Vibrational Energy Distribution Analysis (VEDA): Scopes and limitations

Michał H. Jamróz1
1Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland

Tài liệu tham khảo

Morino, 1952, A note on the classification of normal vibrations of molecules, J. Chem. Phys., 20, 1809, 10.1063/1.1700299 Taylor, 1954, Distribution of kinetic and potential energy in vibrating molecules, J. Chem. Phys., 22, 1780, 10.1063/1.1739902 Miyazawa, 1958, Normal vibrations of nmethylacetamide, J. Chem. Phys., 29, 611, 10.1063/1.1744547 Zerbi, 1963, Urey—Bradley force constants of methanol, J. Chem. Phys., 38, 122, 10.1063/1.1733449 Keresztury, 1971, Alternative calculation of vibrational potential energy distribution, J. Mol. Struct., 10, 304, 10.1016/0022-2860(71)87090-4 Pulay, 1979, Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives, J. Am. Chem. Soc., 101, 2550, 10.1021/ja00504a009 L. Lapinski, P. Pongor, PED-program, Warsaw, 1994. L. Lapinski, M.J. Nowak, BALGA – Computer Program for PED Calculation, Institute of Physics Polish Academy of Sciences, Warsaw. Dobrowolski, 1999, Theoretical vibrational spectra of diformates: diformate anion, J. Mol. Struct., 482-483, 183, 10.1016/S0022-2860(98)00782-0 A. Khvorostov, Photoinduced proton transfer processes observed for thiouracil derivatives (in Polish), PhD disertation supervised by Prof. M. Nowak, Institute of Physics Polish Academy of Sciences, Warsaw, 2006. Dunning, 1989, Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen, J. Chem. Phys., 90, 1007, 10.1063/1.456153 Woon, 1993, Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon, J. Chem. Phys., 98, 1358, 10.1063/1.464303 Frisch, 2009 M.H. Jamróz, Vibrational Energy Distribution Analysis: VEDA 4, program, Warsaw, 2004–2010. <http://www.smmg.pl/> Jamróz, 2006, Vibrational modes of 2,6-, 2,7-, and 2,3-diisopropylnaphthalene. A DFT study, J. Mol. Struct., 787, 172, 10.1016/j.molstruc.2005.10.044 Dobrowolski, 2000, Theoretical IR and Raman spectra of diketene and its 3-methylene isomer, Vibr. Spectr., 22, 19, 10.1016/S0924-2031(99)00039-9 Cyrański, 2012, On two alizarin polymorphs, CrystEngComm., 14, 3667, 10.1039/c2ce06063a Sadlej, 2006, DFT study of vibrational circular dichroism spectra of d-lactic acid–water complexes, Phys. Chem. Chem. Phys., 8, 101, 10.1039/B509351A Dobrowolski, 2007, Theoretical prediction and the first IR-matrix observation of several l-cysteine molecule conformers, ChemPhysChem., 8, 1085, 10.1002/cphc.200600784 Dobrowolski, 2008, IR low-temperature matrix and ab initio study on β-alanine conformers, ChemPhysChem., 9, 2042, 10.1002/cphc.200800383 Dobrowolski, 2010, IR low-temperature matrix, X-ray and ab initio study on l-isoserine conformations, Phys. Chem. Chem. Phys., 12, 10818, 10.1039/c0cp00016g Dobrowolski, 2005, Ar-matrix IR spectra of 5-halouracils interpreted by means of DFT calculations, J. Phys. Chem., 109, 2167, 10.1021/jp045213f Dobrowolski, 2002, Theoretical and IR-matrix isolation studies on the urea and urea-D4, -13C, and -1,3-15N2 substituted molecules, Vibr. Spectr., 29, 261, 10.1016/S0924-2031(01)00187-4 Dobrowolski, 2008, Ar-matrix IR spectra of 2-propanol and its OD, D7 and D8 isotopologues, Vibr. Spectr., 48, 82, 10.1016/j.vibspec.2007.12.017 Jamróz, 2011, Novel and unusual triterpene from black cohosh. Determination of structure of 9,10-seco-9,19-cyclolanostane xyloside (cimipodocarpaside) by NMR, IR and Raman spectroscopy and DFT calculations, Spectrochim. Acta A, 78, 107, 10.1016/j.saa.2010.09.005 Jamróz, 2012, One new and six known triterpene xylosides from Cimicifuga racemosa: FT-IR, Raman and NMR studies and DFT calculations, Spectrochim. Acta A, 93, 10, 10.1016/j.saa.2012.02.064 Sajan, 2013, Ultrafast optical nonlinearity, electronic absorption, vibrational spectra and solvent effect studies of ninhydrin, Spectrochim. Acta A, 109, 331, 10.1016/j.saa.2013.03.001 Sarojini, 2013, Synthesis, structural, spectroscopic studies, NBO analysis, NLO and HOMO-LUMO of 4-methyl-N-(3-nitrophenyl)benzene sulfonamide with experimental and theoretical approaches, Spectrochim. Acta A, 108, 159, 10.1016/j.saa.2013.01.060 Manimaran, 2013, Growth and vibrational spectral investigation of nonlinear optical crystal l-argininum perchlorate-DFT study, Spectrochim. Acta A, 109, 173, 10.1016/j.saa.2013.02.024 Sridevi, 2013, Structural, vibrational, electronic, NMR, NLO and reactivity analyses of (3Z)-3-(2-oxo-2-phenylethylidene)-1,3-dihydro-2H-indol-2-one (OPEDI) by ab initio HF and DFT calculations, Spectrochim. Acta A, 107, 334, 10.1016/j.saa.2013.01.044 Poiyamozhi, 2012, The spectroscopic (FTIR, FT-Raman, UV and NMR), first-order hyperpolarizability and HOMO–LUMO analysis of 4-amino-5-chloro-2-methoxybenzoic acid, J. Mol. Struct., 1024, 1, 10.1016/j.molstruc.2012.05.008 Siddiqui, 2012, Electronic structure, nonlinear optical properties, and vibrational analysis of gemifloxacin by density functional theory, Spectroscopy (New York), 27, 185 Govindarajan, 2012, Vibrational spectroscopic studies, NLO, HOMO–LUMO and electronic structure calculations of α, α, α-trichlorotoluene using HF and DFT, Spectrochim. Acta A, 94, 53, 10.1016/j.saa.2012.03.074 Jesintha John, 2012, Analysis of vibrational spectra and nonlinear optical properties of organic molecule l-alaninium formate, Spectrochim. Acta A, 86, 174, 10.1016/j.saa.2011.09.070 Jayavarthanan, 2012, Vibrational spectra, UV and NMR, first order hyperpolarizability and HOMO–LUMO analysis of 2-amino-4-chloro-6-methylpyrimidine, Spectrochim. Acta A, 97, 811, 10.1016/j.saa.2012.07.064 Fridrichová, 2012, Vibrational spectra of guanylurea(1+) hydrogen phosphite – novel remarkable material for nonlinear optics, Vibr. Spectr., 63, 485, 10.1016/j.vibspec.2012.09.011 Muthu, 2012, Quantum mechanical study and spectroscopic (FT-IR, FT-Raman, 13C, 1H, UV) study, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of 4-[(4-aminobenzene) sulfonyl] aniline by ab initio HF and density functional method, Spectrochim. Acta A, 92, 154, 10.1016/j.saa.2012.02.056 Muthu, 2012, Molecular structure, vibrational spectra, first order hyper polarizability, NBO and HOMO-LUMO analysis of 4-amino-3(4-chlorophenyl) butanoic acid, Solid State Sci., 14, 476, 10.1016/j.solidstatesciences.2012.01.028 Dhas, 2012, Spectroscopic investigation and hydrogen-bonding analysis of triazinones, J. Mol. Model., 18, 3587, 10.1007/s00894-011-1237-7 Walewski, 2012, Thermal fluctuations and infrared spectra of the formamide–formamidine complex, J. Phys. Chem. A, 116, 10412, 10.1021/jp3054636 Soliman, 2012, Molecular structure and vibrational spectra of free and coordinated 3-bromoquinoline: unexpected intramolecular CH⋯O interactions, J. Mol. Struct., 1017, 135, 10.1016/j.molstruc.2012.03.016 Du, 2012, Theoretical study on the adduct of chlorine trifluoride oxide and boron trifluoride-molecular and crystal structures, vibrational spectrum, and thermodynamic properties, Int. J. Quant. Chem., 112, 1291, 10.1002/qua.23127 Rode, 2012, Dobrowolski, on chirality transfer in electron donor-acceptor complexes. A prediction for the sulfinimine BF 3 system, Chirality, 24, 5, 10.1002/chir.21977 Buchanan, 2012, Single-conformation infrared spectra of model peptides in the amide i and amide II regions: experiment-based determination of local mode frequencies and inter-mode coupling, J. Chem. Phys., 137, 094301, 10.1063/1.4747507 Cai, 2012, Secondary structure and vibrational spectral feature of alanine dipeptide, Wuli Huaxue Xuebao/Acta Phys. – Chim. Sinica, 28, 1837, 10.3866/PKU.WHXB201205021 Cai, 2013, Anharmonic vibrational probe for N-methylacetamide in different micro-environments, Vibr. Spectr., 66, 8, 10.1016/j.vibspec.2013.01.005 Alam, 2012, Anharmonic vibrational studies of l-aspartic acid using HF and DFT calculations, Spectrochim. Acta A, 96, 992, 10.1016/j.saa.2012.07.135 Poopari, 2012, Conformational distributions of N-acetyl-l-cysteine in aqueous solutions: a combined implicit and explicit solvation treatment of VA and VCD spectra, ChemPhysChem., 13, 2310, 10.1002/cphc.201200152 Han, 2012, Influence of an unnatural amino acid side chain on the conformational dynamics of peptides, ChemPhysChem., 13, 1522, 10.1002/cphc.201100995 Shanmugasundaram, 2011, Vibrational markers of structural distortion in adenine nucleobases upon DNA damage, Phys. Chem. Chem. Phys., 13, 3851, 10.1039/c0cp01731k Siddiqui, 2009, Vibrational dynamics and potential energy distribution of two well-known neurotransmitter receptors: tyramine and dopamine hydrochloride, J. Theor. Comput. Chem., 8, 433, 10.1142/S0219633609004861 Suresh, 2012, Vibrational spectral investigation and natural bond orbital analysis of anti-rheumatoid drug ethyl 4-nitrophenylacetate – DFT approach, Spectrochim. Acta A, 98, 413, 10.1016/j.saa.2012.08.071 Srivastava, 2012, Vibrational, structural and electronic properties of 6-methyl nicotinic acid by density functional theory, J. Chem. Pharm. Res., 4, 3333 Çirak, 2012, Experimental and computational study on molecular structure and vibrational analysis of a modified biomolecule: 5-Bromo-2′-deoxyuridine, Spectrochim. Acta A, 92, 406, 10.1016/j.saa.2012.02.053 El-Emam, 2012, Structural and spectroscopic characterization of a novel potential chemotherapeutic agent 3-(1-adamantyl)-1-{[4-(2-methoxyphenyl)piperazin-1-yl] methyl}-4-methyl-1H-1,2,4-triazole-5(4H)-thione by first principle calculations, J. Mol. Struct., 1022, 49, 10.1016/j.molstruc.2012.04.074 Saini, 2012, Effects of chemical analytes on zinc tetraphenylporphine thin films studied by vibrational spectroscopy and density functional theory, Vibr. Spectr., 61, 188, 10.1016/j.vibspec.2012.04.004 Liu, 2013, Spectroscopic and vibrational analysis of the methoxypsoralen system: a comparative experimental and theoretical study, J. Mol. Struct., 1035, 13, 10.1016/j.molstruc.2012.08.047 Dhas, 2013, DFT computation and experimental analysis of vibrational and electronic spectra of phenoxy acetic acid herbicides, Spectrochim. Acta A, 108, 89, 10.1016/j.saa.2013.01.081 Meng, 2013, SERS and DFT study of crystal violet, J. Mol. Struct., 1035, 326, 10.1016/j.molstruc.2012.10.066 Wrzosek, 2012, Adsorption of 1,2,4-triazole on a silver electrode: surface-enhanced Raman spectroscopy and density functional theory studies, J. Raman Spectrosc., 43, 1010, 10.1002/jrs.3161 Pandey, 2013, Effect of chlorine substitution on triplet state structure of thioxanthone: a time-resolved resonance Raman study, J. Raman Spectrosc., 44, 270, 10.1002/jrs.4189 Pandey, 2012, Simultaneous detection of two triplets: a time-resolved resonance Raman study, J. Phys. Chem. A, 116, 8484, 10.1021/jp3047467 Pandey, 2011, Time-resolved resonance Raman spectroscopic studies on the triplet excited state of thioxanthone, J. Phys. Chem. A, 115, 7566, 10.1021/jp202387v Merten, 2012, Simultaneous resonance Raman optical activity involving two electronic states, J. Phys. Chem. A, 116, 7329, 10.1021/jp3036082 Jayanth, 2009, Solution structure of the DNA damage lesion 8-oxoguanosine from ultraviolet resonance Raman Spectroscopy, J. Phys. Chem. A, 113, 1459, 10.1021/jp8071519 Kaya, 2013, A palladium(II) complex containing both carbonyl and imine oxime ligands: crystal structure, experimental and theoretical UV–vis, IR and NMR studies, Spectrochim. Acta A, 108, 133, 10.1016/j.saa.2013.01.054 Basova, 2012, Experimental and theoretical study of vibrational spectra of palladium(II) β-diketonates, Vibr. Spectr., 61, 219, 10.1016/j.vibspec.2012.04.003 Parlak, 2012, FT-IR and Raman spectroscopic analysis of some Hofmann type complexes, Spectrochim. Acta A, 99, 12, 10.1016/j.saa.2012.09.020 Keşan, 2012, FT-IR and Raman spectroscopic and quantum chemical investigations of some metal halide complexes of 1-phenylpiperazine, Spectrochim. Acta A, 88, 144, 10.1016/j.saa.2011.12.020 Kalinowska, 2010, Spectroscopic (FT-IR, FT-Raman, UV, 1H, and 13C NMR) and theoretical studies of m-anisic acid and lithium, sodium, potassium, rubidium, and caesium m-anisates, J. Phys. Org. Chem., 23, 37 Samsonowicz, 2008, Experimental (FT-IR, FT-Raman, 1H, 13C NMR) and theoretical study of alkali metal 2-aminobenzoates, J. Mol. Struct., 887, 220, 10.1016/j.molstruc.2007.11.041 Yancheva, 2013, Characterization of the structure, electronic conjugation and vibrational spectra of the radical anions of p- and m-dinitrobenzene: a quantum chemical study, Bulg. Chem. Commun., 45, 24 Sert, 2013, Vibrational analysis of 4-chloro-3-nitrobenzonitrile by quantum chemical calculations, Spectrochim. Acta A, 107, 248, 10.1016/j.saa.2013.01.046 Sudha, 2013, Spectroscopic (FTIR, FT-Raman, NMR and UV) and molecular structure investigations of 1,5-diphenylpenta-2,4-dien-1-one: a combined experimental and theoretical approach, Mol. Sim., 39, 330, 10.1080/08927022.2012.727210 Tanak, 2013, FT-IR, FT-Raman, and DFT computational studies of melaminium nitrate molecular-ionic crystal, J. Mol. Struct., 1034, 363, 10.1016/j.molstruc.2012.10.046 Bilge, 2012, Theoretical molecular structure, vibrational frequencies and nmr investigations of 2-[(1E)-2-aza-2-(5-methyl(2-pyridyl)ethenyl)]-4-bromobenzen-1-ol, Bull. Chem. Soc. Ethiopia, 26, 279, 10.4314/bcse.v26i2.11 Daszkiewicz, 2011, Crystallographic, vibrational and theoretical studies of 2,3-diaminopyridinium selenite, Vibr. Spectr., 57, 326, 10.1016/j.vibspec.2011.09.008 Keefe, 2011, Infrared optical properties and Raman spectra of n-pentane and n-pentane-d12, Vibr. Spectr., 57, 72 Kalinowska, 2010, The effect of alkali metal ions on the electronic structure of p-anisic acid, Spectroscopy, 24, 449, 10.1155/2010/574024 Kucharska, 2010, Molecular and crystal structure, IR and Raman spectra, and quantum chemical calculations for 2-hydroxy-3-cyano-4-methylpyridine, Vibr. Spectr., 53, 189, 10.1016/j.vibspec.2010.02.003 Güneş, 2011, DFT, FT-Raman and FT-IR investigations of 5-methoxysalicylic acid, Spectrochim. Acta A, 82, 504, 10.1016/j.saa.2011.07.089