The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction
Abstract
The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge-charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and a modification of the Coulomb scaling to improve the electrostatic treatment within the second-order terms. These modifications lead to a significant improvement in the description of hydrogen-bonding interactions and proton affinities of biologically relevant molecules.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Generalized Gradient Approximation Made Simple
Perdew, J. P., Burke, K., & Ernzerhof, M. (1996) · Physical Review Letters · doi:10.1103/physrevlett.77.3865 · Cited by 215,824
Density-functional thermochemistry. III. The role of exact exchange
Becke, A. D. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464913 · Cited by 103,767
Density-functional exchange-energy approximation with correct asymptotic behavior
Becke, A. D. (1988) · Physical Review A · doi:10.1103/physreva.38.3098 · Cited by 53,711
Genetic Algorithms in Search, Optimization and Machine Learning
Goldberg, D. E., & Robson, D. (1988) · Cited by 18,391
Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint
Reed, A. E., Curtiss, L. A., & Weinhold, F. (1988) · Chemical Reviews · doi:10.1021/cr00088a005 · Cited by 17,359
Goldberg, D. E., & Shakespeare, W. (2002) · Cited by 16,088
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 14,944
Density Functional Theory of Atoms and Molecules
Parr, R. G. (1980) · Horizons of Quantum Chemistry · doi:10.1007/978-94-009-9027-2_2 · Cited by 11,964
Grimme, S. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20078 · Cited by 5,221
Warshel, A., & Levitt, M. (1976) · Journal of Molecular Biology · doi:10.1016/0022-2836(76)90311-9 · Cited by 4,479
Elstner, M., Porezag, D., Jungnickel, G., Elsner, J., Haugk, M., Frauenheim, T., Suhai, S., & Seifert, G. (1998) · Physical Review B · doi:10.1103/physrevb.58.7260 · Cited by 4,124
Self-citationGaussian-3 (G3) theory for molecules containing first and second-row atoms
Curtiss, L. A., Raghavachari, K., Redfern, P. C., Rassolov, V., & Pople, J. A. (1998) · The Journal of Chemical Physics · doi:10.1063/1.477422 · Cited by 2,865
Porezag, D., Frauenheim, T., Köhler, T., Seifert, G., & Kaschner, R. (1995) · Physical Review B · doi:10.1103/physrevb.51.12947 · Cited by 2,201
Proof that∂E∂ni=εin density-functional theory
Janak, J. F. (1978) · Physical Review B · doi:10.1103/physrevb.18.7165 · Cited by 2,107
Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding
Fersht, A. (2017) · Series in Structural Biology · doi:10.1142/10574 · Cited by 2,039
Gaussian-3 theory using density functional geometries and zero-point energies
Baboul, A. G., Curtiss, L. A., Redfern, P. C., & Raghavachari, K. (1999) · The Journal of Chemical Physics · doi:10.1063/1.478676 · Cited by 1,750
Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes
Shaik, S., Kumar, D., de Visser, S. P., Altun, A., & Thiel, W. (2005) · Chemical Reviews · doi:10.1021/cr030722j · Cited by 1,236
Some remarks on the Pariser-Parr-Pople method
Ohno, K. (1964) · Theoretica Chimica Acta · doi:10.1007/bf00528281 · Cited by 1,033
Elstner, M., Hobza, P., Frauenheim, T., Suhai, S., & Kaxiras, E. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1329889 · Cited by 1,023
Self-citationEmpirical correction to density functional theory for van der Waals interactions
Wu, Q., & Yang, W. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1424928 · Cited by 840
Q UANTUM M ECHANICAL M ETHODS FOR E NZYME K INETICS
Gao, J., & Truhlar, D. G. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.091301.150114 · Cited by 733
Friesner, R. A., & Guallar, V. (2005) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.55.091602.094410 · Cited by 522
Orthogonalization corrections for semiempirical methods
Weber, W., & Thiel, W. (2000) · Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) · doi:10.1007/s002149900083 · Cited by 421
Xantheas, S. S., Burnham, C. J., & Harrison, R. J. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1423941 · Cited by 393
The SCC-DFTB method and its application to biological systems
Elstner, M. (2006) · Theoretical Chemistry Accounts · doi:10.1007/s00214-005-0066-0 · Cited by 387
Self-citationKlopman, G. (1964) · Journal of the American Chemical Society · doi:10.1021/ja01075a008 · Cited by 351
Nam, K., Gao, J., & York, D. M. (2005) · Journal of Chemical Theory and Computation · doi:10.1021/ct049941i · Cited by 310
Self-citationRiccardi, D., Schaefer, P., Yang, Yu, H., Ghosh, N., Prat-Resina, X., König, P., Li, G., Xu, D., Guo, H., et al. (2006) · The Journal of Physical Chemistry B · doi:10.1021/jp056361o · Cited by 300
Self-citationComputational determination of equilibrium geometry and dissociation energy of the water dimer
Klopper, W., M. van Duijneveldt-van de Rijdt, J. G. C., & van Duijneveldt, F. B. (2000) · Physical Chemistry Chemical Physics · doi:10.1039/a910312k · Cited by 264
Hobza, P., Kabel�?, M., ?poner, J., Mejzl�k, P., & Vondr�?ek, J. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(19970715)18:9<1136::aid-jcc3>3.0.co;2-s · Cited by 264
Quantum Chemistry and Molecular Processes
Head-Gordon, M. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp953665+ · Cited by 252
A Self-Consistent Charge Density-Functional Based Tight-Binding Scheme for Large Biomolecules
Elstner, M., Frauenheim, T., Kaxiras, E., Seifert, G., & Suhai, S. (2000) · physica status solidi (b) · Cited by 234
Self-citationElstner, M., Cui, Q., Munih, P., Kaxiras, E., Frauenheim, T., & Karplus, M. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10201 · Cited by 203
Self-citationAn approximate DFT method for QM/MM simulations of biological structures and processes
Elstner, M., Frauenheim, T., & Suhai, S. (2003) · Journal of Molecular Structure: THEOCHEM · doi:10.1016/s0166-1280(03)00286-0 · Cited by 189
Self-citationSCC-DFTB: What Is the Proper Degree of Self-Consistency?
Elstner, M. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp071338j · Cited by 182
Self-citationLooking at Self-Consistent-Charge Density Functional Tight Binding from a Semiempirical Perspective
Otte, N., Scholten, M., & Thiel, W. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp0700130 · Cited by 164
Nam, K., Cui, Q., Gao, J., & York, D. M. (2007) · Journal of Chemical Theory and Computation · doi:10.1021/ct6002466 · Cited by 164
Self-citationShurki, A., & Warshel, A. (2003) · Advances in Protein Chemistry · doi:10.1016/s0065-3233(03)66007-9 · Cited by 159
Krüger, T., Elstner, M., Schiffels, P., et al. (2005) · The Journal of Chemical Physics · doi:10.1063/1.1871913 · Cited by 157
Self-citationRiccardi, D., Schaefer, P., & Cui, Q. (2005) · Journal of Physical Chemistry B · doi:10.1021/jp0517192 · Cited by 154
Self-citationQuantum mechanics simulation of protein dynamics on long timescale
Liu, H., Elstner, M., Kaxiras, E., Frauenheim, T., Hermans, J., & Yang, W. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1114 · Cited by 150
Self-citationElstner, M., Jalkanen, K. J., Knapp‐Mohammady, M., Frauenheim, T., & Suhai, S. (2001) · Chemical Physics · doi:10.1016/s0301-0104(00)00375-x · Cited by 142
Self-citationComparison of SCC-DFTB and NDDO-Based Semiempirical Molecular Orbital Methods for Organic Molecules
Sattelmeyer, K. W., Tirado‐Rives, J., & Jorgensen, W. L. (2006) · The Journal of Physical Chemistry A · doi:10.1021/jp064544k · Cited by 134
Toward Theoretical Analyis of Long-Range Proton Transfer Kinetics in Biomolecular Pumps
König, P. H., Ghosh, N., Hoffmann, M., Elstner, M., Tajkhorshid, E., Frauenheim, T., & Cui, Q. (2006) · The Journal of Physical Chemistry A · doi:10.1021/jp052328q · Cited by 114
Self-citationPerspectives on Semiempirical Molecular Orbital Theory
Thiel, W. (1996) · Advances in chemical physics · doi:10.1002/9780470141526.ch10 · Cited by 107
Key Role of Electrostatic Interactions in Bacteriorhodopsin Proton Transfer
Bondar, A., Fischer, S., Smith, J. C., Elstner, M., & Suhai, S. (2004) · Journal of the American Chemical Society · doi:10.1021/ja047982i · Cited by 96
Self-citationPerformance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules
Zhou, H., Tajkhorshid, E., Frauenheim, T., Suhai, S., & Elstner, M. (2002) · Chemical Physics · doi:10.1016/s0301-0104(01)00695-4 · Cited by 92
Self-citationHan, W., Elstner, M., Jalkanen, K. J., et al. (2000) · International Journal of Quantum Chemistry · doi:10.1002/(sici)1097-461x(2000)78:6<459::aid-qua7>3.0.co;2-r · Cited by 70
Self-citationBernal‐Uruchurtu, M. I., Martins‐Costa, M. T. C., Millot, C., & Ruiz-L�pez, M. F. (2000) · Journal of Computational Chemistry · Cited by 68
Basic ideas for the correction of semiempirical methods describing H-bonded systems
Bernal‐Uruchurtu, M. I., & Ruiz‐López, M. F. (2000) · Chemical Physics Letters · doi:10.1016/s0009-2614(00)01062-9 · Cited by 64
Improvement of semiempirical response properties with charge-dependent response density
Giese, T. J., & York, D. M. (2005) · The Journal of Chemical Physics · doi:10.1063/1.2080007 · Cited by 62
Self-citationQuantum descriptors for biological macromolecules from linear‐scaling electronic structure methods
Khandogin, J., & York, D. M. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20171 · Cited by 59
Self-citationHybrid QM/MM Study of Thio Effects in Transphosphorylation Reactions: The Role of Solvation
Gregersen, B. A., López, X., & York, D. M. (2004) · Journal of the American Chemical Society · doi:10.1021/ja031815l · Cited by 56
Self-citationDescription of peptide and protein secondary structures employing semiempirical methods
M�hle, K., Hofmann, H. ‐., & Thiel, W. (2001) · Journal of Computational Chemistry · Cited by 51
Khandogin, J., Musier‐Forsyth, K., & York, D. M. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00658-2 · Cited by 44
Self-citationTreatment of hydrogen bonding in SINDO1
Jug, K., & Geudtner, G. (1993) · Journal of Computational Chemistry · doi:10.1002/jcc.540140603 · Cited by 42
QCRNA 1.0: A database of quantum calculations for RNA catalysis
Giese, T. J., Gregersen, B. A., Liu, Y., Nam, K., Mayaan, E., Moser, A., Range, K., Faza, O. N., López, C. S., de Lera, Á. R., et al. (2006) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2006.02.011 · Cited by 30
Self-citationTheoretical and computational studies of vectorial processes in biomolecular systems
Cui, Q. (2006) · Theoretical Chemistry Accounts · doi:10.1007/s00214-005-0022-z · Cited by 15
Self-citation
Cited by
Christensen, A. S., Kubař, T., Cui, Q., & Elstner, M. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00584 · Cited by 446
Self-citationYang, Y., Sahai, N., Romanek, C. S., & Chakraborty, S. (2012) · Geochimica et Cosmochimica Acta · doi:10.1016/j.gca.2012.03.018 · Cited by 33
Self-citation
Metadata
- Authors
- Yang, Y., Yu, H., York, D., Cui, Q., & Elstner, M.
- Venue
- The Journal of Physical Chemistry A
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-10-01
- Volume
- 111
- Issue
- 42
- Pages
- 10861-10873
- ISSN
- 1089-5639 (ISSN-L)
- 1520-5215
- OpenAlex
- W1997231673
- Cited by
- 317
- References
- 58
- FWCI
- 4.07
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.