# Punctuation in superscripting with Natbib in Xetex

I'm trying to use the achemso package for my bibliography and citations. I'm also trying to using Xetex to use the Minion Pro fonts. When I just typeset with LaTeX and do everything in Computer Modern I don't have any problems. However, once I switch to using Xetex and add the fontspec code, the citations don't look the way they should; the hyphens don't seem to be superscripted.

Here are the relevant code snippets:

\usepackage[usetitle=true]{achemso}
\usepackage[T1]{fontenc}
%Set up the Minion Pro font
\usepackage{fontspec,xltxtra,xunicode}
\defaultfontfeatures{Ligatures=TeX}
\setromanfont[Ligatures=TeX]{Minion Pro}
\setsansfont[Scale=MatchLowercase,Ligatures=TeX]{Gill Sans}
\setmonofont[Scale=MatchLowercase, Ligatures=TeX]{Andale Mono}

Synthetic devices have been historically easier to construct, and for a number of applications they are still preferred, but advances in nanotechnology have vastly improved our ability to work with small molecules, allowing for biological and chemical drug delivery systems based on polymer nanoparticles, hydrogels, and biological vesicles, among other possibilities \cite{langer_advances_2003,farokhzad_impact_2009,grainger_nanobiomaterials_2008,stevenson_reservoir-based_2012}.


EDIT Added the citations and an image below.

@article{langer_advances_2003,
Abstract = {Biomaterials are widely used in numerous medical applications. Chemical engineering has played a central role in this research and development. Polymers as biomaterials, materials and approaches used in drug and protein delivery systems, materials used as scaffolds in tissue engineering, and nanotechnology and microfabrication techniques applied to biomaterials are reviewed.},
Author = {Langer, Robert and Peppas, Nicholas A.},
Copyright = {Copyright {\copyright} 2003 American Institute of Chemical Engineers ({AIChE)}},
Doi = {10.1002/aic.690491202},
File = {Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/V29GB4KF/Langer and Peppas - 2003 - Advances in biomaterials, drug delivery, and biona.pdf:application/pdf;Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/AGIQ86SV/abstract.html:text/html},
Issn = {1547-5905},
Journal = {{AIChE} Journal},
Language = {en},
Number = {12},
Pages = {2990--3006},
Title = {Advances in biomaterials, drug delivery, and bionanotechnology},
Url = {http://onlinelibrary.wiley.com/doi/10.1002/aic.690491202/abstract},
Urldate = {2013-03-19},
Volume = {49},
Year = {2003},
Bdsk-Url-1 = {http://onlinelibrary.wiley.com/doi/10.1002/aic.690491202/abstract},
Bdsk-Url-2 = {http://dx.doi.org/10.1002/aic.690491202}}

Abstract = {While both organic and inorganic technologies are under development, controlled-release polymer technologies and liposomes will likely continue to have the greatest clinical impact for the foreseeable future.},
Author = {Farokhzad, Omid C. and Langer, Robert},
Doi = {10.1021/nn900002m},
File = {ACS Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/X6KASK8T/Farokhzad and Langer - 2009 - Impact of Nanotechnology on Drug Delivery.pdf:application/pdf;ACS Full Text Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/JX5A7RQ4/nn900002m.html:text/html},
Issn = {1936-0851},
Journal = {{ACS} Nano},
Month = jan,
Number = {1},
Pages = {16--20},
Title = {Impact of Nanotechnology on Drug Delivery},
Url = {http://dx.doi.org/10.1021/nn900002m},
Urldate = {2013-03-19},
Volume = {3},
Year = {2009},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/nn900002m}}

@article{grainger_nanobiomaterials_2008,
Abstract = {Nanomaterials advocated for biomedical applications must exhibit well-controlled surface properties to achieve optimum performance in complex biological or physiological fluids. Dispersed materials with extremely high specific surface areas require as extensive characterization as their macroscale biomaterials analogues. However, current literature is replete with many examples of nanophase materials, most notably nanoparticles, with little emphasis placed on reporting rigorous surface analysis or characterization, or in formal implementation of surface property standards needed to validate structure-property relationships for biomedical applications. Correlations of nanophase surface properties with their stability, toxicity and biodistributions are essential for in vivo applications. Surface contamination is likely, given their processing conditions and interfacial energies. Leaching adventitious adsorbates from high surface area nanomaterials is a possible toxicity mechanism. Polydimethylsiloxane ({PDMS)}, long known as a ubiquitous contaminant in clean room conditions, chemical synthesis and microfabrication, remains a likely culprit in nanosystems fabrication, especially in synthesis, soft lithography and contact molding methods. New standards and expectations for analyzing the interfacial properties of nanoparticles and nano-fabricated technologies are required. Surface science analytical rigor similar to that applied to biomedical devices, nanophases in microelectronics and heterogeneous catalysts should serve as a model for nanomaterials characterization in biomedical technologies.},
Author = {Grainger, D. W. and Castner, D. G.},
Copyright = {Copyright {\copyright} 2008 {WILEY-VCH} Verlag {GmbH} \& Co. {KGaA}, Weinheim},
File = {Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/HIFH3Q2H/Grainger and Castner - 2008 - Nanobiomaterials and Nanoanalysis Opportunities f.pdf:application/pdf;Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/DIVZA4TZ/abstract.html:text/html},
Issn = {1521-4095},
Journal = {Advanced Materials},
Keywords = {Biomaterials, Biomedical applications, Bionanotechnology, Nanoparticles, Polydimethylsiloxane, Surface characterization},
Language = {en},
Number = {5},
Pages = {867--877},
Shorttitle = {Nanobiomaterials and Nanoanalysis},
Title = {Nanobiomaterials and Nanoanalysis: Opportunities for Improving the Science to Benefit Biomedical Technologies},
Urldate = {2013-03-19},
Volume = {20},
Year = {2008},

@article{stevenson_reservoir-based_2012,
Abstract = {This review covers reservoir-based drug delivery systems that incorporate microtechnology, with an emphasis on oral, dermal, and implantable systems. Key features of each technology are highlighted such as working principles, fabrication methods, dimensional constraints, and performance criteria. Reservoir-based systems include a subset of microfabricated drug delivery systems and provide unique advantages. Reservoirs, whether external to the body or implanted, provide a well-controlled environment for a drug formulation, allowing increased drug stability and prolonged delivery times. Reservoir systems have the flexibility to accommodate various delivery schemes, including zero order, pulsatile, and on demand dosing, as opposed to a standard sustained release profile. Furthermore, the development of reservoir-based systems for targeted delivery for difficult to treat applications (e.g., ocular) has resulted in potential platforms for patient therapy.},
Author = {Stevenson, Cynthia L. and Santini Jr., John T. and Langer, Robert},
File = {ScienceDirect Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/PSHDRPIW/Stevenson et al. - 2012 - Reservoir-based drug delivery systems utilizing mi.pdf:application/pdf;ScienceDirect Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/4SI72XH5/S0169409X12000282.html:text/html},
Issn = {0169-{409X}},
Journal = {Advanced Drug Delivery Reviews},
Keywords = {Controlled release, Implant, {MEMS}, Microneedle, Micropump, Ocular, On demand, Pulsatile},
Month = nov,
Number = {14},
Pages = {1590--1602},
Shorttitle = {Emerging micro- and nanotechnologies for the development of novel drug delivery devices and systems},
Title = {Reservoir-based drug delivery systems utilizing microtechnology},
Url = {http://www.sciencedirect.com/science/article/pii/S0169409X12000282},
Urldate = {2013-03-21},
Volume = {64},
Year = {2012},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0169409X12000282},


EDIT 2: I've also tried removing the achemso package and directly just using natbib like so.

\usepackage[super]{natbib}


This results in no hyphens being used, but the commas are now completely out of whack. The commas now look like they are not superscripted, but there are superscripted dots separating the entries

Removing the \defaultfontfeatures seems to be much better, it leads to printing the - as -- instead, so I thought it might be an issue with the ligature for an endash being an underscore. But changing the HyphenChar doesn't really seem to change anything.

-
Welcome to TeX.sx! –  texenthusiast Apr 1 '13 at 18:02
Have you tried removing the instruction \usepackage[T1]{fontenc}? Please consider augmenting your example with the four bib entries. Because you haven't posted the part of the .bib file that contains the four entries cited, it's not possible to replicate your error; when natbib encounters undefined references, a simple ? is printed regardless of citation mode (authoryear,numeric,superscripts). –  Mico Apr 1 '13 at 18:07
Yes I've tried removing the fontenc package, it doesn't seem to do anything. And I didn't think to include the citations before, they're there now. –  Vyas Apr 1 '13 at 18:59
Did you try removing the xltxtra package? Also xunicode is not necessary. –  egreg Apr 1 '13 at 21:19

The culprit is the xltxtra package, which redefines \textsuperscript to use a font feature for which not all characters are available, in particular the hyphen and the en-dash.

Remove the package. And remove also xunicode that shouldn't be loaded explicitly any more.

The following example uses filecontents in order to be self-consistent; you don't need it, just pass the bib file name as usual to \bibliography.

\begin{filecontents*}{\jobname.bib}
Abstract = {Biomaterials are widely used in numerous medical applications. Chemical engineering has played a central role in this research and development. Polymers as biomaterials, materials and approaches used in drug and protein delivery systems, materials used as scaffolds in tissue engineering, and nanotechnology and microfabrication techniques applied to biomaterials are reviewed.},
Author = {Langer, Robert and Peppas, Nicholas A.},
Copyright = {Copyright {\copyright} 2003 American Institute of Chemical Engineers ({AIChE)}},
Doi = {10.1002/aic.690491202},
File = {Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/V29GB4KF/Langer and Peppas - 2003 - Advances in biomaterials, drug delivery, and biona.pdf:application/pdf;Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/AGIQ86SV/abstract.html:text/html},
Issn = {1547-5905},
Journal = {{AIChE} Journal},
Language = {en},
Number = {12},
Pages = {2990--3006},
Title = {Advances in biomaterials, drug delivery, and bionanotechnology},
Url = {http://onlinelibrary.wiley.com/doi/10.1002/aic.690491202/abstract},
Urldate = {2013-03-19},
Volume = {49},
Year = {2003},
Bdsk-Url-1 = {http://onlinelibrary.wiley.com/doi/10.1002/aic.690491202/abstract},
Bdsk-Url-2 = {http://dx.doi.org/10.1002/aic.690491202}}

Abstract = {While both organic and inorganic technologies are under development, controlled-release polymer technologies and liposomes will likely continue to have the greatest clinical impact for the foreseeable future.},
Author = {Farokhzad, Omid C. and Langer, Robert},
Doi = {10.1021/nn900002m},
File = {ACS Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/X6KASK8T/Farokhzad and Langer - 2009 - Impact of Nanotechnology on Drug Delivery.pdf:application/pdf;ACS Full Text Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/JX5A7RQ4/nn900002m.html:text/html},
Issn = {1936-0851},
Journal = {{ACS} Nano},
Month = jan,
Number = {1},
Pages = {16--20},
Title = {Impact of Nanotechnology on Drug Delivery},
Url = {http://dx.doi.org/10.1021/nn900002m},
Urldate = {2013-03-19},
Volume = {3},
Year = {2009},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/nn900002m}}

@article{grainger_nanobiomaterials_2008,
Abstract = {Nanomaterials advocated for biomedical applications must exhibit well-controlled surface properties to achieve optimum performance in complex biological or physiological fluids. Dispersed materials with extremely high specific surface areas require as extensive characterization as their macroscale biomaterials analogues. However, current literature is replete with many examples of nanophase materials, most notably nanoparticles, with little emphasis placed on reporting rigorous surface analysis or characterization, or in formal implementation of surface property standards needed to validate structure-property relationships for biomedical applications. Correlations of nanophase surface properties with their stability, toxicity and biodistributions are essential for in vivo applications. Surface contamination is likely, given their processing conditions and interfacial energies. Leaching adventitious adsorbates from high surface area nanomaterials is a possible toxicity mechanism. Polydimethylsiloxane ({PDMS)}, long known as a ubiquitous contaminant in clean room conditions, chemical synthesis and microfabrication, remains a likely culprit in nanosystems fabrication, especially in synthesis, soft lithography and contact molding methods. New standards and expectations for analyzing the interfacial properties of nanoparticles and nano-fabricated technologies are required. Surface science analytical rigor similar to that applied to biomedical devices, nanophases in microelectronics and heterogeneous catalysts should serve as a model for nanomaterials characterization in biomedical technologies.},
Author = {Grainger, D. W. and Castner, D. G.},
Copyright = {Copyright {\copyright} 2008 {WILEY-VCH} Verlag {GmbH} \& Co. {KGaA}, Weinheim},
File = {Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/HIFH3Q2H/Grainger and Castner - 2008 - Nanobiomaterials and Nanoanalysis Opportunities f.pdf:application/pdf;Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/DIVZA4TZ/abstract.html:text/html},
Issn = {1521-4095},
Journal = {Advanced Materials},
Keywords = {Biomaterials, Biomedical applications, Bionanotechnology, Nanoparticles, Polydimethylsiloxane, Surface characterization},
Language = {en},
Number = {5},
Pages = {867--877},
Shorttitle = {Nanobiomaterials and Nanoanalysis},
Title = {Nanobiomaterials and Nanoanalysis: Opportunities for Improving the Science to Benefit Biomedical Technologies},
Urldate = {2013-03-19},
Volume = {20},
Year = {2008},

@article{stevenson_reservoir-based_2012,
Abstract = {This review covers reservoir-based drug delivery systems that incorporate microtechnology, with an emphasis on oral, dermal, and implantable systems. Key features of each technology are highlighted such as working principles, fabrication methods, dimensional constraints, and performance criteria. Reservoir-based systems include a subset of microfabricated drug delivery systems and provide unique advantages. Reservoirs, whether external to the body or implanted, provide a well-controlled environment for a drug formulation, allowing increased drug stability and prolonged delivery times. Reservoir systems have the flexibility to accommodate various delivery schemes, including zero order, pulsatile, and on demand dosing, as opposed to a standard sustained release profile. Furthermore, the development of reservoir-based systems for targeted delivery for difficult to treat applications (e.g., ocular) has resulted in potential platforms for patient therapy.},
Author = {Stevenson, Cynthia L. and Santini Jr., John T. and Langer, Robert},
File = {ScienceDirect Full Text PDF:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/PSHDRPIW/Stevenson et al. - 2012 - Reservoir-based drug delivery systems utilizing mi.pdf:application/pdf;ScienceDirect Snapshot:/Users/vramasub/Library/Application Support/Firefox/Profiles/5g5hcrdl.default/zotero/storage/4SI72XH5/S0169409X12000282.html:text/html},
Issn = {0169-{409X}},
Journal = {Advanced Drug Delivery Reviews},
Keywords = {Controlled release, Implant, {MEMS}, Microneedle, Micropump, Ocular, On demand, Pulsatile},
Month = nov,
Number = {14},
Pages = {1590--1602},
Shorttitle = {Emerging micro- and nanotechnologies for the development of novel drug delivery devices and systems},
Title = {Reservoir-based drug delivery systems utilizing microtechnology},
Url = {http://www.sciencedirect.com/science/article/pii/S0169409X12000282},
Urldate = {2013-03-21},
Volume = {64},
Year = {2012},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0169409X12000282},
\end{filecontents*}

\documentclass{article}
\usepackage[usetitle=true]{achemso}
%Set up the Minion Pro font
\usepackage{fontspec}
\setmainfont[Ligatures=TeX]{Minion Pro}
\setsansfont[Scale=MatchLowercase,Ligatures=TeX]{Gill Sans}
\setmonofont[Scale=MatchLowercase, Ligatures=TeX]{Andale Mono}

\begin{document}

Synthetic devices have been historically easier to construct, and for a number of
applications they are still preferred, but advances in nanotechnology have vastly improved
our ability to work with small molecules, allowing for biological and chemical drug
delivery systems based on polymer nanoparticles, hydrogels, and biological vesicles, among
other possibilities
grainger_nanobiomaterials_2008,
stevenson_reservoir-based_2012}.

\bibliography{\jobname}
\end{document}


If you really need other features from xltxtra such as \vfrac or \showhyphens, then load it by

\usepackage[no-sscript]{xltxtra}

-
Thanks! That fixed the problem. This was my first time trying to use XeLaTeX, so I didn't want to mess with the packages related to fontspec. Thanks for the fix. –  Vyas Apr 1 '13 at 21:50