Publications Piet van Duijnen

111G.J. Linker, P. Th. van Duijnen, P.H.M. van Loosdrecht, R. BroerThe thermal metal-insulator phase transition in (EDO-TTF)2PF6
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Mol. Phys., http://dx.doi.org/10.1080/00268976.2016.12637652016
110M. Remko, R. Broer, A. Remková, P. Th. Van DuijnenHow strong are Ca2+-heparin and Zn2+-heparin interactions?
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Chem. Phys. Lett., 621, 12-172015
109G.J. Linker, P. Th. van Duijnen, P.H.M. van Loosdrecht, R. BroerTheoretical study of the ground state of (EDO-TTF)2PF6
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Comp. Theor. Chem., 1069, 105-1112015
108G.-J. Linker, P.H.M. van Loosdrecht, P. Th. van Duijnen, R. BroerPeriodic Hartree-Fock and hybrid density functional calculations on the metallic and the insulating phase of (EDO-TTF)2PF6
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Phys. Chem. Chem. Phys., 17, 30371-303772015
107M. Remko, R. Broer, A. Remková, P. Th. van DuijnenAcidity and metal (Mg2+, Ca2+, Zn2+) affinity of L-γ-carboxyglutamic acid and its peptide analog
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Chem. Phys. Lett., 614, 214-2192014
106P. Th. van Duijnen, H.D. de Gier, R. Broer, R.W.A. HavenithThe behaviour of charge distributions in dielectric media
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Chem. Phys. Lett., 615, 83-882014
105Milan Remko, Ria Broer, Piet Th. van DuijnenHow acidic are monomeric structural units of heparin?
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Chem. Phys. Lett., 590, 187-1912013
104Milan Remko, Piet Th. van Duijnen, Ria BroerStructure and stability of complexes of charged structural units of heparin with arginine and lysine
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RSC Adv., 3, 1789-17962013
103Milan Remko, Piet Th. Van Duijnen, Ria Broer Effect of metal ions (Li+, Na+, K+, Mg2+, and Ca2+) and water on the conformational changes of glycosidic bonds in heparin oligosaccharides
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RSC Adv., 3, 9843-9853 2013
102Gerrit-Jan Linker, Piet Th. van Duijnen, Paul H.M. van Loosdrecht, Ria BroerOff-Planar Geometry and Structural Instability of EDO-TTF Explained by Using the Extended Debye Polarizability Model for Bond Angles
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J. Phys. Chem. A, 116, 7219-72272012
101Layo van het Goor, Piet Th. van Duijnen, Carola Koper, Leonardus W. Jenneskens, Remco W. A. Havenith, František Hartlπ-dimerization of pleiadiene radical cations at low temperatures revealed by UV-vis spectroelectrochemistry and quantum theory
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J Solid State Electrochem 15:2107-21172011
100Gerrit-Jan Linker, Paul H.M. van Loosdrecht, Piet van Duijnen, Ria BroerComparison of ab initio molecular properties of EDO-TTF with the properties of the (EDO-TTF)2PF6 crystal
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Chemical Physics Letters 487, 220-2252010
99MARCEL SWART, PIET TH. VAN DUIJNENAtomic Radii in Molecules for Use in a Polarizable Force Field
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International Journal of Quantum Chemistry, accepted2010
98Piet Th. van Duijnen and Marcel SwartOn the 'atomic' polarizabilities in small Sin clusters and the dielectric constant of 'bulk' silicon
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J.Phys.Chem.C, 114, 20547-205552010
97Milan Remko, Piet Th. Van Duijnen, Ria BroerMolecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans
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Struct. Chem., 21:965-976, DOI 10.1007/s11224-010-9633-72010
96Duijnen, P.Th.van, Swart M. and Jensen L.The discrete reaction field approach for calculating solvent effects
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In: Solvation effects on molecules and biomolecules, S. Canuto, Editor. Springer. p. 39-1032008
95Piet Th. van Duijnen, Shannon N. Greene, and Nigel G. J. RichardsTime-dependent density functional theory/discrete reaction field spectra of open shell systems: The visual spectrum of [FeIII(PyPepS)2]- in aqueous solution
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J. Chem. Phys. 127, 0451052007
94Milan Remko, Piet Th. Van Duijnen and Claus-Wilhelm von der LiethStructure and stability of Li(I) and Na(I) - Carboxylate, sulfate and phosphate complexes
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Journal of Molecular Structure: THEOCHEM 814 119-1252007
93Jensen L. and Duijnen, P.Th. vanThe Discrete Solvent Reaction Field model: A Quantum mechanics/Molecular mechanics model for calculating nonlinear optical properties of molecules in the condensed phase
In: Atoms, molecules and clusters in electric fields. Theoretical approaches to the calculation of electric polarizability, G. Maroulis, Editor. Imperial College Press: London. p. 1-43. 2006
92L. Jensen, M.Swart, P.Th. van Duijnen, and J. AutschbachCircular Dichroism Spectrum of [Co(en)3]3+ in Water: A Discrete Solvent Reaction Field Study
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Int.J.Quantum Chem. Vol 106, 2479-24882006
91P. Th. van Duijnen and T.L. NetzelExplicit Solvent DRF INDOs/CIS Computations of Charge Transfer State Energetics in a Pyrenyldeoxyuridine Nucleoside Model
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J.Phys.Chem.A, 110, 2204-22132006
90 M.Swart, P.Th. van DuijnenDRF90: a Polarizable Force Field.
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Molec. Simul. Vol. 32, No. 62006
89L. Jensen and P.Th. van DuijnenThe refractive index and third-order nonlinear susceptibility of C60 in the condensed phase, calculated with the Discrete Reaction Field solvent model
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Int. J. Quantum Chem., 2005. 102(1): p. 612-6192005
88L. Jensen, M.Swart, and P.Th. van DuijnenMicroscopic and macroscopic polarization witin a combined quantum mechanics and molecuar mechanics model
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J. Chem.Phys., 2005. 122: p. 034103/142005
87F. C. Grozema, M. Swart, R.W.J. Zijlstra, J. J. Piet, L. D.A. Siebbeles, and P.Th. van DuijnenQM/MM study of the role of the solvent in the formation of the charge separated excited state in 9, 9'-bianthryl.
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J.Am.Chem.Soc., 2005. 127: p. 11019-110282005
86L. Jensen and P.Th. van DuijnenThe second-harmonic generation of p-nitroaniline in 1,4-dioxane: A quantum mechanical/molecular mechanics study
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J.Chem.Phys., 123, 074307 (2005)2005
85F.C. Grozema, P. Th. van Duijnen, L.D.A. Siebbeles, A. Goossens, S.W. de LeeuwElectronic structure of thienylene vinylene oligomers: singlet excited sates, triplet excited states, cations, and dications
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J. Phys. Chem. B, 108, 16139-161462004
84M.Swart, J.G.Snijders, P.Th.van DuijnenPolarizabilities of amino acid residues
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JCSME 4 (2004) 419-4252004
83L.Jensen, P.Th. van Duijnen, J.G.SnijdersA Discrete Solvent Reaction field Model within Density Functional Theory
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J. Chem. Phys. 118, 514-5212003
82L.Jensen, P.Th. van Duijnen, J.G.SnijdersA discrete solvent reaction field model for calculating frequency-dependent hyperpolarizabilities of molecules in solution
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J. Chem. Phys. 119 (24) 12998-130062003
81L.Jensen, P.Th. van Duijnen, J.G.SnijdersA Discrete Solvent Reaction Field Model for calculating molecular linear response properties in solution
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J. Chem. Phys. 119, 3800-38092003
80M.Remko, P.Th.van Duijnen, M.SwartTheoretical study of molecular structure, tautomerism, and geometrical isomerism of N-methyl and N-phenyl substituted cyclic imidazolines, oxazolines and thiazolines
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J. Struct. Chem. 14, 271-2782003
79L.Jensen, P.Th. van Duijnen, J.G.Snijders, D.P.ChongTime-Dependent Density Functional study of the second hyperpolarizability of BB-, NN- and BN-substituted C60
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Chem. Phys. Lett. 359, 524-5292002
78F.Grozema, P.Th..van Duijnen, Y. A. Berlinc, M.A. Ratner,L.D.A.SiebbelesIntramolecular Charge Transport Along Isolated Chains of Conjugated Polymers:
Effect of Torsional Disorder and Polymerization Defects

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J. Phys. Chem. B, 7791-77952002
77T.la Cour Jansen, M.Swart, L.Jensen, P.Th.van Duijnen, J.G.Snijders, K.DuppenCollision effects in the nonlinear Raman response of liquid carbon disulfide
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J. Chem. Phys. 116, 3277-32852002
76F.C.Grozema, L.P.Candeias, M.Swart, P.Th.van Duijnen, J.Wildeman, G.Hadziioanou, L.D.A.Siebbeles, J M.WarmanTheoretical and experimental studies of the opto-electronic properties of positively charged oligo(phenylene vinylene)s: Effects of chain length and alkoxy substitution
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J. Chem. Phys. 117, 11366-113782002
75L.Jensen, M.Swart, P.Th. van Duijnen, J.G.SnijdersMedium perturbations on the molecular polarizability calculated within a localized dipole interaction model
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J. Chem. Phys. 117, 3316-33202002
74P.Th..van Duijnen, A.H.de Vries, M.Swart, F.GrozemaPolarizabilities in the Condensed Phase and the Local Fields Problem.
A Direct Reaction Field formulation.

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J. Chem. Phys. 117, 8442-84532002
73M.Swart, P.Th.van Duijnen, J.G.SnijdersA charge analysis derived from an atomic multipole expansion
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J. Comput. Chem. 22, 79-882001
72R.W.J.Zijlstra, F.C.Grozema, M.Swart, B.L.Feringa, P.Th.van Duijnen Solvent induced charge separation in the excited states of symmetrical ethylene:
A Direct Reaction Field study

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J. Phys. Chem. A 105, 3583-35902001
71R.Telesca, H.Bolink, S.Yunoki, G.Hadziioannou, P.Th.van Duijnen, H.T.Jonkman, J.G.Snijders, G.A.SawatzkyA Density Functional Study of the Evolution of the Electronic Structure of Oligomers of Thiophene
Towards a Model Hamiltonian

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Phys. Rev. B 63, 155112, 1-112001
70M.Remko, M.Smieko, P.Th.van DuijnenSubstituent Effects on Gas-Phase Acidities of Formic Acid and Its Silicon and Sulfur Derivatives R-M(=X)XH (M = C, Si; X = O, S; R = H, F, Cl, OH, NH2, and CH3)
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Mol. Phys. 98, 709-7142000
69P.Th.van Duijnen, M.Swart, F.C.GrozemaQM/MM calculations of (hyper-)polarizabilities with the Direct Reaction Field approach
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ACS Symposium Series 712, 220-2321999
68F.C.Grozema, R.W.J.Zijlstra, P.Th.van DuijnenMany-Body Interactions Calculated with the Direct Reaction Field Model
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Chem. Phys. 246, 217-2271999
67M.Remko, P.Th.van DuijnenThe gas-phase acidities of substituted dithiosilanoic acids
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Chem. Phys. Lett. 308, 242-2481999
66F.C.Grozema, R.W.Zijlstra, M.Swart, P.Th.van DuijnenOn the Iodine-Benzene complex. Potential energy surface and transition probabilities studied at several levels of theory
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Int. J. Quant. Chem. 75, 709-7231999
65M.Swart, P.Th.van Duijnen, J.G.SnijdersMean polarizabilities of organic molecules. A comparison of Restricted Hartree Fock, Density Functional Theory and Direct Reaction Field results
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J. Mol. Struct. (THEOCHEM) 458, 11-171999
64P.Th.van Duijnen, F.C.Grozema, M.SwartSome applications of the Direct Reaction Field approach
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J. Mol. Struct. (THEOCHEM) 464, 193-2001999
63R.W.J.Zijlstra, W.F.Jager, B.de Lange, P.Th.van Duijnen, B.L.Feringa, H.Goto, A.Saito, N.Koumura, N.HaradaChemistry of Unique Chiral Olefins. 4. Theoretical Studies of the Racemization Mechanism of trans- and cis- 1,1',2,2',3,3',4,4'-Octahydro-4,4'-biphenanthrylidenes
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J. Org. Chem. 64, 1667-16741999
62P.Th.van Duijnen, M.SwartMolecular and atomic polarizabilities : Thole's model Revisited
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J. Phys. Chem. A 102, 2399-24071998
61F.C.Grozema, P.Th.van DuijnenSolvent effects on the n to p* transition of acetone in various solvents
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J. Phys. Chem. A 102, 7984-79891998
60A.C.Dros, R.W.J.Zijlstra, P.Th.van Duijnen, A.L.Spek, H.Kooijman, R.M.KelloggUnusual Conformational Aspects of some Novel Chiral Non-racemic Pyridinyl-2-Phosphonates
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Tetrahedron 54, 7787-78121998
59P.Th.van DuijnenTheo Thole as a Ph.D. "student"
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J. El. Spectr. Rel. Phen. 86, 17-211997
58A.H.de Vries, P.Th.van Duijnen, R.W.J.Zijlstra, M.SwartThole's interacting polarizability model in computational chemistry practice
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J. El. Spectr. Rel. Phen. 86, 49-561997
57M.Y.Nguyen, G.Raspoet, L.G.Vanquickenborne, P.Th.van DuijnenHow many water molecules are involved in the neutral hydration of carbon oxide?
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J. Phys. Chem. A 101, 7379-73881997
56R.W.J.Zijlstra, P.Th.van Duijnen, B.L.Feringa, T.Steffen, K.Duppen, D.A.WiersmaExcited state dynamics of tetraphenylethene: ultrafast Stoke shift, isomerization and charge separation
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J. Phys. Chem. A 101, 9828-98361997
55R.Duchateau, T.Tuinstra, E.A.C.Brusee, A.Meetsma, P.Th.van Duijnen, J.H.TeubenAlternatives for Cyclopentadienyl Ligands in Organometallic Chemistry: Bis(N,O-Bis(tert-Butyl)Alkoxydiethylsilylamido) Yttrium compounds
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Organometallics 16, 3511-35221997
54R.W.J.Zijlstra, P.Th.van Duijnen, A.H.de VriesPolarization of the excited states of twisted ethylene in a non-symmetrical environment
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Chem. Phys. 204, 439-461996
53A.H.de Vries, P.Th.van DuijnenSolvatochromism of the p*<n transition of acetone by combined quantum mechanical-classical mechanical calculations
Int. J. Quant. Chem. 57, 1067-10761996
52P.Th.van Duijnen, A.H.de VriesDirect reaction field force field: a consistent way to connect and combine quantum-chemical and classical descriptions of molecules
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Int. J. Quant. Chem. 60, 1111-11321996
51R.Duchateau, C.T.van Wee, A.Meetsma, P.Th.van Duijnen, J.H.TeubenAncillary ligand effects in Organoyttrium chemistry: Synthesis,Characterization and electronic strcture of Bis(benzamidinato)yttrium compounds.
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Organometallics 15, 2279-22901996
50P.Th.van Duijnen, A.H.de VriesUtopia dielectrica
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Int. J. Quant. Chem. S29, 523-5311995
49A.H.de Vries, P.Th.van Duijnen, A.H.Juffer, J.A.C.Rullmann, J.P.Dijkman, H.Merenga, B.T.TholeImplementation of reaction field methods in quantum chemistry computer codes
J. Comput. Chem. 16, 37-551995
48P.Th.van DuijnenEmbedding in quantum chemistry: the direct recationfield approach
New challenges in computional quantum chemistry, R. Broer, P. J. C. Aerts and P. S. Bagus(Ed.) Dept. of Chemical Physics andMaterials Science, Groningen1994
47A.H.de Vries, P.Th.van Duijnen, A.H.JufferSuccess and pitfalls of the dielectric continuum model in quantum chemical calculations
Int. J. Quant. Chem. S27, 451-4661993
46A.H.de Vries, P.Th.van DuijnenTheoretical calculation of tautomer equilibria of 4-substituted imidazoles in the gas phase and in solution
Biophys. Chem. 43, 139-1471992
45M.Remko, S.Scheiner, P.Th.van DuijnenAb initio investigations of interactions between models of local anesthetics and polar groups of membranes
QSAR in design of bioacitve compounds, A. J. Hopfinger(Ed.), J.R.Prous Science Publishers, Barcelona, p.831992
44P.Th.van Duijnen, A.H.Juffer, H.P.DijkmanQuantum chemistry in the condensed phase: an extended direct reaction field approach
THEOCHEM 92, 195-2051992
43J.P.Dijkman, P.Th.van DuijnenPapain in aqueous solution and the role of Asp-158 in the mechanism: an ab initio SCF + DRF + BEM study
Int. J. Quant. Chem. S18, 49-591991
42P.Th.van Duijnen, J.A.C.RullmannIntermolecular interactions with the direct reaction field method
Int. J. Quant. Chem. 38, 181-1891990
41H.van der Werff, P.Th.van Duijnen, A.J.PenningsDeformation energetics of chain defects of polyethylene
Macromolecules 23, 2935-29401990
40J.A.C.Rullmann, P.Th.van DuijnenPotential energy models of biological macromolecules: a case for ab initio quantum chemistry
Rep. Mol. Theory 1, 1-211990
39J.A.C.Rullmann, M.N.Bellido, P.Th.van DuijnenThe active site of papaine: all-atom study of interactions with protein matrix and solvent
J. Mol. Biol. 206, 101-1181989
38S.J.Picken, W.F.van Gunsteren, P.Th.van Duijnen, W.H.de JeuA molecular dynamics study of the nematic phase of 4-n-pentyl-4'-cyanobiphenyl
Liq. Cryst. 6, 357-3711989
37J.A.C.Rullmann, P.Th.van DuijnenA polarizable water model for calculation of hydration energies
Mol. Phys. 63, 451-4751988
36J.A.C.Rullmann, P.Th.van DuijnenAnalysis of discrete and continuum dielectric models; application to the calculation of protonation energies in solution
Mol. Phys. 61, 293-3111987
35M.Remko, P.Th.van Duijnen, I.Sekerka, J.Cizmárik,Ab initio and PCILO investigations of local anaesthetic-model membrane interactions
Drugs Exptl. Clin. Res. 21, 7131986
34P.Th.van DuijnenQuantum chemistry and enzymes: a next step
Enzyme 36, 93-1001986
33P.Th.van DuijnenComputed structure/function realtionships of proteins and their possible model dependence
Theoretical chemistry of biological systems., G. Naray-Szabo (Ed.) Elsevier, Amsterdam, p.1011986
32P.Th.van Duijnen, J.C.de Jager, B.T.TholeDo parallel b-strands have dipole moments? An ab initio molecular-orbital-direct reaction field study
Biopolymers 24, 735-451985
31R.J.van der Wal, P.Th.van Duijnen, A.VosNote on the oxygen lone-pair densities observed in trans-2,5 diehtyl-3-hexene-2,5 diolhemihydrate, C8H16O2.1/2H2O
Acta Cryst. B 39, 646-6471984
30M.Remko, I.Sekerka, P.Th.van DuijnenQuantum-chemical study of phenylcarbamates with local anesthetic activity
Arch. Pharm. 31, 45-531984
29B.T.Thole, P.Th.van DuijnenReaction field effects on proton transfer in the active site of actinidin
Biophys. Chem. 18, 53-91983
28B.T.Thole, P.Th.van Duijnen, J.C.de JagerAb initio calculations with the direct reaction field Hamiltonian
Struct. Dyn.: Nucleic Acids Proteins, Proc. Int. Symp., Meeting Date 1982, 95-105. Editor(s): Clementi, Enrico; Sarma, Ramaswamy H. Publisher: Adenine Press, Guilderland, N. Y.1983
27M.Remko, P.Th.van DuijnenAb initio investigations of local anesthetic-phospholipid model membrane interactions
THEOCHEM 13, 451-4571983
26M.Remko, P.Th.van DuijnenAb initio investigations on the local anesthetics procaine, lidocaine and heptacaine
THEOCHEM 14, 1-101983
25B.T.Thole, P.Th.van DuijnenA general population analysis preserving the dipole moment
Theor. Chim. Acta 63, 209-2211983
24P.Th.van Duijnen, B.T.TholeCooperative effects in a-helixes: An ab initio molecular orbital study
Biopolymers 21, 1748-17611982
23B.T.Thole, P.Th.van DuijnenThe direct reaction-field Hamiltonian: analysis of the dispersion term and application to the water dimer
Chem. Phys. 71, 211-2201982
22P.Th.van Duijnen, B.T.TholeEnvironmental effects on proton transfer. Ab initio calculations on systems in a semiclassical, polarizable environment
Quantum Theory Chem. React., Volume 3, 85-95. Editor(s): Daudel, Raymond. Publisher: Reidel, Dordrecht, Neth.1982
21P.Th.van Duijnen, B.T.TholeElectric field of a-helices
Stud. Phys. Theor. Chem. 18 (Steric Eff. Biomol.), 347-3581982
20P.Th.van DuijnenOn the inactivity of thiol-subtilisin. The role of the intramolecular electric field
Biophys. Chem. 13, 133-91981
19P.Th.van Duijnen, B.T.TholeThe a-helix as an ion channel. An ab initio molecular orbital study
Chem. Phys. Lett. 83, 129-331981
18P.Th.van DuijnenAb initio calculations as a numerical experiment
Chemisch Magazine, 401-4031981
17P.Th.van DuijnenQuantum chemistry and enzymes
J. Mol. Catal. 11, 263-2731981
16B.T.Thole, P.Th.van DuijnenQuantum mechanics of solvent effects
Proc. - Semin. Comput. Methods Quantum Chem., 5th, 326-30 Publisher: Max-Planck-Inst. Phys. Astrophys. Inst. Astrophys., Garching, Fed. Rep. Ger.1981
15P.Th.van Duijnen, B.T.TholeDerivation of a new and general population analysis preserving at least the dipole moment
Proc. - Semin. Comput. Methods Quantum Chem., 5th, 332-40 Publisher: Max-Planck-Inst. Phys. Astrophys. Inst. Astrophys., Garching, Fed. Rep. Ger.1981
14P.Th.van Duijnen, P.J.C.AertsChemical bonding without orbitals
Chemisch Magazine, 302-3061980
13P.Th.van Duijnen, B.T.Thole, R.Broer, W.C.NieuwpoortActive site a-helix in papain and the stability of the ion pair RS-...ImH+
Int. J. Quant. Chem. 17, 651-6711980
12B.T.Thole, P.Th.van DuijnenOn the quantum mechanical treatment of solvent effects
Theor. Chim. Acta 55, 307-181980
11P.Th.van Duijnen, B.T.Thole, W.G.J.HolOn the role of the active site helix in papain, an ab initio molecular orbital study
Biophys. Chem. 9, 273-2801979
10W.G.J.Hol, P.Th.van Duijnen, H.J.C.BerendsenThe a-helix dipole and the properties of proteins
Nature 273 (5662), 443-4461978
9W.C.Nieuwpoort, D.Post, P.Th.van DuijnenCalibration constant for 57Fe Mössbauer isomer shifts derived from ab initio selfconsistent-field calculations on octahedral FeF6 and Fe(CN)6clusters
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Phys. Rev. B 17, 91-981978
8R.Broer, P.Th.van Duijnen, W.C.NieuwpoortAb Initio molecular orbital studies on the active site of papain
Chem. Phys. Lett. 42, 525-5291976
7P.Th.van Duijnen, P.van der Ploeg, H.Hogeveen, W.F.J.HuurdemanDiels-Alder reactivity of hydrocarbons containing unsaturatively bridged small rings
Tetrahedron Lett. 8, 573-5761975
6P.Th.van DuijnenMolecular integrals over generalized Gaussian basis sets
Int. J. Quant. Chem. 8, 179-1911974
5H.Hogeveen, P.W.Kwant, J.Postma, P.Th.van DuijnenElectronic spectra of pyramidal dications. (CCH3)62+ and (CH)62+
Tetrahedron Lett. 49/50, 4351-43541974
4P.Th.van Duijnen Ellipsoidal gaussian orbitals
Dissertation Universiteit van Amsterdam, promotor prof.dr.W.C.Nieuwpoort1972
3D.B.Cook, P.Th.van DuijnenMolecular integrals in terms of ellipsoidal Gaussian-type orbitals
Chem. Phys. Lett. 8, 201-2071971
2P.Th.van Duijnen, D.B.CookAb initio calculations with small ellipsoidal gaussian basis sets. I
Mol. Phys. 21, 475-4831971
1P.Th.van Duijnen, D.B.CookAb initio calculations with small ellipsoidal gaussian basis sets. II
Mol. Phys. 22, 637-6471971