Tapas Kar | Utah State University (original) (raw)

Papers by Tapas Kar

Research paper thumbnail of Some remarks on multi-center bond index

The basic mathematical structure and the inherent limitations of the bond index model are critica... more The basic mathematical structure and the inherent limitations of the bond index model are critically examined. It is then compared with a similar model where the bonding indices are defined in terms of multi-center effective pair populations derived from pair densities. The two models, although they differ in the basic approach, are shown to be equivalent for bond indices of even rank deduced from an RHF wavefunction.

Research paper thumbnail of Rules for BN-substitution in BCN-fullerenes. Separation of BN and C domains

Research paper thumbnail of Site and chirality selective chemical modifications of boron nitride nanotubes (BNNTs) via Lewis acid-base interactions

Physical chemistry chemical physics : PCCP, Jan 7, 2015

The pristine BNNTs contain both Lewis acid (boron) and Lewis base (nitrogen) centers at their sur... more The pristine BNNTs contain both Lewis acid (boron) and Lewis base (nitrogen) centers at their surface. Interactions of ammonia and borane molecules, representatives of Lewis base and acid as adsorbates respectively, with matching sites at the surface of BNNTs, have been explored in the present DFT study. Adsorption energies suggest stronger chemisorption (about 15-20 kcal mol(-1)) of borane than ammonia (about 5-10 kcal mol(-1)) in both armchair (4,4) and zigzag (8,0) variants of the tube. NH3 favors (8,0) over the (4,4) tube, whereas BH3 exhibits the opposite preference, indicating some chirality dependence on acid-base interactions. A new feature of bonding is found in BH3/AlH3-BNNTs (at the edge site) complexes, where one hydrogen of the guest molecule is involved in three-center two-electron bonding, in addition to dative covalent bond (N: → B). This interaction causes a reversal of electron flow from borane/alane to BNNT, making the tube an electron acceptor, suggesting tailori...

Research paper thumbnail of Segmentation and additive approach: A reliable technique to study noncovalent interactions of large molecules at the surface of single-wall carbon nanotubes

Journal of computational chemistry, Aug 31, 2016

This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to st... more This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to study exohedral noncovalent functionalization of single-walled carbon nanotubes with large molecules, such as polymers and biomolecules, by segmenting the entire system into smaller units to reduce computational cost. A key criterion of the segmentation process is the preservation of the molecular structure responsible for stabilization of the entire system in smaller segments. Noncovalent interaction of linoleic acid (LA, C18 H32 O2 ), a fatty acid, at the surface of a (10,0) zigzag nanotube is considered for test purposes. Three smaller segmented models have been created from the full (10,0)-LA system and interaction energies were calculated for these models and compared with the full system at different levels of theory, namely ωB97XD, LDA. The success of this SAA is confirmed as the sum of the interaction energies is in very good agreement with the total interaction energy. Besides red...

Research paper thumbnail of Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy

Journal of Molecular Modeling

Research paper thumbnail of Evaluation of lignans from Piper cubeba against Schistosoma mansoni adult worms: A combined experimental and theoretical study

Chemistry & biodiversity, Jan 18, 2018

Six dibenzylbutyrolactonic lignans ((-)-hinokinin (1), (-)-cubebin (2), (-)-yatein (3), (-)-5-met... more Six dibenzylbutyrolactonic lignans ((-)-hinokinin (1), (-)-cubebin (2), (-)-yatein (3), (-)-5-methoxy-yatein (4), dihydrocubebin (5) and dihydroclusin (6)) were isolated from Piper cubeba seed extract and evaluated against Schistosoma mansoni. All lignans, except 5, were able to separate the adult worm pairs and reduce the egg numbers during the 24 h of incubation. Lignans 1, 3 and 4 (containing a lactone ring) were the most efficient concerning anti-parasitary activity. Comparing structures 3 and 4, the presence of the methoxy group at position 5 appears to be important for this activity. Considering 1 and 3, it is possible to see that the substitution pattern change (methylenedioxy or methoxyl groups) in positions 3' and 4' alter the biological response, with 1 being the second most active compound. Computational calculations suggest that the activity of compound 4 can be correlated with the largest lipophilicity value.

Research paper thumbnail of Solvation Enhances the Distinction between Carboxylated Armchair and Zigzag Single-Wall Carbon Nanotubes (SWNT-COOH)

The Journal of Physical Chemistry C

Research paper thumbnail of Ultraviolet Optical Absorption Spectra of Water Clusters: From Molecular Dimer to Nanoscaled Cage-Like Hexakaidecahedron

Journal of Computational and Theoretical Nanoscience

Research paper thumbnail of Ab initio SCF study of the ground state electronic structure of SN2+2, SN2, SN2−2, S2N+ and S2N−

Journal of Molecular Structure: THEOCHEM

Research paper thumbnail of Electronic Structure, Stability, and Nature of Bonding of the Complexes of C2H2 and C2H4 with H+, Li+, and Na+ Ions. Extensive ab Initio and Density Functional Study

ABSTRACT The ground-state geometries of the complexes Of C2H2 and C2H4 with H+, Li+, and Na+ ions... more ABSTRACT The ground-state geometries of the complexes Of C2H2 and C2H4 with H+, Li+, and Na+ ions have been optimized at the B3LYP and MP2(full) levels of theory using several basis sets'. The difference in the direction of tilting of the terminal H atoms noticed in C2H3+ and C2H5+ seems to be an artifact of the methods of calculation and basis sets. The dissociation energies (DEs) of the complexes have been calculated using B3LYP, MP2(full) and CCSD(T)=full methods. When ZPE (zero-point energy) and BSSE (basis set superposition error) corrections are included the DEs at the CCSD(T)=full level of theory are obtained for a number of basis sets in very good agreement with the experimental values, wherever available. The nature of bonding of the complexes has been deduced on the basis of charge transfer, bond indices, localized MOs, and topological properties of electron density. Both bond indices and LMOs indicate the presence of three-center bonding in all the complexes. In the protonated species the bonding is found to be predominantly covalent; in the Li+ and Na+ complexes also the covalent interaction plays a fairly important role.

Research paper thumbnail of AIN, GaN, AlxGa1―xN nanotubes and GaN/AlxGa1―xN nanotube heterojunctions

Research paper thumbnail of A closer look into the causes of discrepancy between Löwdin and Mulliken atomic charges

Journal of Molecular Structure: THEOCHEM, 1991

ABSTRACT

Research paper thumbnail of Effect of spin contamination in UHF wavefunctions on charge density-based local quantities

Journal of Molecular Structure: THEOCHEM, 1996

ABSTRACT

Research paper thumbnail of Natural populations and charge transfer in hydrogen and alkali bihalide ions

Journal of Molecular Structure: THEOCHEM, 1994

Research paper thumbnail of Theoretical study of multi-centre bonding using a delocalised MO approach

Journal of Molecular Structure: THEOCHEM, 1992

The nature of the bonding in about thirty electron-deficient molecules has been studied on the ba... more The nature of the bonding in about thirty electron-deficient molecules has been studied on the basis of two-centre and multi-centre (mainly three-centre) bond indices and atomic valencies calculated from ab initio SCF density matrices using 4-3lG (or 6-31G) and 6-31G* (or 6-31G**) basis sets. For comparison, the density matrices corresponding to nonorthogonal and symmetrically orthogonalised basis functions have been employed. The nature of the bonding deduced on the basis of bond indices and valencies has been confirmed by localised MO calculations. It has been observed that a three-centre bond is invariably associated with a positive and significantly high value (a 0.1) of the bond index. For a four-centre bonding interaction the corresponding bond index is generally positive, but rather small.

Research paper thumbnail of Borazine and Benzene Homo- and Heterodimers

The Journal of Physical Chemistry a, Apr 1, 2009

The homodimers of benzene and borazine as well as a heterodimer consisting of one benzene (bz) an... more The homodimers of benzene and borazine as well as a heterodimer consisting of one benzene (bz) and one borazine (bor) molecule are investigated using MP2, SCS-MP2, and CCSD(T) theories in conjunction with basis sets of up to quadruple-zeta quality. Dimer geometries were completely optimized using the resolution of the identity approximation of MP2 with a QZVPP basis set and characterized by computation of harmonic vibrational frequencies using triple-zeta basis sets. While significant higher order correlation effects beyond MP2 are important for the benzene dimer, these are very small for the borazine dimer and intermediate for the heterodimer. The spin-component scaling (SCS) correction of MP2 produces binding energies for the borazine dimer that are too low but yields very good agreement with CCSD(T) for the heterodimer. The decrease in the intermolecular distance in the sandwich (S) configurations from bz(2) via bz-bor to bor(2) is accompanied by an increased binding energy and a change from second-order stationary points to a minimum for bor(2). The T isomer is less stable than the S configuration for bor(2), but it is preferred over the S and a parallel-displaced (PD) arrangement in the heterodimer. The following order of stability is obtained for the minima at the extrapolated CCSD(T) level: T(bz-bor) > S(bor(2)) > PD(bz-bor) > PD(bor(2)) > T(bor(2)) > PD(bz(2)). The most stable isomer at all levels of theory, T(bz-bor), features a NH...pi interaction.

Research paper thumbnail of Substitution patterns in mono-BN-fullerenes: Cn (n = 20, 24, 28, 32, 36, and 40)

The Journal of Physical Chemistry a, Sep 1, 2004

ABSTRACT

Research paper thumbnail of Comparison of atomic charges, valencies and bond orders in some hydrogen-bonded complexes calculated from Mulliken and Löwdin SCF density matrices

Journal of Molecular Structure THEOCHEM

ABSTRACT

Research paper thumbnail of Effect of basis set on Mulliken and Löwdin atomic charges, bond orders and valencies of some polar molecules

Journal of Molecular Structure THEOCHEM

ABSTRACT

Research paper thumbnail of Molecular orbital calculations of valency within the framework of a general non-singular transformation of the atomic orbital basis sets

Journal of Molecular Structure: THEOCHEM, 1990

ABSTRACT

Research paper thumbnail of Some remarks on multi-center bond index

The basic mathematical structure and the inherent limitations of the bond index model are critica... more The basic mathematical structure and the inherent limitations of the bond index model are critically examined. It is then compared with a similar model where the bonding indices are defined in terms of multi-center effective pair populations derived from pair densities. The two models, although they differ in the basic approach, are shown to be equivalent for bond indices of even rank deduced from an RHF wavefunction.

Research paper thumbnail of Rules for BN-substitution in BCN-fullerenes. Separation of BN and C domains

Research paper thumbnail of Site and chirality selective chemical modifications of boron nitride nanotubes (BNNTs) via Lewis acid-base interactions

Physical chemistry chemical physics : PCCP, Jan 7, 2015

The pristine BNNTs contain both Lewis acid (boron) and Lewis base (nitrogen) centers at their sur... more The pristine BNNTs contain both Lewis acid (boron) and Lewis base (nitrogen) centers at their surface. Interactions of ammonia and borane molecules, representatives of Lewis base and acid as adsorbates respectively, with matching sites at the surface of BNNTs, have been explored in the present DFT study. Adsorption energies suggest stronger chemisorption (about 15-20 kcal mol(-1)) of borane than ammonia (about 5-10 kcal mol(-1)) in both armchair (4,4) and zigzag (8,0) variants of the tube. NH3 favors (8,0) over the (4,4) tube, whereas BH3 exhibits the opposite preference, indicating some chirality dependence on acid-base interactions. A new feature of bonding is found in BH3/AlH3-BNNTs (at the edge site) complexes, where one hydrogen of the guest molecule is involved in three-center two-electron bonding, in addition to dative covalent bond (N: → B). This interaction causes a reversal of electron flow from borane/alane to BNNT, making the tube an electron acceptor, suggesting tailori...

Research paper thumbnail of Segmentation and additive approach: A reliable technique to study noncovalent interactions of large molecules at the surface of single-wall carbon nanotubes

Journal of computational chemistry, Aug 31, 2016

This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to st... more This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to study exohedral noncovalent functionalization of single-walled carbon nanotubes with large molecules, such as polymers and biomolecules, by segmenting the entire system into smaller units to reduce computational cost. A key criterion of the segmentation process is the preservation of the molecular structure responsible for stabilization of the entire system in smaller segments. Noncovalent interaction of linoleic acid (LA, C18 H32 O2 ), a fatty acid, at the surface of a (10,0) zigzag nanotube is considered for test purposes. Three smaller segmented models have been created from the full (10,0)-LA system and interaction energies were calculated for these models and compared with the full system at different levels of theory, namely ωB97XD, LDA. The success of this SAA is confirmed as the sum of the interaction energies is in very good agreement with the total interaction energy. Besides red...

Research paper thumbnail of Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy

Journal of Molecular Modeling

Research paper thumbnail of Evaluation of lignans from Piper cubeba against Schistosoma mansoni adult worms: A combined experimental and theoretical study

Chemistry & biodiversity, Jan 18, 2018

Six dibenzylbutyrolactonic lignans ((-)-hinokinin (1), (-)-cubebin (2), (-)-yatein (3), (-)-5-met... more Six dibenzylbutyrolactonic lignans ((-)-hinokinin (1), (-)-cubebin (2), (-)-yatein (3), (-)-5-methoxy-yatein (4), dihydrocubebin (5) and dihydroclusin (6)) were isolated from Piper cubeba seed extract and evaluated against Schistosoma mansoni. All lignans, except 5, were able to separate the adult worm pairs and reduce the egg numbers during the 24 h of incubation. Lignans 1, 3 and 4 (containing a lactone ring) were the most efficient concerning anti-parasitary activity. Comparing structures 3 and 4, the presence of the methoxy group at position 5 appears to be important for this activity. Considering 1 and 3, it is possible to see that the substitution pattern change (methylenedioxy or methoxyl groups) in positions 3' and 4' alter the biological response, with 1 being the second most active compound. Computational calculations suggest that the activity of compound 4 can be correlated with the largest lipophilicity value.

Research paper thumbnail of Solvation Enhances the Distinction between Carboxylated Armchair and Zigzag Single-Wall Carbon Nanotubes (SWNT-COOH)

The Journal of Physical Chemistry C

Research paper thumbnail of Ultraviolet Optical Absorption Spectra of Water Clusters: From Molecular Dimer to Nanoscaled Cage-Like Hexakaidecahedron

Journal of Computational and Theoretical Nanoscience

Research paper thumbnail of Ab initio SCF study of the ground state electronic structure of SN2+2, SN2, SN2−2, S2N+ and S2N−

Journal of Molecular Structure: THEOCHEM

Research paper thumbnail of Electronic Structure, Stability, and Nature of Bonding of the Complexes of C2H2 and C2H4 with H+, Li+, and Na+ Ions. Extensive ab Initio and Density Functional Study

ABSTRACT The ground-state geometries of the complexes Of C2H2 and C2H4 with H+, Li+, and Na+ ions... more ABSTRACT The ground-state geometries of the complexes Of C2H2 and C2H4 with H+, Li+, and Na+ ions have been optimized at the B3LYP and MP2(full) levels of theory using several basis sets'. The difference in the direction of tilting of the terminal H atoms noticed in C2H3+ and C2H5+ seems to be an artifact of the methods of calculation and basis sets. The dissociation energies (DEs) of the complexes have been calculated using B3LYP, MP2(full) and CCSD(T)=full methods. When ZPE (zero-point energy) and BSSE (basis set superposition error) corrections are included the DEs at the CCSD(T)=full level of theory are obtained for a number of basis sets in very good agreement with the experimental values, wherever available. The nature of bonding of the complexes has been deduced on the basis of charge transfer, bond indices, localized MOs, and topological properties of electron density. Both bond indices and LMOs indicate the presence of three-center bonding in all the complexes. In the protonated species the bonding is found to be predominantly covalent; in the Li+ and Na+ complexes also the covalent interaction plays a fairly important role.

Research paper thumbnail of AIN, GaN, AlxGa1―xN nanotubes and GaN/AlxGa1―xN nanotube heterojunctions

Research paper thumbnail of A closer look into the causes of discrepancy between Löwdin and Mulliken atomic charges

Journal of Molecular Structure: THEOCHEM, 1991

ABSTRACT

Research paper thumbnail of Effect of spin contamination in UHF wavefunctions on charge density-based local quantities

Journal of Molecular Structure: THEOCHEM, 1996

ABSTRACT

Research paper thumbnail of Natural populations and charge transfer in hydrogen and alkali bihalide ions

Journal of Molecular Structure: THEOCHEM, 1994

Research paper thumbnail of Theoretical study of multi-centre bonding using a delocalised MO approach

Journal of Molecular Structure: THEOCHEM, 1992

The nature of the bonding in about thirty electron-deficient molecules has been studied on the ba... more The nature of the bonding in about thirty electron-deficient molecules has been studied on the basis of two-centre and multi-centre (mainly three-centre) bond indices and atomic valencies calculated from ab initio SCF density matrices using 4-3lG (or 6-31G) and 6-31G* (or 6-31G**) basis sets. For comparison, the density matrices corresponding to nonorthogonal and symmetrically orthogonalised basis functions have been employed. The nature of the bonding deduced on the basis of bond indices and valencies has been confirmed by localised MO calculations. It has been observed that a three-centre bond is invariably associated with a positive and significantly high value (a 0.1) of the bond index. For a four-centre bonding interaction the corresponding bond index is generally positive, but rather small.

Research paper thumbnail of Borazine and Benzene Homo- and Heterodimers

The Journal of Physical Chemistry a, Apr 1, 2009

The homodimers of benzene and borazine as well as a heterodimer consisting of one benzene (bz) an... more The homodimers of benzene and borazine as well as a heterodimer consisting of one benzene (bz) and one borazine (bor) molecule are investigated using MP2, SCS-MP2, and CCSD(T) theories in conjunction with basis sets of up to quadruple-zeta quality. Dimer geometries were completely optimized using the resolution of the identity approximation of MP2 with a QZVPP basis set and characterized by computation of harmonic vibrational frequencies using triple-zeta basis sets. While significant higher order correlation effects beyond MP2 are important for the benzene dimer, these are very small for the borazine dimer and intermediate for the heterodimer. The spin-component scaling (SCS) correction of MP2 produces binding energies for the borazine dimer that are too low but yields very good agreement with CCSD(T) for the heterodimer. The decrease in the intermolecular distance in the sandwich (S) configurations from bz(2) via bz-bor to bor(2) is accompanied by an increased binding energy and a change from second-order stationary points to a minimum for bor(2). The T isomer is less stable than the S configuration for bor(2), but it is preferred over the S and a parallel-displaced (PD) arrangement in the heterodimer. The following order of stability is obtained for the minima at the extrapolated CCSD(T) level: T(bz-bor) > S(bor(2)) > PD(bz-bor) > PD(bor(2)) > T(bor(2)) > PD(bz(2)). The most stable isomer at all levels of theory, T(bz-bor), features a NH...pi interaction.

Research paper thumbnail of Substitution patterns in mono-BN-fullerenes: Cn (n = 20, 24, 28, 32, 36, and 40)

The Journal of Physical Chemistry a, Sep 1, 2004

ABSTRACT

Research paper thumbnail of Comparison of atomic charges, valencies and bond orders in some hydrogen-bonded complexes calculated from Mulliken and Löwdin SCF density matrices

Journal of Molecular Structure THEOCHEM

ABSTRACT

Research paper thumbnail of Effect of basis set on Mulliken and Löwdin atomic charges, bond orders and valencies of some polar molecules

Journal of Molecular Structure THEOCHEM

ABSTRACT

Research paper thumbnail of Molecular orbital calculations of valency within the framework of a general non-singular transformation of the atomic orbital basis sets

Journal of Molecular Structure: THEOCHEM, 1990

ABSTRACT