Laurence Nafie | Syracuse University (original) (raw)

Papers by Laurence Nafie

Research paper thumbnail of Theory of vibrational circular dichroism

The Journal of Physical Chemistry, 1985

Research paper thumbnail of Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments

Molecules, 2018

Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolu... more Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed.

Research paper thumbnail of A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion

Theoretical Chemistry Accounts, Apr 18, 2007

Research paper thumbnail of Calculation of Vibrational Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Molecular Chirality and Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Measurement of Vibrational Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Instrumentation for Raman Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Vibrational CD Spectrometers

Encyclopedia of Spectroscopy and Spectrometry, 2017

Vibrational circular dichroism (VCD) is defined as circular dichroism (CD) in vibrational transit... more Vibrational circular dichroism (VCD) is defined as circular dichroism (CD) in vibrational transitions of molecules. Hence, a VCD spectrometer is an infrared spectrometer that can measure the CD associated with infrared vibrational absorption bands. After presenting briefly the principles of a typical VCD measurement, three different VCD spectrometer designs are discussed. The simplest of these is the dispersive VCD spectrometer, and this design is used to illustrate the basic concepts associated with the electronic processing of VCD spectra. The two subsequent cases involving Fourier transform VCD spectrometers are more complex, but share the same underlying conceptual basis as the dispersive VCD spectrometer. Finally, the principal applications of VCD spectroscopy, which include measurements of the conformation, absolute configuration and enantiomeric excess of chiral molecules are discussed.

Research paper thumbnail of Raman optical activity: Spectral simulation of the conformer dependent CCl stretching vibrations in 1-chloro-2-methylbutane

Journal of Raman Spectroscopy, 1979

... PL Prasad and Laurence A. Nafie Department of Chemistry, Syracuse University, Syracuse, New Y... more ... PL Prasad and Laurence A. Nafie Department of Chemistry, Syracuse University, Syracuse, New York 13210, USA Duane F. Burow Department of Chemistry, University of Toledo, Toledo, Ohio 43606, USA ... 4, eds. RJH Clark and R. E. Hester, pp. 271-321. ...

Research paper thumbnail of Isolation, Total Synthesis, and Absolute Configuration Determination of Renoprotective Dimeric NAcetyldopamineAdenine Hybrids from the Insect Aspongopus chinensis

Research paper thumbnail of Chapter 3 Instrumental methods of infrared and Raman vibrational optical activity

Techniques and Instrumentation in Analytical Chemistry, 1994

Abstract We present the basic concepts and methods for the measurement of infrared and Raman vibr... more Abstract We present the basic concepts and methods for the measurement of infrared and Raman vibrational optical activity (VOA). These two forms of VOA are referred to as infrared vibrational circular dichroism (VCD) and Raman optical activity (ROA), respectively The principal aim of the article is to provide detailed descriptions of the instrumentation and measurement methods associated with VCD and ROA in general, and Fourier transform VCD and multichannel CCD ROA, in particular. Although VCD and ROA are closely related spectroscopic techniques, the instrumentation and measurement techniques differ markedly. These two forms of VOA will be compared and the reasons behinds their differences, now and in the future, will be explored.

Research paper thumbnail of Circular Dichroism Measurement Using Fourier Transform Interferometry

Proceedings of SPIE, Dec 1, 1989

ABSTRACT

Research paper thumbnail of Fourier Transform Vibrational Circular Dichroism In The amide I band Of Polypeptides

Proceedings of SPIE, Dec 20, 1985

ABSTRACT

Research paper thumbnail of Fourier Transform Vibrational Circular Dichroism Of Carbonyl Stretching Modes In N-urethanyl-a-amino acids

Proceedings of SPIE, Dec 20, 1985

ABSTRACT

Research paper thumbnail of Vibrational circular dichroism in the carbon-hydrogen stretching region of (+)-3(R)-methylcyclohexanone and chiral deuteriated isotopomers

Journal of the American Chemical Society, Feb 3, 1988

Research paper thumbnail of Stereochemical Aspects of Vibrational Optical Activity

Topics in Stereochemistry, Feb 26, 2007

Research paper thumbnail of Determination of the absolute configuration and solution conformation of the antifungal agents ketoconazole, itraconazole, and miconazole with vibrational circular dichroism

Chirality, 2005

The absolute configuration assignments of three antifungal agents, (+)-(2R,4S)-ketoconazole, (+)-... more The absolute configuration assignments of three antifungal agents, (+)-(2R,4S)-ketoconazole, (+)-(2R,4S)-itraconazole (with (S)-configuration at the sec-butyl group) and (+)-(S)-miconazole nitrate have been confirmed by using vibrational circular dichroism (VCD). For these three antifungal drugs, this study also provides evidence for the most abundant conformations of miconazole and for the relative conformations of the azole, dichlorophenyl, and methoxyphenyl groups in ketoconazole and itraconazole, in chloroform solution.

Research paper thumbnail of Vibrational circular dichroism in amino acids and peptides. 10. Fourier transform VCD and Fourier self-deconvolution of the amide I region of poly(γ-benzyl-L-glutamate)

Biopolymers, May 1, 1985

Vibrational CD (VCD) spectra have been obtained in the amide I region of poly(γ‐benzyl‐L‐glutamat... more Vibrational CD (VCD) spectra have been obtained in the amide I region of poly(γ‐benzyl‐L‐glutamate), using a Fourier transform ir VCD spectrometer operating at 4‐cm−1 resolution. These results reveal a new negative VCD band at 1650 cm−1 in addition to the previously observed negative positive VCD couplet centered at 1660 cm−1. Fourier self‐deconvolution (FSD) of the VCD spectrum reveals three strong VCD component bands, rather than just two, as originally supposed. FSD also resolves the absorbance spectrum into two components corresponding to the parallel polarized A mode at lower frequency, and an unresolved perpendicular polarized E1 mode at higher frequency. The VCD spectrum is reassigned on the basis of this new spectral data and the FSD‐VCD results are analyzed for the Moffitt contribution and the so‐called helical contribution. Comparison with theory shows the VCD to be more intense than expected, particularly for the helical term. Charge flow between subunits is suggested as an additional source of VCD intensity that is presently not included in theoretical exciton descriptions. The splitting of the E1 mode and the large VCD contribution attributed to the helical term implies a deviation of the polypeptide structure from perfect helical symmetry and, as a result, a mixing of the A and E1 vibrational modes.

Research paper thumbnail of SSSCPreds: Deep Neural Network-Based Software for the Prediction of Conformational Variability and Application to SARS-CoV-2

Research paper thumbnail of Isotopic difference spectra as an aide in determining absolute configuration using vibrational optical activity: Vibrational circular dichroism of13C- and2H-labelled nonamethoxy cyclotriveratrylene

Chirality, 2008

The use of isotopic difference spectra in vibrational optical activity is demonstrated as a suppl... more The use of isotopic difference spectra in vibrational optical activity is demonstrated as a supplemental aide in determining the absolute configuration of chiral molecules. It is shown that IR and VCD difference spectra associated with isotopic substitution observed in experimental spectra can be accurately reproduced by density functional theory calculations when the IR and VCD spectra of the original isotopomer are calculated to reasonable accuracy. Results for isotopically substituted nonamethoxy cyclotriveratrylene are presented to illustrate the degree of agreement between measured and calculated IR and VCD difference spectra for several isotopomers of this molecule. These findings highlight the utility of isotoptic substitution as an aide to verifying the determination of absolute configuration using vibrational optical activity. Chirality, 2008. © 2008 Wiley‐Liss, Inc.

Research paper thumbnail of Theory of vibrational circular dichroism

The Journal of Physical Chemistry, 1985

Research paper thumbnail of Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments

Molecules, 2018

Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolu... more Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed.

Research paper thumbnail of A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion

Theoretical Chemistry Accounts, Apr 18, 2007

Research paper thumbnail of Calculation of Vibrational Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Molecular Chirality and Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Measurement of Vibrational Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Instrumentation for Raman Optical Activity

Vibrational Optical Activity, 2011

Research paper thumbnail of Vibrational CD Spectrometers

Encyclopedia of Spectroscopy and Spectrometry, 2017

Vibrational circular dichroism (VCD) is defined as circular dichroism (CD) in vibrational transit... more Vibrational circular dichroism (VCD) is defined as circular dichroism (CD) in vibrational transitions of molecules. Hence, a VCD spectrometer is an infrared spectrometer that can measure the CD associated with infrared vibrational absorption bands. After presenting briefly the principles of a typical VCD measurement, three different VCD spectrometer designs are discussed. The simplest of these is the dispersive VCD spectrometer, and this design is used to illustrate the basic concepts associated with the electronic processing of VCD spectra. The two subsequent cases involving Fourier transform VCD spectrometers are more complex, but share the same underlying conceptual basis as the dispersive VCD spectrometer. Finally, the principal applications of VCD spectroscopy, which include measurements of the conformation, absolute configuration and enantiomeric excess of chiral molecules are discussed.

Research paper thumbnail of Raman optical activity: Spectral simulation of the conformer dependent CCl stretching vibrations in 1-chloro-2-methylbutane

Journal of Raman Spectroscopy, 1979

... PL Prasad and Laurence A. Nafie Department of Chemistry, Syracuse University, Syracuse, New Y... more ... PL Prasad and Laurence A. Nafie Department of Chemistry, Syracuse University, Syracuse, New York 13210, USA Duane F. Burow Department of Chemistry, University of Toledo, Toledo, Ohio 43606, USA ... 4, eds. RJH Clark and R. E. Hester, pp. 271-321. ...

Research paper thumbnail of Isolation, Total Synthesis, and Absolute Configuration Determination of Renoprotective Dimeric NAcetyldopamineAdenine Hybrids from the Insect Aspongopus chinensis

Research paper thumbnail of Chapter 3 Instrumental methods of infrared and Raman vibrational optical activity

Techniques and Instrumentation in Analytical Chemistry, 1994

Abstract We present the basic concepts and methods for the measurement of infrared and Raman vibr... more Abstract We present the basic concepts and methods for the measurement of infrared and Raman vibrational optical activity (VOA). These two forms of VOA are referred to as infrared vibrational circular dichroism (VCD) and Raman optical activity (ROA), respectively The principal aim of the article is to provide detailed descriptions of the instrumentation and measurement methods associated with VCD and ROA in general, and Fourier transform VCD and multichannel CCD ROA, in particular. Although VCD and ROA are closely related spectroscopic techniques, the instrumentation and measurement techniques differ markedly. These two forms of VOA will be compared and the reasons behinds their differences, now and in the future, will be explored.

Research paper thumbnail of Circular Dichroism Measurement Using Fourier Transform Interferometry

Proceedings of SPIE, Dec 1, 1989

ABSTRACT

Research paper thumbnail of Fourier Transform Vibrational Circular Dichroism In The amide I band Of Polypeptides

Proceedings of SPIE, Dec 20, 1985

ABSTRACT

Research paper thumbnail of Fourier Transform Vibrational Circular Dichroism Of Carbonyl Stretching Modes In N-urethanyl-a-amino acids

Proceedings of SPIE, Dec 20, 1985

ABSTRACT

Research paper thumbnail of Vibrational circular dichroism in the carbon-hydrogen stretching region of (+)-3(R)-methylcyclohexanone and chiral deuteriated isotopomers

Journal of the American Chemical Society, Feb 3, 1988

Research paper thumbnail of Stereochemical Aspects of Vibrational Optical Activity

Topics in Stereochemistry, Feb 26, 2007

Research paper thumbnail of Determination of the absolute configuration and solution conformation of the antifungal agents ketoconazole, itraconazole, and miconazole with vibrational circular dichroism

Chirality, 2005

The absolute configuration assignments of three antifungal agents, (+)-(2R,4S)-ketoconazole, (+)-... more The absolute configuration assignments of three antifungal agents, (+)-(2R,4S)-ketoconazole, (+)-(2R,4S)-itraconazole (with (S)-configuration at the sec-butyl group) and (+)-(S)-miconazole nitrate have been confirmed by using vibrational circular dichroism (VCD). For these three antifungal drugs, this study also provides evidence for the most abundant conformations of miconazole and for the relative conformations of the azole, dichlorophenyl, and methoxyphenyl groups in ketoconazole and itraconazole, in chloroform solution.

Research paper thumbnail of Vibrational circular dichroism in amino acids and peptides. 10. Fourier transform VCD and Fourier self-deconvolution of the amide I region of poly(γ-benzyl-L-glutamate)

Biopolymers, May 1, 1985

Vibrational CD (VCD) spectra have been obtained in the amide I region of poly(γ‐benzyl‐L‐glutamat... more Vibrational CD (VCD) spectra have been obtained in the amide I region of poly(γ‐benzyl‐L‐glutamate), using a Fourier transform ir VCD spectrometer operating at 4‐cm−1 resolution. These results reveal a new negative VCD band at 1650 cm−1 in addition to the previously observed negative positive VCD couplet centered at 1660 cm−1. Fourier self‐deconvolution (FSD) of the VCD spectrum reveals three strong VCD component bands, rather than just two, as originally supposed. FSD also resolves the absorbance spectrum into two components corresponding to the parallel polarized A mode at lower frequency, and an unresolved perpendicular polarized E1 mode at higher frequency. The VCD spectrum is reassigned on the basis of this new spectral data and the FSD‐VCD results are analyzed for the Moffitt contribution and the so‐called helical contribution. Comparison with theory shows the VCD to be more intense than expected, particularly for the helical term. Charge flow between subunits is suggested as an additional source of VCD intensity that is presently not included in theoretical exciton descriptions. The splitting of the E1 mode and the large VCD contribution attributed to the helical term implies a deviation of the polypeptide structure from perfect helical symmetry and, as a result, a mixing of the A and E1 vibrational modes.

Research paper thumbnail of SSSCPreds: Deep Neural Network-Based Software for the Prediction of Conformational Variability and Application to SARS-CoV-2

Research paper thumbnail of Isotopic difference spectra as an aide in determining absolute configuration using vibrational optical activity: Vibrational circular dichroism of13C- and2H-labelled nonamethoxy cyclotriveratrylene

Chirality, 2008

The use of isotopic difference spectra in vibrational optical activity is demonstrated as a suppl... more The use of isotopic difference spectra in vibrational optical activity is demonstrated as a supplemental aide in determining the absolute configuration of chiral molecules. It is shown that IR and VCD difference spectra associated with isotopic substitution observed in experimental spectra can be accurately reproduced by density functional theory calculations when the IR and VCD spectra of the original isotopomer are calculated to reasonable accuracy. Results for isotopically substituted nonamethoxy cyclotriveratrylene are presented to illustrate the degree of agreement between measured and calculated IR and VCD difference spectra for several isotopomers of this molecule. These findings highlight the utility of isotoptic substitution as an aide to verifying the determination of absolute configuration using vibrational optical activity. Chirality, 2008. © 2008 Wiley‐Liss, Inc.