Morphology and Optical Properties of RF Sputtering Deposited Indium Nitride Layers Under Different N2/Ar Ratio.

InN thin films were prepared using reactive radio frequency sputtering on (111) Si substrates under different N2/Ar ratio. The surface morphology and optical properties of InN thin films were characterized by X-ray diffraction, atomic force microscopy, scanning electron microscope, energy dispersive spectrometer, and UV-visible-NIR spectrophotometer at room temperature. It was found that the growth rate and surface RMS roughness of InN layers all significantly decreased with the increasing of N2 content in the sputtering gas. All the InN films were wurtzite structure with the proportion of N2 increasing from 40% to 100% in the mixture gas. The highly c-axis orientation InN films could only be obtained in the composition ratios of N2 higher than 90%. The atomic percentage of N is much higher than that of In at high N2 content films, which mainly due to the chemical reaction on the surface of Si substrate. The apparent optical band gap energy is estimated at 1.83 eV. However, the InN absorption band tail is strongly influenced by the sputtering due to a change in the species of the plasma.

[Biological effects of upregulated expression of transfected FOLR1 gene on SKOV3 cell lines acted by cisplatin].

OBJECTIVE: To explore biological effects of up-regulated expression of transfected FOLR1 gene on SKOV3 cell lines following action by cisplatin (DDP) . METHODS: Three groups of cells originated from the same SKOV3 cell line were used in this research, including the SKOV3 cell line(blank control), the cell line transfected with lentiviral pWPI plasmid(no-load control) and the cell line transfected with FOLR1 gene via lentiviral pWPI plasmid(experimental group). Next, the mRNA and protein expression of FOLR1 gene in the three groups were detected by reverse transcription (RT) -PCR and western blot, respectively. Methyl thiazolyl tetrazolium (MTT) assay was used to analysis cells growth curve and identify their sensitivity to cisplatin, and their half inhibition concentration(IC50) values were calculated. Based on the IC50 value(3.6 µg/ml) in the experimental group, different levels of cisplatin concentration (0.5×IC50, 1×IC50, 2×IC50, respectively) were administered to the three groups of cells, and the inhibition rates, apoptosis rates as well as apoptosis proportion of each group after 24, 48, 72 hours were further recorded.Finally, the residual cisplatin concentrations in the three group cells acted successively by 1×IC50 cisplatin for 48 hours were measured by high performance liquid chromatography (HPLC) . P value less than 0.05 were defined as statistically significant. RESULTS: RT-PCR and western blot detection showed that stable mRNA and protein expression of the FOLR1 gene in the experimental group while the other two groups were not. MTT assay demonstrated that higher cell growth rate, sensitivity to cisplatin(IC50 = 3.6 µg/ml) and inhibition rate in the experimental group compared with those in the other two groups (P < 0.05) , which showed no significance in intergroup comparison(P > 0.05). Flow cytometry showed apoptosis rates among three groups increased with higher cisplatin concentrations and longer action duration in dosage-time dependent manner (P < 0.05) , and the proportion of S phase cells increased with higher cisplatin concentration in dosage-dependent manner (P < 0.05) ;for the same concentration and duration, the experimental group showed significantly different apoptosis rates and S phase cells compared with the other two groups, which demonstrated no significance in intergroup comparison (P > 0.05) . After action by cisplatin(3.6 µg/ml) for 48 hours, HPLC showed significantly higher residual cisplatin concentration (2.60 ± 0.21) µg/10(6) cell counts in experimental group than those in no-load control group (1.49 ± 0.12) µg/10(6) cell counts and blank control group(1.54 ± 0.11) µg/10(6) cell counts, respectively (P < 0.05) , and the comparison within the latter two groups showed no significance (P > 0.05). CONCLUSION: Up-regulated expression of the transfected FOLR1 gene in SKOV3 cells may be associated with higher sensitivity to cisplatin, residual cisplatin concentration and higher proportion of S phase cells, and tended to inhibit cancer cells growth and induce apoptosis.

Regenerative Effect of Mesenchymal Stem Cell on Cartilage Damage in a Porcine Model.

Osteoarthritis (OA) is a major public and animal health challenge with significant economic consequences. Cartilage degradation plays a critical role in the initiation and progression of degenerative joint diseases, such as OA. Mesenchymal stem cells (MSCs) have become increasingly popular in the field of cartilage regeneration due to their promising results. The objective of this preclinical study was to evaluate the regenerative effects of mesenchymal stem cells (MSCs) in the repair of knee cartilage defects using a porcine model. Seven healthy LYD breed white pigs, aged 9-10 weeks and weighing approximately 20 ± 3 kg, were used in the experimental protocol. Full-thickness defects measuring 8 mm in diameter and 5 mm in depth were induced in the lateral femoral condyle of the posterior limbs in both knee joints using a sterile puncture technique while the knee was maximally flexed. Following a 1-week induction phase, the pig treatment groups received a 0.3 million/kg MSC transplant into the damaged knee region, while the placebo group received a control solution as a treatment. Magnetic resonance imaging (MRI), computerized tomography (CT), visual macroscopic examination, histological analysis, and cytokine concentration analysis were used to assess cartilage regeneration. The findings revealed that human adipose-derived mesenchymal stem cells (hADSCs) were more effective in repairing cartilage than pig umbilical cord-derived mesenchymal stem cells (pUCMSCs). These results suggest that MSC-based treatments hold promise as a treatment option for cartilage repair, which aid in the treatment of OA. However, further studies with larger sample sizes and longer follow-up periods are required to fully demonstrate the safety and efficacy of these therapies in both animals and humans.

Theoretical study of triatomic silver (Ag3) and its ions with coupled-cluster methods and correlation-consistent basis sets.

Coupled-cluster calculations including non-iterative effects of triple excitations (CCSD(T)) have been made with correlation-consistent basis sets to study a range of properties of Ag3, Ag3(-), and Ag3(+). The methodology was tested on atomic and diatomic silver systems. The accuracy achieved for these systems suggests that predictive-quality results can be expected for the triatomic systems. Properties of the triatomic systems studied include structures and energies of ground and excited states (bent and linear geometries), dissociation energies, ionization energies, and vertical electron detachment energies. In the absence of experimental structural data, the present calculated data serve as reliable predictions. The calculated dissociation energies are near the middle of the experimental range (253 ± 13 kJ mol(-1)). The calculated ionization energies clearly favor the lower of the two experimental measurements (i.e. 5.66 eV). Our calculated vertical electron detachment energies of linear Ag3(-) match the observed photoelectron data fairly well. Overall the higher levels of theory used in the present study achieve consistent accuracy for a range of properties. In contrast, some prior density-functional theory studies provide good results for certain properties, but are lacking in accuracy for others. Another feature of the present study is that it has not been necessary to empirically correct results on the triatomic systems because of known deficiencies in the results on atomic and diatomic systems. The majority of prior wave function-based studies cannot make this claim.

Theoretical investigation into the structural, thermochemical, and electronic properties of the decathio[10]circulene.

For the first time, a theoretical study has been performed on the prototypical decathio[10]circulene (C(20)S(10)) species, which is an analogue of the novel octathio[8]circulene "Sulflower" molecule (C(16)S(8)). Examinations of the singlet and triplet states of C(20)S(10) were made at the B3LYP/6-311G(d) level. Local minima of C(2) and C(s) symmetry were found for the lowest singlet and triplet states, respectively. The stability of C(20)S(10) was assessed by calculating the ΔH°(f) of C(16)S(8) and C(20)S(10) and the ΔH(o) for their decomposition into C(2)S units. Frontier molecular orbital plots show that structural adjacent steric factors along with the twist and strain orientations of C(20)S(10) do not disturb the aromatic π-delocalizing effects. In fact, C(20)S(10) maintains the same p(z) HOMO character as C(16)S(8). These similarities are further verified by density-of-states characterization. Calculated infrared spectra of C(16)S(8) and C(20)S(10) show broad similarities. Molecular electrostatic potential results reveal that eight of the peripheral sulfur atoms are the most electronegative atoms in the molecule, while the interior ten-membered ring exhibits virtually no electronegativity.

Theoretical characterization of the F(2)O(3) molecule by coupled-cluster methods.

Coupled-cluster calculations with extended basis sets that include noniterative connected triple excitations (CCSD(T)) have been used to study the FOOOF isomer of F(2)O(3). Second-order Moller-Plessett perturbation theory (MP2) and density-functional theory (B3LYP functional) calculations have also been performed for comparison. Two local minima of similar energy, namely, conformers of C(2) and C(s) symmetry have been located. Structures, harmonic vibrational frequencies, and standard enthalpies and free energies of formation have been calculated. The calculated bond lengths of F(2)O(3) are more characteristic of those in F(2)O and a "normal" peroxide than the unusual bond lengths in F(2)O(2). Both conformers have equal F-O and O-O bond lengths, contrary to a recent suggestion of an unsymmetrical structure. The harmonic vibrational frequencies can aid possible identification of gaseous F(2)O(3). The calculated Δ(f)H° and Δ(f)G° are 110 and 173 kJ mol(-1), respectively. These values are based on extrapolation of CCSD(T) results with augmented triple- and quadruple-ζ basis sets and are expected to be within chemical accuracy (i.e., 1 kcal mol(-1) or 4 kJ mol(-1)). F(2)O(3) is calculated to be stable to decomposition to either FO + FOO or F(2) + O(3), but unstable to decomposition to its elements, to F(2)O(2) + (1)/(2)O(2), and to F(2)O + O(2).

Iron porphyrins with different imidazole ligands. A theoretical comparative study.

A theoretical comparative study of a series of five- and six-coordinate iron porphyrins, FeP(L) and FeP(L)(O(2)), has been carried out using DFT methods, where P = porphine and L = imidazole (Im), 1-methylimidazole (1-MeIm), 2-methylimidazole (2-MeIm), 1,2-dimethylimidazole (1,2-Me(2)Im), 4-ethylimidazole (4-EtIm), or histidine (His). Two ligated "picket-fence" iron porphyrins, FeTpivPP(2-MeIm) and FeTpivPP(2-MeIm)(O(2)), were also included in the study for comparison. A number of density functionals were employed in the computations to obtain reliable results. The performance of functionals and basis set effects were investigated in detail on FeP, FeP(Im), and FeP(Im)(O(2)), for which certain experimental information is available and there are some previous calculations in the literature for comparison. Many subtle distinctions in the effects of the different imidazole ligands on the structures and energetics of the deoxy- and oxy iron porphyrins are revealed. While FeP(2-MeIm) is identified to be high spin (S = 2), the ground state of FeP(1-MeIm) may be an admixture of a high-spin (S = 2) and an intermediate-spin (S = 1) state. The ground state of FeP(L)(O(2)) may be different with different L. A weaker Fe-L bond more likely leads to an open-shell singlet ground state for the oxy complex. The 2-methyl group in 2-MeIm, which increases steric contact between the ligand and the porphyrinato skeleton, weakens the Fe-O(2) bond, and thus iron porphyrins with 2-MeIm mimic T-state (low affinity) hemoglobin. The calculated FeP(2-MeIm)-O(2) bonding energy is comparable to the FeTpivPP(2-MeIm)-O(2) one, in agreement with the fact that the picket-fence iron porphyrin binds O(2) with affinity similar to that of myoglobin but different from the result obtained by the CPMD scheme. Im and 4-EtIm closely resemble His, the biologically axial base, and so future computations on hemoprotein models can be simplified safely by using Im.

Structure, bonding, and linear optical properties of a series of silver and gold nanorod clusters: DFT/TDDFT studies.

DFT/TDDFT calculations have been carried out for a series of silver and gold nanorod clusters (Ag(n), Au(n), n = 12-120) whose structures are of cigar-type. Pentagonal Ag(n) clusters with n = 49-121 and hexagonal Au(n) clusters with n = 14-74 were also calculated for comparison. Metal-metal distances, binding energies per atom, ionization potentials, and electron affinities were determined, and their trends with cluster size were examined. The TDDFT calculated excitation energies and oscillator strengths were fit by a Lorentz line shape modification, which gives rise to the simulated absorption spectra. The significant features of the experimental spectra for actual silver and gold nanorod particles are well reproduced by the calculations on the clusters. The calculated spectral patterns are also in agreement with previous theoretical results on different-type Ag(n) clusters. Many differences in the calculated properties are found between the Ag(n) and Au(n) clusters, which can be explained by relativistic effects.

Theoretical study of the tautomerism, structures, and vibrational frequencies of the phosphaalkenes XP=C(CH3)2 (X = H, F, Cl, Br, OH, Ar(F) (Ar(F) = 2,6-(CF3)2C6H3)).

Ab initio theoretical calculations have been used to study the influence of phosphorus substituents, Y, on the tautomerism between the vinylphosphine XP(H)C(CH(3))=CH(2) and the phosphaalkene XP=C(CH(3))(2) (X = H, F, Cl, Br, OH, and Ar(F); Ar(F) = 2,6-(CF(3))(2)C(6)H(3)) and on the acidity of the aforementioned vinylphosphine. The stabilization of the phosphaalkene and the increased acidity of the vinylphosphine by Ar(F) are possible factors in the successful synthesis of certain isolable phosphaalkenes. In this work, the properties of Ar(F) are assessed theoretically. Density functional theory using the B3LYP functional has been used for all substituents. In addition, coupled-cluster singles and doubles with noniterative triples (CCSD(T)) has been used for X = H, F, Cl, Br, and OH. The phosphaalkene is favored over the vinylphosphine for all substituents, with F having the strongest stabilizing effect. Cl, Br, and OH have stronger stabilizing effects than Ar(F). In contrast, the most acidic vinylphosphine is that with Ar(F). To aid in the interpretation and analysis of future experimental work, CCSD(T) calculations were used to provide structures and vibrational frequencies for the series XP=C(CH(3))(2) (X = H, F, Cl, Br). The influence of the substituent on geometries and C=P and X-P stretching frequencies was examined, and comparisons were made with the CH(2)=PX series.

Coupled-cluster study of isomers of H2SO2.

A theoretical study has been made on six isomers of H2SO2 using coupled-cluster singles and doubles with noniterative triple excitations (CCSD(T)). The isomers studied are sulfoxylic acid (S(OH)2; C2 and Cs conformers), sulfinic acid (HS(=O)OH; 2 C1 conformers), dihydrogen sulfone (H2SO2; C2v), sulfhydryl hydroperoxide (HSOOH; C1), thiadioxirane (Cs), and dihydrogen persulfoxide (H2SOO; Cs). Molecular geometries, harmonic vibrational frequencies, and infrared intensities of all species were obtained using the CCSD(T) method and the 6-311++G(2d,2p) basis set. All aforementioned species were found to be local minima, with the exception of thiadioxirane, which has one imaginary frequency. A prior possible infrared observation of sulfinic acid was reassessed on the basis of the present data. In agreement with previous MP2 results, the present CCSD(T) data provide support for at most 4 of the 8 observed frequencies. The CCSD(T) frequencies and intensities should be of assistance in future identification of H2SO2 isomers by vibrational spectroscopy. Relative energies were calculated using the CCSD(T) method and several larger basis sets. As found previously, the lowest energy species is C2 S(OH)2, followed by Cs S(OH)2, HS(=O)OH, H2SO2, HSOOH, thiadioxirane, and H2SOO. Expanding the basis set significantly reduces the relative energies of HS(=O)OH and H2SO2. The CCSD(T) method was used with extended basis sets (up to aug-cc-pV(Q+d)Z) and basis set extrapolation in two reaction schemes to calculate the DeltaH degrees t (25 degrees C) of C2 S(OH)2. The two reaction schemes gave -285.8 and -282.7 kJ mol-1, which are quite close to a prior theoretical estimate (-290 kJ mol-1).

[Studies on flavonoid glycosides of Sarcandra glabra].

OBJECTIVE: To in vestigate the chemical constituents of Sarcandra glabra and obtain a more comprehensive understanding on its effective components. METHOD: The constituents were isolated by various column chromatographic method and their structures were elucidated by physico-chemical properties and spectroscopic analysis. RESULT: Five flavonoid glycosides were isolated and identified as kaempferol-3-O-beta-D-glucuronide (1), quercetin-3-O-alpha-D-glucuronide (2), quercetin-3-O-beta-D-glucuronopyranoside methyl ester (3), 5, 7, 4'-trihydroxy-8-C-beta-D-glucopyranosyl flavanone (4), neoastilbin (5), 5-O-caffeoylquinic acid methyl ester (6), 3, 4-dihydroxybenzoic acid (7), isofraxidin (8). CONCLUSION: Compounds 1-6 were isolated from the genus Sarcandra for the first time. The glucuroide compounds compounds 1-3, were first isolated from the genus Sarcandra.

FOLR1 increases sensitivity to cisplatin treatment in ovarian cancer cells.

BACKGROUND: Whether there is a mechanistic link between FOLR1 and response to cisplatin has not been extensively examined. In this study, we determine the expression of FOLR1 in ovarian cancer and examine if FOLR1 levels influence response to cisplatin. RESULTS: (1) FOLR1 protein expression was lowest in normal ovarian tissue, higher in benign ovarian tumors, and highest in malignant tumors (P < 0.01). (2) FOLR1 expression was decreased in platinum drug-resistant ovarian tumors compared to sensitive tumors (P < 0.01). Consistent with this, FOLR1 expression in tumors progressing following cisplatin treatment was lower than levels in tumors in remission (P < 0.01). (3) FOLR1 was successfully overexpressed at both the mRNA and protein levels following transfection in SKOV3 cells. (4) SKOV3 cells with FOLR1 overexpression were the most sensitive to cisplatin treatment (IC50 = 3.60 µg/ml) and exhibited the highest inhibition rates in the presence of the drug (P < 0.05). (5) The rate of apoptosis of SKOV3 cells increased with cisplatin treatment in a dose- and time-dependent manner (P < 0.05). Cisplatin also induced S phase arrest in a concentration-dependent manner (P < 0.05). Apoptosis and S phase proportion were significantly altered by FOLR1 overexpression (P < 0.05). CONCLUSION: FOLR1 may be a useful biomarker for ovarian cancer, and it may be useful as a therapeutic application to improve sensitivity to cisplatin treatment.

Interaction of metal porphyrins with fullerene C60: a new insight.

The electronic structure and bonding in the noncovalent, supramolecular complexes of fullerene C60 with a series of first-row transition metal porphines MP (M=Fe, Co, Ni, Cu, Zn) have been re-examined with DFT methods. A dispersion correction was made for the C60-MP binding energy through an empirical method (J. Comput. Chem. 2004, 25, 1463). Several density functionals and two types of basis sets were employed in the calculations. Our calculated results are rather different from those obtained in a recent paper (J. Phys. Chem. A 2005, 109, 3704). The ground state of C60.FeP is predicted to be high spin (S=2); the low-spin (S=0), closed-shell state is even higher in energy than the intermediate-spin (S=1) state. With only one electron in the Co-dz2 orbital, the calculated Co-C60 distance is in fact rather short, about 0.1 A longer than the Fe-C60 distance in high-spin C60.FeP. Double occupation of an M-dz2 orbital in MP prevents close association of any axial ligand, and so the Ni-C60, Cu-C60, and Zn-C60 distances are much longer than the Co-C60 one. The evaluated MP-C60 binding energies (Ebind) are 0.8 eV (18.5 kcal/mol) for M=Fe/Co and 0.5 eV (11.5 kcal/mol) for M=Ni/Cu/Zn (Ebind is about 0.2 eV larger in the case of C60-MTPP). They are believed to be reliable and accurate based on our dispersion-corrected DFT calculations that included the counterpoise (CP) correction. The effects of the C60 contact on the redox properties of MP were also examined.

Two-step phase shifting differential-recording digital holographic microscopy.

We present two-step phase-shifting differential-recording digital holographic microscopy (TPD-DH in microscopy) for phase imaging of microscopic transparent elements. Two CCDs are employed to record two interferograms at two different defocusing distances. The interferograms on the two CCD cameras are shifted for a phase retarder 0 and π via an all-optics phase shifting unit. A novel algorithm is proposed to reconstruct both amplitude and phase distributions of the object wave from the recorded interferograms. This method has the same spectrum bandwidth and measurement accuracy with those of conventional four-step phase-shifting interferometry (FS-PSI), whereas it reduces the measurement time by half.

Metal Oxide Nanomaterials in Nanomedicine: Applications in Photodynamic Therapy and Potential Toxicity.

Metal oxide nanomaterials have exhibited excellent performance as nanomedicines in photodynamic therapy (PDT) for cancer and infection treatment. Their unique and tunable physicochemical properties advance them as promising alternatives in drug delivery, early diagnosis, imaging, and treatment against various tumors and infectious diseases. Moreover, the implementation of nanophototherapy in deep tissue sites is enhanced by advancements in photosensitization technology. Notwithstanding the progress made in emerging metal oxide nanomaterials-derived PDT, the potential toxicity towards adjunct tissues associated with this approach remains challenging. Regulation and legislation have also been recommended and subsequently enacted in response to public concerns related to large-scale production, transportation, use, and disposal of those nanomaterials. Consequently, a quantitative structure-activity relationship (QSAR) paradigm has been adopted and is widely used in evaluating and predicting the side effects of nanomedicines, thus influencing their design and fabrication. This article briefly reviews the application of metal oxide nanomaterials in PDT and their associated adverse impacts as reported in recent publications. The future trends and implications of this platform in nanomedicine are also highlighted. However, more studies and efforts have to be carried out for developing novel nano-therapeutics with high selectivity, sensitivity, biocompatibility, and minimal side effects in PDT.

Using experimental data of Escherichia coli to develop a QSAR model for predicting the photo-induced cytotoxicity of metal oxide nanoparticles.

A quantitative structure-activity relationship (QSAR) study of seventeen metal oxide nanoparticles (MNPs), in regard to their photo-induced toxicity to bacteria Escherichia coli, was developed by using quantum chemical methods. A simple and statistically significant QSAR model (F=33.83, R(2)=0.87) was successfully developed for the dark group based on two descriptors, absolute electronegativity of the metal and the metal oxide. Similarly, a best correlation (F=20.51, R(2)=0.804) was obtained to predict the photo-induced toxicity of MNPs by using two descriptors, molar heat capacity and average of the alpha and beta LUMO (lowest unoccupied molecular orbital) energies of the metal oxide. Revelation of these influential molecular descriptors may be useful in elucidating the mechanisms of nanotoxicity and for predicting the environmental risk associated with release of the MNPs. In addition, the developed model may have a role in the future design and manufacture of safe nanomaterials.

Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study.

DFT and dispersion-corrected DFT calculations were carried out to probe the factors that distort the heme structure in Heme-Nitric oxide/OXygen-binding (H-NOX) protein domains. Various model systems that include heme, heme+surrounding residues, and heme+surrounding residues+additional protein environment were examined; the latter system was calculated with a quantum mechanics/molecular mechanics (QM/MM) method. The computations were extended to a myoglobin (Mb) protein, in which the heme structure is quite planar, in contrast to that in H-NOX. The natural tendency of the heme is to be planar. The strong structural distortion in H-NOX is mainly brought about by the intermolecular interactions between the whole heme molecule (heme ring plus its peripheral substituents) and the surrounding residues, among which the polar residues (Tyr140, Pro115, Mse98) play major roles in distorting the heme structure. The two peripheral propionate substituents that are oriented on the same side of the heme plane can also make the molecule distort, but the distortion caused by this factor is not significant. In Mb, the surrounding residues considered are all nonpolar and do not cause a structural distortion. The different structural features of the heme macrocycle in the different proteins (H-NOX and Mb) are reproduced by the calculations. The dispersion correction is necessary, since it improves the calculated structures. The effects of the distortion on the binding affinity of the axial ligand to the heme were also examined.

Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study.

The binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron-histidine (Fe-His) binding. The Heme-AB (AB = O2, NO) and Fe-His binding energies in iron porphyrin FeP(His)(AB), myoglobin Mb(AB), H-NOX(AB), and Tyr140 → Phe mutated H-NOX[Y140F(AB)] were determined for comparison. The calculated stabilization of bound O2 is even higher in H-NOX than that in a myoglobin (Mb), consistent with the observation that the H-NOX domain of T. tengcongensis has a very high affinity for its oxygen molecule. Among the two different X-ray crystal structures for the Tt H-NOX protein, the calculated results for both AB = O2 and NO appear to support the crystal structure with the PDB code 1XBN , where the Trp9 and Asn74 residues do not form a hydrogen-bonding network with Tyr140. A hydrogen bond interaction from the polar residue does not have obvious effects on the Fe-His binding strength, but a dispersion contribution to Ebind(Fe-His) may be significant, depending on the crystal structure used. We speculate that the Fe-His binding strength in the deoxy form of a native protein could be an important factor in determining whether the bond of His to Fe is broken or maintained upon binding of NO to Fe.

Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.

The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.

FeP(Im)-AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O(2)).

Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (E(bond)) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O(2)). The results indicate that an accurate prediction of E(bond) for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield E(bond) values of ca.1.1, 1.2, and 0.4 eV for AB = CO, NO, and O(2), respectively, which are in reasonable agreement with experimental data (0.78 - 0.85 eV for CO, 0.99 eV for NO, and 0.44 - 0.53 eV for O(2)). The other functionals show more or less deficiency for one or two of the systems. The performances of the various functionals in describing the spin-state energetics of the five-coordinate FeP(Im) complex were also examined.