iucr.bib

@article{allen2010bond,
  title={Bond lengths in organic and metal-organic compounds revisited: X—H bond lengths from neutron diffraction data},
  author={Allen, Frank H and Bruno, Ian J},
  journal={ActaCryst.},
  volume={B66},
  number={3},
  pages={380--386},
  year={2010},
  publisher={International Union of Crystallography}
}

@article{becke1988multicenter,
  title={A multicenter numerical integration scheme for polyatomic molecules},
  author={Becke, Axel D},
  journal={ J. Chem. Phys.},
  volume={88},
  number={4},
  pages={2547--2553},
  year={1988},
  publisher={AIP}
}



@article{brunger1987crystallographic,
  title={Crystallographic R factor refinement by molecular dynamics},
  author={Br{\"u}nger, Axel T and Kuriyan, John and Karplus, Martin},
  journal={Science},
  volume={235},
  number={4787},
  pages={458--460},
  year={1987},
  publisher={American Association for the Advancement of Science}
}
@article{borbulevych2014accurate,
  title={Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package},
  author={Borbulevych, Oleg Y and Plumley, Joshua A and Martin, Roger I and Merz, Kenneth M and Westerhoff, Lance M},
  journal={ActaCryst.},
  volume={D70},
  number={5},
  pages={1233--1247},
  year={2014},
  publisher={International Union of Crystallography}
}



@article{capelli2014hirshfeld,
  title={Hirshfeld atom refinement},
  author={Capelli, Silvia C and B{\"u}rgi, H-B and Dittrich, Birger and Grabowsky, Simon and Jayatilaka, Dylan},
  journal={IUCrJ},
  volume={1},
  number={5},
  pages={361--379},
  year={2014},
  publisher={International Union of Crystallography}
}

@article{blakeley2015sub,
  title={Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential},
  author={Blakeley, Matthew P and Hasnain, Samar S and Antonyuk, Svetlana V},
  journal={IUCrJ},
  volume={2},
  number={4},
  pages={464--474},
  year={2015},
  publisher={International Union of Crystallography}
}


@article{collins2015energy,
  title={Energy-based molecular fragmentation methods},
  author={Collins, Michael A and Bettens, Ryan PA},
  journal={Chem.Rev.},
  volume={115},
  number={12},
  pages={5607--5642},
  year={2015},
  publisher={ACS Publications}
}

@book{coppens1997x,
  title={X-ray charge densities and chemical bonding},
  author={Coppens, Philip},
  year={1997},
  publisher={International Union of Crystallography}
}



@article{dittrich2002reproducability,
  title={Reproducability and transferability of topological properties; experimental charge density of the hexapeptide cyclo-(d, l-Pro) \_2--(l-Ala) \_4 monohydrate},
  author={Dittrich, B and Korits{\'a}nszky, T and Grosche, M and Scherer, Wolfgang and Flaig, R and Wagner, A and Krane, HG and Kessler, H and Riemer, C and Schreurs, AMM and others},
  journal={ActaCryst.},
  volume={B58},
  number={4},
  pages={721--727},
  year={2002},
  publisher={International Union of Crystallography}
}

@article{dittrich2005invariom,
  title={The invariom model and its application: refinement of D, L-serine at different temperatures and resolution},
  author={Dittrich, B and H{\"u}bschle, Ch B and Messerschmidt, M and Kalinowski, R and Girnt, D and Luger, P},
  journal={ActaCryst.},
  volume={A61},
  number={3},
  pages={314--320},
  year={2005},
  publisher={International Union of Crystallography}
}



@article{dittrich2013generalized,
  title={The generalized invariom database (GID)},
  author={Dittrich, B and H{\"u}bschle, CB and Pr{\"o}pper, K and Dietrich, F and Stolper, T and Holstein, J},
  journal={ActaCryst.},
  volume={B69},
  number={2},
  pages={91--104},
  year={2013},
  publisher={International Union of Crystallography}
}



@article{destro1995bond,
  title={Bond lengths, and beyond},
  author={Destro, RICCARDO and Merati, FEL1CITA},
  journal={ActaCryst.},
  volume={B51},
  number={4},
  pages={559--570},
  year={1995},
  publisher={International Union of Crystallography}
}

@article{doll1997quantum,
  title={Quantum chemical approach to cohesive properties of NiO},
  author={Doll, Klaus and Dolg, Michael and Fulde, Peter and Stoll, Hermann},
  journal={Phys. Rev. B},
  volume={55},
  number={16},
  pages={10282},
  year={1997},
  publisher={APS}
}

@article{dunning1989gaussian,
  title={Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen},
  author={Dunning, Thom H},
  journal={ J. Chem. Phys.},
  volume={90},
  number={2},
  pages={1007--1023},
  year={1989},
  publisher={AIP}
}




@article{field1990combined,
  title={A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations},
  author={Field, Martin J and Bash, Paul A and Karplus, Martin},
  journal={J. Comput. Chem.},
  volume={11},
  number={6},
  pages={700--733},
  year={1990},
  publisher={Wiley Online Library}
}


@article{fugel2018probing,
  title={Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2},
  author={Fugel, Malte and Jayatilaka, Dylan and Hupf, Emanuel and Overgaard, Jacob and Hathwar, Venkatesha R and Macchi, Piero and Turner, Michael J and Howard, Judith AK and Dolomanov, Oleg V and Puschmann, Horst and others},
  journal={IUCrJ},
  volume={5},
  number={1},
  pages={32--44},
  year={2018},
  publisher={International Union of Crystallography}
}



@article{gao1992priori,
  title={A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations},
  author={Gao, Jiali and Xia, Xinfu},
  journal={Science},
  volume={258},
  number={5082},
  pages={631--635},
  year={1992},
  publisher={American Association for the Advancement of Science}
}



@article{grabowsky2009transferability,
  title={Transferability and reproducibility in electron-density studies--bond-topological and atomic properties of tripeptides of the type l-alanyl-Xl-alanine},
  author={Grabowsky, Simon and Kalinowski, Roman and Weber, Manuela and F{\"o}rster, Diana and Paulmann, Carsten and Luger, Peter},
  journal={ActaCryst.},
  volume={B65},
  number={4},
  pages={488--501},
  year={2009},
  publisher={International Union of Crystallography}
}


@article{grabowsky2017quantum,
  title={Quantum crystallography},
  author={Grabowsky, Simon and Genoni, Alessandro and B{\"u}rgi, Hans-Beat},
  journal={ Chem. Sci.},
  volume={8},
  number={6},
  pages={4159--4176},
  year={2017},
  publisher={Royal Society of Chemistry}
}

@article{jayatilaka2008x,
  title={X-ray structure refinement using aspherical atomic density functions obtained from quantum-mechanical calculations},
  author={Jayatilaka, Dylan and Dittrich, Birger},
  journal={ActaCryst.},
  volume={A64},
  number={3},
  pages={383--393},
  year={2008},
  publisher={International Union of Crystallography}
}

@article{massa1995quantum,
  title={Quantum crystallography and the use of kernel projector matrices},
  author={Massa, L and Huang, L and Karle, J},
  journal={Int. J. Quantum Chem.},
  volume={56},
  number={S29},
  pages={371--384},
  year={1995},
  publisher={Wiley Online Library}
}


@article{mezey1995macromolecular,
  title={Macromolecular density matrices and electron densities with adjustable nuclear geometries},
  author={Mezey, Paul G},
  journal={J. Math. Chem.},
  volume={18},
  number={2},
  pages={141--168},
  year={1995},
  publisher={Springer}
}


@article{monard1999combined,
  title={Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems},
  author={Monard, Gerald and Merz, Kenneth M},
  journal={Acc.  Chem.  Res.},
  volume={32},
  number={10},
  pages={904--911},
  year={1999},
  publisher={ACS Publications}
}

@article{reuter2000frontier,
  title={Frontier bonds in QM/MM methods: A comparison of different approaches},
  author={Reuter, Nathalie and Dejaegere, Annick and Maigret, Bernard and Karplus, Martin},
  journal={J. Phys. Chem. A},
  volume={104},
  number={8},
  pages={1720--1735},
  year={2000},
  publisher={ACS Publications}
}


@article{ryde2002quantum,
  title={Quantum chemical geometry optimizations in proteins using crystallographic raw data},
  author={Ryde, Ulf and Olsen, Lars and Nilsson, Kristina},
  journal={J. Comput. Chem.},
  volume={23},
  number={11},
  pages={1058--1070},
  year={2002},
  publisher={Wiley Online Library}
}


@article{schwarzenbach1995statistical,
  title={Statistical descriptions in crystallography. II. Report of a Working Group on Expression of Uncertainty in Measurement},
  author={Schwarzenbach, D and Abrahams, SC and Flack, HD and Prince, E and Wilson, AJC},
  journal={ActaCryst.},
  volume={A51},
  number={4},
  pages={565--569},
  year={1995},
  publisher={International Union of Crystallography}
}


@article{soderhjelm2008accurate,
  title={How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations},
  author={S\"{o}derhjelm, P\"{a}r and Ryde, Ulf},
  journal={J. Phys. Chem. A},
  volume={113},
  number={3},
  pages={617--627},
  year={2008},
  publisher={ACS Publications}
}

@article{sheldrick2015crystal,
  title={Crystal structure refinement with SHELXL},
  author={Sheldrick, George M},
  journal={ActaCryst.},
  volume={c71},
  number={1},
  pages={3--8},
  year={2015},
  publisher={International Union of Crystallography}
}


@article{singh1986combined,
  title={A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl+ Cl- exchange reaction and gas phase protonation of polyethers},
  author={Singh, U Chandra and Kollman, Peter A},
  journal={J. Comput. Chem.},
  volume={7},
  number={6},
  pages={718--730},
  year={1986},
  publisher={Wiley Online Library}
}

@article{stanton1993calculation,
  title={Calculation of solvation free energies using a density functional/molecular dynamics coupled potential},
  author={Stanton, Robert V and Hartsough, David S and Merz Jr, Kenneth M},
  journal={J.Phys.Chem.},
  volume={97},
  number={46},
  pages={11868--11870},
  year={1993},
  publisher={ACS Publications}
}

@article{stoll1992correlation,
  title={Correlation energy of diamond},
  author={Stoll, Hermann},
  journal={Phys. Rev. B},
  volume={46},
  number={11},
  pages={6700},
  year={1992},
  publisher={APS}
}


@article{thery1994quantum,
  title={Quantum mechanical computations on very large molecular systems: The local self-consistent field method},
  author={Th{\'e}ry, Vincent and Rinaldi, Daniel and Rivail, Jean-Louis and Maigret, Bernard and Ferenczy, Gy{\"o}rgy G},
  journal={J. Comput. Chem.},
  volume={15},
  number={3},
  pages={269--282},
  year={1994},
  publisher={Wiley Online Library}
}

@article{walker1993molecular,
  title={Molecular electron density lego approach to molecule building},
  author={Walker, P Duane and Mezey, Paul G},
  journal={Am.Chem.Soc.},
  volume={115},
  number={26},
  pages={12423--12430},
  year={1993},
  publisher={ACS Publications}
}


@article{walker1994ab,
  title={Ab initio quality electron densities for proteins: A MEDLA approach},
  author={Walker, P Duane and Mezey, Paul G},
  journal={Am.Chem.Soc.},
  volume={116},
  number={26},
  pages={12022--12032},
  year={1994},
  publisher={ACS Publications}
}

@article{walker1994realistic,
  title={Realistic, detailed images of proteins and tertiary structure elements: ab initio quality electron density calculations for bovine insulin},
  author={Walker, P Duane and Mezey, Paul G},
  journal={Can. J. Chem. },
  volume={72},
  number={12},
  pages={2531--2536},
  year={1994},
  publisher={NRC Research Press}
}




@article{warshel1976theoretical,
  title={Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme},
  author={Warshel, Arieh and Levitt, Michael},
  journal={J. Mol. Biol. },
  volume={103},
  number={2},
  pages={227--249},
  year={1976},
  publisher={Elsevier}
}


@article{woinska2014hirshfeld,
  title={Hirshfeld atom refinement for modelling strong hydrogen bonds},
  author={Woi{\'n}ska, Magdalena and Jayatilaka, Dylan and Spackman, Mark A and Edwards, Alison J and Dominiak, Paulina M and Wo{\'z}niak, Krzysztof and Nishibori, Eiji and Sugimoto, Kunihisa and Grabowsky, Simon},
  journal={ActaCryst.},
  volume={A70},
  number={5},
  pages={483--498},
  year={2014},
  publisher={International Union of Crystallography}
}
@article{woinska2016hydrogen,
  title={Hydrogen atoms can be located accurately and precisely by x-ray crystallography},
  author={Woi{\'n}ska, Magdalena and Grabowsky, Simon and Dominiak, Paulina M and Wo{\'z}niak, Krzysztof and Jayatilaka, Dylan},
  journal={Sci. Adv},
  volume={2},
  number={5},
  pages={e1600192},
  year={2016},
  publisher={American Association for the Advancement of Science}
}



@article{zheng2017q,
  title={Q| R: quantum-based refinement},
  author={Zheng, Min and Reimers, Jeffrey R and Waller, Mark P and Afonine, Pavel V},
  journal={ActaCryst.},
  volume={D73},
  number={1},
  pages={45--52},
  year={2017},
  publisher={International Union of Crystallography}
}



@article{zhang2003molecular,
  title={Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein--molecule interaction energy},
  author={Zhang, Da W and Zhang, JZH},
  journal={ J. Chem. Phys.},
  volume={119},
  number={7},
  pages={3599--3605},
  year={2003},
  publisher={AIP}
}

@article{zhurov2011importance,
  title={Importance of the consideration of anharmonic motion in charge-density studies: a comparison of variable-temperature studies on two explosives, RDX and HMX},
  author={Zhurov, Vladimir V and Zhurova, Elizabeth A and Stash, Adam I and Pinkerton, A Alan},
  journal={ActaCryst.},
  volume={A67},
  number={2},
  pages={160--173},
  year={2011},
  publisher={International Union of Crystallography}
}
@article{zhurov2013charge,
  title={Charge Density Analysis of an Organic Ferroelectric. Croconic Acid: an Experimental and Theoretical Study},
  author={Zhurov, Vladimir V and Pinkerton, A Alan},
  journal={Z. Anorg. Allg. Chem.},
  volume={639},
  number={11},
  pages={1969--1978},
  year={2013},
  publisher={Wiley Online Library}
}

@misc {malaspina2019,
	Title = {Fast and Accurate Quantum Crystallography: from Small to Large, from Light to Heavy},
	Author = {Malaspina, Lorraine and Wieduwilt, Erna and Bergmann, Justin and Kleemiss, Florian and Meyer, Benjamin and Ruiz-López, Manuel and Pal, Rumpa and Hupf, Emanuel and Beckmann, Jens and Piltz, Ross and Edwards, Alison J. and Grabowsky, Simon and Genoni, Alessandro},
	DOI = {10.26434/chemrxiv.9120407.v2},
	Publisher = {ChemRxiv},
	Year = {2019},
	URL = {https://doi.org/10.26434/chemrxiv.9120407.v2},
}

@article{Kobayashi2019,
author = {Kobayashi, Rika and Addicoat, Matthew A. and Gilbert, Andrew T.B. and Amos, Roger D. and Collins, Michael A.},
title = {The SMFA program for quantum chemistry calculations on large molecules},
journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
volume = {9},
number = {5},
pages = {e1413},
keywords = {macro molecules, quantum chemistry},
doi = {10.1002/wcms.1413},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/wcms.1413},
year = {2019}
}
















%%%%fragmmentation
@article{yang1991direct,
  title={Direct calculation of electron density in density-functional theory},
  author={Yang, Weitao},
  journal={Phys. Rev. Lett.},
  volume={66},
  number={11},
  pages={1438},
  year={1991},
  publisher={APS}
}
@article{lee1996linear,
  title={Linear-scaling semiempirical quantum calculations for macromolecules},
  author={Lee, Tai-Sung and York, Darrin M and Yang, Weitao},
  journal={ J. Chem. Phys.},
  volume={105},
  number={7},
  pages={2744--2750},
  year={1996},
  publisher={AIP}
}
@article{yang1995density,
  title={A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules},
  author={Yang, Weitao and Lee, Tai-Sung},
  journal={ J. Chem. Phys.},
  volume={103},
  number={13},
  pages={5674--5678},
  year={1995},
  publisher={AIP}
}
@article{kohn1996density,
  title={Density functional and density matrix method scaling linearly with the number of atoms},
  author={Kohn, Walter},
  journal={Phys. Rev. Lett.},
  volume={76},
  number={17},
  pages={3168},
  year={1996},
  publisher={APS}
}
@article{dixon1996semiempirical,
  title={Semiempirical molecular orbital calculations with linear system size scaling},
  author={Dixon, Steven L and Merz Jr, Kenneth M},
  journal={ J. Chem. Phys.},
  volume={104},
  number={17},
  pages={6643--6649},
  year={1996},
  publisher={AIP}
}
@article{gogonea2000quantum,
  title={Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schr{\"o}dinger equation for large molecular systems using a composite density functional--semiempirical Hamiltonian},
  author={Gogonea, Valentin and Westerhoff, Lance M and Merz Jr, Kenneth M},
  journal={ J. Chem. Phys.},
  volume={113},
  number={14},
  pages={5604--5613},
  year={2000},
  publisher={AIP}
}
@article{stewart1996application,
  title={Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations},
  author={Stewart, James JP},
  journal={Int. J. Quantum Chem.},
  volume={58},
  number={2},
  pages={133--146},
  year={1996},
  publisher={Wiley Online Library}
}
@article{daniels1997semiempirical,
  title={Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems containing thousands of atoms},
  author={Daniels, Andrew D and Millam, John M and Scuseria, Gustavo E},
  journal={ J. Chem. Phys.},
  volume={107},
  number={2},
  pages={425--431},
  year={1997},
  publisher={AIP}
}
@article{daniels1999best,
  title={What is the best alternative to diagonalization of the Hamiltonian in large scale semiempirical calculations?},
  author={Daniels, Andrew D and Scuseria, Gustavo E},
  journal={ J. Chem. Phys.},
  volume={110},
  number={3},
  pages={1321--1328},
  year={1999},
  publisher={AIP}
}
@article{scuseria1999linear,
  title={Linear scaling density functional calculations with Gaussian orbitals},
  author={Scuseria, Gustavo E},
  journal={J. Phys. Chem. A},
  volume={103},
  number={25},
  pages={4782--4790},
  year={1999},
  publisher={ACS Publications}
}

@article{Merz:05,
  title={Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics},
  author={Yu, N. and Yennawar H. P. and Merz, K. M.},
  journal={Acta Cryst. D},
  volume={61},
  pages={322--332},
  year={2005}
}
@article{northey2019ab,
  title={Ab Initio Fragment Method for Calculating Molecular X-ray Diffraction},
  author={Northey, T and Kirrander, A},
  journal={The Journal of Physical Chemistry A},
  volume={123},
  number={15},
  pages={3395--3406},
  year={2019},
  publisher={ACS Publications}
}

@article{Thiel:09,
  title={QM/MM Methods for Biomolecular Systems},
  author={Senn, H M. and Thiel, W.},
  journal={Angew. Chem. Int. Ed.},
  volume={48},
  pages={1198--1229},
  year={2009}
}
@article{Ryde:qmmmrev,
  title={QM/MM calculations on proteins},
  author={Ryde, U.},
  journal={Meth. Enz.},
  volume={577},
  pages={119--158},
  year={2016}
}
@article{tonto,
  title={Tonto: A Fortran Based Object-Oriented System for Quantum Chemistry and Crystallography},
  author={Jayatilaka, D. and Grimwood, D. J.},
  journal={Computational Science - ICCS},
  volume={4},
  pages={142-151},
  year={2003}
}
@article{grimme:12,
  title={Fully Ab Initio Protein--Ligand Interaction Energies with Dispersion Corrected Density Functional Theory},
  author={Jens Antony and Stefan Grimme},
  journal={J. Comp. Chem.},
  volume={33},
  pages={1730--1739},
  year={2012}
}