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Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide

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Abstract

Results from force fields implemented in HyperChem, a program frequently used in studies of bioactive compounds, have been compared using the example of the conformational analysis of a 1-carbonylthiosemicarbazide that exhibits strong antibacterial activity. By comparing these results with the original force fields and the experimental NMR ROESY spectrum, it was shown that these implementations can lead to erroneous results.

The most stable conformations of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide obtained with the Amber, CHARMM, and OPLS force fields; note that—confusingly—the most stable conformations obtained with these three force fields are very different

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References

  1. Warshel A, Levitt M (1976) Theoretical studies of enzymatic reactions: dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227–249

    Article  CAS  Google Scholar 

  2. Chen IJ, Follope N (2011) Is conformational sampling of drug-like molecules a solved problem? Drug Develop Res 72:85–94

    Article  CAS  Google Scholar 

  3. Guével RL, Oger F, Lecorgne A, Dudasova Z, Chevance S, Bondon A, Barath P, Simonneaux G, Salbert G (2009) Identification of small molecule regulators of the nuclear receptor HNF4α based on naphthofuran scaffolds. Bioorg Med Chem 17:7021–7030

    Article  Google Scholar 

  4. Paoletta S, Steventon GB, Wildeboer D, Ehrman TM, Hylands PJ, Barlow DJ (2008) Screening of herbal constituents for aromatase inhibitory activity. Bioorg Med Chem 16:8466–8470

    Article  CAS  Google Scholar 

  5. Narayanasamy S, Thirumamagal BTS, Johnsamuel J, Byun Y, Al-Madhoun AS, Usova E, Cosquer GY, Yan J, Bandyopadhyaya AK, Tiwari R, Eriksson S, Tjarks W (2006) Hydrophilically enhanced 3-carboranyl thymidine analogues (3CTAs) for boron neutron capture therapy (BNCT) of cancer. Bioorg Med Chem 14:6886–6899

    Article  CAS  Google Scholar 

  6. Farkas V, Vass E, Hanssens I, Majer Z, Hollósi M (2005) Cyclic peptide models of the Ca2+-binding loop of a-lactalbumin. Bioorg Med Chem 13:5310–5320

    Google Scholar 

  7. Khlebnikov AI, Schepetkin IA, Quinn MT (2008) Structure–activity relationship analysis of N-benzoylpyrazoles for elastase inhibitory activity: a simplified approach using atom pair descriptors. Bioorg Med Chem 16:2791–2802

    Article  CAS  Google Scholar 

  8. Dheyongera JP, Geldenhuys WJ, Dekker TG, Matsabisa MG, Van der Schyf CJ (2005) Antimalarial activity of thioacridone compounds related to the acronycine alkaloid. Bioorg Med Chem 13:1653–1659

    Article  CAS  Google Scholar 

  9. Plonska-Ocypa K, Sicinski RR, Plum LA, Grzywacz P, Frelek J, Clagett-Dame M, DeLuca HF (2009) 13-Methyl-substituted des-C,D analogs of (20S)-1α,25-dihydroxy-2-methylene-19-norvitamin D3 (2MD): synthesis and biological evaluation. Bioorg Med Chem 17:1747–1763

    Google Scholar 

  10. Abdel-Aziz AA-M, El-Subbagh HI, Kunieda T (2005) Lewis acid-promoted transformation of 2-alkoxypyridines into 2-aminopyridines and their antibacterial activity. Part 2: remarkably facile C–N bond formation. Bioorg Med Chem 13:4929–4935

    Google Scholar 

  11. Katritzky AR, Dobchev DA, Tulp I, Karelson M, Carlson DA (2006) QSAR study of mosquito repellents using Codessa Pro. Bioorg Med Chem Lett 16:2306–2311

    Article  CAS  Google Scholar 

  12. Fiorentino A, D’Abrosca B, Pacifico S, Iacovino R, Mastellone C, Di Blasio B, Monaco P (2006) Distachyasin: a new antioxidant metabolite from the leaves of Carex distachya. Bioorg Med Chem Lett 16:6096–6101

    Google Scholar 

  13. Stout EP, Prudhomme J, Le Roch K, Fairchild CR, Franzblau SG, Aalbersberg W, Hay ME, Kubanek J (2010) Unusual antimalarial meroditerpenes from tropical red macroalgae. Bioorg Med Chem Lett 20:5662–5665

    Article  CAS  Google Scholar 

  14. El-Ayaan U, Abdel-Aziz AA-M, Al-Shihry S (2007) Solvatochromism, DNA binding, antitumor activity and molecular modeling study of mixed-ligand copper(II) complexes containing the bulky ligand: bis[N-(p-tolyl)imino]acenaphthene. Eur J Med Chem 42:1325–1333

    Google Scholar 

  15. Thakur A, Thakur M, Bharadwaj A, Thakur S (2008) SAR and QSAR studies: modelling of new DAPY derivatives. Eur J Med Chem 43:471–477

    Google Scholar 

  16. Gupta AK, Gupta RA, Soni LK, Kaskhedikar SG (2008) Exploration of physicochemical properties and molecular modeling studies of 2-sulfonyl-phenyl-3-phenyl-indole analogs as cyclooxygenase-2 inhibitors. Eur J Med Chem 43:1297–1303

    Article  CAS  Google Scholar 

  17. Abdel-Aziz AA-M (2007) Novel and versatile methodology for synthesis of cyclic imides and evaluation of their cytotoxic, DNA binding, apoptotic inducing activities and molecular modeling study. Eur J Med Chem 42:614–626

    Article  CAS  Google Scholar 

  18. El-Kerdawy MM, El-Bendary ER, Abdel-Aziz AA-M, El-wasseef DR, Abd El-Aziz NI (2010) Synthesis and pharmacological evaluation of novel fused thiophene derivatives as 5-HT2A receptor antagonists: molecular modeling study. Eur J Med Chem 45:1805–1820

  19. Rescifina A, Chiacchio U, Corsaro A, Piperno A, Romeo R (2011) Isoxazolidinyl polycyclic aromatic hydrocarbons as DNA-intercalating antitumor agents. Eur J Med Chem 46:129–136

    Article  CAS  Google Scholar 

  20. da Silva SL, Calgarotto AK, Maso V, Damico DCS, Baldasso P, Veber CL, Villar JAFP, Oliveira ARM, Comar M Jr, Oliveira KMT, Marangoni S (2009) Molecular modeling and inhibition of phospholipase A2 by polyhydroxy phenolic compounds. Eur J Med Chem 44:312–321

    Article  Google Scholar 

  21. Alieva IN, Mustafayeva NN, Gojayev NM (2006) Conformational analysis of the N-terminal sequence Met1–Val60 of the tyrosine hydroxylase. J Mol Struct 785:76–84

    Article  CAS  Google Scholar 

  22. de Sousa AS, Fernandes MA, Nxumalo W, Balderson JL, Jeftič T, Cukrowski I, Marques HM (2008) Sc(III) porphyrins. The molecular structure of two Sc(III) porphyrins and a re-evaluation of the parameters for the molecular mechanics modelling of Sc(III) porphyrins. J Mol Struct 872:47–55

    Google Scholar 

  23. Gaber M, El-Daly SA, El-Sayed YSY (2009) Synthesis, spectral, thermal and theoretical studies of Cu(II) complexes with 3-[4′-dimethylaminophenyl]-1-(2-pyridyl)prop-2-en-1-one (DMAPP). J Mol Struct 922:51–57

    Google Scholar 

  24. Mautner FA, Taylor ER, Rozas DM, Massoud SS (2009) Synthesis and structural characterization of dicopper(II) and dipalladium(II) complexes of 1,1,2,2-tetrakis(carboxamido-2-methylpyridyl)ethane. J Mol Struct 936:250–256

    Article  CAS  Google Scholar 

  25. Bairagya HR, Mukhopadhyay BP, Bhattacharya S (2009) Role of the conserved water molecules in the binding of inhibitor to IMPDH-II (human): a study on the water mimic inhibitor design. J Mol Struct THEOCHEM 908:31–39

    Google Scholar 

  26. Pichierri F (2010) Macrodipoles of potassium and chloride ion channels as revealed by electronic structure calculations. J Mol Struct THEOCHEM 950:79–82

    Article  CAS  Google Scholar 

  27. Jankowski CK, Martel J-L, Fermandjian S, Maroun RG (2005) Study of potential HIV-1 inhibition glutaric dialdehyde adducts. J Mol Struct THEOCHEM 731:83–87

    Google Scholar 

  28. Gikas E, Bazoti FN, Tsarbopoulos A (2007) Conformation of oleuropein, the major bioactive compound of Olea europea. J Mol Struct THEOCHEM 821:125–132

    Google Scholar 

  29. Fendri A, Frikha F, Miled N, Bacha AB, Gargouri Y (2007) Modulating the activity of avian pancreatic lipases by an alkyl chain reacting with an accessible sulfhydryl group. Biochem Biophys Res Commun 360:765–771

    Article  CAS  Google Scholar 

  30. Lorin A, Lins L, Stroobant V, Brasseur R, Charloteaux B (2007) Determination of the minimal fusion peptide of bovine leukemia virus gp30. Biochem Biophys Res Commun 355:649–653

    Article  CAS  Google Scholar 

  31. Shi YH, Song YL, Lin DH, Tan J, Roller PP, Li Q, Long YQ, Song GQ (2005) Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin. Biochem Biophys Res Commun 330:1254–1261

    Article  CAS  Google Scholar 

  32. Dupiereux I, Zorzi W, Lins L, Brasseur R, Colson P, Heinen E, Elmoualij B (2005) Interaction of the 106–126 prion peptide with lipid membranes and potential implication for neurotoxicity. Biochem Biophys Res Commun 331:894–901

    Article  CAS  Google Scholar 

  33. Katsara M, Yuriev E, Ramsland PA, Deraos G, Tselios T, Matsoukas J, Apostolopoulos V (2008) Mannosylation of mutated MBP83–99 peptides diverts immune responses from Th1 to Th2. Mol Immunol 45:3661–3670

    Article  CAS  Google Scholar 

  34. Solórzano-Vargas RS, Vasilevko V, Acero G, Ugen KE, Martinez R, Govezensky T, Vazquez-Ramirez R, Kubli-Garfias C, Cribbs DH, Manoutcharian K, Gevorkian G (2008) Epitope mapping and neuroprotective properties of a human single chain FV antibody that binds an internal epitope of amyloid-beta 1–42. Mol Immunol 45:881–886

    Article  Google Scholar 

  35. Zoroddu MA, Medici S, Peana M (2009) Copper and nickel binding in multi-histidinic peptide fragments. J Inorg Biochem 103:1214–1220

    Article  CAS  Google Scholar 

  36. Kulon K, Valensin D, Kamysz W, Valensin G, Nadolski P, Porciatti E, Gaggelli E, Kozłowski H (2008) The His–His sequence of the antimicrobial peptide demegen P-113 makes it very attractive ligand for Cu2+. J Inorg Biochem 102:960–972

    Google Scholar 

  37. Christofis P, Katsarou M, Papakyriakou A, Sanakis Y, Katsaros N, Psomas G (2005) Mononuclear metal complexes with Piroxicam: synthesis, structure and biological activity. J Inorg Biochem 99:2197–2210

    Google Scholar 

  38. Mucha A, Bal W, Jeżowska-Bojczuk M (2008) Comparative studies of coordination properties of puromycin and puromycin aminonucleoside towards copper(II) ions. J Inorg Biochem 102:46–52

    Article  CAS  Google Scholar 

  39. Deconinck E, Xu QS, Put R, Coomans D, Massart DL, Vander Heyden Y (2005) Prediction of gastro-intestinal absorption using multivariate adaptive regression splines. J Pharm Biomed Anal 39:1021–1030

    Article  CAS  Google Scholar 

  40. Al Omari AA, Al Omari MM, Badwan AA, Al-Sou’od KA (2011) Effect of cyclodextrins on the solubility and stability of candesartan cilexetil in solution and solid state. J Pharm Biomed Anal 54:503–509

    Article  CAS  Google Scholar 

  41. Deconinck E, Hancock T, Coomans D, Massart DL, Heyden YV (2005) Classification of drugs in absorption classes using the classification and regression trees (CART) methodology. J Pharm Biomed Anal 39:91–103

    Article  CAS  Google Scholar 

  42. Pescitelli G, Bilia AR, Bergonzi MC, Vincieri FF, Di Bari L (2010) Cyclodextrins as carriers for kavalactones in aqueous media: Spectroscopic characterization of (S)-7,8-dihydrokavain and β-cyclodextrin inclusion complex. J Pharm Biomed Anal 52:479–483

    Article  CAS  Google Scholar 

  43. Kumar RR, Perumal S (2007) A facile synthesis and highly atom economic 1,3-dipolar cycloaddition of hexahydropyrido[3,4-c][1,5]benzothiazepines with nitrile oxide: stereoselective formation of hexahydro-[1,2,4]oxadiazolo[5,4-d]pyrido[3,4-c][1,5]benzothiazepines. Tetrahedron 63:7850–7857

    Google Scholar 

  44. Campayo L, Calzado F, Cano MC, Yunta MJR, Pardo M, Navarro P, Jimeno ML, Gómez-Contreras F, Sanz AM (2005) New acyclic receptors containing pyridazine units. The influence of π-stacking on the selective transport of lipophilic phenethylamines. Tetrahedron 61:11965–11975

    Article  CAS  Google Scholar 

  45. Saghiyan AS, Dadayan SA, Petrosyan SG, Manasyan LL, Geolchanyan AV, Djamgaryan SM, Andreasyan SA, Maleev VI, Khrustalev VN (2006) New chiral NiII complexes of Schiff’s bases of glycine and alanine for efficient asymmetric synthesis of α-amino acids. Tetrahedron Asymmetr 17:455–467

    Google Scholar 

  46. Alajarín M, López-Leonardo C, Berná J, Sánchez-Andrada P (2007) Center-to-propeller and propeller-to-propeller stereocontrol in a series of macrobicyclic tri-λ5-phosphazenes. Tetrahedron Lett 48:3583–3586

    Article  Google Scholar 

  47. Garmy N, Taїeb N, Yahi N, Fantini J (2005) Apical uptake and transepithelial transport of sphingosine monomers through intact human intestinal epithelial cells: physicochemical and molecular modeling studies. Arch Biochem Biophys 440:91–100

    Google Scholar 

  48. You Z, Omura S, Ikeda H, Cane DE (2007) Pentalenolactone biosynthesis: molecular cloning and assignment of biochemical function to PtlF, a short-chain dehydrogenase from Streptomyces avermitilis, and identification of a new biosynthetic intermediate. Arch Biochem Biophys 459:233–240

    Google Scholar 

  49. Bouffioux O, Berquand A, Eeman M, Paquot M, Dufrêne YF, Brasseur R, Deleu M (2007) Molecular organization of surfactin–phospholipid monolayers: effect of phospholipid chain length and polar head. Biochim Biophys Acta 1768:1758–1768

    Google Scholar 

  50. Concu R, Dea-Ayuela MA, Perez-Montoto LG, Prado-Prado FJ, Uriarte E, Bolás-Fernández F, Podda G, Pazos A, Munteanu CR, Ubeira FM, González-Díaz H (2009) 3D Entropy and moments prediction of enzyme classes and experimental-theoretic study of peptide fingerprints in Leishmania parasites. Biochim Biophys Acta 1794:1784–1794

    Google Scholar 

  51. Petraccone L, Martino L, Duro I, Oliviero G, Borbone N, Piccialli G, Giancola C (2007) Physico-chemical analysis of G-quadruplex containing bunch-oligonucleotides. Int J Biol Macromol 40:242–247

    Article  CAS  Google Scholar 

  52. Noble JE, Wang L, Cole KD, Gaigalas AK (2005) The effect of overhanging nucleotides on fluorescence properties of hybridising oligonucleotides labelled with Alexa-488 and FAM fluorophores. Biophys Chem 113:255–263

    Article  CAS  Google Scholar 

  53. Taraszewska J, Koźbiał M (2005) Complexation of Ketoconazole by native and modified cyclodextrins. J Incl Phenom Macro 53:155–161

    Article  CAS  Google Scholar 

  54. Baker ES, Dupuis NF, Bowers MT (2009) Aminoglycoside antibiotics: A-site specific binding to 16S. Int J Mass Spectrom 283:105–111

    Article  CAS  Google Scholar 

  55. Matsingou Ch, Dimas K, Demetzos C (2006) Design and development of liposomes incorporating a bioactive labdane-type diterpene. In vitro growth inhibiting and cytotoxic activity against human cancer cell lines. Biomed Pharmacother 60:191–199

    Article  CAS  Google Scholar 

  56. Liu H, Du Y-M, Kennedy JF (2007) Hydration energy of the 1,4-bonds of chitosan and their breakdown by ultrasonic treatment. Carbohyd Polym 68:598–600

    Article  CAS  Google Scholar 

  57. Banerjee A, Sengupta PK (2006) Encapsulation of 3-hydroxyflavone and fisetin in b-cyclodextrins: excited state proton transfer fluorescence and molecular mechanics studies. Chem Phys Lett 424:379–386

    Google Scholar 

  58. Singh BK, Jetley UK, Sharma RK, Garg BS (2007) Synthesis, characterization and biological activity of complexes of 2-hydroxy-3,5-dimethylacetophenoneoxime (HDMAOX) with copper(II), cobalt(II), nickel(II) and palladium(II). Spectrochim Acta A 68:63–73

    Article  Google Scholar 

  59. Melnig V, Apostu MO, Tura V, Ciobanu C (2005) Optimization of polyurethane membranes. Morphology and structure studies. J Membrane Sci 267:58–67

    Article  CAS  Google Scholar 

  60. TarushiA CP, Psomas G (2007) Synthesis, characterization and interaction with DNA of mononuclear metal complexes with oxolinic acid. Polyhedron 26:3963–3972

    Article  Google Scholar 

  61. Setaki D, Tataridis D, Stamatiou G, Kolocouris A, Foscolos GB, Fytas G, Kolocouris N, Padalko E, Neyts J, De Clercq E (2006) Synthesis, conformational characteristics and anti-influenza virus A activity of some 2-adamantylsubstituted azacycles. Bioorg Chem 34:248–273

    Article  CAS  Google Scholar 

  62. Parks WM, Bottrill AR, Pierrat OA, Durrant MC, Maxwell A (2007) The action of the bacterial toxin, microcin B17, on DNA gyrase. Biochimie 89:500–507

    Article  CAS  Google Scholar 

  63. Fatiha M, Khatmi DE, Largate L (2010) Theoretical approach in the study of the inclusion processes of sulconazole with β-cyclodextrin. J Mol Liq 154:1–5

    Article  CAS  Google Scholar 

  64. Hutter MC (2006) Stability of the guanine-cytosine radical cation in DNA base pairs triplets. Chem Phys 326:240–245

    Article  CAS  Google Scholar 

  65. Deconinck E, Ates H, Callebaut N, Van Gyseghem E, Heyden YV (2007) Evaluation of chromatographic descriptors for the prediction of gastro-intestinal absorption of drugs. J Chromatogr A 1138:190–202

    Article  CAS  Google Scholar 

  66. Furusjö E, Svenson A, Rahmberg M, Andersson M (2006) The importance of outlier detection and training set selection for reliable environmental QSAR predictions. Chemosphere 63:99–108

    Article  Google Scholar 

  67. Ezabadi IR, Camoutsis C, Zoumpoulakis P, Geronikaki A, Soković M, Glamoćilija J, Ćirić A (2008) Sulfonamide-1,2,4-triazole derivatives as antifungal and antibacterial agents: synthesis, biological evaluation, lipophilicity, and conformational studies. Bioorg Med Chem 16:1150–1161

    Article  CAS  Google Scholar 

  68. Kuş C, Ayhan-Kılcıgil G, Özbey S, Kaynak FB, Kaya M, Çoban T, Can-Eke B (2008) Synthesis and antioxidant properties of novel N-methyl-1,3,4-thiadiazol-2-amine and 4-methyl-2 H-1,2,4-triazole-3(4H)-thione derivatives of benzimidazole class. Bioorg Med Chem 16:4294–4303

    Google Scholar 

  69. Önkol T, Doğruer DS, Uzun L, Adak S, Özkan S, Şahin MF (2008) Synthesis and antimicrobial activity of new 1,2,4-triazole and 1,3,4-thiadiazole derivatives. J Enzym Inhib Med Chem 23:277–284

    Article  Google Scholar 

  70. Shams HZ, Mohareb RM, Helal MH, Mahmoud AE (2007) Synthesis, structure elucidation, and biological evaluation of some fused and/or pendant thiophene, pyrazole, imidazole, thiazole, triazole, triazine, and coumarin systems based on cyanoacetic 2-[(benzoylamino)thioxomethyl] hydrazide. Phosphorus Sulfur Silicon Relat Elem 182:237–263

    Article  CAS  Google Scholar 

  71. Siwek A, Stączek P, Wujec M, Stefańska J, Kosikowska U, Malm A, Jankowski S, Paneth P (2011) Biological and docking studies of topoisomerase IV inhibition by thiosemicarbazides. J Mol Model doi:10.1007/s00894-010-0889-z

    Google Scholar 

  72. HyperCube Inc. (2007) HyperChem 8.0.3. HyperCube Inc., Gainsville

  73. Cornell WD, Cieplak P, Bayly ChI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PAJ (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179–5197

    Article  CAS  Google Scholar 

  74. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616

    Article  CAS  Google Scholar 

  75. Jorgensen WL, Tirado-Rives J (1988) The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657–1666

    Article  CAS  Google Scholar 

  76. Frisch MJ et al. (2009) Gaussian 09, revision A.02. Gaussian Inc., Wallingford

  77. Zhao Y, Schultz NE, Truhlar DG (2006) Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. J Chem Theor Comput 2:364–382

    Article  Google Scholar 

  78. Zhao Y, Truhlar DG (2008) Density functionals with broad applicability in chemistry. Acc Chem Res 41:157–167

    Article  CAS  Google Scholar 

  79. Ditchfield R, Hehre WJ, Pople J (1971) Self–consistent molecular–orbital methods. IX. An extended Gaussian–type basis for molecular–orbital studies of organic molecules. J Chem Phys 54:724–728

    Article  CAS  Google Scholar 

  80. Clark T, Chandrasekhar J, Spitznagel GW, PvR S (1983) Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li–F. J Comput Chem 4:294–301

    Article  CAS  Google Scholar 

  81. Frisch MJ, Pople JA, Binkley JS (1984) Self–consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets. J Chem Phys 80:3265–3269

    Article  CAS  Google Scholar 

  82. Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113:6378–6396

    Article  CAS  Google Scholar 

  83. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652

    Article  CAS  Google Scholar 

  84. Burke K, Perdew JP, Wang Y (1998) In: Dobson JF, Vignale G, Das MP (eds) Electronic density functional theory: recent progress and new directions. Plenum, New York (eds)

  85. McLean AD, Chandler GS (1980) Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18. J Chem Phys 72:5639–5648

    Google Scholar 

  86. Cancès MT, Mennucci B, Tomasi J (1997) A new integral equation formalism for the polarizable continuum model: theoretical background and applications to isotropic and anisotropic dielectrics. J Chem Phys 107:3032–3041

    Google Scholar 

  87. Cossi M, Barone V, Mennucci B, Tomasi J (1998) Ab initio study of ionic solutions by a polarizable continuum dielectric model. Chem Phys Lett 286:253–260

    Article  CAS  Google Scholar 

  88. Mennucci B, Tomasi J (1997) Continuum solvation models: a new approach to the problem of solute’s charge distribution and cavity boundaries. J Chem Phys 106:5151–5158

    Google Scholar 

  89. Siwek A, Paneth P (2007) Computational studies of the cyclization of thiosemicarbazides. J Phys Org Chem 20:463–468

    Article  CAS  Google Scholar 

  90. Lodola A, Sirirak J, Fey N, Rivara S, Mor M, Mulholland AJ (2010) Structural fluctuations in enzyme-catalyzed reactions: determinants of reactivity in fatty acid amide hydrolase from multivariate statistical analysis of quantum mechanics/molecular mechanics paths. J Chem Theor Comput 6:2948–2960

    Article  CAS  Google Scholar 

  91. Schrödinger, LLC (2009) Impact, version 56107. Schrödinger, LLC, New York

  92. Aliev AE, Courtier-Murias D (2010) Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly. J Phys Chem B 114:12358–12375

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Chodzki 4a, 20–093, Lublin, Poland

    Agata Siwek

  2. Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90–924, Lodz, Poland

    Katarzyna Świderek

  3. Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90–924, Lodz, Poland

    Stefan Jankowski

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  1. Agata Siwek
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Siwek, A., Świderek, K. & Jankowski, S. Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide. J Mol Model 18, 843–849 (2012). https://doi.org/10.1007/s00894-011-1117-1

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