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Ab Initio and Density Functional Theory Studies on D-Serine

Hannah Ruben, J. Sharmi Kumar, A. Bright

Abstract


The Hartee-Fock and density functional method (B3LYP) with 6–311++G (d, p) basis set were employed to study the structural and spectroscopic properties of amino acid D-serine in ground state. The structural and vibrational parameters of amino acid D-serine were obtained using optimised conformer. Using Vibrational Energy Distribution Analysis (VEDA) 4 program and theoretically obtained FTIR and FT-Raman data complete assignment of vibrations and analysis of fundamental modes of the compound were done. Thermodynamic properties, Mulliken charges and natural charges were also determined. Stability of the molecule arising from hyper conjugative interactions and charge delocalization has been analyzed using Natural Bond Orbital (NBO) analysis. The first order hyperpolarizability (b) and Molecular Electrostatic Potential (MESP) of the molecule were computed using DFT calculations. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge-Independent Atomic Orbital (GIAO) method. 

Keywords


D-Serine, DFT, NBO, MESP

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References


Lamzin VS, Dauter Z, Wilson KS. How nature deals with stereoisomers. Curropin Struct biol. 1995; 5:830–6.

Hashimoto A, Nishikawa T, Hayashi T, et al. The presence of free D-serine in rat brain. Febslett. 1992; 269:33–6.

Hashimoto A, Kumashiro S, Nishikawa t, et al. Embryonic development and postnatal changes in free D-aspartate and D-serine in the human prefrontal cortex. J Neurochem. 1993;61: 348–51.

Gustafson EC, Stevens ER, Wolosker H, Miller RF, Endogenous D-serine contributes to nMda receptor-mediated light-evoked responses in the vertebrate retina. J Neurophysiol. 2007;98: 122–30.

Junjaud G, Rouaud E, Turpin F, Mothet JP, Billard JM, Age-related effects of the neuromodulator D-serine on neurotransmission and synaptic potentiation in the Ca1 hippocampal area of the rat. J Neurochem. 2006;98:1159–66.

Mothet JP, Parent AT, Wolosker H, et al. D-Serine is an endogenous ligand for the glycine site of the n-methyl-d-aspartate receptor. PNAS. 2000;97:4926–31.

Katsuki H, Nonaka M, Shirakawa H, Kume T, Akaike A, Endogenous D-serine is involved in induction of neuronal death by n-methyl-d-aspartate and simulated ischemia in rat cerebrocortical slices. J Pharmacol Exp Ther. 2004;311:836–44.

Kartvelishvily E, Shleper M, Balan L, Dumin E, Wolosker H, Neuron-derived D-serine release provides a novel means to activate n-methyl-d-aspartate receptors. J biol Chem. 2006; 281:14151–62.

Katsuki h, Watanabe Y, Fujimoto S, Kume T, Akaike A, Contribution of endogenous glycine and D-serine to excitotoxic and ischemic cell death in rat cerebrocortical slice cultures. Life Sci. 2007;81:740–9.

Williams SM, Diaz CM, Macnab LT, Sullivan RK, Pow DV, Immunocytochemical analysis of D-serine distribution in the mammalian brain reveals novel anatomical compartmentalizations in glia and neurons. Glia 2006 March; 53(4):401–11.

Kartvelishvily E, Shleper M, Balan L, Dumin E, Wolosker H, Neuron-derived D-serine release provides a novel means to activate N-methyl-D-aspartate receptors. J Biol Chem 2006 May 19;281(20):14151–62.

Yoshikawa M, Nakajima K, Takayasu N, Noda S, Sato Y, Kawaguchi M et al. Expression of the mRNA and protein of serine racemase in primary cultures of rat neurons. Eur J Pharmacol 2006 October 24;548(1–3):74–6.

MJ Frisch, GW Trucks, HB Schlegel, GE Scuseria, MA Robb, JR Cheeseman, G Scalmani, V Barone, B. Mennucci, GA Petersson, H Nakatsuji, M Caricato, X Li, HP Hratchian, AF Izmaylov, J Bloino, G Zheng, JL Sonnenberg, M Hada, M Ehara, K Toyota, R Fukuda, J Hasegawa, M Ishida, T Nakajima, Y Honda, O Kitao, H Nakai, T Vreven, JA Montgomery, Jr., JE Peralta, F Ogliaro, M Bearpark, JJ Heyd, E Brothers, KN Kudin, VN Staroverov, R Kobayashi, J Normand, K Raghavachari, A Rendell, JC Burant, SS Iyengar, J Tomasi, M Cossi, N Rega, JM Millam, M Klene, JE Knox, JB Cross, V Bakken, C Adamo, J Jaramillo, R Gomperts, RE Stratmann, O Yazyev, AJ Austin, R Cammi, C Pomelli, JW Ochterski, RL Martin, K Morokuma, VG Zakrzewski, GA Voth, P Salvador, JJ Dannenberg, S Dapprich, AD Daniels, O Farkas, JB Foresman, JV Ortiz, J Cioslowski, DJ Fox, Gaussian, Inc., Wallingford CT, 2009.

HB Schlegel, Optimization of equilibrium geometries and transition structures, J Comput. Chem. 3 (2) (1982) 214–218.

JC Colleter, M Gadret, Acta Crystallogr. 24(1968) 519.

J Coates, RA Meyers, Interpretation of Infrared Spectra, A Practical Approach, John Wiley & Sons Ltd., Chichester, 2000.

MT Gulluoglu, Y Erdogdu, J Karpagam, N Sundaraganesan, S Yurdakul. J. Mol. Struct. 990 (2011) 17.

DP Dilella, HD Stidham. J. Raman Spectrosc. 9 (1980) 103.

Turgay Polat, Senay Yurdakul. J. Mol. Structure 1053 (2013) 27–37.

M Silverstein, GC Basseleer, C Moril, Spectrometric Identification of Organic Compounds, Wiley, New York, 1981.

NB Colthup, LH Daly, SE Wiberley, Introduction to Infrared and Raman Spectroscopy, Academic Press, New York, 1990.

BC Smith, Infrared Spectral Interpretation, CRC press, Boca Raton, FL, 1996.

G Mariappan, N, Sundaraganesan, S Manoharan, Specto. Acta part A, 95 (2012) 86–99.

JHS Green, DJ Harrison, W Kynaston, Spectrochim. Acta 1971, 27A, 2199.

MW Wong, Chem. Phys. Lett. 256 (1996) 391–399

A Dreuw, M Head-Gordon, Chem. Rev. 105 (2005) 4009–4037.

K Fukui, Science 218 (1982) 747–754

R Meenashi, Mol. Simulat. 36 (6) (2010) 425.

H William, An Introduction to Organic Chemistry, Holden-Day, Inc., 1977.

L Xiao-Hong et al. Theor. Chem. 969 (2011) 27–34.

R Zhang, B Dub, G Sun, Y Sun, Spectrochim. Acta A 75 (2010) 1115–1124.

BT Gowda, S Foro, H Fuess, ActaCryst. B63 (2007) 2340.

HO Kalinowski, S Berger, S Barun, Carbon-13 NMR Spectroscopy, John Wiley & Sons, Chichester, 1988.

FA Cotton, CW Wilkinson, Advanced Inorganic Chemistry, 3rd Ed., Inter-science publisher, NewYork, 1972.

AE Reed, F Weinhold. J. Chem. Phys. 83 (1985) 1736–1740.

S Sebastin, N Sundaraganesan, Spectrochim. Acta A 75 (2010) 941–952

E Scrocco, J Tomasi, Adv. Quantum Chem. (1979) 11–115.

P Acebad, S Blaya, L Carretero. J. Phys. B: Atom. Mol. Opt. Phys. 36 (2003) 2445–2454.


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