NMR properties of hydrogen-bonded glycine cluster in gas phase

Carvalho, J.; Silva, Arnaldo Machado da; Ghosh, Angsula; Chaudhuri, Puspitapallab

doi:10.1016/j.molstruc.2016.06.011

Cited by 7 publications

(7 citation statements)

References 81 publications

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“…However, it possesses many different conformations due to the internal rotational degrees of freedom associated with the CC, CN, and CO bonds and possible formation of intramolecular H‐bond. The optimized structure of the glycine molecule used in the present work, as shown in Figure , corresponds to the most stable and abundant Cs conformations, obtained earlier by ab initio calculations and identified experimentally …”

Section: Resultsmentioning

confidence: 66%

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NMR spin–spin coupling constants in hydrogen‐bonded glycine clusters

Chaudhuri

Canuto

Provasi

2018

Int J of Quantum Chemistry

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The influence of the hydrogen bond formation on the NMR spin–spin coupling constants (SSCC), including the Fermi contact (FC), the diamagnetic spin‐orbit, the paramagnetic spin‐orbit, and the spin dipole term, has been investigated systematically for the homogeneous glycine cluster, in gas phase, containing up to three monomers. The one‐bond and two‐bond SSCCs for several intramolecular (through covalent bond) and intermolecular (across the hydrogen‐bond) atomic pairs are calculated employing the density functional theory with B3LYP and KT3 functionals and different types of extended basis sets. The ab initio SOPPA(CCSD) is used as benchmark for the SSCCs of the glycine monomer. The hydrogen bonding is found to cause significant variations in the one‐bond SSCCs, mostly due to contribution from electronic interactions. However, the nature of variation depends on the type of oxygen atom (proton‐acceptor or proton‐donor) present in the interaction. Two‐bond intermolecular coupling constants vary more than the corresponding one‐bond constants when the size of the cluster increases. Among the four Ramsey terms that constitute the total SSCC, the FC term is the most dominant contributor followed by the paramagnetic spin‐orbit term in all one‐bond interaction.

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Section: Resultsmentioning

confidence: 66%

“…In last few years, several experimental and theoretical works have been performed to investigate the H‐bonded interaction of GLY with water molecule . However, very few studies have been reported on the noncovalent interactions of GLY with itself or with molecules other than water like HCN and THF …”

Section: Introductionmentioning

confidence: 99%

NMR spin–spin coupling constants in hydrogen‐bonded glycine clusters

Chaudhuri

Canuto

Provasi

2018

Int J of Quantum Chemistry

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“…A hydrogen bond is an important interaction dominating the structural conformation of a DNA double chain and the reactivity of clusters . The strength of the hydrogen bond sometimes determines the reaction mechanism of the clusters …”

Section: Introductionmentioning

confidence: 99%

Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization

Tachikawa

2017

J Comput Chem

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Reactions of water dimer cation (H2O)2+ following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of (H2O)2+: ground state ( A″-like state) and the first excited state ( A'-like state). All trajectories on the ground-state PES lead to the proton-transferred product: H O (Wd)-H O(Wa) → OH(Wd)-H O (Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively. Time of proton transfer (PT) varied widely from 15 to 40 fs (average time of PT = 30.9 fs). The trajectories on the excited-state PES gave two products: an intermediate complex with a face-to-face structure (H O-OH ) and a PT product. However, the proton was transferred to the opposite direction, and the reverse PT was found on the excited-state PES: H O(Wd)-H O (Wa) → H O (Wd)-OH(Wa). This difference occurred because the ionizing water molecule in the dimer switched between the ground and excited states. The reaction mechanism of (H2O)2+ and the effects of ZPE are discussed on the basis of the results. © 2017 Wiley Periodicals, Inc.

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“…Both HCN and GLY have featured in innumerous theoretical and experimental quantum‐chemical investigations. Moreover, different models of quantum chemical calculations have been used, in last few years, to investigate on the hydrogen‐bonded interaction of HCN and GLY with same or other molecules . In this respect, it is important to know how AAN molecules interact with other molecules in space.…”

Section: Introductionmentioning

confidence: 99%

“…The process of hydrogen bond (H‐bond) formation in biomolecular systems and, in particular, the effect of intramolecular and intermolecular H‐bonded interaction on chemical and structural properties of molecules are topics of continuing interest in science. H‐bond formation has investigated with a great variety of techniques and different aspects of H‐bonds in molecular systems are being reported regularly . Because of the sensitivity of the vibrational spectrum to the hydrogen bond formation, IR spectroscopy provides a definitive criterion for the detection of hydrogen bonds.…”

Section: Introductionmentioning

confidence: 99%

Effect of hydrogen‐bonded interactions on the energetics and spectral properties of the astromolecule aminoacetonitrile

Chakraborty

Lima

Silva

et al. 2017

Int J of Quantum Chemistry

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A detailed and systematic electronic structure calculation has been performed to analyze the hydrogen-bonded interaction of aminoacetonitrile (H 2 NCH 2 CN) with hydrogen cyanide (HCN) andGlycine (H 2 NCH 2 COOH). Both HCN and aminoacetonitrile have already been detected in the interstellar medium (ISM) and their active role in the molecular mechanisms of glycine production has already been recognized. Four different density functional models have been used to study the effect of hydrogen bond formation on the energetic stability and vibrational spectra of the aminoacetonitrile-HCN and aminoacetonitrile-glycine complexes in gas phase. The aminoacetonitrile-glycine dimer is energetically far more stable than all forms of aminoacetonitrile-HCN dimers. Elastic and inelastic scattering of light off the hydrogen-bonded clusters have been investigated in details via Rayleigh and Raman spectroscopic parameters. The dipole moments and depolarization ratios are found to be sensitive on the type of hydrogen-bond network. The mean polarizabilty show appreciable dependence on the choice of the DFT-model. In general, all the chemical groups (OH, CN, NH 2 , and CH) that participate directly in the hydrogen bond formation suffer appreciable variation in the intensity of vibration. K E Y W O R D S hydrogen-bonded astromolecule, polarizability, Raman spectra, Rayleigh scattering, vibrational frequency shift 1 | I N TR ODU C TI ON Aminoacetonitrile (AAN) is a small organic compound that contains an amino group (NH 2 ) at one end and nitrile group (CN) at the other. The discovery of AAN in the constellation Sagittarius B2 (Sgr B2), in 2008, [1] is a significant event in astrochemistry, as it plays the central role in the Strecker amino acid synthesis mechanism. [2][3][4][5] Amino acids are the building blocks of proteins and, therefore, the key ingredients for the origin of life. The existence of amino acids in interstellar medium (ISM) has been a topic of interest for many years. As it is well known, the possible origin of life and its existence in interstellar space is an important aspect of exobiology and planetary chemistry. Among the 20 a-amino acids commonly found in proteins, glycine (GLY), with chemical formula NH 2 CH 2 COOH, is the simplest one. Although several attempts to detect the glycine have been carried out over the past few years, identification of isolated glycine is not firmly established yet. [6][7][8][9][10][11] In 2003, the interstellar glycine was reportedly identified in the hot molecular cores Sgr B2 (N-LMH), Orion KL, and W51 e1/e2. [10] But, the procedure of the assignment of the spectral lines used in this report suffered criticism. [11] However, the detection of GLY in the comet 81P/Wild 2 by NASA's Stardust mission in 2009 [12] brought new enthusiasm to the search of extraterrestrial amino acids. In 2016, Stardust results have been confirmed by the identification of volatile glycine along with methylamine and ethylamine in the shroud of gases surrounding the Comet 67P/Churyumov-Gerasimenko by the use ...

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NMR properties of hydrogen-bonded glycine cluster in gas phase

Cited by 7 publications

References 81 publications

NMR spin–spin coupling constants in hydrogen‐bonded glycine clusters

NMR spin–spin coupling constants in hydrogen‐bonded glycine clusters

Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization

Effect of hydrogen‐bonded interactions on the energetics and spectral properties of the astromolecule aminoacetonitrile

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