benzenoid ring. Further, a convenient strategy to design electron rich π-systems is provided on the basis of topographical analysis of molecular electrostatic potential.
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- 2013
6. Accurate prediction of cation-π interaction energy using substituent effects
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Fareed Bhasha Sayyed and Cherumuttathu H. Suresh
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chemistry.chemical_compound ,Crystallography ,Reaction rate constant ,Linear relationship ,Hammett equation ,chemistry ,Computational chemistry ,Cation π ,Substituent ,Aromaticity ,Density functional theory ,Interaction energy ,Physical and Theoretical Chemistry - Abstract
Substituent effects on cation-π interactions have been quantified using a variety of Φ-X···M(+) complexes where Φ, X, and M(+) are the π-system, substituent, and cation, respectively. The cation-π interaction energy, E(M(+)), showed a strong linear correlation with the molecular electrostatic potential (MESP) based measure of the substituent effect, ΔV(min) (the difference between the MESP minimum (V(min)) on the π-region of a substituted system and the corresponding unsubstituted system). This linear relationship is E(M(+)) = C(M(+))(ΔV(min)) + E(M(+))' where C(M(+)) is the reaction constant and E(M(+))' is the cation-π interaction energy of the unsubstituted complex. This relationship is similar to the Hammett equation and its first term yields the substituent contribution of the cation-π interaction energy. Further, a linear correlation between C(M(+))() and E(M(+))()' has been established, which facilitates the prediction of C(M(+)) for unknown cations. Thus, a prediction of E(M(+)) for any Φ-X···M(+) complex is achieved by knowing the values of E(M(+))' and ΔV(min). The generality of the equation is tested for a variety of cations (Li(+), Na(+), K(+), Mg(+), BeCl(+), MgCl(+), CaCl(+), TiCl(3)(+), CrCl(2)(+), NiCl(+), Cu(+), ZnCl(+), NH(4)(+), CH(3)NH(3)(+), N(CH(3))(4)(+), C(NH(2))(3)(+)), substituents (N(CH(3))(2), NH(2), OCH(3), CH(3), OH, H, SCH(3), SH, CCH, F, Cl, COOH, CHO, CF(3), CN, NO(2)), and a large number of π-systems. The tested systems also include multiple substituted π-systems, viz. ethylene, acetylene, hexa-1,3,5-triene, benzene, naphthalene, indole, pyrrole, phenylalanine, tryptophan, tyrosine, azulene, pyrene, [6]-cyclacene, and corannulene and found that E(M)(+) follows the additivity of substituent effects. Further, the substituent effects on cationic sandwich complexes of the type C(6)H(6)···M(+)···C(6)H(5)X have been assessed and found that E(M(+)) can be predicted with 97.7% accuracy using the values of E(M(+))' and ΔV(min). All the Φ-X···M(+) systems showed good agreement between the calculated and predicted E(M(+))() values, suggesting that the ΔV(min) approach to substituent effect is accurate and useful for predicting the interactive behavior of substituted π-systems with cations.
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- 2012
7. Quantitative assessment of substituent effects on cation-π interactions using molecular electrostatic potential topography
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Cherumuttathu H. Suresh and Fareed Bhasha Sayyed
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Models, Molecular ,Chemistry ,Chemistry, Physical ,Linear dependency ,Cation π ,Static Electricity ,Substituent ,Benzene ,Electrons ,Hydrogen Bonding ,Interaction energy ,chemistry.chemical_compound ,Kinetics ,Models, Chemical ,Computational chemistry ,Additive function ,Cations ,Quantitative assessment ,Thermodynamics ,Physical and Theoretical Chemistry - Abstract
A molecular electrostatic potential (MESP) topography based approach has been proposed to quantify the substituent effects on cation-π interactions in complexes of mono-, di-, tri-, and hexasubstituted benzenes with Li(+), Na(+), K(+), and NH(4)(+). The MESP minimum (V(min)) on the π-region of C(6)H(5)X showed strong linear dependency to the cation-π interaction energy, E(M(+)). Further, cation-π distance correlated well with V(min)-π distance. The difference between V(min) of C(6)H(5)X and C(6)H(6) (ΔV(min)) is proposed as a good parameter to quantify the substituent effect on cation-π interaction. Compared to benzene, electron-donating groups stabilize the di-, tri-, and hexasubstituted cation-π complexes while electron-withdrawing groups destabilize them. In multiple substituted complexes, E(M(+)) is almost equal (∼95%) to the sum of the individual substituent contributions (E(M(+)) ≈ Σ(ΔE(M(+)))), suggesting that substituent effect on cation-π interactions is largely additive. The ΔV(min) of C(6)H(5)X systems and additivity feature have been used to make predictions on the interaction energies of 80 multiple substituted cation-π complexes with above 97% accuracy. The average mean absolute deviation of the V(min)-predicted interaction energy, E(M(+))(V) from the calculated E(M(+)) is -0.18 kcal/mol for Li(+), -0.09 kcal/mol for Na(+), -0.43 kcal/mol for K(+), and -0.67 kcal/mol for NH(4)(+), which emphasize the predictive power of V(min) as well as the additive feature of the substituent effect.
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- 2011
8. Substituent effects in cation-π interactions: a unified view from inductive, resonance, and through-space effects
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Cherumuttathu H. Suresh and Fareed Bhasha Sayyed
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chemistry.chemical_compound ,Crystallography ,chemistry ,Computational chemistry ,Hydrocarbons, Halogenated ,Cations ,Cation π ,Sodium ,Substituent ,Quantum Theory ,Physical and Theoretical Chemistry ,Resonance (chemistry) ,Space (mathematics) - Abstract
The quantification of inductive (I), resonance (R), and through-space (TS) effects of a variety of substituents (X) in cation-π interactions of the type C₆H₅X···Na⁺ is achieved by modeling C₆H₅-(Φ₁)(n)-X···Na⁺ (1), C₆H₅-(Φ₂)(n)-X···Na⁺ (2), C₆H₅-(Φ(2perpendicular))(n)-X···Na⁺ (2'), and C₆H₆ ···HX···Na⁺ (3), where Φ₁ = -CH₂CH₂-, Φ₂ = -CHCH-, Φ(2perpendicular) indicates that Φ₂ is perpendicular to the plane of C₆H₅, and n = 1-5. The cation-π interaction energies of 1, 2, 2', and 3, relative to X = H and fitted to polynomial equations in n have been used to extract the substituent effect E₀¹, E₀², E₀(2'), and E₀³ for n = 0, the C₆H₅X···Na⁺ systems. E₀¹ is made up of inductive (E(I)) and through-space (E(TS)) effects while the difference (E₀² - E₀(2')) is purely resonance (E(R)) and E₀³ is attributed to the TS contribution (E(TS)) of the X. The total interaction energy of C₆H₅X···Na⁺ is nearly equal to the sum of E(I), E(R), and E(TS), which brings out the unified view of cation-π interaction in terms of I, R, and TS effects. The electron-withdrawing substituents contribute largely by TS effect, whereas the electron-donating substituents contribute mainly by resonance effect to the total cation-π interaction energy.
- Published
- 2011
9. Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT
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Fareed Bhasha Sayyed, Cherumuttathu H. Suresh, and Joshy P. Yesudas
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Protein Conformation ,Low-barrier hydrogen bond ,Protein Data Bank (RCSB PDB) ,Ring (chemistry) ,Ligands ,Catalysis ,Inorganic Chemistry ,HIV-1 protease ,HIV Protease ,Drug Discovery ,Molecule ,Non-covalent interactions ,Computer Simulation ,Protein Interaction Domains and Motifs ,Physical and Theoretical Chemistry ,chemistry.chemical_classification ,Protein Tyrosine Phosphatase, Non-Receptor Type 1 ,Binding Sites ,biology ,Ligand ,Chemistry ,Hydrogen bond ,Organic Chemistry ,Water ,Hydrogen Bonding ,Computer Science Applications ,Crystallography ,Computational Theory and Mathematics ,Models, Chemical ,biology.protein ,Software - Abstract
A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria. Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein, (iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously–the structural water–is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant portions of the corresponding structures are also extracted in the output. The application potential of this program is tested using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L.
- Published
- 2010
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