Glake Hill | Jackson State University (original) (raw)
Papers by Glake Hill
Physical Chemistry Chemical Physics, 2010
Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqu... more Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase Marie-Pierre Gaigeot, Phys. Chem. Chem. Phys.
Journal of Physical Chemistry A, 2008
An ab initio nonequilibrium Green&amp... more An ab initio nonequilibrium Green's function study of the electron-transport properties of the adenine, thymine, cytosine, and guanine DNA bases located between gold electrodes has been performed. One-electron transmission spectra were calculated for both gold and sulfur-modified gold electrodes, which are model conditions of scanning tunneling microscopy (STM) experiments with the different tips. It is shown that the nature of chemical bonding between molecules and metal electrodes plays the most significant role in the overall conductance of the systems. The distance between electrodes and the size of molecules are less important, at least when both sides of the molecule form chemical contact with the electrodes. On the basis of the obtained results, a simple two-pass DNA sequencing scheme is suggested.
Although a vast amount of experimental information is available on the elongation, compression, a... more Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic level. Since this area of work is relatively new, this paper reports the results of computer simulation of elongation and compression of B-DNA structures providing new insights into high- energy forms of DNA implicated in these processes.
An ab initio Green's function study of the electron transport properties of the selected metal-po... more An ab initio Green's function study of the electron transport properties of the selected metal-porphyrin complexes has been performed. Transmission spectra and current-voltage dependence have been calculated for the porphyrin molecule located between gold electrodes in the presence of interaction with metal atoms, which are most common in biochemistry (Fe(II), Fe(III), Mn(II), and Zn(II)). It was shown that the estimated Fermi level almost coincides with the LUMO level of Fe(II)-porphyrin and Fe(III)-porphyrin, resulting in significant conductance at small voltage biases. Conductance of Mn(II)-porphyrin and Zn(II)-porphyrin are much lower, and decrease from Mn to Zn. It was confirmed that performing spin-unrestricted calculations is essential to account splitting of the original molecular orbitals levels. Preformed calculations demonstrate the principal possibility of experimental realization of porphyrin based nanosensors.
Chemical Physics Letters, 2011
... Phys. Lett. 512 (2011) 92]. Authors: Khan, Sadia Afrin; Senapathi, Dulal; Senapathi, Tapas; L... more ... Phys. Lett. 512 (2011) 92]. Authors: Khan, Sadia Afrin; Senapathi, Dulal; Senapathi, Tapas; Liao, Meng-Sheng; Bonifassi, P.; Fan, Zhen; Singh, Anant Kumar; Neeley, Adria; Hill, Glake; Huang, Ming-Ju; Watts, John D.; Ray, Paresh Chandra. ...
Chemical Physics Letters, 2011
Using solution-based method, silver quantum clusters of different sizes (Ag 20 , Ag 140 and Ag 98... more Using solution-based method, silver quantum clusters of different sizes (Ag 20 , Ag 140 and Ag 980 ) have been synthesized and their first hyper-polarizabilities were measured using hyper-Rayleigh scattering technique. We have shown that nonlinear optical properties of silver quantum cluster are highly dependent on the size of quantum cluster. Time-dependent density functional theory calculations using the Amsterdam Density Functional (ADF) program package are used to evaluate linear and nonlinear optical properties of silver tetrahedral Ag n (n = 10, 20, 35, 56) clusters. Both theoretical and experimental data have shown that nonlinear as well as linear optical properties are highly dependent on the size of silver quantum cluster.
International Journal of Quantum Chemistry, 2001
Studies of structures, energetics, and charge distribution were performed for ground and lowest e... more Studies of structures, energetics, and charge distribution were performed for ground and lowest excited electronic states of MeCl2(NH3)2, Me=Pd and Pt complexes. Despite the similarity of the Pd and Pt elements, the differences in isomerization energies, ground-excited state separation energy, and electronic density distribution are significant. The MeN and MeCl bonds possess a different nature with the Cl accepting and the NH3 group donating electrons to the central metal. The bonds are more polarized in Pt-based complexes. The electronic excitations involve mostly the metal atom, and although they do not change the structure drastically, the excitations do, however, impact the charge distribution. Interaction energy decomposition for the ground state indicates that ammonia–metal interactions are dominated by the energy delocalization term. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 213–219, 2001
Chemical Physics Letters, 2003
For the first time, the physical nature of intermolecular interactions between 10 DNA stacked bas... more For the first time, the physical nature of intermolecular interactions between 10 DNA stacked bases has been examined by an interaction energy decomposition method based on the variation-perturbation theory. The dominant correlation term including dispersion interactions is found to be cancelled to a considerable extent by exchange and delocalization contributions leaving the relatively smaller long range electrostatic contribution as the most important factor determining relative stacking interaction energies. The electrostatic multipole component closely mimics the trend of total interaction energy in all considered systems.
Polymer, 2011
The molecular interactions of phosphorous ylide (PY) and hypohalous acids HOX (X = F, Cl and Br) ... more The molecular interactions of phosphorous ylide (PY) and hypohalous acids HOX (X = F, Cl and Br) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. The patterns including non-classical hydrogen bond HÁ Á ÁC, halogen bond XÁ Á ÁC, classical hydrogen bonds HÁ Á ÁX and HÁ Á ÁO, and FÁ Á ÁP interactions were found for complex formation between PY and HOX molecules. From the predicted models, stabilities of the XÁ Á ÁC and HÁ Á ÁC types complexes are greater than other types. Quantum theories of atoms in molecules (AIM) and natural bond orbitals (NBO) methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the secondorder perturbation energies E (2) and the charge transfer qCT in the studied systems.
Journal of Biomolecular Structure & Dynamics, 2003
We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pa... more We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6–31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6–31G(d,p), MP2/6–31++G(d,p), and MP2/6–311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.
Journal of Biomolecular Structure & Dynamics, 2003
Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) ... more Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries of the local minima were optimized without symmetry restrictions by the gradient procedure at DFT level of theory and were verified by energy second derivative calculations. The standard 6–31G(d) basis set was used. The single-point calculations have been performed at the MP2/6–31G(d,p), MP2/6–31++G(d,p), and MP2/6–311++G(2d,2p) levels of theory. The geometrical parameters, relative stability and counterpoise corrected interaction energies are reported. Also, using a variation-perturbation energy decomposition scheme we have found the vital contributions to the total interaction energy.
Journal of Physical Chemistry B, 2006
Minor tautomers of nucleic acid bases can result by intramolecular proton transfer. These rare ta... more Minor tautomers of nucleic acid bases can result by intramolecular proton transfer. These rare tautomers could be stabilized through the addition of methyl groups to DNA bases. A comprehensive theoretical study of tautomers of methylated derivatives of guanine, adenine, cytosine, thymine, and uracil was performed. Molecular geometries of all tautomers were obtained at the density functional theory and MP2 levels with the 6-31G(d,p) basis set, and single-point calculations were performed at the CCSD(T)/6-311G(d,p) level. Tautomers obtained by protonation at the preferred protonation site for methylated isolated bases were compared to their nonmethylated counterparts. The effects of methylation on the relative stabilities of nucleic acid base tautomers are also studied and discussed in this work. The results suggest that some sites on the bases may not be mutagenic and may even stabilize the canonical Watson-Crick form. The results also indicate that a number of methylation sites can stabilize the tautomers, suggesting possible mechanisms for mutagenic changes.
Structural Chemistry, 2010
Molecularly imprinted polymers can be used for molecular recognition and design of detection devi... more Molecularly imprinted polymers can be used for molecular recognition and design of detection devices. During molecular imprinting, a monomer, such as methacrylic acid, is used to encapsulate a template like an explosive. Selective lock–key system build through specific intermolecular interactions is formed. The 2,6-dinitrotoluene has been chosen for this study as an example of highly energetic material whose detection is in demand. This study presents density functional theory and MP2 calculations on structural and vibrational properties of dinitrotoluene–methacrylic acid complex as well as description of the nature of interactions within this complex. Additionally, theoretical and experimental IR spectra along with vibrational assignments are reported.
Journal of Physical Chemistry C, 2010
The foreign atom doping influences the properties of carbon materials, and it is a possible way o... more The foreign atom doping influences the properties of carbon materials, and it is a possible way of designing materials of desired characteristics. Density functional calculations have been carried out on various isomers of boron-doped (4,0) and (9,0) carbon nanotubes as templates to investigate the doping effect on the structure and electronic properties on such systems. The results indicate that these boron-doped carbon nanotubes show local structural changes, mostly due to the elongation of bonds. The insertion of heteroatoms perturbs the π-conjugation system, which, in effect, destabilizes the material through higher energy cost of formation. The position of the foreign atom controls the new organization of electron density and leads to one of two possible distributions, viz., global (where electron density is distributed over the molecular surface) or local (localized distribution of electron density). This feature, in turn, can influence the bonding of the reactants while interacting with the surface. The charge distribution at a particular boron-doped site always possesses the local characteristics with a positively charged boron atom surrounded by negatively charged carbons. Such a character is also a measure of the driving force for influencing the substitution reaction in the vicinity of boron through an ionic mechanism.
Journal of Biomolecular Structure & Dynamics, 2003
Ab initio techniques were used to determine the effects of protonation and methylation on cytosin... more Ab initio techniques were used to determine the effects of protonation and methylation on cytosine's molecular geometry, molecular affinities, relative stability, and structural rigidity. The geometries of local minima were fully optimized by the gradient procedure at DFT and MP2 levels of theory with the medium size 6–31G(d,p) basis set. The results of energetic analysis indicate that N(3)-methyl-cytosine and C(5)-methyl-cytosine are the most stable derivatives for monocationic and neutral species, respectively. The structural rigidity of each species was assessed by an analysis of normal out-of-plane frequencies, the amplitudes, and by the contribution of internal coordinates to the potential energy distributions. The obtained evidence suggests that methylation increases the overall structural flexibility of cytosine and that all molecules in this study populate a non-planar conformation 50% of the time.
Physical Chemistry Chemical Physics, 2010
Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqu... more Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase Marie-Pierre Gaigeot, Phys. Chem. Chem. Phys.
Journal of Physical Chemistry A, 2008
An ab initio nonequilibrium Green&amp... more An ab initio nonequilibrium Green's function study of the electron-transport properties of the adenine, thymine, cytosine, and guanine DNA bases located between gold electrodes has been performed. One-electron transmission spectra were calculated for both gold and sulfur-modified gold electrodes, which are model conditions of scanning tunneling microscopy (STM) experiments with the different tips. It is shown that the nature of chemical bonding between molecules and metal electrodes plays the most significant role in the overall conductance of the systems. The distance between electrodes and the size of molecules are less important, at least when both sides of the molecule form chemical contact with the electrodes. On the basis of the obtained results, a simple two-pass DNA sequencing scheme is suggested.
Although a vast amount of experimental information is available on the elongation, compression, a... more Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic level. Since this area of work is relatively new, this paper reports the results of computer simulation of elongation and compression of B-DNA structures providing new insights into high- energy forms of DNA implicated in these processes.
An ab initio Green's function study of the electron transport properties of the selected metal-po... more An ab initio Green's function study of the electron transport properties of the selected metal-porphyrin complexes has been performed. Transmission spectra and current-voltage dependence have been calculated for the porphyrin molecule located between gold electrodes in the presence of interaction with metal atoms, which are most common in biochemistry (Fe(II), Fe(III), Mn(II), and Zn(II)). It was shown that the estimated Fermi level almost coincides with the LUMO level of Fe(II)-porphyrin and Fe(III)-porphyrin, resulting in significant conductance at small voltage biases. Conductance of Mn(II)-porphyrin and Zn(II)-porphyrin are much lower, and decrease from Mn to Zn. It was confirmed that performing spin-unrestricted calculations is essential to account splitting of the original molecular orbitals levels. Preformed calculations demonstrate the principal possibility of experimental realization of porphyrin based nanosensors.
Chemical Physics Letters, 2011
... Phys. Lett. 512 (2011) 92]. Authors: Khan, Sadia Afrin; Senapathi, Dulal; Senapathi, Tapas; L... more ... Phys. Lett. 512 (2011) 92]. Authors: Khan, Sadia Afrin; Senapathi, Dulal; Senapathi, Tapas; Liao, Meng-Sheng; Bonifassi, P.; Fan, Zhen; Singh, Anant Kumar; Neeley, Adria; Hill, Glake; Huang, Ming-Ju; Watts, John D.; Ray, Paresh Chandra. ...
Chemical Physics Letters, 2011
Using solution-based method, silver quantum clusters of different sizes (Ag 20 , Ag 140 and Ag 98... more Using solution-based method, silver quantum clusters of different sizes (Ag 20 , Ag 140 and Ag 980 ) have been synthesized and their first hyper-polarizabilities were measured using hyper-Rayleigh scattering technique. We have shown that nonlinear optical properties of silver quantum cluster are highly dependent on the size of quantum cluster. Time-dependent density functional theory calculations using the Amsterdam Density Functional (ADF) program package are used to evaluate linear and nonlinear optical properties of silver tetrahedral Ag n (n = 10, 20, 35, 56) clusters. Both theoretical and experimental data have shown that nonlinear as well as linear optical properties are highly dependent on the size of silver quantum cluster.
International Journal of Quantum Chemistry, 2001
Studies of structures, energetics, and charge distribution were performed for ground and lowest e... more Studies of structures, energetics, and charge distribution were performed for ground and lowest excited electronic states of MeCl2(NH3)2, Me=Pd and Pt complexes. Despite the similarity of the Pd and Pt elements, the differences in isomerization energies, ground-excited state separation energy, and electronic density distribution are significant. The MeN and MeCl bonds possess a different nature with the Cl accepting and the NH3 group donating electrons to the central metal. The bonds are more polarized in Pt-based complexes. The electronic excitations involve mostly the metal atom, and although they do not change the structure drastically, the excitations do, however, impact the charge distribution. Interaction energy decomposition for the ground state indicates that ammonia–metal interactions are dominated by the energy delocalization term. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 213–219, 2001
Chemical Physics Letters, 2003
For the first time, the physical nature of intermolecular interactions between 10 DNA stacked bas... more For the first time, the physical nature of intermolecular interactions between 10 DNA stacked bases has been examined by an interaction energy decomposition method based on the variation-perturbation theory. The dominant correlation term including dispersion interactions is found to be cancelled to a considerable extent by exchange and delocalization contributions leaving the relatively smaller long range electrostatic contribution as the most important factor determining relative stacking interaction energies. The electrostatic multipole component closely mimics the trend of total interaction energy in all considered systems.
Polymer, 2011
The molecular interactions of phosphorous ylide (PY) and hypohalous acids HOX (X = F, Cl and Br) ... more The molecular interactions of phosphorous ylide (PY) and hypohalous acids HOX (X = F, Cl and Br) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. The patterns including non-classical hydrogen bond HÁ Á ÁC, halogen bond XÁ Á ÁC, classical hydrogen bonds HÁ Á ÁX and HÁ Á ÁO, and FÁ Á ÁP interactions were found for complex formation between PY and HOX molecules. From the predicted models, stabilities of the XÁ Á ÁC and HÁ Á ÁC types complexes are greater than other types. Quantum theories of atoms in molecules (AIM) and natural bond orbitals (NBO) methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the secondorder perturbation energies E (2) and the charge transfer qCT in the studied systems.
Journal of Biomolecular Structure & Dynamics, 2003
We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pa... more We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6–31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6–31G(d,p), MP2/6–31++G(d,p), and MP2/6–311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.
Journal of Biomolecular Structure & Dynamics, 2003
Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) ... more Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries of the local minima were optimized without symmetry restrictions by the gradient procedure at DFT level of theory and were verified by energy second derivative calculations. The standard 6–31G(d) basis set was used. The single-point calculations have been performed at the MP2/6–31G(d,p), MP2/6–31++G(d,p), and MP2/6–311++G(2d,2p) levels of theory. The geometrical parameters, relative stability and counterpoise corrected interaction energies are reported. Also, using a variation-perturbation energy decomposition scheme we have found the vital contributions to the total interaction energy.
Journal of Physical Chemistry B, 2006
Minor tautomers of nucleic acid bases can result by intramolecular proton transfer. These rare ta... more Minor tautomers of nucleic acid bases can result by intramolecular proton transfer. These rare tautomers could be stabilized through the addition of methyl groups to DNA bases. A comprehensive theoretical study of tautomers of methylated derivatives of guanine, adenine, cytosine, thymine, and uracil was performed. Molecular geometries of all tautomers were obtained at the density functional theory and MP2 levels with the 6-31G(d,p) basis set, and single-point calculations were performed at the CCSD(T)/6-311G(d,p) level. Tautomers obtained by protonation at the preferred protonation site for methylated isolated bases were compared to their nonmethylated counterparts. The effects of methylation on the relative stabilities of nucleic acid base tautomers are also studied and discussed in this work. The results suggest that some sites on the bases may not be mutagenic and may even stabilize the canonical Watson-Crick form. The results also indicate that a number of methylation sites can stabilize the tautomers, suggesting possible mechanisms for mutagenic changes.
Structural Chemistry, 2010
Molecularly imprinted polymers can be used for molecular recognition and design of detection devi... more Molecularly imprinted polymers can be used for molecular recognition and design of detection devices. During molecular imprinting, a monomer, such as methacrylic acid, is used to encapsulate a template like an explosive. Selective lock–key system build through specific intermolecular interactions is formed. The 2,6-dinitrotoluene has been chosen for this study as an example of highly energetic material whose detection is in demand. This study presents density functional theory and MP2 calculations on structural and vibrational properties of dinitrotoluene–methacrylic acid complex as well as description of the nature of interactions within this complex. Additionally, theoretical and experimental IR spectra along with vibrational assignments are reported.
Journal of Physical Chemistry C, 2010
The foreign atom doping influences the properties of carbon materials, and it is a possible way o... more The foreign atom doping influences the properties of carbon materials, and it is a possible way of designing materials of desired characteristics. Density functional calculations have been carried out on various isomers of boron-doped (4,0) and (9,0) carbon nanotubes as templates to investigate the doping effect on the structure and electronic properties on such systems. The results indicate that these boron-doped carbon nanotubes show local structural changes, mostly due to the elongation of bonds. The insertion of heteroatoms perturbs the π-conjugation system, which, in effect, destabilizes the material through higher energy cost of formation. The position of the foreign atom controls the new organization of electron density and leads to one of two possible distributions, viz., global (where electron density is distributed over the molecular surface) or local (localized distribution of electron density). This feature, in turn, can influence the bonding of the reactants while interacting with the surface. The charge distribution at a particular boron-doped site always possesses the local characteristics with a positively charged boron atom surrounded by negatively charged carbons. Such a character is also a measure of the driving force for influencing the substitution reaction in the vicinity of boron through an ionic mechanism.
Journal of Biomolecular Structure & Dynamics, 2003
Ab initio techniques were used to determine the effects of protonation and methylation on cytosin... more Ab initio techniques were used to determine the effects of protonation and methylation on cytosine's molecular geometry, molecular affinities, relative stability, and structural rigidity. The geometries of local minima were fully optimized by the gradient procedure at DFT and MP2 levels of theory with the medium size 6–31G(d,p) basis set. The results of energetic analysis indicate that N(3)-methyl-cytosine and C(5)-methyl-cytosine are the most stable derivatives for monocationic and neutral species, respectively. The structural rigidity of each species was assessed by an analysis of normal out-of-plane frequencies, the amplitudes, and by the contribution of internal coordinates to the potential energy distributions. The obtained evidence suggests that methylation increases the overall structural flexibility of cytosine and that all molecules in this study populate a non-planar conformation 50% of the time.