A series of one-photon absorption spectra for fluorene-based donor-pi-acceptor molecules is prese... more A series of one-photon absorption spectra for fluorene-based donor-pi-acceptor molecules is presented and spectroscopically assigned, based upon the results obtained from time-dependent density functional theory. The computed excitation energies were generally shown to be in good agreement with experiment, particularly when compared to results from measurements carried out in a nonpolar solvent, which were available for some molecules. The computed oscillator strengths may resolve discordant experimental values in some cases, for example, for AF-380, AF-270, and AF-295. However, a quantitative comparison between computed and observed oscillator strengths is complicated by band overlapping. Thus, the computed extinction coefficients obtained by summing over the Gaussian bands are useful in such cases.
We report a comprehensive time-dependent density functional theory (TDDFT) study of one-photon an... more We report a comprehensive time-dependent density functional theory (TDDFT) study of one-photon and two-photon absorption (OPA and TPA, respectively) spectra for donor-pi-acceptor molecules. The calculated excitation energies were generally shown to be in good agreement with experiment, particularly when compared to results from measurements carried out in a nonpolar solvent, although the oscillator strengths were overestimated in some cases. Calculated TPA cross sections applying the two-state approximation were shown to be highly dependent on the form of the line-shape function used. Although a good agreement with experimental TPA spectra was generally observed, the wide range in the experimentally measured values and lack of systematic experimental data on solvent effects limited a detailed comparison as yet.
In our ongoing studies to gain insight into the photophysical properties of nonlinear optical mat... more In our ongoing studies to gain insight into the photophysical properties of nonlinear optical materials, including reverse saturable and two-photon absorbing organic molecules, also in the condensed phase, we recently reported a series of systematic studies using time-dependent density functional theory. Further validation and quantitative prediction of properties for extended molecular systems will be reported. In addition, two-photon absorption cross-sections and excitation energies for a series of substituted stilbenes, including combinations of donor-donor, acceptor-acceptor, and donor acceptor molecular systems, in careful comparison with experimental data, will be discussed in detail.
Page 1. 5998 J. Am. Chem. SOC. 1991, 113, 5998-6001 Systematic Survey of Cyclic Silicon-Oxygen Co... more Page 1. 5998 J. Am. Chem. SOC. 1991, 113, 5998-6001 Systematic Survey of Cyclic Silicon-Oxygen Compounds Michael W. Schmidt,t Kiet A. Nguyen,? Mark S. Gordon,*'t and John A. Montgomery, Jr.t Contribution from the ...
Page 1. Theoretical studies of spin-forbidden radiation less decay in polyatomic systems. II. Rad... more Page 1. Theoretical studies of spin-forbidden radiation less decay in polyatomic systems. II. Radiationless decay of aN 2 0 2 Kiet A. Nguyen and Mark S. Gordon Iowa State University, Ames, Iowa 50011-3111 John A. Montgomery, Jr. ...
A macrocyclic, peptidomimetic inhibitor of peptide deformylase was designed by covalently cross-l... more A macrocyclic, peptidomimetic inhibitor of peptide deformylase was designed by covalently cross-linking the P1' and P3' side chains. The macrocycle, which contains an N-formylhydroxylamine side chain as the metal-chelating group, was synthesized from a diene precursor via olefin metathesis using Grubbs's catalyst. The cyclic inhibitor showed potent inhibitory activity toward Escherichia coli deformylase (K(I) = 0.67 nM) and antibacterial activity against both Gram-positive and Gram-negative bacteria (MIC = 0.7-12 microg/mL).
Proceedings of Spie the International Society For Optical Engineering, 2009
The optical properties of gold nanoclusters of size 2 - 20 have been investigated using time-depe... more The optical properties of gold nanoclusters of size 2 - 20 have been investigated using time-dependent density functional theory (TDDFT) to simulate their linear absorption spectra. Relativistic effects have been included by using pseudopotentials, with the Douglas-Kroll (DK) approximation, and with the zero-order regular approximation (ZORA). The improved model core potential with scaled relativistic effects (iMCP-SR2) used in combination with either the BP86, BLYP, or B3LYP exchange-correlation density functional was found to fairly accurately model the spectra of clusters for which measured spectra are available, although the all-electron ZORA method was best both for accuracy and computational efficiency. The effects on the optical properties of organic chromophores from coordination with small gold clusters were preliminarily studied. The extent of enhancement of the absorption properties is seen to depend on the size and structure of the gold cluster.
The emergence of bacterial pathogens resistant to current antibiotics has caused an urgent demand... more The emergence of bacterial pathogens resistant to current antibiotics has caused an urgent demand for new treatments. Peptide deformylase (PDF) has become an exciting target for designing novel antibiotics. To facilitate the screening of PDF inhibitors, three robust, coupled assays have been developed. The first method couples the PDF reaction with that of formate dehydrogenase. Formate dehydrogenase oxidizes formate into CO2 with a concomitant reduction of NAD+ to NADH, which can be monitored spectrophotometrically. The second method involves Aeromonas aminopeptidase (AAP) as the coupling enzyme and an artificial substrate, f-Met-Leu-p-nitroanilide. The sequential action of PDF and AAP releases p-nitroanilide as a highly chromogenic product. In the third method, f-Met-Lys-7-amino-4-methylcoumarin is used as the substrate. Deformylation by PDF gives an excellent substrate for dipeptidyl peptidase I, which releases the dipeptide Met-Lys and fluorogenic 7-amino-4-methylcoumarin. The combination of these assay methods should meet the needs of most laboratories.
Although two-photon absorbing organic materials are increasingly recognized as important for a va... more Although two-photon absorbing organic materials are increasingly recognized as important for a variety of technological applications, it is difficult to obtain predictive molecular structure-to-property relationships for these compounds. In this study we investigate the potential of time-dependent density functional theory as an accurate and computationally feasible method for the prediction of two-photon absorption spectra. We show that the calculated excited-state energies for the smaller conjugated polyenes and their phenylated analogs are in good agreement with experiment, as well as with the highest level of theoretical predictions to date. Calculated two-photon absorption cross-sections are reported for these compounds, and compared with previously calculated values and with available experimental data. Our results indicate that these moelcular systems may have a larger potential as two-photon absorbing materials than has been previously estimated.
In our continuing efforts to design nonlinear optical materials, conjugated polyenes that exhibit... more In our continuing efforts to design nonlinear optical materials, conjugated polyenes that exhibit the two-photon absorption mechanism, are being studied. The accurate prediction of the absorption frequencies and cross-sections for the relatively large molecular systems of interest is difficult due to both the high level of ab initio calculations required for evaluating excited state energies and transition dipole moments, as well as the modeling of the material's behavior in the condensed phase. In this study we present multi-configurational self-consistent field geometry optimization results, in the gas-phase and in solution, for hexatriene, octatetraene, and several of their substituted analogs. Solvent effects are modeled using our newly developed effective fragment potential method. Transition dipole moment calculations are also discussed, from which the two-photon absorption cross-sections are estimated. This approach consists the first stage towards defining a general approach to predict the optical properties of two-photon absorbing materials in solution.
A series of one-photon absorption spectra for fluorene-based donor-pi-acceptor molecules is prese... more A series of one-photon absorption spectra for fluorene-based donor-pi-acceptor molecules is presented and spectroscopically assigned, based upon the results obtained from time-dependent density functional theory. The computed excitation energies were generally shown to be in good agreement with experiment, particularly when compared to results from measurements carried out in a nonpolar solvent, which were available for some molecules. The computed oscillator strengths may resolve discordant experimental values in some cases, for example, for AF-380, AF-270, and AF-295. However, a quantitative comparison between computed and observed oscillator strengths is complicated by band overlapping. Thus, the computed extinction coefficients obtained by summing over the Gaussian bands are useful in such cases.
We report a comprehensive time-dependent density functional theory (TDDFT) study of one-photon an... more We report a comprehensive time-dependent density functional theory (TDDFT) study of one-photon and two-photon absorption (OPA and TPA, respectively) spectra for donor-pi-acceptor molecules. The calculated excitation energies were generally shown to be in good agreement with experiment, particularly when compared to results from measurements carried out in a nonpolar solvent, although the oscillator strengths were overestimated in some cases. Calculated TPA cross sections applying the two-state approximation were shown to be highly dependent on the form of the line-shape function used. Although a good agreement with experimental TPA spectra was generally observed, the wide range in the experimentally measured values and lack of systematic experimental data on solvent effects limited a detailed comparison as yet.
In our ongoing studies to gain insight into the photophysical properties of nonlinear optical mat... more In our ongoing studies to gain insight into the photophysical properties of nonlinear optical materials, including reverse saturable and two-photon absorbing organic molecules, also in the condensed phase, we recently reported a series of systematic studies using time-dependent density functional theory. Further validation and quantitative prediction of properties for extended molecular systems will be reported. In addition, two-photon absorption cross-sections and excitation energies for a series of substituted stilbenes, including combinations of donor-donor, acceptor-acceptor, and donor acceptor molecular systems, in careful comparison with experimental data, will be discussed in detail.
Page 1. 5998 J. Am. Chem. SOC. 1991, 113, 5998-6001 Systematic Survey of Cyclic Silicon-Oxygen Co... more Page 1. 5998 J. Am. Chem. SOC. 1991, 113, 5998-6001 Systematic Survey of Cyclic Silicon-Oxygen Compounds Michael W. Schmidt,t Kiet A. Nguyen,? Mark S. Gordon,*'t and John A. Montgomery, Jr.t Contribution from the ...
Page 1. Theoretical studies of spin-forbidden radiation less decay in polyatomic systems. II. Rad... more Page 1. Theoretical studies of spin-forbidden radiation less decay in polyatomic systems. II. Radiationless decay of aN 2 0 2 Kiet A. Nguyen and Mark S. Gordon Iowa State University, Ames, Iowa 50011-3111 John A. Montgomery, Jr. ...
A macrocyclic, peptidomimetic inhibitor of peptide deformylase was designed by covalently cross-l... more A macrocyclic, peptidomimetic inhibitor of peptide deformylase was designed by covalently cross-linking the P1' and P3' side chains. The macrocycle, which contains an N-formylhydroxylamine side chain as the metal-chelating group, was synthesized from a diene precursor via olefin metathesis using Grubbs's catalyst. The cyclic inhibitor showed potent inhibitory activity toward Escherichia coli deformylase (K(I) = 0.67 nM) and antibacterial activity against both Gram-positive and Gram-negative bacteria (MIC = 0.7-12 microg/mL).
Proceedings of Spie the International Society For Optical Engineering, 2009
The optical properties of gold nanoclusters of size 2 - 20 have been investigated using time-depe... more The optical properties of gold nanoclusters of size 2 - 20 have been investigated using time-dependent density functional theory (TDDFT) to simulate their linear absorption spectra. Relativistic effects have been included by using pseudopotentials, with the Douglas-Kroll (DK) approximation, and with the zero-order regular approximation (ZORA). The improved model core potential with scaled relativistic effects (iMCP-SR2) used in combination with either the BP86, BLYP, or B3LYP exchange-correlation density functional was found to fairly accurately model the spectra of clusters for which measured spectra are available, although the all-electron ZORA method was best both for accuracy and computational efficiency. The effects on the optical properties of organic chromophores from coordination with small gold clusters were preliminarily studied. The extent of enhancement of the absorption properties is seen to depend on the size and structure of the gold cluster.
The emergence of bacterial pathogens resistant to current antibiotics has caused an urgent demand... more The emergence of bacterial pathogens resistant to current antibiotics has caused an urgent demand for new treatments. Peptide deformylase (PDF) has become an exciting target for designing novel antibiotics. To facilitate the screening of PDF inhibitors, three robust, coupled assays have been developed. The first method couples the PDF reaction with that of formate dehydrogenase. Formate dehydrogenase oxidizes formate into CO2 with a concomitant reduction of NAD+ to NADH, which can be monitored spectrophotometrically. The second method involves Aeromonas aminopeptidase (AAP) as the coupling enzyme and an artificial substrate, f-Met-Leu-p-nitroanilide. The sequential action of PDF and AAP releases p-nitroanilide as a highly chromogenic product. In the third method, f-Met-Lys-7-amino-4-methylcoumarin is used as the substrate. Deformylation by PDF gives an excellent substrate for dipeptidyl peptidase I, which releases the dipeptide Met-Lys and fluorogenic 7-amino-4-methylcoumarin. The combination of these assay methods should meet the needs of most laboratories.
Although two-photon absorbing organic materials are increasingly recognized as important for a va... more Although two-photon absorbing organic materials are increasingly recognized as important for a variety of technological applications, it is difficult to obtain predictive molecular structure-to-property relationships for these compounds. In this study we investigate the potential of time-dependent density functional theory as an accurate and computationally feasible method for the prediction of two-photon absorption spectra. We show that the calculated excited-state energies for the smaller conjugated polyenes and their phenylated analogs are in good agreement with experiment, as well as with the highest level of theoretical predictions to date. Calculated two-photon absorption cross-sections are reported for these compounds, and compared with previously calculated values and with available experimental data. Our results indicate that these moelcular systems may have a larger potential as two-photon absorbing materials than has been previously estimated.
In our continuing efforts to design nonlinear optical materials, conjugated polyenes that exhibit... more In our continuing efforts to design nonlinear optical materials, conjugated polyenes that exhibit the two-photon absorption mechanism, are being studied. The accurate prediction of the absorption frequencies and cross-sections for the relatively large molecular systems of interest is difficult due to both the high level of ab initio calculations required for evaluating excited state energies and transition dipole moments, as well as the modeling of the material's behavior in the condensed phase. In this study we present multi-configurational self-consistent field geometry optimization results, in the gas-phase and in solution, for hexatriene, octatetraene, and several of their substituted analogs. Solvent effects are modeled using our newly developed effective fragment potential method. Transition dipole moment calculations are also discussed, from which the two-photon absorption cross-sections are estimated. This approach consists the first stage towards defining a general approach to predict the optical properties of two-photon absorbing materials in solution.
In Vietnam, the load induced by earthquake had not been considered in the structure design until ... more In Vietnam, the load induced by earthquake had not been considered in the structure design until 2006, when the Code Design of Structures for Earthquake Resistances was first issued. However, this Code is prepared only for the building design. Hence, there still exists the quest regarding the importance of seismic load in the design of Port Structures which are often associated with high seismic risk. The aim of this study is to look into whether it is necessary to consider this type of load in the Port structure design.
Uploads
Papers