Kurt Kistler - Academia.edu (original) (raw)

Papers by Kurt Kistler

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

arXiv (Cornell University), Mar 27, 2024

DNA regulation and repair processes require direct interactions between proteins and DNA at speci... more DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses-both at the ensemble and singlemolecule levels-to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.

Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-sp... more Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of ‘internally-labeled’ (iCy3)2dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conform...

Regulatory Toxicology and Pharmacology, 2016

The study objective was to determine the effect of variable power applied to the atomizer of refi... more The study objective was to determine the effect of variable power applied to the atomizer of refillable tank based e-cigarette (EC) devices. Five different devices were evaluated, each at four power levels. Aerosol yield results are reported for each set of 25 EC puffs, as mass/puff, and normalized for the power applied to the coil, in mass/watt. The range of aerosol produced on a per puff basis ranged from 1.5 to 28 mg, and, normalized for power applied to the coil, ranged from 0.27 to 1.1 mg/watt. Aerosol samples were also analyzed for the production of formaldehyde, acetaldehyde, and acrolein, as DNPH derivatives, at each power level. When reported on mass basis, three of the devices showed an increase in total aldehyde yield with increasing power applied to the coil, while two of the devices showed the opposite trend. The mass of formaldehyde, acetaldehyde, and acrolein produced per gram of total aerosol produced ranged from 0.01 to 7.3 mg/g, 0.006 to 5.8 mg/g, and <0.003 to 0.78 mg/g, respectively. These results were used to estimate daily exposure to formaldehyde, acetaldehyde, and acrolein from EC aerosols from specific devices, and were compared to estimated exposure from consumption of cigarettes, to occupational and workplace limits, and to previously reported results from other researchers.

Journal of Chemical Education, 2014

This article shows the potential for using video responses to specific questions as part of the a... more This article shows the potential for using video responses to specific questions as part of the assessment process in an organic chemistry class. These exercises have been used with a postbaccalaureate cohort of 40 students, learning in an online environment, over a period of four years. A second cohort of 25 second-year students taking the organic chemistry course onsite has been using these exercises over a period of three years. The questions in this exercise require the students to use a molecular model kit. The problems presented to the students involve standard concepts in organic chemistry relating to geometric issues with molecules or organic reactions. This method of assessment allows the instructor to see a student's higher-order thinking on a particular topic to a greater degree than is generally afforded with clicker questions. Students are acclimated to this new environment for assessment through practice exercises that are evaluated and critiqued, but not counted towards a grade. A transition to similar exercises follows that counts towards the students' grades. Constructive feedback to the students for their nongraded and graded responses, as well as the types of errors and misconceptions they display in their videos, are also described.

Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco, 2015

The purpose of this study was to evaluate sweet-flavored electronic cigarette (EC) liquids for th... more The purpose of this study was to evaluate sweet-flavored electronic cigarette (EC) liquids for the presence of diacetyl (DA) and acetyl propionyl (AP), which are chemicals approved for food use but are associated with respiratory disease when inhaled. In total, 159 samples were purchased from 36 manufacturers and retailers in 7 countries. Additionally, 3 liquids were prepared by dissolving a concentrated flavor sample of known DA and AP levels at 5%, 10%, and 20% concentration in a mixture of propylene glycol and glycerol. Aerosol produced by an EC was analyzed to determine the concentration of DA and AP. DA and AP were found in 74.2% of the samples, with more samples containing DA. Similar concentrations were found in liquid and aerosol for both chemicals. The median daily exposure levels were 56 μg/day (IQR: 26-278 μg/day) for DA and 91 μg/day (IQR: 20-432 μg/day) for AP. They were slightly lower than the strict NIOSH-defined safety limits for occupational exposure and 100 and 10 ...

The journal of physical chemistry. A, Jan 6, 2007

The ultrafast radiationless decay mechanism for cytosine has been shown to be in part dependent u... more The ultrafast radiationless decay mechanism for cytosine has been shown to be in part dependent upon high vertical excitation, while slower fluorescence displayed in some cytosine analogs is generally linked to lower vertical excitation energies. To probe how excitation energies relate to pyrimidine structure, substituent effects on the vertical excitation energies for a number of derivatives of 2-pyrimidin-(1H)-one (2P) have been calculated using multireference configuration-interaction ab initio methods. Substitutions using groups with pi electron donating, withdrawing and conjugation-extending properties at the C(4) and C(5) positions on the 2P system give predictive trends for the first three singlet excited-state energies. The S(1) pipi* energies of 2P derivatives involving C4 substitution vary linearly with the Hammett substituent parameter sigma(P)+. Cytosine is shown to have the highest bright pipi* energy of the 2P derivatives presented, with that energy being strongly depe...

The Journal of biological chemistry, Jan 8, 1994

The catalysis of the hydration of CO2 by human carbonic anhydrase II (HCA II) includes the transf... more The catalysis of the hydration of CO2 by human carbonic anhydrase II (HCA II) includes the transfer of a proton from zinc-bound water to histidine 64 utilizing a network of intervening hydrogen-bonded water molecules, then the proton is transferred to buffer in solution. We used stopped-flow spectrophotometry and 18O exchange between CO2 and water measured by mass spectrometry to compare catalytic constants dependent on proton transfer in HCA II and in the mutant H64A HCA II containing the replacement His64-->Ala. Maximal velocities and oxygen-18 exchange catalyzed by H64A HCA II showed that nearly all of the proton transfer with this mutant proceeded through the imidazole buffer. The following parameters were very similar or identical in catalysis by H64A HCA II compared with catalysis by wild-type HCA II both in the presence of large concentrations of imidazole (100 mM): the maximal rate of initial velocity and of exchange of 18O between CO2 and water, solvent hydrogen isotope ...

ABSTRACT Nonadiabatic processes play an important role on the excited state dynamics of chemical ... more ABSTRACT Nonadiabatic processes play an important role on the excited state dynamics of chemical systems. Conical intersections (actual potential energy surface crossings) of two states have been established to facilitate nonadiabatic processes of molecules and radicals in the gas phase. More recently three-state conical intersections have made their appearance and may also play a key role in nonadiabatic processes. Here we present studies where the importance of conical intersections is being investigated in photoinitiated processes of biologically relevant systems, and particularly the nucleobases and their analogs. Large scale ab initio multireference configuration interaction methods (MRCI) are being used. Our results show the presence of many seams of two- or three-state conical intersections that can complicate the potential energy surfaces and dynamics of these systems. Solvent effects on conical intersections are first being investigated using clusters of water with the system. A mixed quantum mechanical/ classical mechanical (QM/MM) approach where the solute is described with the MRCI method will also be presented as a means to study the effect of the solvent on excited states.

ABSTRACT Three-state conical intersections, actual degeneracies between three electronic states t... more ABSTRACT Three-state conical intersections, actual degeneracies between three electronic states that are not imposed by symmetry, have been shown in recent years to be present in many polyatomic molecules. These features may exist when there are at least five degrees of freedom present in the molecule. Their importance and effect on nonadiabatic dynamics, however, are not well understood. We have investigated the importance of two- and three-state conical intersections in photoinitiated processes of biologically relevant systems, and particularly the nucleic acid bases and their analogs. Three-state conical intersections have been located using multi-reference configuration-interaction ab initio methods. The potential energy surfaces for each base contain many different seams of three-state intersections. Paths along seams from these intersections are shown to be connected to well characterized stationary points involved in radiationless decay pathways. Nonadiabatic coupling terms have also been calculated, and the effects of the proximal third state on these quantities are detailed. In particular, it is shown that when one of these loops incorporates more than one seam point there is a profound and predictable effect on the phase of the nonadiabatic coupling terms, and as such provides a diagnostic for the presence and location of additional seams.

International Journal of Chemistry, 2013

A series of novel 3-cyclohexyl-2-phenyl-1,3-thiazolidin-4-one derivatives with substituents on th... more A series of novel 3-cyclohexyl-2-phenyl-1,3-thiazolidin-4-one derivatives with substituents on the 2-phenyl ring were synthesized, and a study of their solid state and solution conformations was effected. In solution the thiazolidin-4-one ring preferred the C2 phenyl in a pseudo-equatorial orientation and the solid state indicated a preference for the C2 phenyl being in a pseudo-axial orientation. Less robust substituent chemical shift (SCS) correlations utilizing 13 C NMR were observed in this instance than in prior studies. Molecular modeling studies using Møller-Plessett second-order perturbation theory (MP2) indicate that the thiazolidinone ring and cyclohexyl ring conformations exhibit a global minimum consistent with the solution studies.

Multi-scale Quantum Models for Biocatalysis, 2009

ABSTRACT This chapter reviews current computational studies of the photophysical behavior of DNA ... more ABSTRACT This chapter reviews current computational studies of the photophysical behavior of DNA and RNA bases. The theoretical concepts and electronic structure methods appropriate for computational photophysical and photochemical studies are presented. The natural nucleobases have ultrashort excited state lifetimes and very low quantum yields for fluorescence. Quantum chemical calculations revealing radiationless decay pathways that quench fluorescence are discussed

The photophysical properties of gas phase 5-methyl-2-pyrimidinone, a fluorescent DNA/RNA pyrimidi... more The photophysical properties of gas phase 5-methyl-2-pyrimidinone, a fluorescent DNA/RNA pyrimidine analog, have been calculated using multi-reference configuration-interaction with three levels of dynamical electron correlation included. The bright state at vertical excitation is S2 (pipi*) at 4.42 eV. An S1-S2 seam originates close to vertical, and a gradient pathway from this seam leads to a global minimum on the S1 surface. A conical intersection between S1 and S0 (ci01) was found, but all levels of theory show that this conical intersection is significantly higher than the minimum, supporting fluorescence from S1. The details for this energetic inaccessibility, and the emission energy calculated (2.36 - 2.75 eV), depend on the level of theory used. Pathways along the S1 surface when no dynamical or intermediate dynamical correlation is included show a small barrier along with a second minimum in the S1 path from vertical to ci01. When higher level of correlation is included (˜1...

The photophysical and photochemical behavior of nucleobases is very important because of their bi... more The photophysical and photochemical behavior of nucleobases is very important because of their biological role as the building blocks in DNA and RNA. Great progress has been made in understanding the excited-state properties of single bases. In order to understand the photophysical properties of nucleobases in complex environments we have investigated their excited states (a) in aqueous solutions and (b) as pi-stacked dimers in DNA. The solvatochromic shifts of the excited states of pyrimidine nucleobases in aqueous solution have been investigated using a combined QM/MM procedure where the quantum mechanical solute is described using high level multireference configuration interaction methods while molecular dynamics simulations are used to obtain the structure of the solvent around the solute in an average way. The excited states of pi-stacked nucleobases have also been investigated using various ab initio methods. The effect of the environment on the excited states and conical int...

The Journal of Physical Chemistry B, 2008

2-Aminopurine (2AP) is an adenine analogue that has a high fluorescence quantum yield. Its fluore... more 2-Aminopurine (2AP) is an adenine analogue that has a high fluorescence quantum yield. Its fluorescence yield decreases significantly when the base is incorporated into DNA, making it a very useful real-time probe of DNA structure. However, the basic mechanism underlying 2AP fluorescence quenching by base stacking is not well understood. A critical element in approaching this problem is obtaining an understanding of the electronic structure of the excited state. We have explored the excited state properties of 2AP and 2-amino,9methylpurine (2A9MP) in frozen solutions using Stark spectroscopy. The experimental data were correlated with high level ab initio (MRCI) calculations of the dipole moments, µ b 0 and µ b 1 , of the ground and excited states. The magnitude and direction of the dipole moment change, ∆µ b 01 ) µ b 1µ b 0 , of the lowest energy optically allowed transition was determined. While other studies have reported on the magnitude of the dipole moment change, we believe that this is the first report of the direction of ∆µ b, a quantity that will be of great value in interpreting absorption spectral changes of the 2AP chromophore. Polarizability changes due to the transition were also obtained.

The Journal of Physical Chemistry B, 2010

The singlet excited electronic states of two pi-stacked thymine molecules and their splittings du... more The singlet excited electronic states of two pi-stacked thymine molecules and their splittings due to electronic coupling have been investigated with a variety of computational methods. Focus has been given on the effect of intermolecular distance on these energies and couplings. Single-reference methods, CIS, CIS(2), EOM-CCSD, TDDFT, and the multireference method CASSCF, have been used, and their performance has been compared. It is found that the excited-state energies are very sensitive to the applied method but the couplings are not as sensitive. Inclusion of diffuse functions in the basis set also affects the excitation energies significantly but not the couplings. TDDFT is inadequate in describing the states and their coupling, while CIS(2) gives results very similar to EOM-CCSD. Excited states of cytosine and adenine pi-stacked dimers were also obtained and compared with those of thymine dimers to gain a more general picture of excited states in pi-stacked DNA base dimers. The coupling is very sensitive to the relative position and orientation of the bases, indicating great variation in the degree of delocalization of the excited states between stacked bases in natural DNA as it fluctuates.

The Journal of Physical Chemistry B, 2012

Using a single-mode Holstein Hamiltonian with through-space excitonic couplings evaluated quantum... more Using a single-mode Holstein Hamiltonian with through-space excitonic couplings evaluated quantum mechanically, the absorption, circular dichroism, and photoluminescence spectral line shapes of a chiral perylene diimide dimer complex were accurately reproduced. In general, a dimer consisting of two chromophores related through a C(2) rotation is neither a J- nor an H-aggregate because oscillator strength is divided between the top and bottom of the exciton band. The division gives rise to the two Davydov components per vibronic band in the absorption spectrum. Nevertheless, it is shown that the vibronic structure of the absorption component polarized in the same direction as the lower (upper) Davydov component is identical to what one would obtain from an ideal J- (H-) aggregate. Emission generally contains both polarization components, but the component polarized in the same direction as the lower (upper) Davydov component behaves similarly to the emission from an ideal J- (H-) aggregate. The basic photophysical behavior also applies to molecular crystals containing two molecules per unit cell in which the interactions between inequivalent molecules dominate over interactions between equivalent molecules.