Glycine Fragments Research Articles

Lipophilic poly(glycolide) blocks in morpholin-2-one-based CARTs for plasmid DNA delivery: Polymer regioregularity, sequence of lipophilic/polyamine blocks, and nanoparticle stability as factors of transfection efficiency

In the present work, monosubstituted glycolides (G2–G4) derived from the (L)-tyrosine-based glycolide G1 and containing –CH2C6H4OR substituents (R = decanoyl, oleoyl, C(O)CH(n-C6H13)(n-C8H17)) have been used to design biodegradable and biocompatible lipophilic blocks in N-BOC-morpholin-2-one (M1)-based Charge-Altering Releasable Transporters (CARTs). Copolymers of dodecyl carbonate C1 (the ‘benchmark’ lipophilic comonomer) and M1, having direct (P1) or inverse (P2) block sequences; copolymers of G2–G4 and M1, having inverse block sequences and irregular, head-to-head in places, microstructures of the poly(glycolide) blocks (P3–P7); and copolymers of G2 and M1, having solely alternating head-to-tail microstructures of the poly(glycolide) blocks and direct (P8) or inverse (P9) block sequences, have been synthesized. DLS studies have shown that, after deprotection, the copolymers P1′–P9′ form liposomal particles in aqueous medium, differing considerably in their colloidal behavior, which depended on the length of the polyamine fragment and the nature of the lipophilic block. The ability of P1′–P9′ to deliver the plasmid pEGFP-N1 into cultured HEK293T cells (transfection efficiency) has been assessed at N/P ratios of the corresponding polyplexes in the range 1:1–50:1 by flow cytometry and further confirmed by fluorescence microscopy. Transfection experiments have demonstrated that the CARTs P1′, P4′, and P6′, containing ten (2-oxyethyl)glycine fragments, are about four times more efficient in delivering pDNA than commercial agents (Lipofectamine™ 3000, PEI MAX, X-tremeGENE™ 9, and GenJet™ In Vitro DNA Transfection Reagent). A correlation between the results of those studies and DLS / ζ-potential measurements has been established for P1′ and P4′: the transfection is efficient, if N/P ratios are equal to those favoring ζ-potential inversion at physiological pH. We conclude that glycolide-based CARTs show significant promise for further development as non-viral NA delivery vehicles and that DLS should be regarded as an efficient method of primary screening of amphiphilic copolymers, as well as copolymer-NA complexes and formulations thereof.

Functional analysis of the cystatin A gene response to SGIV infection in orange-spotted grouper, Epinephelus coioides

Cystatin A (CyA), an inhibitor of cysteine protease, was widely studied in immune defense and cancer therapy. However, the function of CyA and its potential molecular mechanism during virus infection in fish remain unknown. In our study, we cloned the open reading frame (ORF) of CyA homology from orange-spotted grouper (Ec-CyA) consisting of 303 nucleotides and encoding a 101-amino acid protein. Ec-CyA included two conserved sequences containing one N-terminal glycine fragment and one QXVXG sequence (48aa-52aa) without the signal peptide. Tissue distribution analysis showed that Ec-CyA was highly expressed in spleen and head kidney. Moreover, further analysis indicated that the expression of Ec-CyA increased during SGIV simulation in grouper spleen (GS) cells. Subcellular localization assay demonstrated that Ec-CyA was mainly distributed in cytoplasm in GS cells. Overexpressed Ec-CyA promoted the mRNA level of viral genes MCP, VP19 and LITAF. Meanwhile, SGIV-induced apoptosis in fat head minnow (FHM) cells was facilitated, as well as the activation of caspase-3/7, caspase-9. In addition, Ec-CyA overexpression down-regulated the expression of interferon (IFN) related molecules including ISG15, IFN, IRF3, MAVS, MyD88, TRAF6 and up-regulated proinflammatory factors such as IL-1β, IL-8 and TNF-α. At the same time, Ec-CyA-overexpressing inhibited the activity of IFN and ISRE promoter, but induced NF-κB promoter activity by luciferase reporter gene assay. In summary, our findings suggested that Ec-CyA was involved in innate immune response and played a key role in DNA virus infection.

Molecular and Heterogenized Cp*Ir Water Oxidation Catalysts Bearing Glyphosate and Glyphosine as Ancillary and Anchoring Ligands

AbstractTwo hybrid materials (1_TiO2 and 2_TiO2) were designed and prepared by anchoring novel [Cp*Ir(κ3‐O,N,O‐glyphosate)] (1; glyphosate=N‐(phosphonomethyl)glycine) and [Cp*Ir(κ3‐O,N,O‐glyphosine)] (2; glyphosine=N,N‐bis(phosphonomethyl)glycine) complexes onto rutile TiO2. Characterization in solution (NMR spectroscopy) and solid state (X‐Ray diffractometry) indicates that 1 and 2 are stabilized by the two arms of the glycine fragment, whereas they have (2) or can easily generate (1 and 2) a dandling phosphonate arm suitable for their anchoring on TiO2. As a matter of fact, they exhibit rather elongated Ir–OP (1: 2.1405 Å, 2: 2.142 Å) and short Ir–OC (1: 2.0784 Å, 2: 2.086 Å) and Ir–N (1: 2.155 Å, 2: 2.207 Å) bonds. NMR spectra of 2 show a dynamic process that exchanges the two phosphonate moieties, consistently with an easy –OP detachment from Ir. Both molecular and heterogenized species were tested as catalysts in water oxidation (WO) driven by NaIO4. 1 (TOF up to 96 min−1) and 2 (26 min−1) proved to be effective molecular catalysts; more importantly, 1_TiO2 and 2_TiO2 showed very high activity (TOF ∼200 min−1), which remained rather constant over seven successive runs, even if substantial leaching of the noble metal in solution occurred during the first catalytic tests. TON was very high and limited only by the amount of NaIO4 used. These results show the potentialities of mixed carboxylate/phosphonate ligands for the development of highly active water oxidation catalysts.

Relation between biomolecular dissociation and energy of secondary electrons generated in liquid water by fast heavy ions

In this work, we measured and simulated the dissociation of biomolecules in liquid water induced by secondary electrons ejected from water molecules during fast heavy-ion irradiation. We calculated the energy spectra of secondary electrons generated along carbon ion tracks in liquid water in the Bragg peak region. The calculation was done using the Particle and Heavy Ion Transport code System (PHITS) in carbon track structure mode. This mode enables simulation of inelastic collisions along a carbon ion track based on the cross sections considered in the Monte Carlo code KURBUC. To understand the biomolecular dissociation processes in our previous MeV-SIMS experiments with microdroplet targets of glycine solution, we calculated the collision spectra of secondary electrons produced near liquid surfaces using PHITS. Furthermore, we examined the relationship between the secondary electron energy and formation of positive and negative glycine fragments. The results showed that the formation of methylene amine cations is caused by secondary electrons with energies of 13–100 eV. The formation of glycine-related negative ions such as cyanide anion, formate anion, and deprotonated glycine was found to be caused by low-energy (less than 13 eV) secondary electrons. These ions are known products of dissociative electron attachment.

Secondary electron-induced biomolecular fragmentation in fast heavy-ion irradiation of microdroplets of glycine solution.

The influence of secondary electrons on radiation damage of biomolecules in water was studied by fast heavy-ion irradiation of biomolecular solutions. Water microdroplets containing the amino acid glycine under vacuum were irradiated by fast carbon projectiles with energies of 0.8-8.0 MeV. A variety of fragments from the droplets were observed by time-of-flight secondary-ion mass spectrometry: methylene amine cation and formate anion originating from the cleavage of C-Cα bonds, cyanide anion generated by cleavage of multiple bonds, and protonated and deprotonated glycine. The dependence of the yield of each fragment on projectile energy was examined; different behavior was observed for positive and negative fragments. Considering that biomolecular fragmentation may be induced by secondary electrons ejected from the water molecules surrounding biomolecules, we calculated the cross section for ejection of secondary electrons from liquid water. We found that the formation of both positive and negative glycine fragment ions correlated with the predicted emission of secondary electrons at different projectile energies. The formation of [Gly-H]- fragments, typical for gas phase dissociative electron attachment to amino acids, is shown to be caused by electrons from the low-energy part of the secondary electron distribution.

Insights into the dissociative ionization of glycine by PEPICO experiments.

The fragmentation of glycine (NH2CH2COOH) has been studied by photoelectron-photoion coincidence, PEPICO, experiments at 60 eV photon energy. Glycine practically fragments at the ionization threshold, with the charge being on the H2NCH2+ moiety, due to ejection of an electron from the nitrogen lone pair of the highest occupied molecular orbital. To observe the formation of the complementary cation COOH+ further energy is needed. The flexibility with respect to rotation about the C-C, C-N and C-O bonds makes glycine exist in the gas phase in several conformers of both Cs and C1 point group symmetry in the neutral as well as ion states. The ionization can lead to stabilization of some conformations, rearrangements and, last but not least, H migration between the two moieties. The results of these experiments prove the sensitivity of PEPICO to pin point all these processes.

Spectral Luminescent Properties of the Glycine Molecule in a Gas Discharge

We have experimentally studied the luminescence spectra of glycine powder in the plasma of a repetitively pulsed longitudinal discharge in argon–glycine and helium–glycine mixtures. We have identified the main fragments of the glycine molecule emitting in the 200–1000 nm region. The emitting molecules due to fragmentation of glycine and dissociation of the carboxyl (−COOH) and amino (−NH2) groups are nitrogen, carbon monoxide, and cyanogen molecules.

Synthesis of new decasubstituted pillar[5]arenes containing glycine fragments and their interactions with Bismarck brown Y

New water-soluble decasubstituted pillar[5]arenes containing glycine and glycylglycine fragments were synthesized and characterized. The UV, DLS and TEM study showed that interaction of self-associates of the glycylglycine derivatives with Bismarck brown Y produced particles of about 59 nm in size.

New binuclear Ni(II)–glycinate homologues: electrochemically distinguishable diastereomers

A voltammetric investigation of the electrochemical reduction and oxidation of a homologous series of binuclear diastereomeric (SR)- and (SS)-Ni(II) α-amino acid /Schiff-base complexes in which two Ni-containing moieties are linked via glycine fragments (LNi–Gly–(CH2)n–Gly–NiL; n=0,1,2) and which contain an auxiliary chiral aromatic moiety – (S)-o-[N-(N'-benzylprolyl) amino]benzophenone was performed at a Pt electrode in acetonitrile. These complexes constitute an interesting example of the influence of the absolute configuration of the stereocenters on the electrochemical behavior of the diastereomers and on the redox potential values. To distinguish between the diastereomers, cyclic voltammetry is more sensitive than UV–vis spectroscopy. For n=0, the difference between the λmax values for the (SR) and the (SS) diastereomers is large enough to differentiate them. With an increase in the number of the methylene units between two Ni–glycine moieties in the binuclear complex spectral characteristics for (SR) and (SS) diastereomers become almost identical whereas the voltammetric characteristics remain sufficiently different to allow the differentiation even for n=2.1H, 13C NMR data and DFT computation revealed that the electronic density in (SR)- LNi–Gly–(CH2)n–Gly–NiL (n=0,1,2) is distributed non-uniformly between the two parts of the diastereomeric molecule both in the neutral complexes and their radical cation. Their dipole moment as well as their frontier orbitals were calculated. The HOMO and LUMO are not located on the same mononuclear units and their location alternates between the two units in the homologous series. Thus, there is an alternation of the reduction and oxidation sites. As a consequence, both the oxidation and the reduction of the (SR)-complexes are easier than those of to their (SS) counterparts, which results in a smaller difference between the oxidation and the reduction potentials for the SR diastereomers. This provides an electrochemical way to probe the absolute configuration of the α-carbon atoms of the diaminodicarboxylic acid moiety in these Ni(II) binuclear complexes.

Peptide bond formation via glycine condensation in the gas phase.

Four unique gas phase mechanisms for peptide bond formation between two glycine molecules have been mapped out with quantum mechanical electronic structure methods. Both concerted and stepwise mechanisms, each leading to a cis and trans glycylglycine product (four mechanisms total), were examined with the B3LYP and MP2 methods and Gaussian atomic orbital basis sets as large as aug-cc-pVTZ. Electronic energies of the stationary points along the reaction pathways were also computed with explicitly correlated MP2-F12 and CCSD(T)-F12 methods. The CCSD(T)-F12 computations indicate that the electronic barriers to peptide bond formation are similar for all four mechanisms (ca. 32-39 kcal mol(-1) relative to two isolated glycine fragments). The smallest barrier (32 kcal mol(-1)) is associated with the lone transition state for the concerted mechanism leading to the formation of a trans peptide bond, whereas the largest barrier (39 kcal mol(-1)) was encountered along the concerted pathway leading to the cis configuration of the glycylglycine dipeptide. Two significant barriers are encountered for the stepwise mechanisms. For both the cis and trans pathways, the early electronic barrier is 36 kcal mol(-1) and the subsequent barrier is approximately 1 kcal mol(-1) lower. A host of intermediates and transition states lie between these two barriers, but they all have very small relative electronic energies (ca. ± 4 kcal mol(-1)). The isolated cis products (glycylglycine + H2O) are virtually isoenergetic with the isolated reactants (within -1 kcal mol(-1)), whereas the trans products are about 5 kcal mol(-1) lower in energy. In both products, however, the water can hydrogen bond to the dipeptide and lower the energy by roughly 5-9 kcal mol(-1). This study indicates that the concerted process leading to a trans configuration about the peptide bond is marginally favored both thermodynamically (exothermic by ca. 5 kcal mol(-1)) and kinetically (barrier height ≈ 32 kcal mol(-1)) according to the CCSD(T)-F12/haTZ electronic energies. The other pathways have slightly larger barrier heights (by 4-8 kcal mol(-1)).

Soft x-ray ionization induced fragmentation of glycine.

X-ray absorption commonly involves dissociative core ionization producing not only momentum correlated charged fragments but also low- and high-energy electrons capable of inducing damage in living tissue. This gives a natural motivation for studying the core ionization induced fragmentation processes in biologically important molecules such as amino acids. Here the fragmentation of amino acid glycine following carbon 1s core ionization has been studied. Using photoelectron-photoion-photoion coincidence technique, a detailed analysis on fragmentation of the sample molecule into pairs of momentum correlated cations has been carried out. The main characteristics of core ionization induced fragmentation of glycine were found to be the rupture of the C-Cα bond and the presence of the CNH(2)(+) fragment.

Combined theoretical studies on solvation and hydrogen bond interactions in glycine tripeptide

The theoretical conformational analysis of glycine tripeptide (GT) has been carried out by molecular dynamics (MD) method in order to find minimum energy conformations. The MD studies on GT with water have been carried out for over 10 ns with a time step of 2 fs using fixed charge force field (AMBER ff03). By adding the solvation effect using water as a solvent, the GT conformers identified in this study exhibit α-helical conformation. Compared with the earlier reports, this MD study is able to identify the energetically favourable GT conformations. The obtained geometry of the five most stable GT conformations was optimised using the density functional theory method at B3LYP/6-311G** level of theory. Subsequently, the effects of solvation on the conformational characteristics of five most stable GT conformers with four water molecules (the number of water molecules in the first solvation shell of GT obtained from MD study) were investigated using the same method and the same level of theory. The effect of microsolvation on the fifth GT conformer has been studied with a cluster of 11 water molecules as the first hydration shell which generates folded structure. The interaction energies of all the complexes are calculated by correcting the basis set superposition error. The strong hydrogen bond mainly contributes to the interaction energies. The atoms in molecules theory and natural bond orbital analysis were used to study the origin of H-bonds. A good correlation between the structural parameters and the properties of charge density is found. NMR calculations show that the C = O carbons of the amine groups of the first and middle glycine fragments have maximum chemical shifts.

The effect of the amphoteric properties of amino acids in the zwitterionic form on the structure of iodine complex compounds in aqueous solutions

The donor–acceptor interactions in three model systems: water–glycine (a), water–glycine–KI3 (b), water–glycine–KI3–LiCl–ethanol (c) were investigated by UV-, IR-spectroscopy, and the quantum-chemical DFT-B3PW91/midi method.UV- and IR spectrum data for the considered systems agree well with the results of calculations of the spectral characteristics of glycine cluster that consists of six molecules, and models that simulate the influence of the zwitterionic form of glycine on the structure of complex iodine compounds in the systems (b–c).Localization of a negative and a positive charge at the ends of a zwitterion makes it possible for a cluster of glycine zwitterions to be formed in water. In such cluster glycine molecules are located under each other so that the protonated group is always under (or above) the carboxy group. Glycine fragments are bound by strong hydrogen bonds and also by hydrogen bonding interactions with water molecules. In the water–glycine–KI3–LiCl–ethanol system the cluster of glycine zwitterions splits the iodide ion into I− and I2 (I− reacts with the protonated amino group, and I2 with the carboxy group). This creates conditions for the formation of an iodine complex compound, in which molecular iodine reveals the acceptor properties towards glycine, and the donor properties towards the LiCl–ethanol complex.

Photochemical degradation of citrate buffers leads to covalent acetonation of recombinant protein therapeutics

Novel acetone and aldimine covalent adducts were identified on the N-termini and lysine side chains of recombinant monoclonal antibodies. Photochemical degradation of citrate buffers, in the presence of trace levels of iron, is demonstrated as the source of these modifications. The link between degradation of citrate and the observed protein modifications was conclusively established by tracking the citrate decomposition products and protein adducts resulting from photochemical degradation of isotope labeled (13)C citrate by mass spectrometry. The structure of the acetone modification was determined by nuclear magnetic resonance (NMR) spectroscopy on modified-free glycine and found to correspond to acetone linked to the N-terminus of the amino acid through a methyl carbon. Results from mass spectrometric fragmentation of glycine modified with an acetone adduct derived from (13)C labeled citrate indicated that the three central carbons of citrate are incorporated onto protein amines in the presence of iron and light. While citrate is known to stoichiometrically decompose to acetone and CO(2) through various intermediates in photochemical systems, it has never been shown to be a causative agent in protein carbonylation. Our results point to a previously unknown source for the generation of reactive carbonyl species. This work also highlights the potential deleterious impact of trace metals on recombinant protein therapeutics formulated in citrate buffers.

Versatile Access to 2‐Aminocyclobutene‐1‐carboxylic Acid Derivatives and Their Incorporation into Small Peptides

AbstractUnder a newly developed set of mild conditions [EtN(iPr)2, LiI, DMF, 20 °C, 3 d], methyl 2‐chloro‐2‐cyclopropylideneacetate (1) smoothly undergoes Michael addition ofvarious benzylamines (4 examples) with ensuing ring enlargement and elimination to give in very good yields (81–99 %) the correspondingly substituted methyl 2‐(benzylamino)cyclobutenecarboxylates 3a–d, which were subsequently converted into the N‐Boc‐protected derivatives 4a–d. After hydrolysis of the esters, the free β‐amino acids 5a,b were cleanly condensed with the methyl esters of glycine, (S)‐proline, (S)‐phenylglycine and (S)‐tryptophan to give the dipeptides 6a–8a, 9b in 58–89 % yield. The cyclic dipeptides 15e,f, consisting of a 2‐aminocyclobutenecarboxylic acid and a glycine fragment, were obtained in 38 and 45 % yield, respectively, upon treatment of the spirocyclopropanated chlorohexahydrodiazepinediones 10e,f with sodium cyanide in DMSO at elevated temperatures. Palladium‐catalyzed hydrogenation of 4a afforded methyl N‐Boc‐2‐aminocyclobutanecarboxylate 19 as a mixture of cis and trans isomers.

Vacuum Ultraviolet Photofragmentation of Sarcosine: Photoionization Mass Spectrometric and Theoretical Insights

Vacuum ultraviolet (VUV) photon-induced ionization and fragmentation of N-methyl glycine (sarcosine) were investigated with infrared laser desorption/tunable synchrotron VUV photoionization mass spectrometry (IR LD/VUV PIMS) and theoretical calculations. Fragment-controllable mass spectra of sarcosine were measured at various photon energies. By tuning the photon energy, the fragments at m/z 44, 45, 43, 42, 30, and 60 were gradually detected. The ionization energy of the precursor was obtained by measuring the photoionization efficiency spectrum. Possible formation pathways of the fragment ions at m/z 44 (CH(3)NHCH(2)(+)), 45 (CH(3)NH(2)CH(2)(+)), 43 (CH(2)NHCH(2)(+)), 42 (CH(2)NCH(2)(+)), 30 (CH(2)NH(2)(+)), and 60 (CH(2)COOH(2)(+)) were discussed in detail with the help of calculations at the G3B3 and B3LYP/6-31++G(d,p) levels.

Structure and fragmentation of glycine, alanine, serine and cysteine radical cations. A theoretical study

The structure of glycine, alanine, serine and cysteine radical cations, as well as their C α–R fragmentations have been studied at the B3LYP/6-31++G(d,p) level of theory. For all systems the loss of COOH is found to be the most favourable process. However, when R 1 size increases, fragmentations that lead to R 1 or R 1 + start become competitive. The energy of a C α–R fragmentation can be related to the ionization potential of the two generated fragments, in such a way that the preferred process is the one that leaves the positive charge in the fragment with a lower ionization potential.

Investigations of double proton transfer and one-electron oxidation behavior in double H-bonded glycine–formamide complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycine–formamide complex have been investigated employing the B3LYP/6-311++G** level of theory. The relevant quantities involved in the DPT process, such as interaction energies, tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. Compared with the intramolecular proton transfer (PT) in isolated glycine, the participation of a formamide molecule favors the PT of glycine kinetically. The DPT process proceeds with a concerted mechanism rather than a stepwise one since no zwitterionic complexes have been located during the DPT process. Correspondingly, the calculated forward and reverse barrier heights are 12.62 and 2.01 kcal/mol, respectively. However, both of them have been reduced to 9.35 and −1.16 kcal/mol when zero-point vibrational energy (ZPVE) corrections are included, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously. Additionally, the one-electron oxidation behavior for the double H-bonded glycine–formamide complex has also been investigated. The oxidation product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to formamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 9.20 and 8.26 eV, respectively.

Double proton transfer and one‐electron oxidation behavior in double H‐bonded glycinamide–glycine complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.

Theoretical prediction of gas-phase infrared spectra of imidazo[1,2- a]pyrazinediones and imidazo[1,2- a]imidazo[1,2- d]pyrazinediones derived from glycine

Imidazo[1,2- a]pyrazine-3,6-diones and imidazo[1,2- a]imidazo[1,2- d]pyrazine-3,8-diones can be produced by pyrolysis of simple amino acids. While such bicyclic and tricyclic amidines were detected and characterized by IR spectroscopy for some α-substituted amino acids, the parent systems composed of glycine fragments are unknown up to now. IR spectra for five amidines derived from glycine were calculated by using different semi-empirical (PM3, AM1, MNDO and MINDO/3), HF, and hybrid DFT (B3LYP, B3P86 and B3PW91) methods in conjunction with 6-31G( d) basis set (for HF and DFT). Vibration frequencies in the experimental IR spectra were predicted based upon the B3LYP data, by correcting the calculated wavenumbers by a scaling factor of 0.959. The behavior of most characteristic bands ( ν C X , ν NH, etc.) and their shifts with respect to such bands in the spectra of alanine and α-aminoisobutyric acid derivatives studied before, are discussed. Performance of the semi-empirical methods was tested, bearing in mind possible future needs for IR spectra predictions for larger molecular systems of similar chemical nature; the use of MINDO/3 and MNDO is recommended. A basis set effect on the B3LYP fundamental vibration frequencies for hexahydroimidazo[1,2- a]pyrazine-3,6-dione was studied by varying Pople basis sets from minimal STO-3G to 6-311++G( d, p). No significant improvements were found beyond the 6-31G( d) basis set, which thus can be recommended to predict IR spectra for the amidines and similar molecules.