@article { ISI:000301225000022, title = {Converting ab initio energies to enthalpies of formation of free radicals. I. new atom equivalents for alkyl radicals}, journal = {Aiche Journal}, volume = {58}, number = {2}, year = {2012}, month = {FEB}, pages = {600-609}, publisher = {WILEY-BLACKWELL}, address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}, abstract = {

A simple method is presented to convert ab initio computed total energies to the standard enthalpy of formation (Delta H-f(o)) of a large number of saturated alkyl radicals (especially those that are relatively highly branched), for which experimental data are scarcely available. For this purpose a new set of radical atom-equivalents (AEQ) and their unique combinations were defined and the energy values of the latter assigned. The theory level and the basis set requirement for the quantum chemistry calculation of the molecular energy were found to be moderate. The Delta H-f(o) predictions appear to be quite accurate with reference to limited available experimental data and are better than values calculated by the group-additivity and the difference methods. The strategy provides an inexpensive way of harnessing the power of computational chemistry and combining it with the organization and insight from the group-additivity method sans any empirical corrections. (C) 2011 American Institute of Chemical Engineers AIChE J, 58: 600-609, 2012

}, keywords = {atom-equivalents, computational chemistry, enthalpy of formation, free radicals, goup additivity method}, issn = {0001-1541}, doi = {10.1002/aic.12596}, author = {Bhattacharya, Arijit} } @article {43949, title = {Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis}, journal = {Journal of Chemical Sciences}, volume = {129}, year = {2017}, month = {MAY}, pages = {515-531}, type = {Article}, abstract = {

Abstract: Molecular Property Diagnostic Suite (MPDS TB) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). MPDS TB tool has nine modules which are classified into data library (1{\textendash}3), data processing (4{\textendash}5) and data analysis (6{\textendash}9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein target analysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains tools for chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal, MPDS TB 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. Graphical Abstract: SYNOPSIS: A web-based MPDS TB Galaxy tool is developed for assessing therapeutic potential of molecules. MPDS TB is categorized into Data Library, Data Processing and Data Analysis. It can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. [Figure not available: see fulltext.] {\textcopyright} 2017, Indian Academy of Sciences.

}, keywords = {chemical analysis, Chemoinformatics, computational chemistry, Diagnosis, Drug discovery portal, Information analysis, Libraries, Molecular graphics, Molecules, Neglected diseases, Open science, Portals, tuberculosis, Web-based technology, Websites}, issn = {0974-3626}, doi = {10.1007/s12039-017-1268-4}, author = {Gaur, A. S. and Bhardwaj, A. and Sharma, A. and John, L. and Vivek, M. R. and Tripathi, N. and Bharatam, P. V. and Kumar, R. and Janardhan, S. and Mori, A. and Banerji, A. and Lynn, A. M. and Hemrom, A. J. and Passi, A. and Singh, A. and Kumar, A. and Muvva, C. and Madhuri, C. and Choudhury, C. and Kumar, D. A. and Pandit, D. and Bharti, D. R. and Kumar, D. and Singam, E. A. and Raghava, G. P. and Sailaja, H. and Jangra, H. and Raithatha, K. and Tanneeru, K. and Chaudhary, K. and Karthikeyan, M. and Prasanthi, M. and Kumar, N. and Yedukondalu, N. and Rajput, N. K. and Saranya, P. S. and Narang, P. and Dutta, Prantu and Krishnan, R.} } @article {45730, title = {Computational survey of ligand properties on iron(III)-iron(II) redox potential: exploring natural attenuation of nitroaromatic compounds}, journal = {Monatshefte Fur Chemie}, volume = {148}, year = {2017}, month = {APR}, pages = {655-668}, type = {Article}, abstract = {

This study is a computational investigation of the ligand effect on the redox potential of iron redox couple aimed at screening these systems for novel applications. The influence of common and naturally available organic compounds with diverse ligand characteristics (nature of donor site, chelation, pre-organization, degree of back acceptance) on the redox potential of iron(III)-iron(II) redox couple has been theoretically calculated using an appropriate level of density functional theory (DFT). The DFT calculated redox potentials of iron complexes are explored to supplement, corroborate, and predict the experimental behavior of the studied systems towards environmental reduction of nitroaromatic compounds to corresponding anilines. The comparative avidity of iron complexes with cysteine derivatives for the reduction of nitroaromatic compounds has been theoretically explored and based on structure-activity relationship; new iron complexes with a range of reactivity and enhanced ability towards nitroaromatic reduction have been predicted.

}, keywords = {Catechol derivatives, computational chemistry, Density functional theory, Iron complexes, Ligand effect on redox potential, Natural attenuation, Nitroaromatic compounds}, issn = {0026-9247}, doi = {10.1007/s00706-016-1813-8}, author = {Rizvi, Masood Ahmad and Mane, Manoj and Khuroo, Mohammad Akbar and Peerzada, Ghulam Mustafa} } @article {46826, title = {Synthesis of novel of 2, 5-disubstituted 1, 3, 4-oxadiazole derivatives and their in vitro anti-inflammatory, anti-oxidant evaluation, and molecular docking study}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {30}, year = {2020}, month = {JUN}, pages = {127136}, type = {Article}, abstract = {

A series of novel 2, 5-disubstituted 1, 3, 4-Oxadiazole derivatives as a potential anti-inflammatory, and antioxidant agent were synthesized via cyclisation. Hydrazide molecule treated with substituted acids in the presence of phosphorus oxychloride (POCl3) as an efficient reagent as well as solvent by conventional method with shorter reaction time and excellent yield. The newly synthesized 1, 3, 4-oxadiazole derivatives exhibited excellent to good anti-inflammatory and anti-oxidant activities compaired to the standard drugs. Molecular docking study on the crucial anti-inflammatory target-cyclooxygenase-2 (COX-2) revealed the ability of the scaffold to correctly recognize the active site and achieve significant bonded and non-bonded interactions with key residues therein. This study could identify potential compounds which can be pertinent starting points for structure-based drug design to obtain newer anti-inflammatory agents.

}, keywords = {1, 3, 4-Oxadiazole, Anti-inflammatory, Anti-Oxidant, Biological activity, computational chemistry}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2020.127136}, author = {Kashid, Bharat B. and Salunkhe, Pravin H. and Dongare, Balasaheb B. and More, Kishor R. and Khedkar, Vijay M. and Ghanwat, Anil A.} } @article {46660, title = {Estimation of reaction kinetics for aromatic and heterocycles nitration in mixed acids through computational chemistry approach}, journal = {International Journal of Chemical Kinetics}, volume = {53}, year = {2021}, month = {MAR}, pages = {319-332}, type = {Article}, abstract = {

Nitration of aromatic compounds and heterocycles in mixed acid environment is one of the regularly performed large-scale reactions in the chemical industry. Although the reaction mechanism of nitration of aromatics in mixed acid is well established, the development of a methodology for the evaluation of kinetics of exothermic aromatic nitrations in a simplified and accurate way is necessary. Here we evaluate the applicability of a kinetic evaluation methodology based on Hammett{\textquoteright}s acidity function, acidity function, and empirical activity coefficient for the nitration reaction. The contributions from the functional groups on the aromatic ring and quantitative structure-activity relationships technique are considered for these evaluations. Natural bond orbital and magnetic index nucleus independent chemical shift analyses were carried out to obtain the substitution constants. The rate constant and activation energy values were evaluated at various temperatures and sulfuric acid strengths. The results were validated by comparing with the experimental data from the literature for several molecules. The effect of various functional groups (viz carbonyl, carboxyl, methyl, and amine) substituted on the benzene ring was also evaluated. For a few identified substrates, the data were used for estimation of residence time needed for complete conversion in continuous stirred tank reactor and in a plug flow reactor to quantify the effect of substitution constant and strength of sulfuric acid. The approach will help select a suitable reactor.

}, keywords = {Aromatic nitration, computational chemistry, Hammett analogy, mixed acids, Reaction kinetics, reactor selection}, issn = {0538-8066}, doi = {10.1002/kin.21445, Early Access Date = OCT 2020}, author = {Jadhav, Pandurang M. and Pandey, Raj K. and Kulkarni, Amol A.} } @article {48383, title = {Computational insights into hydroboration with acyclic alpha-Borylamido-germylene and stannylene catalysts: Cooperative dual catalysis the key to system efficiency}, journal = {Polyhedron}, volume = {222}, year = {2022}, month = {AUG}, pages = {115907}, type = {Article}, abstract = {

The chemistry of low valent main group compounds has grown as an alternative to the chemistry of less abundant and less green transition metal complexes. It has been found that low valent compounds such as carbenes, silylenes, stannylenes and germylenes are efficient for activating small molecules and for catalysis. However, the reaction mechanism and the factors that affect the rate of reaction are not completely understood. In this computational investigation with density functional theory (DFT), we investigate and demonstrate the efficiency of a new mechanism for the hydroboration of aldehydes by germylenes and stannylenes, in the presence of the common hydroborating agent, pinacolborane, HBpin. This mechanism involves an HBpin molecule as an additional catalyst that cooperates with the germylene or stannylene catalyst to efficiently carry out the hydroboration. This mechanism is first demonstrated to work for experimentally reported systems, and then shown to be efficient for newly proposed germylene and stannylene systems. These new systems are alpha-Borylamido-germylene ((2,6-iPr(2)C(6)H(3)NBCy(2))(2)Ge(II)) and alpha-Borylamido-stannylene((2,6-iPr(2)C(6)H(3)NBCy(2))(2)Sn(II)). These new insights will help researchers look into low valent germylene and stannylene chemistry from a new perspective.

}, keywords = {Catalysis of hydroboration, computational chemistry, Germylenes and stannylenes, Main group chemistry, New mechanism}, issn = {0277-5387}, doi = {10.1016/j.poly.2022.115907}, author = {Banerjee, Subhrashis and Vanka, Kumar} } @article {48490, title = {Can Li atoms anchored on boron- and nitrogen-doped graphene catalyze dinitrogen molecules to ammonia? a DFT study}, journal = {ChemPhysChem}, volume = {24}, year = {2023}, month = {JUN}, type = {Article}, abstract = {

The most successful electrochemical conversion of ammonia from dinitrogen molecule reported to date is through a Li mediated mechanism. In the framework of the above fact and that Li anchored graphene is an experimentally feasible system, the present work is a computational experiment to identify the potential of Li anchored graphene as a catalyst for N-2 to NH3 conversion as a function of (a) minimum number of Li atoms needed for anchoring on graphene sheets and (b) the role of chemical modification of graphene surfaces. The studies bring forth an understanding that Li anchored graphene sheets are potential catalysts for ammonia conversion with preferential adsorption of N-2 through end-on configuration on Li atoms anchored on doped and pristine graphene surfaces. This mode of adsorption being characteristic of Nitrogen Reduction Reaction (NRR) through enzymatic pathway, examination of the same followed by analysis of electronic properties demonstrates that tri-Li atoms (Tri Atom Catalysts, TACs) are more efficient as catalysts for NRR as compared to two Li atoms (Di Atom Catalysts, DACs). Either way, the rate determining step was found to be *NH2 -\>*NH3 step (mixed pathway) with Delta G(max)=1.02 eV and *NH2-*NH3 -\>*NH2 step (enzymatic pathway) with Delta G(max)=1.11 eV for 1B doped TAC and DAC on graphene sheet, respectively. Consequently, this work identifies the viability of Li anchored graphene based 2-D sheets as hetero-atom catalyst for NRR.

}, keywords = {computational chemistry, Graphene Sheet, heterogeneous catalysis, Li Nanoparticles, Nitrogen Reduction Reaction}, issn = {1439-4235}, doi = {10.1002/cphc.202200750}, author = {Verma, Tushar Singh and Samal, Pragnya Paramita and Selvaraj, Kaliaperumal and Krishnamurty, Sailaja} }