The decline of tufa deposition in an alkaline fen ecosystem in East-Central Europe and its impact on biotic assemblages: Insights from monitoring and paleoecological data.

Protection and restoration of the CaCO3 depositing alkaline fens require an in-depth understanding of these unique and declining ecosystems. The present study investigates the development of the formerly heavy tufa depositing alkaline fen in East-Central Europe after CaCO3 precipitation markedly declined ca. 5400 cal yr BP. By combining palaeoecological and monitoring data, we aim to identify the limiting factors for tufa deposition and to recognise the vegetation and mollusc response to the change. Investigation of the current fen ecosystem included a botanical and malacological inventory and a monthly monitoring of the physicochemical properties of the groundwater emerging at the fen. It was also tested whether CaCO3 precipitates there. Transformations of the fen ecosystem since the mid-Holocene tufa decline were recognized by applying plant macrofossil and malacological analyses supplemented with organic matter and CaCO3 contents and the radiocarbon chronologies of the sediment cores. Although macroscopic tufa is currently not observed at the fen surface, the monitoring study revealed the microscopic calcite crystals at the glass slides during the spring and summer. A combination of cooling, gradual depletion of the Ca2+ pool, acidification of soils, and water table fluctuations was likely responsible for limiting tufa deposition in the mid-Holocene and maintaining this state during the late Holocene. Share of the calciphilous species' macrofossils (e.g. moss Tomentypnum nitens) declined following the sedimentary CaCO3 drop, whereas the contribution of species associated with high nutrient levels raised (e.g. Juncus articulatus). Inspection of the contemporary vegetation of the fen revealed that only Carex paniculata is associated with the calcium-rich substrate. The response of molluscs to the decline in tufa deposition remains unclear as mollusc shells did not preserve in CaCO3-depleted sediments, except for the youngest deposits. The present-day malacofauna consists of 21 species, including two rare and protected calciphilous species, namely Vertigo angustior and V. geyeri.

Multiproxy paleoceanographic study from the western Barents Sea reveals dramatic Younger Dryas onset followed by oscillatory warming trend.

The Younger Dryas (YD) is recognized as a cool period that began and ended abruptly during a time of general warming at the end of the last glacial. New multi-proxy data from a sediment gravity core from Storfjordrenna (western Barents Sea, 253 m water depth) reveals that the onset of the YD occurred as a single short-lived dramatic environment deterioration, whereas the subsequent warming was oscillatory. The water masses in the western Barents Sea were likely strongly stratified at the onset of the YD, possibly due to runoff of meltwater combined with perennial sea-ice cover, the latter may last up to several decades without any brake-up. Consequently, anoxic conditions prevailed at the bottom of Storfjordrenna, leading to a sharp reduction of benthic biota and the appearance of vivianite microconcretions which formation is favoured by reducing conditions. While the anoxic conditions in Storfjordrenna were transient, the unfavorable conditions for benthic foraminifera lasted for c. 1300 years. We suggest that the Pre-Boreal Oscillation, just after the onset of the Holocene, may have been a continuation of the oscillatory warming trend during the YD.

Pnictogen bonding in pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes.

This paper presents a study of pnictogen bonding in a series of pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes. The whole series was studied computationally. Moreover, the pyrazine complexes with PCl5 and SbCl5 were prepared and characterized experimentally. It was found that the Pn-N distances are only slightly elongated when compared to the sum of covalent radii. The conformation of PnX5 changed considerably upon the complex formation, which resulted in a significant change of the dipole moment of the PnX5 fragment and a considerably more positive σ-hole on the pnictogen atom. Finally, interaction energies were decomposed in order to provide a deeper insight into the nature of the studied pnictogen-bonded complexes. Graphical abstract The conformation of PnX5 changed considerably upon the complex formation, which resulted in a considerably more positive σ-hole on the pnictogen atom.

Theoretical investigation of the halogen bonded complexes between carbonyl bases and molecular chlorine.

The halogen bonded complexes between six carbonyl bases and molecular chlorine are investigated theoretically. The interaction energies calculated at the CCSD(T)/aug-cc-pVTZ level range between -1.61 and -3.50 kcal mol(-1). These energies are related to the ionization potential, proton affinity, and also to the most negative values (V(s,min)) on the electrostatic potential surface of the carbonyl bases. A symmetry adapted perturbation theory decomposition of the energies has been performed. The interaction results in an elongation of the Cl-Cl bond and a contraction of the CF and CH bonds accompanied by a blue shift of the ν(CH) vibrations. The properties of the Cl2 molecules are discussed as a function of the σ*(Cl-Cl) occupation, the hybridization, and the occupation of the Rydberg orbitals of the two chlorine atoms. Our calculations predict a large enhancement of the infrared and Raman intensities of the ν(Cl-Cl) vibration on going from isolated to complexed Cl2.

X-ray crystal structure, vibrational spectra and DFT calculations of 3-chloro-7-azaindole: a case of dual N-H⋯N hydrogen bonds in dimers.

3-Chloro-7-azaindole (3Cl7AI) is the carrier ligand in a new anticancer platinum(II) agent cis-[PtCl2(3Cl7AI)2]. In this work 3Cl7AI has been studied by a single crystal X-ray diffraction, infrared and Raman spectroscopy and density functional calculations. The compound crystallizes in the monoclinic system, space group P21/n, with a=12.3438(3), b=3.85964(11), c=14.4698(4)Å, ß=100.739(2)°, V=677.31(3)Å(3) and Z=4. In the crystal, a pair of 3Cl7AI molecules forms a centrosymmetric dimer linked by the moderately strong dual N-H⋯N hydrogen bonds. The nitrogen atom in the pyrrole ring acts as the proton donor, while the nitrogen atom in the pyridine ring is the proton acceptor. The FT-IR and FT-Raman spectra (3500-60 cm(-1)) have been recorded. The theoretical studies on the molecular structures and vibrational spectra of the monomeric and dimeric forms of 3Cl7AI and its N-deuterated derivative were performed using the B3LYP method with 6-311++G(d,p) basis set. The theoretically predicted Raman spectrum for the dimer shows very good agreement with experiment. Detailed vibrational assignments for the two isotopomers have been made on the basis of the calculated potential energy distributions (PEDs). The dual N-H⋯N hydrogen bonds in 3Cl7AI dimer are characterized by a very broad and complicated structure of the absorption band between 3300 and 2500 cm(-1), which is caused by multiple Fermi resonances between the N-H stretching vibration and various combinations bands.

Raman and infrared spectroscopy, DFT calculations, and vibrational assignment of the anticancer agent picoplatin: performance of long-range corrected/hybrid functionals for a platinum(II) complex.

Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.

Assessment of new DFT methods for predicting vibrational spectra and structure of cisplatin: which density functional should we choose for studying platinum(II) complexes?

Ten different DFT methods, including several recently developed functionals have been tested for their performances in prediction of infrared and Raman spectra and molecular structure of cisplatin. The assessed DFT methods cover the range from meta-GGA to hybrid, double hybrid and long-range corrected hybrid models (M06-L, M06, M06-2X, PBE0, mPW1PW, B3LYP, B2PLYP, CAM-B3LYP, ωB97XD and LC-ωPBE). The calculated structural parameters and theoretical spectra have been compared to the corresponding experimental data. It is shown that the LC-ωPBE scheme is superior to other DFT methods in predicting the geometry of cisplatin. Unfortunately, the M06-L, M06-2X and B3LYP functionals are deficient in the evaluation of the strength of two Pt←NH3 coordination bonds in cisplatin (the calculated bond lengths are too long and the Pt-N stretching frequencies are underestimated). Both the PBE0 and mPW1PW functionals, in conjunction with the LanL2TZ(f) basis set for Pt give very similar theoretical results and seem to be the best methods for predicting the IR and Raman spectra of cisplatin. The long-range corrected functionals (LC-ωPBE, ωB97XD and CAM-B3LYP) have shown good performances in predicting the frequencies of Pt-ligand vibrations and are promising new tools for theoretical study of novel platinum(II) compounds.

Comparison of whole genome amplification and nested-PCR methods for preimplantation genetic diagnosis for BRCA1 gene mutation on unfertilized oocytes-a pilot study.

BACKGROUND: Preimplantation genetic diagnosis (PGD) remains nowadays a valid alternative for couples at high-risk of having a child with a genetic disease and for women older than 37-40 years with the high risk of chromosomal aneuploidies in the embryos. However the use of PGD for high penetrance recessive, dominant and X-liked disorders occurring in early life is documented, debate exists regarding its appropriateness in lower penetrance and late-onset cancer susceptibility syndromes. The data regarding the efficacy of different molecular techniques used in PGD are still lacking. We therefore sought to assess the different molecular techniques used in PGD for detecting three most frequent BRCA1 gene mutations: 5382insC, 185delAG and C61G. METHODS: Anonymous donors of the oocytes and control healthy blood samples were extracted and analyzed in the Fertility and Reproductive Center Invicta in Gdansk. Preimplantation genetic diagnosis for the most frequent mutations: 185delAG, 5382insC, C61G in BRCA 1 gene was carried out on single, unfertilized oocytes, in metaphase of second meiotic division, not qualified to IVF. Positive mutation controls were represented by cell lines from the Coriell Institute for Medical Research: GM14090 (185delAG), GM14097 (C61G), GM13715 (5382insC). RESULTS: Repeatability of the results acquired from the WGA analysis for the mutation 5382insC was 38%. The repeatability of the nested-PCR analysis in the second round of the amplification was labile for the mutation 5382insC and 185delAG and was ranged from 47% to 57%. However, the repeatability for the mutation C61G was 100%. CONCLUSIONS: Our results suggest that the nested-PCR technique remains more sensitive and specific method as compared to WGA. WGA performed on the single cells did not reflect expected results. The repeatability of the WGA methodology remains questionable, and any analysis attempt does not guarantee reliable results. Further evaluation is strongly needed to propose the most accurate molecular technique used in PGD for detecting three most frequent BRCA1 gene mutations: 5382insC, 185delAG and C61G.

Theoretical studies of the interaction between enflurane and water.

Increase of the atmospheric concentration of halogenated organic compounds is partially responsible for a change of the global climate. In this work we have investigated the interaction between halogenated ether and water, which is one of the most important constituent of the atmosphere. The structures of the complexes formed by the two most stable conformers of enflurane (a volatile anaesthetic) with one and two water molecules were calculated by means of the counterpoise CP-corrected gradient optimization at the MP2/6-311++G(d,p) level. In these complexes the CH…O(w) hydrogen bonds are formed, with the H…O(w) distances varying between 2.23 and 2.32 Å. A small contraction of the CH bonds and the blue shifts of the ν(CH) stretching vibrations are predicted. There is also a weak interaction between one of the F atoms and the H atom of water, with the H(w)…F distances between 2.41 and 2.87 Å. The CCSD(T)/CBS calculated stabilization energies in these complexes are between -5.89 and -4.66 kcal mol(-1), while the enthalpies of formation are between -4.35 and -3.22 kcal mol(-1). The Cl halogen bonding between enflurane and water has been found in two complexes. The intermolecular (Cl···O) distance is smaller than the sum of the corresponding van der Waals radii. The CCSD(T)/CBS stabilization energies for these complexes are about -2 kcal mol(-1).

Blue shifts and unusual intensity changes in the infrared spectra of the enflurane···acetone complexes: spectroscopic and theoretical studies.

Blue-shifting C-H···O hydrogen-bonded complexes between enflurane (CHFCl-CF(2)-O-CHF(2)) and deuterated acetone have been identified in CCl(4) solution by FT-IR spectroscopy. For the two ν(C-H) stretching vibrations of enflurane the observed blue shifts are +17 and +11 cm(-1). The corresponding two infrared ν(C-H) bands show the opposite changes of their intensity, one is decreasing, and the other is significantly increasing, upon formation of the hydrogen bonding. The structures, binding energies, and theoretical infrared spectra of the enflurane-acetone complexes were calculated by MP2 and B3LYP methods using the 6-311++G(d,p) basis set. The interaction energies were evaluated by the complete basis set limit (CBS) calculations at the HF, MP2, and CCSD(T) levels of theory. Although the MP2 method slightly overestimates the blue shifts, the MP2 predicted frequency difference and the relative IR intensities of two ν(C-H) stretching bands for the enflurane-acetone complexes show good agreement with experiment. Unfortunately, the B3LYP method predicts incorrect IR intensities of these hydrogen-bonded systems. The NBO analysis was performed to unravel the origin of the unusual intensity changes of two ν(C-H) stretching bands, in enflurane complexes.

Halogen bonded complexes between volatile anaesthetics (chloroform, halothane, enflurane, isoflurane) and formaldehyde: a theoretical study.

The structures and intermolecular interactions in the halogen bonded complexes of anaesthetics (chloroform, halothane, enflurane and isoflurane) with formaldehyde were studied by ab initio MP2 and CCSD(T) methods. The CCSD(T)/CBS calculated binding energies of these complexes are between -2.83 and -4.21 kcal mol(-1). The largest stabilization energy has been found for the C-Br···O bonded halothane···OCH(2) complex. In all complexes the C-X bond length (where X = Cl, Br) is slightly shortened, in comparison to a free compound, and an increase of the C-X stretching frequency is observed. The electrostatic interaction was excluded as being responsible for the C-X bond contraction. It is suggested that contraction of the C-X bond length can be explained in terms of the Pauli repulsion (the exchange overlap) between the electron pairs of oxygen and halogen atoms in the investigated complexes. This is supported by the DFT-SAPT results, which indicate that the repulsive exchange energy overcompensates the electrostatic one. Moreover, the dispersion and electrostatic contributions cover about 95% of the total attraction forces, in these complexes.

Theoretical investigation of the conformation, acidity, basicity and hydrogen bonding ability of halogenated ethers.

MP2/6-311++G(d,p) calculations have been carried out to investigate the conformation, protonation and the hydrogen bonding interactions with water of several halogenated ethers (CH(3)OCH(2)Cl, CH(2)ClOCH(2)Cl, CH(3)OCHCl(2), CHFClOCHF(2)). The optimized geometries, ν(CH) harmonic vibrational frequencies and the SAPT decomposition of the interaction energies are studied. The interaction with one water molecule gives several stable structures characterized by O(w)H(w)...O and CH...O(w) hydrogen bonds or by O...Cl halogen bonding. The MP2/CBS calculated binding energies of different complexes between the halogenated ethers and water vary between 1.7 and 7.7 kcal mol(-1). The energies of these structures are discussed as a function of the proton affinity of the ethers and the deprotonation enthalpy of the CH bonds. The contraction of the CH bonds and blue shifts of the corresponding stretching vibrations in the O-protonated ethers and their O...H(w)O(w) complexes are compared. A natural bond orbital analysis has revealed that substitution of the H atoms by one or several halogen atoms has a great influence on the hyperconjugative effects from the two non-equivalent O lone pairs to relevant antibonding orbitals, and the subsequent geometry of the hydrogen bonded complexes.

Adenine ribbon stabilized by Watson-Crick and Hoogsteen hydrogen bonds: WFT and DFT study.

The self-organized adenine ribbon is studied theoretically. The experimental evidence for the formation of such a ribbon has been found in the crystal structure of the supramolecular system [Dobrzynska and Jerzykiewicz, J. Am. Chem. Soc., 2004, 126, 11118], and the striking structural feature is the fact that both the Watson-Crick and Hoogsteen faces of adenine are involved in the hydrogen bonding within the ribbon. The structure and physical properties of the monomer and five clusters of adenine (Ade)(n) (where n = 2, 3, 4, 5, 6) with AA2(2) configuration have been studied by means of the B3LYP, RI-TPSS, RI-TPSS-D (augmented with the dispersion term) and RI-MP2 methods using the 6-311+G(d,p), cc-pVTZ and TZVP basis sets. It is shown that among the investigated adenine clusters only the dimer has the planar structure. The evaluation of the three-body contribution to the total binding energy of adenine trimer has been performed at different levels of theory. All the methods consistently indicate that this term is positive and small (less than 0.5 kcal mol(-1)) which corresponds to a weak anti-cooperative effect, in adenine trimer. The differences between the total electronic energies obtained at the RI-TPSS/TZVP-D and RI-TPSS/TZVP levels of theory have shown that the London dispersion forces stabilize the adenine cluster containing 12 or more molecules by about -8 kcal mol(-1) per molecule. The results from the DFT symmetry adapted perturbation theory analysis have revealed that the contribution of dispersion to the binding energy of the adenine ribbon is about 25%.

The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine.

The amino group in adenine plays a key role in formation of hydrogen bonds in nucleic acids and in other molecular systems. Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. Ab initio MP2 and density functional B3LYP methods with various basis sets have been used to calculate the optimized structure and the infrared spectrum of adenine (the N9-H tautomer). Calculations at the MP2 level with larger basis sets tend to decrease the degree of pyramidalization of the C-NH2 group, whereas the B3LYP method consistently yields the planar or nearly planar structure of adenine. MP2 complete basis set (CBS) limit method with the aug-cc-pVTZ --> aug-cc-pVQZ (aTZ --> aQZ) extrapolation scheme has predicted very small planarization barrier of adenine, 0.015 kcal/mol, which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III, J. Chem. Phys. 2006, 124, 044303. Similar results were obtained in calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be concluded that the amino group in adenine, in the gas phase, is very flexible with a small degree of nonplanarity. Extremely low planarization barrier implies that adenine requires very little energy to conform the structure of the amino group to formation of the complementary hydrogen bonds with other molecules. This fact is very important for base pairing in nucleic acids or other polymers containing adenine residues. The anharmonic frequencies of adenine have been calculated at the B3LYP/6-311++G(df,pd) level of theory. The theoretical results show excellent agreement with the available experimental data. The revised assignment of the infrared spectrum of adenine in Ar matrix has been made. The predicted anharmonic frequency of the NH2 inversion, 181 cm(-1), is supported by the experimental data. It is demonstrated that the vibrational frequencies and potential energy distribution (PED) obtained from the B3LYP calculations are more reliable than those obtained at the MP2 level.

Theoretical and experimental studies of enflurane. Infrared spectra in solution, in low-temperature argon matrix and blue shifts resulting from dimerization.

Theoretical studies are performed on enflurane (CHFCl-CF(2)-O-CHF(2)) to investigate the conformational properties and vibrational spectra. Calculations are carried out at the B3LYP/6-31G(d) level along with a natural bond orbital (NBO) analysis. Experimental infrared spectra are investigated in carbon tetrachloride solution at room temperature and in argon matrix at 12 K. In agreement with previously reported data (Pfeiffer, A.; Mack, H.-G.; Oberhammer, H. J. Am. Chem. Soc. 1998, 120, 6384), it is shown that the four most stable conformers possess a trans configuration of the C-C-O-C skeleton and a gauche orientation of the CHF(2) group (with respect to the central C-O bond). These conformations are favored by electrostatic interaction between the H atom of the CHF(2) group and the F atoms of the central CF(2) group. Hyperconjugation effects from the O lone pairs to the antibonding orbitals of the neighboring C-H and C-F bonds also contribute to the stability of the four conformers. The vibrational frequencies, infrared intensities, and potential energy distributions are calculated at the same level of theory for the most stable conformers. On the basis of the theoretical results, these conformers are identified in an argon matrix. The influence of the concentration on the nu(CH) vibrations suggests the formations of higher aggregates in solution. Theoretical calculations are carried out on the enflurane dimer. The results show that the dimer is formed between two enflurane conformers having the largest stability. The dimer has an asymmetric cyclic structure, the two enflurane molecules being held together by two nonequivalent C-H...F hydrogen bonds, the C-H bond of the CHFCl group acting as a proton donor, and one of the F atoms of the CHF(2) groups acting as a proton acceptor. The theory predicts a contraction of 0.0014-0.0025 A of the two CH bonds involved in the interaction along with a blue shift of 30-38 cm(-1) of the corresponding nu(C-H) bands, in good agreement with the blue shifts of 35-39 cm(-1) observed in an argon matrix.

Theoretical Raman and infrared spectra, and vibrational assignment for para-halogenoanilines: DFT study.

The theoretical IR and Raman spectra of para-halogenoanilines, 4-XC(6)H(4)NH(2) (X=F, Cl and Br) were calculated by using the density functional B3LYP method with the 6-311++G(df,pd) basis set. The theoretical spectra show very good agreement with experiment. The rigorous normal coordinate analyses have been performed, and the detailed vibrational assignment has been made on the basis of the calculated potential energy distributions (PEDs). Several ambiguities and contradictions in the previously reported vibrational assignments have been clarified. The "marker bands" and the effects of the halogen substituent on the characteristic aniline bands in the IR and Raman spectra are discussed.

FT-Raman and FT-IR spectra, vibrational assignments and density functional studies of 5-bromo-2-nitropyridine.

The Fourier transform Raman and Fourier transform infrared spectra of 5-bromo-2-nitropyridine were recorded in the solid phase. The equilibrium geometry, natural atomic charges, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-311++G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. A detailed interpretations of the infrared and Raman spectra of 5-bromo-2-nitropyridine is reported on the basis of the calculated potential energy distribution (PED). The theoretical spectrograms for the Raman and IR spectra of the title molecule have been constructed.

Vibrational spectra of 1-methylthymine: matrix isolation, solid state and theoretical studies.

The infrared spectra of 1-methylthymine (1-MeT) in argon and nitrogen cryogenic matrices are presented, for the first time. The molecular structure, conformations, vibrational frequencies, infrared intensities and Raman scattering activities of 1-MeT have been calculated by the DFT(B3LYP), MP2 and HF methods using the D95V** basis set. The theoretically predicted intensity pattern of the IR and Raman bands has proved to be of great help in assigning the experimental spectra. Rigorous normal coordinate analysis has been performed, at each level of theory. The unequivocal and complete vibrational assignment for 1-MeT has been made on the basis of the calculated potential energy distribution (PED). Comparison of the experimental matrix isolation spectra with the theoretical results has revealed that the B3LYP method is superior to both the MP2 and HF methods in predicting the frequencies of uracil derivatives. The MP2 method consistently underestimates the frequencies of the out-of-plane gamma(C=O) and gamma(C-H) bending modes, while the HF method yields the reverse order of the frequencies of two nu(C=O) stretching vibrations. Investigation of the frequency shift of several bands, on passing from matrix isolation to solid state spectra, has provided information on the strength of intermolecular hydrogen bonding in the crystal of 1-MeT. Several ambiguities in the earlier assignments of the vibrational spectra of polycrystalline 1-MeT have been clarified.

Vibrational spectra of 1-methyluracilate complex with silver(I) and theoretical studies of the 1-MeU anion.

The FT-Raman and FT-infrared spectra of (1-methyluracilato)silver, [Ag(C(5)H(5)N(2)O(2))] in the solid state have been studied. The complex is a polymer in which one silver ion is linearly bonded to two 1-MeU ligands through the deprotonated N(3) sites and another silver ion is tetrahedrally coordinated to the four 1-MeU ligands through the O2 and O4 carbonyl oxygen atoms. The harmonic vibrational frequencies, infrared intensities and Raman scattering activities of the N(3)-deprotonated 1-methyluracilate anion have been calculated using density functional (B3LYP) and ab initio (HF and MP2) methods with the 6-31G(d,p) and 6-31++G(df,pd) basis sets. The calculated potential energy distribution (PED) for the 1-MeU anion has proved to be of great help in assigning the spectra of the title complex. It can be concluded that the two strong Raman bands at 1263 and 796 cm(-1) are diagnostic for the N3-deprotonation of the 1-methyluracilate ring and complexation with silver ion. The linear N-Ag-N stretching vibrations are assigned to the bands at 448 and 362 cm(-1) (IR) and 453, 362 cm(-1) (Raman). The Ag-O stretching vibrations are assigned to the bands in the range of 280-250 cm(-1).

Study of the nature of improper blue-shifting hydrogen bonding and standard hydrogen bonding in the X3CH...OH2 and XH...OH2 complexes (X = F, Cl, Br, I): A correlated Ab initio study.

Weak hydrogen bonding was studied in the XH...OH2 and X3CH...OH2 complexes (X = F, Cl, Br, I) using the correlated MP2 ab initio method with relativistic Stuttgart/Dresden pseudopotentials and basis set (SDD). The accuracy of the method was tested for selected nonrelativistic complexes by performing MP2 calculations with all-electron basis sets (6-311G** and TZVPP). The characteristics of bonding in the hydrogen halide complexes correspond to the standard H-bonding (an elongation of the X-H bond and red shift of its stretch frequency), whereas those in the X3CH...OH2 complexes (X = F, Cl) are typical of improper blue-shifting H-bonding (a contraction of the CH bond and blue shift of the respective stretch frequency). A natural bond orbital analysis revealed some important differences between both classes of complexes: a) the electron density transfer (EDT) in the former complexes is considerably larger than that in the latter complexes: b) the EDT in the former complexes is almost completely directed to the sigma*-antibonding orbital of the XH bond, which causes a weakening of this bond, its elongation, and a concomitant decrease of the XH stretch frequency. In the latter complexes, only a small portion of the EDT goes to the sigma*-antibonding orbital of the CH bond of the proton donor and a larger part is transferred to the remote (nonparticipating) part of the proton donor. As a consequence, the structural reorganization of the proton donor occurred, leading to the contraction of the C-H bond. The fact that a small red shift of the C-H stretch frequency was found in bromoform-water and iodoform-water complexes was explained by the competition of both the above-mentioned mechanisms with dominating passage of electron density to the sigma*-antibonding orbital of the C-H bond. For an explanation of all the geometric features of both types of complexes, it is however necessary to consider both charge transfer and electrostatic effects. The electrostatic effects fail sometimes to interpret the geometry changes in the proton donor.