Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications.

Christensen, Anders S.; Kubař, Tomáš; Cui, Qiang; Elstner, Marcus

doi:10.1021/acs.chemrev.5b00584

Cited by 446Advanced Chemical Physics StudiesCrystallography and molecular interactionsAdvanced Physical and Chemical Molecular Interactions

Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications.

Open access

Christensen, Anders S., Kubař, Tomáš, Cui, Qiang, Elstner, Marcus·2016·Chemical Reviews

DOI 10.1021/acs.chemrev.5b00584PMC PMC4867870

Open this paper in CoChat — free account

Abstract

Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.

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

Crossref · 10.1021/acs.chemrev.5b00584

Cites

336 of 336 references verified0 citation errors · 0 not checkable

Statistics

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.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

In the last 10 years, important advances were made in computing hardware, quantum algorithms to compute molecular wave functions, more reliable semi-empirical quantum methods, and new hybrid QM/MM methods.
“In the last 10 years, important advances were made in computing hardware (e.g., Graphics Processing Units – GPUs), in the development of quantum algorithms to compute molecular wave functions (Dixon and Merz, 1997; Birgin et al., 2013), the development of more reliable semi-empirical quantum methods (Christensen et al., 2016; Yilmazer and Korth, 2016), and development of new hybrid QM/MM methods (”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Christensen et al., 2016
QM methods are particularly useful when molecular recognition involves bond formation, π-stacking, cation-π, halogen bonding, and polarization and charge transfer effects.
“This is particularly true when dealing with systems where the molecular recognition involves bond formation, π-stacking, cation-π, halogen bonding (i.e., σ-hole bonding), and polarization and charge transfer effects (Christensen et al., 2016).”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Christensen et al., 2016

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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 · see citing works
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 · see citing works
A consistent and accurate <i>ab initio</i> parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
Grimme, S., Antony, J., Ehrlich, S., & Krieg, H. (2010) · The Journal of Chemical Physics · doi:10.1063/1.3382344 · Cited by 59,686 · see citing works
Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction
Grimme, S. (2006) · Journal of Computational Chemistry · doi:10.1002/jcc.20495 · Cited by 30,925 · see citing works
Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
Weigend, F., & Ahlrichs, R. (2005) · Physical Chemistry Chemical Physics · doi:10.1039/b508541a · Cited by 30,761 · see citing works
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
Zhao, Y., & Truhlar, D. G. (2007) · Theoretical Chemistry Accounts · doi:10.1007/s00214-007-0310-x · Cited by 30,407 · see citing works
Effect of the damping function in dispersion corrected density functional theory
Grimme, S., Ehrlich, S., & Goerigk, L. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21759 · Cited by 28,221 · see citing works
Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
Stephens, P. J., Devlin, F. J., Chabalowski, C. F., & Frisch, M. J. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100096a001 · Cited by 23,329 · see citing works
The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors
Boys, S. F., & Bernardi, F. (1970) · Molecular Physics · doi:10.1080/00268977000101561 · Cited by 22,268 · see citing works
GROMACS: Fast, flexible, and free
van der Spoel, D., Lindahl, E. R., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20291 · Cited by 19,292 · see citing works
The influence of polarization functions on molecular orbital hydrogenation energies
Hariharan, P. C., & Pople, J. A. (1973) · Theoretical Chemistry Accounts · doi:10.1007/bf00533485 · Cited by 15,848 · see citing works
Density-functional theory of atoms and molecules
Patterson, J. D. (1989) · Annals of Nuclear Energy · doi:10.1016/0306-4549(89)90016-9 · Cited by 12,625 · see citing works
Density Functional Theory of Atoms and Molecules
Parr, R. G. (1980) · Springer eBooks · doi:10.1007/978-94-009-9027-2_2 · Cited by 12,016 · see citing works
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
Dewar, M. J., Zoebisch, E., Healy, E. F., & Stewart, J. (1985) · Journal of the American Chemical Society · doi:10.1021/ja00299a024 · Cited by 11,560 · see citing works
Electronic structure calculations on workstation computers: The program system turbomole
Ahlrichs, R., Bär, M. R., Häser, M., Horn, H. W., & Kölmel, C. (1989) · Chemical Physics Letters · doi:10.1016/0009-2614(89)85118-8 · Cited by 8,439 · see citing works
Optimization of parameters for semiempirical methods I. Method
Stewart, J. J. P. (1989) · Journal of Computational Chemistry · doi:10.1002/jcc.540100208 · Cited by 7,645 · see citing works
Accurate description of van der Waals complexes by density functional theory including empirical corrections
Grimme, S. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20078 · Cited by 5,212 · see citing works
Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters
Dewar, M. J., & Thiel, W. (1977) · Journal of the American Chemical Society · doi:10.1021/ja00457a004 · Cited by 4,584 · see citing works
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
Elstner, M., Porezag, D. V., Jungnickel, G., Elsner, J., Haugk, M., Frauenheim, T., Suhai, S., & Seifert, G. (1998) · Physical review. B, Condensed matter · doi:10.1103/physrevb.58.7260 · Cited by 4,130 · see citing works
Self-citation
Optimization of parameters for semiempirical methods II. Applications
Stewart, J. J. P. (1989) · Journal of Computational Chemistry · doi:10.1002/jcc.540100209 · Cited by 3,746 · see citing works
Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
Stewart, J. J. P. (2007) · Journal of Molecular Modeling · doi:10.1007/s00894-007-0233-4 · Cited by 3,652 · see citing works
Approximate molecular orbital theory
Pople, J. A., & Beveridge, D. L. (1970) · Medical Entomology and Zoology · Cited by 3,570 · see citing works
Absolute electronegativity and hardness: application to inorganic chemistry
Pearson, R. G. (1988) · Inorganic Chemistry · doi:10.1021/ic00277a030 · Cited by 3,496 · see citing works
Molecular Electronic‐Structure Theory
Helgaker, T., Jørgensen, P., & Olsen, J. (2000) · doi:10.1002/9781119019572 · Cited by 2,594 · see citing works
Challenges for Density Functional Theory
Cohen, A. J., Mori‐Sánchez, P., & Yang, W. (2011) · Chemical Reviews · doi:10.1021/cr200107z · Cited by 2,529 · see citing works
Insights into Current Limitations of Density Functional Theory
Cohen, A. J., Mori-Sánchez, P., & Yang, W. (2008) · Science · doi:10.1126/science.1158722 · Cited by 2,527 · see citing works
Halogen bonding: the σ-hole
Clark, T., Hennemann, M., Murray, J. S., & Politzer, P. (2006) · Journal of Molecular Modeling · doi:10.1007/s00894-006-0130-2 · Cited by 2,321 · see citing works
GLYCAM06: A generalizable biomolecular force field. Carbohydrates
Kirschner, K. N., Yongye, A. B., Tschampel, S. M., González‐Outeiriño, J., Daniels, C. R., Foley, B. L., & Woods, R. J. (2007) · Journal of Computational Chemistry · doi:10.1002/jcc.20820 · Cited by 2,253 · see citing works
Basis-set convergence in correlated calculations on Ne, N2, and H2O
Asger Halkier, A., Helgaker, T. U., Jørgensen, P., Klopper, W., Henrik Koch, A., Olsen, J., & Wilson, A. K. (1998) · Chemical Physics Letters · doi:10.1016/s0009-2614(98)00111-0 · Cited by 2,193 · see citing works
Water as an active constituent in cell biology
Ball, P. (2008) · Chemical Reviews · doi:10.1021/cr068037a · Cited by 2,177 · see citing works
Supramolecular Binding Thermodynamics by Dispersion‐Corrected Density Functional Theory
Grimme, S. (2012) · Chemistry - A European Journal · doi:10.1002/chem.201200497 · Cited by 2,132 · see citing works
Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
Stewart, J. J. P. (2012) · Journal of Molecular Modeling · doi:10.1007/s00894-012-1667-x · Cited by 2,028 · see citing works
An intermediate neglect of differential overlap technique for spectroscopy: Pyrrole and the azines
Ridley, J. E., & Zerner, M. C. (1973) · Theoretical Chemistry Accounts · doi:10.1007/bf00528484 · Cited by 1,972 · see citing works
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
Jurečka, P., Šponer, J., Černý, J., & Hobza, P. (2006) · Physical Chemistry Chemical Physics · doi:10.1039/b600027d · Cited by 1,854 · see citing works
A Medicinal Chemist’s Guide to Molecular Interactions
Bissantz, C., Kuhn, B., & Ståhl, M. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100112j · Cited by 1,741 · see citing works
Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures
Pople, J. A., Santry, D. P., & Segal, G. A. (1965) · The Journal of Chemical Physics · doi:10.1063/1.1701475 · Cited by 1,723 · see citing works
DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method
Aradi, B., Hourahine, B., & Frauenheim, T. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp070186p · Cited by 1,708 · see citing works
Theory of Intermolecular Forces
Stone, A. J. (1969) · Elsevier eBooks · doi:10.1016/c2013-0-02436-x · Cited by 1,693 · see citing works
Interaction of the van der Waals Type Between Three Atoms
Axilrod, B. M., & Teller, E. (1943) · The Journal of Chemical Physics · doi:10.1063/1.1723844 · Cited by 1,685 · see citing works
Halogen bonds in biological molecules
Auffinger, P., Hays, F. A., Westhof, É., & Ho, P. S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407607101 · Cited by 1,644 · see citing works
A density-functional model of the dispersion interaction
Becke, A. D., & Johnson, E. R. (2005) · The Journal of Chemical Physics · doi:10.1063/1.2065267 · Cited by 1,624 · see citing works
Perspective: Fifty years of density-functional theory in chemical physics
Becke, A. D. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4869598 · Cited by 1,542 · see citing works
The Theory of Intermolecular Forces
Stone, A. J. (1996) · doi:10.1093/oso/9780198558842.001.0001 · Cited by 1,532 · see citing works
Zur Theorie und Systematik der Molekularkr�fte
London, F. (1930) · The European Physical Journal A · doi:10.1007/bf01421741 · Cited by 1,515 · see citing works
Molecular electronic-structure theory
Ratner, M. A. (2000) · Cited by 1,506 · see citing works
Interatomic Potentials from First-Principles Calculations: The Force-Matching Method
Ercolessi, F., & Adams, J. B. (1994) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/26/8/005 · Cited by 1,455 · see citing works
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
Kr�utler, V., A, W. F. V. G., & Hünenberger, P. H. (2001) · Journal of Computational Chemistry · doi:10.1002/1096-987x(20010415)22:5 · Cited by 1,444 · see citing works
Current Status of the AMOEBA Polarizable Force Field
Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., et al. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp910674d · Cited by 1,440 · see citing works
An overview of halogen bonding
Politzer, P., Lane, P., Concha, M. C., Ma, Y., & Murray, J. S. (2006) · Journal of Molecular Modeling · doi:10.1007/s00894-006-0154-7 · Cited by 1,432 · see citing works
Linear scaling electronic structure methods
Goedecker, S. (1999) · Reviews of Modern Physics · doi:10.1103/revmodphys.71.1085 · Cited by 1,383 · see citing works
Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals—Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions
Goerigk, L., & Grimme, S. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct100466k · Cited by 1,364 · see citing works
Deriving effective mesoscale potentials from atomistic simulations
Reith, D., Pütz, M., & Müller‐Plathe, F. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10307 · Cited by 1,314 · see citing works
Metalloproteins and metal sensing
Waldron, K. J., Rutherford, J. C., Ford, D., & Robinson, N. J. (2009) · Nature · doi:10.1038/nature08300 · Cited by 1,269 · see citing works
A post-Hartree-Fock model of intermolecular interactions: Inclusion of higher-order corrections
Johnson, E. R., & Becke, A. D. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2190220 · Cited by 1,232 · see citing works
Biomolecular simulation: a computational microscope for molecular biology.
Dror, R., Dirks, R. M., Grossman, J. P., Xu, H., & Shaw, D. (2012) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-042910-155245 · Cited by 1,176 · see citing works
Interatomic Potentials from First-Principles Calculations – The Force-Matching MethodPreprint
Ercolessi, F., & Adams, J. B. (1994) · Cited by 1,160 · see citing works
Molecular dynamics and protein function
Karplus, M., & Kuriyan, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408930102 · Cited by 1,154 · see citing works
Metal ions in biological catalysis: from enzyme databases to general principles
Andreini, C., Bertini, I., Cavallaro, G., Holliday, G. L., & Thornton, J. M. (2008) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-008-0404-5 · Cited by 1,150 · see citing works
DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
Gaus, M., Cui, Q., & Elstner, M. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct100684s · Cited by 1,111 · see citing works
Self-citation
Approximate Self-Consistent Molecular Orbital Theory. II. Calculations with Complete Neglect of Differential Overlap
Pople, J. A., & Segal, G. A. (1965) · The Journal of Chemical Physics · doi:10.1063/1.1701476 · Cited by 1,082 · see citing works
Direct calculation of electron density in density-functional theory
Yang, W. (1991) · Physical Review Letters · doi:10.1103/physrevlett.66.1438 · Cited by 1,057 · see citing works
Some remarks on the Pariser-Parr-Pople method
Ohno, K. (1964) · Theoretical Chemistry Accounts · doi:10.1007/bf00528281 · Cited by 1,034 · see citing works
Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment
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 · see citing works
Self-citation
S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures
Řezáč, J., Riley, K. E., & Hobza, P. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct2002946 · Cited by 1,022 · see citing works
Parametrization and Benchmark of DFTB3 for Organic Molecules
Gaus, M., Goez, A., & Elstner, M. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300849w · Cited by 1,003 · see citing works
Self-citation
Simulating water with rigid non-polarizable models: a general perspective
Vega, C., & Abascal, J. L. F. (2011) · Physical Chemistry Chemical Physics · doi:10.1039/c1cp22168j · Cited by 992 · see citing works
Consistent structures and interactions by density functional theory with small atomic orbital basis sets
Grimme, S., Brandenburg, J. G., Bannwarth, C., & Hansen, A. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4927476 · Cited by 925 · see citing works
A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems
Kruse, H., & Grimme, S. (2012) · The Journal of Chemical Physics · doi:10.1063/1.3700154 · Cited by 900 · see citing works
Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
Lyubartsev, A. P., & Laaksonen, A. (1995) · Physical Review E · doi:10.1103/physreve.52.3730 · Cited by 852 · see citing works
Empirical 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 838 · see citing works
In pursuit of the ab initio limit for conformational energy prototypes
Császár, A. G., Allen, W. D., & Schaefer, H. F. (1998) · The Journal of Chemical Physics · doi:10.1063/1.476449 · Cited by 718 · see citing works
Exploring the Accuracy Limits of Local Pair Natural Orbital Coupled-Cluster Theory
Liakos, D. G., Sparta, M., Kesharwani, M. K., Martin, J. M. L., & Neese, F. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct501129s · Cited by 702 · see citing works
RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I
Rocha, G. B., Freire, R. O., Simas, A. M., et al. (2006) · Journal of Computational Chemistry · doi:10.1002/jcc.20425 · Cited by 684 · see citing works
Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock
Bikádi, Z., & Hazai, E. (2009) · Journal of Cheminformatics · doi:10.1186/1758-2946-1-15 · Cited by 671 · see citing works
Computer Modeling of Halogen Bonds and Other σ-Hole Interactions
Kolář, M. H., & Hobza, P. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00560 · Cited by 662 · see citing works
Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations
Jurečka, P., Černý, J., Hobza, P., & Salahub, D. R. (2006) · Journal of Computational Chemistry · doi:10.1002/jcc.20570 · Cited by 646 · see citing works
Exchange-hole dipole moment and the dispersion interaction
Becke, A. D., & Johnson, E. R. (2005) · The Journal of Chemical Physics · doi:10.1063/1.1884601 · Cited by 630 · see citing works
A simple polarizable model of water based on classical Drude oscillators
Lamoureux, G., MacKerell, A. D., & Roux, B. (2003) · The Journal of Chemical Physics · doi:10.1063/1.1598191 · Cited by 618 · see citing works
Water Molecule Dipole in the Gas and in the Liquid Phase
Silvestrelli, P. L., & Parrinello, M. (1999) · Physical Review Letters · doi:10.1103/physrevlett.82.3308 · Cited by 614 · see citing works
Accounting for electronic polarization in non-polarizable force fields
Leontyev, I. V., & Stuchebrukhov, A. A. (2011) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp01971b · Cited by 532 · see citing works
\mathcal{O}(N) methods in electronic structure calculations
Bowler, D. R., & Miyazaki, T. (2012) · Reports on Progress in Physics · doi:10.1088/0034-4885/75/3/036503 · Cited by 516 · see citing works
A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method
Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., & Karplus, M. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp0029109 · Cited by 515 · see citing works
Self-citation
Corrected small basis set Hartree‐Fock method for large systems
Sure, R., & Grimme, S. (2013) · Journal of Computational Chemistry · doi:10.1002/jcc.23317 · Cited by 514 · see citing works
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods.
Řezáč, J., & Hobza, P. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct200751e · Cited by 471 · see citing works
Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit?
Řezáč, J., & Hobza, P. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400057w · Cited by 470 · see citing works
Development of a “First Principles” Water Potential with Flexible Monomers. II: Trimer Potential Energy Surface, Third Virial Coefficient, and Small Clusters
Babin, V., Medders, G. R., & Paesani, F. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500079y · Cited by 445 · see citing works
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
Izvekov, S., Parrinello, M., Burnham, C. J., & Voth, G. A. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1739396 · Cited by 433 · see citing works
Orthogonalization corrections for semiempirical methods
Weber, W., & Thiel, W. (2000) · Theoretical Chemistry Accounts · doi:10.1007/s002149900083 · Cited by 433 · see citing works
Wavefunction methods for noncovalent interactions
Hohenstein, E., & Sherrill, C. (2012) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.84 · Cited by 430 · see citing works
Investigations into the Nature of Halogen Bonding Including Symmetry Adapted Perturbation Theory Analyses
Riley, K. E., & Hobza, P. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct700216w · Cited by 428 · see citing works
Solvation. A molecular dynamics study of a dipeptide in water
Rossky, P. J., & Karplus, M. (1979) · Journal of the American Chemical Society · doi:10.1021/ja00502a001 · Cited by 411 · see citing works
Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine
Riley, K. E., Murray, J. S., Fanfrlík, J., et al. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1015-6 · Cited by 405 · see citing works
Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters
Bryantsev, V. S., Diallo, M. S., van Duin, A. C. T., & Goddard, W. A. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct800549f · Cited by 403 · see citing works
Localized bond orbitals and the correlation problem
Diner, S., Malrieu, J., & Claverie, P. (1969) · Theoretical Chemistry Accounts · doi:10.1007/bf00527316 · Cited by 401 · see citing works
Localized bond orbitals and the correlation problem
Diner, S., Malrieu, J., Jordan, F., et al. (1969) · Theoretical Chemistry Accounts · doi:10.1007/bf00528246 · Cited by 370 · see citing works
Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes
Řezáč, J., Fanfrlík, J., Salahub, D. R., et al. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct9000922 · Cited by 358 · see citing works
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand−Macromolecule Complexes. A Bottom-Up Strategy
Gresh, N., Cisneros, G. A., Darden, T. A., & Piquemal, J. (2007) · Journal of Chemical Theory and Computation · doi:10.1021/ct700134r · Cited by 357 · see citing works
Force Field for Peptides and Proteins based on the Classical Drude Oscillator
Lopes, P. E. M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., & MacKerell, A. D. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400781b · Cited by 356 · see citing works
A benchmark for non-covalent interactions in solids
Otero‐de‐la‐Roza, A., & Johnson, E. R. (2012) · The Journal of Chemical Physics · doi:10.1063/1.4738961 · Cited by 354 · see citing works
Basis set convergence of the coupled-cluster correction, $\delta _{\text{MP2}}^{\text{CCSD(T)}}$δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases
Marshall, M. S., Burns, L. A., & Sherrill, C. D. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3659142 · Cited by 351 · see citing works
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 349 · see citing works
Self-citation
Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields
Beachy, M. D., Chasman, D., Murphy, R. B., et al. (1997) · Journal of the American Chemical Society · doi:10.1021/ja962310g · Cited by 338 · see citing works
Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections
Temelso, B., Archer, K. A., & Shields, G. C. (2011) · The Journal of Physical Chemistry A · doi:10.1021/jp2069489 · Cited by 337 · see citing works
Concurrent Coupling of Length Scales in Solid State Systems
Rudd, R. E., & Broughton, J. Q. (2000) · physica status solidi (b) · doi:10.1002/(sici)1521-3951(200001)217:1 · Cited by 335 · see citing works
Density functional tight binding
Elstner, M., & Seifert, G. (2014) · Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences · doi:10.1098/rsta.2012.0483 · Cited by 335 · see citing works
Self-citation
Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study
Graf, J., Nguyen, P. H., Stock, G., & Schwalbe, H. (2007) · Journal of the American Chemical Society · doi:10.1021/ja0660406 · Cited by 333 · see citing works
Understanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals
Reilly, A. M., & Tkatchenko, A. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4812819 · Cited by 332 · see citing works
Electron distribution in water
Badyal, Y. S., Saboungi, M., Price, D. L., Shastri, S. D., Haeffner, D. R., & Soper, A. K. (2000) · The Journal of Chemical Physics · doi:10.1063/1.481541 · Cited by 332 · see citing works
Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules
Řezáč, J., Riley, K. E., & Hobza, P. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300647k · Cited by 325 · see citing works
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
Yang, Y., Yu, H. B., York, D. M., et al. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp074167r · Cited by 316 · see citing works
Is polyproline II a major backbone conformation in unfolded proteins?
Shi, Z., Woody, R. W., & Kallenbach, N. R. (2002) · Advances in protein chemistry · doi:10.1016/s0065-3233(02)62008-x · Cited by 314 · see citing works
Basis set consistent revision of the S22 test set of noncovalent interaction energies.
Takatani, T., Hohenstein, E., Malagoli, M., Marshall, M. S., & Sherrill, C. (2010) · Journal of Chemical Physics · doi:10.1063/1.3378024 · Cited by 314 · see citing works
The accuracy of quantum chemical methods for large noncovalent complexes
Sedlak, R., Janowski, T., Pitoňák, M., Řezáč, J., Pulay, P., & Hobza, P. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400036b · Cited by 312 · see citing works
An Efficient a Posteriori Treatment for Dispersion Interaction in Density-Functional-Based Tight Binding
Zhechkov, L., Heine, T., Patchkovskii, S., Seifert, G., & Duarte, H. A. (2005) · Journal of Chemical Theory and Computation · doi:10.1021/ct050065y · Cited by 303 · see citing works
Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study
Řeha, D., Kabeláč, M., Ryjáček, F., et al. (2002) · Journal of the American Chemical Society · doi:10.1021/ja011490d · Cited by 302 · see citing works
Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems
Kubillus, M., Kubař, T., Gaus, M., Řezáč, J., & Elstner, M. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct5009137 · Cited by 302 · see citing works
Self-citation
Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements
Stewart, J. J. P. (2004) · Journal of Molecular Modeling · doi:10.1007/s00894-004-0183-z · Cited by 302 · see citing works
Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes
Riccardi, D., Schaefer, P., Yang, Y., Yu, H. B., 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 · see citing works
Self-citation
New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
Lee, J., Scheraga, H. A., & Rackovsky, S. R. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(19970715)18:9 · Cited by 300 · see citing works
PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods
Repasky, M. P., Chandrasekhar, J., & Jorgensen, W. L. (2002) · Journal of Computational Chemistry · doi:10.1002/jcc.10162 · Cited by 295 · see citing works
A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods
Korth, M., Pitoňák, M., Řezáč, J., et al. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct900541n · Cited by 275 · see citing works
Extension of MNDO to d Orbitals: Parameters and Results for the Second-Row Elements and for the Zinc Group
Thiel, W., & Voityuk, A. A. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp952148o · Cited by 274 · see citing works
Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents
Jorgensen, W. L., & Schyman, P. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300180w · Cited by 264 · see citing works
Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace‐Ala‐Nme and Ace‐Gly‐Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
Hu, H., Elstner, M., & Hermans, J. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10279 · Cited by 264 · see citing works
Self-citation
Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set
Gráfová, L., Pitoňák, M., Řezáč, J., et al. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct1002253 · Cited by 262 · see citing works
Noncovalent interactions in biochemistry
Riley, K. E., & Hobza, P. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.8 · Cited by 257 · see citing works
Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package
Seabra, G. D. M., Walker, R. C., Elstner, M., Case, D. A., & Roitberg, A. E. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp070071l · Cited by 257 · see citing works
Self-citation
Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model
Banks, J. L., Kaminski, G. A., Zhou, R., et al. (1999) · The Journal of Chemical Physics · doi:10.1063/1.478043 · Cited by 253 · see citing works
The role of quantum mechanics in structure-based drug design
Raha, K., Peters, M. B., Wang, B., Yu, N., Wollacott, A. M., Westerhoff, L. M., & Merz, K. M. (2007) · Drug Discovery Today · doi:10.1016/j.drudis.2007.07.006 · Cited by 253 · see citing works
Parameter Calibration of Transition-Metal Elements for the Spin-Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method: Sc, Ti, Fe, Co, and Ni
Zheng, G., Witek, H. A., Bobadova‐Parvanova, P., Irle, S., Musaev, D. G., Prabhakar, R. S., Morokuma, K., Lundberg, M., Elstner, M., Köhler, C., et al. (2007) · Journal of Chemical Theory and Computation · doi:10.1021/ct600312f · Cited by 250 · see citing works
Self-citation
GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations
Maia, J. D. C., Urquiza‐Carvalho, G. A., Mangueira, C. P., et al. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct3004645 · Cited by 250 · see citing works
Theoretical Calculation of Absolute Radii of Atoms and Ions. Part 1. The Atomic Radii
Ghosh, D. C., & Biswas, R. (2002) · International Journal of Molecular Sciences · doi:10.3390/i3020087 · Cited by 249 · see citing works
Theoretical Study of Aqueous N-Acetyl- l -alanine N‘-Methylamide: Structures and Raman, VCD, and ROA Spectra
Han, W., Jalkanen, K. J., Elstner, M., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp972299m · Cited by 248 · see citing works
Self-citation
Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries
Řezáč, J., Riley, K. E., & Hobza, P. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct200523a · Cited by 247 · see citing works
Semiempirical molecular orbital calculations with linear system size scaling
Dixon, S. L., & Merz, K. M. (1996) · The Journal of Chemical Physics · doi:10.1063/1.471382 · Cited by 244 · see citing works
Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields
Korth, M. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct100408b · Cited by 244 · see citing works
SINDO1. A semiempirical SCF MO method for molecular binding energy and geometry I. Approximations and parametrization
Nanda, D. N., & Jug, K. (1980) · Theoretical Chemistry Accounts · doi:10.1007/bf00574898 · Cited by 243 · see citing works
Comprehensive Benchmark of Association (Free) Energies of Realistic Host–Guest Complexes
Sure, R., & Grimme, S. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00296 · Cited by 243 · see citing works
Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective
Wolters, L. P., & Bickelhaupt, F. M. (2012) · ChemistryOpen · doi:10.1002/open.201100015 · Cited by 242 · see citing works
A chemical potential equalization method for molecular simulations
York, D. M., & Yang, W. (1996) · The Journal of Chemical Physics · doi:10.1063/1.470886 · Cited by 234 · see citing works
Molecular mechanical study of halogen bonding in drug discovery
Ibrahim, M. A. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21836 · Cited by 223 · see citing works
A semiempirical model for the two-center repulsion integrals in the NDDO approximation
Dewar, M. J. S., & Thiel, W. (1977) · Theoretical Chemistry Accounts · doi:10.1007/bf00548085 · Cited by 211 · see citing works
Simulations of peptide conformational dynamics and thermodynamics
Brooks, C. L., & Case, D. A. (1993) · Chemical Reviews · doi:10.1021/cr00023a008 · Cited by 210 · see citing works
Large-Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein−Ligand Complexes
Raha, K., & Merz, K. M. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm048973n · Cited by 209 · see citing works
An Improved Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Set of Parameters for Simulation of Bulk and Molecular Systems Involving Titanium
Dolgonos, G., Aradi, B., Moreira, N. H., et al. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct900422c · Cited by 207 · see citing works
Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results
Tobias, D. J., & Brooks, C. L. (1992) · The Journal of Physical Chemistry · doi:10.1021/j100188a054 · Cited by 205 · see citing works
A Method for Estimating Electronic Repulsion Integrals Over LCAO MO'S in Complex Unsaturated Molecules
Parr, R. G. (1952) · The Journal of Chemical Physics · doi:10.1063/1.1700802 · Cited by 200 · see citing works
Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB)
Brandenburg, J. G., & Grimme, S. (2014) · The Journal of Physical Chemistry Letters · doi:10.1021/jz500755u · Cited by 198 · see citing works
Preparation of Water-Soluble Cationic Phosphorus-Containing Dendrimers as DNA Transfecting Agents
Loup, C., Zanta, M.-A., Caminade, A., Majoral, J., & Meunier, B. (1999) · Chemistry - A European Journal · doi:10.1002/(sici)1521-3765(19991203)5:12 · Cited by 196 · see citing works
Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications
Lu, X., Gaus, M., Elstner, M., & Cui, Q. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp506557r · Cited by 192 · see citing works
Self-citation
An 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 191 · see citing works
Self-citation
Assessment of the MP2 Method, along with Several Basis Sets, for the Computation of Interaction Energies of Biologically Relevant Hydrogen Bonded and Dispersion Bound Complexes
Riley, K. E., & Hobza, P. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp073358r · Cited by 183 · see citing works
SCC-DFTB: What Is the Proper Degree of Self-Consistency?
Elstner, M. (2007) · The Journal of Physical Chemistry A · doi:10.1021/jp071338j · Cited by 183 · see citing works
Self-citation
Density functional tight binding: application to organic and biological molecules
Gaus, M., Cui, Q., & Elstner, M. (2014) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1156 · Cited by 182 · see citing works
Self-citation
A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations
Grimme, S. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500573f · Cited by 182 · see citing works
Parameterization of NDDO wavefunctions using genetic algorithms. An evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations for organic reactions
Rossi, I., & Truhlar, D. G. (1995) · Chemical Physics Letters · doi:10.1016/0009-2614(94)01450-a · Cited by 178 · see citing works
Structure and IR Spectrum of Phenylalanyl–Glycyl–Glycine Tripetide in the Gas‐Phase: IR/UV Experiments, Ab Initio Quantum Chemical Calculations, and Molecular Dynamic Simulations
Řeha, D., Valdés, H., Vondrášek, J., et al. (2005) · Chemistry - A European Journal · doi:10.1002/chem.200500465 · Cited by 176 · see citing works
Communication: The effect of dispersion corrections on the melting temperature of liquid water
Yoo, S., & Xantheas, S. S. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3573375 · Cited by 170 · see citing works
Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples
Řezáč, J., Jurečka, P., Riley, K. E., Černý, J., Valdés, H., Pluháčková, K., Berka, K., Řezáč, T., Pitoňák, M., Vondrášek, J., et al. (2008) · Collection of Czechoslovak Chemical Communications · doi:10.1135/cccc20081261 · Cited by 169 · see citing works
Density functional based calculations for Fen (n⩽32)
Köhler, C., Seifert, G., & Frauenheim, T. (2004) · Chemical Physics · doi:10.1016/j.chemphys.2004.03.034 · Cited by 167 · see citing works
A Comparison of the CHARMM, AMBER and ECEPP Potentials for Peptides. II. φ-ψ Maps for N-Acetyl Alanine N′-Methyl Amide: Comparisons, Contrasts and Simple Experimental Tests
Roterman, I., Lambert, M. H., Gibson, K. D., et al. (1989) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.1989.10508503 · Cited by 167 · see citing works
Modeling zinc in biomolecules with the self consistent charge‐density functional tight binding (SCC‐DFTB) method: Applications to structural and energetic analysis
Elstner, M., Cui, Q., Munih, P., Kaxiras, E., Frauenheim, T., & Karplus, M. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10201 · Cited by 165 · see citing works
Self-citation
Looking 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 · see citing works
Toward Accurate Theoretical Thermochemistry of First Row Transition Metal Complexes
Jiang, W., DeYonker, N. J., Determan, J. J., & Wilson, A. K. (2011) · The Journal of Physical Chemistry A · doi:10.1021/jp205710e · Cited by 160 · see citing works
Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales
Shi, Z., Chen, K., Liu, Z., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507124102 · Cited by 159 · see citing works
Density functional tight binding: values of semi-empirical methods in an ab initio era
Cui, Q., & Elstner, M. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp00908h · Cited by 158 · see citing works
Self-citation
Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data
Krüger, T., Elstner, M., Schiffels, P., et al. (2005) · The Journal of Chemical Physics · doi:10.1063/1.1871913 · Cited by 157 · see citing works
Self-citation
Bulk Liquid Water at Ambient Temperature and Pressure from MP2 Theory
Ben, M. D., Schönherr, M., Hutter, J., & VandeVondele, J. (2013) · The Journal of Physical Chemistry Letters · doi:10.1021/jz401931f · Cited by 157 · see citing works
A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding
Raha, K., & Merz, K. M. (2004) · Journal of the American Chemical Society · doi:10.1021/ja038496i · Cited by 156 · see citing works
Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field
Valdés, H., Pluháčková, K., Pitoňák, M., et al. (2008) · Physical Chemistry Chemical Physics · doi:10.1039/b719294k · Cited by 156 · see citing works
Beyond the MNDO model: Methodical considerations and numerical results
Kolb, M., & Thiel, W. (1993) · Journal of Computational Chemistry · doi:10.1002/jcc.540140704 · Cited by 152 · see citing works
Quantum 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 · see citing works
Self-citation
Do Bridging Water Molecules Dictate the Structure of a Model Dipeptide in Aqueous Solution?
Poon, C., Samulski, E. T., Weise, C. F., et al. (2000) · Journal of the American Chemical Society · doi:10.1021/ja993953+ · Cited by 148 · see citing works
Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods
Jensen, J. H. (2015) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp00628g · Cited by 145 · see citing works
Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein−Ligand Complexes
Faver, J. C., Benson, M. L., He, X. D., Roberts, B. P., Wang, B., Marshall, M. S., Kennedy, M. R., Sherrill, C. D., & Merz, K. M. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct100563b · Cited by 141 · see citing works
Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations
Elstner, M., Jalkanen, K. J., Knapp‐Mohammady, M., et al. (2001) · Chemical Physics · doi:10.1016/s0301-0104(00)00375-x · Cited by 140 · see citing works
Self-citation
On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds
Kolář, M. H., & Hobza, P. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct2008389 · Cited by 139 · see citing works
Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules
McNamara, J. P., & Hillier, I. H. (2007) · Physical Chemistry Chemical Physics · doi:10.1039/b701890h · Cited by 136 · see citing works
Comparison 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 · see citing works
Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches
Li, A., Muddana, H. S., & Gilson, M. K. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct401111c · Cited by 131 · see citing works
A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle
Chelli, R., & Procacci, P. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1515773 · Cited by 129 · see citing works
N-Acetyl-L-alanine N′-methylamide: a density functional analysis of the vibrational absorption and vibrational circular dichroism spectra
Jalkanen, K. J., & Suhai, S. (1996) · Chemical Physics · doi:10.1016/0301-0104(96)00042-0 · Cited by 126 · see citing works
Toward an Accurate Density-Functional Tight-Binding Description of Zinc-Containing Compounds
Moreira, N. H., Dolgonos, G., Aradi, B., da Rosa, A. L., & Frauenheim, T. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct800455a · Cited by 125 · see citing works
A halogen-bonding correction for the semiempirical PM6 method
Řezáč, J., & Hobza, P. (2011) · Chemical Physics Letters · doi:10.1016/j.cplett.2011.03.009 · Cited by 124 · see citing works
Further analysis and comparative study of intermolecular interactions using dimers from the S22 database
Molnar, L. F., He, X., Wang, B., & Merz, K. M. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3173809 · Cited by 123 · see citing works
Intrinsic backbone preferences are fully present in blocked amino acids
Avbelj, F., Grdadolnik, S. G., Grdadolnik, J., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510420103 · Cited by 123 · see citing works
Some remarks on the Pariser-Parr-Pople method
Ohno, K. (1970) · Theoretical Chemistry Accounts · doi:10.1007/bf00527570 · Cited by 122 · see citing works
Correct electrostatic treatment of noncovalent interactions: the importance of polarization
Clark, T., Politzer, P. A., & Murray, J. S. (2014) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1210 · Cited by 121 · see citing works
A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands
Fanfrlík, J., Bronowska, A. K., Řezáč, J., Přenosil, O., Konvalinka, J., & Hobza, P. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp1032965 · Cited by 121 · see citing works
Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models
Goyal, P., Qian, H.-J., Irle, S., Lu, X., Roston, D., Mori, T., Elstner, M., & Cui, Q. (2014) · Journal of Physical Chemistry B · doi:10.1021/jp503372v · Cited by 120 · see citing works
Self-citation
Molecular orbital calculations on carbonium ions. II. Methyl, ethyl, and vinyl cations. The series C3H7+
Sustmann, R., WILLIAMS, J. E. J., Dewar, M. J. S., et al. (1969) · Journal of the American Chemical Society · doi:10.1021/ja01047a026 · Cited by 115 · see citing works
Benchmarking DFT and semiempirical methods on structures and lattice energies for ten ice polymorphs
Brandenburg, J. G., Maas, T., & Grimme, S. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4916070 · Cited by 114 · see citing works
Improved interaction energy benchmarks for dimers of biological relevance
Podeszwa, R., Patkowski, K., & Szalewicz, K. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/b926808a · Cited by 114 · see citing works
Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods
Řezáč, J., Huang, Y., Hobza, P., & Beran, G. J. O. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00281 · Cited by 110 · see citing works
Theoretical Calculation of Absolute Radii of Atoms and Ions. Part 2. The Ionic Radii
Ghosh, D. C., & Biswas, R. (2003) · International Journal of Molecular Sciences · doi:10.3390/i4060379 · Cited by 110 · see citing works
The electronic properties of water molecules in water clusters and liquid water
Tu, Y., & Laaksonen, A. (2000) · Chemical Physics Letters · doi:10.1016/s0009-2614(00)01026-5 · Cited by 107 · see citing works
Perspectives on Semiempirical Molecular Orbital Theory
Thiel, W. (1996) · Advances in chemical physics · doi:10.1002/9780470141526.ch10 · Cited by 106 · see citing works
Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches
Burns, L. A., Marshall, M. S., & Sherrill, C. D. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4903765 · Cited by 104 · see citing works
DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1–20
Elstner, M., Jalkanen, K. J., Knapp‐Mohammady, M., et al. (2000) · Chemical Physics · doi:10.1016/s0301-0104(00)00100-2 · Cited by 101 · see citing works
Self-citation
Low-Cost Quantum Chemical Methods for Noncovalent Interactions
Brandenburg, J. G., Hochheim, M., Bredow, T., & Grimme, S. (2014) · The Journal of Physical Chemistry Letters · doi:10.1021/jz5021313 · Cited by 98 · see citing works

Flagged first, then by citations

Research works printed but not linked: 5

Weinhold F.; Landis C. R. Valency and Bonding; Cambridge University Press: Cambridge, UK, 2005.
Elstner M.; Porezag D.; Jungnickel G.; Elsner J.; Haugk M.; Frauenheim T.; Suhai S.; Seifert G. Self-Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Complex Materials Properties. Phys. Rev. B: Condens. Matter Mater. Phys. 1998, 58, 7260– 7268. 10.1103/PhysRevB.58.7260. · DOI
Muto Y. Forces Between Nonpolar Molecules. J. Phys.-Math. Soc. Jpn. 1943, 17, 629– 631.
Řezáč J.; Riley K. E.; Hobza P. Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules. J. Chem. Theory Comput. 2012, 8, 4285– 4292. 10.1021/ct300647k. 26605592 · DOI
Tvaroška I.; Kožár T. Theoretical Studies on the Conformation of Saccharides XI. Stereochemistry of Methyl α- and Methyl β-d-glucopyranosides in Solution. Chem. Pap. 1987, 41, 501– 510.

Sorted by citations

Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges
Guedes, I. A., Pereira, F. S. S., & Dardenne, L. E. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.01089 · Cited by 331 · see citing works
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., et al. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04100 · Cited by 136 · see citing works
Self-citation
Generalized Density-Functional Tight-Binding Repulsive Potentials from Unsupervised Machine Learning
Kranz, J. J., Kubillus, M., Ramakrishnan, R., von Lilienfeld, O. A., & Elstner, M. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00933 · Cited by 63 · see citing works
Self-citation
Recent advances in automated protein design and its future challenges
Setiawan, D., Brender, J., & Zhang, Y. (2018) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2018.1465922 · Cited by 26 · see citing works

THE PHOTOCHEMICAL METHODS OF IMMOBILIZATION BIOMOLECULES ON POLYMER MATERIALS
Zhong, Y. (2001)
Design of Sub-40nm FinFET Based Label Free Biosensor
Kesherwani, S., Daga, M., & Mishra, G. P. (2022) · Silicon · doi:10.1007/s12633-022-01936-9 · Cited by 22 · see citing works
Biomolecule-sensitive Hydrogels
Miyata, T. (2013) · Royal Society of Chemistry eBooks · doi:10.1039/9781849734318-00261 · Cited by 6 · see citing works
A general approach for biomimetic mineralization of MOF particles using biomolecules
Zou, D., Yu, L., Sun, Q., Hui, Y., Tengjisi, Liu, Y., Yang, G., Wibowo, D., & Zhao, C. (2020) · Colloids and Surfaces B Biointerfaces · doi:10.1016/j.colsurfb.2020.111108 · Cited by 50 · see citing works
Biomolecule and its Types
Upadhay, S. (2021) · Natural Products Chemistry & Research · doi:10.35248/2329-6836.21.9.404

Authors: Christensen, A. S., Kubař, T., Cui, Q., & Elstner, M.
Affiliations: University of Wisconsin–Madison (US)
Karlsruhe Institute of Technology , , Kaiserstrasse 12 , ,
Karlsruhe Institute of Technology (DE)
Corresponding author: Cui, Qiang
Elstner, Marcus
ORCID: Christensen, Anders S.
Cui, Qiang
Elstner, Marcus
Venue: Chemical Reviews
Publisher: American Chemical Society (ACS)
Published: 2016-04-13
Volume: 116
Issue: 9
Pages: 5301-5337
ISSN: 0009-2665 (ISSN-L)
1520-6890
DOI: 10.1021/acs.chemrev.5b00584
PMC: PMC4867870
OpenAlex: W2337403656
Cited by: 446
References: 336
Citations by year: 2026: 25 · 2025: 54 · 2024: 51 · 2023: 48 · 2022: 59 · 2021: 52 · 2020: 46 · 2019: 35 · 2018: 36 · 2017: 25 · 2016: 13 · 2015: 1
FWCI: 1.85
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: other-oa
pubs.acs.org/page/policy/authorchoice_termsofuse.html (vor, 365 d)
Locations: Chemical Reviews (publishedVersion, other-oa)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institute of General Medical Sciences (R01-GM106443)
Division of Chemistry (CHE-1300209)
Topics: Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Crystallography and molecular interactions
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords: non-covalent interactions, biomolecules, aqueous solutions, organic materials, soft matter, conformational sampling, linear-scaling methods, large molecular systems
MeSH terms: Algorithms, Ligands, Metals, Peptides, Proteins, Quantum Theory, Water

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

Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications.

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Self-check

Cites

Cited by

Related

Record

About these checks